diff --git a/README b/README
new file mode 100644
index 0000000000..54877d3f2d
--- /dev/null
+++ b/README
@@ -0,0 +1,71 @@
+
+Where to start
+~~~~~~~~~~~~~~
+A good place to start is the "doc" directory, where you
+will find "user" guides for the MOM.
+
+How to run the MOM tests
+~~~~~~~~~~~~~~~~~~~~~~~~~
+MOM tests provided in exp directory divide in two types,
+both using the GFDL shared infrastructure (FMS) :
+
+1. Solo models : Run stand alone MOM Ocean model.
+2. Coupled models: Run MOM coupled with GFDL ice model
+ (besides null versions of atmosphere and land models).
+
+To run Solo models:
+ a. cd to exp and run mom4p1_solo_compile.csh first.
+ b. Modify the 'name' variable in the script
+ mom4p1_solo_run.csh to be the name of the test you
+ want to run. A list of available tests is included in the script.
+ c. Get the required input data for the test from GFDL ftp site.
+ You can get the info by running the script mom4p1_solo_run.csh
+ and following the instructions.
+ d. Run mom4p1_solo_run.csh
+ e. The results go into subdir name/workdir
+
+To run Coupled models:
+ Do the same steps above to mom4p1_coupled_compile.csh and mom4p1_coupled_run.csh
+
+To run EBM models:
+ Do the same steps above to mom4p1_ebm_compile.csh and mom4p1_ebm_run.csh
+
+
+
+Warning: The Solo and Coupled run scripts have been tested only on 10 and 24, ia64
+ processors respectively.
+Warning: Some of these tests require a large disk space to save the input data.
+ Choose a partition with enough space (1-2 G) to untar the code and data bundels.
+Warning: If you want to use the same root directory for all three experiments we suggest to
+ compile in the order of increasing complexity: solo -> coupled -> ebm .
+ You may have to remove some of the existing .o and .mod files
+ if you want to compile ebm experiment after the coupled experiment.
+ E.g., you probably have to: cd ../exec; rm mpp*.o mpp*.mod fms_io*.o fms_io*.mod
+
+Note: IBM platform users might want to add the following line to the top of the run scripts
+ setenv LDR_CNTRL MAXDATA=0xD0000000@DSA
+
+
+Note: The compile scripts provide the basic capability to use static memory allocation
+ which might be faster on some platforms. In that case you need to adjust the values
+ of domain bounds properly according to the number of processors and layout.
+
+
+Summary of directory contents
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+bin/
+ -- mkmf script for creating Makefiles
+ -- template files for the mkmf script
+ -- assorted other scripts
+
+exp/
+ -- all MOM experiments (test cases)
+
+src/
+ -- source code for all models
+
+src/postprocessing/
+ -- source code for postprocessing programs
+
+src/preprocessing/
+ -- source code for preprocessing programs
diff --git a/bin/.prepare_pubrel.csh.swp b/bin/.prepare_pubrel.csh.swp
new file mode 100644
index 0000000000..d655e66061
Binary files /dev/null and b/bin/.prepare_pubrel.csh.swp differ
diff --git a/bin/diag_table_chk b/bin/diag_table_chk
index f988da66e3..55423a43cb 100755
--- a/bin/diag_table_chk
+++ b/bin/diag_table_chk
@@ -1,8 +1,8 @@
#! /usr/bin/perl
-# $Author: fms $
-# $Revision: 17.0 $
-# $Date: 2009/08/10 20:51:27 $
+# $Author: Niki.Zadeh $
+# $Revision: 1.1.2.1 $
+# $Date: 2013/12/18 17:47:53 $
# Perl script to parse the diag_table. Count the number of files to
# be used, and the max number of fields per file used.
diff --git a/bin/environs.ibm.xlf b/bin/environs.ibm.xlf
new file mode 100644
index 0000000000..57deddb846
--- /dev/null
+++ b/bin/environs.ibm.xlf
@@ -0,0 +1,3 @@
+export OMP_NUM_THREADS=1
+export BG_APPTHREADDEPTH=1
+
diff --git a/bin/environs.ncrc2.gnu b/bin/environs.ncrc2.gnu
new file mode 100644
index 0000000000..64609814a0
--- /dev/null
+++ b/bin/environs.ncrc2.gnu
@@ -0,0 +1,15 @@
+ source $MODULESHOME/init/csh
+ module use -a /ncrc/home2/fms/local/modulefiles
+ module unload PrgEnv-pgi PrgEnv-pathscale PrgEnv-intel PrgEnv-gnu PrgEnv-cray
+ module unload netcdf fre fre-commands
+ module load PrgEnv-gnu
+ module load hdf5/1.8.8
+ module load netcdf/4.2.0
+ module list
+ setenv MPICH_MAX_SHORT_MSG_SIZE 8000
+ setenv KMP_STACKSIZE 512m
+ setenv NC_BLKSZ 1M
+
+ setenv mpirunCommand "aprun -n"
+ setenv PATH ${PATH}:.
+
diff --git a/bin/environs.ncrc2.intel b/bin/environs.ncrc2.intel
index f71429b8a3..fda798ef01 100644
--- a/bin/environs.ncrc2.intel
+++ b/bin/environs.ncrc2.intel
@@ -4,7 +4,7 @@
#
source $MODULESHOME/init/csh
module rm PrgEnv-pgi PrgEnv-pathscale netcdf
- module load PrgEnv-intel/4.0.30
+ module load PrgEnv-intel
module swap intel intel/12.0.5.220
module load hdf5/1.8.7
module load netcdf/4.1.3
diff --git a/bin/environs.workstation.gfort b/bin/environs.workstation.gfort
new file mode 100644
index 0000000000..124be6ea84
--- /dev/null
+++ b/bin/environs.workstation.gfort
@@ -0,0 +1,2 @@
+ setenv mpirunCommand "mpirun -np"
+
diff --git a/bin/environs.workstation.intel b/bin/environs.workstation.intel
new file mode 100644
index 0000000000..cd80b1f614
--- /dev/null
+++ b/bin/environs.workstation.intel
@@ -0,0 +1,17 @@
+ source $MODULESHOME/init/csh
+ module use -a /home/fms/local/modulefiles
+ module purge
+ module load ifort.11.0.074
+ module load icc.11.0.074
+ module load idb.10.1.35
+ module load hdf5-1.8.3
+ module load netcdf-4.0.1
+ setenv OMP_NUM_THREADS 1
+#
+ setenv NC_BLKSZ 64K
+ setenv FMS_ARCHIVE /archive/fms
+ setenv PATH ${PATH}:.
+ setenv netcdf3_inc_dir "/usr/local/netcdf-3.6.2/include"
+ setenv netcdf3_lib_dir "/usr/local/netcdf-3.6.2/lib"
+ setenv mpirunCommand "mpirun -np"
+
diff --git a/bin/list_files_with_tag b/bin/list_files_with_tag
index 40a0432f1f..08a8cfca4f 100755
--- a/bin/list_files_with_tag
+++ b/bin/list_files_with_tag
@@ -4,7 +4,7 @@
# Returns list of files under CVS control, relative to current
# directory, which can be updated or checked out with the tag tagname.
#Modified to also list files not currently checked out (arl, 4/2002)
-#Version: $Id: list_files_with_tag,v 10.0 2003/10/27 22:46:40 fms Exp $
+#Version: $Id: list_files_with_tag,v 1.1.2.1 2013/12/18 17:47:54 Niki.Zadeh Exp $
#test that a tagname was given as an argument
if( "$#ARGV" ne "0" ) {
diff --git a/bin/list_paths b/bin/list_paths
index 2b2efa81d0..1cb890bf5f 100755
--- a/bin/list_paths
+++ b/bin/list_paths
@@ -1,5 +1,5 @@
#!/bin/csh -ef
-# $Id: list_paths,v 10.1 2010/05/19 18:42:43 fms Exp $
+# $Id: list_paths,v 1.1.2.1 2013/12/18 17:47:54 Niki.Zadeh Exp $
#-----------------------------------------------------------------------
# list_paths: CVS administrative script
#
@@ -93,6 +93,6 @@ echo "Documentation in current working directory" > $ou
echo "
- A main program that couples component models for atmosphere, ocean, land,
- and sea ice on independent grids.
-
-
-
-
-
- This version couples model components representing atmosphere, ocean, land
- and sea ice on independent grids. Each model component is represented by a
- data type giving the instantaneous model state.
-
- The component models are coupled to allow implicit vertical diffusion of
- heat and moisture at the interfaces of the atmosphere, land, and ice models.
- As a result, the atmosphere, land, and ice models all use the same time step.
- The atmospheric model has been separated into down and up calls that
- correspond to the down and up sweeps of the standard tridiagonal elimination.
-
- The ocean interface uses explicit mixing. Fluxes to and from the ocean must
- be passed through the ice model. This includes atmospheric fluxes as well as
- fluxes from the land to the ocean (runoff).
-
- This program contains the model's main time loop. Each iteration of the
- main time loop is one coupled (slow) time step. Within this slow time step
- loop is a fast time step loop, using the atmospheric time step, where the
- tridiagonal vertical diffusion equations are solved. Exchange between sea
- ice and ocean occurs once every slow timestep.
-
-
MAIN PROGRAM EXAMPLE
- --------------------
-
- DO slow time steps (ocean)
-
- call flux_ocean_to_ice
-
- call ICE_SLOW_UP
-
- DO fast time steps (atmos)
-
- call flux_calculation
-
- call ATMOS_DOWN
-
- call flux_down_from_atmos
-
- call LAND_FAST
-
- call ICE_FAST
-
- call flux_up_to_atmos
-
- call ATMOS_UP
-
- END DO
-
- call ICE_SLOW_DN
-
- call flux_ice_to_ocean
-
- call OCEAN
-
- END DO
- The date that the current integration starts with.
-
-[integer, dimension(6), default: 0]
-
-
-force_date_from_namelist
-
-
- Flag that determines whether the namelist variable current_date should
- override the date in the restart file INPUT/coupler.res. If the restart
- file does not exist then force_date_from_namelist has not effect, the value of current_date
- will be used.
-
-[logical, default: .false.]
-
-
-calendar
-
-
- The calendar type used by the current integration. Valid values are consistent
- with the time_manager module: 'julian', 'noleap', or 'thirty_day'. The value
- 'no_calendar' can not be used because the time_manager's date function are used.
- All values must be lowercase.
-
-[character(maxlen=17), default: '']
-
-
-months
-
-
- The number of months that the current integration will be run for.
-
-[integer, default: 0]
-
-
-days
-
-
- The number of days that the current integration will be run for.
-
-[integer, default: 0]
-
-
-hours
-
-
- The number of hours that the current integration will be run for.
-
-[integer, default: 0]
-
-
-minutes
-
-
- The number of minutes that the current integration will be run for.
-
-[integer, default: 0]
-
-
-seconds
-
-
- The number of seconds that the current integration will be run for.
-
-[integer, default: 0]
-
-
-dt_atmos
-
-
- Atmospheric model time step in seconds, including the fast coupling with
- land and sea ice.
-
-[integer, default: 0]
-
-
-dt_cpld
-
-
- Time step in seconds for coupling between ocean and atmospheric models:
- must be an integral multiple of dt_atmos and dt_ocean. This is the "slow" timestep.
-
-[integer, default: 0]
-
-
-do_atmos, do_ocean, do_ice, do_land, do_flux
-
-
- If true (default), that particular model component (atmos, etc.) is run.
- If false, the execution of that component is skipped. This is used when
- ALL the output fields sent by that component to the coupler have been
- overridden using the data_override feature. For advanced users only:
- if you're not sure, you should leave these values at TRUE.
-
-[logical]
-
-
-concurrent
-
-
- If true, the ocean executes concurrently with the atmosphere-land-ocean
- on a separate set of PEs.
- If false (default), the execution is serial: call atmos... followed by
- call ocean...
- If using concurrent execution, you must set one of
- atmos_npes and ocean_npes, see below.
-
-[logical]
-
-
-atmos_npes, ocean_npes
-
-
- If concurrent is set to true, we use these to set the list of PEs on which
- each component runs.
- At least one of them must be set to a number between 0 and NPES.
- If exactly one of these two is set non-zero, the other is set to the
- remainder from NPES.
- If both are set non-zero they must add up to NPES.
-
-[integer]
-
-
-atmos_nthreads, ocean_nthreads
-
-
- We set here the number of OpenMP threads to use
- separately for each component (default 1)
-
-[integer]
-
-
-use_lag_fluxes
-
-
- If true, then mom4 is forced with SBCs from one coupling timestep ago
- If false, then mom4 is forced with most recent SBCs.
- For a leapfrog MOM coupling with dt_cpld=dt_ocean, lag fluxes
- can be shown to be stable and current fluxes to be unconditionally unstable.
- For dt_cpld>dt_ocean there is probably sufficient damping.
- use_lag_fluxes is set to TRUE by default.
-
-[logical]
-
-
-restart_interval
-
-
- The time interval that write out intermediate restart file. The format is (yr,mo,day,hr,min,sec).
- When restart_interval is all zero, no intermediate restart file will be written out.
-
-[integer, dimension(6), default: 0]
-
-
-
-
-
-
-
-
-
-
-
ERROR MESSAGES
-
-
-
-
-FATAL error during execution of program coupler_main
-
-
-no namelist value for current_date
-
-
- A namelist value for current_date must be given if no restart file for
- coupler_main (INPUT/coupler.res) is found.
-
-
-FATAL error during execution of program coupler_main
-
-
-invalid namelist value for calendar
-
-
- The value of calendar must be 'julian', 'noleap', or 'thirty_day'.
- See the namelist documentation.
-
-
-FATAL error during execution of program coupler_main
-
-
-no namelist value for calendar
-
-
- If no restart file is present, then a namelist value for calendar
- must be specified.
-
-
-FATAL error during execution of program coupler_main
-
-
-initial time is greater than current time
-
-
- If a restart file is present, then the namelist value for either
- current_date or start_date was incorrectly set.
-
-
-FATAL error during execution of program coupler_main
-
-
-run length must be multiple of ocean time step
-
-
- There must be an even number of ocean time steps for the requested run length.
-
-
-WARNING error during execution of program coupler_main
-
-
-final time does not match expected ending time
-
-
- This error should probably not occur because of checks done at initialization time.
-
-
-
-
-
-
-
-
NOTES
-
-
-
-
1.If no value is set for current_date, start_date, or calendar (or default value
- specified) then the value from restart file "INPUT/coupler.res" will be used.
- If neither a namelist value or restart file value exist the program will fail.
- 2.The actual run length will be the sum of months, days, hours, minutes, and
- seconds. A run length of zero is not a valid option.
- 3.The run length must be an intergal multiple of the coupling timestep dt_cpld.
- The flux_exchange module provides interfaces to couple the following component
- models: atmosphere, ocean, land, and ice. All interpolation between physically
- distinct model grids is handled by the exchange grid (xgrid_mod) with the
- interpolated quantities being conserved.
-
-
-
-
-
-
-
1.This version of flux_exchange_mod allows the definition of physically independent
- grids for atmosphere, land and sea ice. Ice and ocean must share the same physical
- grid (though the domain decomposition on parallel systems may be different).
- Grid information is input through the grid_spec file (URL). The masked region of the
- land grid and ice/ocean grid must "tile" each other. The masked region of the ice grid
- and ocean grid must be identical.
-
- ATMOSPHERE |----|----|----|----|----|----|----|----|
-
- LAND |---|---|---|---|xxx|xxx|xxx|xxx|xxx|xxx|
-
- ICE |xxx|xxx|xxx|xxx|---|---|---|---|---|---|
-
- OCEAN |xxx|xxx|xxx|xxx|---|---|---|---|---|---|
-
- where |xxx| = masked grid point
-
-
- The atmosphere, land, and ice grids exchange information using the exchange grid xmap_sfc.
-
- The land and ice grids exchange runoff data using the exchange grid xmap_runoff.
-
- Transfer of data between the ice bottom and ocean does not require an exchange
- grid as the grids are physically identical. The flux routines will automatically
- detect and redistribute data if their domain decompositions are different.
-
- To get information from the atmosphere to the ocean it must pass through the
- ice model, first by interpolating from the atmospheric grid to the ice grid,
- and then transferring from the ice grid to the ocean grid.
- 2.Each component model must have a public defined data type containing specific
- boundary fields. A list of these quantities is located in the NOTES of this document.
-
- 3.The surface flux of sensible heat and surface evaporation can be implicit functions
- of surface temperature. As a consequence, the parts of the land and sea-ice models
- that update the surface temperature must be called on the atmospheric time step
-
- 4.The surface fluxes of all other tracers and of momentum are assumed to be explicit
- functions of all surface parameters
-
- 5.While no explicit reference is made within this module to the implicit treatment
- of vertical diffusion in the atmosphere and in the land or sea-ice models, the
- module is designed to allow for simultaneous implicit time integration on both
- sides of the surface interface.
-
- 6.Due to #5, the diffusion part of the land and ice models must be called on the
- atmospheric time step.
-7. Any field passed from one component to another may be "faked" to a
- constant value, or to data acquired from a file, using the
- data_override feature of FMS. The fields to override are runtime
- configurable, using the text file <tt>data_table</tt> for input.
- See the data_override_mod documentation for more details.
-
- We DO NOT RECOMMEND exercising the data override capabilities of
- the FMS coupler until the user has acquired considerable
- sophistication in running FMS.
-
- Here is a listing of the override capabilities of the flux_exchange
- module:
-
- FROM the atmosphere boundary TO the exchange grid (in sfc_boundary_layer):
-
- t_bot, q_bot, z_bot, p_bot, u_bot, v_bot, p_surf, slp, gust
-
- FROM the ice boundary TO the exchange grid (in sfc_boundary_layer):
-
- t_surf, rough_mom, rough_heat, rough_moist, albedo, u_surf, v_surf
-
- FROM the land boundary TO the exchange grid (in sfc_boundary_layer):
-
- t_surf, t_ca, q_ca, rough_mom, rough_heat, albedo
-
- FROM the exchange grid TO land_ice_atmos_boundary (in
- sfc_boundary_layer):
-
- t, albedo, land_frac, dt_t, dt_q, u_flux, v_flux, dtaudu, dtaudv,
- u_star, b_star, rough_mom
-
- FROM the atmosphere boundary TO the exchange grid (in
- flux_down_from_atmos):
-
- flux_sw, flux_lw, lprec, fprec, coszen, dtmass, delta_t,
- delta_q, dflux_t, dflux_q
-
- FROM the exchange grid TO the land boundary (in
- flux_down_from_atmos):
-
- t_flux, q_flux, lw_flux, sw_flux, lprec, fprec, dhdt, dedt, dedq,
- drdt, drag_q, p_surf
-
- FROM the exchange grid TO the ice boundary (in flux_down_from_atmos):
-
- u_flux, v_flux, t_flux, q_flux, lw_flux, lw_flux_dn, sw_flux,
- sw_flux_dn, lprec, fprec, dhdt, dedt, drdt, coszen, p
-
- FROM the land boundary TO the ice boundary (in flux_land_to_ice):
-
- runoff, calving
-
- FROM the ice boundary TO the ocean boundary (in flux_ice_to_ocean):
-
- u_flux, v_flux, t_flux, q_flux, salt_flux, lw_flux, sw_flux,
- lprec, fprec, runoff, calving, p
-
- FROM the ocean boundary TO the ice boundary (in flux_ocean_to_ice):
-
- u, v, t, s, frazil, sea_level
-
- FROM the ice boundary TO the atmosphere boundary (in flux_up_to_atmos):
-
- t_surf
-
- FROM the land boundary TO the atmosphere boundary (in
- flux_up_to_atmos):
-
- t_ca, t_surf, q_ca
-
- See NOTES below for an explanation of the field names.
- Returns fluxes and derivatives corrected for the implicit treatment of atmospheric
- diffusive fluxes, as well as the increments in the temperature and specific humidity
- of the lowest atmospheric layer due to all explicit processes as well as the diffusive
- fluxes through the top of this layer.
-
- Initializes the interpolation routines,diagnostics and boundary data
-
-
-
-
-INPUT
-
-
-
-
-
Time
- current time
- [time_type]
-
-
-
Atm
- A derived data type to specify atmosphere boundary data.
- [atmos_data_type]
-
-
-
Land
- A derived data type to specify land boundary data.
- [land_data_type]
-
-
-
Ice
- A derived data type to specify ice boundary data.
- [ice_data_type]
-
-
-
Ocean
- A derived data type to specify ocean boundary data.
- [ocean_public_type]
-
-
-
dt_atmos
- Atmos time step in secs.
- [integer]
-
-
-
dt_cpld
- Coupled time step in secs.
- [integer]
-
-
-
-
-
-INPUT/OUTPUT
-
-
-
-
-
atmos_ice_boundary
- A derived data type to specify properties and fluxes passed from atmosphere to ice.
- [atmos_ice_boundary_type]
-
-
-
land_ice_atmos_boundary
- A derived data type to specify properties and fluxes passed from exchange grid to
- the atmosphere, land and ice.
- [land_ice_atmos_boundary_type]
-
-
-
land_ice_boundary
- A derived data type to specify properties and fluxes passed from land to ice.
- [land_ice_boundary_type]
-
-
-
ice_ocean_boundary
- A derived data type to specify properties and fluxes passed from ice to ocean.
- [ice_ocean_boundary_type]
-
-
-
ocean_ice_boundary
- A derived data type to specify properties and fluxes passed from ocean to ice.
- [ocean_ice_boundary_type]
-
-
-
-
-
-
-
-
-
sfc_boundary_layer
-
-call sfc_boundary_layer ( dt, Time, Atm, Land, Ice, Boundary )
-
-
-DESCRIPTION
-
-
-
-
The following quantities in the land_ice_atmos_boundary_type are computed:
-
-
- t_surf_atm = surface temperature (used for radiation) (K)
- albedo_atm = surface albedo (used for radiation) (nondimensional)
- rough_mom_atm = surface roughness for momentum (m)
- land_frac_atm = fractional area of land beneath an atmospheric
- grid box
- dtaudu_atm, dtaudv_atm = derivatives of wind stress w.r.t. the
- lowest level wind speed (Pa/(m/s))
- flux_u_atm = zonal wind stress (Pa)
- flux_v_atm = meridional wind stress (Pa)
- u_star_atm = friction velocity (m/s)
- b_star_atm = buoyancy scale (m2/s)
-
- (u_star and b_star are defined so that u_star**2 = magnitude
- of surface stress divided by density of air at the surface,
- and u_star*b_star = buoyancy flux at the surface)
-
-
-
-
-
-INPUT
-
-
-
-
-
dt
- time step.
- [real]
-
-
-
Time
- current time
- [time_type]
-
-
-
-
-
-INPUT/OUTPUT
-
-
-
-
-
Atm
- A derived data type to specify atmosphere boundary data.
- [atmos_data_type]
-
-
-
Land
- A derived data type to specify land boundary data.
- [land_data_type]
-
-
-
Ice
- A derived data type to specify ice boundary data.
- [ice_data_type]
-
-
-
Boundary
- A derived data type to specify properties and fluxes passed from exchange grid to
- the atmosphere, land and ice.
- [land_ice_atmos_boundary_type]
The following elements from Atmos_boundary are used as input:
-
- flux_u_atm = zonal wind stress (Pa)
- flux_v_atm = meridional wind stress (Pa)
-
-
- The following elements of Land_boundary are output:
-
- flux_t_land = sensible heat flux (W/m2)
- flux_q_land = specific humidity flux (Kg/(m2 s)
- flux_lw_land = net longwave flux (W/m2), uncorrected for
- changes in surface temperature
- flux_sw_land = net shortwave flux (W/m2)
- dhdt_land = derivative of sensible heat flux w.r.t.
- surface temperature (on land model grid) (W/(m2 K)
- dedt_land = derivative of specific humidity flux w.r.t.
- surface temperature (on land model grid) (Kg/(m2 s K)
- drdt_land = derivative of upward longwave flux w.r.t.
- surface temperature (on land model grid) (W/(m2 K)
- lprec_land = liquid precipitation, mass for one time step
- (Kg/m2)
- fprec_land = frozen precipitation, mass for one time step
- (Kg/m2)
-
-
- The following elements of Ice_boundary are output:
-
- flux_u_ice = zonal wind stress (Pa)
- flux_v_ice = meridional wind stress (Pa)
- coszen_ice = cosine of the zenith angle
-
-
-
-
-
-INPUT
-
-
-
-
-
Time
- current time
- [time_type]
-
-
-
Land
- A derived data type to specify land boundary data.
- [land_data_type]
-
-
-
Ice
- A derived data type to specify ice boundary data.
- [ice_data_type]
-
-
-
Atmos_boundary
- A derived data type to specify properties and fluxes passed from exchange grid to
- the atmosphere, land and ice.
- [land_ice_atmos_boundary_type]
-
-
-
-
-
-INPUT/OUTPUT
-
-
-
-
-
Atm
- A derived data type to specify atmosphere boundary data.
- [atmos_data_type]
-
-
-
Land_boundary
- A derived data type to specify properties and fluxes passed from atmosphere to land.
- [atmos_land_boundary_type]
-
-
-
Ice_boundary
- A derived data type to specify properties and fluxes passed from atmosphere to ice.
- [atmos_ice_boundary_type]
The following elements are transferred from the Land to the Land_ice_boundary:
-
- discharge --> runoff (kg/m2)
- discharge_snow --> calving (kg/m2)
-
-
-
-
-
-INPUT
-
-
-
-
-
Time
- current time
- [time_type]
-
-
-
Land
- A derived data type to specify land boundary data.
- [land_data_type]
-
-
-
Ice
- A derived data type to specify ice boundary data.
- [ice_data_type]
-
-
-
-
-
-INPUT/OUTPUT
-
-
-
-
-
Land_Ice_Boundary
- A derived data type to specify properties and fluxes passed from land to ice.
- [land_ice_boundary_type]
-
-
-
-
-
-
-
-
-
flux_ice_to_ocean
-
-call flux_ice_to_ocean ( Time, Ice, Ocean, Ice_Ocean_Boundary )
-
-
-DESCRIPTION
-
-
-
-
The following quantities are transferred from the Ice to the ice_ocean_boundary_type:
-
- flux_u = zonal wind stress (Pa)
- flux_v = meridional wind stress (Pa)
- flux_t = sensible heat flux (W/m2)
- flux_q = specific humidity flux (Kg/m2/s)
- flux_salt = salt flux (Kg/m2/s)
- flux_sw = net (down-up) shortwave flux (W/m2)
- flux_lw = net (down-up) longwave flux (W/m2)
- lprec = mass of liquid precipitation since last
- time step (Kg/m2)
- fprec = mass of frozen precipitation since last
- time step (Kg/m2)
- runoff = mass (?) of runoff since last time step
- (Kg/m2)
- p_surf = surface pressure (Pa)
-
-
-
-
-
-INPUT
-
-
-
-
-
Time
- current time
- [time_type]
-
-
-
Ice
- A derived data type to specify ice boundary data.
- [ice_data_type]
-
-
-
Ocean
- A derived data type to specify ocean boundary data.
- [ocean_public_type]
-
-
-
-
-
-INPUT/OUTPUT
-
-
-
-
-
Ice_Ocean_Boundary
- A derived data type to specify properties and fluxes passed from ice to ocean.
- [ice_ocean_boundary_type]
-
-
-
-
-
-
-
-
-
flux_ocean_to_ice
-
-call flux_ocean_to_ice ( Time, Ocean, Ice, Ocean_Ice_Boundary)
-
-
-DESCRIPTION
-
-
-
-
The following quantities are transferred from the Ocean to the ocean_ice_boundary_type:
-
- t_surf = surface temperature (deg K)
- frazil = frazil (???)
- u_surf = zonal ocean current/ice motion (m/s)
- v_surf = meridional ocean current/ice motion (m/s
-
-
-
-
-
-INPUT
-
-
-
-
-
Time
- current time
- [time_type]
-
-
-
Ocean
- A derived data type to specify ocean boundary data.
- [ocean_public_type]
-
-
-
Ice
- A derived data type to specify ice boundary data.
- [ice_data_type]
-
-
-
-
-
-INPUT/OUTPUT
-
-
-
-
-
Ocean_Ice_Boundary
- A derived data type to specify properties and fluxes passed from ocean to ice.
- [ocean_ice_boundary_type]
-
-
-
-
-
-
-
-
-
flux_check_stocks
-
-
-DESCRIPTION
-
-
- Will print out any difference between the integrated flux (in time
- and space) feeding into a component, and the stock stored in that
- component.
-
-
-
-
-
-
-
-
flux_init_stocks
-
-
-DESCRIPTION
-
-
- This will call the various component stock_pe routines to store the
- the initial stock values.
-
-
-
-
-
-
-
-
generate_sfc_xgrid
-
-call generate_sfc_xgrid ( Land, Ice )
-
-
-DESCRIPTION
-
-
- Optimizes the exchange grids by eliminating land and ice partitions with no data.
-
-
-
-
-INPUT
-
-
-
-
-
Land
- A derived data type to specify land boundary data.
- [land_data_type]
-
-
-
Ice
- A derived data type to specify ice boundary data.
- [ice_data_type]
-
-
-
-
-
-
-
-
-
flux_up_to_atmos
-
-call flux_up_to_atmos ( Time, Land, Ice, Land_Ice_Atmos_Boundary, Land_boundary, Ice_boundary )
-
-
-DESCRIPTION
-
-
- Corrects the fluxes for consistency with the new surface temperatures in land
- and ice models. Final increments for temperature and specific humidity in the
- lowest atmospheric layer are computed and returned to the atmospheric model
- so that it can finalize the increments in the rest of the atmosphere.
-
The following elements of the land_ice_atmos_boundary_type are computed:
- dt_t = temperature change at the lowest
- atmospheric level (deg k)
- dt_q = specific humidity change at the lowest
- atmospheric level (kg/kg)
-
-
-
-
-
-INPUT
-
-
-
-
-
Time
- Current time.
- [time_type]
-
-
-
-
-
-INPUT/OUTPUT
-
-
-
-
-
Land
- A derived data type to specify land boundary data.
- [land_data_type]
-
-
-
Ice
- A derived data type to specify ice boundary data.
- [ice_data_type]
-
-
-
Land_Ice_Atmos_Boundary
- A derived data type to specify properties and fluxes passed from exchange grid to
- the atmosphere, land and ice.
- [land_ice_atmos_boundary_type]
-
-
-
-
-
-
-
-
-
flux_ice_to_ocean_stocks
-
-call flux_ice_to_ocean_stocks ( Ice )
-
-
-DESCRIPTION
-
-
- Integrate the fluxes over the surface and in time.
-
-
-
-
-INPUT
-
-
-
-
-
Time
- A derived data type to specify ice boundary data.
- [ice_data_type]
- This subroutine updates the stocks of Ocean by the amount of input that the Ocean gets from Ice component.
- Unlike subroutine flux_ice_to_ocean_stocks() that uses Ice%fluxes to update the stocks due to the amount of output from Ice
- this subroutine uses Ice_Ocean_boundary%fluxes to calculate the amount of input to the Ocean. These fluxes are the ones
- that Ocean model uses internally to calculate its budgets. Hence there should be no difference between this input and what
- Ocean model internal diagnostics uses.
- This bypasses the possible mismatch in cell areas between Ice and Ocean in diagnosing the stocks of Ocean
- and should report a conserving Ocean component regardless of the glitches in fluxes.
-
- The use of this subroutine in conjunction with subroutine flux_ice_to_ocean_stocks() will also allow to directly
- diagnose the amount "stocks lost in exchange" between Ice and Ocean
-
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&flux_exchange_nml
-
-
-
-
-
-z_ref_heat
-
-
- eference height (meters) for temperature and relative humidity
- diagnostics (t_ref,rh_ref,del_h,del_q)
-
-[real, default: 2.0]
-
- By default, the global exchange grid u_star will not be interpolated from
- atmospheric grid, this is different from Jakarta behavior and will
- change answers. So to perserve Jakarta behavior and reproduce answers
- explicitly set this namelist variable to .true. in input.nml.
- Talk to mw, ens for details.
-
-[logical, default: false]
-
-
-do_runoff
-
-
- Turns on/off the land runoff interpolation to the ocean.
-
-[logical, default: .TRUE.]
-
-
-
-
-
-
-
-
-
-
DIAGNOSTIC FIELDS
-
Diagnostic fields may be output to a netcdf file by
- specifying the module name identifier and the desired field names (given below) in
- file diag_table. See the documentation for diag_manager.
field description (units) ------------------------- fractional amount of land (none)
-wind speed for flux calculations (m/s)
-drag coeff for moisture (none)
-drag coeff for heat (none)
-drag coeff for momentum (none)
-surface roughness for moisture (m)
-surface roughness for heat (m)
-surface roughness for momentum (m)
-friction velocity (m/s)
-buoyancy scale (m/s)
-moisture scale (kg water/kg air)
-temperature at btm level (deg_k)
-u wind component at btm level (m/s)
-v wind component at btm level (m/s)
-specific humidity at btm level (kg/kg)
-pressure at btm level (pa)
-height of btm level (m)
-gust scale (m/s)
-relative humidity at ref height (percent)
-temperature at ref height (deg_k)
-zonal wind component at ref height (m/s)
-meridional wind component at ref height (m/s)
-ref height interp factor for heat (none)
-ref height interp factor for momentum (none)
-ref height interp factor for moisture (none)
-zonal wind stress (pa)
-meridional wind stress (pa)
-fractional amount of sea ice (none)
-surface temperature (deg_k)
-canopy air temperature (deg_k)
-surface specific humidity (kg/kg)
-sensible heat flux (w/m2)
-evaporation rate (kg/m2/s)
-net (down-up) longwave flux (w/m2)
-
-
-
-
-
-
-
-
-
-
-
-
ERROR MESSAGES
-
-
-
-
-FATAL in flux_exchange_init
-
-
-grid_spec.nc incompatible with atmosphere resolution
-
-
- The atmosphere grid size from file grid_spec.nc is not compatible with the atmosphere
- resolution from atmosphere model.
-
-
-FATAL in flux_exchange_init
-
-
-grid_spec.nc incompatible with atmosphere longitudes (see xba.dat and yba.dat)
-
-
- longitude from file grid_spec.nc ( from field yba ) is different from the longitude from atmosphere model.
-
-
-FATAL in flux_exchange_init
-
-
-grid_spec.nc incompatible with atmosphere longitudes (see xba.dat and yba.dat)
-
-
- longitude from file grid_spec.nc ( from field xba ) is different from the longitude from atmosphere model.
-
-
-FATAL in flux_exchange_init
-
-
-grid_spec.nc incompatible with atmosphere latitudes (see grid_spec.nc)
-
-
- latgitude from file grid_spec.nc is different from the latitude from atmosphere model.
-
-
-FATAL in sfc_boundary_layer
-
-
-must call flux_exchange_init first
-
-
- flux_exchange_init has not been called before calling sfc_boundary_layer.
-
-
-FATAL in flux_ocean_to_ice
-
-
-Ocean_Ice_Boundary%xtype must be DIRECT or REDIST.
-
-
- The value of variable xtype of ice_ocean_boundary_type data must be DIRECT or REDIST.
-
-
-
-
-
-
-
-
NOTES
-
-
-
-
MAIN PROGRAM EXAMPLE
- --------------------
-
- DO slow time steps (ocean)
-
- call flux_ocean_to_ice
-
- call ICE_SLOW_UP
-
-
- DO fast time steps (atmos)
-
- call sfc_boundary_layer
-
- call ATMOS_DOWN
-
- call flux_down_from_atmos
-
- call LAND_FAST
-
- call ICE_FAST
-
- call flux_up_to_atmos
-
- call ATMOS_UP
-
- END DO
-
- call ICE_SLOW_DN
-
- call flux_ice_to_ocean
-
- call OCEAN
-
- END DO
-
- LAND_FAST and ICE_FAST must update the surface temperature
-
- =======================================================================
-
- REQUIRED VARIABLES IN DEFINED DATA TYPES FOR COMPONENT MODELS
- --------------------------------------------------------------
-
- type (atmos_boundary_data_type) :: Atm
- type (surf_diff_type) :: Atm%Surf_Diff
-
- real, dimension(:)
-
- Atm%lon_bnd longitude axis grid box boundaries in radians
- must be monotonic
- Atm%lat_bnd latitude axis grid box boundaries in radians
- must be monotonic
-
- real, dimension(:,:)
-
- Atm%t_bot temperature at lowest model level
- Atm%q_bot specific humidity at lowest model level
- Atm%z_bot height above the surface for the lowest model level (m)
- Atm%p_bot pressure at lowest model level (pa)
- Atm%u_bot zonal wind component at lowest model level (m/s)
- Atm%v_bot meridional wind component at lowest model level (m/s)
- Atm%p_surf surface pressure (pa)
- Atm%slp sea level pressure (pa)
- Atm%gust gustiness factor (m/s)
- Atm%flux_sw net shortwave flux at the surface
- Atm%flux_lw downward longwave flux at the surface
- Atm%lprec liquid precipitation (kg/m2)
- Atm%fprec water equivalent frozen precipitation (kg/m2)
- Atm%coszen cosine of the zenith angle
-
- (the following five fields are gathered into a data type for convenience in passing
- this information through the different levels of the atmospheric model --
- these fields are rlated to the simultaneous implicit time steps in the
- atmosphere and surface models -- they are described more fully in
- flux_exchange.tech.ps and
- in the documntation for vert_diff_mod
-
-
- Atm%Surf_Diff%dtmass = dt/mass where dt = atmospheric time step ((i+1) = (i-1) for leapfrog) (s)
- mass = mass per unit area of lowest atmosphehic layer (Kg/m2))
- Atm%Surf_Diff%delta_t increment ((i+1) = (i-1) for leapfrog) in temperature of
- lowest atmospheric layer (K)
- Atm%Surf_Diff%delta_q increment ((i+1) = (i-1) for leapfrog) in specific humidity of
- lowest atmospheric layer (nondimensional -- Kg/Kg)
- Atm%Surf_Diff%dflux_t derivative of implicit part of downward temperature flux at top of lowest
- atmospheric layer with respect to temperature
- of lowest atmospheric layer (Kg/(m2 s))
- Atm%Surf_Diff%dflux_q derivative of implicit part of downward moisture flux at top of lowest
- atmospheric layer with respect to specific humidity of
- of lowest atmospheric layer (Kg/(m2 s))
-
-
- integer, dimension(4)
-
- Atm%axes Axis identifiers returned by diag_axis_init for the
- atmospheric model axes: X, Y, Z_full, Z_half.
-
- -----------------------------------------------
-
- type (land_boundary_data_type) :: Land
-
- real, dimension(:)
-
- Land%lon_bnd longitude axis grid box boundaries in radians
- must be monotonic
- Land%lat_bnd latitude axis grid box boundaries in radians
- must be monotonic
-
- logical, dimension(:,:,:)
-
- Land%mask land/sea mask (true for land)
- Land%glacier glacier mask (true for glacier)
-
- real, dimension(:,:,:)
-
- Land%tile_size fractional area of each tile (partition)
-
- Land%t_surf surface temperature (deg k)
- Land%albedo surface albedo (fraction)
- Land%rough_mom surface roughness for momentum (m)
- Land%rough_heat surface roughness for heat/moisture (m)
- Land%stomatal stomatal resistance
- Land%snow snow depth (water equivalent) (kg/m2)
- Land%water water depth of the uppermost bucket (kg/m2)
- Land%max_water maximum water depth allowed in the uppermost bucket (kg/m2)
-
- -----------------------------------------------
-
-
- type (ice_boundary_data_type) :: Ice
-
- real, dimension(:)
-
- Ice%lon_bnd longitude axis grid box boundaries for temperature points
- in radians (must be monotonic)
- Ice%lat_bnd latitude axis grid box boundaries for temperature points
- in radians (must be monotonic)
- Ice%lon_bnd_uv longitude axis grid box boundaries for momentum points
- in radians (must be monotonic)
- Ice%lat_bnd_uv latitude axis grid box boundaries for momentum points
- in radians (must be monotonic)
-
- logical, dimension(:,:,:)
-
- Ice%mask ocean/land mask for temperature points
- (true for ocean, with or without ice)
- Ice%mask_uv ocean/land mask for momentum points
- (true for ocean, with or without ice)
- Ice%ice_mask optional ice mask (true for ice)
-
- real, dimension(:,:,:)
-
- Ice%part_size fractional area of each partition of a temperature grid box
- Ice%part_size_uv fractional area of each partition of a momentum grid box
-
- the following fields are located on the ice top grid
-
- Ice%t_surf surface temperature (deg k)
- Ice%albedo surface albedo (fraction)
- Ice%rough_mom surface roughness for momentum (m)
- Ice%rough_heat surface roughness for heat/moisture (m)
- Ice%u_surf zonal (ocean/ice) current at the surface (m/s)
- Ice%v_surf meridional (ocean/ice) current at the surface (m/s)
-
- the following fields are located on the ice bottom grid
-
- Ice%flux_u zonal wind stress (Pa)
- Ice%flux_v meridional wind stress (Pa)
- Ice%flux_t sensible heat flux (w/m2)
- Ice%flux_q specific humidity flux (kg/m2/s)
- Ice%flux_sw net (down-up) shortwave flux (w/m2)
- Ice%flux_lw net (down-up) longwave flux (w/m2)
- Ice%lprec mass of liquid precipitation since last time step (Kg/m2)
- Ice%fprec mass of frozen precipitation since last time step (Kg/m2)
- Ice%runoff mass of runoff water since last time step (Kg/m2)
-
- -----------------------------------------------
-
- type (ocean_boundary_data_type) :: Ocean
-
- real, dimension(:)
-
- Ocean%Data%lon_bnd longitude axis grid box boundaries for temperature
- points on the ocean DATA GRID (radians)
- Ocean%Data%lat_bnd latitude axis grid box boundaries for temperature
- points on the ocean DATA GRID (radians)
- Ocean%Data%lon_bnd_uv longitude axis grid box boundaries for momentum
- points on the ocean DATA GRID (radians)
- Ocean%Data%lat_bnd_uv latitude axis grid box boundaries for momentum
- points on the ocean DATA GRID (radians)
-
- Ocean%Ocean%lon_bnd longitude axis grid box boundaries for temperature
- points on the ocean MODEL GRID (radians)
- Ocean%Ocean%lat_bnd latitude axis grid box boundaries for temperature
- points on the ocean MODEL GRID (radians)
- Ocean%Ocean%lon_bnd_uv longitude axis grid box boundaries for momentum
- points on the ocean MODEL GRID (radians)
- Ocean%Ocean%lat_bnd_uv latitude axis grid box boundaries for momentum
- points on the ocean MODEL GRID (radians)
-
- Note: The data values in all longitude and latitude grid box boundary
- array must be monotonic.
-
- logical, dimension(:,:)
-
- Ocean%Data%mask ocean/land mask for temperature points on the ocean
- DATA GRID (true for ocean)
- Ocean%Data%mask_uv ocean/land mask for momentum points on the ocean
- DATA GRID (true for ocean)
-
- Ocean%Ocean%mask ocean/land mask for temperature points on the ocean
- MODEL GRID (true for ocean)
- Ocean%Ocean%mask_uv ocean/land mask for momentum points on the ocean
- MODEL GRID (true for ocean)
-
- real, dimension(:,:)
-
- Ocean%t_surf_data surface temperature on the ocean DATA GRID (deg k)
-
- Ocean%t_surf surface temperature on the ocean MODEL GRID (deg k)
- Ocean%u_surf zonal ocean current at the surface on the ocean
- MODEL GRID (m/s)
- Ocean%v_surf meridional ocean current at the surface on the
- ocean MODEL GRID (m/s)
- Ocean%frazil frazil at temperature points on the ocean MODEL GRID
-
-
diff --git a/src/coupler/surface_flux.F90 b/src/coupler/surface_flux.F90
index 33aff01d50..1f78542001 100644
--- a/src/coupler/surface_flux.F90
+++ b/src/coupler/surface_flux.F90
@@ -1,31 +1,27 @@
-! ============================================================================
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+!! !!
+!! GNU General Public License !!
+!! !!
+!! This file is part of the Flexible Modeling System (FMS). !!
+!! !!
+!! FMS is free software; you can redistribute it and/or modify it !!
+!! under the terms of the GNU General Public License as published by !!
+!! the Free Software Foundation, either version 3 of the License, or !!
+!! (at your option) any later version. !!
+!! !!
+!! FMS is distributed in the hope that it will be useful, !!
+!! but WITHOUT ANY WARRANTY; without even the implied warranty of !!
+!! MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the !!
+!! GNU General Public License for more details. !!
+!! !!
+!! You should have received a copy of the GNU General Public License !!
+!! along with FMS. if not, see: http://www.gnu.org/licenses/gpl.txt !!
+!! !!
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+
module surface_flux_mod
-!-----------------------------------------------------------------------
-! GNU General Public License
-!
-! This program is free software; you can redistribute it and/or modify it and
-! are expected to follow the terms of the GNU General Public License
-! as published by the Free Software Foundation; either version 2 of
-! the License, or (at your option) any later version.
-!
-! MOM is distributed in the hope that it will be useful, but WITHOUT
-! ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
-! or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
-! License for more details.
-!
-! For the full text of the GNU General Public License,
-! write to: Free Software Foundation, Inc.,
-! 675 Mass Ave, Cambridge, MA 02139, USA.
-! or see: http://www.gnu.org/licenses/gpl.html
-!-----------------------------------------------------------------------
!
-! Steve Klein
-! Isaac Held
-! Bruce Wyman
-
-! V. Balaji
-! Sergey Malyshev
-! Elena Shevliakova
+! GFDL
!
!
!
@@ -191,14 +187,14 @@ module surface_flux_mod
interface surface_flux
! module procedure surface_flux_0d
module procedure surface_flux_1d
-! module procedure surface_flux_2d
+ module procedure surface_flux_2d
end interface
!
!-----------------------------------------------------------------------
-character(len=*), parameter :: version = '$Id: surface_flux.F90,v 19.0 2012/01/06 20:36:33 fms Exp $'
-character(len=*), parameter :: tagname = '$Name: siena_201207 $'
+character(len=*), parameter :: version = '$Id: surface_flux.F90,v 20.0 2013/12/13 23:27:45 fms Exp $'
+character(len=*), parameter :: tagname = '$Name: tikal $'
logical :: do_init = .true.
@@ -726,6 +722,7 @@ subroutine surface_flux_init
! read namelist
#ifdef INTERNAL_FILE_NML
read (input_nml_file, surface_flux_nml, iostat=io)
+ ierr = check_nml_error(io,'surface_flux_nml')
#else
if ( file_exist('input.nml')) then
unit = open_namelist_file ()
@@ -754,8 +751,8 @@ end subroutine surface_flux_init
!~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~!
! Over-ocean fluxes following Large and Yeager (used in NCAR models) !
-! Original code: Michael.Winton
-! Update Jul2007: Stephen.Griffies (ch and ce exchange coeff bugfix)
+! Original code: GFDL.Climate.Model.Info
+! Update Jul2007: GFDL.Climate.Model.Info (ch and ce exchange coeff bugfix)
!~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~!
!
subroutine ncar_ocean_fluxes (u_del, t, ts, q, qs, z, avail, &
diff --git a/src/coupler/surface_flux.html b/src/coupler/surface_flux.html
deleted file mode 100644
index 47111e4f49..0000000000
--- a/src/coupler/surface_flux.html
+++ /dev/null
@@ -1,458 +0,0 @@
-
-
-
-Module surface_flux_mod
-
-
-
-
-PUBLIC INTERFACE
-
- ~ PUBLIC ROUTINES
- ~ NAMELIST
-
-
- Radiative energy flux temperature sensitivity
- [real, dimension(:)]
-
-
-
dhdt_atm
- Derivative of sensible heat flux over temp at the lowest atmos level.
- [real, dimension(:)]
-
-
-
dedq_atm
- Derivative of water vapor flux over temp at the lowest atmos level.
- [real, dimension(:)]
-
-
-
dtaudu_atm
- Derivative of zonal wind stress w.r.t the lowest level zonal
- wind speed of the atmos
- [real, dimension(:)]
-
-
-
dtaudv_atm
- Derivative of meridional wind stress w.r.t the lowest level meridional
- wind speed of the atmos
- [real, dimension(:)]
-
-
-
dt
- Time step (it is not used presently)
- [real]
-
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&surface_flux_nml
-
-
-
-
-
-no_neg_q
-
-
- If q_atm_in (specific humidity) is negative (because of numerical truncation),
- then override with 0.
-
-[logical, default: .false.]
-
-
-use_virtual_temp
-
-
- If true, use virtual potential temp to calculate the stability of the surface layer.
- if false, use potential temp.
-
-[logical, default: .true.]
-
-
-alt_gustiness
-
-
- An alternative formulation for gustiness calculation.
- A minimum bound on the wind speed used influx calculations, with the bound
- equal to gust_const
-
-[logical, default: .false.]
-
-
-old_dtaudv
-
-
- The derivative of surface wind stress w.r.t. the zonal wind and
- meridional wind are approximated by the same tendency.
-
-[logical, default: .false.]
-
-
-use_mixing_ratio
-
-
- An option to provide capability to run the Manabe Climate form of the
- surface flux (coded for legacy purposes).
-
-[logical, default: .false.]
-
-
-gust_const
-
-
- Constant for alternative gustiness calculation.
-
-[, default: 1.0]
-
-
-gust_min
-
-
- Minimum gustiness used when alt_gustiness = false.
-
-[, default: 0.0]
-
-
-ncar_ocean_flux
-
-
- Use NCAR climate model turbulent flux calculation described by
- Large and Yeager, NCAR Technical Document, 2004
-
-[logical, default: .false.]
-
-
-ncar_ocean_flux_orig
-
-
- Use NCAR climate model turbulent flux calculation described by
- Large and Yeager, NCAR Technical Document, 2004, using the original
- GFDL implementation, which contains a bug in the specification of
- the exchange coefficient for the sensible heat. This option is available
- for legacy purposes, and is not recommended for new experiments.
-
-[logical, default: .false.]
-
-
-raoult_sat_vap
-
-
- Reduce saturation vapor pressures to account for seawater salinity.
-
-[logical, default: .false.]
-
- Interface to the OASIS3
- This module serves as a hook between PRISM2-5/OASIS3 and mom4p1
- Only serial coupling has been tested at this stage (Oct 2009) although there are
- hints for the user for implementing different strategies.
-
- Standard mom surface quantities In Ocean_Ice_Boundary and Ocean_sfc may be passed
-
- The namelist ocean_oasis3_interface_nml contains the quantities to be passed to and from the ocean
-
- The number of fields to be passed to mom from external sources
-
-[integer, default: 0]
-
-
-num_fields_out
-
-
- The number of fields to be passed from mom to external progams
-
-[integer, default: 0]
-
-
-fields_in
-
-
- The fields to be passed to mom from external progams. Currently
- valid names correspond to variables in the Ice_ocean_boundary structure.
- These names must agree with names in the OASIS namcouple file
- WARNING! Note truncation of names of ssw flux components and salt_flx.
-
-[character(maxlen=8), default: '']
-
-
-fields_out
-
-
- The fields to be passed from mom to external progams. Currently
- valid names correspond to variables in the Ocean_sfc structure.
- These names must agree with the 'interpolated' names in the OASIS namcouple file
-
-[character(maxlen=8), default: '']
-
-
-send_before_ocean_update
-
-
- TRUE if coupling strategy requires we send data to coupler BEFORE updating the ocean
-
-[logical, default: .FALSE.]
-
-
-send_after_ocean_update
-
-
- TRUE if coupling strategy requires we send data to coupler AFTER updating the ocean
-
-[logical, default: .FALSE.]
-
- Driver for ocean-only simulations and prototype setup for OASIS3 driver.
-
-
-
-
-
- Driver for the ocean-only simulations. Similar to the FMS coupler, but
- allows one to run the ocean model without compiling other models.
- Much simpler than the full FMS coupler.
-
- This driver also provides the prototype hooks for using MOM with OASIS3,
- with this code surrounded by the cpp-preprocessor option "ifdef OASIS3".
- The couping of MOM to OASIS3 has not been tested at GFDL. Rather,
- CSIRO in Australia uses MOM with OASIS3, with Dave.Bi@csiro.au the primary
- contact for questions regarding MOM and OASIS3.
-
- The date that the current integration starts with. If the restart file
- ocean_solo.res is present, date_init will be taken from there.
-
-[integer, dimension(6), default: 0]
-
-
-calendar
-
-
- The calendar type used by the current integration. Valid values are consistent
- with the time_manager module: 'julian', 'gregorian', 'noleap', or 'thirty_day'.
- The value 'no_calendar' can not be used because the time_manager's date
- function are used.
-
-
-[character(maxlen=17), default: '']
-
-
-months
-
-
- The number of months that the current integration will be run for.
-
-[integer, default: 0]
-
-
-days
-
-
- The number of days that the current integration will be run for.
-
-[integer, default: 0]
-
-
-hours
-
-
- The number of hours that the current integration will be run for.
-
-[integer, default: 0]
-
-
-minutes
-
-
- The number of minutes that the current integration will be run for.
-
-[integer, default: 0]
-
-
-seconds
-
-
- The number of seconds that the current integration will be run for.
-
-[integer, default: 0]
-
-
-dt_cpld
-
-
- Time step in seconds for coupling between ocean and atmospheric models:
- must be an integral multiple of dt_ocean. This is the "slow" timestep.
- Note that for an ocean_solo model, the coupling to an "atmosphere" is the coupling
- to some data files. In this case, dt_cpld represents the time which data is updated.
- For example, if data is "daily", then dt_cpld=86400 should be chosen.
- If data is fixed, then dt_cpld of any integer of dt_ocean is fine, with
- dt_cpld=86400 the default.
-
-[integer, default: 0]
-
-
-n_mask
-
-
- number of region to be masked out. Its value should be less than MAX_PES.
-
-[integer]
-
-
-mask_list(2,MAXPES)
-
-
- The position of the region to be masked out. mask_list(1,:) is the x-layout position
- and mask_list(2,:) is y-layout position.
-
-[integer, dimension(MAX_MASK_REGION,2)]
-
-
-layout_mask
-
-
- Processor domain layout for all the component model. layout_mask need to be set when and only
- when n_mask is greater than 0 ( some domain region is masked out ). When this namelist is set,
- it will overload the layout in each component model. The default value is (0,0).
- Currently we require all the component model has the same layout and same grid size.
-
-[integer, dimension(2)]
-
-
-restart_interval
-
-
- The time interval that write out intermediate restart file. The format is (yr,mo,day,hr,min,sec).
- When restart_interval is all zero, no intermediate restart file will be written out.
-
-[integer, dimension(6), default: 0]
-
-
-
diff --git a/src/mom5/drivers/ocean_solo_nuopc.inc b/src/mom5/drivers/ocean_solo_nuopc.inc
new file mode 100644
index 0000000000..26d016252f
--- /dev/null
+++ b/src/mom5/drivers/ocean_solo_nuopc.inc
@@ -0,0 +1,1779 @@
+!---------------------------------------------------------------
+!------------------ Utilities ----------------------------------
+!
+!This is a set of utilities that convert time management data structures
+!between ESMF and FMS.
+!
+!Author: Fei Liu
+!Wed Feb 20 09:15:23 MST 2013
+!---------------------------------------------------------------
+
+module time_utils_mod
+
+ use fms_mod, only: uppercase
+ use mpp_mod, only: mpp_error, FATAL
+ use time_manager_mod, only: time_type, set_time, set_date, get_date
+ use time_manager_mod, only: GREGORIAN, JULIAN, NOLEAP, THIRTY_DAY_MONTHS, NO_CALENDAR
+ use time_manager_mod, only: fms_get_calendar_type => get_calendar_type
+ use ESMF
+
+ implicit none
+ private
+
+ !-------------------- interface blocks ---------------------
+ interface fms2esmf_cal
+ module procedure fms2esmf_cal_c
+ module procedure fms2esmf_cal_i
+ end interface fms2esmf_cal
+ interface esmf2fms_time
+ module procedure esmf2fms_time_t
+ module procedure esmf2fms_timestep
+ end interface esmf2fms_time
+
+ public fms2esmf_cal
+ public esmf2fms_time
+ public fms2esmf_time
+ public string_to_date
+
+ contains
+
+ !-------------------- module code ---------------------
+
+ function fms2esmf_cal_c(calendar)
+! ! Return Value:
+ type(ESMF_CALKIND_FLAG) :: fms2esmf_cal_c
+! ! Arguments:
+ character(len=*), intent(in) :: calendar
+
+ select case( uppercase(trim(calendar)) )
+ case( 'GREGORIAN' )
+ fms2esmf_cal_c = ESMF_CALKIND_GREGORIAN
+ case( 'JULIAN' )
+ fms2esmf_cal_c = ESMF_CALKIND_JULIAN
+ case( 'NOLEAP' )
+ fms2esmf_cal_c = ESMF_CALKIND_NOLEAP
+ case( 'THIRTY_DAY' )
+ fms2esmf_cal_c = ESMF_CALKIND_360DAY
+ case( 'NO_CALENDAR' )
+ fms2esmf_cal_c = ESMF_CALKIND_NOCALENDAR
+ case default
+ call mpp_error(FATAL, &
+ 'ocean_solo: ocean_solo_nml entry calendar must be one of GREGORIAN|JULIAN|NOLEAP|THIRTY_DAY|NO_CALENDAR.' )
+ end select
+ end function fms2esmf_cal_c
+
+ function fms2esmf_cal_i(calendar)
+! ! Return Value:
+ type(ESMF_CALKIND_FLAG) :: fms2esmf_cal_i
+! ! Arguments:
+ integer, intent(in) :: calendar
+
+ select case(calendar)
+ case(THIRTY_DAY_MONTHS)
+ fms2esmf_cal_i = ESMF_CALKIND_360DAY
+ case(GREGORIAN)
+ fms2esmf_cal_i = ESMF_CALKIND_GREGORIAN
+ case(JULIAN)
+ fms2esmf_cal_i = ESMF_CALKIND_JULIAN
+ case(NOLEAP)
+ fms2esmf_cal_i = ESMF_CALKIND_NOLEAP
+ case(NO_CALENDAR)
+ fms2esmf_cal_i = ESMF_CALKIND_NOCALENDAR
+ end select
+ end function fms2esmf_cal_i
+
+ function esmf2fms_time_t(time)
+ ! Return Value
+ type(Time_type) :: esmf2fms_time_t
+ ! Input Arguments
+ type(ESMF_Time), intent(in) :: time
+ ! Local Variables
+ integer :: yy, mm, dd, h, m, s
+ type(ESMF_CALKIND_FLAG) :: calkind
+
+ integer :: rc
+
+ call ESMF_TimeGet(time, yy=yy, mm=mm, dd=dd, h=h, m=m, s=s, &
+ calkindflag=calkind, rc=rc)
+ if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ line=__LINE__, &
+ file=__FILE__)) &
+ return ! bail out
+
+ esmf2fms_time_t = Set_date(yy, mm, dd, h, m, s)
+
+ end function esmf2fms_time_t
+
+ function esmf2fms_timestep(timestep)
+ ! Return Value
+ type(Time_type) :: esmf2fms_timestep
+ ! Input Arguments
+ type(ESMF_TimeInterval), intent(in):: timestep
+ ! Local Variables
+ integer :: s
+ type(ESMF_CALKIND_FLAG) :: calkind
+
+ integer :: rc
+
+ call ESMF_TimeIntervalGet(timestep, s=s, calkindflag=calkind, rc=rc)
+ if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ line=__LINE__, &
+ file=__FILE__)) &
+ return ! bail out
+
+ esmf2fms_timestep = set_time(s, 0)
+
+ end function esmf2fms_timestep
+
+ function fms2esmf_time(time, calkind)
+ ! Return Value
+ type(ESMF_Time) :: fms2esmf_time
+ ! Input Arguments
+ type(Time_type), intent(in) :: time
+ type(ESMF_CALKIND_FLAG), intent(in), optional :: calkind
+ ! Local Variables
+ integer :: yy, mm, d, h, m, s
+ type(ESMF_CALKIND_FLAG) :: l_calkind
+
+ integer :: rc
+
+ if(present(calkind)) then
+ l_calkind = calkind
+ else
+ l_calkind = fms2esmf_cal(fms_get_calendar_type())
+ endif
+
+ call get_date(time, yy, mm, d, h, m, s)
+
+ call ESMF_TimeSet(fms2esmf_time, yy=yy, mm=mm, d=d, h=h, m=m, s=s, &
+ calkindflag=l_calkind, rc=rc)
+ if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ line=__LINE__, &
+ file=__FILE__)) &
+ return ! bail out
+
+ end function fms2esmf_time
+
+ function string_to_date(string, rc)
+ character(len=15), intent(in) :: string
+ integer, intent(out), optional :: rc
+ type(time_type) :: string_to_date
+
+ integer :: yr,mon,day,hr,min,sec
+
+ if(present(rc)) rc = ESMF_SUCCESS
+
+ read(string, '(I4.4,I2.2,I2.2,".",I2.2,I2.2,I2.2)') yr, mon, day, hr, min, sec
+ string_to_date = set_date(yr, mon, day, hr, min, sec)
+
+ end function string_to_date
+
+end module time_utils_mod
+
+!--------------- MOM5 Ocean solo model -----------------
+! This is the MOM5 ocean solo model component that's NUOPC compiant.
+! The public ocean_solo_SS method sets up all the model services such as
+! initialize, run and finalize.
+!
+! Author: Fei.Liu@gmail.com
+!
+
+module ocean_solo_mod
+ use constants_mod, only: constants_init
+ use data_override_mod, only: data_override_init, data_override
+ use diag_manager_mod, only: diag_manager_init, diag_manager_end
+ use field_manager_mod, only: field_manager_init
+ use fms_mod, only: fms_init, fms_end, open_namelist_file, check_nml_error
+ use fms_mod, only: close_file, file_exist, uppercase
+ use fms_io_mod, only: fms_io_exit
+ use mpp_domains_mod, only: domain2d, mpp_get_compute_domain
+ use mpp_io_mod, only: mpp_open, MPP_RDONLY, MPP_ASCII, MPP_OVERWR, MPP_APPEND, mpp_close, MPP_SINGLE
+ use mpp_mod, only: input_nml_file, mpp_error, FATAL, NOTE, mpp_pe, mpp_npes, mpp_set_current_pelist
+ use mpp_mod, only: stdlog, stdout, mpp_root_pe, mpp_clock_id
+ use mpp_mod, only: mpp_clock_begin, mpp_clock_end, MPP_CLOCK_SYNC
+ use mpp_mod, only: MPP_CLOCK_DETAILED, CLOCK_COMPONENT, MAXPES
+ use time_interp_external_mod, only: time_interp_external_init
+ use time_manager_mod, only: set_calendar_type, time_type, increment_date
+ use time_manager_mod, only: set_time, set_date, get_time, get_date, month_name
+ use time_manager_mod, only: GREGORIAN, JULIAN, NOLEAP, THIRTY_DAY_MONTHS, NO_CALENDAR
+ use time_manager_mod, only: operator( <= ), operator( < ), operator( >= )
+ use time_manager_mod, only: operator( + ), operator( - ), operator( / )
+ use time_manager_mod, only: operator( * ), operator( /= ), operator( > )
+ use time_manager_mod, only: date_to_string
+ use time_manager_mod, only: fms_get_calendar_type => get_calendar_type
+ use ocean_model_mod, only: ocean_model_init , update_ocean_model, ocean_model_end
+ use ocean_model_mod, only: ocean_model_restart, ocean_public_type, ocean_state_type
+ use ocean_types_mod, only: ice_ocean_boundary_type
+
+ use ESMF
+ use NUOPC
+ use NUOPC_Model, only: &
+ model_routine_SS => routine_SetServices, &
+ model_label_SetClock => label_SetClock, &
+ model_label_Advance => label_Advance
+
+ use time_utils_mod
+
+ implicit none
+ private
+ public ocean_solo_SS
+
+ type ocean_internalstate_type
+ type(ocean_public_type), pointer :: ocean_public_type_ptr
+ type(ocean_state_type), pointer :: ocean_state_type_ptr
+ type(ice_ocean_boundary_type), pointer :: ice_ocean_boundary_type_ptr
+ end type
+
+ type ocean_internalstate_wrapper
+ type(ocean_internalstate_type), pointer :: ptr
+ end type
+
+ contains
+ !-----------------------------------------------------------------------
+ !------------------- Solo Ocean code starts here -----------------------
+ !-----------------------------------------------------------------------
+
+ subroutine ocean_solo_SS(gcomp, rc)
+
+ type(ESMF_GridComp) :: gcomp
+ integer, intent(out) :: rc
+
+ rc = ESMF_SUCCESS
+
+ ! the NUOPC model component will register the generic methods
+ call model_routine_SS(gcomp, rc=rc)
+ if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ line=__LINE__, &
+ file=__FILE__)) &
+ return ! bail out
+
+ ! set entry point for methods that require specific implementation
+ call ESMF_GridCompSetEntryPoint(gcomp, ESMF_METHOD_INITIALIZE, &
+ userRoutine=InitializeP1, phase=1, rc=rc)
+ if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ line=__LINE__, &
+ file=__FILE__)) &
+ return ! bail out
+ call ESMF_GridCompSetEntryPoint(gcomp, ESMF_METHOD_INITIALIZE, &
+ userRoutine=InitializeP2, phase=2, rc=rc)
+ if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ line=__LINE__, &
+ file=__FILE__)) &
+ return ! bail out
+
+ call ESMF_GridCompSetEntryPoint(gcomp, ESMF_METHOD_FINALIZE, &
+ userRoutine=ocean_solo_finalize, rc=rc)
+ if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ line=__LINE__, &
+ file=__FILE__)) &
+ return ! bail out
+
+ ! attach specializing method(s)
+ ! No need to change clock settings
+ !call ESMF_MethodAdd(gcomp, label=model_label_SetClock, &
+ ! userRoutine=SetClock, rc=rc)
+ !if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ ! line=__LINE__, &
+ ! file=__FILE__)) &
+ ! return ! bail out
+
+ call ESMF_MethodAdd(gcomp, label=model_label_Advance, &
+ userRoutine=ModelAdvance, rc=rc)
+ if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ line=__LINE__, &
+ file=__FILE__)) &
+ return ! bail out
+
+ end subroutine
+
+ subroutine InitializeP1(gcomp, importState, exportState, clock, rc)
+
+ type(ESMF_GridComp) :: gcomp
+ type(ESMF_State) :: importState, exportState
+ type(ESMF_Clock) :: clock
+ integer, intent(out) :: rc
+
+ type(ESMF_VM) :: vm
+
+ type (ocean_public_type), pointer :: Ocean_sfc
+ type (ocean_state_type), pointer :: Ocean_state => NULL()
+ type(ice_ocean_boundary_type), pointer :: Ice_ocean_boundary
+
+ ! define some time types
+ type(time_type) :: Time_init ! initial time for experiment
+ type(time_type) :: Time_start ! start time for experiment
+ type(time_type) :: Time_end ! end time for experiment (as determined by dtts)
+ type(time_type) :: Run_len ! length of experiment
+ type(time_type) :: Time
+ type(time_type) :: Time_step_coupled
+ type(time_type) :: Time_restart_init
+ type(time_type) :: Time_restart
+ type(time_type) :: Time_restart_current
+
+
+ integer :: num_cpld_calls = 0
+ integer :: nc
+ integer :: calendar_type=-1
+
+
+ integer :: isc,iec,jsc,jec
+ integer :: unit, io_status, ierr
+
+ integer :: flags=0, override_clock
+ integer :: nfields
+
+ character(len=256) :: version = ''
+ character(len=256) :: tag = ''
+
+ character(len=9) :: month
+ character(ESMF_MAXSTR):: timestamp
+
+ integer :: n, m
+
+ integer :: date_init(6)=0, date(6)
+ integer :: date_restart(6)
+ character(len=17) :: calendar = 'julian'
+ integer :: dt_cpld = 86400
+ integer :: years=0, months=0, days=0, hours=0, minutes=0, seconds=0
+ integer :: layout_mask(2) = (/0 , 0/)
+ integer :: n_mask = 0
+ integer :: mask_list(2,MAXPES)
+ integer, parameter :: mp = 2*MAXPES
+ data ((mask_list(n,m),n=1, 2),m=1,MAXPES) /mp*0/
+ integer :: restart_interval(6) = (/0,0,0,0,0,0/)
+
+ namelist /ocean_solo_nml/ date_init, calendar, months, days, hours, minutes, seconds, dt_cpld, &
+ n_mask, layout_mask, mask_list, restart_interval
+
+ integer :: mpi_comm_mom
+ integer :: stdoutunit,stdlogunit
+ logical :: external_initialization
+
+ type(ocean_internalstate_wrapper) :: ocean_internalstate
+
+ rc = ESMF_SUCCESS
+
+ allocate(Ice_ocean_boundary)
+ !allocate(Ocean_state) ! ocean_model_init allocate this pointer
+ allocate(Ocean_sfc)
+ allocate(ocean_internalstate%ptr)
+ ocean_internalstate%ptr%ice_ocean_boundary_type_ptr => Ice_ocean_boundary
+ ocean_internalstate%ptr%ocean_public_type_ptr => Ocean_sfc
+
+ ! To start we have a dummy ocean that will not import or export anything.
+ !
+ !! importable field: air_pressure_at_sea_level
+ !call NUOPC_StateAdvertiseField(importState, &
+ ! StandardName="air_pressure_at_sea_level", rc=rc)
+ !if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ ! line=__LINE__, &
+ ! file=__FILE__)) &
+ ! return ! bail out
+ !
+ !! importable field: isotropic_shortwave_radiance_in_air
+ !call NUOPC_StateAdvertiseField(importState, &
+ ! StandardName="isotropic_shortwave_radiance_in_air", rc=rc)
+ !if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ ! line=__LINE__, &
+ ! file=__FILE__)) &
+ ! return ! bail out
+
+ ! exportable field: sea_surface_temperature
+ !call NUOPC_StateAdvertiseField(exportState, &
+ ! StandardName="sea_surface_temperature", rc=rc)
+ !if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ ! line=__LINE__, &
+ ! file=__FILE__)) &
+ ! return ! bail out
+
+ !call external_coupler_mpi_init(mpi_comm_mom, external_initialization)
+
+ call constants_init
+
+ flags = MPP_CLOCK_SYNC
+
+ stdoutunit=stdout();stdlogunit=stdlog()
+
+ ! provide for namelist over-ride
+#ifdef INTERNAL_FILE_NML
+ read (input_nml_file, nml=ocean_solo_nml, iostat=io_status)
+ ierr = check_nml_error(io_status,'ocean_solo_nml')
+#else
+ unit = open_namelist_file('input.nml')
+ read (unit, ocean_solo_nml,iostat=io_status)
+ ierr = check_nml_error(io_status,'ocean_solo_nml')
+ call close_file (unit)
+#endif
+ write (stdoutunit,'(/)')
+ write (stdoutunit,'(/47x,a/)') '======== MODEL BEING DRIVEN BY OCEAN_SOLO_MOD ========'
+ write (stdoutunit, ocean_solo_nml)
+ write (stdlogunit, ocean_solo_nml)
+
+ write (stdlogunit,'(/,80("="),/(a))') trim(version), trim(tag)
+
+ ! set the calendar
+
+ select case( uppercase(trim(calendar)) )
+ case( 'GREGORIAN' )
+ calendar_type = GREGORIAN
+ case( 'JULIAN' )
+ calendar_type = JULIAN
+ case( 'NOLEAP' )
+ calendar_type = NOLEAP
+ case( 'THIRTY_DAY' )
+ calendar_type = THIRTY_DAY_MONTHS
+ case( 'NO_CALENDAR' )
+ calendar_type = NO_CALENDAR
+ case default
+ call mpp_error(FATAL, &
+ 'ocean_solo: ocean_solo_nml entry calendar must be one of GREGORIAN|JULIAN|NOLEAP|THIRTY_DAY|NO_CALENDAR.' )
+ end select
+
+ ! get ocean_solo restart : this can override settings from namelist
+ if (file_exist('INPUT/ocean_solo.res')) then
+ call mpp_open(unit,'INPUT/ocean_solo.res',form=MPP_ASCII,action=MPP_RDONLY)
+ read(unit,*) calendar_type
+ read(unit,*) date_init
+ read(unit,*) date
+ call mpp_close(unit)
+ endif
+
+ if (file_exist('INPUT/ocean_solo.intermediate.res')) then
+ call mpp_open(unit,'INPUT/ocean_solo.intermediate.res',form=MPP_ASCII,action=MPP_RDONLY)
+ read(unit,*) date_restart
+ call mpp_close(unit)
+ else
+ date_restart = date_init
+ endif
+
+ call set_calendar_type (calendar_type)
+
+ !!$ initialize pelists for ocean ensembles set current pelist to ensemble member
+ !!$ need to call prior to diagnostics_init
+ !!$ code presently not supported (mjh)
+ !!$ call ocean_ensemble_init()
+
+ call field_manager_init(nfields)
+
+ call diag_manager_init()
+
+ call time_interp_external_init()
+
+ if (sum(date_init) <= 0) then
+ call mpp_error(FATAL,&
+ '==>Error from ocean_solo_mod: date_init must be set either in ocean_solo.res or in ocean_solo_nml')
+ else
+ Time_init = set_date(date_init(1),date_init(2), date_init(3), &
+ date_init(4),date_init(5),date_init(6))
+ endif
+
+ if (file_exist('INPUT/ocean_solo.res')) then
+ Time_start = set_date(date(1),date(2),date(3),date(4),date(5),date(6))
+ else
+ Time_start = Time_init
+ date = date_init
+ endif
+
+ Time_end = increment_date(Time_start, years, months, days, hours, minutes, seconds)
+ Run_len = Time_end - Time_start
+
+
+ Time_step_coupled = set_time(dt_cpld, 0)
+ num_cpld_calls = Run_len / Time_step_coupled
+ Time = Time_start
+
+ Time_restart_init = set_date(date_restart(1), date_restart(2), date_restart(3), &
+ date_restart(4), date_restart(5), date_restart(6) )
+ Time_restart_current = Time_start
+ if(ALL(restart_interval ==0)) then
+ Time_restart = increment_date(Time_end, 1, 0, 0, 0, 0, 0) ! no intermediate restart
+ else
+ Time_restart = increment_date(Time_restart_init, restart_interval(1), restart_interval(2), &
+ restart_interval(3), restart_interval(4), restart_interval(5), restart_interval(6) )
+ if(Time_restart <= Time_start) call mpp_error(FATAL, &
+ '==>Error from program ocean_solo: The first intermediate restart time is no larger than the start time')
+ end if
+
+ !-----------------------------------------------------------------------
+ !------------------- some error checks ---------------------------------
+ if ( num_cpld_calls * Time_step_coupled /= Run_len ) call mpp_error(FATAL, &
+ '==>Error from program ocean_solo: run length must be multiple of cpld time step', FATAL)
+
+ call mpp_open (unit, 'time_stamp.out', form=MPP_ASCII, action=MPP_APPEND,threading=MPP_SINGLE)
+
+ month = month_name(date(2))
+ if ( mpp_pe() == mpp_root_pe() ) write (unit,'(6i4,2x,a3)') date, month(1:3)
+
+ call get_date (Time_end, date(1), date(2), date(3), date(4), date(5), date(6))
+ month = month_name(date(2))
+ if ( mpp_pe() == mpp_root_pe() ) write (unit,'(6i4,2x,a3)') date, month(1:3)
+
+ call mpp_close (unit)
+
+ !----- check the value of layout and setup the maskmap for domain layout.
+ if( n_mask > 0 ) then
+ if( layout_mask(1)*layout_mask(2) - n_mask .NE. mpp_npes() ) call mpp_error(FATAL, &
+ '==>Error from program ocean_solo: layout(1)*layout(2) - n_mask should equal to npes when n_mask>0')
+ call mpp_error(NOTE, &
+ '==>Error from program ocean_solo: layout_mask and mask_list is set in ocean_solo_nml, ' // &
+ 'the value of layout_mask will override the layout specified in ocean_model_mod')
+
+ allocate(Ocean_sfc%maskmap(layout_mask(1), layout_mask(2)) )
+ Ocean_sfc%maskmap = .TRUE.
+ do n=1, n_mask
+ if (mask_list(1,n) .gt. layout_mask(1) ) &
+ call mpp_error( FATAL, &
+ 'program ocean_solo: mask_list elements outside layout defines.' )
+ if (mask_list(2,n) .gt. layout_mask(2) ) &
+ call mpp_error( FATAL, &
+ 'program ocean_solo: mask_list elements outside layout defines.' )
+ Ocean_sfc%maskmap(mask_list(1,n),mask_list(2,n)) = .false.
+ enddo
+ else
+ if( layout_mask(1)*layout_mask(2) .NE. 0 ) call mpp_error(NOTE, &
+ 'program ocean_solo: when no region is masked out, layout_mask need not be set' )
+ end if
+
+
+
+ call ocean_model_init(Ocean_sfc, Ocean_state, Time_init, Time)
+
+ call data_override_init(Ocean_domain_in = Ocean_sfc%domain)
+
+ !override_clock = mpp_clock_id('Override', flags=flags,grain=CLOCK_COMPONENT)
+
+ call mpp_get_compute_domain(Ocean_sfc%domain, isc, iec, jsc, jec)
+
+
+ allocate ( Ice_ocean_boundary% u_flux (isc:iec,jsc:jec), &
+ Ice_ocean_boundary% v_flux (isc:iec,jsc:jec), &
+ Ice_ocean_boundary% t_flux (isc:iec,jsc:jec), &
+ Ice_ocean_boundary% q_flux (isc:iec,jsc:jec), &
+ Ice_ocean_boundary% salt_flux (isc:iec,jsc:jec), &
+ Ice_ocean_boundary% lw_flux (isc:iec,jsc:jec), &
+ Ice_ocean_boundary% sw_flux_vis_dir (isc:iec,jsc:jec), &
+ Ice_ocean_boundary% sw_flux_vis_dif (isc:iec,jsc:jec), &
+ Ice_ocean_boundary% sw_flux_nir_dir (isc:iec,jsc:jec), &
+ Ice_ocean_boundary% sw_flux_nir_dif (isc:iec,jsc:jec), &
+ Ice_ocean_boundary% lprec (isc:iec,jsc:jec), &
+ Ice_ocean_boundary% fprec (isc:iec,jsc:jec), &
+ Ice_ocean_boundary% runoff (isc:iec,jsc:jec), &
+ Ice_ocean_boundary% calving (isc:iec,jsc:jec), &
+ Ice_ocean_boundary% p (isc:iec,jsc:jec))
+
+ Ice_ocean_boundary%u_flux = 0.0
+ Ice_ocean_boundary%v_flux = 0.0
+ Ice_ocean_boundary%t_flux = 0.0
+ Ice_ocean_boundary%q_flux = 0.0
+ Ice_ocean_boundary%salt_flux = 0.0
+ Ice_ocean_boundary%lw_flux = 0.0
+ Ice_ocean_boundary%sw_flux_vis_dir = 0.0
+ Ice_ocean_boundary%sw_flux_vis_dif = 0.0
+ Ice_ocean_boundary%sw_flux_nir_dir = 0.0
+ Ice_ocean_boundary%sw_flux_nir_dif = 0.0
+ Ice_ocean_boundary%lprec = 0.0
+ Ice_ocean_boundary%fprec = 0.0
+ Ice_ocean_boundary%runoff = 0.0
+ Ice_ocean_boundary%calving = 0.0
+ Ice_ocean_boundary%p = 0.0
+
+ call external_coupler_sbc_init(Ocean_sfc%domain, dt_cpld, Run_len)
+
+ ocean_internalstate%ptr%ocean_state_type_ptr => Ocean_state
+ call ESMF_GridCompSetInternalState(gcomp, ocean_internalstate, rc)
+ if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ line=__LINE__, &
+ file=__FILE__)) &
+ return ! bail out
+
+ ! Set some MOM_solo specific attributes to be used during finalize
+ call ESMF_AttributeSet(gcomp, name="dt_cpld", value=dt_cpld, rc=rc)
+ if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ line=__LINE__, &
+ file=__FILE__)) &
+ return ! bail out
+ call ESMF_AttributeSet(gcomp, name="num_cpld_calls", value=num_cpld_calls, rc=rc)
+ if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ line=__LINE__, &
+ file=__FILE__)) &
+ return ! bail out
+ call ESMF_AttributeSet(gcomp, name="calendar_type", value=calendar_type, rc=rc)
+ if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ line=__LINE__, &
+ file=__FILE__)) &
+ return ! bail out
+
+ timestamp = date_to_string(time_restart)
+ call ESMF_AttributeSet(gcomp, name="Time_restart", value=timestamp, rc=rc)
+ if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ line=__LINE__, &
+ file=__FILE__)) &
+ return ! bail out
+
+ timestamp = date_to_string(time_restart_current)
+ call ESMF_AttributeSet(gcomp, name="Time_restart_current", value=timestamp, rc=rc)
+ if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ line=__LINE__, &
+ file=__FILE__)) &
+ return ! bail out
+
+ timestamp = date_to_string(time_end)
+ call ESMF_AttributeSet(gcomp, name="Time_end", value=timestamp, rc=rc)
+ if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ line=__LINE__, &
+ file=__FILE__)) &
+ return ! bail out
+
+ timestamp = date_to_string(time_init)
+ call ESMF_AttributeSet(gcomp, name="Time_init", value=timestamp, rc=rc)
+ if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ line=__LINE__, &
+ file=__FILE__)) &
+ return ! bail out
+
+ timestamp = date_to_string(time_start)
+ call ESMF_AttributeSet(gcomp, name="Time_start", value=timestamp, rc=rc)
+ if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ line=__LINE__, &
+ file=__FILE__)) &
+ return ! bail out
+
+ end subroutine
+
+ !-----------------------------------------------------------------------------
+
+ subroutine InitializeP2(gcomp, importState, exportState, clock, rc)
+ type(ESMF_GridComp) :: gcomp
+ type(ESMF_State) :: importState, exportState
+ type(ESMF_Clock) :: clock
+ integer, intent(out) :: rc
+
+ ! local variables
+ type(ESMF_TimeInterval) :: stabilityTimeStep
+ type(ESMF_Field) :: field
+ type(ESMF_Grid) :: gridIn
+ type(ESMF_Grid) :: gridOut
+
+ rc = ESMF_SUCCESS
+
+ ! To start we have a dummy ocean that will not import or export anything.
+ !
+ !! create a Grid object for Fields
+ !gridIn = NUOPC_GridCreateSimpleXY(10._ESMF_KIND_R8, 20._ESMF_KIND_R8, &
+ ! 100._ESMF_KIND_R8, 200._ESMF_KIND_R8, 10, 100, rc)
+ !if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ ! line=__LINE__, &
+ ! file=__FILE__)) &
+ ! return ! bail out
+ !gridOut = gridIn ! for now out same as in
+ !! importable field: air_pressure_at_sea_level
+ !field = ESMF_FieldCreate(name="pmsl", grid=gridIn, &
+ ! typekind=ESMF_TYPEKIND_R8, rc=rc)
+ !if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ ! line=__LINE__, &
+ ! file=__FILE__)) &
+ ! return ! bail out
+ !call NUOPC_StateRealizeField(importState, field=field, rc=rc)
+ !if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ ! line=__LINE__, &
+ ! file=__FILE__)) &
+ ! return ! bail out
+ !
+ !! importable field: isotropic_shortwave_radiance_in_air
+ !field = ESMF_FieldCreate(name="risw", grid=gridIn, &
+ ! typekind=ESMF_TYPEKIND_R8, rc=rc)
+ !if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ ! line=__LINE__, &
+ ! file=__FILE__)) &
+ ! return ! bail out
+ !call NUOPC_StateRealizeField(importState, field=field, rc=rc)
+ !if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ ! line=__LINE__, &
+ ! file=__FILE__)) &
+ ! return ! bail out
+
+ !! exportable field: sea_surface_temperature
+ !field = ESMF_FieldCreate(name="sst", grid=gridOut, &
+ ! typekind=ESMF_TYPEKIND_R8, rc=rc)
+ !if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ ! line=__LINE__, &
+ ! file=__FILE__)) &
+ ! return ! bail out
+ !call NUOPC_StateRealizeField(exportState, field=field, rc=rc)
+ !if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ ! line=__LINE__, &
+ ! file=__FILE__)) &
+ ! return ! bail out
+
+ end subroutine
+
+ !-----------------------------------------------------------------------------
+
+ ! Ocean solo model uses same clock as parent gridComp
+ !subroutine SetClock(gcomp, rc)
+ ! type(ESMF_GridComp) :: gcomp
+ ! integer, intent(out) :: rc
+ !
+ ! ! local variables
+ ! type(ESMF_Clock) :: clock
+ ! type(ESMF_TimeInterval) :: stabilityTimeStep
+
+ ! rc = ESMF_SUCCESS
+ !
+ ! ! query the Component for its clock, importState and exportState
+ ! call ESMF_GridCompGet(gcomp, clock=clock, rc=rc)
+ ! if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ ! line=__LINE__, &
+ ! file=__FILE__)) &
+ ! return ! bail out
+ !
+ ! ! initialize internal clock
+ ! ! here: parent Clock and stability timeStep determine actual model timeStep
+ ! !TODO: stabilityTimeStep should be read in from configuation
+ ! !TODO: or computed from internal Grid information
+ ! call ESMF_TimeIntervalSet(stabilityTimeStep, m=60, rc=rc)
+ ! if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ ! line=__LINE__, &
+ ! file=__FILE__)) &
+ ! return ! bail out
+ ! call NUOPC_GridCompSetClock(gcomp, clock, stabilityTimeStep, rc=rc)
+ ! if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ ! line=__LINE__, &
+ ! file=__FILE__)) &
+ ! return ! bail out
+
+ !
+ !end subroutine
+
+ !-----------------------------------------------------------------------------
+
+ subroutine ModelAdvance(gcomp, rc)
+ type(ESMF_GridComp) :: gcomp
+ integer, intent(out) :: rc
+
+ ! local variables
+ type(ESMF_Clock) :: clock
+ type(ESMF_State) :: importState, exportState
+ type(ESMF_Time) :: currTime
+ type(ESMF_TimeInterval) :: timeStep
+
+ type (ocean_public_type), pointer :: Ocean_sfc
+ type (ocean_state_type), pointer :: Ocean_state
+ type(ice_ocean_boundary_type), pointer :: Ice_ocean_boundary
+
+ ! define some time types
+ type(time_type) :: Time
+ type(time_type) :: Time_step_coupled
+ type(time_type) :: Time_restart
+ type(time_type) :: Time_restart_current
+
+ character(len=17) :: calendar = 'julian'
+
+ integer :: dt_cpld = 86400
+ integer :: nc
+ integer :: calendar_type=-1
+
+ integer :: date_init(6)=0, date(6)
+ integer :: date_restart(6)
+ integer :: years=0, months=0, days=0, hours=0, minutes=0, seconds=0
+
+ integer :: isc,iec,jsc,jec
+
+ integer :: flags=0, override_clock
+ integer :: nfields
+
+ character(len=9) :: month
+ character(len=64):: timestamp
+ integer :: restart_interval(6) = (/1,0,0,0,0,0/)
+ type(ocean_internalstate_wrapper) :: ocean_internalstate
+
+
+ rc = ESMF_SUCCESS
+
+ ! query the Component for its clock, importState and exportState
+ call ESMF_GridCompGet(gcomp, clock=clock, importState=importState, &
+ exportState=exportState, rc=rc)
+ if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ line=__LINE__, &
+ file=__FILE__)) &
+ return ! bail out
+
+ call ESMF_GridCompGetInternalState(gcomp, ocean_internalstate, rc)
+ if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ line=__LINE__, &
+ file=__FILE__)) &
+ return ! bail out
+
+ Ice_ocean_boundary => ocean_internalstate%ptr%ice_ocean_boundary_type_ptr
+ Ocean_sfc => ocean_internalstate%ptr%ocean_public_type_ptr
+ Ocean_state => ocean_internalstate%ptr%ocean_state_type_ptr
+
+ ! HERE THE MODEL ADVANCES: currTime -> currTime + timeStep
+
+ ! Because of the way that the internal Clock was set in SetClock(),
+ ! its timeStep is likely smaller than the parent timeStep. As a consequence
+ ! the time interval covered by a single parent timeStep will result in
+ ! multiple calls to the ModelAdvance() routine. Every time the currTime
+ ! will come in by one internal timeStep advanced. This goes until the
+ ! stopTime of the internal Clock has been reached.
+
+ call NUOPC_ClockPrintCurrTime(clock, &
+ "------>Advancing OCN from: ", rc=rc)
+ if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ line=__LINE__, &
+ file=__FILE__)) &
+ return ! bail out
+
+ call ESMF_ClockGet(clock, currTime=currTime, timeStep=timeStep, rc=rc)
+ if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ line=__LINE__, &
+ file=__FILE__)) &
+ return ! bail out
+
+ call NUOPC_TimePrint(currTime + timeStep, &
+ "--------------------------------> to: ", rc=rc)
+ if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ line=__LINE__, &
+ file=__FILE__)) &
+ return ! bail out
+
+ Time = esmf2fms_time(currTime)
+ Time_step_coupled = esmf2fms_time(timeStep)
+
+ ! Retrieve some MOM_solo specific attribute
+ call ESMF_AttributeGet(gcomp, name="dt_cpld", value=dt_cpld, rc=rc)
+ if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ line=__LINE__, &
+ file=__FILE__)) &
+ return ! bail out
+ call ESMF_AttributeGet(gcomp, name="Time_restart", value=timestamp, rc=rc)
+ if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ line=__LINE__, &
+ file=__FILE__)) &
+ return ! bail out
+ Time_restart = string_to_date(timestamp)
+ call ESMF_AttributeGet(gcomp, name="Time_restart_current", value=timestamp, rc=rc)
+ if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ line=__LINE__, &
+ file=__FILE__)) &
+ return ! bail out
+ Time_restart_current = string_to_date(timestamp)
+
+ override_clock = mpp_clock_id('Override', flags=flags,grain=CLOCK_COMPONENT)
+ call mpp_clock_begin(override_clock)
+
+ call ice_ocn_bnd_from_data(Ice_ocean_boundary, Time, Time_step_coupled)
+
+ call mpp_clock_end(override_clock)
+
+ call external_coupler_sbc_before(Ice_ocean_boundary, Ocean_sfc, nc, dt_cpld )
+
+ call update_ocean_model(Ice_ocean_boundary, Ocean_state, Ocean_sfc, Time, Time_step_coupled)
+
+ Time = Time + Time_step_coupled
+
+ if( Time >= Time_restart ) then
+ Time_restart_current = Time
+ Time_restart = increment_date(Time, restart_interval(1), restart_interval(2), &
+ restart_interval(3), restart_interval(4), restart_interval(5), restart_interval(6) )
+ timestamp = date_to_string(time_restart_current)
+ write(*,*) '=> NOTE from program ocean_solo: intermediate restart file is written and ', &
+ trim(timestamp),' is appended as prefix to each restart file name'
+ call ocean_model_restart(Ocean_state, timestamp)
+ call ocean_solo_restart(gcomp, Time, Time_restart_current, timestamp)
+ end if
+
+ call external_coupler_sbc_after(Ice_ocean_boundary, Ocean_sfc, nc, dt_cpld )
+
+ ! Set Time_restart_current
+ timestamp = date_to_string(time_restart_current)
+ call ESMF_AttributeSet(gcomp, name="Time_restart_current", value=timestamp, rc=rc)
+ if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ line=__LINE__, &
+ file=__FILE__)) &
+ return ! bail out
+
+ end subroutine
+
+ subroutine ocean_solo_finalize(gcomp, importState, exportState, clock, rc)
+
+ ! input arguments
+ type(ESMF_GridComp) :: gcomp
+ type(ESMF_State) :: importState, exportState
+ type(ESMF_Clock) :: clock
+ integer, intent(out) :: rc
+
+ ! local variables
+ type (ocean_public_type), pointer :: Ocean_sfc
+ type (ocean_state_type), pointer :: Ocean_state
+ type(ocean_internalstate_wrapper) :: ocean_internalstate
+ type(time_type) :: Time, Time_restart_current, Time_end
+ type(ESMF_Time) :: currTime
+ type(ESMF_VM) :: vm
+ integer :: mpi_comm_mom, dt_cpld, num_cpld_calls
+ character(len=64) :: timestamp
+
+ rc = ESMF_SUCCESS
+
+ call ESMF_GridCompGetInternalState(gcomp, ocean_internalstate, rc)
+ if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ line=__LINE__, &
+ file=__FILE__)) &
+ return ! bail out
+
+ Ocean_sfc => ocean_internalstate%ptr%ocean_public_type_ptr
+ Ocean_state => ocean_internalstate%ptr%ocean_state_type_ptr
+
+ call ESMF_ClockGet(clock, currTime=currTime, rc=rc)
+ if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ line=__LINE__, &
+ file=__FILE__)) &
+ return ! bail out
+ Time = esmf2fms_time(currTime)
+
+ call ESMF_VMGetCurrent(vm=vm, rc=rc)
+ if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ line=__LINE__, &
+ file=__FILE__)) &
+ return ! bail out
+
+ call ESMF_VMGet(vm, mpiCommunicator=mpi_comm_mom, rc=rc)
+ if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ line=__LINE__, &
+ file=__FILE__)) &
+ return ! bail out
+
+ ! Retrieve some MOM_solo specific attributes
+ call ESMF_AttributeGet(gcomp, name="dt_cpld", value=dt_cpld, rc=rc)
+ if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ line=__LINE__, &
+ file=__FILE__)) &
+ return ! bail out
+ call ESMF_AttributeGet(gcomp, name="num_cpld_calls", value=num_cpld_calls, rc=rc)
+ if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ line=__LINE__, &
+ file=__FILE__)) &
+ return ! bail out
+ call ESMF_AttributeGet(gcomp, name="Time_end", value=timestamp, rc=rc)
+ if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ line=__LINE__, &
+ file=__FILE__)) &
+ return ! bail out
+ Time_end = string_to_date(timestamp)
+ call ESMF_AttributeGet(gcomp, name="Time_restart_current", value=timestamp, rc=rc)
+ if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ line=__LINE__, &
+ file=__FILE__)) &
+ return ! bail out
+ Time_restart_current= string_to_date(timestamp)
+
+ ! close some of the main components
+
+ call ocean_model_end(Ocean_sfc, Ocean_state, Time)
+
+ call diag_manager_end(Time)
+
+ !! need to reset pelist before calling mpp_clock_end
+ call mpp_set_current_pelist()
+
+ !! write restart file
+ call ocean_solo_restart(gcomp, Time_end, Time_restart_current)
+
+ call external_coupler_restart( dt_cpld, num_cpld_calls )
+
+ call fms_io_exit
+
+ call external_coupler_exit
+
+ call fms_end
+
+ call external_coupler_mpi_exit(mpi_comm_mom, .true.)
+
+ write(*,*) 'MOM: --- completed ---'
+
+ end subroutine
+
+
+ !--- writing restart file that contains running time and restart file writing time.
+ subroutine ocean_solo_restart(gcomp, Time_run, Time_res, time_stamp)
+ type(ESMF_GridComp), intent(in) :: gcomp
+ type(time_type), intent(in) :: Time_run, Time_res
+ character(len=*), intent(in), optional :: time_stamp
+
+ integer :: unit, calendar_type, rc
+ character(len=64) :: timestamp
+ type(Time_type) :: Time_init, Time_start
+ character(len=128) :: file_run, file_res
+ integer :: yr, mon, day, hr, min, sec
+
+ call ESMF_AttributeGet(gcomp, name="calendar_type", value=calendar_type, rc=rc)
+ if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ line=__LINE__, &
+ file=__FILE__)) &
+ return ! bail out
+ call ESMF_AttributeGet(gcomp, name="Time_init", value=timestamp, rc=rc)
+ if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ line=__LINE__, &
+ file=__FILE__)) &
+ return ! bail out
+ Time_init = string_to_date(timestamp)
+ call ESMF_AttributeGet(gcomp, name="Time_start", value=timestamp, rc=rc)
+ if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ line=__LINE__, &
+ file=__FILE__)) &
+ return ! bail out
+ Time_start = string_to_date(timestamp)
+
+ ! write restart file
+ if(present(time_stamp)) then
+ file_run = 'RESTART/'//trim(time_stamp)//'.ocean_solo.res'
+ file_res = 'RESTART/'//trim(time_stamp)//'.ocean_solo.intermediate.res'
+ else
+ file_run = 'RESTART/ocean_solo.res'
+ file_res = 'RESTART/ocean_solo.intermediate.res'
+ endif
+
+ call mpp_open( unit, file_run, nohdrs=.TRUE. )
+ if ( mpp_pe().EQ.mpp_root_pe() )then
+ write( unit, '(i6,8x,a)' )calendar_type, &
+ '(Calendar: no_calendar=0, thirty_day_months=1, julian=2, gregorian=3, noleap=4)'
+
+ call get_date(Time_init,yr,mon,day,hr,min,sec)
+ write( unit, '(6i6,8x,a)' )yr,mon,day,hr,min,sec, &
+ 'Model start time: year, month, day, hour, minute, second'
+ call get_date(Time_run ,yr,mon,day,hr,min,sec)
+ write( unit, '(6i6,8x,a)' )yr,mon,day,hr,min,sec, &
+ 'Current model time: year, month, day, hour, minute, second'
+ end if
+ call mpp_close(unit)
+
+ if(Time_res > Time_start) then
+ call mpp_open( unit, file_res, nohdrs=.TRUE. )
+ if ( mpp_pe().EQ.mpp_root_pe() )then
+ call get_date(Time_res ,yr,mon,day,hr,min,sec)
+ write( unit, '(6i6,8x,a)' )yr,mon,day,hr,min,sec, &
+ 'Current intermediate restart time: year, month, day, hour, minute, second'
+ end if
+ call mpp_close(unit)
+ end if
+
+ end subroutine ocean_solo_restart
+
+!====================================================================
+! get forcing data from data_overide
+ subroutine ice_ocn_bnd_from_data(x, Time, Time_step_coupled)
+
+ type (ice_ocean_boundary_type) :: x
+ type(Time_type), intent(in) :: Time, Time_step_coupled
+
+ type(Time_type) :: Time_next
+
+ Time_next = Time + Time_step_coupled
+
+ call data_override('OCN', 't_flux', x%t_flux , Time_next)
+ call data_override('OCN', 'u_flux', x%u_flux , Time_next)
+ call data_override('OCN', 'v_flux', x%v_flux , Time_next)
+ call data_override('OCN', 'q_flux', x%q_flux , Time_next)
+ call data_override('OCN', 'salt_flux', x%salt_flux , Time_next)
+ call data_override('OCN', 'lw_flux', x%lw_flux , Time_next)
+ call data_override('OCN', 'sw_flux_vis_dir', x%sw_flux_vis_dir, Time_next)
+ call data_override('OCN', 'sw_flux_vis_dif', x%sw_flux_vis_dif, Time_next)
+ call data_override('OCN', 'sw_flux_nir_dir', x%sw_flux_nir_dir, Time_next)
+ call data_override('OCN', 'sw_flux_nir_dif', x%sw_flux_nir_dif, Time_next)
+ call data_override('OCN', 'lprec', x%lprec , Time_next)
+ call data_override('OCN', 'fprec', x%fprec , Time_next)
+ call data_override('OCN', 'runoff', x%runoff , Time_next)
+ call data_override('OCN', 'calving', x%calving , Time_next)
+ call data_override('OCN', 'p', x%p , Time_next)
+
+ end subroutine ice_ocn_bnd_from_data
+
+
+!-----------------------------------------------------------------------------------------
+!
+! Subroutines for enabling coupling to external programs through a third party coupler
+! such as OASIS/PRISM.
+! If no external coupler then these will mostly be dummy routines.
+! These routines can also serve as spots to call other user defined routines
+!-----------------------------------------------------------------------------------------
+
+!-----------------------------------------------------------------------------------------
+#ifdef OASIS3
+
+! Here we provide some hooks for calling an interface between the OASIS3 coupler and MOM.
+! The mom_oasis3_interface module is NOT general and it is expected that the user will
+! heavily modify it depending on the coupling strategy.
+! For clarity all variables should be passed as arguments rather than as globals.
+! This may require changes to the argument lists.
+
+ subroutine external_coupler_mpi_init(mom_local_communicator, external_initialization)
+! OASIS3/PRISM acts as the master and initializes MPI. Get a local communicator.
+! need to initialize prism and get local communicator MPI_COMM_MOM first!
+ use mom_oasis3_interface_mod, only : mom_prism_init
+ implicit none
+ integer, intent(out) :: mom_local_communicator
+ logical, intent(out) :: external_initialization
+ mom_local_communicator = -100 ! Is there mpp_undefined parameter corresponding to MPI_UNDEFINED?
+ ! probably wouldn't need logical flag.
+ call mom_prism_init(mom_local_communicator)
+ external_initialization = .true.
+ end subroutine external_coupler_mpi_init
+!-----------------------------------------------------------------------------------------
+
+!-----------------------------------------------------------------------------------------
+ subroutine external_coupler_sbc_init(Dom, dt_cpld, Run_len)
+! Call to routine initializing arrays etc for transferring via coupler
+! Perform sanity checks and make sure all inputs are compatible
+ use mom_oasis3_interface_mod, only : coupler_init
+ implicit none
+ type(domain2d) :: Dom
+ integer :: dt_cpld
+ type(time_type) :: Run_len
+ call coupler_init(Dom, dt_cpld, Run_len=Run_len)
+ end subroutine external_coupler_sbc_init
+!-----------------------------------------------------------------------------------------
+
+
+!-----------------------------------------------------------------------------------------
+ subroutine external_coupler_sbc_before(Ice_ocean_boundary, Ocean_sfc, nsteps, dt_cpld )
+! Perform transfers before ocean time stepping
+! May need special tratment on first call.
+
+ use mom_oasis3_interface_mod, only : from_coupler, into_coupler
+
+ implicit none
+ type (ice_ocean_boundary_type), intent(INOUT) :: Ice_ocean_boundary
+ type (ocean_public_type) , intent(INOUT) :: Ocean_sfc
+ integer , intent(IN) :: nsteps, dt_cpld
+
+ integer :: rtimestep ! Receive timestep
+ integer :: stimestep ! Send timestep
+
+ rtimestep = (nsteps-1) * dt_cpld ! runtime in this run segment!
+ stimestep = rtimestep
+ call from_coupler( rtimestep, Ice_ocean_boundary )
+ call into_coupler( stimestep, Ocean_sfc, before_ocean_update = .true.)
+ end subroutine external_coupler_sbc_before
+!-----------------------------------------------------------------------------------------
+
+
+!-----------------------------------------------------------------------------------------
+ subroutine external_coupler_sbc_after(Ice_ocean_boundary, Ocean_sfc, nsteps, dt_cpld )
+! Perform transfers after ocean time stepping
+
+ use mom_oasis3_interface_mod, only : into_coupler
+
+ implicit none
+ type (ice_ocean_boundary_type) :: Ice_ocean_boundary
+ type (ocean_public_type) :: Ocean_sfc
+ integer :: nsteps, dt_cpld
+
+ integer :: stimestep ! Send timestep
+
+ stimestep = nsteps * dt_cpld ! runtime in this run segment!
+ call into_coupler(stimestep, Ocean_sfc, before_ocean_update = .false.)
+ end subroutine external_coupler_sbc_after
+!-----------------------------------------------------------------------------------------
+!-----------------------------------------------------------------------------------------
+ subroutine external_coupler_restart( dt_cpld, num_cpld_calls )
+! Clean up as appropriate and write a restart
+ use mom_oasis3_interface_mod, only : write_coupler_restart
+ implicit none
+ integer, intent(in) :: dt_cpld, num_cpld_calls
+ integer :: timestep
+ timestep = num_cpld_calls * dt_cpld
+ call write_coupler_restart(timestep, write_restart=.true.)
+ end subroutine external_coupler_restart
+
+
+!-----------------------------------------------------------------------------------------
+ subroutine external_coupler_exit
+! Clean up as appropriate
+! Final call to external program
+ use mom_oasis3_interface_mod, only : mom_prism_terminate
+ call mom_prism_terminate
+ end subroutine external_coupler_exit
+!-----------------------------------------------------------------------------------------
+
+!-----------------------------------------------------------------------------------------
+ subroutine external_coupler_mpi_exit(mom_local_communicator, external_initialization)
+! mpp_exit wont call MPI_FINALIZE if mom_local_communicator /= MPI_COMM_WORLD
+ implicit none
+ integer, intent(in) :: mom_local_communicator
+ logical, intent(in) :: external_initialization
+ integer :: ierr
+ call MPI_FINALIZE(ierr)
+ return
+ end subroutine external_coupler_mpi_exit
+!-----------------------------------------------------------------------------------------
+
+#else
+
+!-----------------------------------------------------------------------------------------
+
+! Dummy subroutines.
+
+ subroutine external_coupler_mpi_init(mom_local_communicator, external_initialization)
+ implicit none
+ integer, intent(out) :: mom_local_communicator
+ logical, intent(out) :: external_initialization
+ external_initialization = .false.
+ mom_local_communicator = -100 ! Is there mpp_undefined parameter corresponding to MPI_UNDEFINED?
+ ! probably wouldn't need logical flag.
+ return
+ end subroutine external_coupler_mpi_init
+
+!-----------------------------------------------------------------------------------------
+ subroutine external_coupler_sbc_init(Dom, dt_cpld, Run_len)
+ implicit none
+ type(domain2d) :: Dom
+ integer :: dt_cpld
+ type(time_type) :: Run_len
+ return
+ end subroutine external_coupler_sbc_init
+
+ subroutine external_coupler_sbc_before(Ice_ocean_boundary, Ocean_sfc, nsteps, dt_cpld )
+ implicit none
+ type (ice_ocean_boundary_type), intent(INOUT) :: Ice_ocean_boundary
+ type (ocean_public_type) , intent(INOUT) :: Ocean_sfc
+ integer , intent(IN) :: nsteps, dt_cpld
+ return
+ end subroutine external_coupler_sbc_before
+
+
+ subroutine external_coupler_sbc_after(Ice_ocean_boundary, Ocean_sfc, nsteps, dt_cpld )
+ type (ice_ocean_boundary_type) :: Ice_ocean_boundary
+ type (ocean_public_type) :: Ocean_sfc
+ integer :: nsteps, dt_cpld
+ return
+ end subroutine external_coupler_sbc_after
+
+ subroutine external_coupler_restart( dt_cpld, num_cpld_calls )
+ implicit none
+ integer, intent(in) :: dt_cpld, num_cpld_calls
+ return
+ end subroutine external_coupler_restart
+
+ subroutine external_coupler_exit
+ return
+ end subroutine external_coupler_exit
+
+!-----------------------------------------------------------------------------------------
+ subroutine external_coupler_mpi_exit(mom_local_communicator, external_initialization)
+ implicit none
+ integer, intent(in) :: mom_local_communicator
+ logical, intent(in) :: external_initialization
+ return
+ end subroutine external_coupler_mpi_exit
+!-----------------------------------------------------------------------------------------
+
+#endif
+
+end module ocean_solo_mod
+
+
+!----------------Earth System Model driver -------------------
+! Standard 1 component earth system model driver NUOPC compliant
+!
+module esm_mod
+ use constants_mod, only: constants_init
+ use data_override_mod, only: data_override_init, data_override
+ use diag_manager_mod, only: diag_manager_init, diag_manager_end
+ use field_manager_mod, only: field_manager_init
+ use fms_mod, only: fms_init, fms_end, open_namelist_file, check_nml_error
+ use fms_mod, only: close_file, file_exist, uppercase
+ use fms_io_mod, only: fms_io_exit
+ use mpp_domains_mod, only: domain2d, mpp_get_compute_domain
+ use mpp_io_mod, only: mpp_open, MPP_RDONLY, MPP_ASCII, MPP_OVERWR, MPP_APPEND, mpp_close, MPP_SINGLE
+ use mpp_mod, only: input_nml_file, mpp_error, FATAL, NOTE, mpp_pe, mpp_npes, mpp_set_current_pelist
+ use mpp_mod, only: stdlog, stdout, mpp_root_pe, mpp_clock_id
+ use mpp_mod, only: mpp_clock_begin, mpp_clock_end, MPP_CLOCK_SYNC
+ use mpp_mod, only: MPP_CLOCK_DETAILED, CLOCK_COMPONENT, MAXPES
+ use time_interp_external_mod, only: time_interp_external_init
+ use time_manager_mod, only: set_calendar_type, time_type, increment_date
+ use time_manager_mod, only: set_time, set_date, get_time, get_date, month_name
+ use time_manager_mod, only: GREGORIAN, JULIAN, NOLEAP, THIRTY_DAY_MONTHS, NO_CALENDAR
+ use time_manager_mod, only: operator( <= ), operator( < ), operator( >= )
+ use time_manager_mod, only: operator( + ), operator( - ), operator( / )
+ use time_manager_mod, only: operator( * ), operator( /= ), operator( > )
+ use time_manager_mod, only: date_to_string
+ use time_manager_mod, only: fms_get_calendar_type => get_calendar_type
+ use ocean_model_mod, only: ocean_model_init , update_ocean_model, ocean_model_end
+ use ocean_model_mod, only: ocean_model_restart, ocean_public_type, ocean_state_type
+ use ocean_types_mod, only: ice_ocean_boundary_type
+
+
+ use ESMF
+ use NUOPC
+ use NUOPC_Driver, only: &
+ driver_routine_SS => routine_SetServices, &
+ driver_type_IS => type_InternalState, &
+ driver_label_IS => label_InternalState, &
+ driver_setMC => label_SetModelCount, &
+#ifdef WITHPETLISTS
+ driver_label_SetModelPetLists => label_SetModelPetLists, &
+#endif
+ driver_label_SetModelServices => label_SetModelServices
+
+ use time_utils_mod
+
+ use ocean_solo_mod
+
+ implicit none
+ private
+ public SetServices
+
+ contains
+
+ !-----------------------------------------------------------------------
+ !------------------- Earth System Model code starts here ---------------
+ !-----------------------------------------------------------------------
+ subroutine SetServices(gcomp, rc)
+ type(ESMF_GridComp) :: gcomp
+ integer, intent(out) :: rc
+
+ rc = ESMF_SUCCESS
+
+ ! NUOPC_Driver registers the generic methods
+ call driver_routine_SS(gcomp, rc=rc)
+ if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ line=__LINE__, &
+ file=__FILE__)) &
+ return ! bail out
+
+ ! attach specializing method(s)
+#ifdef WITHPETLISTS
+ call ESMF_MethodAdd(gcomp, label=driver_label_SetModelPetLists, &
+ userRoutine=SetModelPetLists, rc=rc)
+ if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ line=__LINE__, &
+ file=__FILE__)) &
+ return ! bail out
+#endif
+
+ call ESMF_MethodAdd(gcomp, label=driver_setMC, &
+ userRoutine=setModelCount, rc=rc)
+ if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ line=__LINE__, &
+ file=__FILE__)) &
+ return ! bail out
+
+ call ESMF_MethodAdd(gcomp, label=driver_label_SetModelServices, &
+ userRoutine=SetModelServices, rc=rc)
+ if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ line=__LINE__, &
+ file=__FILE__)) &
+ return ! bail out
+
+ end subroutine
+
+ !-----------------------------------------------------------------------------
+
+#ifdef WITHPETLISTS
+
+ subroutine SetModelPetLists(gcomp, rc)
+ type(ESMF_GridComp) :: gcomp
+ integer, intent(out) :: rc
+
+ ! local variables
+ integer :: localrc
+ type(driver_type_IS) :: is
+ integer :: petCount, i
+
+ rc = ESMF_SUCCESS
+
+ ! query Component for its internal State
+ nullify(is%wrap)
+ call ESMF_UserCompGetInternalState(gcomp, driver_label_IS, is, rc)
+ if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ line=__LINE__, &
+ file=__FILE__)) &
+ return ! bail out
+
+ ! get the petCount
+ call ESMF_GridCompGet(gcomp, petCount=petCount, rc=rc)
+ if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ line=__LINE__, &
+ file=__FILE__)) &
+ return ! bail out
+
+ ! set petList for OCN -> second half of PETs
+ allocate(is%wrap%modelPetLists(petCount))
+ do i=0, petCount-1
+ is%wrap%modelPetLists(i) = i ! PET labeling goes from 0 to petCount-1
+ enddo
+
+ end subroutine
+#endif
+
+ subroutine setModelCount(gcomp, rc)
+ type(ESMF_GridComp) :: gcomp
+ integer, intent(out) :: rc
+
+ ! local variables
+ integer :: localrc
+ type(driver_type_IS) :: is
+ integer :: petCount, i
+
+ rc = ESMF_SUCCESS
+
+ ! query Component for its internal State
+ nullify(is%wrap)
+ call ESMF_UserCompGetInternalState(gcomp, driver_label_IS, is, rc)
+ if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ line=__LINE__, &
+ file=__FILE__)) &
+ return ! bail out
+
+ !Only ocean model exists
+ is%wrap%modelCount=1
+
+ end subroutine
+
+ subroutine SetModelServices(gcomp, rc)
+ type(ESMF_GridComp) :: gcomp
+ integer, intent(out) :: rc
+
+ ! local variables
+ integer :: localrc
+ type(driver_type_IS) :: is
+ type(ESMF_Grid) :: grid
+ type(ESMF_Field) :: field
+ type(ESMF_Time) :: startTime
+ type(ESMF_Time) :: stopTime
+ type(ESMF_TimeInterval) :: timeInterval
+ type(ESMF_TimeInterval) :: timeStep
+ type(ESMF_Clock) :: internalClock
+
+ integer :: n, m, unit, io_status, ierr
+ ! Read clock information from namelist
+ integer :: date_init(6)=0, date(6)
+ integer :: date_restart(6)
+ character(len=17) :: calendar = 'julian'
+ integer :: dt_cpld = 86400
+ integer :: years=0, months=0, days=0, hours=0, minutes=0, seconds=0
+ integer :: layout_mask(2) = (/0 , 0/)
+ integer :: n_mask = 0
+ integer :: mask_list(2,MAXPES)
+ integer, parameter :: mp = 2*MAXPES
+ data ((mask_list(n,m),n=1, 2),m=1,MAXPES) /mp*0/
+ integer :: restart_interval(6) = (/0,0,0,0,0,0/)
+
+ namelist /ocean_solo_nml/ date_init, calendar, months, days, hours, minutes, seconds, dt_cpld, &
+ n_mask, layout_mask, mask_list, restart_interval
+
+ rc = ESMF_SUCCESS
+
+#ifdef INTERNAL_FILE_NML
+ read (input_nml_file, nml=ocean_solo_nml, iostat=io_status)
+ ierr = check_nml_error(io_status,'ocean_solo_nml')
+#else
+ unit = open_namelist_file('input.nml')
+ read (unit, ocean_solo_nml,iostat=io_status)
+ ierr = check_nml_error(io_status,'ocean_solo_nml')
+ call close_file (unit)
+#endif
+
+ write(*,*) 'Time is', date_init(1), date_init(2), date_init(3), &
+ date_init(4), date_init(5), date_init(6)
+ ! query Component for its internal State
+ nullify(is%wrap)
+ call ESMF_UserCompGetInternalState(gcomp, driver_label_IS, is, rc)
+ if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ line=__LINE__, &
+ file=__FILE__)) &
+ return ! bail out
+
+ ! SetServices for OCN
+ call ESMF_GridCompSetServices(is%wrap%modelComp(1), ocean_solo_SS, userRc=localrc, rc=rc)
+ if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ line=__LINE__, &
+ file=__FILE__)) &
+ return ! bail out
+ if (ESMF_LogFoundError(rcToCheck=localrc, msg=ESMF_LOGERR_PASSTHRU, &
+ line=__LINE__, &
+ file=__FILE__, &
+ rcToReturn=rc)) &
+ return ! bail out
+
+ ! set the model clock
+ call ESMF_TimeIntervalSet(timeStep, s=dt_cpld, rc=rc)
+ if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ line=__LINE__, &
+ file=__FILE__)) &
+ call ESMF_Finalize(endflag=ESMF_END_ABORT)
+
+ call ESMF_TimeSet(startTime, yy=date_init(1), mm=date_init(2), &
+ dd=date_init(3), h=date_init(4), m=date_init(5), s=date_init(6), &
+ calkindflag=fms2esmf_cal(calendar), rc=rc)
+ if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ line=__LINE__, &
+ file=__FILE__)) &
+ call ESMF_Finalize(endflag=ESMF_END_ABORT)
+
+ call ESMF_TimeIntervalSet(timeInterval, mm=months, d=days, h=hours, &
+ m=minutes, s=seconds, rc=rc)
+ if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ line=__LINE__, &
+ file=__FILE__)) &
+ call ESMF_Finalize(endflag=ESMF_END_ABORT)
+
+ stopTime = startTime + timeInterval
+
+ internalClock = ESMF_ClockCreate(name="Application Clock", &
+ timeStep=timeStep, startTime=startTime, stopTime=stopTime, rc=rc)
+ if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ line=__LINE__, &
+ file=__FILE__)) &
+ call ESMF_Finalize(endflag=ESMF_END_ABORT)
+
+ call ESMF_GridCompSet(gcomp, clock=internalClock, rc=rc)
+ if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ line=__LINE__, &
+ file=__FILE__)) &
+ return ! bail out
+
+ end subroutine
+
+end module esm_mod
+
+program ocean_solo
+!
+!This is an updated ocean solo model application using NUOPC framework.
+!
+!Author: Fei Liu
+!Thu Feb 7 10:09:06 MST 2013
+!
+! Matt Harrison
+!
+!
+! Dave Bi (for OASIS3 hooks)
+!
+!
+! Niki Zadeh (for OASIS3 hooks)
+!
+!
+! V. Balaji
+!
+!
+! Stephen Griffies
+!
+!
+!
+! Driver for ocean-only simulations and prototype setup for OASIS3 driver.
+!
+!
+!
+! Driver for the ocean-only simulations. Similar to the FMS coupler, but
+! allows one to run the ocean model without compiling other models.
+! Much simpler than the full FMS coupler.
+!
+! This driver also provides the prototype hooks for using MOM with OASIS3,
+! with this code surrounded by the cpp-preprocessor option "ifdef OASIS3".
+! The couping of MOM to OASIS3 has not been tested at GFDL. Rather,
+! CSIRO in Australia uses MOM with OASIS3, with Dave.Bi@csiro.au the primary
+! contact for questions regarding MOM and OASIS3.
+!
+!
+!
+!
+!
+! The date that the current integration starts with. If the restart file
+! ocean_solo.res is present, date_init will be taken from there.
+!
+!
+! The calendar type used by the current integration. Valid values are consistent
+! with the time_manager module: 'julian', 'gregorian', 'noleap', or 'thirty_day'.
+! The value 'no_calendar' can not be used because the time_manager's date
+! function are used.
+!
+!
+!
+! The number of months that the current integration will be run for.
+!
+!
+! The number of days that the current integration will be run for.
+!
+!
+! The number of hours that the current integration will be run for.
+!
+!
+! The number of minutes that the current integration will be run for.
+!
+!
+! The number of seconds that the current integration will be run for.
+!
+!
+! Time step in seconds for coupling between ocean and atmospheric models:
+! must be an integral multiple of dt_ocean. This is the "slow" timestep.
+! Note that for an ocean_solo model, the coupling to an "atmosphere" is the coupling
+! to some data files. In this case, dt_cpld represents the time which data is updated.
+! For example, if data is "daily", then dt_cpld=86400 should be chosen.
+! If data is fixed, then dt_cpld of any integer of dt_ocean is fine, with
+! dt_cpld=86400 the default.
+!
+!
+! number of region to be masked out. Its value should be less than MAX_PES.
+!
+!
+! The position of the region to be masked out. mask_list(1,:) is the x-layout position
+! and mask_list(2,:) is y-layout position.
+!
+!
+! Processor domain layout for all the component model. layout_mask need to be set when and only
+! when n_mask is greater than 0 ( some domain region is masked out ). When this namelist is set,
+! it will overload the layout in each component model. The default value is (0,0).
+! Currently we require all the component model has the same layout and same grid size.
+!
+!
+! The time interval that write out intermediate restart file. The format is (yr,mo,day,hr,min,sec).
+! When restart_interval is all zero, no intermediate restart file will be written out.
+!
+!
+!
+!
+!
+!
+! 1.The actual run length will be the sum of months,
+! days, hours, minutes, and seconds. A run length of zero
+! is not a valid option.
+! 2.The run length must be an integral multiple of the coupling
+! timestep dt_cpld.
+!
+!
+!
+ use constants_mod, only: constants_init
+ use data_override_mod, only: data_override_init, data_override
+ use diag_manager_mod, only: diag_manager_init, diag_manager_end
+ use field_manager_mod, only: field_manager_init
+ use fms_mod, only: fms_init, fms_end, open_namelist_file, check_nml_error
+ use fms_mod, only: close_file, file_exist, uppercase
+ use fms_io_mod, only: fms_io_exit
+ use mpp_domains_mod, only: domain2d, mpp_get_compute_domain
+ use mpp_io_mod, only: mpp_open, MPP_RDONLY, MPP_ASCII, MPP_OVERWR, MPP_APPEND, mpp_close, MPP_SINGLE
+ use mpp_mod, only: input_nml_file, mpp_error, FATAL, NOTE, mpp_pe, mpp_npes, mpp_set_current_pelist
+ use mpp_mod, only: stdlog, stdout, mpp_root_pe, mpp_clock_id
+ use mpp_mod, only: mpp_clock_begin, mpp_clock_end, MPP_CLOCK_SYNC
+ use mpp_mod, only: MPP_CLOCK_DETAILED, CLOCK_COMPONENT, MAXPES
+ use time_interp_external_mod, only: time_interp_external_init
+ use time_manager_mod, only: set_calendar_type, time_type, increment_date
+ use time_manager_mod, only: set_time, set_date, get_time, get_date, month_name
+ use time_manager_mod, only: GREGORIAN, JULIAN, NOLEAP, THIRTY_DAY_MONTHS, NO_CALENDAR
+ use time_manager_mod, only: operator( <= ), operator( < ), operator( >= )
+ use time_manager_mod, only: operator( + ), operator( - ), operator( / )
+ use time_manager_mod, only: operator( * ), operator( /= ), operator( > )
+ use time_manager_mod, only: date_to_string
+ use time_manager_mod, only: fms_get_calendar_type => get_calendar_type
+
+ use ocean_model_mod, only: ocean_model_init , update_ocean_model, ocean_model_end
+ use ocean_model_mod, only: ocean_model_restart, ocean_public_type, ocean_state_type
+ use ocean_types_mod, only: ice_ocean_boundary_type
+
+
+ use ESMF
+ use time_utils_mod
+ use esm_mod
+
+ implicit none
+
+
+ !-------------------- main code starts here ---------------------
+ integer :: rc, urc, mpi_comm_mom
+ type(ESMF_VM) :: vm
+ type(ESMF_GridComp) :: esmComp
+
+ ! Initialize ESMF
+ call ESMF_Initialize(logkindflag=ESMF_LOGKIND_MULTI, rc=rc)
+ if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ line=__LINE__, &
+ file=__FILE__)) &
+ call ESMF_Finalize(endflag=ESMF_END_ABORT)
+
+ call ESMF_VMGetCurrent(vm, rc=rc)
+ if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ line=__LINE__, &
+ file=__FILE__)) &
+ call ESMF_Finalize(endflag=ESMF_END_ABORT)
+
+ call ESMF_VMGet(vm, mpiCommunicator=mpi_comm_mom, rc=rc)
+ if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ line=__LINE__, &
+ file=__FILE__)) &
+ call ESMF_Finalize(endflag=ESMF_END_ABORT)
+
+ call fms_init(mpi_comm_mom)
+
+ call ESMF_LogWrite("MOM5 ocean solo STARTING", ESMF_LOGMSG_INFO, rc=rc)
+ if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ line=__LINE__, &
+ file=__FILE__)) &
+ call ESMF_Finalize(endflag=ESMF_END_ABORT)
+
+ ! Create the earth system Component
+ esmComp = ESMF_GridCompCreate(name="mom_solo", rc=rc)
+ if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ line=__LINE__, &
+ file=__FILE__)) &
+ call ESMF_Finalize(endflag=ESMF_END_ABORT)
+
+ ! SetServices for the earth system Component
+ call ESMF_GridCompSetServices(esmComp, SetServices, userRc=urc, rc=rc)
+ if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ line=__LINE__, &
+ file=__FILE__)) &
+ call ESMF_Finalize(endflag=ESMF_END_ABORT)
+ if (ESMF_LogFoundError(rcToCheck=urc, msg=ESMF_LOGERR_PASSTHRU, &
+ line=__LINE__, &
+ file=__FILE__)) &
+ call ESMF_Finalize(endflag=ESMF_END_ABORT)
+
+ ! Call Initialize for the earth system Component
+ call ESMF_GridCompInitialize(esmComp, userRc=urc, rc=rc)
+ if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ line=__LINE__, &
+ file=__FILE__)) &
+ call ESMF_Finalize(endflag=ESMF_END_ABORT)
+ if (ESMF_LogFoundError(rcToCheck=urc, msg=ESMF_LOGERR_PASSTHRU, &
+ line=__LINE__, &
+ file=__FILE__)) &
+ call ESMF_Finalize(endflag=ESMF_END_ABORT)
+
+ ! Call Run for earth the system Component
+ call ESMF_GridCompRun(esmComp, userRc=urc, rc=rc)
+ if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ line=__LINE__, &
+ file=__FILE__)) &
+ call ESMF_Finalize(endflag=ESMF_END_ABORT)
+ if (ESMF_LogFoundError(rcToCheck=urc, msg=ESMF_LOGERR_PASSTHRU, &
+ line=__LINE__, &
+ file=__FILE__)) &
+ call ESMF_Finalize(endflag=ESMF_END_ABORT)
+
+ ! Call Finalize for the earth system Component
+ call ESMF_GridCompFinalize(esmComp, userRc=urc, rc=rc)
+ if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ line=__LINE__, &
+ file=__FILE__)) &
+ call ESMF_Finalize(endflag=ESMF_END_ABORT)
+ if (ESMF_LogFoundError(rcToCheck=urc, msg=ESMF_LOGERR_PASSTHRU, &
+ line=__LINE__, &
+ file=__FILE__)) &
+ call ESMF_Finalize(endflag=ESMF_END_ABORT)
+
+ ! Destroy the earth system Component
+ call ESMF_GridCompDestroy(esmComp, rc=rc)
+ if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ line=__LINE__, &
+ file=__FILE__)) &
+ call ESMF_Finalize(endflag=ESMF_END_ABORT)
+
+ call ESMF_LogWrite("MOM5 ocean solo FINISHED", ESMF_LOGMSG_INFO, rc=rc)
+ if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+ line=__LINE__, &
+ file=__FILE__)) &
+ call ESMF_Finalize(endflag=ESMF_END_ABORT)
+
+ ! Finalize ESMF
+ call ESMF_Finalize()
+
+end program ocean_solo
diff --git a/src/mom5/ocean_bgc/ocean_bgc_restore.F90 b/src/mom5/ocean_bgc/ocean_bgc_restore.F90
index e9cef5872d..8db434cea9 100644
--- a/src/mom5/ocean_bgc/ocean_bgc_restore.F90
+++ b/src/mom5/ocean_bgc/ocean_bgc_restore.F90
@@ -357,8 +357,8 @@ module ocean_bgc_restore_mod
integer :: package_index
logical :: module_initialized = .false.
-character(len=128) :: version = '$Id: ocean_bgc_restore.F90,v 1.1.2.1 2012/05/15 15:55:19 smg Exp $'
-character(len=128) :: tagname = '$Name: mom5_siena_08jun2012_smg $'
+character(len=128) :: version = '$Id: ocean_bgc_restore.F90,v 20.0 2013/12/14 00:09:28 fms Exp $'
+character(len=128) :: tagname = '$Name: tikal $'
! Input parameters:
!
diff --git a/src/mom5/ocean_bgc/ocean_bgc_restore.html b/src/mom5/ocean_bgc/ocean_bgc_restore.html
deleted file mode 100644
index 7230014e82..0000000000
--- a/src/mom5/ocean_bgc/ocean_bgc_restore.html
+++ /dev/null
@@ -1,455 +0,0 @@
-
-
-
-Module ocean_bgc_restore_mod
-
-
-
-
-PUBLIC INTERFACE
-
- ~ PUBLIC ROUTINES
-
-
- After Numerical recipes:
-
- Given an array XX of length N, and a given value of X, returns a
- value of J such that X is between XX(J) and XX(J+1). XX must be
- monotonic, either increasing or decreasing. J=0 or J=N is
- returned to indicate that X is out of range.
- New features:
-
- If "period" is specified, then the array, xx, is considered
- to be periodic with a period of "period". If "x_in" is out
- of range, then add or subtract "period" once to attempt to
- make "x_in" be in range.
-
- If "nearest" is specified, and true, then return "j" such
- that it is the element of "xx" which is nearest to the value
- of "x_in" (where "x_in" may have been modified by the value
- "period", above). With this option, "j" will be in
- the range 1 <= j <= n.
-
-
-
-
-
-
-
-
ocean_bgc_restore_bbc
-
-
-DESCRIPTION
-
-
- calculate the surface boundary conditions
-
-
-
-
-
-
-
-
ocean_bgc_restore_end
-
-
-DESCRIPTION
-
-
- Clean up various BIOTIC quantities for this run.
-
-
-
-
-
-
-
-
ocean_bgc_restore_restart
-
-
-DESCRIPTION
-
-
- Write out restart files registered through register_restart_file
-
-
-
-
-
-
-
-
ocean_bgc_restore_sbc
-
-
-DESCRIPTION
-
-
- Calculate the surface boundary conditions
-
-
-
-
-
-
-
-
ocean_bgc_restore_flux_init
-
-
-DESCRIPTION
-
-
- Set up any extra fields needed by the ocean-atmosphere gas fluxes
-
-
-
-
-
-
-
-
ocean_bgc_restore_init
-
-
-DESCRIPTION
-
-
- Set up any extra fields needed by the tracer packages
-
- Save pointers to various "types", such as Grid and Domains.
-
-
-
-
-
-
-
-
ocean_bgc_restore_init_sfc
-
-
-DESCRIPTION
-
-
- Initialize surface fields for flux calculations
-
- Note: this subroutine should be merged into ocean_bgc_restore_start
-
-
-
-
-
-
-
-
ocean_bgc_restore_sum_sfc
-
-
-DESCRIPTION
-
-
- Sum surface fields for flux calculations
-
-
-
-
-
-
-
-
ocean_bgc_restore_zero_sfc
-
-
-DESCRIPTION
-
-
- Sum surface fields for flux calculations
-
-
-
-
-
-
-
-
ocean_bgc_restore_avg_sfc
-
-
-DESCRIPTION
-
-
- Sum surface fields for flux calculations
-
-
-
-
-
-
-
-
ocean_bgc_restore_sfc_end
-
-
-DESCRIPTION
-
-
- Initialize surface fields for flux calculations
-
-
-
-
-
-
-
-
ocean_bgc_restore_source
-
-
-DESCRIPTION
-
-
- compute the source terms for the BIOTICs, including boundary
- conditions (not done in setvbc, to minimize number
- of hooks required in MOM base code)
-
-
-
-
-
-
-
-
ocean_bgc_restore_start
-
-
-DESCRIPTION
-
-
- Initialize variables, read in namelists, calculate constants for a given run
- and allocate diagnostic arrays
-
-
-
-
-
-
-
-
set_array
-
-
-DESCRIPTION
-
-
- Set up an array covering the model domain with a user-specified
- value, in user-specified regions. There are a given number of
- 2-d regions specified by the values slat, nlat, wlon and elon.
- The longitudes are for a cyclic domain, and if wlon and elon
- are on opposite sides of the cut, the correct thing will
- be done. Elon is considered to be east of wlon, so if elon is
- less than wlon, then the region east of elon to the cut will be
- filled, and the region from the cut to wlon will be filled.
-
- After setting up the array in this routine, it may prove useful
- to allow fine-tuning the settings via an array in a namelist.
-
- Arguments:
- Input:
- num_regions = number of user-specified regions which will be
- filled
-
- wlon = 1-d array of western (starting) longitudes for the
- rectangular regions
-
- elon = 1-d array of eastern (ending) longitudes for the
- rectangular regions
-
- slat = 1-d array of southern (starting) latitudes for the
- rectangular regions
-
- nlat = 1-d array of northern (ending) latitudes for the
- rectangular regions
-
- Note: if slat >= nlat, then nothing is done
- for that region
-
- set_value = the value to assign to array in the user-specified
- regions
-
- unset_value = the value to assign to array outside of the
- user-specified regions
-
- name = character variable used in informative messages
-
- coastal_only = true to limit changes only to coastal points
- (i.e., at least one bordering point is land)
-
- Output:
-
- array = 2-d array which will contain the set- and unset-
- values. The array is assumed to have a border
- one unit wide on all edges, ala MOM. A cyclic
- boundary condition will be set if requested.
-
- Press, W. H., S. A. Teukosky, W. T. Vetterling, B. P. Flannery, 1992.
- Numerical Recipes in FORTRAN, Second Edition, Cambridge University Press.
-
-
- Enting, I.G., T. M. L. Wigley, M. Heimann, 1994. Future Emissions
- and concentrations of carbon dioxide: key ocean / atmosphere /
- land analyses, CSIRO Aust. Div. Atmos. Res. Tech. Pap. No. 31,
- 118 pp.
-
- This subroutine:
- Initializes the generic tracer packages and adds their tracers to the list
- Adds the tracers in the list of generic tracers to the set of MOM tracers
- (i.e., make them elements of T_prog or T_diag)
-
-
-
-
-
-
-
-
ocean_generic_zero_sfc
-
-call ocean_generic_zero_sfc (IOB_struc)
-
-
-DESCRIPTION
-
-
- This is need since MOM coupler values are acumulated and then divided by time ocean steps.
-
-
-
-
-
-
-
-
ocean_generic_sum_sfc
-
-call ocean_generic_sum_sfc (Disd,Djsd, Ocean, T_prog, Dens, Time )
-
-
-DESCRIPTION
-
-
- This subroutine calculates the surface state and set coupler values for
- those generic tracers that havd flux exchange with atmosphere.
-
- IDEALIZED OCEAN BIOGEOCHEMISTRY *
- *
- An idealized biogeochemical cycling module, in which the ecosystem and *
- particles are treated implicitly. This is intended as a first-order *
- complexity complement to more intricate ecosystem/biogeochemical models *
- such as BLING, or the GFDL TOPAZ model. *
-
- iBGC is not intended to simulate marine biogeochemistry in the most *
- accurate sense possible - that is left to the more complex models. *
- Instead, it is intended as a tool for basic research, being easily *
- modified, simply understood, and readily used in idealized configurations.*
-
- Note that the model parameters are not particularly well tuned for any *
- ocean model, and the user should feel free to alter anything as they see *
- fit. *
-
-
-
-
-
-
-
-* Inorganic nutrients are incorporated into organic matter in the presence *
-* of light. Once in the organic pool, the nutrient elements are recycled *
-* between organisms and labile reservoirs as long as light is present in *
-* sufficient abundance to fuel continued growth. In the absence of light, *
-* inorganic nutrients gradually accumulate once again. The ideal nutrient *
-* tracers are intended to capture the fundamental dynamics of these *
-* light-dependent inorganic-organic transitions, but in a very simple, *
-* transparent way that depends only on the physical circulation and the *
-* availability of PAR. Thus, they ignore the complexities of ecosystems, *
-* in terms of uptake dynamics and remineralization pathways. Although this *
-* will certainly decrease their ability to reproduce the observed *
-* distributions of nutrients in the ocean, they are computationally *
-* inexpensive and easy to interpret, features which will hopefully give *
-* them some utility. *
-* The simplest ideal nutrient tracer, ideal_n, is non-conservative, *
-* designed to quickly approach equilibrium (order 10 years), avoiding the *
-* need for long integrations. The slightly less straightforward, *
-* conservative tracers are remineralized through the water column and *
-* therefore approach steady state on much longer, multi-centennial *
-* timescales. *
-*
-* The core behaviour of the ideal nutrients are given by the exponential, *
-* exp(-IRR/IRRk). IRR is the available light (average SW radiation, in *
-* W/m2, within the grid cell) and IRRk (in W/m2) determines the light *
-* level at which the phytoplankton growth rate approaches saturation. *
-* Thus, this term is 1 when IRR is 0, and approaches 0 as IRR increases. A *
-* larger value for IRRk causes the exponential to approach 0 more slowly, *
-* ie. to saturate at a higher light level. *
-*
-* Uptake is determined by the product of the 1 minus the exponential term, *
-* a maximum uptake velocity (Vmax, in s-1), and limitation caused by the *
-* concentration of the ideal nutrient itself, N (in mol kg-1): *
-* *
-* -Vmax * (1 - exp( -IRR / IRRk )) * (N / N + k) *
-* *
-* The last term causes nutrient uptake to slow as the nutrient *
-* concentration approaches 0, according to Michaelis-Menten dynamics. *
-* *
-* In ideal_n, regeneration is simply a constant rate, R. *
-*
-* Starting from this simple foundation, biogeochemical functionality is *
-* added by creating a macronutrient (iPO4) with identical uptake to *
-* ideal_n, but for which mass is conserved within the ocean. This is *
-* achieved by separating the uptake into dissolved and particulate *
-* organic matter, the latter of which is instantaneously remineralized *
-* throughout the water column below according to a variant of the OCMPIP2 *
-* protocol. This calculates the remineralization rate at each level as a *
-* function of the temperature, base remineralization rate, and sinking *
-* rate (itself a function of depth). Any flux reaching the bottom box is *
-* instantly remineralized there to conserve mass within the ocean. *
-* Meanwhile, Dissolved Organic Phosphorus (iDOP) is transported within the *
-* ocean, decaying to PO4 at a temperature-dependent rate. *
-*
-* Given the apparent importance of iron (Fe) as a limiting micronutrient *
-* in the oceans, it seemed interesting to try making another PO4 tracer, *
-* limited by Fe, in addition to the basic limitations given above: this is *
-* called iPO4f. The iron input is highly idealized, and the scavenging *
-* function very simple, but iron-limitation develops and modulates *
-* growth rate through iron-light colimitation in a way that may not be *
-* totally unlike the real ocean. The Fe-limited PO4 cycle is completely *
-* independent of the non-Fe-limited PO4, and they can be run on their own *
-* or in parallel for comparison.
-*
-* A full biogeochemical simulation can then be made by selecting one of *
-* the iPO4s as the central bgc variable (default is iPO4). Biological *
-* consumption and production of other quantities, including a number of *
-* gases and idealized gas tracers, are then determined from the generally *
-* reliable Redfield stoichiometries. *
-*
-* Isotopic fractionations are simulated by multiplying the uptake rate of *
-* the chemical species by the isotopic rate ratio, alpha. The tracer *
-* concentrations of the heavy isotope species are actually *
-* equal to the true concentration divided by the isotopic ratio of the *
-* standard, e.g. 15NO3 = [15NO3] * [14Nair] / [15Nair]. The true value in *
-* permil is given by (15NO3 / NO3 - 1.) * 1000. *
-*
-* Dissolved gases are handled according to the OCMIP2 protocol. The air- *
-* sea exchange code was taken from the ocmip2_abiotic and ocmip2_biotic *
-* modules, with negligible modification. Note that the 14C implementation *
-* differs from that of abiotic, in that biological uptake and remineraliz- *
-* ation of carbon impact the distribution of 14C, analagous to 15N. *
-*
-* Chlorophyll is estimated diagnostically from the net bgc iPO4 (or iPO4f) *
-* uptake rate, with an adjustment for photoadaptation.
-
-
- A general note on nomenclature
- Variables starting with 'j' are source/sink terms; jprod_x is the
- biological production term for the quantity 'x'; jremin_x is the
- remineralization rate of the quantity 'x'. Variables starting with 'fp'
- are sinking particulate flux terms. Most of the 'i's stand for idealized,
- as in iBGC, and help to avoid duplication of arrays and tracer names used
- by TOPAZ and BLING, so that ibgc can be run in parallel with these other
- models. Most of the 'p's stand for particulate, though a lot of them
- stand for phosphorus. So, for example, jprod_pip is the production rate
- of particulate idealized phosphorus through the uptake of iPO4.
-
- Tracer units are generally in mol kg-1, with some exceptions (suntan,
- ideal_n, Fe).
-
- A general note on parameter values:
- Pretty much all of the parameter values were selected ad hoc, from very
- loose principles. They were not particularly well 'tuned' to match any
- given circulation model, though they gave reasonable results with the
- 3-degree ocean model, om1p7. As such, the user should feel free to make
- changes to the default values given here.
- Exceptions to this are: gas exchange parameters, radiocarbon decay,
- nutrient stoichiometry, fractionation factors.
-
- Dynamically allocate arrays for quantities with unknown dimensions.
- These are arrays that only exist temporarily.
-
-
-
-
-
-
-
-
ocean_ibgc_bbc
-
-
-DESCRIPTION
-
-
- This sets up the boundary conditions at the bottom of the water
- column. Here, this does nothing and is just a placeholder.
-
-
-
-
-
-
-
-
ocean_ibgc_end
-
-
-DESCRIPTION
-
-
- Clean up various quantities for this run. This includes writing out
- additional information to ensure reproduction across restarts.
-
-
-
-
-
-
-
-
ocean_ibgc_restart
-
-
-DESCRIPTION
-
-
- Write out restart files registered through register_restart_file
-
-
-
-
-
-
-
-
ocean_ibgc_sbc
-
-
-DESCRIPTION
-
-
- Calculate the surface boundary conditions. This includes things
- like gas exchange, atmospheric deposition, and riverine inputs.
-
-
-
-
-
-
-
-
ocean_ibgc_flux_init
-
-
-DESCRIPTION
-
-
- Set up any extra fields needed by the ocean-atmosphere gas fluxes
-
-
-
-
-
-
-
-
ocean_ibgc_init
-
-
-DESCRIPTION
-
-
- Set up any extra fields needed by the tracer packages
-
- Save pointers to various "types", such as Grid and Domains.
-
-
-
-
-
-
-
-
ocean_ibgc_init_sfc
-
-
-DESCRIPTION
-
-
-
- SURFACE GAS FLUXES
-
- This subroutine coordinates the calculation of gas solubilities in the surface layer,
- and sends the appropriate values to the coupler.
-
- First, for CO2 and 14CO2, the carbon solubility and speciation are calculated by the
- subroutine co2calc, following the OCMIP2 protocol. These calculations are both made
- using total CO2, following which the surface CO2 concentration (CO2*, also known as
- H2CO3*) is scaled by the DI14C/DIC ratio to give the surface 14CO2 concentration.
- The speciation calculation uses in situ temperature, salinity, idealized PO4 and
- idealized SiO4 (which must be scaled to real SiO4 units, since I'm using PO4 units
- for iSiO4).
- Oxygen solubility is calculated here, using in situ temperature and salinity.
-
- The actual gas fluxes will be calculated in the coupler using a piston velocity (Kw),
- Flux = Kw * (alpha - csurf)
- and returned as elements of ice_ocean_boundary_fluxes%bc in the ocean_ibgc_sbc
- subroutine.
-
-
-
-
-
-
-
-
ocean_ibgc_sum_sfc
-
-
-DESCRIPTION
-
-
- Sum surface fields for flux calculations.
-
-
-
-
-
-
-
-
ocean_ibgc_zero_sfc
-
-
-DESCRIPTION
-
-
- Sum surface fields for flux calculations.
-
-
-
-
-
-
-
-
ocean_ibgc_avg_sfc
-
-
-DESCRIPTION
-
-
- Sum surface fields for flux calculations.
-
-
-
-
-
-
-
-
ocean_ibgc_sfc_end
-
-
-DESCRIPTION
-
-
- Finish up stuff for surface fields for flux calculations.
-
-
-
-
-
-
-
-
ocean_ibgc_source
-
-
-DESCRIPTION
-
-
- Compute the source terms for the ideal nutrients, including boundary
- conditions (not done in setvbc, to minimize number
- of hooks required in MOM base code)
-
-
-
-
-
-
-
-
ocean_ibgc_start
-
-
-DESCRIPTION
-
-
- Initialize variables, read in namelists, calculate constants for a given run
- and allocate diagnostic arrays
-
-
-
-
-
-
-
-
ocean_ibgc_tracer
-
-
-DESCRIPTION
-
-
- Perform things that should be done in tracer, but are done here
- in order to minimize the number of hooks necessary in the MOM4 basecode.
-
- Here, it is used only to set the values of preformed iPO4 and iDIC in
- the mixed layer.
-
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_ibgc_nml
-
-
-
-
-
-do_ideal
-
-
- If true, then do ideal_n and suntan. This does not require any other
- part of the model.
-
-[logical]
-
-
-do_po4
-
-
- If true, then do the non-Fe-limited P cycle, iPO4 and iDOP. If either
- this or do_po4f is true, PO4_pre and chl will be calculated as well. If
- both do_po4 and do_po4f are true, po4 will be the master variable,
- unless bgc_felim is true.
-
-[logical]
-
-
-do_po4f
-
-
- If true, then do the Fe-limited P cycle, with iFe, iPO4f and DOP. If
- either this or do_po4 is true, PO4_pre and chl will be calculated as well.
- If both do_po4 and do_po4f are true, po4 will be the master variable,
- unless do_bgc_felim is true.
-
-[logical]
-
-
-do_bgc_felim
-
-
- If true, then use PO4f as the master variable for biogeochemical
- calculations (gases, PO4_pre, chl, isotopes). Requires that do_PO4f be true.
-
-[logical]
-
-
-do_gasses
-
-
- If true, then do the gases Dissolved Inorganic Carbon (iDIC) and oxygen
- (iO2). Requires that do_po4 and/or do_po4f be true.
-
-[logical]
-
-
-do_carbon_comp
-
-
- If true, then do the dissolved inorganic carbon component tracers,
- Saturation DIC (iDIC_sat) and preformed DIC (iDIC_pre). Requires
- that do_po4 and/or do_po4f be true, and that do_gasses be true.
-
-[logical]
-
-
-do_radiocarbon
-
-
- If true, then do the radiocarbon tracers (iDI14C and iDO14C). Requires
- that do_po4 and/or do_po4f be true, and that do_gasses be true.
-
-[logical]
-
-
-do_isio4
-
-
- If true, then do silica cycle and silicon isotopes, iSiO4 and i30SiO4.
-
-[logical]
-
-
-do_no3_iso
-
-
- If true, then do NO3 isotopes, i15NO3, iN18O3 and iDO15N. Requires that
- do_po4 and/or do_po4f be true.
-
-[logical]
-
-
-
-
-
-
-
-
-
-
-
REFERENCES
-
-
-
-
- The basic nutrient uptake equations will be described in an upcoming paper
- by Galbraith et al. (in prep.). The remainder of the biogeochemistry
- module may be documented more officially elsewhere. All are welcome to use
- ibgc model output for the purposes of publication; however, please contact
- Eric Galbraith (Eric.Galbraith@mcgill.ca) for the appropriate reference.
-
- Ocean perturbation CO2 module, based on Sarmiento, Orr and Siegenthaler, 1992
-
-
-
-
-
- Implementation of routines to solve the Ocean perturbation CO2
- simulations as outlined by "A Perturbation Simulation of
- CO2 Uptake in an Ocean General Circulation Model", Jorge L. Sarmiento,
- James C. Orr and Ulrich Siegenthaler, 1992, JGR, 97,
- pp 3621-3645.
-
- Set up any extra fields needed by the ocean-atmosphere gas fluxes
-
-
-
-
-
-
-
-
ocean_pert_co2_init
-
-
-DESCRIPTION
-
-
- Set up any extra fields needed by the tracer packages
-
- Save pointers to various "types", such as Grid and Domains.
-
-
-
-
-
-
-
-
ocean_pert_co2_init_sfc
-
-
-DESCRIPTION
-
-
- Initialize surface fields for flux calculations
-
- Note: this subroutine should be merged into ocean_pert_co2_start
-
-
-
-
-
-
-
-
ocean_pert_co2_sum_sfc
-
-
-DESCRIPTION
-
-
- Sum surface fields for flux calculations
-
-
-
-
-
-
-
-
ocean_pert_co2_zero_sfc
-
-
-DESCRIPTION
-
-
- Sum surface fields for flux calculations
-
-
-
-
-
-
-
-
ocean_pert_co2_avg_sfc
-
-
-DESCRIPTION
-
-
- Sum surface fields for flux calculations
-
-
-
-
-
-
-
-
ocean_pert_co2_sfc_end
-
-
-DESCRIPTION
-
-
- Initialize surface fields for flux calculations
-
-
-
-
-
-
-
-
ocean_pert_co2_source
-
-
-DESCRIPTION
-
-
- compute the source terms, including boundary
- conditions (not done in setvbc, to minimize number
- of hooks required in MOM base code)
-
-
-
-
-
-
-
-
ocean_pert_co2_start
-
-
-DESCRIPTION
-
-
- Initialize variables, read in namelists, calculate constants
- for a given run and allocate diagnostic arrays
-
-
-
-
-
-
-
-
-
-
-
-
-
-
REFERENCES
-
-
-
-
- A Perturbation Simulation of
- CO2 Uptake in an Ocean General Circulation Model, Jorge L. Sarmiento,
- James C. Orr and Ulrich Siegenthaler, 1992, JGR, 97,
- pp 3621-3645.
-
- This module has simple implementation of preformed phosphate.
- Where,
- po4_pre=po4, if z <= mld
-
- It is an optional package that requires TOPAZ, ocmip2_biotic, or ocean_bgc_restore to be running.
-
- Various mixed layer depth options are available and can be
- set via namelist
-
- 1 = kpp mixed layer (default)
- 2 = buoyancy criteria defined mixed layer, where this buoyancy
- references in situ density
- 3 = buoyancy criteria defined mixed layer, where this buoyancy
- references potential density
-
-
- Clean up various PO4_PRE quantities for this run.
-
-
-
-
-
-
-
-
ocean_po4_pre_sbc
-
-
-DESCRIPTION
-
-
- Calculate the surface boundary conditions
-
-
-
-
-
-
-
-
ocean_po4_pre_flux_init
-
-
-DESCRIPTION
-
-
- Set up any extra fields needed by the ocean-atmosphere gas fluxes
-
-
-
-
-
-
-
-
ocean_po4_pre_init
-
-
-DESCRIPTION
-
-
- Set up any extra fields needed by the tracer packages
-
- Save pointers to various "types", such as Grid and Domains.
-
-
-
-
-
-
-
-
ocean_po4_pre_init_sfc
-
-
-DESCRIPTION
-
-
- Initialize surface fields for flux calculations
-
- Note: this subroutine should be merged into ocean_po4_pre_start
-
-
-
-
-
-
-
-
ocean_po4_pre_sum_sfc
-
-
-DESCRIPTION
-
-
- Sum surface fields for flux calculations
-
-
-
-
-
-
-
-
ocean_po4_pre_zero_sfc
-
-
-DESCRIPTION
-
-
- Sum surface fields for flux calculations
-
-
-
-
-
-
-
-
ocean_po4_pre_avg_sfc
-
-
-DESCRIPTION
-
-
- Sum surface fields for flux calculations
-
-
-
-
-
-
-
-
ocean_po4_pre_sfc_end
-
-
-DESCRIPTION
-
-
- Finish up stuff for surface fields for flux calculations
-
-
-
-
-
-
-
-
ocean_po4_pre_source
-
-
-DESCRIPTION
-
-
- compute the source terms for the PO4_PREs, including boundary
- conditions (not done in setvbc, to minimize number
- of hooks required in MOM base code)
-
-
-
-
-
-
-
-
ocean_po4_pre_start
-
-
-DESCRIPTION
-
-
- Initialize variables, read in namelists, calculate constants for a given run
- and allocate diagnostic arrays
-
-
-
-
-
-
-
-
ocean_po4_pre_tracer
-
-
-DESCRIPTION
-
-
- Perform things that should be done in tracer, but are done here
- in order to minimize the number of hooks necessary in the MOM4 basecode
-
-
-
-
-
-
-
-
set_array
-
-
-DESCRIPTION
-
-
- Set up an array covering the model domain with a user-specified
- value, in user-specified regions. There are a given number of
- 2-d regions specified by the values slat, nlat, wlon and elon.
- The longitudes are for a cyclic domain, and if wlon and elon
- are on opposite sides of the cut, the correct thing will
- be done. Elon is considered to be east of wlon, so if elon is
- less than wlon, then the region east of elon to the cut will be
- filled, and the region from the cut to wlon will be filled.
-
- After setting up the array in this routine, it may prove useful
- to allow fine-tuning the settings via an array in a namelist.
-
- Arguments:
- Input:
- num_regions = number of user-specified regions which will be
- filled
-
- wlon = 1-d array of western (starting) longitudes for the
- rectangular regions
-
- elon = 1-d array of eastern (ending) longitudes for the
- rectangular regions
-
- slat = 1-d array of southern (starting) latitudes for the
- rectangular regions
-
- nlat = 1-d array of northern (ending) latitudes for the
- rectangular regions
-
- Note: if slat >= nlat, then nothing is done
- for that region
-
- set_value = the value to assign to array in the user-specified
- regions
-
- unset_value = the value to assign to array outside of the
- user-specified regions
-
- name = character variable used in informative messages
-
- coastal_only = true to limit changes only to coastal points
- (i.e., at least one bordering point is land)
-
- Output:
-
- array = 2-d array which will contain the set- and unset-
- values. The array is assumed to have a border
- one unit wide on all edges, ala MOM. A cyclic
- boundary condition will be set if requested.
-
- Clean up various ABIOTIC quantities for this run.
-
-
-
-
-
-
-
-
ocmip2_abiotic_restart
-
-
-DESCRIPTION
-
-
- Write out restart files registered through register_restart_file
-
-
-
-
-
-
-
-
ocmip2_abiotic_sbc
-
-
-DESCRIPTION
-
-
- Calculate the surface boundary conditions
-
-
-
-
-
-
-
-
ocmip2_abiotic_flux_init
-
-
-DESCRIPTION
-
-
- Set up any extra fields needed by the ocean-atmosphere gas fluxes
-
-
-
-
-
-
-
-
ocmip2_abiotic_init
-
-
-DESCRIPTION
-
-
- Set up any extra fields needed by the tracer packages
-
- Save pointers to various "types", such as Grid and Domains.
-
-
-
-
-
-
-
-
ocmip2_abiotic_init_sfc
-
-
-DESCRIPTION
-
-
- Initialize surface fields for flux calculations
-
- Note: this subroutine should be merged into ocmip2_abiotic_start
-
-
-
-
-
-
-
-
ocmip2_abiotic_sum_sfc
-
-
-DESCRIPTION
-
-
- Sum surface fields for flux calculations
-
-
-
-
-
-
-
-
ocmip2_abiotic_zero_sfc
-
-
-DESCRIPTION
-
-
- Sum surface fields for flux calculations
-
-
-
-
-
-
-
-
ocmip2_abiotic_avg_sfc
-
-
-DESCRIPTION
-
-
- Sum surface fields for flux calculations
-
-
-
-
-
-
-
-
ocmip2_abiotic_sfc_end
-
-
-DESCRIPTION
-
-
- Initialize surface fields for flux calculations
-
-
-
-
-
-
-
-
ocmip2_abiotic_source
-
-
-DESCRIPTION
-
-
- compute the source terms for the ABIOTICs, including boundary
- conditions (not done in setvbc, to minimize number
- of hooks required in MOM base code)
-
-
-
-
-
-
-
-
ocmip2_abiotic_start
-
-
-DESCRIPTION
-
-
- Initialize variables, read in namelists, calculate constants
- for a given run and allocate diagnostic arrays
-
-
-
-
-
-
-
-
ocmip2_abiotic_tracer
-
-
-DESCRIPTION
-
-
- Perform things that should be done in tracer, but are done here
- in order to minimize the number of hooks necessary in the MOM4 basecode
-
- Press, W. H., S. A. Teukosky, W. T. Vetterling, B. P. Flannery, 1992.
- Numerical Recipes in FORTRAN, Second Edition, Cambridge University Press.
-
-
- Enting, I.G., T. M. L. Wigley, M. Heimann, 1994. Future Emissions
- and concentrations of carbon dioxide: key ocean / atmosphere /
- land analyses, CSIRO Aust. Div. Atmos. Res. Tech. Pap. No. 31,
- 118 pp.
-
- After Numerical recipes:
-
- Given an array XX of length N, and a given value of X, returns a
- value of J such that X is between XX(J) and XX(J+1). XX must be
- monotonic, either increasing or decreasing. J=0 or J=N is
- returned to indicate that X is out of range.
- New features:
-
- If "period" is specified, then the array, xx, is considered
- to be periodic with a period of "period". If "x_in" is out
- of range, then add or subtract "period" once to attempt to
- make "x_in" be in range.
-
- If "nearest" is specified, and true, then return "j" such
- that it is the element of "xx" which is nearest to the value
- of "x_in" (where "x_in" may have been modified by the value
- "period", above). With this option, "j" will be in
- the range 1 <= j <= n.
-
-
-
-
-
-
-
-
ocmip2_biotic_bbc
-
-
-DESCRIPTION
-
-
- calculate the surface boundary conditions
-
-
-
-
-
-
-
-
ocmip2_biotic_end
-
-
-DESCRIPTION
-
-
- Clean up various BIOTIC quantities for this run.
-
-
-
-
-
-
-
-
ocmip2_biotic_restart
-
-
-DESCRIPTION
-
-
- Write out restart files registered through register_restart_file
-
-
-
-
-
-
-
-
ocmip2_biotic_sbc
-
-
-DESCRIPTION
-
-
- Calculate the surface boundary conditions
-
-
-
-
-
-
-
-
ocmip2_biotic_flux_init
-
-
-DESCRIPTION
-
-
- Set up any extra fields needed by the ocean-atmosphere gas fluxes
-
-
-
-
-
-
-
-
ocmip2_biotic_init
-
-
-DESCRIPTION
-
-
- Set up any extra fields needed by the tracer packages
-
- Save pointers to various "types", such as Grid and Domains.
-
-
-
-
-
-
-
-
ocmip2_biotic_init_sfc
-
-
-DESCRIPTION
-
-
- Initialize surface fields for flux calculations
-
- Note: this subroutine should be merged into ocmip2_biotic_start
-
-
-
-
-
-
-
-
ocmip2_biotic_sum_sfc
-
-
-DESCRIPTION
-
-
- Sum surface fields for flux calculations
-
-
-
-
-
-
-
-
ocmip2_biotic_zero_sfc
-
-
-DESCRIPTION
-
-
- Sum surface fields for flux calculations
-
-
-
-
-
-
-
-
ocmip2_biotic_avg_sfc
-
-
-DESCRIPTION
-
-
- Sum surface fields for flux calculations
-
-
-
-
-
-
-
-
ocmip2_biotic_sfc_end
-
-
-DESCRIPTION
-
-
- Initialize surface fields for flux calculations
-
-
-
-
-
-
-
-
ocmip2_biotic_source
-
-
-DESCRIPTION
-
-
- compute the source terms for the BIOTICs, including boundary
- conditions (not done in setvbc, to minimize number
- of hooks required in MOM base code)
-
-
-
-
-
-
-
-
ocmip2_biotic_start
-
-
-DESCRIPTION
-
-
- Initialize variables, read in namelists, calculate constants
- for a given run and allocate diagnostic arrays
-
-
-
-
-
-
-
-
set_array
-
-
-DESCRIPTION
-
-
- Set up an array covering the model domain with a user-specified
- value, in user-specified regions. There are a given number of
- 2-d regions specified by the values slat, nlat, wlon and elon.
- The longitudes are for a cyclic domain, and if wlon and elon
- are on opposite sides of the cut, the correct thing will
- be done. Elon is considered to be east of wlon, so if elon is
- less than wlon, then the region east of elon to the cut will be
- filled, and the region from the cut to wlon will be filled.
-
- After setting up the array in this routine, it may prove useful
- to allow fine-tuning the settings via an array in a namelist.
-
- Arguments:
- Input:
- num_regions = number of user-specified regions which will be
- filled
-
- wlon = 1-d array of western (starting) longitudes for the
- rectangular regions
-
- elon = 1-d array of eastern (ending) longitudes for the
- rectangular regions
-
- slat = 1-d array of southern (starting) latitudes for the
- rectangular regions
-
- nlat = 1-d array of northern (ending) latitudes for the
- rectangular regions
-
- Note: if slat >= nlat, then nothing is done
- for that region
-
- set_value = the value to assign to array in the user-specified
- regions
-
- unset_value = the value to assign to array outside of the
- user-specified regions
-
- name = character variable used in informative messages
-
- coastal_only = true to limit changes only to coastal points
- (i.e., at least one bordering point is land)
-
- Output:
-
- array = 2-d array which will contain the set- and unset-
- values. The array is assumed to have a border
- one unit wide on all edges, ala MOM. A cyclic
- boundary condition will be set if requested.
-
- Press, W. H., S. A. Teukosky, W. T. Vetterling, B. P. Flannery, 1992.
- Numerical Recipes in FORTRAN, Second Edition, Cambridge University Press.
-
-
- Enting, I.G., T. M. L. Wigley, M. Heimann, 1994. Future Emissions
- and concentrations of carbon dioxide: key ocean / atmosphere /
- land analyses, CSIRO Aust. Div. Atmos. Res. Tech. Pap. No. 31,
- 118 pp.
-
- Set up any extra fields needed by the ocean-atmosphere gas fluxes
-
-
-
-
-
-
-
-
ocmip2_cfc_init
-
-
-DESCRIPTION
-
-
- Set up any extra fields needed by the tracer packages
-
- Save pointers to various "types", such as Grid and Domains.
-
-
-
-
-
-
-
-
ocmip2_cfc_init_sfc
-
-
-DESCRIPTION
-
-
- Initialize surface fields for flux calculations
-
- Note: this subroutine should be merged into ocmip2_cfc_start
-
-
-
-
-
-
-
-
ocmip2_cfc_sum_sfc
-
-
-DESCRIPTION
-
-
- Sum surface fields for flux calculations
-
-
-
-
-
-
-
-
ocmip2_cfc_zero_sfc
-
-
-DESCRIPTION
-
-
- Sum surface fields for flux calculations
-
-
-
-
-
-
-
-
ocmip2_cfc_avg_sfc
-
-
-DESCRIPTION
-
-
- Sum surface fields for flux calculations
-
-
-
-
-
-
-
-
ocmip2_cfc_sfc_end
-
-
-DESCRIPTION
-
-
- Initialize surface fields for flux calculations
-
-
-
-
-
-
-
-
ocmip2_cfc_source
-
-
-DESCRIPTION
-
-
- compute the source terms for the CFCs, including boundary
- conditions (not done in setvbc, to minimize number
- of hooks required in MOM base code)
-
-
-
-
-
-
-
-
ocmip2_cfc_start
-
-
-DESCRIPTION
-
-
- Initialize variables, read in namelists, calculate constants
- for a given run and allocate diagnostic arrays
-
- Calculate the fugacity of CO2 at the surface in thermodynamic
- equilibrium with the current alkalinity (Alk) and total dissolved
- inorganic carbon (DIC) at a particular temperature and salinity
- using an initial guess for the total hydrogen
- ion concentration (htotal)
-
- Calculate CO2 solubility, alpha, from
- temperature (t) and salinity (s).
-
- INPUT
-
- isd = first i-limit of the arrays with halo
- ied = last i-limit of the arrays with halo
- jsd = first j-limit of the arrays with halo
- jed = last j-limit of the arrays with halo
- isc = first i-limit of the arrays for computation
- iec = last i-limit of the arrays for computation
- jsc = first j-limit of the arrays for computation
- jec = last j-limit of the arrays for computation
-
- t = temperature (degrees C)
-
- s = salinity (PSU)
-
- mask = land mask array (0.0 = land)
-
- OUTPUT
- alpha = Solubility of CO2 for air? (mol/kg/atm unless scaled)
-
- IMPORTANT: Some words about units - (JCO, 4/4/1999)
-
- - Models may carry tracers in mol/m^3 (on a per volume basis)
-
- - Conversely, this routine, which was written by observationalists
- (C. Sabine and R. Key), passes input arguments in umol/kg
- (i.e., on a per mass basis)
-
- - Thus, if the input or output units need to be changed from/to mol/m^3
- then set scale to an appropriate value. For example, if the model
- uses mol/m^3, then scale should be set to something like 1.0/1024.5
- to convert from mol/m^3 to mol/kg.
-
-
-
-
-
-
-
-
-
ocmip2_co2calc
-
-
-DESCRIPTION
-
-
- Calculate co2* from total alkalinity and total CO2 at
- temperature (t) and salinity (s).
- It is assumed that init_ocmip2_co2calc has already been called with
- the T and S to calculate the various coefficients.
-
- INPUT
-
- isd = first i-limit of the arrays with halo
- ied = last i-limit of the arrays with halo
- jsd = first j-limit of the arrays with halo
- jed = last j-limit of the arrays with halo
- isc = first i-limit of the arrays for computation
- iec = last i-limit of the arrays for computation
- jsc = first j-limit of the arrays for computation
- jec = last j-limit of the arrays for computation
-
- mask = land mask array (0.0 = land)
-
- t = temperature (degrees C)
-
- s = salinity (PSU)
-
- dic_in = total inorganic carbon (mol/kg unless scaled)
- where 1 T = 1 metric ton = 1000 kg
-
- ta_in = total alkalinity (eq/kg unless scaled)
-
- pt_in = inorganic phosphate (mol/kg unless scaled)
-
- sit_in = inorganic silicate (mol/kg unless scaled)
-
- htotallo = factor to set lower limit of htotal range
-
- htotalhi = factor to set upper limit of htotal range
-
- htotal = H+ concentraion
-
- OUTPUT
- co2star = CO2*water (kg/kg unless scaled)
- alpha = Solubility of CO2 for air? (kg/kg/atm unless scaled)
- pco2surf = oceanic pCO2 (ppmv)
-
- k1 = activity factors for carbonate species
-
- k2 (see below)
-
- invtk = 1/(t+273.15)
-
- IMPORTANT: Some words about units - (JCO, 4/4/1999)
-
- - Models may carry tracers in mol/m^3 (on a per volume basis)
-
- - Conversely, this routine, which was written by observationalists
- (C. Sabine and R. Key), passes input arguments in umol/kg
- (i.e., on a per mass basis)
-
- - Thus, if the input or output units need to be changed from/to mol/m^3
- then set scale to an appropriate value. For example, if the model
- uses mol/m^3, then scale should be set to something like 1.0/1024.5
- to convert from mol/m^3 to mol/kg.
-
-
-
-
-
-
-
-
-
drtsafe
-
-
-DESCRIPTION
-
-
- File taken from Numerical Recipes. Modified R. M. Key 4/94
-
-
-
-
-
-
-
-
ta_iter_1
-
-
-DESCRIPTION
-
-
- This routine expresses TA as a function of DIC, htotal and constants.
- It also calculates the derivative of this function with respect to
- htotal. It is used in the iterative solution for htotal. In the call
- "x" is the input value for htotal, "fn" is the calculated value for TA
- and "df" is the value for dTA/dhtotal
-
- Ocean Carbon Model Intercomparison Study II: HE module
-
-
-
-
-
- Implementation of routines to solve the OCMIP-2 HE
- simulations as outlined in the Helium-HOWTO documentation,
- revision 1.6, 1999/04/29.
- Modified Jan 2008 b1d. Separated atmospheric and mantle component
- and added a factor to chance the source strength
-
- Called each time-step
- calculate the bottom boundary conditions
-
-
-
-
-
-
-
-
ocmip2_he_end
-
-
-DESCRIPTION
-
-
- Called once at the end of the run
- Clean up various HE quantities for this run.
-
-
-
-
-
-
-
-
ocmip2_he_restart
-
-
-DESCRIPTION
-
-
- Write out restart files registered through register_restart_file
-
-
-
-
-
-
-
-
ocmip2_he_sbc
-
-
-DESCRIPTION
-
-
- Called each time-step
- Calculate the surface boundary conditions
-
-
-
-
-
-
-
-
ocmip2_he_flux_init
-
-
-DESCRIPTION
-
-
- Called once at the beginning of the run
- Set up any extra fields needed by the ocean-atmosphere gas fluxes
-
-
-
-
-
-
-
-
ocmip2_he_init
-
-
-DESCRIPTION
-
-
- Called once at the beginning of the run
- Set up any extra fields needed by the tracer packages
- Save pointers to various "types", such as Grid and Domains.
-
-
-
-
-
-
-
-
ocmip2_he_init_sfc
-
-
-DESCRIPTION
-
-
- Called once at the beginning of the run
- Initialize surface fields for flux calculations
-
-
-
-
-
-
-
-
-
ocmip2_he_sum_sfc
-
-
-DESCRIPTION
-
-
- Called for FMS coupler
- ocean_tpm_sum_sfc: Accumulate data for the coupler
- Sum surface fields for flux calculations
-
-
-
-
-
-
-
-
ocmip2_he_zero_sfc
-
-
-DESCRIPTION
-
-
- Zero out the fields for the coupler to allow
- for accumulation for the next time period
-
-
-
-
-
-
-
-
ocmip2_he_avg_sfc
-
-
-DESCRIPTION
-
-
- Called for FMS coupler
- ocean_tpm_avg_sfc: Take the time-mean of the fields for the coupler
- Sum surface fields for flux calculations
-
-
-
-
-
-
-
-
ocmip2_he_sfc_end
-
-
-DESCRIPTION
-
-
- Called for FMS coupler
- ocean_tpm_sfc_end: Save out fields for the restart.
-
-
-
-
-
-
-
-
ocmip2_he_source
-
-
-DESCRIPTION
-
-
- compute the source terms for the HEs, including boundary
- conditions (not done in setvbc, to minimize number
- of hooks required in MOM base code)
- As described by J-C Dutay et al.'s Helium HOWTO.
- Mantle Helium has a source due to emission of helium rich waters
- along ocean ridges on the seafloor. Globally integrated, the source
- term amounts to 1000 moles of He-3 per year. Regionally, sources are
- partitioned as a function of ridge position, length and spreading rate.
- A loss term exists in the air-sea flux of mantle helium.
-
- The loss term is calculated in the subroutine ocmip2_he_sbc.
-
-
-
-
-
-
-
-
ocmip2_he_start
-
-
-DESCRIPTION
-
-
- Initialize variables, read in namelists, calculate constants
- for a given run and allocate diagnostic arrays
-
-
-
-
-
-
-
-
ocmip2_he_tracer
-
-
-DESCRIPTION
-
-
- Perform things that should be done in tracer, but are done here
- in order to minimize the number of hooks necessary in the MOM4 basecode
-
- This is the main "driver" module for the Lagrangian blob scheme. This
- module calls other modules that contain the individual parameterisations.
-
- Please note that the preprocessor option MOM_STATIC_ARRAYS is NOT
- supported. This is because to run a model where the memeory statically
- allocated without the blob framework will incur a large, unnecessary
- increase in memory requirements.
-
-
-
-
-
- This module is the top-level module of the Lagrangian blob framework.
- It calls routines to form blobs, to integrate their properties, to
- transfer them from one dynamic regime to another, and also calculates
- the L system contribution towards grid cell thickness.
-
- This module also handles some framework wide variables, mostly
- associated with system wide diagnostics and the system wide accounting
- required to ensure the Eulerian model and the Lagrangian model can coexist.
-
- It should be noted that many of the parameterisations are not mutually
- exclusive. As such, care should be excercised when creating namelists
- for experiments.
-
- Initialises the Lagrangian blob module by setting up module wide
- variables and calling initialisation scripts for the related modules,
- as well as the Lagrangian system itself.
-
- Infrastructure for communicating between PE's, interpolation of E
- system variables to a blob, communicating model wide namelist values
- and variables to other modules and picking up restarts is all done.
-
-
-
-
-
-
-
-
init_blob_thickness
-
-
-DESCRIPTION
-
-
- Initialises the L_system thickness, based on the existing blobs
-
-
-
-
-
-
-
-
ocean_blob_update
-
-
-DESCRIPTION
-
-
- Updates the Lagrangian blobs by calling routines that run during the
- explicit in time part of the time step.
-
-
-
-
-
-
-
-
ocean_blob_cell_update
-
-
-DESCRIPTION
-
-
-
- For bottom blobs, it diagnoses the blobs vertical position in the
- models native vertical coordinate.
-
- For free blobs, it searches for the vertical grid cell that a free
- blob resides in.
-
- We require the information regarding the vertical grid cell that a
- blob resides in prior to the calculation of total grid cell thickness
- and prior to the calculation of the vertical advection velocity.
-
- In order to figure out which grid cell the blob is in, we need to
- employ different strategies for different coordinate system (see notes
- for details).
-
- For any blobs that penetrate the free surface (which is unlikely, but
- not impossible) we immediately kill them, returning their properties
- to the surface grid cell of the (i,j) column that they belong to.
-
- We recalculate a blobs density and volume for taup1, based on the pressure
- at the centre of the grid cell that it resides in.
-
-
-
-
-
-
-
-
-
update_L_thickness
-
-
-DESCRIPTION
-
-
- Calculates the contribution to thickness of all the blobs for the
- L system arrays in the Thickness strcture.
-
- The mass per unit area from the blobs is also calculated for the
- upper and lower part of each grid cell and stored in the L_system
- structure. The calculate of mass per unit area is required for
- pressure calculations.
-
- We note that in DEPTH_BASED models, the value for density used is
- rho0, while it is the actual density in PRESSURE_BASED models. For
- the L_system mass per unit area, the actual density is used for
- all supported coordinates.
-
-
-
-
-
-
-
-
calculate_rhoT
-
-
-DESCRIPTION
-
-
- Calculates the density of the combined E and L systems.
-
- It needs to be done here so that the blobs are taken into account.
-
-
-
-
-
-
-
-
-
ocean_blob_implicit
-
-
-DESCRIPTION
-
-
- Updates the Lagrangian blobs by calling routines that run during the
- implicit in time part of the time step.
-
-
-
-
-
-
-
-
adjust_L_thickness
-
-
-DESCRIPTION
-
-
- blob_thickness is called after new blobs are formed implicitly in
- time. blob_thickness provides the same function as
- update_L_thickness, with a couple of subtle differences.
-
- At the point that this routine is called, we:
- 1/ Know the vertical position of an "old" blob relative to the geoid
- and in the Eulerian model's native vertical coordinate. We do
- not know a blobs depth relative to the sea surface.
- 2/ Know the vertical position relative to the sea surface for "new"
- blobs, but we do not know its position relative to the geoid or in
- the Euerlian model's native vertical coordinate.
-
- So, blob_thickness uses the logical new, which is part of the blob
- derived type, to distinguish between new blobs and old blobs. New
- blobs have their position (upper or lower part of a grid cell)
- calculated using the depth relative to the sea surface height, while
- blobs that are not new have their position calculated using the
- Eulerian models native coordinate.
-
- The accumulation of thickness and mass per unit area are done in the
- same was as is done in update_L_thickness.
-
-
-
-
-
-
-
-
ocean_blob_diagnose_depth
-
-
-DESCRIPTION
-
-
- When blobs are created implicitly in time, the sea surface height has
- not been calcualted in pressure based models (but depth has). However,
- the prognostic variable for blobs is the geodepth and not the depth. So,
- for a new blob, we set the depth when it is formed and then calculate
- the geodepth here. For existing blobs, we diagnose the depth using
- eta_t and geodepth.
-
- We note that in GEOPOTENTIAL coordinates, depth and geodepth are
- equivalent, and so we set them to be equivalent for the blobs too.
-
-
-
-
-
-
-
-
ocean_blob_end
-
-
-DESCRIPTION
-
-
- Writes restarts and do checksums for the blobs at the end of a run.
-
-
-
-
-
-
-
-
write_all_blobs
-
-
-DESCRIPTION
-
-
- A convenient subroutine for debugging that dumps blob details from
- every list
-
-
-
-
-
-
-
-
entrainment_checksum
-
-
-DESCRIPTION
-
-
- Do the entrainment checksums
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_blob_nml
-
-
-
-
-
-use_this_module
-
-
- Must be true to use this module.
- Default is use_this_module=.false.
-
-[logical]
-
-
-debug_this_module
-
-
- Writes additional diagnostic data to fms.out. This
- also controls debug output for the other related blob
- modules.
- Default is debug_this_module=.false.
-
-[logical]
-
-
-really_debug
-
-
- Be careful what you wish for, this outputs A LOT of
- diagnostics to standard out!
- Default is debug_this_module=.false.
-
-[logical]
-
-
-do_bitwise_exact_sum
-
-
- When global sum outputs are done there is additional
- computational expense to ensure that they are bitwise
- the same across an arbitrary number of processors.
- However, for debugging purposes, it can be useful
- for global sums to be the same. Note, that this differs
- from bitwise_reproduction in that it do_bitwise_exact_sum
- only applies to the mpp_global_sum diagnostic.
- Note that this flag controls the output for all associated
- blob modules.
- Default is do_bitwise_exact_sum=.false.
-
-[logical]
-
-
-bitwise_reproduction
-
-
- There is additional cost involved in ensuring that
- results are reproducable across an arbitrary number of
- processors and across restarts.
- Bitwise reproduction is a very memory intensive operation and should
- only be used for debugging. For bitwise_reproduction=.true. We need
- to process blobs and their histories in the same relative order
- regardless of domain decomposition and restarts. To do so, we save the
- "history" of each blob subcycle is saved to a number of arrays (which
- can be a very memory intensive process) and process them in order.
- Note that this flag controls reproducability for all associated
- blob modules.
- Bitwise reproducibility is only possible with the appropriate
- compiler flags AND when the simulation is run on hardware that is
- capable of producing bitwise reproduction.
- Default is bitwise_reproduction=.false.
-
-[logical]
-
-
-blob_small_mass
-
-
- Will delete blobs of mass less than blob_small_mass.
- Note that this variable is for all associated blob
- modules. The deletion of blobs is a conservative
- action, any mass/tracer fields that are nonzero
- have the remaining properties transferred back to the
- Eulerian system. So, in principle, blob_small_mass
- can actually be a relatively large number, and the
- model will remain conservative. It has been found in
- certain test cases (with very low tracer values) that
- setting blob_small_mass to be very small (i.e. <1e2)
- that roundoff error can cause non-trivial errors. So,
- it is recommended that blob_small_mass be no smaller than
- than 1e3 kg (which is approximately 1.0m**3 -- a very small
- blob!)
- Default is blob_small_mass=1.e3
-
-[real, units: kg]
-
-
-mass_prop_thickness
-
-
- Sets the maximum proportion of a grid cell that the
- Lagrangian system may occupy. This is actually calculated
- separately (and therefore must be satisfied separately) for
- the uppper and lower portions of a grid cell.
- Default is blob_small_mass=0.7
-
-[real, units: dimensionless]
-
-
-
-
-
-
-
-
-
-
-
REFERENCES
-
-
-
-
- S.M. Griffies, Elements of MOM4p1 (2009)
- NOAA/Geophysical Fluid Dynamics Laboratory
-
-
-
diff --git a/src/mom5/ocean_blobs/ocean_blob.xml b/src/mom5/ocean_blobs/ocean_blob.xml
deleted file mode 100644
index 9db8c3d09c..0000000000
--- a/src/mom5/ocean_blobs/ocean_blob.xml
+++ /dev/null
@@ -1,187 +0,0 @@
-
-
- Michael L. Bates
- Stephen M. Griffies
-
- This is the main "driver" module for the Lagrangian blob scheme. This
- module calls other modules that contain the individual parameterisations.
-
- Please note that the preprocessor option MOM_STATIC_ARRAYS is NOT
- supported. This is because to run a model where the memeory statically
- allocated without the blob framework will incur a large, unnecessary
- increase in memory requirements.
-
- This module is the top-level module of the Lagrangian blob framework.
- It calls routines to form blobs, to integrate their properties, to
- transfer them from one dynamic regime to another, and also calculates
- the L system contribution towards grid cell thickness.
-
- This module also handles some framework wide variables, mostly
- associated with system wide diagnostics and the system wide accounting
- required to ensure the Eulerian model and the Lagrangian model can coexist.
-
- It should be noted that many of the parameterisations are not mutually
- exclusive. As such, care should be excercised when creating namelists
- for experiments.
-
- S.M. Griffies, Elements of MOM4p1 (2009)
- NOAA/Geophysical Fluid Dynamics Laboratory
-
- Must be true to use this module.
- Default is use_this_module=.false.
-
- Writes additional diagnostic data to fms.out. This
- also controls debug output for the other related blob
- modules.
- Default is debug_this_module=.false.
-
- Be careful what you wish for, this outputs A LOT of
- diagnostics to standard out!
- Default is debug_this_module=.false.
-
- When global sum outputs are done there is additional
- computational expense to ensure that they are bitwise
- the same across an arbitrary number of processors.
- However, for debugging purposes, it can be useful
- for global sums to be the same. Note, that this differs
- from bitwise_reproduction in that it do_bitwise_exact_sum
- only applies to the mpp_global_sum diagnostic.
- Note that this flag controls the output for all associated
- blob modules.
- Default is do_bitwise_exact_sum=.false.
-
- There is additional cost involved in ensuring that
- results are reproducable across an arbitrary number of
- processors and across restarts.
- Bitwise reproduction is a very memory intensive operation and should
- only be used for debugging. For bitwise_reproduction=.true. We need
- to process blobs and their histories in the same relative order
- regardless of domain decomposition and restarts. To do so, we save the
- "history" of each blob subcycle is saved to a number of arrays (which
- can be a very memory intensive process) and process them in order.
- Note that this flag controls reproducability for all associated
- blob modules.
- Bitwise reproducibility is only possible with the appropriate
- compiler flags AND when the simulation is run on hardware that is
- capable of producing bitwise reproduction.
- Default is bitwise_reproduction=.false.
-
- Will delete blobs of mass less than blob_small_mass.
- Note that this variable is for all associated blob
- modules. The deletion of blobs is a conservative
- action, any mass/tracer fields that are nonzero
- have the remaining properties transferred back to the
- Eulerian system. So, in principle, blob_small_mass
- can actually be a relatively large number, and the
- model will remain conservative. It has been found in
- certain test cases (with very low tracer values) that
- setting blob_small_mass to be very small (i.e. <1e2)
- that roundoff error can cause non-trivial errors. So,
- it is recommended that blob_small_mass be no smaller than
- than 1e3 kg (which is approximately 1.0m**3 -- a very small
- blob!)
- Default is blob_small_mass=1.e3
-
- Sets the maximum proportion of a grid cell that the
- Lagrangian system may occupy. This is actually calculated
- separately (and therefore must be satisfied separately) for
- the uppper and lower portions of a grid cell.
- Default is blob_small_mass=0.7
-
- Initialises the Lagrangian blob module by setting up module wide
- variables and calling initialisation scripts for the related modules,
- as well as the Lagrangian system itself.
-
- Infrastructure for communicating between PE's, interpolation of E
- system variables to a blob, communicating model wide namelist values
- and variables to other modules and picking up restarts is all done.
-
- Initialises the L_system thickness, based on the existing blobs
-
- Updates the Lagrangian blobs by calling routines that run during the
- explicit in time part of the time step.
-
-
- For bottom blobs, it diagnoses the blobs vertical position in the
- models native vertical coordinate.
-
- For free blobs, it searches for the vertical grid cell that a free
- blob resides in.
-
- We require the information regarding the vertical grid cell that a
- blob resides in prior to the calculation of total grid cell thickness
- and prior to the calculation of the vertical advection velocity.
-
- In order to figure out which grid cell the blob is in, we need to
- employ different strategies for different coordinate system (see notes
- for details).
-
- For any blobs that penetrate the free surface (which is unlikely, but
- not impossible) we immediately kill them, returning their properties
- to the surface grid cell of the (i,j) column that they belong to.
-
- We recalculate a blobs density and volume for taup1, based on the pressure
- at the centre of the grid cell that it resides in.
-
-
- Calculates the contribution to thickness of all the blobs for the
- L system arrays in the Thickness strcture.
-
- The mass per unit area from the blobs is also calculated for the
- upper and lower part of each grid cell and stored in the L_system
- structure. The calculate of mass per unit area is required for
- pressure calculations.
-
- We note that in DEPTH_BASED models, the value for density used is
- rho0, while it is the actual density in PRESSURE_BASED models. For
- the L_system mass per unit area, the actual density is used for
- all supported coordinates.
-
- Calculates the density of the combined E and L systems.
-
- It needs to be done here so that the blobs are taken into account.
-
-
- Updates the Lagrangian blobs by calling routines that run during the
- implicit in time part of the time step.
-
- blob_thickness is called after new blobs are formed implicitly in
- time. blob_thickness provides the same function as
- update_L_thickness, with a couple of subtle differences.
-
- At the point that this routine is called, we:
- 1/ Know the vertical position of an "old" blob relative to the geoid
- and in the Eulerian model's native vertical coordinate. We do
- not know a blobs depth relative to the sea surface.
- 2/ Know the vertical position relative to the sea surface for "new"
- blobs, but we do not know its position relative to the geoid or in
- the Euerlian model's native vertical coordinate.
-
- So, blob_thickness uses the logical new, which is part of the blob
- derived type, to distinguish between new blobs and old blobs. New
- blobs have their position (upper or lower part of a grid cell)
- calculated using the depth relative to the sea surface height, while
- blobs that are not new have their position calculated using the
- Eulerian models native coordinate.
-
- The accumulation of thickness and mass per unit area are done in the
- same was as is done in update_L_thickness.
-
- When blobs are created implicitly in time, the sea surface height has
- not been calcualted in pressure based models (but depth has). However,
- the prognostic variable for blobs is the geodepth and not the depth. So,
- for a new blob, we set the depth when it is formed and then calculate
- the geodepth here. For existing blobs, we diagnose the depth using
- eta_t and geodepth.
-
- We note that in GEOPOTENTIAL coordinates, depth and geodepth are
- equivalent, and so we set them to be equivalent for the blobs too.
-
- Writes restarts and do checksums for the blobs at the end of a run.
-
- A convenient subroutine for debugging that dumps blob details from
- every list
-
- Do the entrainment checksums
-
diff --git a/src/mom5/ocean_blobs/ocean_blob_diag.html b/src/mom5/ocean_blobs/ocean_blob_diag.html
deleted file mode 100644
index d054ecdb66..0000000000
--- a/src/mom5/ocean_blobs/ocean_blob_diag.html
+++ /dev/null
@@ -1,250 +0,0 @@
-
-
-
-Module ocean_blob_diag_mod
-
-
-
-
-PUBLIC INTERFACE
-
- ~ PUBLIC ROUTINES
-
-
- Controls the diagnostic output from individual blobs.
-
-
-
-
-
- Controls the diagnostics from individual blobs. Blob diagnostics
- are snapshots at full E system time steps of blob properties. There is
- no averaging of individual blob properties. The properties that can be
- output are set in a diagnostic file. The name of the diagnostic file
- is specified in the namelist.
-
- Accummulates the blob diagnostics by creating a linked list of
- diagnostic blobs. The blobs are kept in the linked list until
- there are more than dump_num of them. Then, they are written
- (using write_blobs), and erased from memory.
-
-
-
-
-
-
-
-
varid
-
-
-DESCRIPTION
-
-
- Reads the variable id of a netcdf file.
-
-
-
-
-
-
-
-
blob_diag_end
-
-
-DESCRIPTION
-
-
-
-
-
-
-
-
-
-
-
write_blobs
-
-
-DESCRIPTION
-
-
- Write the diagnostics of individual blobs.
-
-
-
-
-
-
-
-
handle_error
-
-
-DESCRIPTION
-
-
- Handles any errors from the reading/writing of netcdf files. It
- should (hopefully) provide some sort of useful idea of what went
- wrong.
-
-
-
diff --git a/src/mom5/ocean_blobs/ocean_blob_diag.xml b/src/mom5/ocean_blobs/ocean_blob_diag.xml
deleted file mode 100644
index 2b1fb5583c..0000000000
--- a/src/mom5/ocean_blobs/ocean_blob_diag.xml
+++ /dev/null
@@ -1,52 +0,0 @@
-
-
- Michael L. Bates
- Stephen M. Griffies
-
- Controls the diagnostic output from individual blobs.
-
- Controls the diagnostics from individual blobs. Blob diagnostics
- are snapshots at full E system time steps of blob properties. There is
- no averaging of individual blob properties. The properties that can be
- output are set in a diagnostic file. The name of the diagnostic file
- is specified in the namelist.
-
- Logical as to whether diagnostics should be saved or not.
- Default is .false.
-
- Name of file to look for blob diagnostic information.
- Default is "blob_diag_table"
-
- The number of entried to keep in memory before writing
- them to file. The higher the number, the more memory that
- the module will take up, but, it should lower the frequency of
- IO operations.
- Default is 2000000
-
- The frequency (in number of E system time steps) that blob
- diagnostics should be saved.
- Default is 1
-
- Initialises the blob diagnostic module.
-
- Accummulates the blob diagnostics by creating a linked list of
- diagnostic blobs. The blobs are kept in the linked list until
- there are more than dump_num of them. Then, they are written
- (using write_blobs), and erased from memory.
-
- Reads the variable id of a netcdf file.
-
-
- Write the diagnostics of individual blobs.
-
- Handles any errors from the reading/writing of netcdf files. It
- should (hopefully) provide some sort of useful idea of what went
- wrong.
-
- Creates a new netcdf file.
-
- Opens an existing netcdf file.
-
- Closes an existing netcdf file.
-
diff --git a/src/mom5/ocean_blobs/ocean_blob_dynamic_bottom.html b/src/mom5/ocean_blobs/ocean_blob_dynamic_bottom.html
deleted file mode 100644
index aaaea33161..0000000000
--- a/src/mom5/ocean_blobs/ocean_blob_dynamic_bottom.html
+++ /dev/null
@@ -1,545 +0,0 @@
-
-
-
-Module ocean_blob_dynamic_bottom_mod
-
-
-
-
-PUBLIC INTERFACE
-
- ~ PUBLIC ROUTINES
- ~ NAMELIST
-
-
- This module runs the dynamic bottom blob implementation of the embedded
- Lagrangian buoyancy blob framework. The module forms new dynamic
- bottom blobs, integrates the properties of existing blobs, and handles
- the transfer of free blobs to bottom blobs.
-
-
-
-
-
- Bottom blobs are formed using the subroutine dynamic_bottom_form_new,
- which is called from the main blob driver module. Bottom blobs are
- formed explicitly in time, directly after the integration of existing
- blobs.
-
- The properties of a bottom blob are also integrated in this module,
- that is, position, velocity, mass and tracer content. Position and
- velocity are integrated using an adaptive step Runge-Kutta scheme.
- There are several schemes available of varying order.
-
- The module also recieves blobs that are transferring from the free
- blob dynamic regime to the bottom blob dynamic regime (i.e. free
- blobs that have interacted with topography).
-
- Initialises the dynamic free blobs by checking the namelist and also
- inherited namelists (from ocean_blob_nml). Also sets up some useful
- constants (including spatially varying constants) - particularly for
- the formation of bottom blobs. It also allocates memory to special
- halo=2 masks and sets up the blob buffers for sending blobs from one
- PE to another.
-
-
-
-
-
-
-
-
blob_dynamic_bottom_update
-
-
-DESCRIPTION
-
-
- This routine calls the routine to update blob positions. When
- bitwise_reproduction=.false., it also figures out when to continue
- the integration of blobs that have changed PE's.
-
-
-
-
-
-
-
-
dynamic_update
-
-
-DESCRIPTION
-
-
- This routine contains the RK scheme used to integrate the position
- and velocity of blobs. It also does many checks for (and
- subsequently handles) things like grounding of blobs, blobs going to
- different PEs, blobs that separate from topography, blobs that
- detrain to less than small_mass and blobs going outside the compute
- domain.
-
- It also does the interpolation of E system variables to a blob.
-
-
-
-
-
-
-
-
transfer_free_to_bottom
-
-
-DESCRIPTION
-
-
- Takes free blobs that have interacted with topography and turns them
- into bottom blobs.
-
-
-
-
-
-
-
-
dynamic_bottom_form_new
-
-
-DESCRIPTION
-
-
- Initialises blobs that are formed when an on-shelf/off-shelf
- instability occurs. The method used for determining an instability
- and the initial conditions are based on that of Campin and Goosse
- (1999).
-
- When the density difference between the shallow ocean cell and the
- deep ocean cell (referenced to the deep ocean cell) exceeds the
- namelist variable rho_threshold, a blob is formed. The deep ocean
- cell is chosen based on which deep ocean cell (in the k plane)
- the blob topography intersects.
-
- After formation, the new blobs are added to the bottom blob linked
- list, and, their properties are integrated, starting at time taup1.
-
-
-
-
-
-
-
-
blob_dynamic_bottom_end
-
-
-DESCRIPTION
-
-
- Clears memory to give a nice clean ending to the run.
-
-
-
-
-
-
-
-
packbuffer
-
-
-DESCRIPTION
-
-
- Packs a buffer with all the information needed to send a blob from
- one PE to another.
-
-
-
-
-
-
-
-
unpackbuffer
-
-
-DESCRIPTION
-
-
- Unpacks a received buffer.
-
-
-
-
-
-
-
-
increase_buffer
-
-
-DESCRIPTION
-
-
- Increases the buffer size for sending blobs from one PE to another.
-
-
-
-
-
-
-
-
send_buffer
-
-
-DESCRIPTION
-
-
- Sends a buffer to an adjoining PE
-
-
-
-
-
-
-
-
receive_buffer
-
-
-DESCRIPTION
-
-
- Receives a buffer from an adjoining PE
-
-
-
-
-
-
-
-
clear_buffer
-
-
-DESCRIPTION
-
-
- Clears the contents of a buffer
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_blob_dynamic_bottom_nml
-
-
-
-
-
-use_this_module
-
-
- Must be true to use this module.
- Default is use_this_module=.false.
-
-[logical]
-
-
-blob_overflow_mu
-
-
- Frictional dissipation rate used for calculating initial
- properties of bottom blobs. Corresponds to mu in Campin and
- Goosse (1999). Units are 1/s.
- Default is blob_overflow_mu=1.0e-4
-
-[real]
-
-
-blob_overflow_delta
-
-
- Fraction of a grid cell participating in an overflow event.
- Corresponds to delta in Campin and Goosse (1999). Dimensionless.
- Default is blob_overflow_mu=1.0e-4
-
-[real]
-
-
-drag
-
-
- Coefficient of drag used for bottom stress drag.
- Corresponds to Cd in Price and Baringer (1994). Dimensionless.
- Default is drag=3.0e-3
-
-[real]
-
-
-det_param
-
-
- The detrainment parameter (kg m^2/s).
- Corresponds to Gamma in the notes.
- Default is det_param=5.0e-8
-
-
-[real]
-
-
-max_detrainment
-
-
- The Maximum allowable detrainment velocity (m/s).
- Default is max_detrainment=1.0e-3
-
-[real]
-
-
-rel_error
-
-
- Relative error for the RK scheme (dimensionless).
- A smaller number is more accurate, but,
- is more computationally expensive. Corresponds to
- zeta* in the notes.
- Must be 0<rel_error<=1.0
- Default is rel_error=0.01
-
-[real]
-
-
-safety_factor
-
-
- Safety factor for the RK scheme (dimensionless).
- A smaller number should reduce the number
- of rejected steps, but, decreases the locally
- extrapolated step. Corresponds to varrho in
- the notes.
- Must be 0<safety_factor<=1.0
- Default is safety_factor=0.8
-
-[real]
-
-
-minstep
-
-
- Minimum step size (in seconds) for a blob.
- Default is minstep=9.0
-
-[real]
-
-
-elastic
-
-
- The elasticity of a blob's collision with
- the topography. Corresponds to epsilon in
- the notes. Should have values 0<=elastic<=1.0
- Values greater than 1 would be super-elastic,
- and values less than 0 would send the blob
- in the opposite direction than it should be
- going in.
- Default is elastic=1.0
-
-[real]
-
-
-min_do_levels
-
-
- Minimum number of deep ocean levels for
- overflows to be considered. That is, how many
- k levels lower should the deep ocean water column
- be than the shelf/shallow ocean column. Value
- must be greater than 0.
- Default is min_do_levels=1
-
-[integer]
-
-
-rho_threshold
-
-
- The density difference required before a blob
- is formed. rho_threshold must be greater than
- zero.
- Default is rho_threshold=0.01
-
-[real]
-
-
-large_speed
-
-
- A value for error checking. If the speed of a
- blob exceeds large_speed in any of x,y,z then
- a warning flag is raised.
- Default is large_speed=10.0
-
-[real]
-
-
-no_rotation
-
-
- Sets the coriolis parameter to zero regardless
- of latitude
- Default is no_rotation=.false.
-
-[real]
-
-
-critical_richardson
-
-
- The critical Richardson number for the entrainment
- velocity. Default is based on Price and Baringer
- (1994).
- Default is critical_richardson=0.8
-
-[real]
-
-
-
-
-
-
-
-
-
-
-
REFERENCES
-
-
-
-
- Price, J.F., Baringer, M.O'N. (1994) Outflows and deep water production
- by marginal seas. Progress in Oceanography 33(3), 161-200.
-
-
- Campin, J-.M., Goosse, H. (1999) Parameterization of a density-driven
- downsloping flow for a coarse-resolution ocean model in z-coordinate.
- Tellus 51A(3), 412-430.
-
-
- Bogacki, P., Shampine, L.F. (1989) A 3(2) pair of Runge-Kutta formulas.
- Applied Mathematical Letters 2(4), 321-325.
-
-
- Cash, J.R., Karp, A.H. (1990) A variable order Runge-Kutta method for
- initial value problems with rapidly varying right-hand sides.
- ACM Transactions on Mathematical Software 16(3), 201-222.
-
-
-
diff --git a/src/mom5/ocean_blobs/ocean_blob_dynamic_bottom.xml b/src/mom5/ocean_blobs/ocean_blob_dynamic_bottom.xml
deleted file mode 100644
index 3f803d07d4..0000000000
--- a/src/mom5/ocean_blobs/ocean_blob_dynamic_bottom.xml
+++ /dev/null
@@ -1,168 +0,0 @@
-
-
- Michael L. Bates
- Stephen M. Griffies
-
- This module runs the dynamic bottom blob implementation of the embedded
- Lagrangian buoyancy blob framework. The module forms new dynamic
- bottom blobs, integrates the properties of existing blobs, and handles
- the transfer of free blobs to bottom blobs.
-
- Bottom blobs are formed using the subroutine dynamic_bottom_form_new,
- which is called from the main blob driver module. Bottom blobs are
- formed explicitly in time, directly after the integration of existing
- blobs.
-
- The properties of a bottom blob are also integrated in this module,
- that is, position, velocity, mass and tracer content. Position and
- velocity are integrated using an adaptive step Runge-Kutta scheme.
- There are several schemes available of varying order.
-
- The module also recieves blobs that are transferring from the free
- blob dynamic regime to the bottom blob dynamic regime (i.e. free
- blobs that have interacted with topography).
-
- Price, J.F., Baringer, M.O'N. (1994) Outflows and deep water production
- by marginal seas. Progress in Oceanography 33(3), 161-200.
-
- Campin, J-.M., Goosse, H. (1999) Parameterization of a density-driven
- downsloping flow for a coarse-resolution ocean model in z-coordinate.
- Tellus 51A(3), 412-430.
-
- Bogacki, P., Shampine, L.F. (1989) A 3(2) pair of Runge-Kutta formulas.
- Applied Mathematical Letters 2(4), 321-325.
-
- Cash, J.R., Karp, A.H. (1990) A variable order Runge-Kutta method for
- initial value problems with rapidly varying right-hand sides.
- ACM Transactions on Mathematical Software 16(3), 201-222.
-
- Must be true to use this module.
- Default is use_this_module=.false.
-
- Frictional dissipation rate used for calculating initial
- properties of bottom blobs. Corresponds to mu in Campin and
- Goosse (1999). Units are 1/s.
- Default is blob_overflow_mu=1.0e-4
-
- Fraction of a grid cell participating in an overflow event.
- Corresponds to delta in Campin and Goosse (1999). Dimensionless.
- Default is blob_overflow_mu=1.0e-4
-
- Coefficient of drag used for bottom stress drag.
- Corresponds to Cd in Price and Baringer (1994). Dimensionless.
- Default is drag=3.0e-3
-
- The detrainment parameter (kg m^2/s).
- Corresponds to Gamma in the notes.
- Default is det_param=5.0e-8
-
-
- The Maximum allowable detrainment velocity (m/s).
- Default is max_detrainment=1.0e-3
-
- Relative error for the RK scheme (dimensionless).
- A smaller number is more accurate, but,
- is more computationally expensive. Corresponds to
- zeta* in the notes.
- Must be 0<rel_error<=1.0
- Default is rel_error=0.01
-
- Safety factor for the RK scheme (dimensionless).
- A smaller number should reduce the number
- of rejected steps, but, decreases the locally
- extrapolated step. Corresponds to varrho in
- the notes.
- Must be 0<safety_factor<=1.0
- Default is safety_factor=0.8
-
- Minimum step size (in seconds) for a blob.
- Default is minstep=9.0
-
- The elasticity of a blob's collision with
- the topography. Corresponds to epsilon in
- the notes. Should have values 0<=elastic<=1.0
- Values greater than 1 would be super-elastic,
- and values less than 0 would send the blob
- in the opposite direction than it should be
- going in.
- Default is elastic=1.0
-
- Minimum number of deep ocean levels for
- overflows to be considered. That is, how many
- k levels lower should the deep ocean water column
- be than the shelf/shallow ocean column. Value
- must be greater than 0.
- Default is min_do_levels=1
-
- The density difference required before a blob
- is formed. rho_threshold must be greater than
- zero.
- Default is rho_threshold=0.01
-
- A value for error checking. If the speed of a
- blob exceeds large_speed in any of x,y,z then
- a warning flag is raised.
- Default is large_speed=10.0
-
- Sets the coriolis parameter to zero regardless
- of latitude
- Default is no_rotation=.false.
-
- The critical Richardson number for the entrainment
- velocity. Default is based on Price and Baringer
- (1994).
- Default is critical_richardson=0.8
-
- Initialises the dynamic free blobs by checking the namelist and also
- inherited namelists (from ocean_blob_nml). Also sets up some useful
- constants (including spatially varying constants) - particularly for
- the formation of bottom blobs. It also allocates memory to special
- halo=2 masks and sets up the blob buffers for sending blobs from one
- PE to another.
-
- This routine calls the routine to update blob positions. When
- bitwise_reproduction=.false., it also figures out when to continue
- the integration of blobs that have changed PE's.
-
- This routine contains the RK scheme used to integrate the position
- and velocity of blobs. It also does many checks for (and
- subsequently handles) things like grounding of blobs, blobs going to
- different PEs, blobs that separate from topography, blobs that
- detrain to less than small_mass and blobs going outside the compute
- domain.
-
- It also does the interpolation of E system variables to a blob.
-
- Takes free blobs that have interacted with topography and turns them
- into bottom blobs.
-
- Initialises blobs that are formed when an on-shelf/off-shelf
- instability occurs. The method used for determining an instability
- and the initial conditions are based on that of Campin and Goosse
- (1999).
-
- When the density difference between the shallow ocean cell and the
- deep ocean cell (referenced to the deep ocean cell) exceeds the
- namelist variable rho_threshold, a blob is formed. The deep ocean
- cell is chosen based on which deep ocean cell (in the k plane)
- the blob topography intersects.
-
- After formation, the new blobs are added to the bottom blob linked
- list, and, their properties are integrated, starting at time taup1.
-
- Clears memory to give a nice clean ending to the run.
-
- Packs a buffer with all the information needed to send a blob from
- one PE to another.
-
- Unpacks a received buffer.
-
- Increases the buffer size for sending blobs from one PE to another.
-
- Sends a buffer to an adjoining PE
-
- Receives a buffer from an adjoining PE
-
- Clears the contents of a buffer
-
diff --git a/src/mom5/ocean_blobs/ocean_blob_dynamic_free.html b/src/mom5/ocean_blobs/ocean_blob_dynamic_free.html
deleted file mode 100644
index 5b373c87fd..0000000000
--- a/src/mom5/ocean_blobs/ocean_blob_dynamic_free.html
+++ /dev/null
@@ -1,358 +0,0 @@
-
-
-
-Module ocean_blob_dynamic_free_mod
-
-
-
-
-PUBLIC INTERFACE
-
- ~ PUBLIC ROUTINES
-
-
- This module runs the dynamic free blob implementation of the embedded
- Lagrangian blob framework. The module forms new dynamic free blobs,
- integrates the properties of existing blobs, and handles the transfer
- of bottom blobs to free blobs.
-
-
-
-
-
- Free blobs are formed using the subroutine blob_dynamic_free_implicit,
- which is called from the blob driver module. Free blobs must be formed
- implicitly in time so that the surface forcing has already been applied.
-
- The properties of free blobs are also integrated in this module, that is,
- position, velocity, mass and tracer content. Position and velocity are
- integrated using an adaptive step Runge-Kutta scheme. There are several
- schemes available of varying order.
-
- The module also receives blobs that are transferring from the bottom
- blob dynamic regime to the free blob regime (i.e. they have separated
- from the bottom boundary).
-
- Initialises the dynamic free blobs by checking the namelist and also
- inherited namelists (from ocean_blob_nml). Also sets up some useful
- constants, allocates memory to special halo=2 masks and sets up
- the blob buffers for sending blobs from one PE to another.
-
-
-
-
-
-
-
-
blob_dynamic_free_implicit
-
-
-DESCRIPTION
-
-
- Initialises dynamic blobs in vertical statically unstable regions.
- Due to the instability condition, blobs should be formed after the
- surface forcing has been applied (which is a major source of
- instability in the water column). The surface forcing is applied
- implicitly in time in MOM, therefore, we must form blobs implicitly
- in time.
-
- If N^2<bv_freq_threshold, then, two blobs are formed. One rising
- and one sinking. The rising blobs is destroyed immediately (after
- it has been moved up one cell) and its properties returned to the E
- system. The sinking blob is added to a linked list, and its
- properties integrated at a later time step.
-
-
-
-
-
-
-
-
blob_dynamic_free_update
-
-
-DESCRIPTION
-
-
- This routine calls the routine to update blob positions. When
- bitwise_reproduction=.false., it also figures out when to continue
- the integration of blobs that have changed PE's.
-
-
-
-
-
-
-
-
dynamic_update
-
-
-DESCRIPTION
-
-
- This routine contains the RK scheme used to integrate the position
- and velocity of blobs. It also does many checks for (and
- subsequently handles) things like grounding of blobs, blobs going to
- different PEs, blobs that interact with topography, blobs that
- detrain to less than small_mass and blobs going outside the compute
- domain.
-
- It also does the interpolation of E system variables to a blob.
-
-
-
-
-
-
-
-
transfer_bottom_to_free
-
-
-DESCRIPTION
-
-
- Takes bottom blobs that have separated from the bottom boundary and
- turns it into a free blob.
-
-
-
-
-
-
-
-
blob_dynamic_free_end
-
-
-DESCRIPTION
-
-
- Clears memory to give a nice clean ending to the run.
-
-
-
-
-
-
-
-
packbuffer
-
-
-DESCRIPTION
-
-
- Packs a buffer with all the information needed to send a blob from
- one PE to another.
-
-
-
-
-
-
-
-
unpackbuffer
-
-
-DESCRIPTION
-
-
- Unpacks a received buffer.
-
-
-
-
-
-
-
-
increase_buffer
-
-
-DESCRIPTION
-
-
- Increases the buffer size for sending blobs from one PE to another.
-
-
-
-
-
-
-
-
send_buffer
-
-
-DESCRIPTION
-
-
- Sends a buffer to an adjoining PE
-
-
-
-
-
-
-
-
receive_buffer
-
-
-DESCRIPTION
-
-
- Receives a buffer from an adjoining PE
-
-
-
-
-
-
-
-
clear_buffer
-
-
-DESCRIPTION
-
-
- Clears the contents of a buffer
-
-
-
-
-
-
-
-
-
-
-
-
-
-
REFERENCES
-
-
-
-
- Bogacki, P., Shampine, L.F., (1989) A 3(2) pair of Runge-Kutta formulas.
- Applied Mathematical Letters 2(4), 321-325.
-
-
- Cash, J.R., Karp, A.H. (1990) A variable order Runge-Kutta method for
- initial value problems with rapidly varying right-hand sides.
- ACM Transactions on Mathematical Software 16(3), 201-222.
-
-
- Griffies, S.M., Harrison, M.J., Pacanowski, R.C., Rosati, A. (2004)
- A Technical Guide to MOM4. GFDL Ocean Group Technical Report No. 5.
- NOAA/Geophysical Fluid Dynamics Laboratory.
-
-
- Marshall, J., Schott, F. (1999) Open-ocean convection: Observations, theory,
- and models. Reviews of Geophysics 37(1), 1-64.
-
-
-
diff --git a/src/mom5/ocean_blobs/ocean_blob_dynamic_free.xml b/src/mom5/ocean_blobs/ocean_blob_dynamic_free.xml
deleted file mode 100644
index 56fc3144bd..0000000000
--- a/src/mom5/ocean_blobs/ocean_blob_dynamic_free.xml
+++ /dev/null
@@ -1,150 +0,0 @@
-
-
- Michael L. Bates
- Stephen M. Griffies
-
- This module runs the dynamic free blob implementation of the embedded
- Lagrangian blob framework. The module forms new dynamic free blobs,
- integrates the properties of existing blobs, and handles the transfer
- of bottom blobs to free blobs.
-
- Free blobs are formed using the subroutine blob_dynamic_free_implicit,
- which is called from the blob driver module. Free blobs must be formed
- implicitly in time so that the surface forcing has already been applied.
-
- The properties of free blobs are also integrated in this module, that is,
- position, velocity, mass and tracer content. Position and velocity are
- integrated using an adaptive step Runge-Kutta scheme. There are several
- schemes available of varying order.
-
- The module also receives blobs that are transferring from the bottom
- blob dynamic regime to the free blob regime (i.e. they have separated
- from the bottom boundary).
-
- Bogacki, P., Shampine, L.F., (1989) A 3(2) pair of Runge-Kutta formulas.
- Applied Mathematical Letters 2(4), 321-325.
-
- Cash, J.R., Karp, A.H. (1990) A variable order Runge-Kutta method for
- initial value problems with rapidly varying right-hand sides.
- ACM Transactions on Mathematical Software 16(3), 201-222.
-
- Griffies, S.M., Harrison, M.J., Pacanowski, R.C., Rosati, A. (2004)
- A Technical Guide to MOM4. GFDL Ocean Group Technical Report No. 5.
- NOAA/Geophysical Fluid Dynamics Laboratory.
-
- Marshall, J., Schott, F. (1999) Open-ocean convection: Observations, theory,
- and models. Reviews of Geophysics 37(1), 1-64.
-
- Must be true to use this module.
- Default is use_this_module=.false.
-
- Rayleigh drag coefficient (1/s) for new blobs that
- are formed due to the vertical instability
- criterion. Corresponds to alpha in the notes.
- Default is rayleigh_drag_new=1.0e-5
-
- Rayleigh drag coefficient (1/s) for bottom blobs
- that become free blobs. Corresponds to alpha in
- the notes.
- Default is rayleigh_drag_bot=1.0e-7
-
- Decide which method to use to integrate the
- blobs. Choices are 'BS_RK3(2)' or 'CK_RK5(4)'
- for the Bogaki-Shampine or Cash-Karp methods
- respectively.
- Default is update_method='CK_RK5(4)
-
- Relative error for the RK scheme (dimensionless).
- A smaller number is more accurate, but,
- is more computationally expensive. Corresponds to
- zeta* in the notes.
- Must be 0<rel_error<=1.0
- Default is rel_error=0.01
-
- Safety factor for the RK scheme (dimensionless).
- A smaller number should reduce the number
- of rejected steps, but, decreases the locally
- extrapolated step. Corresponds to varrho in
- the notes.
- Must be 0<safety_factor<=1.0
- Default is safety_factor=0.8
-
- Minimum step size (in seconds) for a blob.
- Default is minstep=9.0
-
- An Adjustment for blob size, 0<size_fact<=1.0
- Corresponds to Lambda in the notes.
- Default is size_fact=1.0
-
- The detrainment parameter (kg m^2/s).
- Corresponds to Gamma in the notes.
- Default is det_param=5.0e-8
-
- The Maximum allowable detrainment velocity (m/s).
- Default is max_detrainment=1.0e-3
-
- The buoyancy frequency threshold at which
- the scheme will start to create blobs, i.e.
- blobs will be formed when N^2<bv_freq_threshold
- Default is bv_freq_threshold=-1.0e-15
-
- Whether to use the buoyancy frequency calculated
- from the combined E and L system (true) or, from
- the E system only (false).
- Default is full_N2=.true.
-
- A value for error checking. If the speed of a
- blob exceeds large_speed in any of x,y,z then
- a warning flag is raised.
- Default is large_speed=10.0
-
- Initialises the dynamic free blobs by checking the namelist and also
- inherited namelists (from ocean_blob_nml). Also sets up some useful
- constants, allocates memory to special halo=2 masks and sets up
- the blob buffers for sending blobs from one PE to another.
-
- Initialises dynamic blobs in vertical statically unstable regions.
- Due to the instability condition, blobs should be formed after the
- surface forcing has been applied (which is a major source of
- instability in the water column). The surface forcing is applied
- implicitly in time in MOM, therefore, we must form blobs implicitly
- in time.
-
- If N^2<bv_freq_threshold, then, two blobs are formed. One rising
- and one sinking. The rising blobs is destroyed immediately (after
- it has been moved up one cell) and its properties returned to the E
- system. The sinking blob is added to a linked list, and its
- properties integrated at a later time step.
-
- This routine calls the routine to update blob positions. When
- bitwise_reproduction=.false., it also figures out when to continue
- the integration of blobs that have changed PE's.
-
- This routine contains the RK scheme used to integrate the position
- and velocity of blobs. It also does many checks for (and
- subsequently handles) things like grounding of blobs, blobs going to
- different PEs, blobs that interact with topography, blobs that
- detrain to less than small_mass and blobs going outside the compute
- domain.
-
- It also does the interpolation of E system variables to a blob.
-
- Takes bottom blobs that have separated from the bottom boundary and
- turns it into a free blob.
-
- Clears memory to give a nice clean ending to the run.
-
- Packs a buffer with all the information needed to send a blob from
- one PE to another.
-
- Unpacks a received buffer.
-
- Increases the buffer size for sending blobs from one PE to another.
-
- Sends a buffer to an adjoining PE
-
- Receives a buffer from an adjoining PE
-
- Clears the contents of a buffer
-
diff --git a/src/mom5/ocean_blobs/ocean_blob_static_bottom.html b/src/mom5/ocean_blobs/ocean_blob_static_bottom.html
deleted file mode 100644
index be577db17c..0000000000
--- a/src/mom5/ocean_blobs/ocean_blob_static_bottom.html
+++ /dev/null
@@ -1,380 +0,0 @@
-
-
-
-Module ocean_blob_static_bottom_mod
-
-
-
-
-PUBLIC INTERFACE
-
- ~ PUBLIC ROUTINES
- ~ NAMELIST
-
-
- Contains static bottom blob parameterisations, namely the Campin and
- Goossee (1999) scheme and some variations.
-
-
-
-
-
- Presently, there is only one static bottom blob scheme implemented
- (although, there are three potential variants), and there are no plans
- to implement any additional schemes.
-
- The scheme that is implemented emulates the Campin and Goossee (1999)
- scheme, as well as having two additional variations for this scheme,
- in which the "plumbing" is change.
-
- Details of the variations can be found in Bates et al. (2010) and are
- controlled by the namelist options overflow_no_return and
- overflow_one_return.
-
- Run the Lagrangian blob model for the Overflow schemes. These
- schemes are static schemes and uses Lagrangian blobs to transport
- tracer and mass down slopes where an onshelf/offshelf instability
- exists.
-
- This scheme is activated by setting the namelist variable
- blob_overflow=.true.
-
- There are three flavours to this scheme, which are detailed in
- sections 2.4 and 2.5 of Bates et al. for further details. The three
- flavours are:
- 1/ A Campin and Goosse (1999) scheme in which the full "plumbing" of
- water going off shelf to the deep ocean and deep ocean waters
- returning on shelf is specified (described in full in section 2.4
- of Bates et al.)
- 2/ Only the lateral part of the plumbing is specified and all vertical
- movement of water within the deep ocean column is taken care of
- (described in full in section 2.5 of Bates et al.). This option is
- activated by setting the namelist variable overflow_one_return=.true.
- 3/ Only the movement of shelf water to the deep ocean column is
- explicitly dealt with (described in full in section 2.5 of Bates
- et al.). This option is activated by setting the namelist variable
- overflow_no_return=.true.
-
- Other namelist variables associated with this scheme are:
- blob_overflow_mu (real), which is the coefficient of friction used
- used to calculate the overflow velocity,
- blob_overflow_delta (real), which is the fraction of a grid cell that
- participates in any one overflow event,
- blob_overflow_umax (real), which is the maximum overflow velocity.
- Depending on the flavour of scheme chosen and the impact that you want
- it to have, typical values should be O(0.01) to O(1).
-
-
-
-
-
-
-
-
blob_static_bottom_end
-
-
-DESCRIPTION
-
-
- Does what is necessary to finish the run.
-
-
-
-
-
-
-
-
allocate_buffer
-
-
-DESCRIPTION
-
-
- Increases the buffer size for sending blobs from one PE to another.
-
-
-
-
-
-
-
-
increase_buffer
-
-
-DESCRIPTION
-
-
- Increases the buffer size for sending blobs from one PE to another.
-
-
-
-
-
-
-
-
send_buffer
-
-
-DESCRIPTION
-
-
- Sends a buffer to an adjoining PE
-
-
-
-
-
-
-
-
receive_buffer
-
-
-DESCRIPTION
-
-
- Receives a buffer from an adjoining PE
-
-
-
-
-
-
-
-
clear_buffer
-
-
-DESCRIPTION
-
-
- Clears the contents of a buffer
-
-
-
-
-
-
-
-
deallocate_buffer
-
-
-DESCRIPTION
-
-
- Deallocates memory from a buffer (usually at the end of a run).
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_blob_static_bottom_nml
-
-
-
-
-
-blob_overflow
-
-
- if true, will use a Campin and Goosse (1999) style overflow
- formulation.
- Default is blob_overflow=.false.
-
-[logical]
-
-
-blob_overflow_mu
-
-
- Frictional dissipation used in blob_overflow scheme
- Default is blob_overflow_mu=1.0e-4
-
-[real, units: 1/s]
-
-
-blob_overflow_delta
-
-
- Fraction of grid cell participating in overflow
- Valid values are 0<=delta<=1
- Default is blob_overflow_delta=1/3
-
-[real]
-
-
-blob_overflow_umax
-
-
- Maximum downslope speed allowed for overflow
- Default is blob_overflow_umax=0.01
-
-[real, units: m/s]
-
-
-overflow_no_return
-
-
- When .false. creates return blobs to replicate the
- original Campin and Goosse scheme. When .true. only
- creates blobs that sink. See further overflow_one_return
-
-[logical]
-
-
-overflow_one_return
-
-
- Creates a single return blob when .true. Cannot be .true.
- when overflow_no_return is also .true.
-
-[logical]
-
-
-
-
-
-
-
-
-
-
-
REFERENCES
-
-
-
-
- Bates, M.L., Griffies, S.M., England, M.H., Adcroft, A.J. (2009)
- Lagrangian blobs of buoyancy embedded in Eulerian models: a framework
- to parameterise vertical and downslope motion of gravitationally unstable
- water parcels. Unpublished Notes.
-
-
- S.M. Griffies, Elements of mom4p1 (2009)
- NOAA/Geophysical Fluid Dynamics Laboratory
-
-
- Campin, J.-M., Goossee, H., 1999, Parameterization of density-driven
- downsloping flow for a coarse-resolution ocean model in z-coordinate.
- Tellus 51A (3), 412-430
-
-
-
diff --git a/src/mom5/ocean_blobs/ocean_blob_static_bottom.xml b/src/mom5/ocean_blobs/ocean_blob_static_bottom.xml
deleted file mode 100644
index 777da47073..0000000000
--- a/src/mom5/ocean_blobs/ocean_blob_static_bottom.xml
+++ /dev/null
@@ -1,103 +0,0 @@
-
-
- Michael L. Bates
- Stephen M. Griffies
-
- Contains static bottom blob parameterisations, namely the Campin and
- Goossee (1999) scheme and some variations.
-
- Presently, there is only one static bottom blob scheme implemented
- (although, there are three potential variants), and there are no plans
- to implement any additional schemes.
-
- The scheme that is implemented emulates the Campin and Goossee (1999)
- scheme, as well as having two additional variations for this scheme,
- in which the "plumbing" is change.
-
- Details of the variations can be found in Bates et al. (2010) and are
- controlled by the namelist options overflow_no_return and
- overflow_one_return.
-
- Bates, M.L., Griffies, S.M., England, M.H., Adcroft, A.J. (2009)
- Lagrangian blobs of buoyancy embedded in Eulerian models: a framework
- to parameterise vertical and downslope motion of gravitationally unstable
- water parcels. Unpublished Notes.
-
- S.M. Griffies, Elements of mom4p1 (2009)
- NOAA/Geophysical Fluid Dynamics Laboratory
-
- Campin, J.-M., Goossee, H., 1999, Parameterization of density-driven
- downsloping flow for a coarse-resolution ocean model in z-coordinate.
- Tellus 51A (3), 412-430
-
- if true, will use a Campin and Goosse (1999) style overflow
- formulation.
- Default is blob_overflow=.false.
-
- Frictional dissipation used in blob_overflow scheme
- Default is blob_overflow_mu=1.0e-4
-
- Fraction of grid cell participating in overflow
- Valid values are 0<=delta<=1
- Default is blob_overflow_delta=1/3
-
- Maximum downslope speed allowed for overflow
- Default is blob_overflow_umax=0.01
-
- When .false. creates return blobs to replicate the
- original Campin and Goosse scheme. When .true. only
- creates blobs that sink. See further overflow_one_return
-
- Creates a single return blob when .true. Cannot be .true.
- when overflow_no_return is also .true.
-
- Initialises the static bottom blob module.
-
- Run the Lagrangian blob model for the Overflow schemes. These
- schemes are static schemes and uses Lagrangian blobs to transport
- tracer and mass down slopes where an onshelf/offshelf instability
- exists.
-
- This scheme is activated by setting the namelist variable
- blob_overflow=.true.
-
- There are three flavours to this scheme, which are detailed in
- sections 2.4 and 2.5 of Bates et al. for further details. The three
- flavours are:
- 1/ A Campin and Goosse (1999) scheme in which the full "plumbing" of
- water going off shelf to the deep ocean and deep ocean waters
- returning on shelf is specified (described in full in section 2.4
- of Bates et al.)
- 2/ Only the lateral part of the plumbing is specified and all vertical
- movement of water within the deep ocean column is taken care of
- (described in full in section 2.5 of Bates et al.). This option is
- activated by setting the namelist variable overflow_one_return=.true.
- 3/ Only the movement of shelf water to the deep ocean column is
- explicitly dealt with (described in full in section 2.5 of Bates
- et al.). This option is activated by setting the namelist variable
- overflow_no_return=.true.
-
- Other namelist variables associated with this scheme are:
- blob_overflow_mu (real), which is the coefficient of friction used
- used to calculate the overflow velocity,
- blob_overflow_delta (real), which is the fraction of a grid cell that
- participates in any one overflow event,
- blob_overflow_umax (real), which is the maximum overflow velocity.
- Depending on the flavour of scheme chosen and the impact that you want
- it to have, typical values should be O(0.01) to O(1).
-
- Does what is necessary to finish the run.
-
- Increases the buffer size for sending blobs from one PE to another.
-
- Increases the buffer size for sending blobs from one PE to another.
-
- Sends a buffer to an adjoining PE
-
- Receives a buffer from an adjoining PE
-
- Clears the contents of a buffer
-
- Deallocates memory from a buffer (usually at the end of a run).
-
diff --git a/src/mom5/ocean_blobs/ocean_blob_static_free.html b/src/mom5/ocean_blobs/ocean_blob_static_free.html
deleted file mode 100644
index 9d93ea67e3..0000000000
--- a/src/mom5/ocean_blobs/ocean_blob_static_free.html
+++ /dev/null
@@ -1,250 +0,0 @@
-
-
-
-Module ocean_blob_static_free_mod
-
-
-
-
-PUBLIC INTERFACE
-
- ~ PUBLIC ROUTINES
- ~ NAMELIST
-
-
- This module controls and runs the free static Lagrangian blob
- parameterisations.
-
-
-
-
-
- There are three available static blob schemes. None are sanctioned
- for their physical integrity, but they have been important in the
- development and testing of the Lagrangian framework.
-
- The first free static scheme emulates the NCON scheme of Cox (1984).
- The second is a scheme that acts in a diffusive manner, while the third
- swaps the properties of adjacent grid cells. Details of all three schemes
- can be found in Bates et al. (2010).
-
- A subroutine that is called by the main driver blob module,
- ocean_blob_mod. The present module in turn calls the three available
- static schemes. They are not mutually exclusive and so may be run
- in any combination.
-
- Note that only the NCON-like scheme has been implemented.
-
-
-
-
-
-
-
-
blob_ncon_like_scheme
-
-
-DESCRIPTION
-
-
- Run the Lagrangian blob model for the NCon-like scheme. This scheme
- is a static scheme and uses Lagrangian blobs to homogenise adjacent
- vertical grid cells by by transferring mass and tracer between them.
-
- This scheme is activated by setting the namelist variable
- blob_ncon_like=.true. The number of times that the domain is checked
- for instability is set by the integer namelist variable ncon_blob, of
- which the default value is 7.
-
- It is based on the original convective adjustment scheme of
- Cox (1984).
-
- See section 2.1 of Bates et al. for further details.
-
-
-
-
-
-
-
-
blob_static_free_end
-
-
-DESCRIPTION
-
-
- Ends the free static module.
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_blob_static_free_nml
-
-
-
-
-
-blob_ncon_like
-
-
- If true, will use NCon-like formulation.
- Default blob_ncon_like = .true.
-
-[logical]
-
-
-blob_diff_like
-
-
- If true, will use the diffusion-like formulation.
- Default is "blob_diff_like=.false.
-
-[logical]
-
-
-blob_swap_like
-
-
- If true, will use the swap-like formulation.
- Default is blob_switch_like=.false.
-
-[logical]
-
-
-ncon_blob
-
-
- The number of times that the water column is checked and adjusted
- for instability.
-
-[integer]
-
-
-
-
-
-
-
-
-
-
-
REFERENCES
-
-
-
-
- S.M. Griffies, Elements of mom4p1 (2009)
- NOAA/Geophysical Fluid Dynamics Laboratory
-
-
- Cox, M.D., 1984, A Primitive Equation, 3-Dimensional Model of the
- Ocean. NOAA/Geophysical Fluid Dynamics Laboratory
-
-
-
diff --git a/src/mom5/ocean_blobs/ocean_blob_static_free.xml b/src/mom5/ocean_blobs/ocean_blob_static_free.xml
deleted file mode 100644
index eb0ad38321..0000000000
--- a/src/mom5/ocean_blobs/ocean_blob_static_free.xml
+++ /dev/null
@@ -1,61 +0,0 @@
-
-
- Michael L. Bates
- Stephen M. Griffies
-
- This module controls and runs the free static Lagrangian blob
- parameterisations.
-
- There are three available static blob schemes. None are sanctioned
- for their physical integrity, but they have been important in the
- development and testing of the Lagrangian framework.
-
- The first free static scheme emulates the NCON scheme of Cox (1984).
- The second is a scheme that acts in a diffusive manner, while the third
- swaps the properties of adjacent grid cells. Details of all three schemes
- can be found in Bates et al. (2010).
-
- S.M. Griffies, Elements of mom4p1 (2009)
- NOAA/Geophysical Fluid Dynamics Laboratory
-
- Cox, M.D., 1984, A Primitive Equation, 3-Dimensional Model of the
- Ocean. NOAA/Geophysical Fluid Dynamics Laboratory
-
- If true, will use NCon-like formulation.
- Default blob_ncon_like = .true.
-
- If true, will use the diffusion-like formulation.
- Default is "blob_diff_like=.false.
-
- If true, will use the swap-like formulation.
- Default is blob_switch_like=.false.
-
- The number of times that the water column is checked and adjusted
- for instability.
-
- Initialises the free static schemes.
-
- A subroutine that is called by the main driver blob module,
- ocean_blob_mod. The present module in turn calls the three available
- static schemes. They are not mutually exclusive and so may be run
- in any combination.
-
- Note that only the NCON-like scheme has been implemented.
-
- Run the Lagrangian blob model for the NCon-like scheme. This scheme
- is a static scheme and uses Lagrangian blobs to homogenise adjacent
- vertical grid cells by by transferring mass and tracer between them.
-
- This scheme is activated by setting the namelist variable
- blob_ncon_like=.true. The number of times that the domain is checked
- for instability is set by the integer namelist variable ncon_blob, of
- which the default value is 7.
-
- It is based on the original convective adjustment scheme of
- Cox (1984).
-
- See section 2.1 of Bates et al. for further details.
-
- Ends the free static module.
-
diff --git a/src/mom5/ocean_blobs/ocean_blob_util.html b/src/mom5/ocean_blobs/ocean_blob_util.html
deleted file mode 100644
index 797666aa4a..0000000000
--- a/src/mom5/ocean_blobs/ocean_blob_util.html
+++ /dev/null
@@ -1,644 +0,0 @@
-
-
-
-Module ocean_blob_util_mod
-
-
-
-
-PUBLIC INTERFACE
-
- ~ PUBLIC ROUTINES
-
-
- This module contains subroutines that are common (or are likely to
- need be common to future implementations) to some or all of the
- various modules that run the Lagrangian blob scheme.
-
-
-
-
-
- This module contains subroutines that are common (or may be common
- in a future implementation) to some of the modules that make up the
- blobs framework.
-
- Some of the subroutines contained herein perform tasks such as
- performing checksums, checking a linked lists for very small blobs
- (and deleting them), inserting blobs into a list, a bunch of routines
- for writing blob restart and history files, grid cell search algorithms,
- buffer manipulations, computations etc.
-
- The module has no namelist. All potential namelist variables are
- controlled through the ocean_blob_mod namelist.
-
- Performs global sums and checksums for all blob types (for diagnostic
- purposes).
-
-
-
-
-
-
-
-
lagrangian_system_chksum
-
-
-DESCRIPTION
-
-
-
- Performs checksums for the Lagrangian_system derived type. This is
- the derived type that stores all of the "gridded" blob variables,
- and is essential for the accounting required to interact with the
- Eulerian model in a conservative manner. The checksums are for
- diagnostic purposes.
-
-
-
-
-
-
-
-
-
E_and_L_totals
-
-
-DESCRIPTION
-
-
- Gives a brief summary of the total mass, volume and tracer content
- of the E, L and total systems. Usually used for debuggin purposes.
-
-
-
-
-
-
-
-
write_blobs
-
-
-DESCRIPTION
-
-
- Dumps most of the information carried around by blobs, for all blobs
- in a particular list. Useful for debugging.
-
-
-
-
-
-
-
-
blob_delete
-
-
-DESCRIPTION
-
-
- Deletes all (nearly) zero mass blob objects from the linked list.
- The size of the blobs that are deleted is controlled by the variable
- blob_small_mass in the ocean_blob_nml.
-
-
-
-
-
-
-
-
unlink_blob
-
-
-DESCRIPTION
-
-
- Unlinks a blob from a doubly linked list. It returns pointers to
- the blob, the head of the list, the (formerly) previous blob in the
- list and the (formerly) next blob in the list.
-
-
-
-
-
-
-
-
insert_blob
-
-
-DESCRIPTION
-
-
- Inserts a blob to the linked list. The relative order of blobs in
- a linked list determines whether bitwise reproduction is possible.
-
- Regardless of bitwise reproducability or not, we must ensure that
- blobs always appear in the same relative order when we are using
- dynamic blobs because if we have a situation where dztL>dztT, we
- start destroying blobs to enforce dztL<dztT. In order that we do
- not significantly change answers, we must always destroy the same
- blob, regardless of domain decomposition, restarts, etc. So, we must
- always sort blobs so they appear in the linked list in the same
- relative order.
-
-
-
-
-
-
-
-
count_blob
-
-
-DESCRIPTION
-
-
- Allocates a blob its hash and a number. These two numbers can
- uniquely identify any blob. The hash and number is based on the grid
- cell of origin. Each grid cell has a unique hash. We have an array
- which keeps track of the number of blobs formed in a grid cell. These
- two numbers give the unique identifier. So, we also need to increment
- the counter array.
-
-
-
-
-
-
-
-
put_att
-
-
-DESCRIPTION
-
-
- Writes an attribute to a netcdf file.
-
-
-
-
-
-
-
-
inq_var
-
-
-DESCRIPTION
-
-
- Gets the variable identifier from a netcdf file.
-
-
-
-
-
-
-
-
get_double
-
-
-DESCRIPTION
-
-
- Gets the value of a "double" variable from a netcdf file
-
-
-
-
-
-
-
-
get_int
-
-
-DESCRIPTION
-
-
- Gets the value of an integer variable from a netcdf file
-
-
-
-
-
-
-
-
put_double
-
-
-DESCRIPTION
-
-
- Writes the value of a "double" variable to a netcdf file
-
-
-
-
-
-
-
-
put_int
-
-
-DESCRIPTION
-
-
- Writes the value of an integer variable to a netcdf file
-
-
-
-
-
-
-
-
def_var
-
-
-DESCRIPTION
-
-
- Defines a netcdf variable
-
-
-
-
-
-
-
-
give_error_code
-
-
-DESCRIPTION
-
-
- Gives error descriptions for netcdf calls.
-
-
-
-
-
-
-
-
hashfun
-
-
-DESCRIPTION
-
-
- Calculates the hash
-
-
-
-
-
-
-
-
blob_util_end
-
-
-DESCRIPTION
-
-
- Does what is necessary to shut down the module.
-
-
-
-
-
-
-
-
check_ijcell
-
-
-DESCRIPTION
-
-
- Checks whether a blob (horizontally) resides in a grid cell or not.
- If it does not it figures out which direction the blob is in and
- checks the neighbouring grid cell, until it finds which grid cell
- the blob resides in.
-
- It uses a cross product technique from computational geometry
- (Cormen et al., 2001).
-
-
-
-
-
-
-
-
check_kcell
-
-
-DESCRIPTION
-
-
- Searches for which (vertical) grid cell a blob resides in).
-
-
-
-
-
-
-
-
kill_blob
-
-
-DESCRIPTION
-
-
- Kills a blob by returning all of its remaining properties to the E
- system.
-
-
-
-
-
-
-
-
free_blob_memory
-
-
-DESCRIPTION
-
-
- Frees the heap memory taken up by a blob.
-
-
-
-
-
-
-
-
allocate_interaction_memory
-
-
-DESCRIPTION
-
-
- Allocates the history arrays for a blob (only used when
- bitwise_reproduction=.true. in the ocean_blob_nml).
-
-
-
-
-
-
-
-
reallocate_interaction_memory
-
-
-DESCRIPTION
-
-
- Different blobs can have different history memory requirements.
- When they change from one type of blob to another, we need to change
- the memory allocated to a blob to reflect the new requirements. This
- is only necessary if bitwise_reproduction=.true. in the ocean_blob_nml.
-
-
-
-
-
-
-
-
interp_tcoeff
-
-
-DESCRIPTION
-
-
- Used for the horizontal interpolation of T grid variables. The
- routine returns coefficients required for inverse distance
- weighting (Shephard, 1968).
-
-
-
-
-
-
-
-
interp_ucoeff
-
-
-DESCRIPTION
-
-
- Used for the horizontal interpolation of U grid variables. The
- routine returns coefficients required for inverse distance
- weighting (Shephard, 1968).
-
-
-
-
-
-
-
-
check_cyclic
-
-
-DESCRIPTION
-
-
- Checks and adjusts blob position and grid cell index
- for cylclic/periodic domains, as well as
- the Murray (1996) tripolar grid.
-
-
-
-
-
-
-
-
-
-
-
-
-
-
REFERENCES
-
-
-
-
- Cormen, T. H, Leiserson, C. E. Rivest, R. L., Stein, C. (2001) Introduction
- to Algorithms. The MIT Press.
-
-
- Shepard, D. (1968) A two-dimensional interpolation function for
- irregularly-spaced data. In: Proceedings of the 1968 23rd ACM national
- conference. ACM '68. ACM, New York, NY, USA, pp. 517-524.
-
-
- Murray, R. J. (1996) Explicit generation of orthogonal grids for
- ocean models. Journal of Computational Physics 126, 251-273.
-
-
-
diff --git a/src/mom5/ocean_blobs/ocean_blob_util.xml b/src/mom5/ocean_blobs/ocean_blob_util.xml
deleted file mode 100644
index a4bed2ba4d..0000000000
--- a/src/mom5/ocean_blobs/ocean_blob_util.xml
+++ /dev/null
@@ -1,134 +0,0 @@
-
-
- Michael L. Bates
- Stephen M. Griffies
-
- This module contains subroutines that are common (or are likely to
- need be common to future implementations) to some or all of the
- various modules that run the Lagrangian blob scheme.
-
- This module contains subroutines that are common (or may be common
- in a future implementation) to some of the modules that make up the
- blobs framework.
-
- Some of the subroutines contained herein perform tasks such as
- performing checksums, checking a linked lists for very small blobs
- (and deleting them), inserting blobs into a list, a bunch of routines
- for writing blob restart and history files, grid cell search algorithms,
- buffer manipulations, computations etc.
-
- The module has no namelist. All potential namelist variables are
- controlled through the ocean_blob_mod namelist.
-
- Cormen, T. H, Leiserson, C. E. Rivest, R. L., Stein, C. (2001) Introduction
- to Algorithms. The MIT Press.
-
- Shepard, D. (1968) A two-dimensional interpolation function for
- irregularly-spaced data. In: Proceedings of the 1968 23rd ACM national
- conference. ACM '68. ACM, New York, NY, USA, pp. 517-524.
-
- Murray, R. J. (1996) Explicit generation of orthogonal grids for
- ocean models. Journal of Computational Physics 126, 251-273.
-
- Initialises this module.
-
- Performs global sums and checksums for all blob types (for diagnostic
- purposes).
-
-
- Performs checksums for the Lagrangian_system derived type. This is
- the derived type that stores all of the "gridded" blob variables,
- and is essential for the accounting required to interact with the
- Eulerian model in a conservative manner. The checksums are for
- diagnostic purposes.
-
-
- Gives a brief summary of the total mass, volume and tracer content
- of the E, L and total systems. Usually used for debuggin purposes.
-
- Dumps most of the information carried around by blobs, for all blobs
- in a particular list. Useful for debugging.
-
- Deletes all (nearly) zero mass blob objects from the linked list.
- The size of the blobs that are deleted is controlled by the variable
- blob_small_mass in the ocean_blob_nml.
-
- Unlinks a blob from a doubly linked list. It returns pointers to
- the blob, the head of the list, the (formerly) previous blob in the
- list and the (formerly) next blob in the list.
-
- Inserts a blob to the linked list. The relative order of blobs in
- a linked list determines whether bitwise reproduction is possible.
-
- Regardless of bitwise reproducability or not, we must ensure that
- blobs always appear in the same relative order when we are using
- dynamic blobs because if we have a situation where dztL>dztT, we
- start destroying blobs to enforce dztL<dztT. In order that we do
- not significantly change answers, we must always destroy the same
- blob, regardless of domain decomposition, restarts, etc. So, we must
- always sort blobs so they appear in the linked list in the same
- relative order.
-
- Allocates a blob its hash and a number. These two numbers can
- uniquely identify any blob. The hash and number is based on the grid
- cell of origin. Each grid cell has a unique hash. We have an array
- which keeps track of the number of blobs formed in a grid cell. These
- two numbers give the unique identifier. So, we also need to increment
- the counter array.
-
- Writes an attribute to a netcdf file.
-
- Gets the variable identifier from a netcdf file.
-
- Gets the value of a "double" variable from a netcdf file
-
- Gets the value of an integer variable from a netcdf file
-
- Writes the value of a "double" variable to a netcdf file
-
- Writes the value of an integer variable to a netcdf file
-
- Defines a netcdf variable
-
- Gives error descriptions for netcdf calls.
-
- Calculates the hash
-
- Does what is necessary to shut down the module.
-
- Checks whether a blob (horizontally) resides in a grid cell or not.
- If it does not it figures out which direction the blob is in and
- checks the neighbouring grid cell, until it finds which grid cell
- the blob resides in.
-
- It uses a cross product technique from computational geometry
- (Cormen et al., 2001).
-
- Searches for which (vertical) grid cell a blob resides in).
-
- Kills a blob by returning all of its remaining properties to the E
- system.
-
- Frees the heap memory taken up by a blob.
-
- Allocates the history arrays for a blob (only used when
- bitwise_reproduction=.true. in the ocean_blob_nml).
-
- Different blobs can have different history memory requirements.
- When they change from one type of blob to another, we need to change
- the memory allocated to a blob to reflect the new requirements. This
- is only necessary if bitwise_reproduction=.true. in the ocean_blob_nml.
-
- Used for the horizontal interpolation of T grid variables. The
- routine returns coefficients required for inverse distance
- weighting (Shephard, 1968).
-
- Used for the horizontal interpolation of U grid variables. The
- routine returns coefficients required for inverse distance
- weighting (Shephard, 1968).
-
- Checks and adjusts blob position and grid cell index
- for cylclic/periodic domains, as well as
- the Murray (1996) tripolar grid.
-
diff --git a/src/mom5/ocean_core/ocean_advection_velocity.F90 b/src/mom5/ocean_core/ocean_advection_velocity.F90
index 1b95156848..77cfa4a02d 100644
--- a/src/mom5/ocean_core/ocean_advection_velocity.F90
+++ b/src/mom5/ocean_core/ocean_advection_velocity.F90
@@ -226,12 +226,13 @@ module ocean_advection_velocity_mod
private inflow_nboundary_init
character(len=128) :: version=&
- '$Id: ocean_advection_velocity.F90,v 1.1.2.8.16.2 2013/04/03 19:00:31 smg Exp $'
+ '$Id: ocean_advection_velocity.F90,v 20.0.4.1 2014/01/22 17:19:10 smg Exp $'
character (len=128) :: tagname = &
- '$Name: mom5_siena_201303_smg $'
+ '$Name: mom5_tikal_22jan2014_smg $'
-logical :: have_obc = .false.
-logical :: module_is_initialized = .FALSE.
+logical :: have_obc = .false.
+logical :: module_is_initialized = .FALSE.
+logical :: prescribe_advection_velocity = .false.
real :: max_advection_velocity = -1.0
logical :: debug_this_module = .false.
@@ -365,6 +366,7 @@ subroutine ocean_advection_velocity_init(Grid, Domain, Time, Time_steps, Thickne
if(read_advection_velocity .or. read_advection_transport) then
call read_advection(Time, Thickness, Adv_vel)
+ prescribe_advection_velocity = .true.
endif
if(constant_advection_velocity) then
@@ -372,6 +374,7 @@ subroutine ocean_advection_velocity_init(Grid, Domain, Time, Time_steps, Thickne
'==>Note: Using ocean_advection_velocity_mod with constant_advection_velocity=.true.'
write(stdoutunit,'(a)') &
' Will hold the advection velocity components constant in time. '
+ prescribe_advection_velocity = .true.
endif
if(use_blobs .and. horz_grid == MOM_CGRID) then
@@ -592,7 +595,7 @@ subroutine ocean_advection_velocity (Velocity, Time, Thickness, Dens, pme, river
! Remap these to get the corresponding advection velocity components
! (uhrho_eu,vhrho_nu) to advect B-grid horizontal momentum.
- if(.not. constant_advection_velocity .and. horz_grid == MOM_BGRID) then
+ if(.not. prescribe_advection_velocity .and. horz_grid == MOM_BGRID) then
do k=1,nk
Adv_vel%uhrho_et(:,:,k) = &
@@ -639,11 +642,11 @@ subroutine ocean_advection_velocity (Velocity, Time, Thickness, Dens, pme, river
endif
- endif ! endif for .not. constant_advection_velocity and MOM_BGRID
+ endif ! endif for .not. prescribe_advection_velocity and MOM_BGRID
! smg: June 2012: C-grid yet to be updated for blobs.
- if(.not. constant_advection_velocity .and. horz_grid == MOM_CGRID) then
+ if(.not. prescribe_advection_velocity .and. horz_grid == MOM_CGRID) then
do k=1,nk
do j=jsd,jed
@@ -666,7 +669,7 @@ subroutine ocean_advection_velocity (Velocity, Time, Thickness, Dens, pme, river
*Grd%tmask(:,:,k)
enddo
- endif ! endif for .not. constant_advection_velocity and MOM_CGRID
+ endif ! endif for .not. prescribe_advection_velocity and MOM_CGRID
if (have_obc) then
@@ -932,7 +935,7 @@ subroutine read_advection(Time, Thickness, Adv_vel)
type(ocean_thickness_type), intent(in) :: Thickness
type(ocean_adv_vel_type), intent(inout) :: Adv_vel
- integer :: k
+ integer :: i,j,k
character(len=128) :: filename
allocate (ue(isd:ied,jsd:jed,nk))
@@ -945,10 +948,19 @@ subroutine read_advection(Time, Thickness, Adv_vel)
filename = 'INPUT/ocean_advect_velocity.nc'
if (file_exist(trim(filename))) then
call read_data(filename,'ue',ue,Dom%domain2d,timelevel=1)
- call mpp_update_domains(ue(:,:,:), Dom%domain2d)
call read_data(filename,'vn',vn,Dom%domain2d,timelevel=1)
- call mpp_update_domains(vn(:,:,:), Dom%domain2d)
call read_data(filename,'wb',wb,Dom%domain2d,timelevel=1)
+ do k=1,nk
+ do j=jsd,jed
+ do i=isd,ied
+ ue(i,j,k) = ue(i,j,k)*Grd%tmask(i,j,k)
+ vn(i,j,k) = vn(i,j,k)*Grd%tmask(i,j,k)
+ wb(i,j,k) = wb(i,j,k)*Grd%tmask(i,j,k)
+ enddo
+ enddo
+ enddo
+ call mpp_update_domains(ue(:,:,:), Dom%domain2d)
+ call mpp_update_domains(vn(:,:,:), Dom%domain2d)
call mpp_update_domains(wb(:,:,:), Dom%domain2d)
else
call mpp_error(FATAL,&
diff --git a/src/mom5/ocean_core/ocean_advection_velocity.html b/src/mom5/ocean_core/ocean_advection_velocity.html
deleted file mode 100644
index 5cc2454f45..0000000000
--- a/src/mom5/ocean_core/ocean_advection_velocity.html
+++ /dev/null
@@ -1,335 +0,0 @@
-
-
-
-Module ocean_advection_velocity_mod
-
-
-
-
-PUBLIC INTERFACE
-
- ~ PUBLIC ROUTINES
- ~ NAMELIST
-
-
- Advection velocity components for tracer and momenta transport, with
- options for B-grid or C-grid.
-
-
-
-
-
- The module computes the horizontal and vertical components to the
- advection velocity on the face of tracer and velocity cells.
- Options are provided for either the B-grid or C-grid.
-
- The three velocity components are related by continuity.
-
- All components are density weighted, and the
- horizontal components are thickness weighted.
-
- Some diagnostics related to fluid mass transport
- classified according to both depth and density classes
- are also computed.
-
-
- Compute thickness weighted and density weighted advection velocity
- components for the B-grid on the T-cells and U-cells.
-
-
-
-
-
-
-
-
check_vert_cfl_blobs
-
-
-DESCRIPTION
-
-
- This routine is useful to check for strong vertical motions in the
- presence of Lagrangian blobs. The CFL check is the same as in the
- module ocean_adv_vel_diag.F90, but we have more local control here
- so it is useful in the development stages of the blobs.
-
-
-
-
-
-
-
-
read_advect_velocity
-
-
-DESCRIPTION
-
-
- For reading in the advection velocity components. Assume that
- the advection velocity components read in from a file are in units
- of meter/sec and placed on the T-cell faces, as in a C-grid ocean model.
-
- This routine assumes that the read-in velocity components already
- have the proper masking.
-
- The main application of this routine is for developing idealized
- test cases for tracer advection.
-
-
-
-
-
-
-
-
inflow_nboundary_init
-
-
-DESCRIPTION
-
-
- Initialize the advection velocity used for specifying a nonzero
- southward inflow introduced to the domain from the northern boundary.
-
-
-
-
-
-
-
-
-
ocean_advection_velocity_end
-
-
-DESCRIPTION
-
-
- Write a restart if necessary
-
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_advection_velocity_nml
-
-
-
-
-
-debug_this_module
-
-
- For debugging.
-
-[logical]
-
-
-inflow_nboundary
-
-
- For adding an inflow velocity from the northern boundary.
- Default is inflow_nboundary=.false.
-
-[logical]
-
-
-read_advection_velocity
-
-
- For reading in a file with specified zonal, meridional,
- and vertical components to the advection velocity.
- The file should have velocity at the east face of T-cell,
- north face, and bottom, just as on a C-grid. The units
- should be m/s for each component. MOM then multiplies
- but the appropriate thickness and density factors to
- generate transport for use in the model.
- Default read_zonal_advection_velocity=.false.
-
-[logical]
-
-
-constant_advection_velocity
-
-
- When reading in the advection velocity components, we
- may choose to keep them constant in time. This facilitates
- idealized tests of tracer advection.
- Default constant_advection_velocity=.false.
-
-[logical]
-
-
-max_advection_velocity
-
-
- This is a check value used to determine if the time steps will result in
- linearly stable advection. If set to a number < 0, then model will estimate the
- value as a function of maximum grid size.
- Note that this time step check is not rigorous, and it depends on the details of
- the advection scheme. Nonetheless, it provides some useful warning for setting the
- time steps in the model.
-
-[real, units: meter/sec]
-
-
-
-
-
-
-
-
-
-
-
REFERENCES
-
-
-
-
- R.C. Pacanowski and S.M. Griffies
- The MOM3 Manual (1999)
-
-
- S.M. Griffies, M.J. Harrison, R.C. Pacanowski, and A. Rosati
- A Technical Guide to MOM4 (2003)
-
-
- S.M. Griffies: Elements of MOM (2012)
-
-
-
-
-
-
-
-
NOTES
-
-
- The expressions for the horizontal components for tracer advection
- allow for a proper conversion between pressure work and buoyancy.
-
-
- The B-grid remapping operators are derived from considerations of linear
- interpolation and volume conservation. A "remapping error" is
- computed to determine consistency between the tracer and velocity
- grid advection velocities. This error is roundoff only for cases
- where the horizontal tracer and velocity grids are linearly related,
- as is the case for the spherical coordinate version of MOM. The
- tripolar version of MOM does not have tracer and velocity grids
- related linearly, and so the "remapping error" is nontrivial. The
- significance of this error is unclear. No adverse effects have been
- identified.
-
-
- The vertical velocity components for both the tracer and velocity cells
- are diagnosed via continuity (either volume or mass conservation depending
- on the use of the Boussinesq or non-Boussinesq versions of MOM).
-
- Update the vertically integrated dynamics using a
- split-explicit algorithm.
-
-
-
-
-
-
- This module time steps the vertically integrated dynamics
- using a predictor-Corrector with adjustable dissipation.
-
- This code uses a split-explicit method. There have been no
- no rigid lid available in MOM since MOM3.
-
- Treatment is provided for both depth-based Boussinesq
- and pressure-based non-Boussinesq vertical coordinates.
-
- Treatment is provided for both a Bgrid or Cgrid horizontal layout.
-
-
- Initialize diagnostic indices for the module.
-
- Diagnose the static arrays.
-
-
-
-
-
-
-
-
eta_terms_diagnose_init
-
-
-DESCRIPTION
-
-
- Initialize diagnostic indices for the eta_terms related diagnostics.
-
-
-
-
-
-
-
-
eta_and_pbot_update
-
-
-DESCRIPTION
-
-
- Time step the surface height or pbot using a "big" time step.
- These fields are coincident in time with ocean tracers.
-
- NOTE: For pbot_t updates, we time step anompb for accuracy, then
- add rho0grav*ht to get pbot_t.
-
-
-
-
-
-
-
-
-
eta_and_pbot_diagnose
-
-
-DESCRIPTION
-
-
- Diagnose surface height or pbot depending on the vertical coordinate.
-
- Note that dzt has been updated to taup1 before this routine is called,
- since we have already called update_tcell_thickness.
-
- Also, compute geodepth_zt in this routine. It is necessary to do
- do this step here, since for pressure coordinate models we do not
- know eta_t(taup1) until this routine.
-
- June 2011: note to smg:
- Consider changing taup1 to tau in rho, since we
- do not yet know the taup1 value. Not a fundamental issue,
- but may be cleaner. It will change bits, however.
-
-
-
-
-
-
-
-
-
eta_and_pbot_tendency
-
-
-DESCRIPTION
-
-
- Compute tendency for surface height or bottom pressure.
-
- If use_blobs=.true., then we include the divergence from
- the Lagrangian system.
-
-
-
-
-
-
-
-
-
update_ocean_barotropic
-
-
-DESCRIPTION
-
-
- Time step the external mode fields using
- a predictor-corrector scheme. Time average these fields to
- update the vertically integrated density weighted velocity
- (urhod,vrhod) and the time averaged surface height eta_t_bar
- or bottom pressure anompb_bar.
-
- NOTE: surface pressure gradient and gradient of anomalous
- bottom pressure are needed for the energy analysis.
-
- Also, if splitting=false or update_velocity_via_uprime=.false.,
- use these for velocity update in ocean_velocity_mod.
-
- Include the tidal forcing if present.
-
- Include geoid perturbation if present.
-
- Use time averaged eta and pbot to ensure the stable pressure gradient
- for use with splitting=false or update_velocity_via_uprime=.false.
-
-
-
-
-
-
-
-
-
ocean_barotropic_forcing
-
-
-DESCRIPTION
-
-
- Construct the vertically integrated forcing. This forcing is to be
- held constant over the barotropic timesteps. At the time of calling
- this routine, accel has the contributions from explicit-time
- forcing, except for the following:
-
- 1. Coriolis force is updated on the barotropic time steps when
- integrating the barotropic dynamics. So it should not
- be included in forcing_bt.
-
- 2. Contributions from smf and bmf are added to forcing_bt to allow
- for simpler handling of vertical friction implicitly in time.
-
- 3. The accel array is already thickness and density weighted, so
- a vertical density weighted integral is here just a vertical sum.
-
-
-
-
-
-
-
-
-
ocean_mass_forcing
-
-
-DESCRIPTION
-
-
- Construct the vertically integrated mass source for
- evolution of the free surface and/or bottom pressure.
-
- Also construct the time tendency for the atmospheric pressure.
-
-
-
-
-
-
-
-
-
pred_corr_tropic_depth_bgrid
-
-
-DESCRIPTION
-
-
- Integrate barotropic dynamics for "nts" timesteps using
- predictor-corrector. Assume depth-like vertical coordinate
- so solve for surface height.
-
- This scheme is more stable than leap_frog since it can run with
- longer time steps to resolve external mode gravity waves. It also
- provides some extra smoothing when pred_corr_gamma > 0 and so the options
- smooth_eta_t_bt_laplacian and smooth_eta_t_bt_biharmonic may not be
- needed.
-
- Time steps Bgrid layout of discrete fields.
-
-
-
-
-
-
-
-
-
pred_corr_tropic_depth_cgrid
-
-
-DESCRIPTION
-
-
- Integrate barotropic dynamics for "nts" timesteps using
- predictor-corrector. Assume depth-like vertical coordinate
- so solve for surface height.
-
- Cgrid horizontal layout.
-
- This scheme is more stable than leap_frog since it can run with
- longer time steps to resolve external mode gravity waves. It also
- provides some extra smoothing when pred_corr_gamma > 0.
- We assume pred_corr_gamma > 0 in this routine.
-
-
-
-
-
-
-
-
-
pred_corr_tropic_press_bgrid
-
-
-DESCRIPTION
-
-
- Integrate barotropic dynamics for "nts" timesteps using
- predictor-corrector. Assume pressure-like vertical coordinate
- so solve here for the bottom pressure.
-
- This scheme provides some smoothing of small spatial scales
- when pred_corr_gamma > 0.
-
- NOTE: the pressure gradient force is based on gradients of
- (pbot_t_bt - rho0*grav*ht) rather than gradients of pbot_t_bt.
- This approach aims to improve accuracy of the pressure force.
-
- Time steps Bgrid layout of discrete fields.
-
-
-
-
-
-
-
-
-
pred_corr_tropic_press_cgrid
-
-
-DESCRIPTION
-
-
- Integrate barotropic dynamics for "nts" timesteps using
- predictor-corrector. Assume pressure-like vertical coordinate
- so solve here for the bottom pressure.
-
- This scheme provides some smoothing of small spatial scales
- with requirement that pred_corr_gamma > 0.
-
- NOTE: the pressure gradient force is based on gradients of
- (pbot_t_bt - rho0*grav*ht) rather than gradients of pbot_t_bt.
- This approach aims to improve accuracy of the pressure force.
-
- Time steps Cgrid layout of discrete fields.
-
-
-
-
-
-
-
-
-
eta_smooth_diagnosed
-
-
-DESCRIPTION
-
-
- Smooth eta_t for case when running with pressure models and wish
- to have a diagnostic eta field smoothed. This option is most
- useful for the Bgrid, which has a checkerboard null mode when
- discretizing gravity waves. The Cgrid has no gravity wave noise
- so may not need this smoother.
-
-
-
-
-
-
-
-
ocean_eta_smooth
-
-
-DESCRIPTION
-
-
- Compute tendency for smoothing eta and tracer.
-
- Use either a laplacian or a biharmonic smoothing operator.
-
- This smoothing option is most useful for the Bgrid, which has
- a checkerboard null mode when discretizing gravity waves. The
- Cgrid has no gravity wave noise so may not need this smoother.
-
- Recommend against using the biharmonic, since it is not a
- positive definite operator and so can lead to extrema.
- Biharmonic is retained for legacy purposes.
-
-
-
-
-
-
-
-
-
ocean_pbot_smooth
-
-
-DESCRIPTION
-
-
- Compute tendency for diffusion of (pbot_t-pbot0) in both pbot_t
- and tracer. Need to consider tracer in order to maintain compability
- between tracer and mass conservation equations.
-
- Use either a laplacian or a biharmonic smoother.
-
- This smoothing option is most useful for the Bgrid, which has
- a checkerboard null mode when discretizing gravity waves. The
- Cgrid has no gravity wave noise so may not need this smoother.
-
- Recommend against using the biharmonic, since it is
- NOT a positive definite operator and so can lead to extrema.
-
-
-
-
-
-
-
-
-
barotropic_integrals
-
-
-DESCRIPTION
-
-
- Compute area averaged fresh water and surface height and ocean mass.
-
-
-
-
-
-
-
-
barotropic_energy
-
-
-DESCRIPTION
-
-
- Compute energetics of vertically integrated flow.
-
-
-
-
-
-
-
-
read_barotropic
-
-
-DESCRIPTION
-
-
- Read in external mode fields from restart file.
-
-
-
-
-
-
-
-
ocean_barotropic_restart
-
-
-DESCRIPTION
-
-
-
- Write out restart files registered through register_restart_file
- Call to reset_field_pointer only needed for fields with a time index.
-
-
-
-
-
-
-
-
-
ocean_barotropic_end
-
-
-DESCRIPTION
-
-
- Write out external mode fields to restart file.
-
-
-
-
-
-
-
-
maximum_convrhoud
-
-
-DESCRIPTION
-
-
- Compute maximum convergence(rho_ud,rho_vd).
-
-
-
-
-
-
-
-
barotropic_chksum
-
-
-DESCRIPTION
-
-
- Compute checksum for external mode fields.
-
-
-
-
-
-
-
-
psi_compute
-
-
-DESCRIPTION
-
-
- Compute quasi-barotropic streamfunctions for diagnostic purposes.
- When no fresh water and steady state, these two streamfunctions
- will be equal, and they will be equal to the rigid lid barotropic
- streamfunction in the Boussinesq case.
-
- Original algorithm: Stephen.Griffies
-
- 13MAR2007: Change units to 10^9 kg/s, which is a "mass Sv"
- This is the natural unit of transport for a mass-based
- vertical coordinate model.
-
- Updated Dec2009 to be compatible with tx_trans and ty_trans
- calculation.
-
-
-
-
-
-
-
-
-
eta_terms_diagnose
-
-
-DESCRIPTION
-
-
- Diagnose various contributions to the sea level.
-
- WARNING: The steric diagnostics from this subroutine are confusing
- when evaluated in a Boussinesq model. The reason is that volume
- conserving Boussinesq models have spurious mass sources, which
- corrupt the bottom pressure signal. One needs to apply corrections
- to make sense of the Boussinesq models for purposes of studying
- mass budgets, including the local contribution to steric effects.
-
- contributions from dynamics, mass, and steric:
-
- eta_nonbouss = (eta_dynamic + eta_water + eta_source) + eta_steric
- = eta_nonsteric + eta_steric
-
- For PRESSURE_BASED vertical coordinates, eta_smooth_tend has
- already been computed in subroutine eta_smooth_diagnosed.
- We do not add this contribution to eta_nonbouss, since this
- piece is not part of the tendencies affecting bottom pressure.
- It is only added for cosmetic reasons. It is for this reason
- that eta_smooth is NOT included in the restart file.
-
- For calculation of the steric contribution, a single time step
- scheme is assumed, which is the recommended time stepping in MOM.
-
- For DEPTH_BASED models, the smoothing of eta is included in
- Ext_mode%source, so eta_smooth_tend is zero for depth-based models.
-
- For PRESSURE_BASED vertical coordinates, eta_nonbouss as computed
- in this routine is very close to the prognostic eta_t. Differences
- arise from any possible smoothing applied to the diagnosed eta_t.
-
-
-
-
-
-
-
-
-
eta_truncate
-
-
-DESCRIPTION
-
-
-
- Truncate eta_t to keep
-
- dzt(1) + eta_t >= frac_crit_cell_height*dzt(1)
-
- and
-
- eta_t <= eta_max
-
- May be needed when run GEOPOTENTIAL models.
-
-
-
-
-
-
-
-
-
eta_check
-
-
-DESCRIPTION
-
-
- Perform diagnostic check on top cell thickness. Useful when
- when use GEOPOTENTIAL vertical coordinate.
-
-
-
-
-
-
-
-
-
tidal_forcing_init
-
-
-DESCRIPTION
-
-
- Initialize fields needed for lunar and solar tidal forcing.
-
-
-
-
-
-
-
-
geoid_forcing_init
-
-
-DESCRIPTION
-
-
- Initialize fields needed for modifying the geoid, relative to the
- standard geoid.
-
-
-
-
-
-
-
-
get_tidal_forcing
-
-
-DESCRIPTION
-
-
- Compute equilibrium tidal forcing.
-
-
-
-
-
-
-
-
ideal_initialize_eta
-
-
-DESCRIPTION
-
-
- Idealized initial condition for eta.
-
-
-
-
-
-
-
-
REMAP_BT_TO_BU_LOCAL
-
-
-DESCRIPTION
-
-
- Local version of the operator, needed here for initialization
- when read in eta information from an initialization file.
- Since barotropic is initialized prior to operators, we need
- to have this operator here locally.
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_barotropic_nml
-
-
-
-
-
-write_a_restart
-
-
- Set true to write a restart. False setting only for rare
- cases where wish to benchmark model without measuring the cost
- of writing restarts and associated chksums.
- Default is write_a_restart=.true.
-
-[logical]
-
-
-zero_tendency
-
-
- If true, will not integrate the barotropic fields.
-
-[logical]
-
-
-zero_forcing_bt
-
-
- Will set to zero all of the terms forcing the barotropic velocity.
-
-[logical]
-
-
-zero_nonlinear_forcing_bt
-
-
- Will set to zero the nonlinear forcing terms, leaving only the smf and bmf
- terms to force the barotropic velocity.
-
-[logical]
-
-
-zero_eta_ic
-
-
- To initialize eta_t to zero.
-
-[logical]
-
-
-zero_eta_t
-
-
- To maintain eta_t at zero, but to allow other fields to evolve.
- For debugging. Default zero_eta_t=.false.
-
-[logical]
-
-
-zero_eta_u
-
-
- To maintain eta_u at zero, but to allow other fields to evolve.
- For debugging. Default zero_eta_u=.false.
-
-[logical]
-
-
-zero_eta_tendency
-
-
- To maintain deta_dt at zero. For debugging.
- Default zero_eta_t=.false.
-
-[logical]
-
-
-ideal_initial_eta
-
-
- To initialize eta_t to an ideal profile. This option overrides
- all other initialization that may have occurred.
- Default=.false.
-
-[logical]
-
-
-ideal_initial_eta_amplitude
-
-
- Amplitude for initializing eta with an ideal profile.
- Default ideal_initial_eta_amplitude = 5.0
-
-[real, units: metre]
-
-
-ideal_initial_eta_xwidth
-
-
- Width in x-direction for sine-wave profile.
- Default xwidth=100e3
-
-[real, units: metre]
-
-
-ideal_initial_eta_ywidth
-
-
- Width in y-direction for sine-wave profile.
- Default ywidth=100e3
-
-[real, units: metre]
-
-
-barotropic_time_stepping_A
-
-
- Use the general approach from MOM4.0, in which the eta_t and
- pbot_t fields are updated with a big time step.
- This is the recommended approach for most applications that
- do not employ and open boundary condition.
- Default barotropic_time_stepping_A=.false.
-
-[logical]
-
-
-barotropic_time_stepping_B
-
-
- Use the alternative approach in which we assume the barotropic
- scheme is a predictor-corrector, which is now the default
- in MOM. We use this assumption so that the eta_t and
- pbot_t fields are updated with a time average. This
- approach is used for open boundary condition applications.
- Default barotropic_time_stepping_A=.false.
-
-[logical]
-
-
-pred_corr_gamma
-
-
- Dimensionless dissipation parameter for the preditor-corrector
- scheme. Setting pred_corr_gamma=0.0 reduces the scheme to a
- forward-backward, but it has been found to be unstable.
- So pred_corr_gamma > 0.0 is recommended. Note that
- pred_corr_gamma > 0.25 may be over-dissipated and so may
- go unstable. Default pred_corr_gamma=0.2.
-
-[real, units: dimensionless]
-
-
-smooth_eta_t_bt_laplacian
-
-
- For spatially smoothing the eta_t field at each barotropic
- time step using a Laplacian operator. This option may not
- be necessary when pred_corr_gamma > 0.0, since the
- predictor-corrector approach has dissipation from
- pred_corr_gamma > 0.0. Also, smoothing is not needed
- in general for Cgrid MOM, since the gravity wave null mode
- only appears for the Bgrid. This option is only
- applicable for DEPTH_BASED vertical coordinates.
- Default smooth_eta_t_bt_laplacian=.false.
-
-[logical]
-
-
-smooth_eta_t_bt_biharmonic
-
-
- For spatially smoothing the eta_t field at each barotropic
- time step using a biharmonic operator. May not be necessary
- when pred_corr_gamma > 0.0, since predictor-corrector has
- dissipation from pred_corr_gamma > 0.0. Also, smoothing is not
- needed in general for Cgrid MOM, since the gravity wave null
- mode only appears for the Bgrid. Applicable just for
- DEPTH_BASED vertical coordinates. WARNING: this operator
- is NOT positive definite, and so can produce spurious
- extrema. It is not generally recommended just for this
- reason. Default smooth_eta_t_bt_laplacian=.false.
-
-[logical]
-
-
-smooth_eta_t_laplacian
-
-
- For spatially smoothing the eta_t field on the big time step
- by using a laplacian operator. For compatibility
- and global conservation, must also introduce a mixing
- to the thickness weighted tracer concentration in the k=1 cell.
- Applicable just for DEPTH_BASED vertical coordinates.
- Also, smoothing is not needed in general for Cgrid MOM,
- since the gravity wave null mode only appears for the Bgrid.
- Default mooth_eta_t_laplacian=.true.
-
-[logical]
-
-
-smooth_eta_t_biharmonic
-
-
- For spatially smoothing the eta_t field on the big time step
- by using a biharmonic operator. For compatibility
- and global conservation, must also introduce a mixing
- to the thickness weighted tracer concentration in the k=1 cell.
- Applicable just for DEPTH_BASED vertical coordinates.
- Also, smoothing is not needed in general for Cgrid MOM,
- since the gravity wave null mode only appears for the Bgrid.
- WARNING: This operator is NOT positive definite, and so can
- produce spurious extrema. It is not recommended just for this
- reason. Default smooth_eta_t_biharmonic=.false.
-
-[logical]
-
-
-eta_offset
-
-
- Uniform offset for use in determining the filter
- acting on tracer when smoothing the surface height.
- Default eta_offset=1e-12.
-
-[real, units: metre]
-
-
-smooth_eta_diag_laplacian
-
-
- For spatially smoothing the diagnosed eta_t field
- using a laplacian operator. This option is used for
- PRESSURE_BASED vertical coordinates, in which case
- the free surface is diagnosed rather than prognosed.
- Also, smoothing is not needed in general for Cgrid MOM,
- since the gravity wave null mode only appears for the Bgrid.
- Default smooth_eta_diag_laplacian=.true.
-
-[logical]
-
-
-smooth_eta_diag_biharmonic
-
-
- For spatially smoothing the diagnosed eta_t field
- using a biharmonic operator. This option is used for
- PRESSURE_BASED vertical coordinates, in which case
- the free surface is diagnosed rather than prognosed.
- Also, smoothing is not needed in general for Cgrid MOM,
- since the gravity wave null mode only appears for the Bgrid.
- Default smooth_eta_diag_biharmonic=.false.
-
-[logical]
-
-
-vel_micom_lap_diag
-
-
- Velocity scale that is used for computing the MICOM Laplacian mixing
- coefficient used in the Laplacian smoothing of diagnosed surface height.
- Default vel_micom_lap_diag=0.2.
-
-[real, units: m/sec]
-
-
-vel_micom_bih_diag
-
-
- Velocity scale that is used for computing the MICOM biharmonic mixing
- coefficient used in the biharmonic smoothing of diagnosed surface height.
- Default vel_micom_bih_diag=0.1.
-
-[real, units: m/sec]
-
-
-smooth_anompb_bt_laplacian
-
-
- For spatially smoothing anomalous pbot_t at each barotropic
- time step using a Laplacian operator. May not be necessary when
- pred_corr_gamma > 0.0, since predictor-corrector has dissipation
- from pred_corr_gamma > 0.0. This option is applicable just
- for PRESSURE_BASED vertical coordinates.
- Also, smoothing is not needed in general for Cgrid MOM,
- since the gravity wave null mode only appears for the Bgrid.
- Default smooth_anompb_bt_laplacian=.false.
-
-[logical]
-
-
-smooth_anompb_bt_biharmonic
-
-
- For spatially smoothing the anomalous pbot_t field at each barotropic
- time step using a biharmonic operator. May not be necessary when
- when pred_corr_gamma > 0.0, since predictor-corrector has dissipation
- from pred_corr_gamma > 0.0. This option is applicable just for
- PRESSURE_BASED vertical coordinates. Also, smoothing is not
- needed in general for Cgrid MOM, since the gravity wave null
- mode only appears for the Bgrid. WARNING: This operator is
- NOT positive definite, and so can produce spurious extrema.
- It is not recommended just for this reason.
- Default smooth_anompb_bt_biharmonic=.false.
-
-[logical]
-
-
-smooth_pbot_t_laplacian
-
-
- For spatially smoothing pbot_t-pbot0 on the big time step
- using a laplacian operator. For compatibility
- and global conservation, must also introduce a mixing
- to the thickness weighted tracer concentration in the k=kbot cell.
- Applicable just for PRESSURE_BASED vertical coordinates.
- Also, smoothing is not needed in general for Cgrid MOM,
- since the gravity wave null mode only appears for the Bgrid.
- Default smooth_pbot_t_laplacian=.true.
-
-[logical]
-
-
-smooth_pbot_t_biharmonic
-
-
- For spatially smoothing pbot_t-pbot0 on the big time step
- by using a biharmonic operator. For compatibility
- and global conservation, must also introduce a mixing
- to the thickness weighted tracer concentration in the k=kbot cell.
- Applicable just for PRESSURE_BASED vertical coordinates.
- Also, smoothing is not needed in general for Cgrid MOM,
- since the gravity wave null mode only appears for the Bgrid.
- WARNING: This operator is NOT positive definite, and so can
- produce spurious extrema. It is not recommended just for this
- reason. Default smooth_pbot_t_biharmonic=.false.
-
-[logical]
-
-
-smooth_pbot_t_biharmonic_legacy
-
-
- For using an older version of the smooth_pbot_t_biharmonic
- scheme. The smooth_pbot_t_biharmonic_legacy option has a
- minor bug, but it is maintained in order to allow for
- backward compatible legacy simulations. It is not
- recommended for new simulations.
- To use it requires also setting smooth_pbot_t_biharmonic=.true.
- Default smooth_pbot_t_biharmonic_legacy=.false.
-
-[logical]
-
-
-pbot_offset
-
-
- Uniform offset for use in determining the filter
- acting on tracer when smoothing the bottom pressure anomaly.
- Default pbot_offset=1e-12.
-
-[real, units: Pa]
-
-
-vel_micom_lap
-
-
- Velocity scale that is used for computing the MICOM Laplacian mixing
- coefficient used in the Laplacian smoothing of surface height
- or anomalous bottom pressure. Default vel_micom_lap=0.05.
-
-[real, units: m/sec]
-
-
-vel_micom_bih
-
-
- Velocity scale that is used for computing the MICOM biharmonic mixing
- coefficient used in the biharmonic smoothing of surface height
- or anomalous bottom pressure. Default vel_micom_bih=0.01.
-
-[real, units: m/sec]
-
-
-udrho_bt_lap
-
-
- The vertically integrated horizontal momentum can be noisy
- on the Bgrid. It is therefore sometimes useful to add a
- smoothing operator to the barotropic time stepping.
- Here, we apply the laplacian friction as coded in the friction
- module using the vertically averaged isotropic viscosity as well as a
- background, and we do so on each barotropic time step. It is an
- expensive option. It is an option rarely used GFDL.
- This options will soon be removed from MOM.
- Default udrho_bt_lap=.false.
-
-[logical]
-
-
-udrho_bt_bih
-
-
- The vertically integrated horizontal momentum on the Bgrid can be
- noisy. It is therefore sometimes useful to add a smoothing
- operator. Here, we apply the biharmonic friction as coded in
- the friction module using the vertically averaged isotropic
- viscosity as well as a background. Do so on each barotropic
- time step, which makes it an expensive option. This option is
- rarely used GFDL. Default udrho_bt_bih=.false.
- This options will soon be removed from MOM.
-
-[logical]
-
-
-udrho_lap
-
-
- The vertically integrated horizontal momentum on the Bgrid can be
- noisy. It is therefore sometimes useful to add a smoothing
- operator. Here, we apply the laplacian friction as coded in
- the friction module using the vertically averaged isotropic
- viscosity as well as a background. Do so just on the baroclinic
- time step, so the option is less expensive than udrho_bt_lap.
- This options will soon be removed from MOM.
- Default udrho_lap=.false.
-
-[logical]
-
-
-udrho_bih
-
-
- The vertically integrated horizontal momentum on the Bgrid can be
- noisy. It is therefore sometimes useful to add a smoothing
- operator. Here, we apply the biharmonic friction as coded in
- the friction module using the vertically averaged isotropic
- viscosity as well as a background. Do so just on the baroclinic
- time step, so the option is less expensive than udrho_bt_lap.
- This options will soon be removed from MOM.
- Default udrho_bih=.false.
-
-[logical]
-
-
-udrho_lap_vel_micom
-
-
- Velocity scale that is used for computing the MICOM Laplacian mixing
- coefficient used in the Laplacian smoothing of udrho.
- This options will soon be removed from MOM.
- Default udrho_lap_vel_micom=.05
-
-[real, units: m/sec]
-
-
-udrho_bih_vel_micom
-
-
- Velocity scale that is used for computing the MICOM biharmonic mixing
- coefficient used in the biharmonic smoothing of udrho.
- This options will soon be removed from MOM.
- Default udrho_bih_vel_micom=.01
-
-[real, units: m/sec]
-
- Forces from 8 lunar and solar tidal constituents.
- Default tidal_forcing_8=.false.
-
-[logical]
-
-
-tidal_forcing_ideal
-
-
- For ideal tidal forcing, which has a bump configuration.
- Default tidal_forcing_ideal=.false.
-
-[logical]
-
-
-alphat
-
-
- Dimensionless self-attraction and loading term. Used only
- when tidal_forcing=.true. Default alphat=0.948.
-
-[real, units: dimensionless]
-
-
-geoid_forcing
-
-
- For modifying the geoid, implemented as a time independent
- tidal forcing. Need to read in a file to obtain the offset
- geoid profile. Default geoid_forcing=.false.
-
-[logical]
-
-
-truncate_eta
-
-
- To truncate the surface height so to ensure positive thickness
- within the top cell. This method will not conserve volume or tracer.
- It is coded for cases when conservation is not critical but wish to
- run GEOPOTENTIAL models w/ large free surface height deviations, such
- as when running with tides and very fine vertical resolution. The preferred
- approach is to use zstar or pstart vertical coordinates.
- Default truncate_eta = .false..
-
-[logical]
-
-
-verbose_truncate
-
-
- For verbose printout on truncate_eta
-
-[logical]
-
-
-frac_crit_cell_height
-
-
- When use GEOPOTENTIAL vertical coordinate, the top model tracer grid
- cell has thickness dzt(i,j,1) = dzt(1) + eta_t(i,j).
- 0 < frac_crit_cell_height <= 1 sets the fraction of dzt(1) that is allowed
- prior to bringing the model down due to overly small dzt(i,j,1).
- Default frac_crit_cell_height=0.20.
-
-[real, units: dimensionless]
-
-
-eta_max
-
-
- The maximum positive eta_t allowed when truncate_eta is true.
- Default eta_max = 5.0.
-
-[real, units: meter]
-
-
-barotropic_halo
-
-
- Set barotropic_halo > 1 to use wide halo in the barotropic time step to improve the
- performance. In barotropic time step, most time is spent on mpp_update_domains. Use
- wide halo to decrease the number of mpp_update_domain calls and hence improve the
- performance. The default value is barotropic_halo=1, which is the older approach
- (non-wide halo). Users are encouraged to experiment with larger halos, as the
- model speedup can be tremendous.
-
-[INTEGER]
-
-
-do_bitwise_exact_sum
-
-
- Set true to do bitwise exact global sum. When it is false, the global
- sum will be non-bitwise_exact, but will significantly increase efficiency.
- Default do_bitwise_exact_sum=.false.
-
-[logical]
-
-
-debug_this_module
-
-
- Print out lots of diagnostics of use for debugging.
- Default debug_this_module=.false.
-
-[logical]
-
-
-verbose_init
-
-
- For brief or full printout on initialization
- Default verbose_init=.true.
-
-[logical]
-
-
-diag_step
-
-
- Frequency for output of ascii barotropic diagnostics.
- Setting diag_step=1 will compute diagnostics each time
- step and print to stdout. This setting is useful when
- developing a model in order to examine various budgets
- and stability issues. But when running production, one
- should set diag_step to a mucch larger number in order to
- reduce i/o and model cost. Default diag_step=-1,
- which means will not compute any of the online diagnostics.
-
-[integer]
-
-
-
-
-
-
-
-
-
-
-
REFERENCES
-
-
-
-
- S.M. Griffies, R.C. Pacanowski, R.M. Schmidt, and V. Balaji
- Tracer Conservation with an Explicit Free Surface Method for
- Z-coordinate Ocean Models
- Monthly Weather Review (2001) vol 129 pages 1081--1098
-
-
- S.M. Griffies
- Fundamentals of Ocean Climate Models
- Princeton University Press (2004)
-
-
- S.M. Griffies, M.J. Harrison, R.C. Pacanowski, and A. Rosati
- A Technical Guide to MOM4 (2004)
-
- Initialize the bottom boundary condition module
-
-
-
-
-
-
-
-
get_ocean_bbc
-
-
-DESCRIPTION
-
-
- Set bottom boundary conditions for velocity and tracer.
-
- Dimensions of bottom momentum flux are
- N/m^2 = (kg/m^3)*(m^2/s^2).
-
- Note the use of rho0 for the conversion from m^2/s^2 to
- (kg/m^3)*(m^2/s^2). We do not know the precise value
- of cdbot, so the rho0 approximate value is well within
- our level of uncertainty. No reason therefore to
- use in situ rho for this conversion, even when using
- non-Boussinesq version of MOM.
-
-
- Note that bmf needs to be computed on the data domain since the
- halo values are accessed in ocean_vert_gotm.F90.
-
-
-
-
-
-
-
-
-
current_wave_drag_diag
-
-
-DESCRIPTION
-
-
- calculates wave-current bottom shear stress
- using model of Grand and Madsen(1979) J. Geophys. Res. 84, C4, 1797
- see Signell et. al (1990) J. Geophys. Res. 95, C6, 9671
-
- input bot_vel: current velocity at u points
- Note: assumed that this is the velocity just above the bottom boundary layer.
-
- A relation between grain size, ripples steepness and and roughness is
- assumed. More general relations are possible but not needed, since
- the output is used only to parameterise resuspension of organic matter
- in the ecosystem model ocean_shared/generic_tracers/generic_ERGOM.F90.
-
- output: effective drag coefficient drag_coeff.
- It is valid for momentum flux from currents into the bottom, but
- from combined waves+current action.
- Velocity%current_wave_stress is the stress from waves and currents
- to the sediment.
-
- Note:
-
- 1/ drag_coeff in this routine arises from both (waves+current);
- That is, ustar**2/uref**2 1 meter above the bottom.
-
- 2/ bottom velocity is taken just above the bottom boundary layer, and
- assumed here to be at lowest u point.
-
- 3/ to understand the calculation of shear stress acting on grains
- at sediment surface ("wrk1_2d(i,j) = (ustar2/ucomb)*0.3152"),
- see Kuhrts et al. (2004) Eqs. (4,5,6,7).
- Assume a thin skin friction layer according to Smith, McLean (1977)
- thickness of the skin friction layer zskin scales with roughness length ruff
- grained sediments are characterised by median diameter d50[m]
- ripples at sea bottom have spacing lambda and height eta with steepness eta/lambda=0.1
- common approx. for grain roughness length = d50/12
- Nielsen (1983) form drag roughness length = (8/30)*eta*(eta/lambda) ==> (8/3000)*lambda
- Yalin (1977) lambda = 1000*d50 ==> form drag = (8/3)*d50
- ruff = grain + form drag = (1/12+8/3)*d50 = (33/12)*d50 = 33*grain
- Smith, McLean (1977) zskin = 0.09*grain*(lambda/grain)**0.8 = 165*grain = 5*ruff
- matching at zskin leads to log(zskin/ruff)/log(zskin/grain)) = log(5)/log(165) = 0.3152
- the current induced skin friction velocity is derived from matching skin friction
- to wave boundary layer.
-
- 4/ Algorithm has yet to be updated for Cgrid.
-
- April 2012
- martin.schmidt@io-warnemuende.de
-
-
-
-
-
-
-
-
-
wave_u_diag
-
-
-DESCRIPTION
-
-
- calculates wave bottom shear stress velocity
- wave friction factor is parametrized by approximation of
- Nielsen (1992), Coastal bottom boundary layers and sediment transport!
-
- April 2012
- martin.schmidt@io-warnemuende.de
-
-
- For incorporating the bottom momentum drag implicitly in time.
- Default is bmf_implicit=.false.
-
-[logical]
-
-
-cdbot_law_of_wall
-
-
- For determining bottom drag coefficient using a constant roughness length.
- Will take maximum between cdbot and the computed value using law of
- wall log-profile. This option of use when have very very
- refined vertical resolution (say on order of meters) near the bottom.
- Terrain following coordinates should use this option since they generally
- have very refined vertical grid spacing on topography.
- Default is cdbot_law_of_wall=.false.
-
-[logical]
-
-
-law_of_wall_rough_length
-
-
- Bottom roughness length. Default is law_of_wall_rough_length=0.01m, following
- the default used in the Princeton Ocean Model (POM). This value
- corresponds to "Law of Wall" physics.
-
-[real, units: metre]
-
-
-cdbot_roughness_length
-
-
- For determining bottom drag coefficient using a map of the roughness length.
- This approach is more relevant for coarse models
- than the constant roughness length used in the cdbot_law_of_wall option.
- Default is cdbot_roughness_length=.false.
-
-[logical]
-
-
-cdbot_roughness_uamp
-
-
- For determining bottom drag coefficient using a map of the roughness length
- and tidal velocity amplitude.
- This approach is more relevant for coarse models
- than the constant roughness length used in the cdbot_law_of_wall option.
- cdbot_lo <= cdbot(i,j) <= cdbot_hi.
- Default is cdbot_roughness_length=.false.
-
-[logical]
-
-
-cdbot_HH
-
-
- H0 in a parameterization of cdbot_roughness_uamp.
- Default is cdbot_HH=1100.0.
-
-[real, units: m]
-
-
-cdbot_UU
-
-
- U0 in a parameterization of cdbot_roughness_uamp.
- Default is cdbot_UU=1.0.
-
-[real, units: m/s]
-
-
-cdbot_wave
-
-
- For determining bottom drag coefficient using a map of the roughness length
- and the surface wind wave field. The modified drag coefficient is calculated
- following Grant and Mattsen. Likewise this method can be improved using
- more sophisticated wave models including swell.
- Default is cdbot_wave=.false.
-
-[logical]
-
-
-uresidual
-
-
- Residual bottom velocity due to unresolved fluctuations (e.g., waves and tides)
- that contribute to bottom dissipation. Should be set to zero when running
- with explicit representation of tidal forcing and when waves are well resolved.
- Default is uresidual=.05.
-
-[real, units: m/s]
-
-
-uvmag_max
-
-
- Maximum magnitude of the bottom velocity used to compute the bottom
- momentum drag. Default is uvmag_max=10.0.
-
-[real, units: m/s]
-
-
-bmf_max
-
-
- Maximum magnitude of the bottom momentum drag.
- Default is bmf_max=1.0.
-
-[real, units: N/m2]
-
-
-debug_this_module
-
-
- For debugging purposes.
-
-[logical]
-
-
-
-
-
-
-
-
-
-
-
REFERENCES
-
-
-
-
- R.C. Pacanowski and S.M. Griffies
- The MOM3 Manual (1999)
-
-
- S.M. Griffies, M.J. Harrison, R.C. Pacanowski, and A. Rosati
- A Technical Guide to MOM4 (2003)
-
- Compute the Coriolis acceleration for either Bgrid or Cgrid.
-
-
-
-
-
- This module computes Coriolis acceleration on either a Bgrid or Cgrid.
- Coriolis and beta parameters are located at B-grid
- velocity point, which equals the C-grid vorticity point.
-
- Compute thickness and density weighted acceleration due to Coriolis
- force on a B-grid.
-
-
-
-
-
-
-
-
coriolis_force_bgrid_implicit
-
-
-DESCRIPTION
-
-
- Contributions to thickness weighted and density weighted
- acceleration from time-implicit Coriolis force.
-
-
-
-
-
-
-
-
coriolis_force_cgrid
-
-
-DESCRIPTION
-
-
-
- Compute thickness and density weighted acceleration due to Coriolis
- force on a C-grid.
-
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_coriolis_nml
-
-
-
-
-
-debug_this_module
-
-
- For debugging.
-
-[logical]
-
-
-use_this_module
-
-
- Must be true to add contributions from Coriolis force.
-
-[logical]
-
-
-acor
-
-
- acor=0.0 means explicit Coriolis force. 0.5 < = acor < 1.0 means semi-implicit,
- and acor = 1.0 is implicit. This option is only relevant for the Bgrid, since
- the C-grid compute Coriolis using 3rd order Adams-Bashforth scheme. For the Bgrid, the
- semi-implicit method removes dtuv time step constraint associated with inertial oscillations,
- but it leads to Coriolis force affecting energy balances.
- If use two-level tendency discretization, then acor=0 is NOT allowed since the
- model will be linearly unstable with growth rate going as f*(delta time).
-
-[real]
-
-
-
-
-
-
-
-
-
-
-
REFERENCES
-
-
-
-
- R.C. Pacanowski and S.M. Griffies
- The MOM3 Manual (1999)
-
-
- S.M. Griffies, M.J. Harrison, R.C. Pacanowski, and A. Rosati
- A Technical Guide to MOM4 (2003)
-
-
- This module computes the in-situ density and its partial derivatives with
- respect to conservative temperature or potential temperature, and with
- respect to salinity.
-
- There are three basic means for performing this calculation.
-
- A/ Linear equation for use in idealized studies
-
- This equation renders density a linear function of potential
- temperature and salinity. All nonlinearities are ignored, as are
- pressure effects.
-
- The valid range for theta and salinity arbitrary for the
- linear equation of state.
-
- B/ pre-TEOS10 method: this method uses density as a rational
- polynomial function of potential temperature, practical salinity,
- and gauge pressure. There is also an implementation that computes
- density as a function of conservative temperature rather than
- potential temperature. The equation of state is based on that
- documented in Jackett, McDougall, Feistel, Wright, and Griffies(2006).
-
- This equation of state is valid over a "cone-shaped" range
- corresponding to
-
- 0psu <= salinity <= 40 psu
-
- -3C <= theta <= 40C "theta" = either conservative or potential temp
-
- 0dbar <= pressure <= 8000dbar
-
- with the cone getting smaller in the deeper ocean where
- theta and salinity vary over a smaller range.
-
- Input variables are the following:
-
- --salinity in psu or g/kg
- --conservative temperature or potential temperature (theta) in deg C
- --pressure in dbars (1bar = 10dbar = 10^5 Newton/m^2 = 10^5 Pascals).
-
- Note that in the ocean, pressure increases roughly by 1dbar for each meter depth.
- Also note that pressure is the "sea pressure", which is the absolute pressure
- minus the pressure of a standard atmosphere, which is 10.1325 dbars.
-
- check values
-
- for "theta" = conservative temperature
- rho(s=20psu,theta=20C,p=1000dbar) = 1017.842890411975 (kg/m^3)
- alpha(s=20psu,theta=20C,p=1000dbar) = 2.436057013634649e-4 (1/C)
- beta(s=20psu,theta=20C,p=1000dbar) = 7.314818108935248e-4 (1/psu)
-
- for "theta" = potential temperature
- rho(s=20psu,theta=20C,p=1000dbar) = 1017.728868019642 (kg/m^3)
- alpha(s=20psu,theta=20C,p=1000dbar) = 2.525481286927133e-4 (1/C)
- beta(s=20psu,theta=20C,p=1000dbar) = 7.379638527217575e-4 (1/psu)
-
- This equation of state should be suitable for purposes of realistic
- global ocean climate modeling.
-
- C/ TEOS10 method: this method makes use of the recommendations from
- the SCOR working group on seawater thermodynamics, 2010. Here, density
- is a function of conservative temperature and absolute salinity.
- The equation is valid from 0 g/kg salinty to a very large value.
-
-
-
- Initialize the EOS coefficients, and write some test values.
-
-
-
-
-
-
-
-
ocean_density_diag
-
-
-DESCRIPTION
-
-
- Diagnostic ocean density fields: neutral density and potential density.
- Also send some diagnostics to diagnostic manager.
-
-
-
-
-
-
-
-
update_ocean_density_salinity
-
-
-DESCRIPTION
-
-
-
- If TEOS-10 is being used then we need to multiply Preformed Salinity and the
- Salinity factor to obtain absolute salinity for use in the TEOS10 EOS.
-
- If not using TEOS10 EOS, then copy the practical salinity into the
- density_salinity field for use in the preTEOS10 EOS or the linear EOS.
-
- Note that halo values are not generally valid for taup1 until the halos
- for index_salt and index_Fdelta have been updated inside of ocean_model.F90.
-
-
-
-
-
-
-
-
-
update_ocean_density
-
-
-DESCRIPTION
-
-
- Diagnose pressure_at_depth and ocean density.
- Also send some diagnostics to diagnostic manager.
-
-
-
-
-
-
-
-
density_field
-
-
-DESCRIPTION
-
-
- Compute density for all grid points.
-
- Note that pressure here is
-
- sea pressure = absolute pressure - press_standard (dbars)
-
- and salinity is in model units (psu or g/kg).
-
-
-
-
-
-
-
-
-
density_level
-
-
-DESCRIPTION
-
-
- Compute density at a particular k-level.
-
- Note that pressure here is
-
- sea pressure = absolute pressure - press_standard (dbars)
-
-
-
-
-
-
-
-
-
density_line
-
-
-DESCRIPTION
-
-
- Compute density at a particular k-level and j index. This scheme
- is used in the vectorized version of the full convection scheme.
-
- Note that pressure here is
-
- sea pressure = absolute pressure - press_standard
-
-
-
-
-
-
-
-
-
neutral_density_field
-
-
-DESCRIPTION
-
-
- Compute neutral density for use in various layer diagnostics.
-
- Two options are presently available:
-
- A/ use rational polynomial (to be done)
-
- B/ use potential density referenced to pressure potrho_press
- McDougall recommends potential density referenced to 2000dbar,
- since the rational polynomial is not too good.
-
- Note that presently, the rational polynomial method defaults to
- potential density referenced to 2000dbar.
- The polynomial approximation from McDougall and Jackett (2005)
- is not recommended (as per Trevor McDougall, 2011). A new polynomial
- is being constructed and should be ready end of 2011.
-
-
-
-
-
-
-
-
-
neutral_density_point
-
-
-DESCRIPTION
-
-
- Compute neutral density for use in various layer diagnostics.
-
- Only test here the rational polynomial
- approximation given by McDougall and Jackett (2005).
- This test needs to be updated.
-
-
-
-
-
-
-
-
-
potential_density
-
-
-DESCRIPTION
-
-
- Compute potential density referenced to some given sea pressure.
-
- Note that potential density referenced to the surface (i.e., sigma_0)
- has a zero sea pressure, so pressure=0.0 should be the argument
- to the function.
-
- Note that pressure here is
- sea pressure = absolute pressure - press_standard (dbars)
-
- input pressure < 0 is an error, and model is brought down.
-
-
-
-
-
-
-
-
-
compute_density_diagnostics
-
-
-DESCRIPTION
-
-
- Diagnostics related to density.
-
-
-
-
-
-
-
-
compute_diagnostic_factors
-
-
-DESCRIPTION
-
-
-
- 1/ Compute ratio |grad neutral rho| / |grad local ref pot rho|
- for use in tform water mass analysis as per Iudicone et al. (2008).
-
- 2/ Compute rho*Area(h)/gamma_h, where "h" is the direction where
- gamma has the largest stratification, and where gamma is the
- locally referenced potential density.
-
-
-
-
-
-
-
-
-
density_sfc
-
-
-DESCRIPTION
-
-
- Compute density as a function of surface salinity, surface theta,
- and in situ sea pressure.
-
- Note that pressure here is
- sea pressure = absolute pressure - press_standard (dbars)
-
- For use in KPP mixed layer scheme
-
-
-
-
-
-
-
-
density_point
-
-
-DESCRIPTION
-
-
- Compute density at a single model grid point.
-
- Note that pressure here is
-
- sea pressure = absolute pressure - press_standard (dbars)
-
-
-
-
-
-
-
-
-
density_derivs_field
-
-
-DESCRIPTION
-
-
- Compute partial derivative of density with respect to
- temperature and with respect to salinity. Hold pressure constant.
-
- Pressure here is
-
- sea pressure = absolute press - press_standard (dbars)
-
-
-
-
-
-
-
-
-
density_derivs_level
-
-
-DESCRIPTION
-
-
- Compute partial derivative of density with respect to
- temperature and with respect to salinity. Hold pressure constant.
-
- Pressure here is sea pressure = absolute press - press_standard
-
-
-
-
-
-
-
-
-
density_derivs_point
-
-
-DESCRIPTION
-
-
- Compute partial derivative of density with respect to
- temperature and with respect to salinity. Do so here for a point.
-
- Pressure here is
-
- sea pressure = absolute pressure - press_standard (dbars)
-
-
-
-
-
-
-
-
-
cabbeling_thermobaricity
-
-
-DESCRIPTION
-
-
- Diagnostic sends for cabbeling and thermobaricity parameters.
-
- Pressure here is
- sea pressure = absolute press - press_standard (dbars)
-
-
-
-
-
-
-
-
-
calc_cabbeling_thermobaricity
-
-
-DESCRIPTION
-
-
- Compute cabbeling and thermobaricity parameters, as defined in
- McDougall (1987).
-
- Pressure here is
- sea pressure = absolute press - press_standard (dbars)
-
-
-
-
-
-
-
-
-
density_delta_z
-
-
-DESCRIPTION
-
-
- rho(k)-rho(k+1) for all i,j with both temperatures referenced to the
- deeper pressure depth.
-
- Of use for KPP scheme.
-
-
-
-
-
-
-
-
density_delta_sfc
-
-
-DESCRIPTION
-
-
- rho(1)-rho(k+1) for all i,j.
-
- Of use for KPP scheme.
-
-
-
-
-
-
-
-
ocean_density_end
-
-
-DESCRIPTION
-
-
-
- Write density and pressure_at_depth to a restart.
-
-
-
-
-
-
-
-
-
ocean_density_restart
-
-
-DESCRIPTION
-
-
- Write out restart files registered through register_restart_file
-
-
-
-
-
-
-
-
ocean_density_chksum
-
-
-DESCRIPTION
-
-
- Compute checksums for density.
-
-
-
-
-
-
-
-
compute_buoyfreq
-
-
-DESCRIPTION
-
-
-
- Diagnose the buoyancy frequency, both at T-points and at
- vertical interfaces of T-cells.
-
- Author: Stephen.Griffies
-
-
-
-
-
-
-
-
-
buoyfreq2
-
-
-DESCRIPTION
-
-
-
- Diagnose the square of the buoyancy frequency at the bottom of
- T-cells, NOT at T-points.
- The algorithm follows that used by the private function
- compute_buoyfreq in the density module.
-
- We take the square of the buoyancy frequency as is, we do not
- smooth or force it to be positive. This allows us to search for
- instabilities.
-
- Authors: m.bates
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_density_nml
-
-
-
-
-
-write_a_restart
-
-
- Set true to write a restart. False setting only for rare
- cases where wish to benchmark model without measuring the cost
- of writing restarts and associated chksums.
- Default is write_a_restart=.true.
-
-[logical]
-
-
-press_standard
-
-
- Standard atmospheric pressure (dbar). The realistic
- EOS used in MOM requires "sea pressure" as an argument
- rather than absolute pressure. Sea pressure is
- absolute pressure minus a standard atmospheric pressure
- of 10.1325dbar.
-
- For models that do have a realistic atmospheric loading, then it
- is appropriate to remove 10.1325dbar prior to computing the EOS.
- For those cases with zero atmospheric pressure, then it is not
- necessary to remove the standard atmosphere. The default for the
- press_standard is 0.0dbar.
-
-[real, units: dbar]
-
-
-t_test
-
-
- Conservative temperature or potential temperature for
- testing the EOS.
-
-[real, units: C]
-
-
-s_test
-
-
- Salinity for testing the EOS.
-
-[real, units: psu or g/kg]
-
-
-p_test
-
-
- Sea pressure for testing the EOS.
-
-[real, units: dbar]
-
-
-tn_test
-
-
- Conservative temperature or potential temperature for
- testing the equation for neutral density.
-
-[real, units: C]
-
-
-sn_test
-
-
- Salinity the equation for neutral density.
-
-[real, units: psu or g/kg]
-
-
-eos_teos10
-
-
- Set to true to use TEOS-10 equation of state, which
- is a function of conservative temperature and absolute
- salinity.
- Default eos_teos10=.false.
-
-[logical]
-
-
-eos_preteos10
-
-
- Set to true to use pre-TEOS-10 equation of state, which
- is a function of potential temperature and practical salinity,
- or conservative temperature and practical salinity.
- Default eos_preteos10=.false.
-
-[logical]
-
-
-eos_linear
-
-
- Set to true to use an idealized linear equation of state, which
- has no pressure dependence, and is a linear function of salinity
- and temperature.
- Default eos_linear=.false.
-
-[logical]
-
-
-alpha_linear_eos
-
-
- Constant "thermal expansion coefficient" for linear EOS
- rho = rho0 - alpha_linear_eos*theta + beta_linear_eos*salinity
-
-[real]
-
-
-beta_linear_eos
-
-
- Constant "saline contraction coefficient" for linear EOS
- rho = rho0 - alpha_linear_eos*theta + beta_linear_eos*salinity
-
-[real]
-
-
-potrho_press
-
-
- Reference sea pressure for computing diagnostic potential density
- of use for computing diagnostics with potential density.
- Default potrho_press=2000.0
-
-[real, units: dbar]
-
-
-potrho_min
-
-
- Minimum potential density used to partition vertical according
- to potential density.
-
-[real, units: kg/m^3]
-
-
-potrho_max
-
-
- Maximum potential density used to partition vertical according
- to potential density.
-
-[real, units: kg/m^3]
-
-
-neutral_density_omega
-
-
- Set to true to compute the neutral density according to
- the omega method based on Klocker and McDougall.
- This approach has not yet been coded. Presently as a
- placeholder we use potential density referenced to 2000dbar.
- Default neutral_density_omega=.false.
-
-[logical]
-
-
-neutral_density_potrho
-
-
- Set to true to compute the neutral density as just
- a selected potential density, set according to potrho_press.
- Since the neutral_density_omega approach has yet to be coded,
- we only have the neutral_density_potrho option to choose from
- at this time.
- Default neutral_density_potrho=.true.
-
-[logical]
-
-
-neutralrho_min
-
-
- Minimum neutral density used to partition vertical according
- to rational polynomial approximation to neutral density.
-
-[real, units: kg/m^3]
-
-
-neutralrho_max
-
-
- Maximum neutral density used to partition vertical according
- to rational polynomial approximation to neutral density.
-
-[real, units: kg/m^3]
-
-
-theta_min
-
-
- Minimum conservative temperature or potential temperature used to
- partition vertical according to temperature.
-
-[real, units: C]
-
-
-theta_max
-
-
- Maximum conservative temperature or potential temperature used to
- partition vertical according to temperature.
-
-[real, units: C]
-
-
-layer_nk
-
-
- Number of classes used to partition vertical according to potential density,
- conservative temperature, or potential temperature. Used for diagnostics.
-
-[integer]
-
-
-buoyfreq_smooth_vert
-
-
- To smooth the vertical temp and salt derivative for diagnosing
- the buoyancy frequency. Default buoyfreq_smooth_vert=.true.
-
-[logical]
-
-
-epsln_drhodz
-
-
- To normalize the inverse vertical derivative of neutral density
- for computing the buoyancy frequency. Default epsln_drhodz=1e-10.
-
-[real, units: kg/m4]
-
-
-epsln_drhodz_diag
-
-
- To normalize the inverse vertical derivative of neutral density
- for computing neutral_rho and wdian diagnostics.
- Default epsln_drhodz_diag=1e-10.
-
-[real, units: kg/m4]
-
-
-smax_diag
-
-
- A diagnostic maximum neutral slope for use in computing which direction
- is deemed the most stratified. For use in computing the stratification_factor
- which is then used to diagnose the dianeutral mass transport.
- smax_diag should corresond to the choice used in neutral diffusion scheme.
- Should have 0 <= smax_diag <= 1.0.
- Default smax_diag=-1.0, in which case we compute the smax according to
- the vertical to horizontal grid aspect ratio. This method ensures that
- the slope is adequately "resolved" by the grid.
-
-[real, units: dimensionless]
-
-
-smax_min_in_column
-
-
- To compute the diagnostic maximum neutral slope within a column as the minimum
- vertical to horizontal grid aspect ratio. This method ensures that
- the slope is adequately "resolved" by the grid, and that all depths use the
- same definition of "resolved", even if presumably thicker grid cells can
- "resolve" larger neutral slopes. This approach is not very useful generally,
- so it is retained only for testing purposes.
- Default smax_min_in_column=.false.
-
-[logical]
-
-
-mask_domain_restart
-
-
- For cases where use the domain masking, it is necessary to initialize the field
- denominator_r to nonzero in order to avoid NaNs in the case when change processor
- layout in between restarts. Note that when use solid wall boundary conditions,
- this logical should remain false in order to bitwise reproduce across restarts.
- Default mask_domain_restart=.false.
-
-[logical]
-
-
-drhodz_diag_stable
-
-
- When computing drhodz_diag, we can enforce that it is negative,
- thus reflecting a stable stratification. The field drhodz_diag
- is used for many water mass transformation diagnostics, such as
- wdian_rho. Allowing for unstable profiles can bias the wdian_rho
- calculation in an improper way, since the magnitude of drhodz_diag
- is very small when it is positive, whereas it is larger magnitude when
- negative. Default drhodz_diag_stable=.true.
-
-[logical]
-
-
-grad_nrho_lrpotrho_compute
-
-
- To perform the diagnostic calculation of grad_nrho_lrpotrho
- for analysis diagnostics. This factor is not well constrained,
- and can be problematic in certain regions. So presently we do
- not recommend computing it, so that the default
- is grad_nrho_lrpotrho_compute=.false.
-
-[logical]
-
-
-grad_nrho_lrpotrho_max
-
-
- Maximum value used for grad_nrho_lrpotrho.
- Default grad_nrho_lrpotrho_max=10.
-
-[real, units: dimensionless]
-
-
-grad_nrho_lrpotrho_min
-
-
- Minimum value used for grad_nrho_lrpotrho.
- Default grad_nrho_lrpotrho_min=1.
-
-[real, units: dimensionless]
-
-
-smooth_stratification_factor
-
-
- For doing an S2D smoothing of the stratification factor used
- for diagnostic purposes. Requires an extra call to mpp update.
- Default smooth_stratification_factor=.false. since the smoothing
- incurs a cost that should be borne only when desired.
-
-[logical]
-
-
-update_diagnostic_factors
-
-
- To update the watermass_factor and stratification_factor
- for use in the water mass transformation diagnostics.
- Default update_diagnostic_factors=.false.
-
-[logical]
-
-
-debug_this_module
-
-
- For debugging nonlinear equation of state
-
-[logical]
-
-
-rho0_density
-
-
- For debugging, it is often useful to have rho=rho0 uniform.
-
-[logical]
-
-
-density_equal_potrho
-
-
- For idealized tests, set the in situ density equal to the
- potential density referenced to potrho_press. All density
- derivatives will also be computed with respect to constant
- potrho_press pressure.
- Default density_equal_potrho=.false.
-
-[logical]
-
-
-do_bitwise_exact_sum
-
-
- Set true to do bitwise exact global sum. When it is false, the global
- sum will be non-bitwise_exact, but will significantly increase
- efficiency.
- default: do_bitwise_exact_sum=.false.
-
-[logical]
-
-
-
-
-
-
-
-
-
-
-
REFERENCES
-
-
-
-
- McDougall T.J., P.M. Barker, R. Feistel and D.R. Jackett, 2011: A
- computationally efficient 48-term expression for the density of
- seawater in terms of Conservative Temperature, and related properties
- of seawater. To be submitted to Ocean Science.
-
-
- IOC, SCOR and IAPSO, 2010: The international thermodynamic equation of
- seawater 2010: Calculation and use of thermodynamic properties.
- Intergovernmental Oceanographic Commission, Manuals and Guides No.
- 56, UNESCO (English), 196 pp.
-
-
- D. Iudicone, G. Madec, and T.J. McDougall (2008)
- Water-mass transformations in a neutral density framework and the
- key role of light penetration. JPO vol 38, pages 1357-1376.
-
-
- Jackett, McDougall, Feistel, Wright, and Griffies (2006)
- Algorithms for density, potential temperature, conservative
- temperature, and freezing temperature of seawater.
- Journal of Atmospheric and Oceanic Technology, 2006,
- volume 23, pages 1709-1728.
-
-
- McDougall and Jackett (2005)
- The material derivative of neutral density
- Journal of Marine Research, vol 63, pages 159-185.
-
-
- Feistel (2003), A new extended Gibbs thermodynamic potential
- of seawater. Progress in Oceanography. vol 58, pages 43-114.
-
-
- S.M. Griffies, M.J. Harrison, R.C. Pacanowski, and A. Rosati
- A Technical Guide to MOM4 (2003)
-
-
- S.M. Griffies, R.C. Pacanowski, R.M. Schmidt, and V. Balaji
- Tracer Conservation with an Explicit Free Surface Method for
- Z-coordinate Ocean Models
- Monthly Weather Review (2001) vol 129 pages 1081--1098
-
-
- T. McDougall (1987)
- Cabbeling, Thermobaricity, and water mass conversion
- JGR vol 92, pages 5448-5464
-
-
-
-
-
-
-
-
NOTES
-
-
-
- Density is computed as a function of conservative temperature (degC)
- or potential temperature (degC), salinity (psu or g/kg), and pressure (dbar).
- The pressure contribution includes that from the free surface height
- and the applied atmospheric and/or sea ice pressure. However, it is referenced
- to standard atmosphere, so that we use the "gauge" pressure rather than the
- full in-situ pressure.
-
- For vert_coordinate==GEOPOTENTIAL, ZSTAR, or ZSIGMA, baroclinic component of
- hydrostatic pressure is not known until density is known. In this case,
- the baroclinic pressure contribution to density is lagged by a time step.
- rho(tau) = rho[theta(tau),s(tau), p_atm(tau) + p_fs(tau) + p_baroclinic(tau-1)].
- This issue does not arise when using vert_coordinate=PRESSURE, PSTAR, or PSIGMA.
-
-
- For setting the ocean domain layout and associated parameters.
-
-
-
-
-
-
-
-
get_local_indices
-
-
-DESCRIPTION
-
-
- For getting local indices from domain derived type.
-
-
-
-
-
-
-
-
get_domain_offsets
-
-
-DESCRIPTION
-
-
- For getting domain offsets from domain derived type.
-
-
-
-
-
-
-
-
get_active_indices
-
-
-DESCRIPTION
-
-
- For getting active domain indices from domain derived type.
-
-
-
-
-
-
-
-
get_global_indices
-
-
-DESCRIPTION
-
-
- For getting global indices from domain derived type.
-
-
-
-
-
-
-
-
reduce_active_domain
-
-
-DESCRIPTION
-
-
- For getting reducing the active domain
-
-
-
-
-
-
-
-
get_halo_sizes
-
-
-DESCRIPTION
-
-
- For getting halo sizes from domain derived type.
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_domains_nml
-
-
-
-
-
-halo
-
-
- For specifying the halo size by hand.
-
-[integer, units: dimensionless]
-
-
-max_tracers
-
-
- temporary - need to call domains_init before tracer_init
- Used for computing mpp_stack_size.
-
-[integer, units: dimensionless]
-
-
-x_cyclic_offset
-
-
- offset to be applied on x-direction boundary condition. Its value could
- be positive or negative and the default value is 0. When the y-direction
- boundary condition is folded-north(tripolar grid), x_cyclic_offset must
- be 0. For torus (cyclic in x and y-direction), at least one of
- x_cyclic_offset and y_cyclic_offset must be 0.
-
-[integer, units: dimensionless]
-
-
-y_cyclic_offset
-
-
- offset to be applied on y-direction boundary condition. Its value could
- be positive or negative and the default value is 0. For torus (cyclic
- in x and y-direction), at least one of x_cyclic_offset and
- y_cyclic_offset must be 0.
-
-[integer, units: dimensionless]
-
-
-
-
-
-
-
-
-
-
-
REFERENCES
-
-
-
-
- S.M. Griffies, M.J. Harrison, R.C. Pacanowski, and A. Rosati
- A Technical Guide to MOM4 (2003)
-
- This module sets up the ocean model grid based on information read in
- from the grid_spec.nc file. It translates the generic names from the
- grid_spec.nc file to the names used by MOM.
-
- Set the ocean grid size. Model expects the grid specification file
- to be called grid_spec.nc.
-
-
-
-
-
-
-
-
set_ocean_hgrid_arrays
-
-
-DESCRIPTION
-
-
- Define horizontal (and some vertical) grid arrays.
-
----------------------------------------------------------------------------------------------------------------------
- Grid% grid_spec grid_spec grid_spec Description
- var field field field
- VERSION_0 VERSION_1 VERSION_2(mosaic)
----------------------------------------------------------------------------------------------------------------------
- ocean_vgrid.nc
- k=1,nk
- zt zt zt zeta(2k-1)
- zw zw zb zeta(2k)
-
- ocean_hgrid.nc
- i=1,ni
- j=1,nj
- grid_x_t gridlon_t grid_x_T x(2i ,2)
- grid_x_u gridlon_vert_t grid_x_C x(2i+1,1)
- grid_y_t gridlat_t grid_y_T y(ni/4,2j)
- grid_y_u gridlat_vert_t grid_y_C y(ni/4,2j+1)
-
-T
- xt(i,j) geolon_t(i,j) x_T(i,j) x(2i,2j)
- yt geolat_t y_T y(2i,2j)
- dtw dtw ds_01_11_T dx(2i-1,2j) distance to western face of t cell
- dte dte ds_11_21_T dx(2i,2j) distance to eastern face of t cell
- dts dts ds_10_11_T dy(2i,2j-1) distance to southern face of t cell
- dtn dtn ds_11_12_T dy(2i,2j) distance to northern face of t cell
-
- dxt dxt ds_01_21_T dx(2i,2j) +dx(2i-1,2j) width of t cell
- dxtn dxtn ds_02_22_T dx(2i-1,2j+1)+dx(2i,2j+1) width of northern face of t cell
- dxte dxte ds_00_20_C dx(2i,2j) +dx(2i+1,2j) distance to adjacent t cell to the east!
- dyt dyt ds_10_12_T dy(2i,2j) +dy(2i,2j-1) height of t cell
- dytn dytn ds_00_02_C dy(2i,2j) +dy(2i,2j+1) distance to adjacent t cell to the north!
- dyte dyte ds_20_22_T dy(2i+1,2j-1)+dy(2i+1,2j) height of eastern face of t cell
-
-C
- NOTE: The "first" (I,J) C-cell is the one shifted NE of the "first" (I,J) T-cell
-
-
- xu geolon_c x_C x(2i+1,2j+1)
- yu geolat_c y_c y(2i+1,2j+1)
- dxu dxu ds_01_21_C dx(2i+1,2j+1)+dx(2i,2j+1) width of u cell
- dxun dxun ds_02_22_C dx(2i,2j+2)+dx(2i+1,2j+2) width of northern face of u cell
- dyu dyu ds_10_12_C dy(2i+1,2j+1)+dy(2i+1,2j) height of u cell
- dyue dyue ds_20_22_C dy(2i+2,2j)+dy(2i+2,2j+1) height of eastern face of u cell
-
- dyun dyun ds_11_12_C dy(2i+1,2j+1)+dy(2i+1,2j+2) distance to adjacent u cell to the north
- +ds_10_11_C(i,j+1) satisfies sum rule dyte(i,j)=dyun(i,j-1)
- dxue dxue ds_11_21_C dx(2i+1,2j+1)+dx(2i+2,2j+1) distance to adjacent u cell to the east!
- +ds_01_11_C(i+1,j)
-
- duw duw ds_01_11_C dx(2i,2j+1) distance to western face of u cell
- due due ds_11_21_C dx(2i+1,2j+1) distance to eastern face of u cell
- dus dus ds_10_11_C dy(2i+1,2j) distance to southern face of u cell
- dun dun ds_11_12_C dy(2i+1,2j+1) distance to northern face of u cell
-
- sin_rot sin_rot angle_C sin(angle_dx(2*i+1,2*j+1) sin of rotation angle at corner cell centers
- cos_rot cos_rot angle_C cos(angle_dx(2*i+1,2*j+1) cos of rotation angle at corner cell centers
-
-Following are the available fields in mosaic files
---------------------------------------------------------
-Mosaic file fields
---------------------------------------------------------
-ocean_hgrid.nc x, y, dx, dy, angle_dx, area
-ocean_vgrid.nc zeta
-topog.nc depth
-
-
-
-
-
-
-
-
-
set_ocean_vgrid_arrays
-
-
-DESCRIPTION
-
-
- Compute vertical (and some horizontal) grids for ocean model.
- Also compute axes information for diagnostic manager.
-
-
-
-
-
-
-
-
axes_info
-
-
-DESCRIPTION
-
-
- Set up axes definitions.
-
-
-
-
-
-
-
-
update_boundaries
-
-
-DESCRIPTION
-
-
- Set halo points at model boundaries equal to values at boundaries
- if no grid connectivity exists. If model is connected along
- boundary (e.g., tripolar) then use mpp_update_domains.
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_grids_nml
-
-
-
-
-
-read_rho0_profile
-
-
- To read in an initial rho0(k) profile to assist in defining the
- initial settings for the pressure increments dst, for use in
- setting the pressure-based vertical coordinate grids. Ideally,
- this profile is determined by the level averaged density in
- the initial conditions. Note that it is essential to have
- rho0_profile have a sensible value at all depths even if there
- is no water there, since there are places where we divide by
- rho0_profile in rock. Also, be mindful that with denser water
- at depth, the pressure levels will be coarser at depth than if
- using the trivial density profile rho0(k)=rho0.
- This option is experimental, so it is recommended that user
- maintain the default read_rho0_profile=.false.
-
-[logical]
-
-
-do_bitwise_exact_sum
-
-
- Set true to do bitwise exact global sum. When it is false, the global
- sum will be non-bitwise_exact, but will significantly increase efficiency.
- The default value is do_bitwise_exact_sum=.false.
-
-[logical]
-
-
-debug_this_module
-
-
- For debugging. Note that most of the debugging stuff
- has been removed, but keep flag around in case need in future.
-
-[logical]
-
-
-verbose_init
-
-
- Prints out lots of initial checksums. Useful to have on, so
- defaulted to true.
-
-[logical]
-
-
-
-
-
-
-
-
-
-
-
REFERENCES
-
-
-
-
- S.M. Griffies, M.J. Harrison, A. Rosati, and R.C. Pacanowski
- A Technical Guide to MOM4 (2003)
-
- Time step the ocean model using either a twolevel staggered scheme
- (the default) or threelevel leap-frog scheme (the older approach).
- Threelevel scheme remains only for legacy purposes and is not
- recommended for normal use.
-
-
-
-
-
- Top level module for ocean model. Contains routines for
- initialization, termination, and update of ocean model state.
-
- Design consideration: declarations of top level ocean variables
- are private to this module and hence are only available to other routines
- through argument lists. For instance, timestep information is passed to
- the various modules on the initialization call and stored internally
- in the respective modules. This is a crucial design consideration sinces
- it maintains modularity and hence maintainability of the code.
-
- Initialize the ocean model.
- Arguments:
- Ocean (inout) - A structure containing various publicly visible ocean
- surface properties after initialization.
- OS (pointer)- A structure whose internal contents are private
- to ocean_model_mod that may be used to contain all
- information about the ocean's interior state.
- Time_init (in) - The start time for the coupled model's calendar.
- Time_in (in) - The time at which to initialize the ocean model.
-
-
-
-
-
-
-
-
update_ocean_model
-
-
-DESCRIPTION
-
-
- Update in time the ocean model fields.
- This subroutine uses the forcing in Ice_ocean_boundary to advance the
- ocean model's state from the input value of Ocean_state (which must be for
- time time_start_update) for a time interval of Ocean_coupling_time_step,
- returning the publicly visible ocean surface properties in Ocean_sfc and
- storing the new ocean properties in Ocean_state.
-
- Arguments:
- Ice_ocean_boundary - A structure containing the various forcing
- fields coming from the ice. It is intent in.
- Ocean_state - A structure containing the internal ocean state.
- Ocean_sfc - A structure containing all the publicly visible ocean
- surface fields after a coupling time step.
- time_start_update - The time at the beginning of the update step.
- Ocean_coupling_time_step - The amount of time over which to advance
- the ocean.
- Note: although several types are declared intent(inout), this is to allow for
- the possibility of halo updates and to keep previously allocated memory.
- In practice, Ice_ocean_boundary is intent in, Ocean_state is private to
- this module and intent inout, and Ocean_sfc is intent out.
-
-
-
-
-
-
-
-
get_ocean_grid_size
-
-
-DESCRIPTION
-
-
- Obtain the ocean grid size.
-
-
-
-
-
-
-
-
get_ocean_domain
-
-
-DESCRIPTION
-
-
- Obtain the ocean domain size.
-
-
-
-
-
-
-
-
ocean_model_init_sfc
-
-
-DESCRIPTION
-
-
- Call ocean_tpm_init_sfc and pass it the needed arguments, most of which
- are local to the ocean model.
-
-
-
-
-
-
-
-
ocean_model_flux_init
-
-
-DESCRIPTION
-
-
- Call ocean_tpm_flux_init and pass it the needed arguments, most of which
- are local to the ocean model.
-
- Currently, no arguments are passed.
-
-
-
-
-
-
-
-
ocean_model_end
-
-
-DESCRIPTION
-
-
- Close down the ocean model
- This subroutine terminates the model run, saving the ocean state in a
- restart file and deallocating any data associated with the ocean.
-
- NOTE from nnz: This module keeps its own Time and does not need the Time_in argument.
- Arguments:
- Ocean_state (type(ocean_state_type), pointer) - A structure containing the internal ocean state.
- Time_in (type(time_type), intent(in)) - The model time, used for writing restarts.
- Ocean_sfc (type(ocean_public_type), optional, intent(inout))- An ocean_public_type structure that is to be
- deallocated upon termination.
-
-
-
-
-
-
-
-
ocean_model_restart
-
-
-DESCRIPTION
-
-
- write out restart file.
-
-
-
-
-
-
-
-
ocean_stock_pe
-
-
-DESCRIPTION
-
-
- Returns stocks of total ocean heat and water water for conservation
- checks. Report here values just on a single PE. Global sums
- are done in the coupler.
-
- This routine is part of a group of similar routines in other
- FMS component models that aims to quantify the conservation of
- scalar properties between the component models when running
- coupled models.
-
-
-
-
-
-
-
-
-
mom4_get_Tsurf
-
-
-DESCRIPTION
-
-
- Return the surface temperature in degrees K
-
-
-
-
-
-
-
-
mom4_get_Ssurf
-
-
-DESCRIPTION
-
-
- Return the surface salinity in psu
-
-
-
-
-
-
-
-
mom4_get_thickness
-
-
-DESCRIPTION
-
-
- Return thickness (in meters) of each layer.
-
-
-
-
-
-
-
-
mom4_get_density
-
-
-DESCRIPTION
-
-
- Return density (in kg/m^3).
-
-
-
-
-
-
-
-
mom4_get_prog_tracer
-
-
-DESCRIPTION
-
-
- Return prognostic tracer data.
-
-
-
-
-
-
-
-
mom4_get_temperature_index
-
-
-DESCRIPTION
-
-
- Return temperature index from prognostic tracer table, which can
- then be used to extract data.
-
-
-
-
-
-
-
-
mom4_get_salinity_index
-
-
-DESCRIPTION
-
-
- Return salt index from prognostic tracer table, which can
- then be used to extract data.
-
-
-
-
-
-
-
-
mom4_get_dimensions
-
-
-DESCRIPTION
-
-
- Return dimensions of data in compute domain
-
-
-
-
-
-
-
-
mom4_get_UVsurf
-
-
-DESCRIPTION
-
-
- Return horizontal velocity vector components (u,v) on the
- A grid (tracer-points).
-
- Note that these velocity components are oriented according to the
- grid lines (i-lines and j-lines). They are generally NOT mapped
- to latitude-longitude lines, unless using a spherical coordinate
- grid specification.
-
-
-
-
-
-
-
-
mom4_get_UV
-
-
-DESCRIPTION
-
-
- Return horizontal velocity vector (u,v) (in m/s) on T points (A mesh).
-
- Note that these velocity components are oriented according to the
- grid lines (i-lines and j-lines). They are generally NOT mapped
- to latitude-longitude lines, unless using a spherical coordinate
- grid specification.
-
-
-
-
-
-
-
-
mom4_U_to_T_2d
-
-
-DESCRIPTION
-
-
- Interpolate (u,v) velocity components from U (B-grid) to
- T points (A-grid).
-
-
-
-
-
-
-
-
mom4_get_latlon_UV
-
use ocean_model_mod real, dimension(isc:, jsc:, :) :: u,v integer :: ierr call mom4_get_latlon_UV (ua, va, ierr)
- array will contain velocity component along x direction upon return
- [real, dimension(isc:, jsc:, :)]
-
-
-
va
- array will contain velocity component along y direction upon return
- [real, dimension(isc:, jsc:, :)]
-
-
-
ierr
- error status will be zero for success and nonzero for failure
- [ineger]
-
-
-
-
-
-
-
-
-
mom4_get_diag_axes
-
-
-DESCRIPTION
-
-
- Return axes indices for diag manager.
-
-
-
-
-
-
-
-
mom4_get_num_diag_tracers
-
use ocean_model_mod mom4_get_num_diag_tracers ()
-
-
-DESCRIPTION
-
-
- This function returns the number of ocean diagnostic tracers if not -1.
- It send a FATAL message if num_diag_tracers is not set (i.e. is -1)
- before this function call.
-
-
-
-
-INPUT
-
-
-
-
-
- No inputs needed.
- []
-
-
-
-
-
-OUTPUT
-
-
-
-
-
- This function returns an integer.
- [integer]
-
-
-
-
-
-
-
-
-
mom4_get_num_prog_tracers
-
use ocean_model_mod mom4_get_num_prog_tracers ()
-
-
-DESCRIPTION
-
-
- This function returns the number of ocean prognostic tracers if not -1.
- It send a FATAL message if num_prog_tracers is not set (i.e. is -1)
- before this function call.
-
-
-
-
-INPUT
-
-
-
-
-
- No inputs needed.
- []
-
-
-
-
-
-OUTPUT
-
-
-
-
-
- This function returns an integer.
- [integer]
-
-
-
-
-
-
-
-
-
mom4_get_surface_tmask
-
use ocean_model_mod real, dimension(:,:), pointer :: temp call mom4_get_surface_tmask (temp)
-
-
-DESCRIPTION
-
-
- This subroutine gets the pointer to a 2D array with values of the tmask
- (land/sea mask for T cells based on s-coordinate) at the ocean surface .
-
-
-
-
-OUTPUT
-
-
-
-
-
surfaceTmask
- pointer to 2 dimensional array of tmask at the ocean surface.
- [real, dimension(:,:),pointer]
-
-
-
-
-
-
-
-
-
mom4_get_ocean_data
-
use ocean_model_mod real, dimension(:,:), pointer :: temp call mom4_get_ocean_data (Ocean,'s_surf',temp)
-
-
-DESCRIPTION
-
-
- This subroutine gets one of the following data arrays of ocean_public_type
- depending on the passed "name" argument, it sends a FATAL signal otherwise
- Ocean%t_surf when name='t_surf'
- Ocean%s_surf when name='s_surf'
- Ocean%u_surf when name='u_surf'
- Ocean%v_surf when name='v_surf'
- Ocean%sea_lev when name='sea_lev'
- Ocean%frazil when name='frazil'
-
-
-
-
-INPUT
-
-
-
-
-
Ocean
- ocean type
- [type(ocean_public_type)]
-
-
-
name
- one of 't_surf','s_surf','u_surf','v_surf','sea_lev','frazil'
- [character(len=*)]
-
-
-
-
-
-OUTPUT
-
-
-
-
-
dataArrayPointer
- pointer to 2 dimensional array corresponding to "name" argument, at the ocean surface.
- [real, dimension(:,:), pointer]
-
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_model_nml
-
-
-
-
-
-layout
-
-
- Processor domain layout for ocean model.
-
-[integer]
-
-
-io_layout
-
-
- Processor IO domain layout for ocean model. The default value is (0,0).
- If either io_layout(1) or (2) is 0, it will default to the number of
- processors in the computational layout, except restart file will default
- to single file if fms_io_nml fileset_write is set to 'single'. When
- both entry of io_layout is positive, io_domain will be defined(a pointer in domain2d)
- and number of distributed files will be layout(1)*layout(2). For example, assume
- the restart file is ocean_velocity.res.nc and the diagnostics file is ocean_daily.nc,
- if the layout = (1,2), the restart files will be ocean_velocity.res.nc.0000 and
- ocean_veloicity.res.nc.0001, the diagnostics files will be ocean_daily.res.nc.0000
- and ocean_daily.res.nc.0001. When the io_domain is defined, restart file and
- diagnostics file name will be controlled by the io_domain (ignoring fms_io_nml fileset_write).
-
-[integer, dimension(2)]
-
-
-dt_ocean
-
-
- Ocean model time step in seconds.
-
-[integer, default: -1]
-
-
-time_tendency
-
-
-
- Possible time stepping schemes are the following.
-
- 1. "threelevel" has the following characteristics
-
- leap-frog for the time tendency which means the
- inviscid/nondissipative processes are at time tau.
-
- forward for lateral mixing processes (dissipation at taum1)
-
- implicit for vertical dissipative (with aidif = 1.0)
-
- semi-implicit for Coriolis (with acor>0)
-
- Because of the need to apply time filters to suppress
- leap-frog splitting, the threelevel time stepping scheme
- does not conserve total tracer content in the model.
-
- 2. "twolevel" has the following characteristics:
-
- staggered 2nd order forward time tendency, which means
- that tracer advection, lateral tracer and velocity mixing,
- are at time tau. Pressure gradients are at taup1.
-
- Adams-Bashforth (either 2nd or 3rd order) for velocity advection
- Third order is default as it is more stable.
-
- implicit vertical mixing (with aidif = 1.0)
-
- semi-implicit for Coriolis (with acor > 0)
-
- This scheme conserves total volume and tracer in the ocean model.
-
-
-[character]
-
-
-vertical_coordinate
-
-
- This string determines the vertical coordinate used in MOM.
-
- There are 3 + 3 options in MOM:
- Depth-based Boussinesq are 'geopotential', 'zstar', 'zsigma',
- Pressure-based non-Boussinesq are 'pressure', 'pstar', and 'psigma'.
-
- The two terrain-following sigma options are not well tested in MOM,
- whereas the other options are standard. The recommended Boussinesq
- vertical coordinate is zstar, and the recommended non-Boussineq
- coordinate is pstar. The default is vertical_coordinate='zstar'.
-
-[character]
-
-
-horizontal_grid
-
-
- This string determines the arrangement of variables on the
- discrete horizontal grid. The standard case is horizontal_grid='bgrid'.
- However, the C-grid is being developed in MOM. It is not yet
- supported for general use. Default horizontal_grid='bgrid'.
-
-[character]
-
-
-impose_init_from_restart
-
-
- Consider the following situation: We have run the model for many years
- and generated restarts. Time%init is then .false. Then, we wish to start
- a series of perturbation experiments from this restart file. The generic
- situation is for Time%init to then be .true. However, we need it to be
- .false. in MOM in order to have a proper reading of the full restart
- information. Setting impose_init_from_restart=.true. will facilitate
- this setup. The default is impose_init_from_restart=.false., in which case
- the model will run through its normal start/stop segments using restarts.
-
-[logical]
-
-
-baroclinic_split
-
-
- baroclinic_split = dtts/dtuv
- = (tracer time step)/(baroclinic time step)
- = (ocean model time step)/(baroclinic time step)
- Transients corrupted if baroclinic_split > 1, so it is recommended
- to use baroclinic_split=1.
-
-[integer]
-
-
-barotropic_split
-
-
- Ratio barotropic_split = dtuv/dtbt
- = (baroclinic time step)/(barotropic time step).
- Must be large enough to resolve the barotropic gravity waves
- captured by the barotropic part of the model.
- Barotropic waves are dissipated when this splitting
- is greater than unity. Model algorithm is not fully
- implemented when barotropic_split=1, so user beware
- if wishing to run an unsplit model simulation.
-
-[integer]
-
-
-surface_height_split
-
-
- Ratio surface_height_split = dtts/dteta
- = (tracer time step)/(surface height time step)
- = (tracer time step)/(bottom pressure time step)
- Typically this split is set to unity for models where baroclinic_split=1,
- but something larger when baroclinic_split is order 10. dteta is the time
- step used for update of eta_t or pbot_t. If surface_height_split is
- not equal to unity, then tracer conservation properties are compromised.
-
-[integer]
-
-
-reinitialize_thickness
-
-
- When initialized with a nontrivial eta field, it is
- necessary to reinitialize the thickness arrays.
-
-[logical]
-
-
-cmip_units
-
-
- For CMIP output, we need to have temperature in deg K and
- mass transport in kg/s. The flag cmip_units=.true. will
- diagnose CMIP5-related fields with the CMIP units for sending
- to the diagnostic manager.
- Default cmip_units=.false.
-
-[logical]
-
- For over-riding the velocity field with values from
- a file. Note that we need separate files for
- (u,v) read into ocean_velocity.F90, as well as
- (udrho,vdrho) read into ocean_barotropic.F90.
- Default use_velocity_override=.false.
-
-[logical]
-
-
-debug
-
-
- For overall model debugging. Set true to print cksums at
- each timestep for debugging purposes.
-
-[logical]
-
-
-mask_table
-
-
- A text file to specify n_mask, layout and mask_list. This table
- aims to reduce the number of processors that are cycling over pure
- land regions. These processors will be masked out of regions that
- which contain all land points.
-
- The default file name of mask_table is "INPUT/ocean_mask_table".
- Please note that the file name must begin with "INPUT/".
-
- The first line of mask_table is the number of region to be masked out.
- The second line is the layout of the model. User need to set ocean_model_nml
- variable layout to be the same as the second line of the mask table.
- The following n_mask line will be the position of the processor to be masked out.
-
- The mask_table could be created by tools check_mask.
-
- For example the mask_table will be as following if n_mask=2, layout=4,6 and
- the processor (1,2) and (3,6) are to be masked out.
- 2
- 4,6
- 1,2
- 3,6
-
-[character]
-
- This module can extrapolate data on the open lateral
- boundaries for MOM. Tracer and surface height
- are extrapolated on the boundary by using implicit radiation
- boundary conditions, velocities are calculated on the boundary
- from a linear equation (omitted advection equation). The
- gradient of each field is supposed to be zero between boundary
- points and the first points accross the boundary.
-
- This scheme has been tested only with the following vertical coordinates:
- vertical_coordinate=='geopotential'
- vertical_coordinate=='zstar'
- Notably, there is no OBC prescription for pressure coordinates.
-
-
- enhance viscosity near open boundary. Maximum viscosity for
- stability is set on the boundary, linearly decreasing to the
- interior value at enh_pnts into the interior.
-
- logical variable that decide whether relax eta or not. Default value is .false.
-
-[logical, dimension(max_obc)]
-
-
-obc_consider_convu
-
-
- logical variable that decide whether to account for one
- component of convu within the boundary. The appropriate behavior
- depends on the model configuration.
- Default value is .false.
-
-[logical, dimension(max_obc)]
-
-
-obc_vert_advel_t
-
-
- logical variable that decide whether to account for vertical
- advection of tracers at the boundary. The appropriate behavior
- depends on the model configuration.
- Default value is .false. (Currently inactive)
-
-[logical, dimension(max_obc)]
-
-
-obc_vert_advel_u
-
-
- logical variable that decide whether to account for vertical
- advection of momentum at the boundary. The appropriate behavior
- depends on the model configuration.
- Default value is .false.
-
-[logical, dimension(max_obc)]
-
-
-obc_relax_eta_profile
-
-
- logical variable that decide whether relax eta to a prescribed profile or not.
- Default value is .false. In this case only the average sea level is relaxed,
- the profile, hence the geostrophic current, is unchanged.
-
-[logical, dimension(max_obc)]
-
-
-obc_relax_tracer
-
-
- logical variable that decide whether relax tracer or not. Default value is .false.
-
-[logical, dimension(max_obc)]
-
-
-obc_flow_relax
-
-
- Integer variable specifying the flow relaxation zone
- (flow realxation of Martinsen and Engedahl (1987). Default value is 1.
-
-[integer, dimension(max_obc)]
-
-
-obc_consider_sources
-
-
- Logical variable specifying if source and SGS terms of the normal tracer
- scheme are valid. Default value is .false..
-
-[logical, dimension(max_obc)]
-
-
-obc_tracer_no_inflow
-
-
- logical variable that decide whether apply orlanski obc on tracer or not. Default value is .false.
-
-[logical, dimension(max_obc)]
-
-
-ctrop_max
-
-
- Maximum value to clip diagnosed barotropic phase speed in terms of sqrt(gH).
- Should be about 1.
-
-[real, dimension(max_obc)]
-
-
-ctrop_min
-
-
- Minimum value to diagnosed barotropic phase speed in terms of sqrt(gH).
- Should be about 0. Default is 0.1.
-
-[real, dimension(max_obc)]
-
-
-ctrop_inc
-
-
- value to be set for barotropic phase speed if incoming waves are diagnosed.
- (in terms of sqrt(gH)) Should be about 0. Default is 0.
-
-[real, dimension(max_obc)]
-
-
-rel_coef_eta_in
-
-
- Relaxation coefficient to be used for incoming wave situation.
-
-[real, dimension(max_obc)]
-
-
-rel_coef_eta_out
-
-
- Relaxation coefficient to be used for outgoing wave situation.
- Should be smaller then or equal to rel_coef_eta_in.
-
-[real, dimension(max_obc)]
-
- Relax sea level at a stripe of rel_eta_pnts. Default = 1.
-
-[integer, dimension(max_obc)]
-
-
-rel_coef_tracer_in
-
-
- Relaxation coefficient to be used for inflow situation.
-
-[real, dimension(max_obc,max_prog_tracers)]
-
-
-rel_coef_tracer_out
-
-
- Relaxation coefficient to be used for outflow situation.
- Should be smaller then or equal to rel_coef_tracer_in.
-
-[real, dimension(max_obc,max_prog_tracers)]
-
-
-rel_clin_pnts
-
-
- Relax a tracer at a stripe of rel_clin_pnts. Default = 1.
-
-[integer, dimension(max_obc,max_prog_tracers)]
-
-
-filename_tracer
-
-
- Filename to read a tracer. It is allowed to put all data for a boundary in one file.
-
-[character, dimension(max_obc,max_prog_tracers)]
-
-
-fieldname_tracer
-
-
- Fieldname of a tracer.
-
-[character, dimension(max_obc,max_prog_tracers)]
-
-
-obc_enhance_visc_back
-
-
- logical variable that decide whether to enhance viscosity at the boundary. Default value is .false.
-
-[logical, dimension(max_obc)]
-
-
-obc_enhance_diff_back
-
-
- logical variable that decide whether to enhance mixing at the boundary. Default value is .false.
-
-[logical, dimension(max_obc)]
-
-
-enh_fac_v
-
-
- 'Safety factor' applied to maximum stable viscosity at the boundary. Default = 0.9
-
-[real, dimension(max_obc)]
-
-
-enh_fac_d
-
-
- Factor applied to enhance mixing at the boundary. Default = 1.
-
-[real, dimension(max_obc)]
-
-
-enh_pnts
-
-
- Enhance viscosity and mixing at a stripe of enh_pnts
- decreasing with the distance from the boundary. Default = 1.
-
-[integer, dimension(max_obc)]
-
-
-debug_phase_speed
-
-
- Includes the phase speed into the model output.
-
-[logical]
-
-
-debug_this_module
-
-
- For debugging.
-
-[logical]
-
-
-nt
-
-
- number of tracers to use open boundary condition.
-
-[integer]
-
- This module can extrapolate data on the open lateral
- boundaries for MOM. Tracer and surface height
- are extrapolated on the boundary by using implicit radiation
- boundary conditions, velocities are calculated on the boundary
- from a linear equation (omitted advection equation). The
- gradient of each field is supposed to be zero between boundary
- points and the first points accross the boundary.
-
- This scheme has been tested only with the following vertical coordinates:
- vertical_coordinate=='geopotential'
- vertical_coordinate=='zstar'
- Notably, there is no OBC prescription for pressure coordinates.
-
-
- logical variable that decide whether relax eta or not. Default value is .false.
-
-[logical, dimension(max_obc)]
-
-
-obc_consider_convu
-
-
- logical variable that decide whether to account for one
- component of convu within the boundary. The appropriate behavior
- depends on the model configuration.
- Default value is .false.
-
-[logical, dimension(max_obc)]
-
-
-obc_vert_advel_t
-
-
- logical variable that decide whether to account for vertical
- advection of tracers at the boundary. The appropriate behavior
- depends on the model configuration.
- Default value is .false. (Currently inactive)
-
-[logical, dimension(max_obc)]
-
-
-obc_vert_advel_u
-
-
- logical variable that decide whether to account for vertical
- advection of momentum at the boundary. The appropriate behavior
- depends on the model configuration.
- Default value is .false.
-
-[logical, dimension(max_obc)]
-
-
-obc_relax_eta_profile
-
-
- logical variable that decide whether relax eta to a prescribed profile or not.
- Default value is .false. In this case only the average sea level is relaxed,
- the profile, hence the geostrophic current, is unchanged.
-
-[logical, dimension(max_obc)]
-
-
-obc_relax_tracer
-
-
- logical variable that decide whether relax tracer or not. Default value is .false.
-
-[logical, dimension(max_obc)]
-
-
-obc_flow_relax
-
-
- Integer variable specifying the flow relaxation zone
- (flow realxation of Martinsen and Engedahl (1987). Default value is 1.
-
-[integer, dimension(max_obc)]
-
-
-obc_consider_sources
-
-
- Logical variable specifying if source and SGS terms of the normal tracer
- scheme are valid. Default value is .false..
-
-[logical, dimension(max_obc)]
-
-
-obc_tracer_no_inflow
-
-
- logical variable that decide whether apply orlanski obc on tracer or not. Default value is .false.
-
-[logical, dimension(max_obc)]
-
-
-ctrop_max
-
-
- Maximum value to clip diagnosed barotropic phase speed in terms of sqrt(gH).
- Should be about 1.
-
-[real, dimension(max_obc)]
-
-
-ctrop_min
-
-
- Minimum value to diagnosed barotropic phase speed in terms of sqrt(gH).
- Should be about 0. Default is 0.1.
-
-[real, dimension(max_obc)]
-
-
-ctrop_inc
-
-
- value to be set for barotropic phase speed if incoming waves are diagnosed.
- (in terms of sqrt(gH)) Should be about 0. Default is 0.
-
-[real, dimension(max_obc)]
-
-
-rel_coef_eta_in
-
-
- Relaxation coefficient to be used for incoming wave situation.
-
-[real, dimension(max_obc)]
-
-
-rel_coef_eta_out
-
-
- Relaxation coefficient to be used for outgoing wave situation.
- Should be smaller then or equal to rel_coef_eta_in.
-
-[real, dimension(max_obc)]
-
- Relax sea level at a stripe of rel_eta_pnts. Default = 1.
-
-[integer, dimension(max_obc)]
-
-
-rel_coef_tracer_in
-
-
- Relaxation coefficient to be used for inflow situation.
-
-[real, dimension(max_obc,max_prog_tracers)]
-
-
-rel_coef_tracer_out
-
-
- Relaxation coefficient to be used for outflow situation.
- Should be smaller then or equal to rel_coef_tracer_in.
-
-[real, dimension(max_obc,max_prog_tracers)]
-
-
-rel_clin_pnts
-
-
- Relax a tracer at a stripe of rel_clin_pnts. Default = 1.
-
-[integer, dimension(max_obc,max_prog_tracers)]
-
-
-filename_tracer
-
-
- Filename to read a tracer. It is allowed to put all data for a boundary in one file.
-
-[character, dimension(max_obc,max_prog_tracers)]
-
-
-fieldname_tracer
-
-
- Fieldname of a tracer.
-
-[character, dimension(max_obc,max_prog_tracers)]
-
-
-obc_enhance_visc_back
-
-
- logical variable that decide whether to enhance viscosity at the boundary. Default value is .false.
-
-[logical, dimension(max_obc)]
-
-
-obc_enhance_diff_back
-
-
- logical variable that decide whether to enhance mixing at the boundary. Default value is .false.
-
-[logical, dimension(max_obc)]
-
-
-enh_fac_v
-
-
- 'Safety factor' applied to maximum stable viscosity at the boundary. Default = 0.9
-
-[real, dimension(max_obc)]
-
-
-enh_fac_d
-
-
- Factor applied to enhance mixing at the boundary. Default = 1.
-
-[real, dimension(max_obc)]
-
-
-enh_pnts
-
-
- Enhance viscosity and mixing at a stripe of enh_pnts
- decreasing with the distance from the boundary. Default = 1.
-
-[integer, dimension(max_obc)]
-
-
-debug_phase_speed
-
-
- Includes the phase speed into the model output.
-
-[logical]
-
-
-debug_this_module
-
-
- For debugging.
-
-[logical]
-
-
-nt
-
-
- number of tracers to use open boundary condition.
-
-[integer]
-
- Set the barotropic domain used in barotropic time step.
-
-
-
-
-INPUT
-
-
-
-
-
Domain_in
- Store the barotropic domain.
- [type(ocean_domain_type)]
-
-
-
-
-
-
-
-
-
get_use_legacy_DIV_UD
-
-
-DESCRIPTION
-
-
- Return the value of ocean_operators_nml variable use_legacy_DIV_UD
-
-
-
-
-
-
-
-
REMAP_NT_TO_NU
-
-
-DESCRIPTION
-
-
- REMAP_NT_TO_NU remaps a normal flux at the north
- face of T-cells to the north face of U-cells
-
-
-
-
-INPUT
-
-
-
-
-
a
- Field to be remapped
- [real, dimension(isd:ied,jsd:jed)]
-
-
-
-
-
-
-
-
-
REMAP_ET_TO_EU
-
-
-DESCRIPTION
-
-
- REMAP_ET_TO_EU remaps a normal flux at the east
- face of T-cells to the east face of U-cells
-
-
-
-
-INPUT
-
-
-
-
-
a
- Field to be remapped
- [real, dimension(isd:ied,jsd:jed)]
-
-
-
-
-
-
-
-
-
REMAP_BT_TO_BU
-
-
-DESCRIPTION
-
-
- REMAP_BT_TO_BU remaps a T-cell thickness or
- vertical velocity on the base of T-cells to U-cells
-
-
-
-
-INPUT
-
-
-
-
-
a
- Field to be remapped
- [real, dimension(isd:ied,jsd:jed)]
-
-
-
-
-
-
-
-
-
DIV_UD
-
-
-DESCRIPTION
-
-
- Compute divergence of vertically integrated velocity.
- For MOM with generalized vertical coordinates, ud has an extra
- density factor built in.
-
- The Bgrid uh and vh fields are located on the corner points, so require
- some backward averaging.
-
- The Cgrid uh and vh fields are located on the T-cell faces, so need no
- spatial averaging.
-
- Bgrid code is a speedier version of
-
- uhy(:,:) = BAY(ud(:,:,1)*dyu(:,:))
-
- vhx(:,:) = BAX(ud(:,:,2)*dxu(:,:))
-
- DIV_UD(ud) = BDX_ET(uhy(:,:)/dyte(:,:)) + BDY_NT(vhx(:,:)/dxtn(:,:))
-
-
-
-
-
-
-
-
-
GRAD_BAROTROPIC_P
-
-
-DESCRIPTION
-
-
- Compute horizontal gradient of the pressure field associated with
- either the free surface height or the bottom pressure.
-
- Account taken here for either Bgrid or Cgrid operators.
- For the Bgrid, the gradient is centered onto the U-cell
- for use in updating barotropic velocity. For the Cgrid, the
- two components are centred on the T-cell faces.
-
- The Bgrid algorithm is a speedier version of
-
- grad_barotropic_p(:,:,1) = FDX_NT(FAY(press(:,:)))
-
- grad_barotropic_p(:,:,2) = FDY_ET(FAX(press(:,:)))
-
-
-
-
-
-
-
-
S2D
-
-
-DESCRIPTION
-
-
- Smooth a 2D field with a 2D version of a 1D filter with weights (1/4, 1/2, 1/4)
-
-
-
-
-INPUT
-
-
-
-
-
a
- Field to be smoothed
- [real, dimension(isd:ied,jsd:jed)]
-
-
-
-
-
-
-
-
-
LAP_T
-
-
-DESCRIPTION
-
-
- Compute horizontal 5-point Laplacian operator on eta_t.
- Result lives at T-cell center.
-
- Redundancy update for tripolar is needed to conserve
- total volume and tracer. It is likely unimportant
- when call LAP_T from within the barotropic loop. Yet it
- is essential when call LAP_T from ocean_surface_smooth.
-
- Mixing coefficient is assumed to be centred on the T-cell.
- It is averaged to compute its value on the i-face and j-face
- for computing fluxes.
-
-
-
-
-
-
-
-
-
FAX
-
-
-DESCRIPTION
-
-
- Forwards average in the i-direction on the X-axis.
- If input is a(i,j) then output is defined at (i+1/2,j)
-
-
-
-
-INPUT
-
-
-
-
-
a
- Field to be averaged
- [real, dimension(isd:ied,jsd:jed)]
-
-
-
-
-
-
-
-
-
BAX
-
-
-DESCRIPTION
-
-
- Backwards average in the i-direction along the X-axis.
- If input is a(i,j) then output is defined at (i-1/2,j)
-
-
-
-
-INPUT
-
-
-
-
-
a
- Field to be averaged
- [real, dimension(isd:ied,jsd:jed)]
-
-
-
-
-
-
-
-
-
FAY
-
-
-DESCRIPTION
-
-
- Forwards average in the j-direction on the Y-axis
- If input is a(i,j) then output is defined at (i,j+1/2)
-
-
-
-
-INPUT
-
-
-
-
-
a
- Field to be averaged
- [real, dimension(isd:ied,jsd:jed)]
-
-
-
-
-
-
-
-
-
BAY
-
-
-DESCRIPTION
-
-
- Backwards average in the j-direction along the Y-axis
- If input is a(i,j) then output is defined at (i,j-1/2)
-
-
-
-
-INPUT
-
-
-
-
-
a
- Field to be averaged
- [real, dimension(isd:ied,jsd:jed)]
-
-
-
-
-
-
-
-
-
BDX_EU
-
-
-DESCRIPTION
-
-
- Backwards Derivative in X of a quantity defined on the East face of a U-cell
- If input is a(i,j) then output is defined at (i-1/2,j)
-
-
-
-
-INPUT
-
-
-
-
-
a
- Field to be finite differenced
- [real, dimension(isd:ied,jsd:jed)]
-
-
-
-
-
-
-
-
-
BDX_ET
-
-
-DESCRIPTION
-
-
- Backwards derivative in X of a quantity defined on the East face of a T-cell.
- If input is a(i,j) then output is defined at (i-1/2,j)
-
-
-
-
-INPUT
-
-
-
-
-
a
- Field to be finite differenced
- [real, dimension(isd:ied,jsd:jed)]
-
-
-
-
-
-
-
-
-
FDX_U
-
-
-DESCRIPTION
-
-
- Forward Derivative in X of a quantity defined on the grid point of a U-cell.
- If input is a(i,j) then output is defined at (i+1/2,j).
-
-
-
-
-INPUT
-
-
-
-
-
a
- Field to be finite differenced
- [real, dimension(isd:ied,jsd:jed)]
-
-
-
-
-
-
-
-
-
FDX_ZT
-
-
-DESCRIPTION
-
-
-
- Forward Derivative in X of a quantity defined on a tracer grid point
- where it is necessary to take derivative with depth held constant.
- When grid points live at different depths, then have an extra
- contribution to the derivative.
-
- Input a(i,j,1) is at the grid point of a T-cell at level k-1.
- Input a(i,j,2) is at the grid point of a T-cell at level k.
-
- Output is defined at (i+1/2,j) which is at the east face in a T-cell at level k.
-
-
-
-
-
-INPUT
-
-
-
-
-
a
- Field to be finite differenced
- [real, dimension(isd:ied,jsd:jed)]
-
-
-
k
- Depth level
- [integer]
-
-
-
-
-
-
-
-
-
FDX_T
-
-
-DESCRIPTION
-
-
-
- Forward Derivative in X of a quantity defined on the grid point
- of a T-cell.
-
- For lateral derivatives where vertical coordinate is held constant.
-
- Input a(i,j) is at the grid point of a T-cell
- Output is defined at (i+1/2,j) which is at the east face in a T-cell.
-
-
-
-
-
-INPUT
-
-
-
-
-
a
- Field to be finite differenced
- [real, dimension(isd:ied,jsd:jed)]
-
-
-
-
-
-
-
-
-
FDY_ZT
-
-
-DESCRIPTION
-
-
- Forward Derivative in Y of a quantity defined on a tracer grid point
- where it is necessary to take derivative with depth held constant.
- When grid points live at different depths, then have an extra
- contribution to the derivative.
-
- Input a(i,j,1) is at the grid point of a T-cell at level k-1.
- Input a(i,j,2) is at the grid point of a T-cell at level k.
-
- Output is defined at (i,j+1/2) which is at the north face in a T-cell at level k.
-
-
-
-
-
-INPUT
-
-
-
-
-
a
- Field to be finite differenced
- [real, dimension(isd:ied,jsd:jed)]
-
-
-
k
- Depth level
- [integer]
-
-
-
-
-
-
-
-
-
FDY_T
-
-
-DESCRIPTION
-
-
- Forward Derivative in Y of a quantity defined on the grid Point
- of a T-cell.
-
- For lateral derivatives where vertical coordinate is held constant.
-
- Input a(i,j) is at the grid point of a T-cell.
- Output is defined at (i,j+1/2) which is at the north face in a T-cell.
-
-
-
-
-
-INPUT
-
-
-
-
-
a
- Field to be finite differenced
- [real, dimension(isd:ied,jsd:jed)]
-
-
-
-
-
-
-
-
-
FDX_NT
-
-
-DESCRIPTION
-
-
- Forward Derivative in X of a quantity defined on the North face of a T-cell.
- If input is a(i,j) then output is defined at (i+1/2,j).
-
-
-
-
-INPUT
-
-
-
-
-
a
- Field to be finite differenced
- [real, dimension(isd:ied,jsd:jed)]
-
-
-
-
-
-
-
-
-
BDY_NU
-
-
-DESCRIPTION
-
-
- Backward Derivative in Y of a quantity defined on the North face of a U-cell.
- If input is a(i,j) then output is defined at (i,j-1/2).
-
-
-
-
-INPUT
-
-
-
-
-
a
- Field to be finite differenced
- [real, dimension(isd:ied,jsd:jed)]
-
-
-
-
-
-
-
-
-
BDY_NT
-
-
-DESCRIPTION
-
-
- Backward Derivative in Y of a quantity defined on the North face of a T-cell.
- If input is a(i,j) then output is defined at (i,j-1/2).
-
-
-
-
-INPUT
-
-
-
-
-
a
- Field to be finite differenced
- [real, dimension(isd:ied,jsd:jed)]
-
-
-
-
-
-
-
-
-
FDY_U
-
-
-DESCRIPTION
-
-
- Forward Derivative in Y of a quantity defined on the grid Point of a U-cell.
- If input is a(i,j) then output is defined at (i,j+1/2).
-
-
-
-
-INPUT
-
-
-
-
-
a
- Field to be finite differenced
- [real, dimension(isd:ied,jsd:jed)]
-
-
-
-
-
-
-
-
-
FDY_ET
-
-
-DESCRIPTION
-
-
- Forward Derivative in Y of a quantity defined on the East face of a T-cell.
- If input is a(i,j) then output is defined at (i,j+1/2).
-
-
-
-
-INPUT
-
-
-
-
-
a
- Field to be finite differenced
- [real, dimension(isd:ied,jsd:jed)]
-
-
-
-
-
-
-
-
-
FDZ_T
-
-
-DESCRIPTION
-
-
- Forward Derivative in Z of a field on the T-cell point at level k.
-
- input a(i,j,1) is at the grid point of a T-cell at level k.
- input a(i,j,2) is at the grid point of a T-cell at level k+1.
-
- output is at (i,j,k+3/2) which is bottom face of T-cell at level k.
-
- minus sign due to convention that z-increases upwards, whereas
- k increases downward.
-
-
-
-
-
-INPUT
-
-
-
-
-
a
- Field to be finite differenced
- [real, dimension(isd:ied,jsd:jed)]
-
-
-
k
- Depth level index
- [integer]
-
-
-
-
-
-
-
-
-
FMX
-
-
-DESCRIPTION
-
-
- Forwards Minimum in the X direction.
- If input is a(i,j) then output is defined at (i+1/2,j).
-
-
-
-
-INPUT
-
-
-
-
-
a
- Field to find minimum
- [real, dimension(isd:ied,jsd:jed)]
-
-
-
-
-
-
-
-
-
FMY
-
-
-DESCRIPTION
-
-
- Forwards Minimum in the Y direction.
- If input is a(i,j) then output is defined at (i,j+1/2).
-
-
-
-
-INPUT
-
-
-
-
-
a
- Field to find minimum
- [real, dimension(isd:ied,jsd:jed)]
-
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_operators_nml
-
-
-
-
-
-use_legacy_DIV_UD
-
-
- Set use_legacy_DIV_UD=.true. to reproduce Riga results for
- DIV_UD on Bgrid. For the case that the model grid is tripolar grid,
- when barotropic_halo > 1 in ocean_barotropic.F90, then
- we must set use_legacy_DIV_UD=.false., since will not reproduce between
- different number of processors if set use_legacy_DIV_UD=.true.
-
- Tests indicate that with wider barotropic halos, there are
- some performance enhancements for use_legacy_DIV_UD=.false.
- Hence, the default is use_legacy_DIV_UD=.false.
-
- For the case that the model grid is regular lat-lon grid,
- use_legacy_DIV_UD could be set to .true. or .false. for
- any positive value of barotropic_halo.
-
- Note that the only difference between the new and old DIV_UD
- is order of operations induced by parentheses, which occurs in the
- tripolar fold region in the Arctic:
- old: DIV_UD(i,j) = (uh_bay - uhim_bay + vh_bax - vhjm_bax)*datr_bt(i,j)
- new: DIV_UD(i,j) = ((uh_bay - uhim_bay) + (vh_bax - vhjm_bax))*datr_bt(i,j)
-
-[logical]
-
-
-
-
-
-
-
-
-
-
-
NOTES
-
-
- All operators will be replaced by generic forms when Fortran
- can properly support functions of allocatable arrays. The
- problems presently with this replacement are are as follows:
- Allocatable arrays cannot be inside of derived types.
- Only pointers to allocatable arrays can be inside derived types.
- Supposedly the former will be allowed in Fortran 95
- Also, functions cannot be typed as a derived type without conflicts
- which preclude using function as general operators operating on
- derived types.
-
-
- Mnemonics for simple operators
-
- 1st letter (direction of operation)
-
- F => Forward direction with respect to the index.
-
- B => Backward direction with respect to the index.
-
- 2nd letter (operation)
-
- D => Derivative
-
- A => Average
-
- M => Minimum
-
- 3rd letter (axis)
-
- X => along the X axis
-
- Y => along the Y axis
-
- Z => along the Z axis
-
- 4th letter (placement of quantity being operated on)
-
- E => East face
-
- N => North face
-
- B => Bottom face
-
- P => Point (grid point within cell)
-
- 5th letter (type of grid cell)
-
- U => U-cell
-
- T => T-cell
-
- Initialize the parameter module, passing cp_ocean back to ocean_model.F90
- and setting all other parameters that will be used throughout the model
- simulation.
-
- Note: we do not enable check_nml_error, since the default settings
- are generally those recommended for simulations.
-
-
-
-
-
-
-
-
-
ocean_parameters_end
-
-
-DESCRIPTION
-
-
- Summarize the basic physical parameters used in the simulation.
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_parameters_nml
-
-
-
-
-
-cp_ocean
-
-
- Specific heat capacity J/(kg degC) for liquid seawater.
- Values are taken from from Jackett etal (2006) for preTEOS10 and
- from TEOS-10 manual for TEOS10 value. The default values differ
- from that in shared/constants since the MOM defaults are more updated.
- Note that there is a check inside of ocean_tempsalt.F90 to ensure that
- cp_ocean=cp_ocean_teos10 if using the teos10 recommendations,
- and cp_ocean=cp_ocean_preteos10 for cases not using teos10.
-
-[real, units: J/(kg degC)]
-
-
-cp_solid_runoff
-
-
- Specific heat capacity J/(kg degC) for solid water runoff via calving land ice.
- Default cp_solid_runoff = 2106.0 is consistent with that used in the
- GFDL land model.
-
-[real, units: J/(kg degC)]
-
-
-cp_liquid_runoff
-
-
- Specific heat capacity J/(kg degC) for liquid water runoff from land.
- Default cp_liquid_runoff = 4218.0 is consistent with that used in the
- GFDL land model.
-
-[real, units: J/(kg degC)]
-
-
-rho0
-
-
- Boussinesq reference density. Default rho0=1035.0
- corresponds to the value in Gill (page 47), where he notes
- that the ocean density typically deviates less than 2 per cent
- from this value. But if using the Boussinesq approximation for
- other water bodies, such as the Baltic, then may wish to change
- rho0 to a more appropriate value.
-
-[real, units: kg/m^3]
-
-
-tfreeze
-
-
- freezing point of fresh water at standard atmos pressure.
- Default tfreeze=273.15
-
-[real, units: Kelvin]
-
-
-omega_earth
-
-
- rotation of earth in radians per second
- Default omega_earth= 7.2921e-5, as per equation (4.1) in Griffies (2004).
-
-[real, units: radians per second]
-
-
-grav
-
-
- Gravitational acceleration at earth surface. Assumed to be constant
- throughout the ocean domain. Default grav=9.8 corresponds to the
- "grav" parameter from shared/constants.F90.
-
-[real, units: m/s^2]
-
-
-von_karman
-
-
- Von Karman constant for law of wall turbulence.
- Default von_karman=0.4.
- Note: due to answer changes on some compilers, von_karman
- has been removed from nml and is now set as a hard-value
- to be consistent with earlier simulations (06mar2012).
-
-[real, units: dimensionless]
-
- Compute the hydrostatic pressure and forces from pressure.
- Includes methods for either Bgrid or Cgrid.
-
-
-
-
-
- This module computes hydrostatic pressure and the pressure force
- acting at a velocity point (traditional finite difference approach).
- This force is used for the linear momentum equation.
-
- This module takes account of the vertical coordinate,
- which determines details of the calculation.
-
- This module allows for either Bgrid or Cgrid calculation.
-
- Compute the horizontal force [Pa=N/m^2] from pressure.
-
- Use the traditional approach whereby the pressure force
- is computed as a finite difference gradient centred
- at the U-cell point.
-
-
-
-
-
-
-
-
-
press_grad_force_depth_bgrid
-
-
-DESCRIPTION
-
-
- Compute the force from pressure using a finite difference method
- to compute the thickness weighted pressure gradient at the
- velocity cell point.
-
- Assume B-grid arrangement here.
-
- For depth-like vertical coordinates, we exclude surface and applied
- pressures (i.e., we are computing here the gradient of the baroclinic
- pressure). The surface and applied pressures are accounted for in
- the barotropic module.
-
- Account is taken of variable partial cell thickness.
-
- 1 = dp/dx; 2 = dp/dy
-
- Thickness weight since this is what we wish to use in update of
- the velocity. Resulting thickness weighted pressure gradient has
- dimensions of Pa = N/m^2 = kg/(m*s^2).
-
- Thickness%dzu should be at tau.
-
-
-
-
-
-
-
-
-
press_grad_force_press_bgrid
-
-
-DESCRIPTION
-
-
- Compute the force from pressure using a finite difference method
- to compute the thickness weighted pressure gradient at the
- velocity cell corner point.
-
- Assume B-grid arrangement here.
-
- For pressure-like vertical coordinates, we omit the bottom pressure
- and bottom geopotential. These pressures are accounted for in the
- barotropic module.
-
- Account is taken of variable partial cell thickness.
-
- 1 = dp/dx; 2 = dp/dy
-
- Thickness weight since this is what we wish to use in update of
- the velocity. Resulting thickness weighted pressure gradient has
- dimensions of Pa = N/m^2 = kg/(m*s^2).
-
- Thickness%dzu should be at tau.
-
-
-
-
-
-
-
-
-
press_grad_force_depth_cgrid
-
-
-DESCRIPTION
-
-
- Compute the force from pressure using a finite difference method
- to compute the thickness weighted pressure gradient at the
- T-cell face, thus acting on the C-grid velocity components.
-
- Assume C-grid arrangement here.
-
- For depth-like vertical coordinates, we exclude surface and applied
- pressures (i.e., we are computing here the gradient of the baroclinic
- pressure). The surface and applied pressures are included in
- ocean_barotropic.
-
- Account is taken of variable partial cell thickness.
-
- 1 = dp/dx; 2 = dp/dy
-
- Thickness weight since this is what we wish to use in update of
- the velocity. Resulting thickness weighted pressure gradient has
- dimensions of Pa = N/m^2 = kg/(m*s^2).
-
- Thickness%dzten should be at time tau.
-
-
-
-
-
-
-
-
-
press_grad_force_press_cgrid
-
-
-DESCRIPTION
-
-
- Compute the force from pressure using a finite difference method
- to compute the thickness weighted pressure gradient at the
- T-cell face, thus acting on the C-grid velocity components.
-
- Assume C-grid arrangement here.
-
- For pressure-like vertical coordinates, we omit the bottom pressure
- and bottom geopotential; these are handled in ocean_barotropic.
-
- Account is taken of variable partial cell thickness.
-
- 1 = dp/dx; 2 = dp/dy
-
- Thickness weight since this is what we wish to use in update of
- the velocity. Resulting thickness weighted pressure gradient has
- dimensions of Pa = N/m^2 = kg/(m*s^2).
-
- Thickness%dzu should be at tau.
-
-
-
-
-
-
-
-
-
pressure_in_dbars
-
-
-DESCRIPTION
-
-
- Compute pressure (dbars) exerted at T cell grid point by weight of
- water column above the grid point.
-
- rho = density in kg/m^3
-
- psurf = surface pressure in Pa= kg/(m*s^2) = hydrostatic pressure
- at z=0 associated with fluid between z=0 and z=eta_t.
- Also include pressure from atmosphere and ice, both of which
- are part of the patm array.
-
- This routine is used by ocean_density to compute the pressure
- used in the equation of state. It is only called when the
- vertical coordinate is DEPTH_BASED.
-
-
-
-
-
-
-
-
-
hydrostatic_pressure
-
-
-DESCRIPTION
-
-
- Hydrostatic pressure [Pa=N/m^2=kg/(m*s^2)] at T cell grid points.
-
- For GEOPOTENTIAL vertical coordinate, integration is
- from z=0 to depth of grid point. This integration results in
- the so-called "baroclinic" pressure.
-
- For ZSTAR or ZSIGMA, vertical coordinate, integration is from z=eta to
- depth of grid point. This is allowed because ZSTAR and ZSIGMA
- absorb the undulations of the surface height into their definition.
-
- If the input density "rho" is an anomoly, the resulting presure
- will be a hydrostatic pressure anomoly. If "rho" is full density,
- the presure will be a full hydrostatic pressure.
-
-
-
-
-
-
-
-
-
geopotential_anomaly
-
-
-DESCRIPTION
-
-
- Geopotential anomaly [m^2/s^2] at T cell grid points.
- Integration here is from z=-H to depth of grid point.
-
- Input should be density anomaly rhoprime = rho-rho0.
-
- This function is needed when computing pressure gradient
- for PRESSURE_BASED vertical coordinates.
-
- WARNING: Thickness%method==FINITEVOLUME has been found to be
- problematic. It remains under development. It is NOT
- supported for general use.
-
-
-
-
-
-
-
-
-
press_grad_force_depth_blob
-
-
-DESCRIPTION
-
-
- This routine respects the partition between Eulerian system mass
- and the Lagrangian system mass associated with the Lagrangian blobs
- model. The pressure gradient from the total (combined Eulerian and
- Lagrangian systems) is calculated. Aside from that, the routine is
- the same as for press_grad_force_depth.
-
- Compute the force from pressure using a finite difference method
- to compute the thickness weighted pressure gradient at the
- velocity cell point.
-
- For depth-like vertical coordinates, we exclude surface and applied
- pressures (i.e., we are computing here the gradient of the baroclinic
- pressure). Account is taken of variable partial cell thickness.
- 1 = dp/dx; 2 = dp/dy
-
- Thickness weight since this is what we wish to use in update of
- the velocity. Resulting thickness weighted pressure gradient has
- dimensions of Pa = N/m^2 = kg/(m*s^2).
-
- Thickness%dzu should be at tau.
-
-
-
-
-
-
-
-
press_grad_force_press_blob
-
-
-DESCRIPTION
-
-
- This routine respects the partition between Eulerian system mass
- and the Lagrangian system mass associated with the Lagrangian blobs
- model. The pressure gradient from the total (combined Eulerian and
- Lagrangian systems) system is calculated. Aside from that, the routine
- is the same as for press_grad_force_press.
-
- Compute the force from pressure using a finite difference method
- to compute the thickness weighted pressure gradient at the
- velocity cell point.
-
- For pressure-like vertical coordinates, we omit the bottom pressure
- and bottom geopotential. Account is taken of variable partial cell
- thickness. 1 = dp/dx; 2 = dp/dy
-
- Thickness weight since this is what we wish to use in update of
- the velocity. Resulting thickness weighted pressure gradient has
- dimensions of Pa = N/m^2 = kg/(m*s^2).
-
- Thickness%dzu should be at tau.
-
-
-
-
-
-
-
-
-
pressure_in_dbars_blob
-
-
-DESCRIPTION
-
-
- This routine respects the partition between Eulerian system mass
- and the Lagrangian system mass associated with the Lagrangian blobs
- model. The pressure from the combined system is calculated.
- Aside from that, the routine is the same as for pressure_in_dbars.
-
- Compute pressure (dbars) exerted at T cell grid point by weight of
- water column above the grid point.
-
- rho = density in kg/m^3
-
- psurf = surface pressure in Pa= kg/(m*s^2) = hydrostatic pressure
- at z=0 associated with fluid between z=0 and z=eta_t.
- Also include pressure from atmosphere and ice, both of which
- are part of the patm array.
-
- This routine is used by ocean_density to compute the pressure
- used in the equation of state. It is only called when the
- vertical coordinate is DEPTH_BASED.
-
-
-
-
-
-
-
-
-
hydrostatic_pressure_blob
-
-
-DESCRIPTION
-
-
- This routine respects the partition between Eulerian system mass
- and the Lagrangian system mass associated with the Lagrangian blobs
- model. The hydrostatic pressure from the combined system is
- calculated. Aside from that, the routine is the same as for
- Hydrostatic_pressure.
-
- Hydrostatic pressure [Pa=N/m^2=kg/(m*s^2)] at T cell grid points.
-
- For GEOPOTENTIAL vertical coordinate, integration is
- from z=0 to depth of grid point. This integration results in
- the so-called "baroclinic" pressure.
-
- For ZSTAR, vertical coordinate, integration is from z=eta to
- depth of grid point. This is allowed because ZSTAR
- absorbs the undulations of the surface height into their definition.
-
- If the input density "rho" is an anomoly, the resulting presure
- will be a hydrostatic pressure anomoly. If "rho" is full density,
- the presure will be a full hydrostatic pressure.
-
-
-
-
-
-
-
-
-
geopotential_anomaly_blob
-
-
-DESCRIPTION
-
-
- This routine respects the partition between Eulerian system mass
- and the Lagrangian system mass associated with the Lagrangian blobs
- model. The geopotential from the combined system is calculated.
- Aside from that, the routine is the same as for geopotential_anomaly.
-
- Geopotential anomaly [m^2/s^2] at T cell grid points.
- Integration here is from z=-H to depth of grid point.
-
- Input should be density anomaly rhoprime = rho-rho0.
-
- This function is needed when computing pressure gradient
- for PRESSURE_BASED vertical coordinates.
-
- WARNING: Thickness%method==FINITEVOLUME has been found to be
- problematic. It remains under development. It is NOT
- supported for general use.
-
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_pressure_nml
-
-
-
-
-
-debug_this_module
-
-
- For debugging.
-
-[logical]
-
-
-zero_correction_term_grad
-
-
- For debugging it is often useful to zero the contribution to the
- pressure gradient that arises from the "correction" term.
- Implemented only for depth based vertical coordinate models.
-
-[logical]
-
-
-zero_diagonal_press_grad
-
-
- For debugging it is often useful to zero the contribution to the
- pressure gradient that arises from the along k-level gradient.
- Implemented only for depth based vertical coordinate models.
-
-[logical]
-
-
-zero_pressure_force
-
-
- For debugging it is often useful to zero the pressure force
- to zero.
-
-[logical]
-
-
-zero_eta_over_h_zstar_pressure
-
-
- For debugging zstar, we drop any eta/H contribution to
- the hydrostatic pressure. This is wrong physically, but
- useful for certain tests.
-
-[logical]
-
- Set up the surface boundary conditions for MOM.
-
-
-
-
-
-
- This module sets up the surface boundary conditions for MOM.
- Also fill Ocean_sfc derived-type used to pass information to other
- component models. Also write diagnostics related to surface
- boundary forcing.
-
- The surface temperature should be the surface insitu temperature,
- which is the same as the surface potential temperature. When the
- model prognostic temperature variable is conservative temperature,
- then the surface potential temperature is carried in T_diag(index_diag_temp).
- The resulting heat flux is potential enthalpy, which is the correct
- field to be forcing the T_prog(index_temp) field when the prognostic
- temperature field is the conservative temperature.
-
- We assume the winds passed to the ocean are on the B-grid
- velocity point. Likewise, we pass the currents back to the coupler
- on the B-grid point. Code will need to be modified if using another
- assumption.
-
-
- Initialize the ocean sbc diagnostics.
- Send some static diagnostics to diagnostic manager.
-
-
-
-
-
-
-
-
initialize_ocean_sfc
-
-
-DESCRIPTION
-
-
- Initialize the ocean surface type, which passes information between ocean
- and other component models.
-
- Note that ocean model sst passed to the atmosphere must be the surface
- potential temperature (which is equated to surface in situ temperature).
- If the ocean prognostic temperature variable is conservative temperature,
- then the sst is carried in T_diag(index_diag_temp). If the prognostic
- temperature is potential temperature, then the sst is carried in
- T_prog(index_temp).
-
- Note that we assume the winds passed to the ocean are on the B-grid
- velocity point. Likewise, we pass the currents back to the coupler
- on the B-grid point. Code will need to be modified if using another
- coupler assumption.
-
- Ocean_sfc%t_surf = time averaged sst (Kelvin) passed to atmosphere/ice model
- Ocean_sfc%s_surf = time averaged sss (psu) passed to atmosphere/ice models
- Ocean_sfc%u_surf = time averaged u-current (m/sec) passed to atmosphere/ice models
- Ocean_sfc%v_surf = time averaged v-current (m/sec) passed to atmosphere/ice models
- Ocean_sfc%sea_lev = time averaged ocean free surface height (m) plus patm/(grav*rho0)
- Ocean_sfc%frazil = time accumulated frazil (J/m^2) passed to ice model. time averaging
- not performed, since ice model needs the frazil accumulated over the
- ocean time steps. Note that Ocean_sfc%frazil is accumulated, whereas
- T_diag%frazil (saved in diagnostic tracer restart file) is instantaneous.
-
-
-
-
-
-
-
-
-
sum_ocean_sfc
-
-
-DESCRIPTION
-
-
- Accumulate the ocean_sfc derived type over the course of the
- ocean component sub-cycling used when coupling to other models.
-
- Note that ocean model sst passed to the atmosphere must be the surface
- potential temperature (which is equated to surface in situ temperature).
- If the ocean prognostic temperature variable is conservative temperature,
- then the sst is carried in T_diag(index_diag_temp). If the prognostic
- temperature is potential temperature, then the sst is carried in
- T_prog(index_temp).
-
- Note that this routine is called after eta_and_pbot_diagnose,
- so Thickness%eta is eta_t(taup1).
-
-
-
-
-
-
-
-
-
zero_ocean_sfc
-
-
-DESCRIPTION
-
-
- Zero the elements of the Ocean_sfc derived type.
-
-
-
-
-
-
-
-
avg_ocean_sfc
-
-
-DESCRIPTION
-
-
- Compute average of ocean surface quantities. This is for coupling,
- where pass time averaged information from ocean to other component
- models. Note that Ocean_sfc%frazil is NOT time averaged. Rather, it
- is accumulated from T_diag(index_frazil)%field in subroutine sum_ocean_sfc.
- Doing so is necessary for heat conservation between ocean and sea
- ice systems. Since it is not time averaged, frazil is not part of
- this averaging subroutine.
-
- Note that ocean model SST passed to the atmosphere is the surface
- potential temperature (which is equal to surface in situ temperature).
- If the ocean prognostic temperature variable is conservative temperature,
- then the sst is carried in T_diag(index_diag_temp). If the prognostic
- temperature is potential temperature, then the sst is carried in
- T_prog(index_temp).
-
- Note that if one removes the averaging, then we take only the
- latest values of the surface fields. This approach has been
- found useful to stabilize the "concurrent" coupling approach.
-
- Note that this routine is called after eta_and_pbot_diagnose,
- so Thickness%eta is eta_t(taup1).
-
-
-
-
-
-
-
-
-
ocean_sfc_restart
-
-
-DESCRIPTION
-
-
- Write out restart files registered through register_restart_file
-
-
-
-
-
-
-
-
ocean_sfc_end
-
-
-DESCRIPTION
-
-
- Save information from Ocean_sfc to restarts. Note that it is
- important in general to distinguish the time accumulated quantity
- Ocean_sfc%frazil, saved here, from the instantaneous quantity
- T_diag%frazil, which is saved in the diagnostic tracer restart file.
-
-
-
-
-
-
-
-
get_ocean_sbc
-
-
-DESCRIPTION
-
-
- Subroutine to get the surface fluxes passed into the ocean from
- other component models.
-
- **momentum fluxes from wind stress and momentum of pme and rivers
- **stokes drift from surface wave model
- **water fluxes and temp/salinity in water fluxes
- **salt fluxes; real or virtual
- **heat fluxes
- **applied surface pressure
-
-
-
-
-
-
-
-
-
flux_adjust
-
-
-DESCRIPTION
-
-
- Subroutine to compute the surface fluxes derived from a
- restoring condition and/or correction from an input file.
-
- We use a convention whereby a positive
- flux enters the ocean: (+) down convention.
-
- When restoring salinity, one may choose to convert this
- flux to an implied water flux, or keep it a salt flux.
- Converting to a water flux will alter the sea level, and
- so alter the concentration of other tracers.
- The default is to keep it as a salt flux.
-
-
-
-
-
-
-
-
-
ocean_sbc_diag
-
-
-DESCRIPTION
-
-
- Compute and send diagnostics from get_ocean_sbc.
-
-
-
-
-
-
-
-
-
-
-DESCRIPTION
-
-
- TEOS-10 expression for latent heat of fusion at the sea surface (p=0dbar)
-
- The following is from the from the matlab routine due to
- McDougall and Barker with respect to the full pressure dependent
- formulation.
-
- Note that the computed latent heat of fusion from this function has
- errors that range between -0.4 and 0.3 J kg^-1, when compared with the
- latent heats of melting derived from the Gibbs functions of ice and of
- seawater (using the SIA code of TEOS-10). However, the underlying data to
- the Gibbs function contains uncertainities of 200 J kg^-1 (IOC et al., 2010).
-
- The reference for this routine is
-
- IOC, SCOR and IAPSO, 2010: The international thermodynamic equation of
- seawater - 2010: Calculation and use of thermodynamic properties.
- Intergovernmental Oceanographic Commission, Manuals and Guides No. 56,
- UNESCO (English), 196 pp. Available from http://www.TEOS-10.org
- See section 3.34 of the TEOS-10 Manual.
-
-
-
-
-
-
-
-
-
-
-DESCRIPTION
-
-
- TEOS-10 expression for latent heat of vaporization at the sea surface
- (p=0dbar).
- The following is from the From the original matlab routine due to
- Barker, McDougall and Feistel
-
- Calculates latent heat, or enthalpy, of evaporation at p = 0 (the
- surface). It is defined as a function of Absolute Salinity, SA, and
- Conservative Temperature, CT, and is valid in the ranges
- 0 < SA < 42 g/kg and 0 < CT < 40 deg C. The errors range between
- -0.4 and 0.6 J/kg
-
- IOC, SCOR and IAPSO, 2010: The international thermodynamic equation of
- seawater - 2010: Calculation and use of thermodynamic properties.
- Intergovernmental Oceanographic Commission, Manuals and Guides No. 56,
- UNESCO (English), 196 pp. Available from http://www.TEOS-10.org
- See section 3.39 of the TEOS-10 Manual.
-
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_sbc_nml
-
-
-
-
-
-use_waterflux
-
-
- Set to true when wish to use real fresh water flux as opposed to virtual
- salt fluxes. This is the recommended method. The alternative virtual
- tracer flux method (use_waterflux=.false.) is not routinely used at
- GFDL, so it may suffer from poor testing.
- Default use_waterflux=.true.
-
-[logical]
-
-
-waterflux_tavg
-
-
- Set to true when aiming to suppress the leap-frog computational mode
- by setting pme and river equal to a time averaged value over the
- present and previous time step. This method requires an extra
- field in the restart file. This method is not needed when using
- the TWO_LEVEL time tendency. It remains for those who wish to
- use the leap-frog THREE_LEVEL time stepping scheme.
- Note that it does not lead to simple checks of conservation across
- model components, since there is a time averaging performed for
- the water flux added to the ocean model. It is generally NOT
- recommended. Default waterflux_tavg=.false.
-
-[logical]
-
-
-use_ideal_runoff
-
-
- To add an idealized liquid runoff read from a file.
- This runoff is assumed to enter the ocean with the same temperature as
- SST, and to be liquid. It is an additional runoff, so that any other
- runoff remains unaltered. The runoff coming from idealized runoff is
- NOT subject to the global normalization realized from
- zero_net_water_coupler=.true.
- Default use_ideal_runoff=.false.
-
-[logical]
-
-
-use_ideal_calving
-
-
- To add an idealized solid runoff or calving read from a file.
- This calving runoff is assumed to require melting, so it extracts
- latent heat of fusion from the liquid ocean
- The runoff coming from idealized cavling is NOT subject to
- the global normalization realized from zero_net_water_coupler=.true.
- Default use_ideal_calving=.false.
-
-[logical]
-
-
-use_waterflux_override_calving
-
-
- Set to true will allow for model to incorporate the latent heating
- from a calving field that comes in through coupled model instantaneous
- interactions, but later will over-ride the mass flux from calving with
- a dataset that is read in from a climatology or observations.
- The idea is to only modify the mass contribution from calving through
- the over-ride, and leave the latent heat contribution untouched.
- Default use_waterflux_override_calving=.false.
-
-[logical]
-
-
-use_waterflux_override_fprec
-
-
- Set to true will allow for model to incorporate the latent heating
- from a fprec field that comes in through coupled model instantaneous
- interactions, but later will over-ride the mass flux from fprec with
- a dataset that is read in from a climatology or observations.
- The idea is to only modify the mass contribution from fprec through
- the over-ride, and leave the latent heat contribution untouched.
- Default use_waterflux_override_fprec=.false.
-
-[logical]
-
-
-use_waterflux_override_evap
-
-
- Set to true will allow for model to incorporate the latent heating
- from an evap field that comes in through coupled model instantaneous
- interactions, but later will over-ride the mass flux from evap with
- a dataset that is read in from a climatology or observations.
- The idea is to only modify the mass contribution from evap through
- the over-ride, and leave the latent heat contribution untouched.
- Default use_waterflux_override_evap=.false.
-
-[logical]
-
-
-temp_restore_tscale
-
-
- Time scale in days for restoring temperature within the top model
- grid cell.
-
-[real, units: day]
-
-
-salt_restore_tscale
-
-
- Time scale in days for restoring salinity within the top model
- grid cell.
-
-[real, units: day]
-
-
-eta_restore_tscale
-
-
- Time scale in days for restoring surface height to produce a modification to
- surface water flux. This option is only available when run with
- use_waterflux=.true.
-
-[real, units: day]
-
-
-use_constant_sst_for_restore
-
-
- To over-ride the sfc_restore.nc value for temp restoring.
- use_constant_sst_for_restore=.false.
-
-[logical]
-
-
-constant_sst_for_restore
-
-
- The SST value used if use_constant_sst_for_restore=.true.
- Default constant_sst_for_restore=12.0
-
-[real, units: degC]
-
-
-salt_restore_as_salt_flux
-
-
- When running a use_waterflux=.true. model, we may choose to add the
- salinity from a restoring condition as a salt flux or convert to
- a fresh water flux. The addition of salt does not alter the sea
- level nor does it alter the concentration of other tracers, whereas
- converting to an implied water flux will alter sea level and other
- concentrations. So we generally recommend the default
- salt_restore_as_salt_flux=.true.
-
-[logical]
-
-
-use_constant_sss_for_restore
-
-
- To over-ride the sfc_restore.nc value for salinity restoring.
- use_constant_sss_for_restore=.false.
-
-[logical]
-
-
-constant_sss_for_restore
-
-
- The SSS value used if use_constant_sss_for_restore=.true.
- Default constant_sss_for_restore=35.0
-
-[real, units: psu]
-
-
-max_delta_salinity_restore
-
-
- When computing the restoring flux for salinity, we can define
- a maximum absolute value for the difference between salinity(k=1)
- and the restoring salinity from a dataset. This approach is useful
- especially in NAtl western boundary, where poor Gulf Stream separation
- can lead to large salinity biases. If restore too much the salinity
- field, we can spuriously transport large amounts of fresh water to the
- subpoloar gyre, thus impacting the overturning circulation too much.
- If max_delta_salinity_restore < 0.0, then will NOT provide a max to the
- delta salinity; will instead compute an unbounded restoring flux.
- Default max_delta_salinity_restore=-0.50.
-
-[real, units: ppt]
-
-
-read_restore_mask
-
-
- For reading in a mask that selects regions of the domain
- that are restored (mask=1) or not restored (mask=0).
- Default read_restore_mask=.false., whereby restore_mask
- is set to tmask(k=1).
-
-[logical]
-
-
-restore_mask_gfdl
-
-
- For modifying the restore mask based on reading in
- the GFDL regional mask. Default restore_mask_gfdl=.false.
-
-[logical]
-
-
-salinity_ref
-
-
- Reference salinity used for converting fresh water flux
- to salt flux.
-
-[real, units: psu]
-
-
-salt_restore_under_ice
-
-
- Logical indicating whether to restore salinity under sea ice or not.
- When .false. then will not restore salinity in regions where we
- use a "frazil" condition as a proxy for where sea-ice is present.
- Do not use sea ice extent from a sea ice model since we generally do
- not pass information regarding ice extent between the sea ice model
- and the ocean model.
-
-[logical]
-
-
-zero_net_salt_restore
-
-
- Logical indicating whether to remove the area mean of the salinity
- restore flux so there is a net zero input of salt to the ocean
- associated with restoring.
-
-[logical]
-
-
-zero_net_salt_correction
-
-
- Logical indicating whether to remove the area mean of the salinity
- correction flux so there is a net zero input of salt to the ocean
- associated with salt correction.
-
-[logical]
-
-
-zero_net_water_restore
-
-
- Logical indicating whether to remove the area mean of the water
- restore flux so there is a net zero input of water to the ocean
- associated with restoring.
-
-[logical]
-
-
-zero_net_water_correction
-
-
- Logical indicating whether to remove the area mean of the water
- correction flux so there is a net zero input of water to the ocean
- associated with water correction.
-
-[logical]
-
-
-zero_net_water_coupler
-
-
- Logical indicating whether to remove the area mean of the water
- passed through the coupler so there is a net zero input of
- fresh water to the ocean associated with p-e+r. Do so by removing
- area mean from pme--keep river values unchanged. Note that a choice
- must be made whether to remove the area mean from rivers or pme.
- We choose pme since it is more evenly distributed than rivers.
- Also note that we DO NOT include the ice melt in this normalization.
- The reason is that we only wish to ensure the ocean+ice system
- has a zero net water. When melt or form sea ice, this only transfers
- water between liquid ocean and solid sea ice, and no normalization is
- appropriate for this case. It is only the water exchanged with the
- land and atmosphere that is normalized.
-
-[logical]
-
-
-zero_net_water_couple_restore
-
-
- This logical keeps the total water forcing on the ocean+ice system
- to a global mean of zero at each time step. We DO NOT include
- the ice melt in this normalization.
- Setting zero_net_water_couple_restore to true may be appropriate when
- running an ice-ocean model using a bulk formulae to compute
- evaporation (e.g., CORE) and when only providing a weak (or zero)
- salinity restoring. It is not appropriate when running a coupled
- ocean-atmosphere model, where the moisture budget should be
- conserved without an artificial removal of the global mean.
-
-[logical]
-
-
-land_model_heat_fluxes
-
-
- For the case where land model passes through the coupler the heat flux
- associated with the liquid runoff and calving land ice fields.
- This heat flux is computed relative to 0C, and takes the form
- heat flux = mass flux of water * temp of water * heat capacity,
- where the water can be either liquid or solid. For many coupled models,
- the water temperature is assumed to be that of the SST. But
- more complete land models now carry the heat of its water relative to 0C,
- in which case the ocean model does not need to assume anything about the
- heat content of the land water.
- Default land_model_heat_fluxes=.false.
-
-[logical]
-
-
-debug_water_fluxes
-
-
- Logical for debugging water fluxes. Must be true for any of the
- options zero_water_fluxes, zero_calving_fluxes, zero_pme_fluxes
- or zero_runoff_fluxes to be enabled.
- Default debug_water_fluxes=.false.
-
-[logical]
-
-
-zero_water_fluxes
-
-
- Logical for debugging to zero the pme, river, and pme_taum1 into
- ocean, over-riding any input from Ice_ocean_boundary.
- Default zero_water_fluxes=.false.
-
-[logical]
-
-
-zero_calving_fluxes
-
-
- Logical for debugging to zero the calving flux passed into the ocean.
- Default zero_calving_fluxes=.false.
-
-[logical]
-
-
-zero_pme_fluxes
-
-
- Logical for debugging to zero the pme flux passed into the ocean.
- Default zero_pme_fluxes=.false.
-
-[logical]
-
-
-zero_runoff_fluxes
-
-
- Logical for debugging to zero the runoff flux passed into the ocean.
- Default zero_runoff_fluxes=.false.
-
-[logical]
-
-
-zero_river_fluxes
-
-
- Logical for debugging to zero the river (calving+runoff) flux passed into the ocean.
- Default zero_river_fluxes=.false.
-
-[logical]
-
-
-convert_river_to_pme
-
-
- Logical for debugging. Here we add the river water input (calving+runoff)
- to pme, then set river=calving=runoff=0.0.
- Default convert_river_to_pme=.false.
-
-[logical]
-
-
-sbc_heat_fluxes_const
-
-
- Logical for setting the surface heat flux from the coupler
- to a global constant. Default is sbc_heat_fluxes_const=.false.
-
-[logical]
-
-
-sbc_heat_fluxes_const_seasonal
-
-
- Logical for setting the surface heat flux from the coupler
- to a global constant, and giving it a seasonally varying amplitude.
- Default is sbc_heat_fluxes_const_seasonal=.false.
-
-[logical]
-
-
-sbc_heat_fluxes_const_value
-
-
- Value for the constant heat flux when using
- sbc_heat_fluxes_const=.true.
- Default sbc_heat_fluxes_const_value=0.0.
-
-[real, units: W/m2]
-
-
-zero_heat_fluxes
-
-
- Logical for debugging to set all heat fluxes into the ocean to zero,
- over-riding any input from Ice_ocean_boundary. Default is .false.
-
-[logical]
-
-
-zero_surface_stress
-
-
- Logical for debugging to zero all surface stress applied to the ocean,
- over-riding any input from Ice_ocean_boundary. Default is .false.
-
-[logical]
-
-
-rotate_winds
-
-
- Set to true when need to rotate the winds onto the ocean model grid.
- This is needed for cases where the winds are on a spherical grid and
- the ocean model uses tripolar=.true. If generate the wind data on
- the ocean model grid, then do not need to rotate, since the rotation
- has already been done.
-
-[logical]
-
-
-max_ice_thickness
-
-
- When coupling MOM to an ice model, the sea ice thickness may need
- to be restricted to prevent vanishing top-level in MOM. Set
- max_ice_thickness (meters) < dzt(k=1) to restrict. This truncation
- avoids the numerical problem but we loose mass conservation in the coupled
- sea ice and ocean system. We also alter the pressure felt on the ocean
- as applied by the sea ice. Different vertical coordinates are needed
- to do the problem more realistically.
-
- Note that the problem of vanishing top layer is removed when use
- either ZSTAR or PSTAR as vertical coordinate.
-
-[real, units: m]
-
-
-ice_salt_concentration
-
-
- The salt concentration of sea ice. This is taken as a bulk value, and should
- be the same as that used by the ice model. Default is ice_salt_concentration=0.005,
- as that is the value used in the GFDL coupled climate model.
-
-[real, units: kg salt / kg ice]
-
-
-runoff_salinity
-
-
- The salinity of river runoff water. Default is runoff_salinity=0.0.
-
-[real, units: g salt / kg runoff water (ppt)]
-
-
-runoff_temp_min
-
-
- The minimum temperature that river runoff into the ocean is assigned.
- Default runoff_temp_min=0.0.
-
-[real, units: DegC]
-
-
-runoffspread
-
-
- Set to true if wish to use the spread_river_horz algorithm to spread
- the river runoff flux horizontally over an area into the ocean wider than
- set by the coupler. This option requires the setup of a table for
- determining the points over which we spread.
- Default runoffspread=.false.
-
-[logical]
-
-
-calvingspread
-
-
- Set to true if wish to use the spread_river_horz algorithm to spread
- the calving flux horizontally over an area into the ocean wider than
- set by the coupler. This option requires the setup of a table for
- determining the points over which we spread.
- Default calvingspread=.false.
-
-[logical]
-
-
-avg_sfc_velocity
-
-
- If set to true, the u and v fields passed up to the sea ice
- are averaged over a coupling interval. TRUE by default.
-
-[logical]
-
-
-avg_sfc_temp_salt_eta
-
-
- If set to true, the t, s and sea_level fields passed up to the sea ice
- are averaged over a coupling interval. TRUE by default.
-
-[logical]
-
-
-use_full_patm_for_sea_level
-
-
- The option use_full_patm_for_sea_level allows for the passing
- of the sea level including the full weight of sea ice back to
- the ice model. This approach maintains the max weight on the liquid
- ocean according to the nml variable max_ice_thickness. But it does
- allow the sea ice to know when there is actually more sea ice than that
- set by max_ice_thickness. This option then provides for a negative
- feedback on the runaway growth of sea ice, since the full pressure acting to
- make the ice flow will be correctly felt. This is a new option, and is not
- fully tested, So the default is use_full_patm_for_sea_level=.false
-
-[logical]
-
-
-do_flux_correction
-
-
- For applying surface flux correction to to a tracer or wind stress field.
- This code is used at GFDL for idealized perturbation experiments, such
- as when one wishes to artificially enhance the wind stress to test
- model sensitivity. It is also appropriate for coupled models that
- may require a modification to the fluxes arrising from a coupled model,
- via reading in information from a pre-defined
- data file,
- Default do_flux_correction=.false.
-
-[logical]
-
-
-temp_correction_scale
-
-
- A scale multiplying the flux correction for temperature.
- Default temp_correction_scale=0.0.
-
-[real, units: dimensionless]
-
-
-salt_correction_scale
-
-
- A scale multiplying the flux correction for salinity.
- Default salt_correction_scale=0.0.
-
-[real, units: dimensionless]
-
-
-tau_x_correction_scale
-
-
- A scale multiplying the flux correction for tau_x.
- Default tau_x_correction_scale=0.0.
-
-[real, units: dimensionless]
-
-
-tau_y_correction_scale
-
-
- A scale multiplying the flux correction for tau_y.
- Default tau_y_correction_scale=0.0.
-
-[real, units: dimensionless]
-
-
-do_bitwise_exact_sum
-
-
- Set true to do bitwise exact global sum. When it is false, the global
- sum will be non-bitwise_exact, but will significantly increase efficiency.
- The default value is do_bitwise_exact_sum=.true. in order to ensure answers
- do not change when alter processors. But if wish to enhance the efficiency
- of coupled ocean-ice models that use one of the global normalization options
- zero_net_salt_restore =.true.
- zero_net_salt_correction =.true.
- zero_net_water_restore =.true.
- zero_net_water_correction =.true.
- zero_net_water_coupler =.true.
- zero_net_water_couple_restore=.true.
- then one may wish to consider setting do_bitwise_exact_sum=.false.
-
-[logical]
-
-
-constant_hlf
-
-
- Treat latent heat of fusion as a constant. Otherwise, use the TEOS-10
- approach in which hlf is function of surface salinity.
- Note, TEOS-10 approach is only valid using Absolute Salinity and
- conservative temperature as the prognostic fields.
- Default constant_hlf = .true., which is the case for pre-TEOS-10 methods.
-
-[logical]
-
-
-constant_hlv
-
-
- Treat latent heat of vaporization as a constant. Otherwise, use the TEOS-10
- approach in which hlf is function of surface salinity.
- Note, TEOS-10 approach is only valid using Absolute Salinity and
- conservative temperature as the prognostic fields.
- Default constant_hlv = .true., which is the case for pre-TEOS-10 methods.
-
-[logical]
-
-
-read_stokes_drift
-
-
- This option is to be used when coupling to a surface wave model such as
- Wavewatch III that provides both the Stokes drift (m/s) velocity at the
- ocean surface, and a decay scale for projecting the Stokes
- drift into the interior. Default read_stokes_drift = .false.
-
-[logical]
-
- Initialize the thickness type.
-
- For pressure-based vertical coordinates, this initialization here
- is preliminary.
-
-
-
-
-
-
-
-
thickness_initialize
-
-
-DESCRIPTION
-
-
- Initialize vertical thicknesses of grid cells.
- For Boussinesq models, this code assumes the
- surface heights eta_t and eta_u are zero.
-
- The values here are relevant for the time=0 initialization
- of the model. Some time independent arrays are also set here,
- but they are over-written if there is a restart file.
-
- For pressure based vertical coordinates, the results here
- assume density = rho0_profile(k). The values are readjusted in
- ocean_thickness_init_adjust after we have determined the initial
- in situ density. This readjustment may involve enforcing an
- initial eta field of zero value, or the default which allows
- for eta to initially be nonzero.
-
-
-
-
-
-
-
-
-
ocean_thickness_init_adjust
-
-
-DESCRIPTION
-
-
-
- When initializing the pressure model, we can choose to initialize
- with a zero surface height, which requires some adjustment of
- bottom depths, or allow the surface height to be nonzero.
-
- The default is a nonzero surface height via
- initialize_zero_eta=.false.
-
-===============================================================
- The following comments refer to the possible issues arising
- from enforcing eta=0 on initialiation via
- initialize_zero_eta=.true.
-
- If we wish to enforce eta=0 on initialization, then we determine
- the depth of ocean needed to ensure a minimum bottom cell
- thickness as set by nml paramter thickness_dzt_min_init.
- This bottom depth is a function of the initial in-situ density
- as well as the nml thickness_dzt_min_init.
-
- If Grid%ht is sufficient according to the specifications of
- thickness_dzt_min_init and the initial in-situ density, then
- model is likely to remain stable, in that there is very small
- chance of losing bottom cell.
- (assuming thickness_dzt_min_init is > 5.0 or so).
-
- If Grid%ht is too shallow, again given the initial rho and
- pressure increments dst, then it is recommended that the user
- modify either the initial density (not easy) or the bottom
- topography (easy). The modifications are often quite trivial,
- depending on thickness_dzt_min_init and how light certain regions
- of the model are. The array "ht_mod" can be saved in the
- diag_table and compared to Grid%ht to see what modifications
- are required. If modificatations are to be made to the original
- grid_spec.nc file, simply use the NCO commands as follows:
-
- 1/ remove the original depth_t array from the original grid spec
- file, and write out a new grid spec file absent the depth_t array.
- ncea -x -v depth_t grid_spec_old.nc grid_spec_new.nc
-
- 2/ append to the new grid spec file the modified bottom topography
- array ht_mod, which was generated in an earlier run of the model.
- ncea -A -v ht_mod history_file_with_ht_mod.nc grid_spec_new.nc
-
- 3/ rename ht_mod to depth_t to conform to standard MOM grid_spec
- name convention.
- ncvarrename new_grid.nc ht_mod depth_t
-
- If there are no modifications required to the depth_t array,
- then it is unlikely that the pressure model will evolve to the
- point of loosing the bottom cell and thus the model will remain
- stable. This conclusion is certainly based on the degree to which
- the model is run with changes in water masses.
-
-===============================================================
-
- NOTE: We generally compute values for the grid increments over
- land. The land values that are in the global halos are not
- going to be available from the restart files. Hence, they
- will need to be recomputed when restarting the model. This
- recalculation is done in dst_land_adjust.
-
- The land values are needed for use in computing U-cell grid
- factors using remapping operators. If we naively place zeros
- in the land, then, for example, rho_dzu next to land will be
- wrong, as it will be based on averaging a non-zero interior
- rho_dzt value with a rho_dzt incorretly set to zero, and so
- lead to spuriously small rho_dzu values next to land. Note that
- the placement of nonzero values of the grid values over land
- is something that is trivially done for the z-models. More care
- is needed with pressure models.
-
-
-
-
-
-
-
-
-
thickness_restart
-
-
-DESCRIPTION
-
-
- Read basic elements of thickness derived type from restart,
- then set remaining elements of the type.
-
- Note that some array elements may be time independent.
- Their values have already been set in thickness_initialize
- or ocean_thickness_init_adjust, and they should not be
- over-written here (in particular, they should not be
- reset here to zero).
-
- To ensure reproducibility across restarts, this routine
- uses the same logic as update_tcell_thickness and
- update_ucell_thickness. This is particularly important
- for the terrain following calculations.
-
- Note that ocean_thickness_init is called prior to
- ocean_operators_init. Hence, we cannot use any
- operators in this subroutine.
-
-
-
-
-
-
-
-
-
calculate_restart_thickness
-
-
-DESCRIPTION
-
-
- This subroutine calculates the total thickness and the E contribution
- to thickness. It is used for the press, pstar and zstar vertical
- coordinates.
-
-
-
-
-
-
-
-
dst_land_adjust
-
-
-DESCRIPTION
-
-
- For computing the grid values inside land in global halos.
- These values are not zero, and so they are not available from
- restart file. They are needed for pressure-based vertical
- coordinate models in order to get the U-cell values at
- global land boundaries via the remap operator.
-
- This step is necessitated by the modifications to dst
- and other arrays made in ocean_thickness_init_adjust.
-
-
-
-
-
-
-
-
update_tcell_thickness
-
-
-DESCRIPTION
-
-
- Update time dependent thickness of T cells. When not using the
- Lagrangian blob scheme. For routines relevant to the blobs, we use:
- 1/ update_tcell_thic_blob
- 2/ update_E_thickness
- 3/ dzt_dst_update
- which are further down the module.
-
- Notes
-
- 1. For pressure-based coordinates, must use rho(tau) since
- rho(taup1) has not yet been computed. This is a limitation of
- the "z-like" algorithm approach used in MOM. It is minor,
- however, since rho(tau) is very close to rho(taup1). Also, this
- approach comes with the advantage of rendering vertical
- physical processes (e.g., diffusion) linear for the general
- coordinates in MOM, just as with geopotential models.
-
- 2. For all coordinates, need to place something reasonable over
- land for dz increments to preclude division by zero.
- For GEOPOTENTIAL and ZSTAR, we just use the time=zero value for dzt.
- For ZSIGMA we set a minimum depth for a fictitious layer over land.
- For PRESSURE and PSTAR, we set rho=rho0_profile and use the time=0 dzt values.
- For PSIGMA, we rho=rho0_profile and use the fictitious layer over land.
- The treatment of these land-points only contributes to the treatment
- of the U-cell grid quantities in the halos and on land, as they are
- computed via the REMAP_ZT_TO_ZU operator.
-
- 3. We need to update s-coordinate increments for GEOPOTENTIAL and
- PRESSURE. It is only for these two coordinates that we modify the
- endpoint values for the s-grid increments.
-
-
-
-
-
-
-
-
-
update_ucell_thickness
-
-
-DESCRIPTION
-
-
- Update time dependent thickness of U cells.
-
- Notes
-
- The computation of the depth arrays is a bit ad hoc. Here are
- the methods and their rationale.
-
- 1. For terrain following coordinates, the remap operator will entrain
- the very shallow layer T-points over land into the four-point averaging.
- This will cause the resulting U-cell depths next to land to be far shallower
- than what they should be. To avoid this problem, we set the U-cell depths the
- same as the T-cell depths. This specification causes no problems for budgets
- or energetic balance since Grid%umask array is already defined according to
- the usual B-grid specification.
-
- 2. For non-terrain and non-geopotential coordinates, compute U-cell thicknesses
- as min of surrounding T-cell thicknesses. This method follows that
- used with earlier MOM versions for the bottom partial step topography.
- Experiments with ZSTAR reveal that we must use the min function for dzu
- computation, rather than the alternative of a remap operator. If using
- the remap operator and nontrivial topography, then the velocity field can
- develop nontrivial noise. We have found that can compute dzwu using the
- remap operator without introducing noise. But we choose to use the
- min function to maintain compatibility with traditional approach in
- geopotential vertical coordinate versions of MOM.
-
- If use_blobs=.true. in the ocean_model_nml, we adopt the following:
- *dzuT = min of surrounting T-cell thickness,
- *dzuL = min of surrounting T-cell thickness,
- *dzu = *dzuT - *dztL
-
-
-
-
-
-
-
-
rho_dzt_tendency
-
-
-DESCRIPTION
-
-
- Compute tendency for rho_dzt. This tendency is a function of the
- vertical coordinate.
-
-
-
-
-
-
-
-
thickness_chksum
-
-
-DESCRIPTION
-
-
-
- Compute checksum for thickness components .
- Only print checksums for fields that should agree across restarts.
-
-
-
-
-
-
-
-
-
thickness_details
-
-
-DESCRIPTION
-
-
-
- For debugging, we print here some details of the grid at a particular
- (i,j) point.
-
-
-
-
-
-
-
-
-
ocean_thickness_restart
-
-
-DESCRIPTION
-
-
- Write out restart files registered through register_restart_file
-
-
-
-
-
-
-
-
ocean_thickness_end
-
-
-DESCRIPTION
-
-
- Write basic elements of thickness derived type to restart
-
-
-
-
-
-
-
-
REMAP_ZT_TO_ZU
-
-
-DESCRIPTION
-
-
- REMAP_ZT_TO_ZU remaps a T-cell thickness or vertical depth on a
- T-cell to the corresponding place on U-cell.
-
- This is the same operator as REMAP_BT_TO_BU.
- It is needed for ocean_thickness_init since this routine is called
- prior to ocean_operators_init. This is a bit awkward, but
- ocean_operators needs thickness values, so it must be called
- after thickness is initialized.
-
-
-
-
-
-
-
-
dzt_dst_update
-
-
-DESCRIPTION
-
-
- Calculate the quantity dzt_dst. dzt_dst is required by the Lagrangian
- blob framework in order to calculate the grid cell the a blob resides
- in at taup1. This information is required prior to the the earliest
- time that we can update the total thickness. As such, we are
- motivated to separate this calculation when use_blobs=.true.
- When use_blobs=.false. the calculation is conducted when the tcell
- thickness is updated.
- We also update coordinate increments for GEOPOTENTIAL and PRESSURE.
- Only for these two coordinates do we need to modify the endpoint
- values for the s-grid increments. Other MOM coordinates have dst
- and dswt constant in time.
-
- Note that at present, GEOPOTENTIAL coordinates are not supported
- by this implementation of the blob framework.
-
-
-
-
-
-
-
-
update_tcell_thick_blob
-
-
-DESCRIPTION
-
-
- The same principle is used as for update_tcell_thickness, however,
- this routine is specific to the Lagrangian blob scheme.
-
- The routine calculates the total tracer grid cell thickness for the
- various vertical coordinate systems (excluding ZSGIMA and PSIGMA).
- Major things to note are:
- 1/ dzt_dst is calculated previously using dzt_dst_update
- 2/ this routine does not calculate the L or E system thicknesses,
- those are calculated separately.
- 3/ This routine is not called unless use_blobs=.true. in
- ocean_model_nml.
-
- Note that the present implementation of the Lagrangian blobs does
- not support ZSIGMA or ZPRESSURE coordinates. GEOPOTENTIAL is also
- not supported.
-
- Also note that we calculate the total density weighted thickness,
- rho_dztT, is calculated differently to how the density weighted
- thickness is calculated without the blobs, rho_dzt.
- rho_dztT(taup1) = rho_dztT(tau) + dtime*rho_dzt_tendency
-
-
-
-
-
-
-
-
update_E_thickness
-
-
-DESCRIPTION
-
-
- Calculates the E system thickness using the basic formulation,
- E_thickness = Total_thickness - L_thickness
-
- Note that this routine is called twice each time step. Once from
- update_ocean_model, and once from the update_ocean_tracer. The
- second call is required after the implicit adjustment involving
- blobs.
-
-
-
-
-
-
-
-
thickness_chksum_blobs
-
-
-DESCRIPTION
-
-
- Compute checksum for thickness components for the Lagrangian and
- total thicknesses.
-
- Only print checksums for fields that should agree across restarts.
-
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_thickness_nml
-
-
-
-
-
-debug_this_module
-
-
- For debugging.
-
-[logical]
-
-
-debug_this_module_detail
-
-
- For debugging pressure coordinate models. Lots of grid information
- printed.
-
-[logical]
-
-
-write_a_restart
-
-
- Set true to write a restart. False setting only for rare
- cases where wish to benchmark model without measuring the cost
- of writing restarts and associated chksums.
- Default is write_a_restart=.true.
-
-[logical]
-
-
-linear_free_surface
-
-
- For debugging, set the thickness of top cell in
- geopotential model to time independent values.
- This option is needed if use the kappa_sort diagnostic.
- Default linear_free_surface=.false.
-
-[logical]
-
-
-thickness_method
-
-
- To determine whether use energetic method or finite volume method
- to compute the thickness of a grid cell. Options are
- thickness_method=energetic or thickness_method=finitevolume.
- There is little overall difference in results for pbot and eta.
- However, it has been found that for realistic bottom topography
- simulations, the vertical velocity component is very noisy with
- the finitevolume approach. So this approach is considered
- experimental. The default is thickness_method='energetic'.
-
-[character]
-
-
-full_step_topography
-
-
- For case where with to only have the dzt be determined by the full step
- bottom topography. This nml option is provided only for backwards
- compatibility with older mom experiments using the full step topog.
-
-[logical]
-
-
-enforce_positive_dzt
-
-
- For cases where wish to run model even with negative thickness.
- Default enforce_positive_dzt=.false.
-
-[logical]
-
-
-epsilon_init_thickness
-
-
- For determining how strict we are to check for the thickness of
- a column when initializing pressure based vertical coordinate models.
-
-[dimensionless]
-
-
-thickness_dzt_min
-
-
- Minimum dzt set when enforce_positive_dzt set true.
- Default thickness_dzt_min=1.0.
-
-[real, units: m]
-
-
-initialize_zero_eta
-
-
- For pressure-based models, we can (with some work) initialize the
- model to have a zero surface height. The recomended approach is to
- allow the surface height to be whatever it wants to be, and let adjustments
- smooth it over time. Default initialize_zero_eta=.false.
-
-[logical]
-
-
-thickness_dzt_min_init
-
-
- For determining a modified bottom depth array
- that is required to ensure pressure model, based on initial
- in-situ density, retains a nontrivial bottom cell thickness
- in the case when initialize_zero_eta=0.0
- Default thickness_dzt_min_init=5.0.
-
-[real, units: m]
-
-
-rescale_mass_to_get_ht_mod
-
-
- Expedient to allow for the computation of ht_mod.
- in the case when initialize_zero_eta=.true. Here,
- we run the pressure based model with a rescaled mass that
- is sufficient to maintain non-negative dzt, at least for
- a short period. This allows for one to run a day integration
- to produce ht_mod. rescale_mass_to_get_ht_mod=.true. will
- produce spurious results in general due to problems with the
- pressure gradient computation. So it is not recommended for
- more than initial day or so. Default rescale_mass_to_get_ht_mod=.false.
-
-[logical]
-
-
-read_rescale_rho0_mask
-
-
- For reading in a basin mask of use to re-define rho0 in
- isolated regions such as the Black Sea. This is used for
- modifying the definition of the pressure or pstar levels
- during the initialization of the thicknesses dst. This
- approach is appropriate in general, but has only been tested
- when modify the pressure levels within a fully enclosed basin.
- Default read_rescale_rho0_mask=.false.
-
-[logical]
-
-
-rescale_rho0_mask_gfdl
-
-
- For specifying the rescale_rho0_mask based on reading in
- the GFDL regional mask. Default rescale_rho0_mask_gfdl=.false.
-
-[logical]
-
-
-rescale_rho0_basin_label
-
-
- For rescaling rho0 in a basin with a number rescale_rho0_basin_label.
- For the Black Sea using GFDL basin masks in OM3,
- rescale_rho0_basin_label=7.0. Default rescale_rho0_basin_label=-1.0
-
-[real]
-
-
-rescale_rho0_value
-
-
- Fractional value for rescaling rho0 in the a region.
- Default rescale_rho0_value=1.0.
-
-[logical]
-
-
-depth_min_for_sigma
-
-
- For sigma coordinates, have minimum depth so that have layers defined
- globally. Masks will zero out results over land, but for numerics
- it is useful to compute everywhere. Default depth_min_for_sigma=0.01.
-
-[real, units: m]
-
-
-read_rho0_profile
-
-
- To read in an initial rho0(z) profile to assist in defining the
- initial settings for the pressure increments dst, for use in
- setting the pressure-based vertical coordinate grids. Ideally,
- this profile is determined by the level averaged density in
- the initial conditions. Note that it is essential to have
- rho0_profile have a sensible value at all depths even if there
- is no water there, since there are places where we divide by
- rho0_profile in rock. Also, be mindful that with denser water
- at depth, the pressure levels will be coarser at depth than if
- using the trivial density profile rho0(k)=rho0.
- This option is experimental, so it is recommended that user
- maintain the default read_rho0_profile=.false.
-
-[logical]
-
-
-pbot0_simple
-
-
- For testing purposes, have this option compute pbot0=g*rho0*ht
- with rho0= constant. Default pbot0_simple=.false.
-
-[logical]
-
-
-update_dzwu_k0
-
-
- A bug in certain versions of MOM4p1 was present, whereby
- Thickness%dzwu(i,j,k=0) was never updated, except for GEOPOTENTIAL
- vertical coordinates. This logical, whose default is
- update_dzwu_k0=.true., is provided for legacy purposes.
- To test the older results, have update_dzwu_k0=.false.
-
-[logical]
-
-
-max_num_bad_print
-
-
- Maximum bad grid cells printout for identifying problematic simulations.
- Default max_num_bad_print=25.
-
-[integer]
-
- Initialize the ocean bottom topography.
-
- There are two reasons to prefer land be at j=1.
-
- A/ MOM employs a northest B-grid. To construct
- horizontal remapping operators, we need information
- about grid factors one row outside of the global
- domain boundaries. In particular, we need j=0
- grid information. However, when constructing the grid spec
- file, we assume nothing about the region outside
- the global domain. So MOM's requirement of j=0
- grid information necessitates extrapolation.
- This extrapolation is done inside ocean_grids.F90, and
- it can lead to non-symmetric values of grid spacing
- for the region j=0 and j=nj, even if the domain global
- limits are symmetric across the equator.
-
- B/ The FMS Sea Ice Simulator (SIS) requires land to be present
- for all points at jsc+joff=1. If this is not the case, then
- the ocean model cannot be coupled to SIS. The SIS requirement
- of all land at jsc+joff=1 is related to the use of a northeast
- B-grid convention. To couple the models, the ocean grid
- must be generated with fill_first_row=.true.
-
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_topog_nml
-
-
-
-
-
-debug_this_module
-
-
- For debugging.
-
-[logical]
-
-
-flat_bottom
-
-
- For debugging, it is often useful to over-ride the grid spec file
- and simply make the domain flat bottom.
-
-[logical]
-
-
-flat_bottom_kmt
-
-
- Number of depth levels to use for the flat_bottom option.
-
-[integer]
-
-
-flat_bottom_ht
-
-
- Depth to make the flat_bottom.
-
-[real]
-
-
-min_thickness
-
-
- min_thickness is only used for Mosaic grid. Since there is no kmt available
- in mosaic grid, need to set min_thickness to configure kmt based on ht and zw.
- Default min_thickness=1.0 metre.
-
-[real]
-
-
-kmt_recompute
-
-
- To recompute the kmt array based on min_thickness. This step is not recommended
- in general, since it can modify the kmt array which may be in the grid spec file.
- But it may be of use for specialized situations, such as when you wish to use
- the same topography file with a refined vertical resolution.
-
-[logical]
-
-
-kmt_recompute_offset
-
-
- To recompute the kmt array based on min_thickness, with an offset
- determined by kmt_recompute_offset. Default kmt_recompute_offset=0.
-
-[integer]
-
- This module contains type declarations and default values for ocean model.
-
-
-
-
-
- This module contains type declarations and default values for ocean model.
- Multiple model realizations need to be distinguished by
- an ensemble_id for use by the diag_manager.
-
- Solve the vertical diffusion equation implicitly using the
- method of inverting a tridiagonal matrix as described in
- Numerical Recipes in Fortran, The art of Scientific Computing,
- Second Edition, Press, Teukolsky, Vetterling, Flannery, 1992
- pages 42,43.
-
- This routine assumes that the variables are defined at grid points,
- and the top and bottom b.c. are flux conditions.
-
- inputs:
-
- z = right hand side terms
-
- nk = number of vertical levels
-
- topbc = top boundary condition
-
- botbc = bottom boundary condition
-
- dcb = vertical mixing coeff at base of cell
-
- tdt = timestep over which do implicit update
-
- kmz = level indicator
-
- mask = land/sea mask
-
- outputs:
-
- z = returned solution
-
-
-
-
-
-
-
-
-
invtri_bmf
-
-
-DESCRIPTION
-
-
- Solve the vertical friction equation implicitly using the
- method of inverting a tridiagonal matrix as described in
- Numerical Recipes in Fortran, The art of Scientific Computing,
- Second Edition, Press, Teukolsky, Vetterling, Flannery, 1992
- pages 42,43.
-
- This routine assumes that the variables are defined at grid points,
- and the top b.c. is a flux condition. The bottom b.c. is assumed
- to be a bottom drag which is implemented implicitly, thus allowing
- for large values of the bottom drag coefficient.
-
- NOTE: This routine is generally only called when doing the bmf
- implicitly in time. The original invtri is used for explicit
- bmf.
-
- inputs:
-
- z = right hand side terms
-
- nk = number of vertical levels
-
- topbc = top boundary condition
-
- botbc = time explicit bottom boundary condition (zero in this routine, since bmf is implicit)
-
- gamma = botttom drag factor scaling the u(taup1) contribution to bottom drag
-
- dcb = vertical mixing coeff at base of cell
-
- tdt = timestep over which do implicit update
-
- kmz = level indicator
-
- mask = land/sea mask
-
- outputs:
-
- z = returned solution
-
-
-
-
-
-
-
-
-
iplot
-
-
-DESCRIPTION
-
-
-
- map integer array "iarray" into characters for printing with
- format (a1) to provide a contour map of the integer field.
- note: max number of unique characters = 80
-
- inputs:
-
- iarray = integer array to be plotted
-
- is = starting index along inner dimension of "iarray"
-
- ie = ending index along inner dimension of "iarray"
-
- js = starting index along outer dimension of "iarray"
-
- je = ending index along outer dimension of "iarray"
-
- output: prints contour map of "iarray"
-
-
-
-
-
-
-
-
-
matrix
-
-
-DESCRIPTION
-
-
- matrix is a general two-dimensional array printing routine,
- input:
-
- array = the array to be printed
-
- istrt = the 1st element of the 1st dimension to be printed
-
- im = the last element of the 1st dimension to be printed
-
- jstrt = the 1st element of the 2nd dimension to be printed
-
- jm = the last element of the 2nd dimension to be printed
- the 2nd dimension is printed in reverse order if both
- jstrt and jm are negative
-
- scale = a scaling factor by which array is divided before
- printing. (if this is zero, no scaling is done.)
- if scale=0, 10 columns are printed across in e format
- if scale>0, 20 columns are printed across in f format
-
- output: print "array" as a matrix
-
-
-
-
-
-
-
-
-
write_timestamp
-
-
-DESCRIPTION
-
-
- Write the time stamp.
-
-
-
-
-
-
-
-
write_chksum_header
-
-
-DESCRIPTION
-
-
- Write the checksum header.
-
-
-
-
-
-
-
-
write_note
-
-
-DESCRIPTION
-
-
- Write a note.
-
-
-
-
-
-
-
-
write_warning
-
-
-DESCRIPTION
-
-
- Write a warning.
-
-
-
-
-
-
-
-
write_line
-
-
-DESCRIPTION
-
-
- Write a message.
-
-
-
-
-
-
-
-
write_chksum_3d
-
-
-DESCRIPTION
-
-
- Write a 3d checksum.
-
-
-
-
-
-
-
-
write_chksum_2d
-
-
-DESCRIPTION
-
-
- Write a 2d checksum.
-
-
-
-
-
-
-
-
write_chksum_2d_int
-
-
-DESCRIPTION
-
-
- Write a 2d integer checksum.
-
-
-
-
-
-
-
-
check_restart
-
-
-DESCRIPTION
-
-
- Write a note regarding the restart setup.
-
-
-
-
-
-
-
-
write_summary
-
-
-DESCRIPTION
-
-
- Write a summary note.
-
-
-
-
-
-
-
-
diagnose_3d
-
-
-DESCRIPTION
-
-
- Helper function for diagnosting 3D data using the grid tmask.
-
-
-
-
-
-
-
-
diagnose_2d
-
-
-DESCRIPTION
-
-
- Helper function for diagnosting 2D data using the grid tmask.
-
-
-
-
-
-
-
-
diagnose_2d_int
-
-
-DESCRIPTION
-
-
- Helper function for diagnosting 2D data using the grid tmask.
-
-
-
-
-
-
-
-
diagnose_3d_int
-
-
-DESCRIPTION
-
-
- Helper function for diagnosting 3D data using the grid tmask.
-
-
- Time explicit contributions to thickness weighted and density
- weighted acceleration.
-
- Omit here the Coriolis force and vertical friction.
- They are omitted in order to facilitate the construction of the
- vertically integrated forcing of the barotropic dynamics.
- They will be added later in ocean_explicit_accel_b.
-
-
-
-
-
-
-
-
-
ocean_explicit_accel_b
-
-
-DESCRIPTION
-
-
-
- Add the contributions from the Coriolis force, computed explicitly
- in time, and those from explicit vertical friction. Add these to
- the thickness weighted and density weighted acceleration.
-
- Note: no visc_cbu_form_drag is included here, since it must
- be handled via implicit vertical friction to maintain stability
- for general cases.
-
-
-
-
-
-
-
-
-
ocean_implicit_accel
-
-
-DESCRIPTION
-
-
-
- Add the time implicit contributions from the Coriolis force
- and vertical friction. Add these to the thickness weighted
- and density weighted acceleration.
-
- Note the contribution from visc_cbu_form_drag is used for
- implicit vertical friction.
-
- Note there is no time implicit Coriolis for Cgrid.
-
-
-
-
-
-
-
-
-
update_ocean_velocity_bgrid
-
-
-DESCRIPTION
-
-
- Update velocity components.
- There are two general methods available.
-
- 1/ update baroclinic velocity; then add (udrho,vdrho) from external
- mode algorithm to get the full velocity field. This method is
- analogous to the older approach with the rigid lid.
-
- 2/ update the full velocity, so there is no need to introduce the
- intermediate step with the baroclinic velocity. To remain stable,
- we must use the time filtered barotropic pressure gradient.
- We then diagnose the vertically integrated horizontal momentum
- (udrho,vdrho) and its convergence, since these fields are needed
- elsewhere.
-
-
-
-
-
-
-
-
-
update_ocean_velocity_cgrid
-
-
-DESCRIPTION
-
-
- Update velocity components, assuming Cgrid layout.
-
- Also assume splitting, so update baroclinic velocity;
- then add (udrho,vdrho) from external mode algorithm to get the
- full velocity field. This method is
- analogous to the older approach with the rigid lid.
-
- As we have already called update_ucell_thickness, the array
- rho_dzten has been udpated to taup1. We use Adv_vel to obtain
- the tau value of (u,v)*rho_dzten, since Adv_vel has been computed
- at the start of the time stepping using (u,v)(tau).
-
-
-
-
-
-
-
-
-
ocean_velocity_restart
-
-
-DESCRIPTION
-
-
-
- Write out restart files registered through register_restart_file
-
-
-
-
-
-
-
-
-
ocean_velocity_end
-
-
-DESCRIPTION
-
-
-
- Write velocity field to a restart
-
-
-
-
-
-
-
-
-
velocity_truncate
-
-
-DESCRIPTION
-
-
- Truncate velocity so that either component
- has magnitude no larger than nml specified value.
-
-
-
-
-
-
-
-
-
ocean_velocity_chksum
-
-
-DESCRIPTION
-
-
- Compute checksum for velocity components
-
-
-
-
-
-
-
-
remap_s_to_depth
-
-
-DESCRIPTION
-
-
-
- Remap in the vertical from s-coordinate to depth and then send to
- diagnostic manager.
-
- This routine is mostly of use for terrain following vertical
- coordinates, which generally deviate a lot from depth or pressure
- coordinates. The zstar and pstar coordinates are very similar
- to z or pressure, so there is no need to do the remapping for
- purposes of visualization.
-
- The routine needs to be made more general and faster.
- It also has been found to be problematic, so it is NOT
- recommended. It remains here as a template for a better algorithm.
- Remapping methods in Ferret are much better.
-
- Use rho_dzu weighting to account for nonBoussinesq.
-
- Author: Stephen.Griffies
-
-
-
-
-
-
-
-
-
stokes_coriolis_force
-
-
-DESCRIPTION
-
-
-
- Time explicit contributions to thickness weighted and density
- weighted acceleration from the Stokes coriolis force, where the
- Stokes drift arises from surface ocean waves. To obtain the
- Stokes drift requires coupling MOM to a surface wave model.
-
- Assume stokes_drift is on U-grid point (smg: to be revisited).
-
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_velocity_nml
-
-
-
-
-
-debug_this_module
-
-
- For debugging.
-
-[logical]
-
-
-write_a_restart
-
-
- Set true to write a restart. False setting only for rare
- cases where wish to benchmark model without measuring the cost
- of writing restarts and associated chksums.
- Default is write_a_restart=.true.
-
-[logical]
-
-
-update_velocity_via_uprime
-
-
- When updating the velocity, this method first computes uprime
- as the updated velocity minus the barotropic pressure gradient.
- This approach is motivated from the rigid lid approach, in which
- the surface pressure was never used to update the barotropic
- fields.
- With the explicit free surface, we have the choice to
- update the full velocity field, with the barotropic contributions
- to the pressure field resulting from a time average in the
- external mode algorithm. This approach is for testing only,
- and it has been found to be unstable for many cases.
-
- update_velocity_via_uprime=.true. uses the older aproach,
- in which the udrho,vdrho fields are taken from the external
- mode module.
-
- update_velocity_via_uprime=.false. only takes the time averaged
- pressure from the external mode, and thus updates the full
- velocity and so recomputes the udrho,vdrho fields.
-
- Default update_velocity_via_uprime=.true.
- The case of update_velocity_via_uprime=.false. is for testing only.
- It is not supported for general use.
-
-[logical]
-
-
-use_constant_velocity
-
-
- For running with time independent constant velocity.
- For use with idealized cases. Default=.false.
-
-[logical]
-
-
-constant_u
-
-
- For running with use_constant_velocity.
- Set the i-velocity component to this value.
- Default constant_u=0.0
-
-[real, units: meter/sec]
-
-
-constant_v
-
-
- For running with use_constant_velocity.
- Set the j-velocity component to this value.
- Default constant_v=0.0
-
-[real, units: meter/sec]
-
-
-zero_tendency
-
-
- For debugging. Will freeze the baroclinic velocity fields.
-
-[logical]
-
-
-zero_tendency_explicit_a
-
-
- For debugging. Will not use explicit-a part of the tendency.
-
-[logical]
-
-
-zero_tendency_explicit_b
-
-
- For debugging. Will not use explicit-b part of the tendency.
-
-[logical]
-
-
-zero_tendency_implicit
-
-
- For debugging. Will not use implicit part of the tendency.
-
-[logical]
-
-
-truncate_velocity
-
-
- Truncate the baroclinic velocity to a maximum value. Useful for cases where
- the initial spin-up initiates spuriously large model velocities that would
- otherwise cause the model to blow-up. Also can be used as a very simple
- "polar filter" in cases where have spherical coordinates and wish to avoid
- using the traditional polar filters.
-
-[logical]
-
-
-truncate_velocity_value
-
-
- Speed above which will truncate the baroclinic velocity
-
-[real, units: meter/sec]
-
-
-truncate_velocity_lat
-
-
- Latitude poleward of which we truncate the velocity. Useful in cases
- when wish to truncate the velocity only in polar regions. Default is 0.0
-
-[real, units: dimensionless]
-
-
-truncate_verbose
-
-
- For verbose printout
-
-[logical]
-
-
-max_cgint
-
-
- Maximum internal gravity wave speed--used for diagnosing conservative
- estimate of stable time steps.
-
-[real]
-
-
-adams_bashforth_epsilon
-
-
- Dimensionless parameter for 2nd order Adams-Bashforth implementation of
- velocity advection. Values between 0.5 and 1.0 are recommended.
- Value of 0.5 leads to second order accurate, but it is formally
- weakly unstable (Durran, Section 2.3.4).
-
-[real, units: dimensionless]
-
-
-adams_bashforth_third
-
-
- For a third order treatment of the velocity advection.
- This is stable and so needs no temporal dissipation
- (Section 2.3.6 of Durran). This is the model default.
-
-[logical]
-
-
-use_stokes_coriolis_force
-
-
- For including the contribution to the Coriolis force from surface wave
- induced Stokes drift. This force requires the coupling to a prognostic
- surface wave model. Default use_stokes_coriolis_force=.false.
-
-[logical]
-
-
-
-
-
-
-
-
-
-
-
REFERENCES
-
-
-
-
- Durran, Numerical Methods for Wave Equations in Geophysical
- Fluid Dynamics (1999).
-
-
- R.C. Pacanowski and S.M. Griffies, The MOM3 Manual (1999).
- NOAA/Geophysical Fluid Dynamics Laboratory
-
-
- S.M. Griffies, R.C. Pacanowski, R.M. Schmidt, and V. Balaji
- Tracer Conservation with an Explicit Free Surface Method for
- Z-coordinate Ocean Models
- Monthly Weather Review (2001) vol 129 pages 1081--1098
-
-
- S.M. Griffies, M.J. Harrison, R.C. Pacanowski, and
- A. Rosati, A Technical Guide to MOM4 (2004).
- NOAA/Geophysical Fluid Dynamics Laboratory
-
-
- S.M. Griffies, Fundamentals of Ocean Climate Models (2004).
- Princeton University Press.
-
-
- Compute thickness weighted and density weighted acceleration
- (kg/m^3)*(m^2/s^2) due to horizontal (constant k-level)
- advection of velocity.
-
-
-
-
-
-
-
-
-
horz_advection_centered
-
-
-DESCRIPTION
-
-
-
- Compute thickness weighted and density weighted acceleration
- (kg/m^3)*(m^2/s^2) due to horizontal (constant k-level)
- advection of velocity.
-
- Use second order centered method for either Bgrid or Cgrid.
-
-
-
-
-
-
-
-
-
horz_advection_upwind
-
-
-DESCRIPTION
-
-
-
- Compute thickness weighted and density weighted acceleration
- (kg/m^3)*(m^2/s^2) due to horizontal (constant k-level)
- advection of velocity.
-
- Use first order upwind method. Not coded for Cgrid, since
- first order upwind method is rarely used.
-
-
-
-
-
-
-
-
-
vert_advection_of_velocity
-
-
-DESCRIPTION
-
-
-
- Compute thickness weighted and density weighted acceleration
- (kg/m^3)*(m^2/s^2) due to vertical advection of velocity.
-
- Include vertical advection due to fresh water entering surface cells.
-
-
-
-
-
-
-
-
-
vert_advection_centered
-
-
-DESCRIPTION
-
-
-
- Compute thickness weighted and density weighted acceleration
- (kg/m^3)*(m^2/s^2) due to vertical advection of velocity.
-
- Include vertical advection due to fresh water entering surface cells.
- Assume upme and uriver are the most fundamental fields, passed through
- the FMS coupler on the Bgrid velocity point. So use these to average
- onto the C-grid velocity points. Likewise, pme and river are fundamental,
- and sit on the T-grid.
-
- Use second order centered method here.
-
-
-
-
-
-
-
-
-
vert_advection_upwind
-
-
-DESCRIPTION
-
-
-
- Compute thickness weighted and density weighted acceleration
- (kg/m^3)*(m^2/s^2) due to vertical advection of velocity.
-
- Include vertical advection due to fresh water entering surface cells.
-
- Use first order upwind method here. Not coded for Cgrid, since
- first order upwind method is rarely used.
-
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_velocity_advect_nml
-
-
-
-
-
-debug_this_module
-
-
- For debugging
-
-[logical]
-
-
-zero_velocity_advect_horz
-
-
- For debugging, it is often useful to remove horizontal advection of velocity.
-
-[logical]
-
-
-zero_velocity_advect_vert
-
-
- For debugging, it is often useful to remove vertical advection of velocity.
-
-[logical]
-
-
-velocity_advect_centered
-
-
- For using the standard second order centered method for
- computing the advection of linear momentum. This is the
- default: velocity_advect_centered=.true.
-
-[logical]
-
-
-velocity_advect_upwind
-
-
- For using the first order upwind method for
- computing the advection of linear momentum.
- Default: velocity_advect_upwind=.false.
-
-[logical]
-
-
-
-
-
-
-
-
-
-
-
REFERENCES
-
-
-
-
- R.C. Pacanowski and S.M. Griffies
- The MOM3 Manual (1999)
-
-
- S.M. Griffies, M.J. Harrison, R.C. Pacanowski, and A. Rosati
- A Technical Guide to MOM4 (2004)
-
-
- R.C. Pacanowski and S.M. Griffies
- The MOM3 Manual (1999)
-
-
- S.M. Griffies: Elements of MOM (2012)
-
-
- Hundsdorder and Trompert (1994), "Method of lines and
- direct discretization: a comparison for linear
- advection", Applied Numerical Mathematics,
- pages 469--490.
-
- Top-level interface between MOM and ocean data assimilation modules
-
-
-
-
-
- Top level module for ocean data assimilation. Contains routines for
- initialization, termination and update of ocean data assimilation increments.
-
- 1.) Get Observations for current model time (and domain)
- based on data window (default=15 days). For PE subdomains,
- data are included if they lie within the region bounded by the
- cell centers on the first x/y halo extent.
-
- 2.)
- IF EAKF (!!not yet implemented!!)
- a.) ensemble state is distributed among NPES as follows:
- Ens01:0:(NPE1-1), Ens02:NPE1:(NPE1+NPE2-1),...,
- EnsN:sum(NPE1+...+NPE(N-1)):NPES
- b.) Redistribute state to ensemble vector using global PEset.
- (Ens01,...,EnsN):0:NPES
- c.) Calculate increments using Ensemble information.
- d.) Re-distribute increments to members and revert to
- original PEset.
- ELSE IF Var2d
- Minimize quadratic CF based on specfied prior correlation maps
- and optionally time-variant prior error variance.
- ELSE ???
-
- ENDIF
-
- 3.) Apply increments to model state based on prior analysis.
- Distribute increments uniformly over analysis period if "do_iau=T".
-
- 4.) Check for convective instability after applying increments.
-
- 5.) Write Profile (observation space) first guess, analysis and mis-fits
-
-========================================================================
-
- Initialize the ocean_adv_vel_diag module containing subroutines
- diagnosing advection velocity related properties of the simulation.
-
-
-
-
-
-
-
-
ocean_adv_vel_diagnostics
-
-
-DESCRIPTION
-
-
- Call diagnostics related to the velocity.
-
-
-
-
-
-
-
-
remapping_check
-
-
-DESCRIPTION
-
-
- Compute remapping error. This error will be roundoff only for model
- grids where the tracer and velocity grid cell distances are
- linearly related. The spherical version of MOM satisfies the
- appropriate relation, and so should maintain roundoff for the
- remapping error. The tripolar version of MOM does not have
- tracer and velocity grids related linearly, and so the
- "remapping error" is nontrivial. The significance of this error
- is unclear. No adverse effects have been identified.
-
-
-
-
-
-
-
-
cfl_check1
-
-
-DESCRIPTION
-
-
- Perform the first of two CFL checks for vertical velocity component.
-
- Vectorized version from Russell.Fiedler@csiro.au computes cfl
- values at a single latitude. The location of the maximum at this
- latitude is calculated via the maxloc() intrinsic. The maximum
- value for this processor is then updated if necessary.
-
-
-
-
-
-
-
-
-
cfl_check2
-
-
-DESCRIPTION
-
-
- Perform the second of two vertical CFL checks.
-
- Bring the model down if too many large Courant numbers detected.
-
-
-
-
-
-
-
-
maximum_bottom_w
-
-
-DESCRIPTION
-
-
- Compute maximum vertical velocity on the bottom of tracer and velocity cells.
- The vertical velocity at bottom of a column of tracer cells should be roundoff.
- For flat bottom simulations, the vertical velocity on the bottom of the
- velocity cell column should also be roundoff. For simulations with topography,
- the vertical velocity on the bottom of a velocity cell column will not vanish
- due to the effects of topography.
-
-
-
-
-
-
-
-
max_continuity_error
-
-
-DESCRIPTION
-
-
- Compute continuity error. Should be roundoff if all is working well.
-
-
-
-
-
-
-
-
transport_on_s
-
-
-DESCRIPTION
-
-
- Compute transports on s-levels (defined by same k-level)
- and send to diag_manager.
-
-
-
-
-
-
-
-
transport_on_nrho
-
-
-DESCRIPTION
-
-
- Classify horizontal transport according to neutral density classes.
-
- NOTE: This diagnostic works with transport through cell faces.
- To get transport_on_nrho, a binning must be done, rather than
- a remapping (as done for trans_rho_gm).
-
- code history:
-
- 2002: Stephen.Griffies
- Zhi.Liang
- Alexander.Pletzer
-
- 2007: updated algorithm with weighting as done in the paper
- Lee, Nurser, Coward, and de Cuevas, 2007:
- "Eddy advective and diffusive transports of heat and salt
- in the Southern Ocean" JPO, vol 37, pages 1376-1393
-
- 2010: updated by Rusty.Benson for optimization.
-
- 2010: Corrected weighting by Stephen.Griffies
-
- 2010: Removed the weighting in favor of a strait rebinning
- approach. The weighting approach was
- unnecessary, and added more cost to the scheme.
-
-
-
-
-
-
-
-
-
transport_on_rho
-
-
-DESCRIPTION
-
-
- Classify horizontal transport according to potential density classes.
-
- Diagnostic makes sense when potrho is monotonically increasing with
- depth, although the algorithm does not explicitly make this assumption.
-
- NOTE: This diagnostic works with transport through cell faces.
- To get transport_on_rho, a binning must be done, rather than
- a remapping (as done for trans_rho_gm).
-
- Code history
-
- 2002: Stephen.Griffies
- Zhi.Liang
- Alexander.Pletzer
-
- 2007: updated algorithm with weighting as done in the paper
- Lee, Nurser, Coward, and de Cuevas, 2007:
- "Eddy advective and diffusive transports of heat and salt
- in the Southern Ocean" JPO, vol 37, pages 1376-1393
-
- 2010: updated by Rusty.Benson for optimization.
- corrected weigthing by Stephen.Griffies
-
- 2010: Removed the weighting in favor of a strait rebinning
- approach. The weighting approach was
- unnecessary, and added more cost to the scheme.
-
-
-
-
-
-
-
-
-
transport_on_theta
-
-
-DESCRIPTION
-
-
- Classify horizontal transport of mass according to potential
- temperature classes. This diagnostic is useful to deduce the
- heat that is transported between potential temperature classes.
-
- Diagnostic makes sense when theta is monotonically decreasing
- with depth, although the algorithm does not explicitly make
- this assumption.
-
- NOTE: This diagnostic works with transport through cell faces.
- To get transport_on_theta, a binning must be done, rather than
- a remapping (as done for trans_rho_gm).
-
- Code history
-
- 2002: Stephen.Griffies
- Zhi.Liang
- Alexander.Pletzer
-
- 2007: updated algorithm with weighting as done in the paper
- Lee, Nurser, Coward, and de Cuevas, 2007:
- "Eddy advective and diffusive transports of heat and salt
- in the Southern Ocean" JPO, vol 37, pages 1376-1393
-
- 2010: updated by Rusty.Benson for optimization.
- corrected weigthing by Stephen.Griffies
-
- 2010: Removed the weighting in favor of a strait rebinning
- approach. The weighting approach was
- unnecessary, and added more cost to the scheme.
-
-
-
-
-
-
-
-
-
vertical_reynolds_check
-
-
-DESCRIPTION
-
-
- This subroutine computes the Reynolds number associated with vertical
- friction visc_cbt and vertical velocity wrho_bt. This check is
- appropriate for either Bgrid or Cgrid.
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_adv_vel_diag_nml
-
-
-
-
-
-max_cfl_value
-
-
- Critical value for Courant number, above which the model will be brought down.
-
-[real, units: dimensionless]
-
-
-large_cfl_value
-
-
- Large value for Courant number, above which will write some diagnostics.
-
-[real, units: dimensionless]
-
-
-verbose_cfl
-
-
- For printing out lots of information about regions of large Courant numbers.
-
-[logical]
-
-
-diag_step
-
-
- Number of time steps between which compute the diagnostics.
-
-[integer, units: dimensionless]
-
- Initialize the ocean_tracer_diag module containing subroutines
- diagnosing tracer related properties of the simulation. These are
- not terms in the equations, but rather they are diagnosed from
- terms.
-
-
-
-
-
-
-
-
ocean_tracer_diagnostics
-
-
-DESCRIPTION
-
-
- Call diagnostics related to the tracer fields.
-
-
-
-
-
-
-
-
calc_mixed_layer_depth
-
-
-DESCRIPTION
-
-
-
- Calculate the mixed layer depth (m), which is defined as the depth ( > 0 )
- where the buoyancy difference with respect to the surface level is
- equal to buoyancy_crit (m/s^2).
-
- Note that the mixed layer depth is taken with respect to the ocean surface
- at z=eta_t, so the mixed layer depth is always positive. That is, the mld
- is here defined as a thickness of water.
-
-
-
-
-
-
-
-
-
mixed_layer_depth
-
-
-DESCRIPTION
-
-
-
- Diagnose mixed layer depth (m).
- Call calc_mixed_layer_depth to determine the mixed layer depth.
- Also compute neutral density at depth of the mixed layer.
-
-
-
-
-
-
-
-
mixed_layer_depth_dtheta
-
-
-DESCRIPTION
-
-
-
- Calculate the depth required to reach a temperature that is
- dtheta cooler than the surface temperature.
-
- Note:
- 1/ mixed_layer_depth_dtheta is taken with respect to the ocean surface
- at z=eta_t.
-
- 2/ mixed_layer_depth_dtheta is no greater than the ocean depth + eta_t.
-
- Coded March 2010 by Stephen.Griffies
-
-
-
-
-
-
-
-
-
compute_subduction
-
-
-DESCRIPTION
-
-
- Diagnose subduction rate (kg/sec) based on kinematic method to compute
- mass transport through base of mixed layer.
-
- Some approximations made for convenience:
- 1/ use velocity at time tau
- use tracer at time tau
- use thickness at time taup1, since all pieces of Thickness
- have already been updated to taup1.
-
- 2/ horizontally interpolate B-grid to C-grid velocity components,
- but then vertically interpolate using mld computed at T-points.
-
- Stephen.Griffies
- March 2012
-
-
-
-
-
-
-
-
tracer_change
-
-
-DESCRIPTION
-
-
-
- Compute change in tracer over a time step and difference between
- this change and the boundary forcing.
-
- This routine is very useful for detecting bugs in tracer routines.
-
-
-
-
-
-
-
-
-
total_tracer
-
-
-DESCRIPTION
-
-
- Compute integrated tracer in model.
-
-
-
-
-
-
-
-
klevel_total_tracer
-
-
-DESCRIPTION
-
-
- Compute integrated tracer on a k-level.
-
-
-
-
-
-
-
-
total_mass
-
-
-DESCRIPTION
-
-
- Compute total ocean tracer cell mass. For Boussinesq fluid,
- mass is determined using rho0 for density.
-
-
-
-
-
-
-
-
total_volume
-
-
-DESCRIPTION
-
-
- Compute total ocean tracer cell volume.
-
-
-
-
-
-
-
-
klevel_total_mass
-
-
-DESCRIPTION
-
-
- Compute ocean tracer cell mass in a k-level. For Boussinesq fluid,
- mass is determined using rho0 for density.
-
-
-
-
-
-
-
-
tracer_integrals
-
-
-DESCRIPTION
-
-
- Compute some integrated tracer diagnostics.
-
-
-
-
-
-
-
-
tracer_land_cell_check
-
-
-DESCRIPTION
-
-
- Check to be sure ocean tracer is zero over land
-
-
-
-
-
-
-
-
mass_conservation
-
-
-DESCRIPTION
-
-
- Compute change in mass over many time steps, and compare to the
- input of mass through surface to check for mass conservation.
-
-============================================================
-
- threelevel scheme
-
- Here is the logic for the accumulation of the fluxes and
- comparisons between mass/volumes at the start and the end.
-
- Consider accumulation over four leap-frog time steps.
- Ignore time filtering.
-
- mass(2) = mass(0) + 2dt*F(1) taup1=2, taum1=0, tau=1
-
- mass(3) = mass(1) + 2dt*F(2) taup1=3, taum1=1, tau=2
-
- mass(4) = mass(2) + 2dt*F(3) taup1=4, taum1=2, tau=3
-
- mass(5) = mass(3) + 2dt*F(4) taup1=5, taum1=3, tau=4
-
- Hence,
-
- [mass(4) + mass(5)] = [mass(0) + mass(1)] + 2dt*[F(1)+F(2)+F(3)+F(4)]
-
- For this example, we have
-
- itts_mass=1 through itte_mass=4 for accumulating fluxes
-
- itt=itts_mass=1=tau we use taum1=0 and tau=1 to get starting mass
-
- itt=itte_mass=4=tau we use tau=4 and taup1=5 to get the final mass
-
-============================================================
-
- twolevel scheme
-
- Here is the logic for the accumulation of the fluxes and
- comparisons between mass/volumes at the start and the end.
-
- Consider accumulation over four time steps.
-
- mass(3/2) = mass(1/2) + dt*F(1) taup1=3/2, taum1=1/2, tau=1
-
- mass(5/2) = mass(3/2) + dt*F(2) taup1=5/2, taum1=3/2, tau=2
-
- mass(7/2) = mass(5/2) + dt*F(3) taup1=7/2, taum1=5/2, tau=3
-
- mass(9/2) = mass(7/2) + dt*F(4) taup1=9/2, taum1=7/2, tau=4
-
- Hence,
-
- mass(9/2) = mass(1/2) + dt*[F(1)+F(2)+F(3)+F(4)]
-
- For this example, we have
-
- itts_mass=1 through itte_mass=4 for accumulating fluxes
-
- itt=itts_mass=1=tau we use taum1=1/2 to get starting mass
-
- itt=itte_mass=4=tau we use taup1=9/2 to get the final mass
-
-
-
-
-
-
-
-
-
tracer_conservation
-
-
-DESCRIPTION
-
-
- Compute change in global integrated tracer over many time steps,
- and compare to the input of tracer through the boundaries to
- check for total tracer conservation.
-
- Accumulate fluxes as in the mass_conservation diagnostic.
-
-
-
-
-
-
-
-
-
diagnose_kappa_sort
-
-
-DESCRIPTION
-
-
- Routine to diagnose the amount of mixing between classes of a
- particular tracer. Temperature is used as default.
- Method follows that used in the paper
-
- Spurious diapycnal mixing associated with advection in a
- z-coordinate ocean model, 2000: S.M. Griffies, R.C.
- Pacanowski, and R.W. Hallberg. Monthly Weather Review, vol 128, 538--564.
-
- This diagnostic is most useful when computing the levels of
- effective dia-tracer mixing occuring in a model run with
- zero buoyancy forcing at the boundaries.
-
- Algorithm notes:
-
- -assumes flat ocean bottom--non-flat bottoms loose the precise relation
- between sorted depth and true ocean depth. This is a minor inconvenience.
- The code is actually written so that the horizontal area of each
- layer can be different. This will allow for this diagnostic to be
- used, say, for simple topography, such as bowl or bump.
-
- -assumes Boussinesq fluid so that consider volume instead of mass of a cell.
- Also his means that dzt = rho0r*rho_dzt
-
- -assumes area integrated eta_t is zero, so domain volume is static.
- This is the case when there are no water boundary fluxes.
-
- -Results are meaningful only when dxt*dyt*dst of each grid cell
- is the same. This is best realized with a beta-plane or f-plane
- geometry, and with zstar vertical coordinate.
-
- My best understanding of this limitation is related to systematic
- biases in roundoff errors that result when the grid cells have
- varying volumes.
-
- If choose to use geopotential vertical coordinate, it is best
- to set linear_free_surface=.true. in ocean_thickness_nml,
- so that Thickness%rho_dzt = rho0%Grd%dzt. The sorting model of
- mixing has not been generalized to evolving layer thicknesses
- with geopotential.
-
- With zstar, the dst is constant in time, and the sorting method
- will sort to a depth in zstar space rather than geopotential space.
- This is a trivial distinction in principle, but should help with
- some roundoff issues in practice.
-
- -assumes tendency=TWO_LEVEL, which is exploited here to save memory.
-
- Numerical roundoff is a real issue with this diagnostic.
- It is critical that full double precision be used
- to garner sensible results.
-
- -defines some global arrays, so requires large memory.
- This feature can be removed if parallel sort is
- implemented. So far, such has not been done.
-
- -Effective kappa is set to zero at top of top-most cell.
- It is then diagnosed as zero (or roundoff) at bottom
- of the column if there are zero boundary buoyancy fluxes.
-
- -when computing density, we do rho=-alpha*theta.
- We drop the rho0 factor in order to reduce roundoff.
- Likewise, we assume alpha=1.0 rather than alpha=alpha_linear_eos
- We use alpha=1.0 to improve precision.
- With alpha=1.0 and rho=-alpha*theta, the rho variable
- is then just minus theta.
-
- -minimum vertical density gradient rho_grad_min is necessary to
- avoid errors with truncation in the division by drho/dz when compute kappa.
- rho_grad_min corresponds roughly to the precision of the computation.
- Physically, with
-
- N^2 = -(g/rho0)(drho/dz)
-
- then rho_grad_min sets a minimum N^2 resolved.
- This corresponds to a frequency f=N/2pi. The typical
- period of inertial oscillations in the deep ocean is 6hrs
- (Pickard and Emery, page 55-56). In the upper ocean, it is
- 10-30 minutes, in pycnocline it is smaller still.
- So to cover the majority of the ocean's stratification,
- we will want to set rho_grad_min to something smaller than 9e-6.
-
- To bin the effective diffusivity, it is also useful to have a max
- vertical density gradient.
-
--versions:
-
- mom4p0 method assumed rigid lid, or zero surface height undulations.
- Fit the following equation to the model data
- \partial_{t}(rho_sort) = (F_{k}-F_{k-1})/dzw
-
- mom4p1 method fits the following equation to model data
- \partial_{t}(dzt_sort*theta_sort) = F_{k} - F_{k-1}
- Fits this equation assuming two-time level tendency
-
- revision: 05/2005
- revision: 07/2007
- Stephen.Griffies
-
-
-
-
-
-
-
-
-
diagnose_kappa_simple
-
-
-DESCRIPTION
-
-
- Routine to diagnose the amount of mixing between classes of a
- particular tracer. Temperature is used as default.
-
- Compute horizontal average of temp to define a stable profile.
- Evolution of this profile defines an effective diffusity.
-
- This diffusivity is different than the one diagnosed
- from the adiabatic sorting approach. The sorting approach is
- more relevant. The two approaches agree when there
- is zero baroclinicity, and the present simple scheme is
- useful ONLY to help debug the sorting routine.
-
-
-
-
-
-
-
-
-
diagnose_depth_of_potrho
-
-
-DESCRIPTION
-
-
-
- Diagnose depth (m) of a potential density surface surface relative to
- the ocean surface at z=eta (not relative to z=0).
-
- Method uses linear interpolation to find the depth of a
- potential rho surface.
-
- Scheme currently does not forward (backwards) interpolate if
- rho surface lies within lowest (uppermost) grid cell.
-
- Diagnostic only makes sense when rho is monotonically
- increasing as go deeper in water column.
-
- Author: Harper.Simmons
- Zhi.Liang
-
-
-
-
-
-
-
-
diagnose_depth_of_theta
-
-
-DESCRIPTION
-
-
-
- Diagnose depth (m) of a potential temperature surface relative to
- the ocean surface at z=eta (not relative to z=0).
-
- Method uses linear interpolation to find the depth of a
- potential temp surface.
-
- Scheme currently does not forward (backwards) interpolate if
- theta surface lies within lowest (uppermost) grid cell.
-
- Diagnostic only makes sense when theta is monotonically
- decreasing as go deeper in water column.
-
- Based on "diagnose_depth_of_potrho" by Harper.Simmons
-
- Author: Stephen.Griffies
- Zhi.Liang
-
-
-
-
-
-
-
-
diagnose_tracer_on_rho
-
-
-DESCRIPTION
-
-
- Diagnose tracer concentration on potential density surface.
- Method based on diagnose_depth_of_potrho diagnostic.
-
- Author: Stephen.Griffies
-
- Updated Oct 2009 to be more vectorized
-
-
-
-
-
-
-
-
-
diagnose_tracer_zrho_on_rho
-
-
-DESCRIPTION
-
-
- Diagnose tracer concentration * dz/drho on potential density surface.
- This product, when integrated over dx*dy*drho, will yield the same
- total tracer (to within roundoff) as the usual tracer concentration
- integrated over dx*dy*dz.
-
- compute abs(dz/drho)==dz/drho in order to have tracer_zrho_on_rho
- with same sign as tracer.
-
- Method based on diagnose_tracer_on_rho diagnostic.
-
- Author: Stephen.Griffies
- Updated Oct 2009 to be more vectorized
-
-
-
-
-
-
-
-
-
calc_potrho_mixed_layer
-
-
-DESCRIPTION
-
-
- Calculate the mixed layer depth and potential density at mixed layer base
- according to depth at which buoyancy is greater than buoyancy_crit
- relative to the surface. Compute the buoyancy using potential
- density, rather than the insitu density, since we aim for this
- diagnostic to be comparable to diagnostics from isopcynal models.
-
- Note that the mixed layer depth is taken with respect to the ocean surface,
- and so the mixed layer depth is always positive. That is, the mld is here
- defined as a thickness of water.
-
-
-
-
-
-
-
-
-
potrho_mixed_layer
-
-
-DESCRIPTION
-
-
- Determine mixed layer depth and potential density at mixed layer base
- according to depth at which buoyancy is greater than buoyancy_crit
- relative to the surface.
- Call calc_potrho_mixed_layer to calculate the quantities.
-
-
-
-
-
-
-
-
-
send_total_mass
-
-
-DESCRIPTION
-
-
- Send total liquid seawater mass to diagnostic manager.
-
-
-
-
-
-
-
-
send_total_volume
-
-
-DESCRIPTION
-
-
- Send total liquid seawater mass to diagnostic manager.
-
-
-
-
-
-
-
-
send_total_tracer
-
-
-DESCRIPTION
-
-
- Send total tracer to diagnostic manager.
-
-
-
-
-
-
-
-
send_global_ave_tracer
-
-
-DESCRIPTION
-
-
- Send global averaged tracer to diagnostic manager.
-
-
-
-
-
-
-
-
send_global_ave_pressure
-
-
-DESCRIPTION
-
-
- Send global averaged pressure to diagnostic manager.
-
-
-
-
-
-
-
-
send_surface_ave_tracer
-
-
-DESCRIPTION
-
-
- Send global averaged surface tracer to diagnostic manager.
- Note the presence of a rho_dzt weighting here...
-
-
-
-
-
-
-
-
send_surface_area_ave_tracer
-
-
-DESCRIPTION
-
-
- Send global area averaged surface tracer to diagnostic manager.
- Note the weigthing is just area, with no thickness nor density.
-
-
-
-
-
-
-
-
send_tracer_variance
-
-
-DESCRIPTION
-
-
-
- Compute the global and k-level tracer variance.
-
-
-
-
-
-
-
-
-
diagnose_eta_tend_3dflux
-
-
-DESCRIPTION
-
-
- Diagnose contribution to global mean sea level evolution arising
- from a 3d MOM flux computed from a parameterization.
-
- fluxes are assumed to have the following dimensions:
- flux_x = (dy*dz)*diffusivity*rho*tracer_derivative_x
- flux_y = (dx*dz)*diffusivity*rho*tracer_derivative_y
- flux_z = diffusivity*rho*tracer_derivative_z
-
- Subroutine history:
- Jan2012 version 1.0: Stephen.Griffies
-
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_tracer_diag_nml
-
-
-
-
-
-tracer_conserve_days
-
-
- Number of days between which compute the tracer conservation diagnostics.
-
-[real, units: days]
-
-
-diag_step
-
-
- Number of time steps between which compute the diagnostics.
-
-[integer, units: dimensionless]
-
-
-debug_diagnose_mixingA
-
-
- Set true for help with debugging the diagnostic for mixing.
-
-[logical]
-
-
-debug_diagnose_mixingB
-
-
- Set true for more help with debugging the diagnostic for mixing.
- Lots of output.
-
-[logical]
-
-
-debug_diagnose_mixingC
-
-
- Set true for more help with debugging the diagnostic for mixing.
- Lots of output.
-
-[logical]
-
-
-debug_diagnose_mixingD
-
-
- Set true for more help with debugging the diagnostic for mixing.
- Lots of output.
-
-[logical]
-
-
-smooth_kappa_sort
-
-
- Number of 1-2-1 smooths applied to kappa_sort
-
-[integer]
-
-
-smooth_dzt_rho_sort
-
-
- Number of 1-2-1 smooths applied to rho_sort
-
-[integer]
-
-
-rho_grad_min
-
-
- min vertical density gradient (kg/m^3/m) used in computing kappa sorted
- in the diagnostic mixing sorted.
-
-[real, units: kg/m^3/m]
-
-
-rho_grad_max
-
-
- max vertical density gradient (kg/m^3/m) used in computing kappa sorted
-
-[real, units: kg/m^3/m]
-
-
-buoyancy_crit
-
-
- Critical buoyancy difference relative to surface for computing mixed
- layer depth. Default buoyancy_crit=0.0003.
-
-[real, units: m/s^2]
-
-
-dtheta_crit
-
-
- Critical temperature difference relative to surface for computing
- mixed_layer_depth_dtheta . Default dtheta_crit=2.0.
-
-[real, units: degC]
-
-
-diagnose_mixing_days
-
-
- Days over which time average the thickness weighted density before taking its
- time tendency for use in computing the effective diapycnal diffusivity.
-
-[real, units: day]
-
-
-psu2ppt
-
-
- The preTEOS10 EOS used in MOM requires salinity to
- use the Practical Salinity Scale (pss). This scale is
- also known as the Practical Salinity Unit (psu).
-
- However, salinity as an absolute concentration in
- parts per thousand is more convenient to use when
- performing budget analyses such as in this module.
- Conversion between pss and ppt depends on the precise
- ratio of ions in the seawater. Hence, the conversion
- is not constant. However, it is close to a constant,
- as reported in Jackett etal (2004). For purposes of
- budgets, we take this conversion as a constant.
- The conversion is
-
- s(ppt) = psu2ppt * s(psu)
-
- where again s(psu) is what MOM carries as its
- prognostic salinity field when preTEOS10 EOS is used.
-
- Jackett etal (2004), correcting a type in equation (53)
- of Feistel (2003), report that
-
- s(ppt) = 1.004867 * s(psu)
-
-
-[real]
-
- Smooth the diagnosed mixed layer depth to be used for subduction
- diagnostics. Default smooth_mld_for_subduction=.true.
-
-[integer]
-
-
-do_bitwise_exact_sum
-
-
- Set true to do bitwise exact global sum. When it is false, the global
- sum will be non-bitwise_exact, but will significantly increase efficiency.
- The default value is false.
-
-[logical]
-
- Compute the global min and max for tracers.
-
- Vectorized using maxloc() and minloc() intrinsic functions by
- Russell.Fiedler@csiro.au (May 2005).
-
- Modified by Zhi.Liang (July 2005)
-
-
-
-
-
-
-
-
-
dzt_min_max
-
-
-DESCRIPTION
-
-
- Compute the global min and max for dzt.
-
- Modified by Stephen.Griffies from subroutine tracer_min_max
-
-
-
-
-
-
-
-
-
tracer_prog_chksum
-
-
-DESCRIPTION
-
-
- Compute checksums for prognostic tracers
-
-
-
-
-
-
-
-
tracer_diag_chksum
-
-
-DESCRIPTION
-
-
- Compute checksums for diagnostic tracers
-
-
-
-
-
-
-
-
tracer_psom_chksum
-
-
-DESCRIPTION
-
-
- Compute checksums for PSOM advection second order moments.
-
-
-
-
-
-
-
-
sort_pick_array
-
-
-DESCRIPTION
-
-
- Simplest, and slowest, sorting algorithm from Numerical Recipes.
- Called "sort_pick" in Numerical Recipes.
-
- Input are two arrays, first array defines the ascending sort
- and second is a slave to the sort.
-
- Typical example is sorting a vector of water parcels lightest
- to densest, with slave being volume of the parcels.
-
- More sophisticated sorting algorithms exist, and may need to
- be coded should this method prove too slow.
-
- This scheme has order N^2 operations, which is a lot.
-
- output has array(1) smallest and a(nsortpts) largest
- with corresponding slave array.
-
- coded Stephen.Griffies June 2005
-
-
-
-
-
-
-
-
-
sort_shell_array
-
-
-DESCRIPTION
-
-
- Shell (or diminishing increment) sort from Numerical Recipes.
- Called "sort_shell" in Numerical Recipes.
-
- Input are two arrays, first array defines the ascending sort
- and second is a slave to the sort array.
-
- Typical example is sorting a vector of water parcels lightest
- to densest, with slave being volume of the parcels.
-
- More sophisticated sorting algorithms exist, and may need to
- be coded should this method prove too slow.
-
- This scheme has order N^(5/4) operations.
-
- output has array(1) smallest and a(nsortpts) largest,
- with corresponding ordering for slave array.
-
- coded Stephen.Griffies June 2005
-
-
-
-
-
-
-
-
-
rebin_onto_rho
-
-
-DESCRIPTION
-
-
- Bin a level input tendency field according to density classes.
- The binning is meant for tendencies and transports, as used in particular
- for the neut_rho, wdian_rho, and tform_rho diagnostics.
-
- Note that if use rebin_onto_rho_all_values=.false. then will
- not be consistent with transport_on_nrho calculation, which includes
- bins all grid cells, including those outside of range for the bounds.
-
- Stephen.Griffies
- April 2012: algorithm made identical to transport_on_nrho as
- computed in ocean_adv_vel_diag.
-
-
-
-
-
-
-
-
-
diagnose_mass_of_layer_orig
-
-
-DESCRIPTION
-
-
-
- Diagnose the mass of a layer as a function of layer and (i,j).
-
- Method uses linear interpolation to find the mass per area of
- layer boundaries, which are then used to get mass per area of
- layer, and then mass through multipication by area.
-
- Scheme currently does not forward (backwards) interpolate if
- layer boundary lies within lowest (uppermost) grid cell.
-
- Diagnostic only makes sense when layer_level is monotonically
- increasing as go deeper in water column.
-
- layer_bounds = neutral density of layer interfaces
- mass_level = mass per area at bottom of tracer cell
- layer_level = neutral density of model grid levels
- mass_layer = diagnosed mass of a neutral density layer
-
-
-
-
-
-
-
-
-
diagnose_mass_of_layer
-
-
-DESCRIPTION
-
-
-
- Diagnose the mass of a layer as a function of layer and (i,j).
-
- Method uses linear interpolation to find the mass per area of
- layer boundaries, which are then used to get mass per area of
- layer, and then mass through multipication by area.
-
- Diagnostic only makes sense when layer_level is monotonically
- increasing as go deeper in water column.
-
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_tracer_util_nml
-
-
-
-
-
-rebin_onto_rho_all_values
-
-
- Set true to if wish to bin all values into density classes, even
- those cells whose density is outside the max and min range of the
- density bins. The default is rebin_onto_rho_all_values=.true.,
- which means those cells with extreme density values will be included.
- This default is consistent with the default computation of
- transport_on_nrho.
-
-[logical]
-
-
-debug_diagnose_mass_of_layer
-
-
- To help debug the algorithm to diagnose mass of fluid within
- a neutral density layer.
- Default: debug_diagnose_mass_of_layer=.false.
-
-[logical]
-
-
-epsln_diagnose_mass_of_layer
-
-
- Relative mass difference allowable between layer and level total mass.
- Default: epsln_diagnose_mass_of_layer=1e-4.
-
-[real]
-
- Numerical diagnostics for velocity related quantities.
-
-
-
-
-
- This module contains some diagnostics for velocity related quantities.
- Account is taken for either Bgrid or Cgrid layout of the velocity
- and related discrete fields.
-
- Initialize the ocean_velocity_diag module containing subroutines
- diagnosing velocity related properties of the simulation. These are
- not terms in the equations, but rather they are diagnosed from
- terms.
-
-
-
-
-
-
-
-
ocean_velocity_diagnostics
-
-
-DESCRIPTION
-
-
- Call diagnostics related to the velocity.
-
-
-
-
-
-
-
-
potential_energy
-
-
-DESCRIPTION
-
-
-
- Compute gravitational potential energy (Joules) relative to z=0
- taken with respect to the value at the initial time step.
-
-
-
-
-
-
-
-
-
kinetic_energy
-
-
-DESCRIPTION
-
-
- Compute global integrated horizontal kinetic energy.
-
-
-
-
-
-
-
-
velocity_land_cell_check
-
-
-DESCRIPTION
-
-
- See if there are any points over land with nonzero ocean velocity
-
-
-
-
-
-
-
-
velocity_change
-
-
-DESCRIPTION
-
-
- Determine the number of points that have large single-time step
- changes in the absolute value of the velocity.
-
-
-
-
-
-
-
-
compute_topostrophy
-
-
-DESCRIPTION
-
-
-
- Diagnose topostrophy as per Greg Holloway.
-
- Stephen.Griffies
- March 2012
-
-
-
-
-
-
-
-
-
compute_vorticity
-
-
-DESCRIPTION
-
-
- Compute z-component to vorticity.
-
-
-
-
-
-
-
-
pressure_conversion
-
-
-DESCRIPTION
-
-
- Perform pressure conversion error analysis. This analysis should be
- computed prior to update_ucell_thickness since we need to use dzu(tau)
- and dzten(tau) here rather than dzu(taup1) or dzten(taup1).
-
- Account taken for Bgrid and Cgrid. However, blobs need to be updated
- for Cgrid.
-
-
-
-
-
-
-
-
-
pressure_energy
-
-
-DESCRIPTION
-
-
- Diagnose u dot grad(p) for diagnostic purposes. These maps
- when summed over all grid points will result in an energy
- that is equal to pint+pext as computed in pressure_conversion.
-
- Account taken of either Bgrid or Cgrid.
-
-
-
-
-
-
-
-
-
friction_energy
-
-
-DESCRIPTION
-
-
- Diagnose u dot Friction for diagnostic purposes.
-
- Account taken for either Bgrid or Cgrid.
-
- NOTE:
-
- A) DO NOT split into baroclinic and barotropic pieces. Just compute
- u dot F using full velocity field u. Otherwise, the calculation emulates
- that done in energy_analysis subroutine.
-
- B) DO NOT remove the effects from bottom drag and from surface stress.
- The reason is that bottom drag and surface stress are incorporated to
- the vertical friction operator, even when doing vertical friction
- implicitly in time. So it is tough to remove these effects in an
- explicitl diagnostic manner. So the u dot vertical friction piece
- includes BOTH surface and bottom stress.
-
-
-
-
-
-
-
-
-
vert_dissipation
-
-
-DESCRIPTION
-
-
- Diagnose dissipation from vertical friction due just to viscosity.
-
- Units W/m^2
-
- Assumptions:
-
- 1/ Ignore bottom drag here...just concerned with viscosity.
-
- 2/ Assume vertical friction is handled implicitly in time.
-
-
-
-
-
-
-
-
-
energy_analysis
-
-
-DESCRIPTION
-
-
- Perform energy analysis by taking scalar product of horizontal
- velocity with the velocity equations and integrating over the ocean volume.
-
- Pressure conversions have already been computed in pressure_conversion
- subroutine. It is necessary to perform that analysis earlier than
- the call to update_ucell_thickness inside ocean_model_mod, whereas
- the remaining elements in the energy analysis can be called at the
- end of the update for velocity.
-
-
-
-
-
-
-
-
cfl_check1_bgrid
-
-
-DESCRIPTION
-
-
- Perform the first of two CFL checks on horizontal velocity.
-
- Assume Bgrid here.
-
- Vectorized version from Russell.Fiedler@csiro.au computes cfl
- values at a single latitude. The location of the maximum at this
- latitude is calculated via the maxloc() intrinsic. The maximum
- value for this processor is then updated if necessary.
-
-
-
-
-
-
-
-
-
cfl_check1_cgrid
-
-
-DESCRIPTION
-
-
- Perform the first of two CFL checks on horizontal velocity.
-
- Assume Cgrid here.
-
- Vectorized version from Russell.Fiedler@csiro.au computes cfl
- values at a single latitude. The location of the maximum at this
- latitude is calculated via the maxloc() intrinsic. The maximum
- value for this processor is then updated if necessary.
-
-
-
-
-
-
-
-
-
cfl_check2_bgrid
-
-
-DESCRIPTION
-
-
- Perform the second of two CFL checks on horizontal velocity.
-
- Assume Bgrid here.
-
- Bring the model down if too many large Courant numbers detected.
-
-
-
-
-
-
-
-
cfl_check2_cgrid
-
-
-DESCRIPTION
-
-
- Perform the second of two CFL checks on horizontal velocity.
-
- Assume Cgrid here.
-
- Bring the model down if too many large Courant numbers detected.
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_velocity_diag_nml
-
-
-
-
-
-diag_step
-
-
- Number of time steps between which compute the diagnostics.
-
-[integer, units: dimensionless]
-
-
-energy_diag_step
-
-
- Perform energy analysis every n timesteps (1==every time step).
- This diagnostic is expensive, so should be used sparingly during
- production runs.
-
-[integer]
-
-
-land_cell_num_max
-
-
- Maximum number of land cells where will printout nonzero velocity points.
- Default land_cell_num_max=100.
-
-[integer, units: dimensionless]
-
-
-max_cfl_value
-
-
- Critical value for Courant number, above which the model will be brought down.
-
-[real, units: dimensionless]
-
-
-large_cfl_value
-
-
- Large value for Courant number, above which will write some diagnostics.
-
-[real, units: dimensionless]
-
-
-verbose_cfl
-
-
- For printing out lots of information about regions of large Courant numbers.
-
-[logical]
-
-
-do_bitwise_exact_sum
-
-
- Set true to do bitwise exact global sum. When it is false, the global
- sum will be non-bitwise_exact, but will significantly increase efficiency.
- The default value is false.
-
-[logical]
-
- Initialize the horizontal biharmonic friction module.
-
-
-
-
-
-
-
-
bih_friction
-
-
-DESCRIPTION
-
-
- Compute the thickness weighted and density weighted accel due to
- lateral biharmonic friction. Add this contribution to Velocity%accel.
-
-
-
-
-
-
-
-
bih_viscosity_check
-
-
-DESCRIPTION
-
-
- To check that the viscosity is not too large.
-
-
-
-
-
-
-
-
bih_reynolds_check
-
-
-DESCRIPTION
-
-
- To check that the Reynolds number is not too large.
-
-
-
-
-
-
-
-
bih_friction_barotropic
-
-
-DESCRIPTION
-
-
-
- This routine computes the biharmonic friction acting on a two-dim
- array. It uses the two-dimensional vertically averaged viscosity
- used in the biharmonic friction module. The intent is to apply this
- 2d operator to the vertically integrated horizontal momentum. We
- ignore the spherical metric terms in this form of the operator,
- since we are aiming for a fast smoothing operator to be applied
- during each of the many barotropic time steps. We also apply
- just the isotropic portion of the more general anisotropic
- biharmonic operator.
-
- This method has only been implemented for Bgrid MOM. It is
- rarely used and remains only for legacy.
-
-
-
-
-
-
-
-
-
ocean_bih_friction_restart
-
-
-DESCRIPTION
-
-
- Write out restart files registered through register_restart_file
-
-
-
-
-
-
-
-
ocean_bih_friction_end
-
-
-DESCRIPTION
-
-
- Write to restart of the vertically averaged viscosity.
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_bih_friction_nml
-
-
-
-
-
-bih_friction_scheme
-
-
- To determine the biharmonic friction scheme: "const" or "general"
-
-[character]
-
-
-debug_this_module
-
-
- For debugging.
-
-[logical]
-
-
-write_a_restart
-
-
- Set true to write a restart. False setting only for rare
- cases where wish to benchmark model without measuring the cost
- of writing restarts and associated chksums.
- Default is write_a_restart=.true.
-
-[logical]
-
-
-
-
-
-
-
-
-
-
-
NOTES
-
-
- The model can generally run with both Laplacian and biharmonic friction
- enabled at the same time. Such has been found useful for some eddying
- ocean simulations.
-
-
-
diff --git a/src/mom5/ocean_param/lateral/ocean_bih_friction.xml b/src/mom5/ocean_param/lateral/ocean_bih_friction.xml
deleted file mode 100644
index e452410a16..0000000000
--- a/src/mom5/ocean_param/lateral/ocean_bih_friction.xml
+++ /dev/null
@@ -1,51 +0,0 @@
-
-
- Stephen M. Griffies
-
- This module calls the appropriate lateral biharmonic friction modules.
-
- This module serves as an interface to the chosen lateral
- biharmonic friction modules.
-
- The model can generally run with both Laplacian and biharmonic friction
- enabled at the same time. Such has been found useful for some eddying
- ocean simulations.
-
- To determine the biharmonic friction scheme: "const" or "general"
-
- For debugging.
-
- Set true to write a restart. False setting only for rare
- cases where wish to benchmark model without measuring the cost
- of writing restarts and associated chksums.
- Default is write_a_restart=.true.
-
- Initialize the horizontal biharmonic friction module.
-
- Compute the thickness weighted and density weighted accel due to
- lateral biharmonic friction. Add this contribution to Velocity%accel.
-
- To check that the viscosity is not too large.
-
- To check that the Reynolds number is not too large.
-
-
- This routine computes the biharmonic friction acting on a two-dim
- array. It uses the two-dimensional vertically averaged viscosity
- used in the biharmonic friction module. The intent is to apply this
- 2d operator to the vertically integrated horizontal momentum. We
- ignore the spherical metric terms in this form of the operator,
- since we are aiming for a fast smoothing operator to be applied
- during each of the many barotropic time steps. We also apply
- just the isotropic portion of the more general anisotropic
- biharmonic operator.
-
- This method has only been implemented for Bgrid MOM. It is
- rarely used and remains only for legacy.
-
-
- Write out restart files registered through register_restart_file
-
- Write to restart of the vertically averaged viscosity.
-
diff --git a/src/mom5/ocean_param/lateral/ocean_bih_tracer.F90 b/src/mom5/ocean_param/lateral/ocean_bih_tracer.F90
index b0f500092d..4d362978df 100644
--- a/src/mom5/ocean_param/lateral/ocean_bih_tracer.F90
+++ b/src/mom5/ocean_param/lateral/ocean_bih_tracer.F90
@@ -108,9 +108,9 @@ module ocean_bih_tracer_mod
integer :: id_ah_biharmonic
character(len=128) :: version=&
- '=>Using: /bih/ocean_bih_tracer.F90 ($Id: ocean_bih_tracer.F90,v 1.1.2.2 2012/06/01 20:47:08 Stephen.Griffies Exp $)'
+ '=>Using: /bih/ocean_bih_tracer.F90 ($Id: ocean_bih_tracer.F90,v 20.0 2013/12/14 00:14:10 fms Exp $)'
character (len=128) :: tagname = &
- '$Name: mom5_siena_08jun2012_smg $'
+ '$Name: tikal $'
type(ocean_grid_type), pointer :: Grd => NULL()
type(ocean_domain_type), pointer :: Dom => NULL()
diff --git a/src/mom5/ocean_param/lateral/ocean_bih_tracer.html b/src/mom5/ocean_param/lateral/ocean_bih_tracer.html
deleted file mode 100644
index 9f2d98fe21..0000000000
--- a/src/mom5/ocean_param/lateral/ocean_bih_tracer.html
+++ /dev/null
@@ -1,242 +0,0 @@
-
-
-
-Module ocean_bih_tracer_mod
-
-
-
-
-PUBLIC INTERFACE
-
- ~ PUBLIC ROUTINES
- ~ NAMELIST
-
-
- Thickness weighted and density weighted time tendency
- for tracer from biharmonic tracer mixing.
-
-
-
-
-
- There are two main options for computing the fluxes.
-
- (1) The lateral fluxes can be aligned with the z-coordinate surfaces,
- in which case the fluxes must be approximated if (i) we use non-geopotential
- vertical coordinates, (ii) next to partial bottom step topography.
- This form of the diffusion is not recommended since it can lead to
- the creation of spurious extrema.
-
- (2) The lateral fluxes can be aligned surfaces of constant vertical
- coordinate. In this case the fluxes are no longer strictly "horizontal."
- Howerver, the operator is simpler and it ensures that no suprious
- extrema are created. It is for this reason that the simpler operator
- is preferred.
-
- The diffusivity used to determine the strength of the tendency can be
- a general function of space yet it is constant in time. A namelist
- option exists that determines this diffusivity as a local function
- of the grid spacing.
-
- Initialize the biharmonic tracer mixing module by
- registering fields for diagnostic output and performing some
- numerical checks to see that diffusivity is set appropriately.
-
-
-
-
-
-
-
-
bih_tracer
-
-
-DESCRIPTION
-
-
- This function computes the thickness weighted and density weighted
- time tendency for tracer from biharmonic mixing.
-
-
-
-
-
-
-
-
delsq_tracer
-
-
-DESCRIPTION
-
-
- Subroutine computes the laplacian operator acting on tracer with unit
- diffusivity. Units of del2_tracer are tracer/length^2
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_bih_tracer_nml
-
-
-
-
-
-use_this_module
-
-
- Must be true to use this module
-
-[logical]
-
-
-horz_z_diffuse
-
-
- To compute fluxes along surfaces of constant depth.
- This operation must necessarily be approximate for the two
- cases (i) non-geopotential vertical coordinates, (2)
- next to partial bottom step topography. There are cases where
- use of this operator can lead to spurious creation of extrema
- due to truncation errors associated with the "slope" term.
- The option to use horz_z_diffuse=.true. is maintained for
- legacy purposes alone.
-
-[logical]
-
-
-horz_s_diffuse
-
-
- To compute diffusion along surfaces of constant vertical s-coordinate.
-
-[logical]
-
-
-abih
-
-
- This is the value for the space-time constant biharmonic diffusivity.
-
-[real, units: m^4/sec]
-
-
-tracer_mix_micom
-
-
- If .true., then the diffusivity is set according to a velocity scale times
- the cube of the grid spacing. It is based on an approach recommended by
- Eric Chassignet that is used in the Miami Isopycnal Model.
-
-[logical]
-
-
-vel_micom
-
-
- Velocity scale that is used for computing the MICOM diffusivity.
-
-[real, units: m/sec]
-
-
-read_diffusivity_mask
-
-
- Allows for reading of a mask that to apply diffusivity
- only in selected regions.
- Default read_diffusivity_mask=.false.
-
-[logical]
-
-
-
diff --git a/src/mom5/ocean_param/lateral/ocean_bih_tracer.xml b/src/mom5/ocean_param/lateral/ocean_bih_tracer.xml
deleted file mode 100644
index 4cbb120f80..0000000000
--- a/src/mom5/ocean_param/lateral/ocean_bih_tracer.xml
+++ /dev/null
@@ -1,62 +0,0 @@
-
-
- Stephen M. Griffies
-
- Thickness weighted and density weighted time tendency
- for tracer from biharmonic tracer mixing.
-
- There are two main options for computing the fluxes.
-
- (1) The lateral fluxes can be aligned with the z-coordinate surfaces,
- in which case the fluxes must be approximated if (i) we use non-geopotential
- vertical coordinates, (ii) next to partial bottom step topography.
- This form of the diffusion is not recommended since it can lead to
- the creation of spurious extrema.
-
- (2) The lateral fluxes can be aligned surfaces of constant vertical
- coordinate. In this case the fluxes are no longer strictly "horizontal."
- Howerver, the operator is simpler and it ensures that no suprious
- extrema are created. It is for this reason that the simpler operator
- is preferred.
-
- The diffusivity used to determine the strength of the tendency can be
- a general function of space yet it is constant in time. A namelist
- option exists that determines this diffusivity as a local function
- of the grid spacing.
-
- Must be true to use this module
-
- To compute fluxes along surfaces of constant depth.
- This operation must necessarily be approximate for the two
- cases (i) non-geopotential vertical coordinates, (2)
- next to partial bottom step topography. There are cases where
- use of this operator can lead to spurious creation of extrema
- due to truncation errors associated with the "slope" term.
- The option to use horz_z_diffuse=.true. is maintained for
- legacy purposes alone.
-
- To compute diffusion along surfaces of constant vertical s-coordinate.
-
- This is the value for the space-time constant biharmonic diffusivity.
-
- If .true., then the diffusivity is set according to a velocity scale times
- the cube of the grid spacing. It is based on an approach recommended by
- Eric Chassignet that is used in the Miami Isopycnal Model.
-
- Velocity scale that is used for computing the MICOM diffusivity.
-
- Allows for reading of a mask that to apply diffusivity
- only in selected regions.
- Default read_diffusivity_mask=.false.
-
- Initialize the biharmonic tracer mixing module by
- registering fields for diagnostic output and performing some
- numerical checks to see that diffusivity is set appropriately.
-
- This function computes the thickness weighted and density weighted
- time tendency for tracer from biharmonic mixing.
-
- Subroutine computes the laplacian operator acting on tracer with unit
- diffusivity. Units of del2_tracer are tracer/length^2
-
diff --git a/src/mom5/ocean_param/lateral/ocean_bihcgrid_friction.F90 b/src/mom5/ocean_param/lateral/ocean_bihcgrid_friction.F90
index 0d709b83b9..421fad9e53 100644
--- a/src/mom5/ocean_param/lateral/ocean_bihcgrid_friction.F90
+++ b/src/mom5/ocean_param/lateral/ocean_bihcgrid_friction.F90
@@ -215,7 +215,6 @@ module ocean_bihcgrid_friction_mod
integer :: id_cos2theta =-1
integer :: id_neptune_bih_u =-1
integer :: id_neptune_bih_v =-1
-integer :: id_neptune_psi =-1
integer :: id_ncar_rescale =-1
integer :: id_along =-1
integer :: id_across =-1
@@ -339,9 +338,9 @@ module ocean_bihcgrid_friction_mod
type(ocean_domain_type), pointer :: Dom => NULL()
character(len=256) :: version=&
- '=>Using: ocean_bihcgrid_friction.F90 ($Id: ocean_bihcgrid_friction.F90,v 1.1.2.7.20.1 2013/04/03 13:25:24 smg Exp $)'
+ '=>Using: ocean_bihcgrid_friction.F90 ($Id: ocean_bihcgrid_friction.F90,v 20.0 2013/12/14 00:14:12 fms Exp $)'
character (len=128) :: tagname = &
- '$Name: mom5_siena_201303_smg $'
+ '$Name: tikal $'
logical :: use_this_module = .false.
logical :: debug_this_module = .false.
diff --git a/src/mom5/ocean_param/lateral/ocean_bihcgrid_friction.html b/src/mom5/ocean_param/lateral/ocean_bihcgrid_friction.html
deleted file mode 100644
index 39fe67af3a..0000000000
--- a/src/mom5/ocean_param/lateral/ocean_bihcgrid_friction.html
+++ /dev/null
@@ -1,560 +0,0 @@
-
-
-
-Module ocean_bihcgrid_friction_mod
-
-
-
-
-PUBLIC INTERFACE
-
- ~ PUBLIC ROUTINES
- ~ NAMELIST
-
-
- This module computes the thickness weighted time tendency for
- horizontal velocity arising from horizontal biharmonic friction.
- Friction is formulated for the C-grid here.
-
-
-
-
-
- This module computes the thickness weighted time tendency for
- horizontal velocity arising from horizontal biharmonic friction.
- The viscosity used to determine the strength of the tendency
- can be a general function of space and time as specified by
- the Smagorinsky approach; a grid-scale dependent
- background viscosity; or other options.
- The form of the friction operator can be isotropic or
- anisotropic in the horizontal plane.
-
- Friction is formulated for the C-grid in this module.
-
-
- Initialize the lateral biharmonic friction module by
- registering fields for diagnostic output and performing some
- numerical checks to see that viscosity is set appropriately.
-
-
-
-
-
-
-
-
bihcgrid_friction
-
-
-DESCRIPTION
-
-
- This routine computes thickness weighted and density weighted
- time tendency for horizontal velocity arising from horizontal
- biharmonic friction.
-
- The algorithm is derived from a functional approach that ensures
- kinetic energy is consistenty dissipated for all flow configurations.
- The stencil is far simpler than the B-grid approach. In particular,
- there are no triads here for the C-grid.
-
- Fundamental to the scheme are the rates of horizontal deformation
- horizontal tension = DT = (dy)(u/dy)_x - (dx)(v/dx)_y
- horizontal strain = DS = (dx)(u/dx)_y + (dy)(v/dy)_x
- Units of the tension and strain are sec^-1.
-
- As shown in Griffies and Hallberg (2000),
- a biharmonic operator with a nonconstant viscosity is guaranteed to
- dissipate kinetic energy *only* when using the sqrt of the biharmonic
- viscosity at each of the two stages of the algorithm.
- The sqrt approach is employed here.
-
-
-
-
-
-
-
-
-
ncar_boundary_scale_read
-
-
-DESCRIPTION
-
-
-
- Read in the 3d ncar boundary scaling field and use this to
- rescale the background viscosities.
-
- To use this routine, we need to already have generated the field
- ncar_rescale using the routine ncar_boundary_scale_create.
-
- The advantage of reading ncar_rescale is that we do not need to
- introduce any global 2d arrays required for ncar_boundary_scale_create.
- So the idea is to pay the price once by running ncar_boundary_scale_create,
- save ncar_rescale, then read that field in during subsequent runs through
- ncar_boundary_scale_read.
-
- Here are the steps:
- 1/ run one time with ncar_boundary_scaling_read=.false.
- and ncar_boundary_scaling=.true.
- Be sure that the field ncar_rescale is saved in diagnostic table.
- To ensure answers agree whether reading ncar_rescale or creating it
- during initialization, it is necessary to save ncar_rescale using the
- double precision option in the diagnostic table (packing=1).
-
- 2/ extract field ncar_rescale from the diagnostics output
- and place into its own file INPUT/ncar_rescale.nc
- example extraction using ncks:
- ncks -v ncar_rescale 19900101.ocean_month.nc ncar_rescale.nc
-
- 3/ set ncar_boundary_scaling_read=.true.
- and ncar_boundary_scaling=.true., and now run the model
- reading in ncar_rescale rather than regenerating
- it during each initialization (which can be a bottleneck
- for large models on huge processor counts).
-
- 4/ As a check that all is fine, save ncar_rescale as a diagnostic
- for both the create and the read stage and make sure they agree.
- Also, all checksums should agree whether reading in ncar_rescale
- or creating it each initialization, so long as the ncar_rescale.nc
- was saved with double precision (see step 1/ above).
-
-
-
-
-
-
-
-
-
ncar_boundary_scale_create
-
-
-DESCRIPTION
-
-
-
- Recale the background viscosities to be larger in the western
- boundary regions. The algorithm is taken directly from the
- anisotropic_ncar routine in ocean_lapgen_friction.F90.
-
- NOTE: The nearest western boundary computations are done along the
- model i-grid lines. Therefore, viscosity based on these are
- only approximate in the high Northern Hemisphere when using
- generalized coordinates with coordinate pole(s) shifted onto
- land.
-
-
-
-
-
-
-
-
-
bihcgrid_viscosity_check
-
-
-DESCRIPTION
-
-
- Subroutine to perform linear stability check for the biharmonic
- operator given a value for the horizontal biharmonic viscosity.
-
-
-
-
-
-
-
-
bihcgrid_reynolds_check
-
-
-DESCRIPTION
-
-
- Subroutine to compute the biharmonic grid Reynolds number. Large
- Reynolds numbers indicate regions where solution may experience
- some grid noise due to lack of enough horizontal friction.
-
-
-
-
-
-
-
-
compute_neptune_velocity
-
-
-DESCRIPTION
-
-
- Compute Neptune velocity.
-
- Method follows that of
- Maltrud and Holloway, 2008: Implementing biharmonic neptune in a
- global eddying ocean model, Ocean Modelling, vol. 21, pages 22-34.
-
- This approach is slightly different than the Eby and Holloway
- method implemented in the laplacian module. There is no fundamental
- reason to favor one versus the other. We use the Maltrud and
- Holloway method here sinc they implemented it for biharmonic.
-
- May 2012
- Stephen.Griffies
-
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_bihcgrid_friction_nml
-
-
-
-
-
-use_this_module
-
-
- Must be true to use this module. Default is false.
-
-[logical]
-
-
-debug_this_module
-
-
- For debugging by printing checksums.
-
-[logical]
-
-
-k_smag_iso
-
-
- This is the dimensionless Smagorinsky coefficient used to set the scale
- of the Smagorinsky isotropic viscosity.
-
-[real, units: dimensionless]
-
-
-k_smag_aniso
-
-
- This is the dimensionless Smagorinsky coefficient used to set the scale
- of the Smagorinsky anisotropic viscosity.
-
-[real, units: dimensionless]
-
-
-vel_micom_iso
-
-
- Velocity scale that is used for computing the MICOM isotropic viscosity.
-
-[real, units: m/sec]
-
-
-vel_micom_aniso
-
-
- Velocity scale that is used for computing the MICOM anisotropic viscosity.
-
-[real, units: m/sec]
-
-
-equatorial_zonal
-
-
- Orient the anisotropic friction within a latitudinal band according to zonal direction.
-
-[logical]
-
-
-equatorial_zonal_lat
-
-
- Latitudinal band to use the zonal friction orientation.
-
-[real]
-
-
-equatorial_no_smag
-
-
- Turn smag off within equatorial_zonal_lat region.
-
-[logical]
-
-
-eq_vel_micom_iso
-
-
- Velocity scale that is used for computing the MICOM isotropic viscosity within
- a user specified equatorial band.
-
-[real]
-
-
-eq_vel_micom_aniso
-
-
- Velocity scale that is used for computing the MICOM anisotropic viscosity within
- a user specified equatorial band.
-
-[real]
-
-
-eq_lat_micom
-
-
- Equatorial latitude band (degrees) within which the MICOM viscosity is set according
- to eq_vel_micom_iso and eq_vel_micom_aniso.
-
-[real]
-
-
-neptune
-
-
- Set to true for computing friction relative to Neptune barotropic velocity.
- Default neptune=.false.
-
-[logical]
-
-
-neptune_length_eq
-
-
- Length scale used to compute Neptune velocity at equator.
-
-[real, units: m]
-
-
-neptune_length_pole
-
-
- Length scale used to compute Neptune velocity at pole.
-
-[real, units: m]
-
-
-neptune_depth_min
-
-
- Minimum depth scale used for computing Neptune velocity.
- Default neptune_depth_min=100.0
-
-[real, units: m]
-
-
-neptune_smooth
-
-
- For doing a horizontal 1-2-1 smoothing on the diagnosed
- neptune velocity scale.
- Default neptune_smooth=.true.
-
-[logical]
-
-
-neptune_smooth_num
-
-
- Number of smoothing passes for neptune velocity.
- Default neptune_smooth_num=1.
-
-[integer]
-
-
-use_side_drag_friction
-
-
- For converting friction at U-cells next to walls into
- a drag law, as per Deremble et al. Use cdbot_array
- from ocean_core/ocean_bbc.F90 to compute drag force.
- Default use_side_drag_friction=.false.
-
-[logical]
-
-
-side_drag_friction_scaling
-
-
- Dimensionless scaling used for cdbot_array when setting
- side drag friction. So the effective side dragy coefficient
- is side_drag_friction_scaling*cdbot_array.
- Default side_drag_friction_scaling=1.0.
-
-[real]
-
-
-side_drag_friction_uvmag_max
-
-
- Maximum magnitude of horizontal velocity used to compute the
- side drag friction. This parameter can be useful especially
- for pressure models where the bottom cells can be quite thin
- and subject to sporadic large magnitudes. We do the same thing with
- bottom drag calculations.
- Default side_drag_friction_uvmag_max=10.0.
-
-[real, units: m/s]
-
-
-side_drag_friction_max
-
-
- Maximum magnitude of the side drag induced friction.
- This parameter can be useful especially for pressure models
- where the bottom cells can be quite thin and subject to sporadic
- large magnitudes. We do the same thing with bottom drag calculations
- in ocean_bbc. Default side_drag_friction_max=1.0.
-
-[real, units: N/m^2]
-
-
-
-
-
-
-
-
-
-
-
REFERENCES
-
-
-
-
- S.M. Griffies and R.W. Hallberg, 2000:
- Biharmonic friction with a Smagorinsky viscosity for use in large-scale
- eddy-permitting ocean models
- Monthly Weather Review, vol. 128, pages 2935-2946
-
-
- R. D. Smith and J. C. McWilliams, 2003:
- Anisotropic horizontal viscosity for ocean models,
- Ocean Modelling, vol. 5, pages 129-156.
-
-
- Maltrud and Holloway, 2008: Implementing biharmonic neptune in a
- global eddying ocean model, Ocean Modelling, vol. 21, pages 22-34.
-
-
- Deremble, Hogg, Berloff, and Dewar, 2011:
- On the application of no-slip lateral boundary conditions to coarsely
- resolved ocean models, Ocean Modelling.
-
-
- Griffies: Elements of MOM (2012)
-
-
-
-
-
-
-
-
NOTES
-
-
- The ocean model can generally run with both Laplacian and biharmonic friction
- enabled at the same time. Such has been found useful for some simulations.
-
-
-
diff --git a/src/mom5/ocean_param/lateral/ocean_bihcgrid_friction.xml b/src/mom5/ocean_param/lateral/ocean_bihcgrid_friction.xml
deleted file mode 100644
index 60469c0fa5..0000000000
--- a/src/mom5/ocean_param/lateral/ocean_bihcgrid_friction.xml
+++ /dev/null
@@ -1,209 +0,0 @@
-
-
- S. M. Griffies
-
- This module computes the thickness weighted time tendency for
- horizontal velocity arising from horizontal biharmonic friction.
- Friction is formulated for the C-grid here.
-
- This module computes the thickness weighted time tendency for
- horizontal velocity arising from horizontal biharmonic friction.
- The viscosity used to determine the strength of the tendency
- can be a general function of space and time as specified by
- the Smagorinsky approach; a grid-scale dependent
- background viscosity; or other options.
- The form of the friction operator can be isotropic or
- anisotropic in the horizontal plane.
-
- Friction is formulated for the C-grid in this module.
-
-
- S.M. Griffies and R.W. Hallberg, 2000:
- Biharmonic friction with a Smagorinsky viscosity for use in large-scale
- eddy-permitting ocean models
- Monthly Weather Review, vol. 128, pages 2935-2946
-
- R. D. Smith and J. C. McWilliams, 2003:
- Anisotropic horizontal viscosity for ocean models,
- Ocean Modelling, vol. 5, pages 129-156.
-
- Maltrud and Holloway, 2008: Implementing biharmonic neptune in a
- global eddying ocean model, Ocean Modelling, vol. 21, pages 22-34.
-
- Deremble, Hogg, Berloff, and Dewar, 2011:
- On the application of no-slip lateral boundary conditions to coarsely
- resolved ocean models, Ocean Modelling.
-
- Griffies: Elements of MOM (2012)
-
- The ocean model can generally run with both Laplacian and biharmonic friction
- enabled at the same time. Such has been found useful for some simulations.
-
- Must be true to use this module. Default is false.
-
- For debugging by printing checksums.
-
- This is the dimensionless Smagorinsky coefficient used to set the scale
- of the Smagorinsky isotropic viscosity.
-
- This is the dimensionless Smagorinsky coefficient used to set the scale
- of the Smagorinsky anisotropic viscosity.
-
- Velocity scale that is used for computing the MICOM isotropic viscosity.
-
- Velocity scale that is used for computing the MICOM anisotropic viscosity.
-
- Orient the anisotropic friction within a latitudinal band according to zonal direction.
-
- Latitudinal band to use the zonal friction orientation.
-
- Turn smag off within equatorial_zonal_lat region.
-
- Velocity scale that is used for computing the MICOM isotropic viscosity within
- a user specified equatorial band.
-
- Velocity scale that is used for computing the MICOM anisotropic viscosity within
- a user specified equatorial band.
-
- Equatorial latitude band (degrees) within which the MICOM viscosity is set according
- to eq_vel_micom_iso and eq_vel_micom_aniso.
-
- Set to true for computing friction relative to Neptune barotropic velocity.
- Default neptune=.false.
-
- Length scale used to compute Neptune velocity at equator.
-
- Length scale used to compute Neptune velocity at pole.
-
- Minimum depth scale used for computing Neptune velocity.
- Default neptune_depth_min=100.0
-
- For doing a horizontal 1-2-1 smoothing on the diagnosed
- neptune velocity scale.
- Default neptune_smooth=.true.
-
- Number of smoothing passes for neptune velocity.
- Default neptune_smooth_num=1.
-
- For converting friction at U-cells next to walls into
- a drag law, as per Deremble et al. Use cdbot_array
- from ocean_core/ocean_bbc.F90 to compute drag force.
- Default use_side_drag_friction=.false.
-
- Dimensionless scaling used for cdbot_array when setting
- side drag friction. So the effective side dragy coefficient
- is side_drag_friction_scaling*cdbot_array.
- Default side_drag_friction_scaling=1.0.
-
- Maximum magnitude of horizontal velocity used to compute the
- side drag friction. This parameter can be useful especially
- for pressure models where the bottom cells can be quite thin
- and subject to sporadic large magnitudes. We do the same thing with
- bottom drag calculations.
- Default side_drag_friction_uvmag_max=10.0.
-
- Maximum magnitude of the side drag induced friction.
- This parameter can be useful especially for pressure models
- where the bottom cells can be quite thin and subject to sporadic
- large magnitudes. We do the same thing with bottom drag calculations
- in ocean_bbc. Default side_drag_friction_max=1.0.
-
- Initialize the lateral biharmonic friction module by
- registering fields for diagnostic output and performing some
- numerical checks to see that viscosity is set appropriately.
-
- This routine computes thickness weighted and density weighted
- time tendency for horizontal velocity arising from horizontal
- biharmonic friction.
-
- The algorithm is derived from a functional approach that ensures
- kinetic energy is consistenty dissipated for all flow configurations.
- The stencil is far simpler than the B-grid approach. In particular,
- there are no triads here for the C-grid.
-
- Fundamental to the scheme are the rates of horizontal deformation
- horizontal tension = DT = (dy)(u/dy)_x - (dx)(v/dx)_y
- horizontal strain = DS = (dx)(u/dx)_y + (dy)(v/dy)_x
- Units of the tension and strain are sec^-1.
-
- As shown in Griffies and Hallberg (2000),
- a biharmonic operator with a nonconstant viscosity is guaranteed to
- dissipate kinetic energy *only* when using the sqrt of the biharmonic
- viscosity at each of the two stages of the algorithm.
- The sqrt approach is employed here.
-
-
-
- Read in the 3d ncar boundary scaling field and use this to
- rescale the background viscosities.
-
- To use this routine, we need to already have generated the field
- ncar_rescale using the routine ncar_boundary_scale_create.
-
- The advantage of reading ncar_rescale is that we do not need to
- introduce any global 2d arrays required for ncar_boundary_scale_create.
- So the idea is to pay the price once by running ncar_boundary_scale_create,
- save ncar_rescale, then read that field in during subsequent runs through
- ncar_boundary_scale_read.
-
- Here are the steps:
- 1/ run one time with ncar_boundary_scaling_read=.false.
- and ncar_boundary_scaling=.true.
- Be sure that the field ncar_rescale is saved in diagnostic table.
- To ensure answers agree whether reading ncar_rescale or creating it
- during initialization, it is necessary to save ncar_rescale using the
- double precision option in the diagnostic table (packing=1).
-
- 2/ extract field ncar_rescale from the diagnostics output
- and place into its own file INPUT/ncar_rescale.nc
- example extraction using ncks:
- ncks -v ncar_rescale 19900101.ocean_month.nc ncar_rescale.nc
-
- 3/ set ncar_boundary_scaling_read=.true.
- and ncar_boundary_scaling=.true., and now run the model
- reading in ncar_rescale rather than regenerating
- it during each initialization (which can be a bottleneck
- for large models on huge processor counts).
-
- 4/ As a check that all is fine, save ncar_rescale as a diagnostic
- for both the create and the read stage and make sure they agree.
- Also, all checksums should agree whether reading in ncar_rescale
- or creating it each initialization, so long as the ncar_rescale.nc
- was saved with double precision (see step 1/ above).
-
-
-
- Recale the background viscosities to be larger in the western
- boundary regions. The algorithm is taken directly from the
- anisotropic_ncar routine in ocean_lapgen_friction.F90.
-
- NOTE: The nearest western boundary computations are done along the
- model i-grid lines. Therefore, viscosity based on these are
- only approximate in the high Northern Hemisphere when using
- generalized coordinates with coordinate pole(s) shifted onto
- land.
-
-
- Subroutine to perform linear stability check for the biharmonic
- operator given a value for the horizontal biharmonic viscosity.
-
- Subroutine to compute the biharmonic grid Reynolds number. Large
- Reynolds numbers indicate regions where solution may experience
- some grid noise due to lack of enough horizontal friction.
-
- Compute Neptune velocity.
-
- Method follows that of
- Maltrud and Holloway, 2008: Implementing biharmonic neptune in a
- global eddying ocean model, Ocean Modelling, vol. 21, pages 22-34.
-
- This approach is slightly different than the Eby and Holloway
- method implemented in the laplacian module. There is no fundamental
- reason to favor one versus the other. We use the Maltrud and
- Holloway method here sinc they implemented it for biharmonic.
-
- May 2012
- Stephen.Griffies
-
-
diff --git a/src/mom5/ocean_param/lateral/ocean_bihcst_friction.F90 b/src/mom5/ocean_param/lateral/ocean_bihcst_friction.F90
index 73d3dd5971..1ef65e688d 100644
--- a/src/mom5/ocean_param/lateral/ocean_bihcst_friction.F90
+++ b/src/mom5/ocean_param/lateral/ocean_bihcst_friction.F90
@@ -137,10 +137,10 @@ module ocean_bihcst_friction_mod
integer :: isd, ied, jsd, jed, isc, iec, jsc, jec, nk
character(len=256) :: version=&
- '=>Using: ocean_bihcst_friction.f90 ($Id: ocean_bihcst_friction.F90,v 1.1.2.4 2012/06/08 20:15:35 Stephen.Griffies Exp $)'
+ '=>Using: ocean_bihcst_friction.f90 ($Id: ocean_bihcst_friction.F90,v 20.0 2013/12/14 00:14:14 fms Exp $)'
character (len=128) :: tagname = &
- '$Name: mom5_siena_08jun2012_smg $'
+ '$Name: tikal $'
logical :: module_is_initialized = .FALSE.
logical :: use_this_module = .false.
diff --git a/src/mom5/ocean_param/lateral/ocean_bihcst_friction.html b/src/mom5/ocean_param/lateral/ocean_bihcst_friction.html
deleted file mode 100644
index 6f6c3d2ef7..0000000000
--- a/src/mom5/ocean_param/lateral/ocean_bihcst_friction.html
+++ /dev/null
@@ -1,305 +0,0 @@
-
-
-
-Module ocean_bihcst_friction_mod
-
-
-
-
-PUBLIC INTERFACE
-
- ~ PUBLIC ROUTINES
- ~ NAMELIST
-
-
- Thickness weighted and density weighted time tendency for velocity
- from horizontal biharmonic friction
-
-
-
-
-
- This module computes the thickness and density weighted time tendency
- for horizontal velocity arising from horizontal biharmonic friction.
- The viscosity used to determine the strength of the tendency
- can be a general function of space yet it is constant in time.
- A namelist option exists that determines this viscosity
- as a local function of the grid spacing.
-
- Initialize the horizontal biharmonic friction module by
- registering fields for diagnostic output and performing some
- numerical checks to see that viscosity is set appropriately.
-
-
-
-
-
-
-
-
bihcst_friction
-
-
-DESCRIPTION
-
-
- This subroutine computes the thickness weighted acceleration on
- horizontal velocity arising from horizontal biharmonic friction.
-
-
-
-
-
-
-
-
delsq_velocity
-
-
-DESCRIPTION
-
-
- Subroutine computes the laplacian operator acting on velocity.
-
-
-
-
-
-
-
-
bihcst_viscosity_check
-
-
-DESCRIPTION
-
-
- Subroutine to perform linear stability check for the biharmonic
- operator given a value for the horizontal biharmonic viscosity.
-
-
-
-
-
-
-
-
bihcst_reynolds_check
-
-
-DESCRIPTION
-
-
- Subroutine to compute the biharmonic grid Reynolds number. Large
- Reynolds numbers indicate regions where solution may experience
- some grid noise due to lack of enough horizontal friction.
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_bihcst_friction_nml
-
-
-
-
-
-use_this_module
-
-
- Must be true to use this module. Default is false.
-
-[logical]
-
-
-debug_this_module
-
-
- For debugging by printing checksums.
-
-[logical]
-
-
-abih
-
-
- This is the value for the space-time constant biharmonic viscosity.
-
-[real, units: m^4/sec]
-
-
-velocity_mix_micom
-
-
- If .true., then the viscosity is set according to a velocity scale times
- the cube of the grid spacing. It is based on an approach recommended by
- Eric Chassignet that is used in the Miami Isopycnal Model.
-
-[logical]
-
-
-vel_micom
-
-
- Velocity scale that is used for computing the MICOM viscosity.
-
-[real, units: m/sec]
-
-
-eq_vel_micom
-
-
- Velocity scale that is used for computing the MICOM viscosity within a latitude
- band surrounding the equator. This is useful for some models of enhanced equatorial
- resolution that can maintain numerical integrity in this region with less friction
- than outside the tropical band.
-
-[real, units: m/sec]
-
-
-eq_lat_micom
-
-
- Equatorial latitude band (degrees) within which the MICOM viscosity is set according
- to eq_vel_micom.
-
-[real]
-
-
-
-
-
-
-
-
-
-
-
REFERENCES
-
-
-
-
- R. J. Murray and C.J.C. Reason,
- A curvilinear version of the Bryan-Cox ocean model
- Journal Computational Physics (2002), vol 171, pages 1-46
-
-
- Elements of MOM (2012), S.M. Griffies
-
-
-
-
-
-
-
-
NOTES
-
-
- The numerical implementation requires one call to mpp_update_domains if
- running the model with halo=1.
-
-
- This scheme has been found to be faster than the Smagorinsky viscosity
- scheme. However, the algorithm here is less robust since it
- contains null modes in the terms associated with the sphericity
- of the earth. Hence, there may be flow configurations that are
- not dissipated.
-
-
- The model can generally run with both Laplacian and biharmonic friction
- enabled at the same time. Such has been found useful for some eddying
- ocean simulations.
-
-
- The numerical implementation in mom4p1 and mom5 does not include the sink due
- to partial bottom cells. This sink was implemented in mom2 and mom3
- and mom4. It is not known how relevant this sink is.
-
-
-
diff --git a/src/mom5/ocean_param/lateral/ocean_bihcst_friction.xml b/src/mom5/ocean_param/lateral/ocean_bihcst_friction.xml
deleted file mode 100644
index 46227e343d..0000000000
--- a/src/mom5/ocean_param/lateral/ocean_bihcst_friction.xml
+++ /dev/null
@@ -1,74 +0,0 @@
-
-
- Stephen M. Griffies
-
- Thickness weighted and density weighted time tendency for velocity
- from horizontal biharmonic friction
-
- This module computes the thickness and density weighted time tendency
- for horizontal velocity arising from horizontal biharmonic friction.
- The viscosity used to determine the strength of the tendency
- can be a general function of space yet it is constant in time.
- A namelist option exists that determines this viscosity
- as a local function of the grid spacing.
-
- R. J. Murray and C.J.C. Reason,
- A curvilinear version of the Bryan-Cox ocean model
- Journal Computational Physics (2002), vol 171, pages 1-46
-
- Elements of MOM (2012), S.M. Griffies
-
- The numerical implementation requires one call to mpp_update_domains if
- running the model with halo=1.
-
- This scheme has been found to be faster than the Smagorinsky viscosity
- scheme. However, the algorithm here is less robust since it
- contains null modes in the terms associated with the sphericity
- of the earth. Hence, there may be flow configurations that are
- not dissipated.
-
- The model can generally run with both Laplacian and biharmonic friction
- enabled at the same time. Such has been found useful for some eddying
- ocean simulations.
-
- The numerical implementation in mom4p1 and mom5 does not include the sink due
- to partial bottom cells. This sink was implemented in mom2 and mom3
- and mom4. It is not known how relevant this sink is.
-
- Must be true to use this module. Default is false.
-
- For debugging by printing checksums.
-
- This is the value for the space-time constant biharmonic viscosity.
-
- If .true., then the viscosity is set according to a velocity scale times
- the cube of the grid spacing. It is based on an approach recommended by
- Eric Chassignet that is used in the Miami Isopycnal Model.
-
- Velocity scale that is used for computing the MICOM viscosity.
-
- Velocity scale that is used for computing the MICOM viscosity within a latitude
- band surrounding the equator. This is useful for some models of enhanced equatorial
- resolution that can maintain numerical integrity in this region with less friction
- than outside the tropical band.
-
- Equatorial latitude band (degrees) within which the MICOM viscosity is set according
- to eq_vel_micom.
-
- Initialize the horizontal biharmonic friction module by
- registering fields for diagnostic output and performing some
- numerical checks to see that viscosity is set appropriately.
-
- This subroutine computes the thickness weighted acceleration on
- horizontal velocity arising from horizontal biharmonic friction.
-
- Subroutine computes the laplacian operator acting on velocity.
-
- Subroutine to perform linear stability check for the biharmonic
- operator given a value for the horizontal biharmonic viscosity.
-
- Subroutine to compute the biharmonic grid Reynolds number. Large
- Reynolds numbers indicate regions where solution may experience
- some grid noise due to lack of enough horizontal friction.
-
diff --git a/src/mom5/ocean_param/lateral/ocean_bihgen_friction.F90 b/src/mom5/ocean_param/lateral/ocean_bihgen_friction.F90
index a718ab5a80..d069923e18 100644
--- a/src/mom5/ocean_param/lateral/ocean_bihgen_friction.F90
+++ b/src/mom5/ocean_param/lateral/ocean_bihgen_friction.F90
@@ -415,9 +415,9 @@ module ocean_bihgen_friction_mod
type(ocean_domain_type), pointer :: Dom => NULL()
character(len=256) :: version=&
- '=>Using: ocean_bihgen_friction.F90 ($Id: ocean_bihgen_friction.F90,v 1.1.2.5.14.1 2013/04/03 13:25:25 smg Exp $)'
+ '=>Using: ocean_bihgen_friction.F90 ($Id: ocean_bihgen_friction.F90,v 20.0 2013/12/14 00:14:16 fms Exp $)'
character (len=128) :: tagname = &
- '$Name: mom5_siena_201303_smg $'
+ '$Name: tikal $'
logical :: use_this_module = .false.
logical :: debug_this_module = .false.
diff --git a/src/mom5/ocean_param/lateral/ocean_bihgen_friction.html b/src/mom5/ocean_param/lateral/ocean_bihgen_friction.html
deleted file mode 100644
index 64c94356f5..0000000000
--- a/src/mom5/ocean_param/lateral/ocean_bihgen_friction.html
+++ /dev/null
@@ -1,742 +0,0 @@
-
-
-
-Module ocean_bihgen_friction_mod
-
-
-
-
-PUBLIC INTERFACE
-
- ~ PUBLIC ROUTINES
- ~ NAMELIST
-
-
- This module computes thickness weighted and density weighted
- time tendency for horizontal velocity arising from
- biharmonic friction.
-
-
-
-
-
- This module computes thickness weighted and density weighted
- time tendency for horizontal velocity arising from biharmonic
- friction.
-
- The viscosity used to determine the strength of the tendency
- can be a general function of space and time as specified by
- the Smagorinsky approach as well as a grid-scale dependent
- background viscosity. The form of the friction operator
- can be isotropic or anisotropic in the lateral plane.
-
- Initialize the horizontal biharmonic friction module by
- registering fields for diagnostic output and performing some
- numerical checks to see that viscosity is set appropriately.
-
-
-
-
-
-
-
-
bihgen_friction
-
-
-DESCRIPTION
-
-
- This subroutine computes the time tendency for horizontal
- velocity (i.e., the acceleration) from horizontal biharmonic friction.
- The algorithm is derived from a functional approach that ensures kinetic
- energy is consistenty dissipated for all flow configurations.
- The triad do-loops are expanded in order to enhance the
- ability of cache-based machines to keep most of the variables
- on-cache.
-
- Fundamental to the scheme are the rates of horizontal deformation
- horizontal tension = DT = (dy)(u/dy)_x - (dx)(v/dx)_y
- horizontal strain = DS = (dx)(u/dx)_y + (dy)(v/dy)_x
- Units of the tension and strain are sec^-1.
-
- Four tensions and four strains are computed for each velocity point,
- corresponding to the four triads surrounding the point.
- The following notation is used to distinguish the triads:
- (0,1)=northwest triad (1,1)=northeast triad,
- (0,0)=southwest triad, (1,0)=southeast triad
-
- A triad contributes when at least one of its velocities is
- not a land point. In order to obtain the correct tension
- and strain next to boundaries, tension and strain should not be
- masked with umask.
-
- As shown in Griffies and Hallberg (2000),
- a biharmonic operator with a nonconstant viscosity is guaranteed to
- dissipate kinetic energy *only* when using the sqrt of the biharmonic
- viscosity at each of the two stages of the algorithm.
- The sqrt approach is employed here.
-
-
-
-
-
-
-
-
-
ncar_boundary_scale_read
-
-
-DESCRIPTION
-
-
-
- Read in the 3d ncar boundary scaling field and use this to
- rescale the background viscosities.
-
- To use this routine, we need to already have generated the field
- ncar_rescale using the routine ncar_boundary_scale_create.
-
- The advantage of reading ncar_rescale is that we do not need to
- introduce any global 2d arrays required for ncar_boundary_scale_create.
- So the idea is to pay the price once by running ncar_boundary_scale_create,
- save ncar_rescale, then read that field in during subsequent runs through
- ncar_boundary_scale_read.
-
- Here are the steps:
- 1/ run one time with ncar_boundary_scaling_read=.false.
- and ncar_boundary_scaling=.true.
- Be sure that the field ncar_rescale is saved in diagnostic table.
- To ensure answers agree whether reading ncar_rescale or creating it
- during initialization, it is necessary to save ncar_rescale using the
- double precision option in the diagnostic table (packing=1).
-
- 2/ extract field ncar_rescale from the diagnostics output
- and place into its own file INPUT/ncar_rescale.nc
- example extraction using ncks:
- ncks -v ncar_rescale 19900101.ocean_month.nc ncar_rescale.nc
-
- 3/ set ncar_boundary_scaling_read=.true.
- and ncar_boundary_scaling=.true., and now run the model
- reading in ncar_rescale rather than regenerating
- it during each initialization (which can be a bottleneck
- for large models on huge processor counts).
-
- 4/ As a check that all is fine, save ncar_rescale as a diagnostic
- for both the create and the read stage and make sure they agree.
- Also, all checksums should agree whether reading in ncar_rescale
- or creating it each initialization, so long as the ncar_rescale.nc
- was saved with double precision (see step 1/ above).
-
-
-
-
-
-
-
-
-
ncar_boundary_scale_create
-
-
-DESCRIPTION
-
-
-
- Recale the background viscosities to be larger in the western
- boundary regions. The algorithm is taken directly from the
- anisotropic_ncar routine in ocean_lapgen_friction.F90.
-
- NOTE: The nearest western boundary computations are done along the
- model i-grid lines. Therefore, viscosity based on these are
- only approximate in the high Northern Hemisphere when using
- generalized coordinates with coordinate pole(s) shifted onto
- land.
-
-
-
-
-
-
-
-
-
BDX_EU_smag
-
-
-DESCRIPTION
-
-
- Compute backwards Derivative in X of a quantity defined on the east
- face of a U-cell. Slightly modified version of BDX_EU used in
- ocean_operators.F90. If input is a(i,j) then output is defined
- at (i-1/2,j).
-
- BDX_EU_smag changes dimensions by m^-3
-
-
-
-
-
-INPUT
-
-
-
-
-
a
- field defined on the east face of a U-cell
- [real, dimension(isd:ied,jsd:jed)]
-
-
-
-
-
-
-
-
-
BDY_NU_smag
-
-
-DESCRIPTION
-
-
- Compute backwards Derivative in Y of a quantity defined on the north
- face of a U-cell. Slightly modified version of BDY_EU used in
- ocean_operators.F90. If input is a(i,j) then output is defined
- at (i,j-1/2).
-
- BDY_EU_smag changes dimensions by m^-3
-
-
-
-
-
-INPUT
-
-
-
-
-
a
- field defined on the north face of a U-cell
- [real, dimension(isd:ied,jsd:jed)]
-
-
-
-
-
-
-
-
-
bihgen_viscosity_check
-
-
-DESCRIPTION
-
-
- Subroutine to perform linear stability check for the biharmonic
- operator given a value for the horizontal biharmonic viscosity.
-
-
-
-
-
-
-
-
bihgen_reynolds_check
-
-
-DESCRIPTION
-
-
- Subroutine to compute the biharmonic grid Reynolds number. Large
- Reynolds numbers indicate regions where solution may experience
- some grid noise due to lack of enough horizontal friction.
-
-
-
-
-
-
-
-
compute_neptune_velocity
-
-
-DESCRIPTION
-
-
- Compute Neptune velocity.
-
- Method follows that of
- Maltrud and Holloway, 2008: Implementing biharmonic neptune in a
- global eddying ocean model, Ocean Modelling, vol. 21, pages 22-34.
-
- March 2012
- Stephen.Griffies
-
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_bihgen_friction_nml
-
-
-
-
-
-use_this_module
-
-
- Must be true to use this module. Default is false.
-
-[logical]
-
-
-debug_this_module
-
-
- For debugging by printing checksums.
-
-[logical]
-
-
-k_smag_iso
-
-
- This is the dimensionless Smagorinsky coefficient used to set the scale
- of the Smagorinsky isotropic viscosity.
-
-[real, units: dimensionless]
-
-
-k_smag_aniso
-
-
- This is the dimensionless Smagorinsky coefficient used to set the scale
- of the Smagorinsky anisotropic viscosity.
-
-[real, units: dimensionless]
-
-
-vel_micom_iso
-
-
- Velocity scale that is used for computing the MICOM isotropic viscosity.
-
-[real, units: m/sec]
-
-
-vel_micom_aniso
-
-
- Velocity scale that is used for computing the MICOM anisotropic viscosity.
-
-[real, units: m/sec]
-
-
-visc_crit_scale
-
-
- Scaling factor used to determine the critical viscosity, above which
- the viscosity is not allowed to reach.
- Use visc_crit_scale < 1.0 for cases where the visc_crit from linear stability
- allows for still too large of a viscosity. Use visc_crit_scale>1.0 when wish
- to allow for larger viscosity. Default is visc_crit_scale=1.0.
-
-[real, units: dimensionless]
-
-
-equatorial_zonal
-
-
- Orient the anisotropic friction within a latitudinal band according
- to zonal direction.
-
-[real]
-
-
-equatorial_zonal_lat
-
-
- Latitudinal band to use the zonal friction orientation.
-
-[real]
-
-
-eq_vel_micom_iso
-
-
- Velocity scale that is used for computing the MICOM isotropic viscosity
- within a user specified equatorial band.
-
-[real]
-
-
-eq_vel_micom_aniso
-
-
- Velocity scale that is used for computing the MICOM anisotropic
- viscosity within a user specified equatorial band.
-
-[real]
-
-
-eq_lat_micom
-
-
- Equatorial latitude band (degrees) within which the MICOM viscosity
- is set according to eq_vel_micom_iso and eq_vel_micom_aniso.
-
-[real]
-
-
-bottom_5point
-
-
- To alleviate problems with small partial cells, it is often necessary
- to reduce the operator to the traditional 5-point Laplacian at the
- ocean bottom. This logical implements this mixing.
- Default bottom_5point=.false.
-
-[logical]
-
-
-vel_micom_bottom
-
-
- Velocity scale that is used for computing the MICOM viscosity for
- 5point Laplacian at the bottom.
-
-[real, units: m/sec]
-
-
-ncar_boundary_scaling
-
-
- To enhance the velocity scale used in western boundaries
- for the isotropic and anisotropic background viscosities,
- we compute a scaling using the algorithm from the laplacian
- NCAR anisotropic scheme.
- Default ncar_boundary_scaling=.false.
-
-[logical]
-
-
-ncar_boundary_scaling_read
-
-
- To read in the ncar boundary scaling field rather than
- generating it during initialization. Generating during
- initialization can be a bottle-neck on fine resolution models
- since there are some global 2d fields needed. So if the
- rescaling is produced once and then saved, it can be read
- in during subsequent runs without incurring the slowdown
- of re-generating the scalings.
- Default ncar_boundary_scaling_read=.false.
-
-[logical]
-
-
-ncar_rescale_power
-
-
- For determining rescaling of the viscosity so to enhance the
- friction near the western boundaries. Default ncar_rescale_power=1.
-
-[integer, units: dimensionless]
-
-
-ncar_vconst_4
-
-
- Inverse damping length for exponential falloff of the velocity scale
- as move eastward away from western boundary. Default ncar_vconst_4=2.e-8.
-
-[real, units: 1/cm]
-
-
-ncar_vconst_5
-
-
- For determining number of grid points in boundary calculation.
- Default ncar_vconst_5=3.
-
-[integer, units: dimensionless]
-
-
-neptune
-
-
- Set to true for computing friction relative to Neptune barotropic velocity.
- Default neptune=.false.
-
-[logical]
-
-
-neptune_length_eq
-
-
- Length scale used to compute Neptune velocity at equator.
- Default neptune_length_eq= 4.2e3 from Maltrud and Holloway.
-
-[real, units: m]
-
-
-neptune_length_pole
-
-
- Length scale used to compute Neptune velocity at pole.
- Default neptune_length_pole= 17.0e3 from Maltrud and Holloway.
-
-[real, units: m]
-
-
-neptune_depth_min
-
-
- Minimum depth scale used for computing Neptune velocity.
- Default neptune_depth_min=100.0 from Maltrud and Holloway.
-
-[real, units: m]
-
-
-neptune_smooth
-
-
- For doing a horizontal 1-2-1 smoothing on the diagnosed
- neptune velocity scale.
- Default neptune_smooth=.true.
-
-[logical]
-
-
-neptune_smooth_num
-
-
- Number of smoothing passes for neptune velocity.
- Default neptune_smooth_num=1.
-
-[integer]
-
-
-neptune_scaling
-
-
- Overall scaling parameter to help tune neptune.
- Default neptune_scaling=1.0
-
-[real]
-
-
-visc_diverge_scaling
-
-
- Dimensionless scaling used for divergence based viscosity.
- Default visc_diverge_scaling=0.0 turns off the scheme.
- visc_diverge_scaling=10.0 produces sensible viscosities for
- 1-degree model. May need tuning for different resolutions.
-
-[real]
-
-
-use_side_drag_friction
-
-
- For converting friction at U-cells next to walls into
- a drag law, as per Deremble et al. Use cdbot_array
- from ocean_core/ocean_bbc.F90 to compute drag force.
- Default use_side_drag_friction=.false.
-
-[logical]
-
-
-side_drag_friction_scaling
-
-
- Dimensionless scaling used for cdbot_array when setting
- side drag friction. So the effective side dragy coefficient
- is side_drag_friction_scaling*cdbot_array.
- Default side_drag_friction_scaling=1.0.
-
-[real]
-
-
-side_drag_friction_uvmag_max
-
-
- Maximum magnitude of horizontal velocity used to compute the
- side drag friction. This parameter can be useful especially
- for pressure models where the bottom cells can be quite thin
- and subject to sporadic large magnitudes. We do the same thing with
- bottom drag calculations.
- Default side_drag_friction_uvmag_max=10.0.
-
-[real, units: m/s]
-
-
-side_drag_friction_max
-
-
- Maximum magnitude of the side drag induced friction.
- This parameter can be useful especially for pressure models
- where the bottom cells can be quite thin and subject to sporadic
- large magnitudes. We do the same thing with bottom drag calculations.
- Default side_drag_friction_max=1.0.
-
-[real, units: N/m^2]
-
-
-
-
-
-
-
-
-
-
-
REFERENCES
-
-
-
-
- S.M. Griffies and R.W. Hallberg, 2000:
- Biharmonic friction with a Smagorinsky viscosity for use
- in large-scale eddy-permitting ocean models
- Monthly Weather Review, vol. 128, pages 2935-2946.
-
-
- R.D. Smith and J.C. McWilliams, 2003:
- Anisotropic horizontal viscosity for ocean models,
- Ocean Modelling, vol. 5, pages 129-156.
-
-
- Maltrud and Holloway, 2008: Implementing biharmonic neptune in a
- global eddying ocean model, Ocean Modelling, vol. 21, pages 22-34.
-
-
- Deremble, Hogg, Berloff, and Dewar, 2011:
- On the application of no-slip lateral boundary conditions to coarsely
- resolved ocean models, Ocean Modelling.
-
-
- S.M. Griffies, 2004:
- Fundamentals of Ocean Climate Models
- Princeton University Press
-
-
- Griffies, Elements of MOM (2012)
-
-
-
-
-
-
-
-
NOTES
-
-
- The ocean model can generally run with both Laplacian and biharmonic
- friction enabled at the same time. Such has been found useful
- for some eddying ocean simulations.
-
-
-
diff --git a/src/mom5/ocean_param/lateral/ocean_bihgen_friction.xml b/src/mom5/ocean_param/lateral/ocean_bihgen_friction.xml
deleted file mode 100644
index c01f155a34..0000000000
--- a/src/mom5/ocean_param/lateral/ocean_bihgen_friction.xml
+++ /dev/null
@@ -1,284 +0,0 @@
-
-
- S. M. Griffies
-
- This module computes thickness weighted and density weighted
- time tendency for horizontal velocity arising from
- biharmonic friction.
-
- This module computes thickness weighted and density weighted
- time tendency for horizontal velocity arising from biharmonic
- friction.
-
- The viscosity used to determine the strength of the tendency
- can be a general function of space and time as specified by
- the Smagorinsky approach as well as a grid-scale dependent
- background viscosity. The form of the friction operator
- can be isotropic or anisotropic in the lateral plane.
-
- S.M. Griffies and R.W. Hallberg, 2000:
- Biharmonic friction with a Smagorinsky viscosity for use
- in large-scale eddy-permitting ocean models
- Monthly Weather Review, vol. 128, pages 2935-2946.
-
- R.D. Smith and J.C. McWilliams, 2003:
- Anisotropic horizontal viscosity for ocean models,
- Ocean Modelling, vol. 5, pages 129-156.
-
- Maltrud and Holloway, 2008: Implementing biharmonic neptune in a
- global eddying ocean model, Ocean Modelling, vol. 21, pages 22-34.
-
- Deremble, Hogg, Berloff, and Dewar, 2011:
- On the application of no-slip lateral boundary conditions to coarsely
- resolved ocean models, Ocean Modelling.
-
- S.M. Griffies, 2004:
- Fundamentals of Ocean Climate Models
- Princeton University Press
-
- Griffies, Elements of MOM (2012)
-
- The ocean model can generally run with both Laplacian and biharmonic
- friction enabled at the same time. Such has been found useful
- for some eddying ocean simulations.
-
- Must be true to use this module. Default is false.
-
- For debugging by printing checksums.
-
- This is the dimensionless Smagorinsky coefficient used to set the scale
- of the Smagorinsky isotropic viscosity.
-
- This is the dimensionless Smagorinsky coefficient used to set the scale
- of the Smagorinsky anisotropic viscosity.
-
- Velocity scale that is used for computing the MICOM isotropic viscosity.
-
- Velocity scale that is used for computing the MICOM anisotropic viscosity.
-
- Scaling factor used to determine the critical viscosity, above which
- the viscosity is not allowed to reach.
- Use visc_crit_scale < 1.0 for cases where the visc_crit from linear stability
- allows for still too large of a viscosity. Use visc_crit_scale>1.0 when wish
- to allow for larger viscosity. Default is visc_crit_scale=1.0.
-
- Orient the anisotropic friction within a latitudinal band according
- to zonal direction.
-
- Latitudinal band to use the zonal friction orientation.
-
- Velocity scale that is used for computing the MICOM isotropic viscosity
- within a user specified equatorial band.
-
- Velocity scale that is used for computing the MICOM anisotropic
- viscosity within a user specified equatorial band.
-
- Equatorial latitude band (degrees) within which the MICOM viscosity
- is set according to eq_vel_micom_iso and eq_vel_micom_aniso.
-
- To alleviate problems with small partial cells, it is often necessary
- to reduce the operator to the traditional 5-point Laplacian at the
- ocean bottom. This logical implements this mixing.
- Default bottom_5point=.false.
-
- Velocity scale that is used for computing the MICOM viscosity for
- 5point Laplacian at the bottom.
-
- To enhance the velocity scale used in western boundaries
- for the isotropic and anisotropic background viscosities,
- we compute a scaling using the algorithm from the laplacian
- NCAR anisotropic scheme.
- Default ncar_boundary_scaling=.false.
-
- To read in the ncar boundary scaling field rather than
- generating it during initialization. Generating during
- initialization can be a bottle-neck on fine resolution models
- since there are some global 2d fields needed. So if the
- rescaling is produced once and then saved, it can be read
- in during subsequent runs without incurring the slowdown
- of re-generating the scalings.
- Default ncar_boundary_scaling_read=.false.
-
- For determining rescaling of the viscosity so to enhance the
- friction near the western boundaries. Default ncar_rescale_power=1.
-
- Inverse damping length for exponential falloff of the velocity scale
- as move eastward away from western boundary. Default ncar_vconst_4=2.e-8.
-
- For determining number of grid points in boundary calculation.
- Default ncar_vconst_5=3.
-
- Set to true for computing friction relative to Neptune barotropic velocity.
- Default neptune=.false.
-
- Length scale used to compute Neptune velocity at equator.
- Default neptune_length_eq= 4.2e3 from Maltrud and Holloway.
-
- Length scale used to compute Neptune velocity at pole.
- Default neptune_length_pole= 17.0e3 from Maltrud and Holloway.
-
- Minimum depth scale used for computing Neptune velocity.
- Default neptune_depth_min=100.0 from Maltrud and Holloway.
-
- For doing a horizontal 1-2-1 smoothing on the diagnosed
- neptune velocity scale.
- Default neptune_smooth=.true.
-
- Number of smoothing passes for neptune velocity.
- Default neptune_smooth_num=1.
-
- Overall scaling parameter to help tune neptune.
- Default neptune_scaling=1.0
-
- Dimensionless scaling used for divergence based viscosity.
- Default visc_diverge_scaling=0.0 turns off the scheme.
- visc_diverge_scaling=10.0 produces sensible viscosities for
- 1-degree model. May need tuning for different resolutions.
-
- For converting friction at U-cells next to walls into
- a drag law, as per Deremble et al. Use cdbot_array
- from ocean_core/ocean_bbc.F90 to compute drag force.
- Default use_side_drag_friction=.false.
-
- Dimensionless scaling used for cdbot_array when setting
- side drag friction. So the effective side dragy coefficient
- is side_drag_friction_scaling*cdbot_array.
- Default side_drag_friction_scaling=1.0.
-
- Maximum magnitude of horizontal velocity used to compute the
- side drag friction. This parameter can be useful especially
- for pressure models where the bottom cells can be quite thin
- and subject to sporadic large magnitudes. We do the same thing with
- bottom drag calculations.
- Default side_drag_friction_uvmag_max=10.0.
-
- Maximum magnitude of the side drag induced friction.
- This parameter can be useful especially for pressure models
- where the bottom cells can be quite thin and subject to sporadic
- large magnitudes. We do the same thing with bottom drag calculations.
- Default side_drag_friction_max=1.0.
-
- Initialize the horizontal biharmonic friction module by
- registering fields for diagnostic output and performing some
- numerical checks to see that viscosity is set appropriately.
-
- This subroutine computes the time tendency for horizontal
- velocity (i.e., the acceleration) from horizontal biharmonic friction.
- The algorithm is derived from a functional approach that ensures kinetic
- energy is consistenty dissipated for all flow configurations.
- The triad do-loops are expanded in order to enhance the
- ability of cache-based machines to keep most of the variables
- on-cache.
-
- Fundamental to the scheme are the rates of horizontal deformation
- horizontal tension = DT = (dy)(u/dy)_x - (dx)(v/dx)_y
- horizontal strain = DS = (dx)(u/dx)_y + (dy)(v/dy)_x
- Units of the tension and strain are sec^-1.
-
- Four tensions and four strains are computed for each velocity point,
- corresponding to the four triads surrounding the point.
- The following notation is used to distinguish the triads:
- (0,1)=northwest triad (1,1)=northeast triad,
- (0,0)=southwest triad, (1,0)=southeast triad
-
- A triad contributes when at least one of its velocities is
- not a land point. In order to obtain the correct tension
- and strain next to boundaries, tension and strain should not be
- masked with umask.
-
- As shown in Griffies and Hallberg (2000),
- a biharmonic operator with a nonconstant viscosity is guaranteed to
- dissipate kinetic energy *only* when using the sqrt of the biharmonic
- viscosity at each of the two stages of the algorithm.
- The sqrt approach is employed here.
-
-
-
- Read in the 3d ncar boundary scaling field and use this to
- rescale the background viscosities.
-
- To use this routine, we need to already have generated the field
- ncar_rescale using the routine ncar_boundary_scale_create.
-
- The advantage of reading ncar_rescale is that we do not need to
- introduce any global 2d arrays required for ncar_boundary_scale_create.
- So the idea is to pay the price once by running ncar_boundary_scale_create,
- save ncar_rescale, then read that field in during subsequent runs through
- ncar_boundary_scale_read.
-
- Here are the steps:
- 1/ run one time with ncar_boundary_scaling_read=.false.
- and ncar_boundary_scaling=.true.
- Be sure that the field ncar_rescale is saved in diagnostic table.
- To ensure answers agree whether reading ncar_rescale or creating it
- during initialization, it is necessary to save ncar_rescale using the
- double precision option in the diagnostic table (packing=1).
-
- 2/ extract field ncar_rescale from the diagnostics output
- and place into its own file INPUT/ncar_rescale.nc
- example extraction using ncks:
- ncks -v ncar_rescale 19900101.ocean_month.nc ncar_rescale.nc
-
- 3/ set ncar_boundary_scaling_read=.true.
- and ncar_boundary_scaling=.true., and now run the model
- reading in ncar_rescale rather than regenerating
- it during each initialization (which can be a bottleneck
- for large models on huge processor counts).
-
- 4/ As a check that all is fine, save ncar_rescale as a diagnostic
- for both the create and the read stage and make sure they agree.
- Also, all checksums should agree whether reading in ncar_rescale
- or creating it each initialization, so long as the ncar_rescale.nc
- was saved with double precision (see step 1/ above).
-
-
-
- Recale the background viscosities to be larger in the western
- boundary regions. The algorithm is taken directly from the
- anisotropic_ncar routine in ocean_lapgen_friction.F90.
-
- NOTE: The nearest western boundary computations are done along the
- model i-grid lines. Therefore, viscosity based on these are
- only approximate in the high Northern Hemisphere when using
- generalized coordinates with coordinate pole(s) shifted onto
- land.
-
-
- Compute backwards Derivative in X of a quantity defined on the east
- face of a U-cell. Slightly modified version of BDX_EU used in
- ocean_operators.F90. If input is a(i,j) then output is defined
- at (i-1/2,j).
-
- BDX_EU_smag changes dimensions by m^-3
-
-
- field defined on the east face of a U-cell
-
- Compute backwards Derivative in Y of a quantity defined on the north
- face of a U-cell. Slightly modified version of BDY_EU used in
- ocean_operators.F90. If input is a(i,j) then output is defined
- at (i,j-1/2).
-
- BDY_EU_smag changes dimensions by m^-3
-
-
- field defined on the north face of a U-cell
-
- Subroutine to perform linear stability check for the biharmonic
- operator given a value for the horizontal biharmonic viscosity.
-
- Subroutine to compute the biharmonic grid Reynolds number. Large
- Reynolds numbers indicate regions where solution may experience
- some grid noise due to lack of enough horizontal friction.
-
- Compute Neptune velocity.
-
- Method follows that of
- Maltrud and Holloway, 2008: Implementing biharmonic neptune in a
- global eddying ocean model, Ocean Modelling, vol. 21, pages 22-34.
-
- March 2012
- Stephen.Griffies
-
-
diff --git a/src/mom5/ocean_param/lateral/ocean_lap_friction.F90 b/src/mom5/ocean_param/lateral/ocean_lap_friction.F90
index 9489915c04..b703798c6e 100644
--- a/src/mom5/ocean_param/lateral/ocean_lap_friction.F90
+++ b/src/mom5/ocean_param/lateral/ocean_lap_friction.F90
@@ -115,9 +115,9 @@ module ocean_lap_friction_mod
integer :: isd, ied, jsd, jed, isc, iec, jsc, jec, nk
character(len=256) :: version=&
- '=>Using: ocean_lap_friction.f90 ($Id: ocean_lap_friction.F90,v 1.1.2.6.6.1 2012/07/10 03:45:18 smg Exp $)'
+ '=>Using: ocean_lap_friction.f90 ($Id: ocean_lap_friction.F90,v 20.0 2013/12/14 00:14:18 fms Exp $)'
character (len=128) :: tagname = &
- '$Name: mom5_siena_08jun2012_smg $'
+ '$Name: tikal $'
logical :: module_is_initialized = .FALSE.
logical :: write_a_restart = .true.
diff --git a/src/mom5/ocean_param/lateral/ocean_lap_friction.html b/src/mom5/ocean_param/lateral/ocean_lap_friction.html
deleted file mode 100644
index 37737acce8..0000000000
--- a/src/mom5/ocean_param/lateral/ocean_lap_friction.html
+++ /dev/null
@@ -1,276 +0,0 @@
-
-
-
-Module ocean_lap_friction_mod
-
-
-
-
-PUBLIC INTERFACE
-
- ~ PUBLIC ROUTINES
- ~ NAMELIST
-
-
- Initialize the horizontal Laplacian friction module.
-
-
-
-
-
-
-
-
lap_friction
-
-
-DESCRIPTION
-
-
- Compute the thickness weighted and density weighted accel due to
- lateral laplacian friction. Add this contribution to Velocity%accel.
-
-
-
-
-
-
-
-
lap_viscosity_check
-
-
-DESCRIPTION
-
-
- To check that the viscosity is not too large.
-
-
-
-
-
-
-
-
lap_reynolds_check
-
-
-DESCRIPTION
-
-
- To check that the Reynolds number is not too large.
-
-
-
-
-
-
-
-
lap_friction_barotropic
-
-
-DESCRIPTION
-
-
-
- This routine computes the laplacian friction acting on a two-dim
- array. It uses the two-dimensional vertically averaged viscosity
- used in the laplacian friction module. The intent is to apply this
- 2d operator to the vertically integrated horizontal momentum. We
- ignore the spherical metric terms in this form of the operator,
- since we are aiming for a fast smoothing operator to be applied
- during each of the many barotropic time steps. We also apply
- just the isotropic portion of the more general anisotropic
- laplacian operator.
-
- This scheme is only meant for the B-grid version of MOM. It
- has not been generalized to the C-grid, since the C-grid has
- less noise in the barotropic gravity waves anyhow, so it is
- unlikely there will need to be extra friction applied to the
- C-grid barotropic equations.
-
-
-
-
-
-
-
-
-
ocean_lap_friction_restart
-
-
-DESCRIPTION
-
-
- Write out restart files registered through register_restart_file
-
-
-
-
-
-
-
-
ocean_lap_friction_end
-
-
-DESCRIPTION
-
-
- Write to restart of the vertically averaged viscosity.
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_lap_friction_nml
-
-
-
-
-
-lap_friction_scheme
-
-
- To determine the laplacian friction scheme: "const" or "general"
-
-[character]
-
-
-debug_this_module
-
-
- For debugging.
-
-[logical]
-
-
-write_a_restart
-
-
- Set true to write a restart. False setting only for rare
- cases where wish to benchmark model without measuring the cost
- of writing restarts and associated chksums.
- Default is write_a_restart=.true.
-
-[logical]
-
-
-
-
-
-
-
-
-
-
-
NOTES
-
-
- The model can generally run with both Laplacian and biharmonic friction
- enabled at the same time. Such has been found useful for some eddying
- ocean simulations.
-
-
-
diff --git a/src/mom5/ocean_param/lateral/ocean_lap_friction.xml b/src/mom5/ocean_param/lateral/ocean_lap_friction.xml
deleted file mode 100644
index c494fe4312..0000000000
--- a/src/mom5/ocean_param/lateral/ocean_lap_friction.xml
+++ /dev/null
@@ -1,54 +0,0 @@
-
-
- Stephen M. Griffies
-
- This module calls the appropriate lateral laplacian friction modules.
-
- This module serves as an interface to the chosen lateral
- laplacian friction modules.
-
- The model can generally run with both Laplacian and biharmonic friction
- enabled at the same time. Such has been found useful for some eddying
- ocean simulations.
-
- To determine the laplacian friction scheme: "const" or "general"
-
- For debugging.
-
- Set true to write a restart. False setting only for rare
- cases where wish to benchmark model without measuring the cost
- of writing restarts and associated chksums.
- Default is write_a_restart=.true.
-
- Initialize the horizontal Laplacian friction module.
-
- Compute the thickness weighted and density weighted accel due to
- lateral laplacian friction. Add this contribution to Velocity%accel.
-
- To check that the viscosity is not too large.
-
- To check that the Reynolds number is not too large.
-
-
- This routine computes the laplacian friction acting on a two-dim
- array. It uses the two-dimensional vertically averaged viscosity
- used in the laplacian friction module. The intent is to apply this
- 2d operator to the vertically integrated horizontal momentum. We
- ignore the spherical metric terms in this form of the operator,
- since we are aiming for a fast smoothing operator to be applied
- during each of the many barotropic time steps. We also apply
- just the isotropic portion of the more general anisotropic
- laplacian operator.
-
- This scheme is only meant for the B-grid version of MOM. It
- has not been generalized to the C-grid, since the C-grid has
- less noise in the barotropic gravity waves anyhow, so it is
- unlikely there will need to be extra friction applied to the
- C-grid barotropic equations.
-
-
- Write out restart files registered through register_restart_file
-
- Write to restart of the vertically averaged viscosity.
-
diff --git a/src/mom5/ocean_param/lateral/ocean_lap_tracer.F90 b/src/mom5/ocean_param/lateral/ocean_lap_tracer.F90
index 455d230150..d72e15e364 100644
--- a/src/mom5/ocean_param/lateral/ocean_lap_tracer.F90
+++ b/src/mom5/ocean_param/lateral/ocean_lap_tracer.F90
@@ -129,9 +129,9 @@ module ocean_lap_tracer_mod
real, dimension(:,:,:), allocatable :: diffusivity_mask ! 3d mask to selectively apply diffusion
character(len=128) :: version=&
- '$Id: ocean_lap_tracer.F90,v 1.1.2.2 2012/06/01 20:47:08 Stephen.Griffies Exp $'
+ '$Id: ocean_lap_tracer.F90,v 20.0 2013/12/14 00:14:20 fms Exp $'
character (len=128) :: tagname = &
- '$Name: mom5_siena_08jun2012_smg $'
+ '$Name: tikal $'
type(ocean_grid_type), pointer :: Grd => NULL()
type(ocean_domain_type), pointer :: Dom => NULL()
diff --git a/src/mom5/ocean_param/lateral/ocean_lap_tracer.html b/src/mom5/ocean_param/lateral/ocean_lap_tracer.html
deleted file mode 100644
index 69628785a6..0000000000
--- a/src/mom5/ocean_param/lateral/ocean_lap_tracer.html
+++ /dev/null
@@ -1,247 +0,0 @@
-
-
-
-Module ocean_lap_tracer_mod
-
-
-
-
-PUBLIC INTERFACE
-
- ~ PUBLIC ROUTINES
- ~ NAMELIST
-
-
- Thickness weighted and density weighted time tendency
- for tracer from lateral laplacian diffusion.
-
-
-
-
-
- This module computes lateral laplacian diffusion of a tracer.
- There are two main options.
-
- (1) The lateral tracer fluxes can be aligned with the z-coordinate surfaces,
- in which case the fluxes must be approximated if (i) we use non-geopotential
- vertical coordinates, (ii) next to partial bottom step topography.
- This form of the diffusion is not recommended since it can lead to
- the creation of spurious extrema.
-
- (2) The lateral tracer fluxes can be aligned surfaces of constant vertical
- coordinate. In this case the fluxes are no longer strictly "horizontal."
- However, the operator is simpler and it ensures that no suprious
- extrema are created. It is for this reason that the simpler operator
- is preferred.
-
- The diffusivity used to determine the strength of the tendency can be
- a general function of space yet it is constant in time. A namelist
- option exists that determines this diffusivity as a local function
- of the grid spacing.
-
- Initialize the laplacian diffusion module by
- registering fields for diagnostic output and performing some
- numerical checks to see that diffusivity is set appropriately.
-
-
-
-
-
-
-
-
lap_tracer
-
-
-DESCRIPTION
-
-
- This function computes the thickness weighted and density weighted
- time tendency for tracer from lateral laplacian diffusion.
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_lap_tracer_nml
-
-
-
-
-
-use_this_module
-
-
- Must be true to use this module. Default is false.
-
-[logical]
-
-
-horz_z_diffuse
-
-
- To compute diffusion along surfaces of constant depth.
- This operation must necessarily be approximate for the two
- cases (i) non-geopotential vertical coordinates, (2)
- next to partial bottom step topography. There are cases where
- use of this operator can lead to spurious creation of extrema
- due to truncation errors associated with the "slope" term.
- For most cases where lateral diffusion is required, we
- will want it to be "diffusive" in the sense that no extrema are
- created. So the default is horz_z_diffuse=.false.
- The option to use horz_z_diffuse=.true. is maintained for
- legacy purposes alone.
-
-[logical]
-
-
-horz_s_diffuse
-
-
- To compute diffusion along surfaces of constant vertical s-coordinate.
- This operation is ensured of obtaining a smoothing operator
- that does not create extrema. It is the default for this
- reason.
-
-[logical]
-
-
-alap
-
-
- This is the value for the space-time constant Laplacian diffusivity.
-
-[real, units: m^2/sec]
-
-
-tracer_mix_micom
-
-
- If .true., then the diffusivity is set according to a velocity scale times
- the grid spacing. It is based on an approach recommended by
- Eric Chassignet that is used in the Miami Isopycnal Model (MICOM).
-
-[logical]
-
-
-vel_micom
-
-
- Velocity scale that is used for computing the MICOM diffusivity.
-
-[real, units: m/sec]
-
-
-read_diffusivity_mask
-
-
- Allows for reading of a mask that to apply diffusivity
- only in selected regions.
- Default read_diffusivity_mask=.false.
-
-[logical]
-
-
-verbose_init
-
-
- For verbose writes during initialization
-
-[logical]
-
-
-
-
-
-
-
-
-
-
-
NOTES
-
-
- The numerical implementation requires no calls to mpp_update_domains.
-
-
-
diff --git a/src/mom5/ocean_param/lateral/ocean_lap_tracer.xml b/src/mom5/ocean_param/lateral/ocean_lap_tracer.xml
deleted file mode 100644
index ad66d67d56..0000000000
--- a/src/mom5/ocean_param/lateral/ocean_lap_tracer.xml
+++ /dev/null
@@ -1,70 +0,0 @@
-
-
- Stephen M. Griffies
-
- Thickness weighted and density weighted time tendency
- for tracer from lateral laplacian diffusion.
-
- This module computes lateral laplacian diffusion of a tracer.
- There are two main options.
-
- (1) The lateral tracer fluxes can be aligned with the z-coordinate surfaces,
- in which case the fluxes must be approximated if (i) we use non-geopotential
- vertical coordinates, (ii) next to partial bottom step topography.
- This form of the diffusion is not recommended since it can lead to
- the creation of spurious extrema.
-
- (2) The lateral tracer fluxes can be aligned surfaces of constant vertical
- coordinate. In this case the fluxes are no longer strictly "horizontal."
- However, the operator is simpler and it ensures that no suprious
- extrema are created. It is for this reason that the simpler operator
- is preferred.
-
- The diffusivity used to determine the strength of the tendency can be
- a general function of space yet it is constant in time. A namelist
- option exists that determines this diffusivity as a local function
- of the grid spacing.
-
- The numerical implementation requires no calls to mpp_update_domains.
-
- Must be true to use this module. Default is false.
-
- To compute diffusion along surfaces of constant depth.
- This operation must necessarily be approximate for the two
- cases (i) non-geopotential vertical coordinates, (2)
- next to partial bottom step topography. There are cases where
- use of this operator can lead to spurious creation of extrema
- due to truncation errors associated with the "slope" term.
- For most cases where lateral diffusion is required, we
- will want it to be "diffusive" in the sense that no extrema are
- created. So the default is horz_z_diffuse=.false.
- The option to use horz_z_diffuse=.true. is maintained for
- legacy purposes alone.
-
- To compute diffusion along surfaces of constant vertical s-coordinate.
- This operation is ensured of obtaining a smoothing operator
- that does not create extrema. It is the default for this
- reason.
-
- This is the value for the space-time constant Laplacian diffusivity.
-
- If .true., then the diffusivity is set according to a velocity scale times
- the grid spacing. It is based on an approach recommended by
- Eric Chassignet that is used in the Miami Isopycnal Model (MICOM).
-
- Velocity scale that is used for computing the MICOM diffusivity.
-
- Allows for reading of a mask that to apply diffusivity
- only in selected regions.
- Default read_diffusivity_mask=.false.
-
- For verbose writes during initialization
-
- Initialize the laplacian diffusion module by
- registering fields for diagnostic output and performing some
- numerical checks to see that diffusivity is set appropriately.
-
- This function computes the thickness weighted and density weighted
- time tendency for tracer from lateral laplacian diffusion.
-
diff --git a/src/mom5/ocean_param/lateral/ocean_lapcgrid_friction.F90 b/src/mom5/ocean_param/lateral/ocean_lapcgrid_friction.F90
index e6a133c403..5a8b7829ff 100644
--- a/src/mom5/ocean_param/lateral/ocean_lapcgrid_friction.F90
+++ b/src/mom5/ocean_param/lateral/ocean_lapcgrid_friction.F90
@@ -351,9 +351,9 @@ module ocean_lapcgrid_friction_mod
type(ocean_domain_type), pointer :: Dom => NULL()
character(len=256) :: version=&
- '=>Using: ocean_lapcgrid_friction.F90 ($Id: ocean_lapcgrid_friction.F90,v 1.1.2.5 2012/06/08 20:15:35 Stephen.Griffies Exp $)'
+ '=>Using: ocean_lapcgrid_friction.F90 ($Id: ocean_lapcgrid_friction.F90,v 20.0 2013/12/14 00:14:22 fms Exp $)'
character (len=128) :: tagname = &
- '$Name: mom5_siena_08jun2012_smg $'
+ '$Name: tikal $'
logical :: use_this_module = .false.
logical :: debug_this_module = .false.
diff --git a/src/mom5/ocean_param/lateral/ocean_lapcgrid_friction.html b/src/mom5/ocean_param/lateral/ocean_lapcgrid_friction.html
deleted file mode 100644
index a27a43ed70..0000000000
--- a/src/mom5/ocean_param/lateral/ocean_lapcgrid_friction.html
+++ /dev/null
@@ -1,574 +0,0 @@
-
-
-
-Module ocean_lapcgrid_friction_mod
-
-
-
-
-PUBLIC INTERFACE
-
- ~ PUBLIC ROUTINES
- ~ NAMELIST
-
-
- This module computes the thickness weighted time tendency for
- horizontal velocity arising from horizontal Laplacian friction.
- Friction is formulated for the C-grid here.
-
-
-
-
-
- This module computes the thickness weighted time tendency for
- horizontal velocity arising from horizontal Laplacian friction.
- The viscosity used to determine the strength of the tendency
- can be a general function of space and time as specified by
- the Smagorinsky approach as well as a grid-scale dependent
- background viscosity. The form of the friction operator
- can be isotropic or anisotropic in the horizontal plane.
-
-
- Friction is formulated for the C-grid here.
-
-
- Initialize the horizontal Laplacian friction module by
- registering fields for diagnostic output and performing some
- numerical checks to see that viscosity is set appropriately.
-
-
-
-
-
-
-
-
lapcgrid_friction
-
-
-DESCRIPTION
-
-
- This routine computes thickness weighted and density weighted
- time tendency for horizontal velocity arising from horizontal
- Laplacian friction.
-
- The algorithm is derived from a functional approach that ensures
- kinetic energy is consistenty dissipated for all flow configurations.
- The stencil is far simpler than the B-grid approach. In particular,
- there are no triads here for the C-grid.
-
- Fundamental to the scheme are the rates of horizontal deformation
- horizontal tension = DT = (dy)(u/dy)_x - (dx)(v/dx)_y
- horizontal strain = DS = (dx)(u/dx)_y + (dy)(v/dy)_x
- Units of the tension and strain are sec^-1.
-
-
-
-
-
-
-
-
-
lapcgrid_viscosity_check
-
-
-DESCRIPTION
-
-
- Subroutine to perform linear stability check for the Laplacian
- operator given a value for the horizontal biharmonic viscosity.
-
-
-
-
-
-
-
-
lapcgrid_reynolds_check
-
-
-DESCRIPTION
-
-
- Subroutine to compute the LLaplacian grid Reynolds number. Large
- Reynolds numbers indicate regions where solution may experience
- some grid noise due to lack of enough horizontal friction.
-
-
-
-
-INPUT
-
-
-
-
-
u
- Horizontal velocity field at time tau
- [real, dimension(isd:ied,jsd:jed,nk,2)]
-
-
-
-
-
-
-
-
-
compute_neptune_velocity
-
-
-DESCRIPTION
-
-
- Compute Neptune velocity for c-grid.
-
- Method follows that used in MOM2 and MOM3 as implemented by
- Greg Holloway (zounds@ios.bc.ca) and Michael Eby (eby@uvic.ca)
- Coded in mom4 by Stephen.Griffies
-
- Neptune is calculated as an equilibrium streamfunction given by
- pnep = -f*snep*snep*ht and is applied through friction whereby
- the solution is damped towards the equilibrium streamfunction
- rather than being damped towards zero kinetic energy.
-
- hu = depth of B-grid velocity corner
- snep = spnep + (senep-spnep)*(0.5 + 0.5*cos(2.0*latitude))
-
- Neptune length scale snep has a value of senep at the
- equator and smoothly changes to spnep at the poles
-
- Reference:
- Holloway, G., 1992: Representing topographic stress for large
- scale ocean models, J. Phys. Oceanogr., 22, 1033-1046
-
- Eby and Holloway, 1994: Sensitivity of a large scale ocean model
- to a parameterization of topographic stress. JPO, vol. 24,
- pages 2577-2588
-
- March 2012
- Stephen.Griffies
- Algorithm updated to Eby and Holloway (1994)
-
- May 2012
- Stephen.Griffies
- upgraded to Cgrid
-
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_lapcgrid_friction_nml
-
-
-
-
-
-use_this_module
-
-
- Must be true to use this module. Default is false.
-
-[logical]
-
-
-debug_this_module
-
-
- For debugging by printing checksums.
-
-[logical]
-
-
-viscosity_scale_by_rossby
-
-
- To scale down the laplacian viscosity according to the relative scale of the
- horizontal grid and the first baroclinic Rossby radius. This is a useful
- scheme for models that resolve the Rossby radius in the lower latitudes, and so
- presumably do not wish to have much laplacian friction, whereas the higher latitudes
- need more friction. Default viscosity_scale_by_rossby=.false.
-
-[logical]
-
-
-viscosity_scale_by_rossby_power
-
-
- The power used to determine the viscosity scaling function.
- Default viscosity_scale_by_rossby_power=2.0.
-
-[real]
-
-
-divergence_damp
-
-
- To damp the divergence field.
-
-[logical]
-
-
-divergence_damp_vel_micom
-
-
- Velocity scale to set the viscosity used with divergence damping.
-
-[real, units: m/s]
-
-
-k_smag_iso
-
-
- This is the dimensionless Smagorinsky coefficient used to set the scale
- of the Smagorinsky isotropic viscosity.
-
-[real, units: dimensionless]
-
-
-k_smag_aniso
-
-
- This is the dimensionless Smagorinsky coefficient used to set the scale
- of the Smagorinsky anisotropic viscosity.
-
-[real, units: dimensionless]
-
-
-vel_micom_iso
-
-
- Velocity scale that is used for computing the MICOM isotropic viscosity.
-
-[real, units: m/sec]
-
-
-vel_micom_aniso
-
-
- Velocity scale that is used for computing the MICOM anisotropic viscosity.
-
-[real, units: m/sec]
-
-
-equatorial_zonal
-
-
- Orient the anisotropic friction within a latitudinal band according to zonal direction.
-
-[logical]
-
-
-equatorial_zonal_lat
-
-
- Latitudinal band to use the zonal friction orientation.
-
-[real]
-
-
-equatorial_no_smag
-
-
- Turn smag off within equatorial_zonal_lat region.
-
-[logical]
-
-
-eq_vel_micom_iso
-
-
- Velocity scale that is used for computing the MICOM isotropic viscosity within
- a user specified equatorial band.
-
-[real]
-
-
-eq_vel_micom_aniso
-
-
- Velocity scale that is used for computing the MICOM anisotropic viscosity within
- a user specified equatorial band.
-
-[real]
-
-
-eq_lat_micom
-
-
- Equatorial latitude band (degrees) within which the MICOM viscosity is set according
- to eq_vel_micom_iso and eq_vel_micom_aniso.
-
-[real]
-
-
-restrict_polar_visc
-
-
- For restricting the background viscosity poleward of a
- latitude. This method may be useful for coupling to an ice model
- in which case the horizontal viscosity may need to be a bit
- smaller to maintain time step constraints. This is because the
- effective friction is larger than that just within the ocean.
-
-[logical]
-
-
-restrict_polar_visc_lat
-
-
- Latitude poleward of which we restrict the viscosity.
-
-[real]
-
-
-restrict_polar_visc_ratio
-
-
- Ratio of the normal critical value that we limit the
- viscosity to be no greater than. If restrict_polar_visc_ratio=1.0
- then there is no special limitation of the viscosity beyond that
- of the one-dimensional stability constraint.
-
-[real]
-
-
-neptune
-
-
- Set to true for computing friction relative to Neptune barotropic velocity.
- Default neptune=.false.
-
-[logical]
-
-
-neptune_length_eq
-
-
- Length scale used to compute Neptune velocity at equator.
-
-[real, units: m]
-
-
-neptune_length_pole
-
-
- Length scale used to compute Neptune velocity at pole.
-
-[real, units: m]
-
-
-neptune_depth_min
-
-
- Minimum depth scale used for computing Neptune velocity.
- Default neptune_depth_min=100.0
-
-[real, units: m]
-
-
-neptune_smooth
-
-
- For doing a horizontal 1-2-1 smoothing on the diagnosed
- neptune velocity scale.
- Default neptune_smooth=.true.
-
-[logical]
-
-
-neptune_smooth_num
-
-
- Number of smoothing passes for neptune velocity.
- Default neptune_smooth_num=1.
-
-[integer]
-
-
-use_side_drag_friction
-
-
- For converting friction at U-cells next to walls into
- a drag law, as per Deremble et al. Use cdbot_array
- from ocean_core/ocean_bbc.F90 to compute drag force.
- Default use_side_drag_friction=.false.
-
-[logical]
-
-
-side_drag_friction_scaling
-
-
- Dimensionless scaling used for cdbot_array when setting
- side drag friction. So the effective side dragy coefficient
- is side_drag_friction_scaling*cdbot_array.
- Default side_drag_friction_scaling=1.0.
-
-[real]
-
-
-side_drag_friction_uvmag_max
-
-
- Maximum magnitude of horizontal velocity used to compute the
- side drag friction. This parameter can be useful especially
- for pressure models where the bottom cells can be quite thin
- and subject to sporadic large magnitudes. We do the same thing with
- bottom drag calculations.
- Default side_drag_friction_uvmag_max=10.0.
-
-[real, units: m/s]
-
-
-side_drag_friction_max
-
-
- Maximum magnitude of the side drag induced friction.
- This parameter can be useful especially for pressure models
- where the bottom cells can be quite thin and subject to sporadic
- large magnitudes. We do the same thing with bottom drag calculations
- in ocean_bbc. Default side_drag_friction_max=1.0.
-
-[real, units: N/m^2]
-
-
-
-
-
-
-
-
-
-
-
REFERENCES
-
-
-
-
- S.M. Griffies and R.W. Hallberg, 2000:
- Biharmonic friction with a Smagorinsky viscosity for use in large-scale
- eddy-permitting ocean models
- Monthly Weather Review, vol. 128, pages 2935-2946
-
-
- R. D. Smith and J. C. McWilliams, 2003:
- Anisotropic horizontal viscosity for ocean models,
- Ocean Modelling, vol. 5, pages 129-156.
-
-
- Maltrud and Holloway, 2008: Implementing biharmonic neptune in a
- global eddying ocean model, Ocean Modelling, vol. 21, pages 22-34.
-
-
- Deremble, Hogg, Berloff, and Dewar, 2011:
- On the application of no-slip lateral boundary conditions to coarsely
- resolved ocean models, Ocean Modelling.
-
-
- Griffies: Elements of MOM (2012)
-
-
-
-
-
-
-
-
NOTES
-
-
- The ocean model can generally run with both Laplacian and biharmonic friction
- enabled at the same time. Such has been found useful for some eddying
- ocean simulations.
-
-
-
diff --git a/src/mom5/ocean_param/lateral/ocean_lapcgrid_friction.xml b/src/mom5/ocean_param/lateral/ocean_lapcgrid_friction.xml
deleted file mode 100644
index 9f3b9bf188..0000000000
--- a/src/mom5/ocean_param/lateral/ocean_lapcgrid_friction.xml
+++ /dev/null
@@ -1,200 +0,0 @@
-
-
- S. M. Griffies
-
- This module computes the thickness weighted time tendency for
- horizontal velocity arising from horizontal Laplacian friction.
- Friction is formulated for the C-grid here.
-
- This module computes the thickness weighted time tendency for
- horizontal velocity arising from horizontal Laplacian friction.
- The viscosity used to determine the strength of the tendency
- can be a general function of space and time as specified by
- the Smagorinsky approach as well as a grid-scale dependent
- background viscosity. The form of the friction operator
- can be isotropic or anisotropic in the horizontal plane.
-
-
- Friction is formulated for the C-grid here.
-
-
- S.M. Griffies and R.W. Hallberg, 2000:
- Biharmonic friction with a Smagorinsky viscosity for use in large-scale
- eddy-permitting ocean models
- Monthly Weather Review, vol. 128, pages 2935-2946
-
- R. D. Smith and J. C. McWilliams, 2003:
- Anisotropic horizontal viscosity for ocean models,
- Ocean Modelling, vol. 5, pages 129-156.
-
- Maltrud and Holloway, 2008: Implementing biharmonic neptune in a
- global eddying ocean model, Ocean Modelling, vol. 21, pages 22-34.
-
- Deremble, Hogg, Berloff, and Dewar, 2011:
- On the application of no-slip lateral boundary conditions to coarsely
- resolved ocean models, Ocean Modelling.
-
- Griffies: Elements of MOM (2012)
-
- The ocean model can generally run with both Laplacian and biharmonic friction
- enabled at the same time. Such has been found useful for some eddying
- ocean simulations.
-
- Must be true to use this module. Default is false.
-
- For debugging by printing checksums.
-
- To scale down the laplacian viscosity according to the relative scale of the
- horizontal grid and the first baroclinic Rossby radius. This is a useful
- scheme for models that resolve the Rossby radius in the lower latitudes, and so
- presumably do not wish to have much laplacian friction, whereas the higher latitudes
- need more friction. Default viscosity_scale_by_rossby=.false.
-
- The power used to determine the viscosity scaling function.
- Default viscosity_scale_by_rossby_power=2.0.
-
- To damp the divergence field.
-
- Velocity scale to set the viscosity used with divergence damping.
-
- This is the dimensionless Smagorinsky coefficient used to set the scale
- of the Smagorinsky isotropic viscosity.
-
- This is the dimensionless Smagorinsky coefficient used to set the scale
- of the Smagorinsky anisotropic viscosity.
-
- Velocity scale that is used for computing the MICOM isotropic viscosity.
-
- Velocity scale that is used for computing the MICOM anisotropic viscosity.
-
- Orient the anisotropic friction within a latitudinal band according to zonal direction.
-
- Latitudinal band to use the zonal friction orientation.
-
- Turn smag off within equatorial_zonal_lat region.
-
- Velocity scale that is used for computing the MICOM isotropic viscosity within
- a user specified equatorial band.
-
- Velocity scale that is used for computing the MICOM anisotropic viscosity within
- a user specified equatorial band.
-
- Equatorial latitude band (degrees) within which the MICOM viscosity is set according
- to eq_vel_micom_iso and eq_vel_micom_aniso.
-
- For restricting the background viscosity poleward of a
- latitude. This method may be useful for coupling to an ice model
- in which case the horizontal viscosity may need to be a bit
- smaller to maintain time step constraints. This is because the
- effective friction is larger than that just within the ocean.
-
- Latitude poleward of which we restrict the viscosity.
-
- Ratio of the normal critical value that we limit the
- viscosity to be no greater than. If restrict_polar_visc_ratio=1.0
- then there is no special limitation of the viscosity beyond that
- of the one-dimensional stability constraint.
-
- Set to true for computing friction relative to Neptune barotropic velocity.
- Default neptune=.false.
-
- Length scale used to compute Neptune velocity at equator.
-
- Length scale used to compute Neptune velocity at pole.
-
- Minimum depth scale used for computing Neptune velocity.
- Default neptune_depth_min=100.0
-
- For doing a horizontal 1-2-1 smoothing on the diagnosed
- neptune velocity scale.
- Default neptune_smooth=.true.
-
- Number of smoothing passes for neptune velocity.
- Default neptune_smooth_num=1.
-
- For converting friction at U-cells next to walls into
- a drag law, as per Deremble et al. Use cdbot_array
- from ocean_core/ocean_bbc.F90 to compute drag force.
- Default use_side_drag_friction=.false.
-
- Dimensionless scaling used for cdbot_array when setting
- side drag friction. So the effective side dragy coefficient
- is side_drag_friction_scaling*cdbot_array.
- Default side_drag_friction_scaling=1.0.
-
- Maximum magnitude of horizontal velocity used to compute the
- side drag friction. This parameter can be useful especially
- for pressure models where the bottom cells can be quite thin
- and subject to sporadic large magnitudes. We do the same thing with
- bottom drag calculations.
- Default side_drag_friction_uvmag_max=10.0.
-
- Maximum magnitude of the side drag induced friction.
- This parameter can be useful especially for pressure models
- where the bottom cells can be quite thin and subject to sporadic
- large magnitudes. We do the same thing with bottom drag calculations
- in ocean_bbc. Default side_drag_friction_max=1.0.
-
- Initialize the horizontal Laplacian friction module by
- registering fields for diagnostic output and performing some
- numerical checks to see that viscosity is set appropriately.
-
- This routine computes thickness weighted and density weighted
- time tendency for horizontal velocity arising from horizontal
- Laplacian friction.
-
- The algorithm is derived from a functional approach that ensures
- kinetic energy is consistenty dissipated for all flow configurations.
- The stencil is far simpler than the B-grid approach. In particular,
- there are no triads here for the C-grid.
-
- Fundamental to the scheme are the rates of horizontal deformation
- horizontal tension = DT = (dy)(u/dy)_x - (dx)(v/dx)_y
- horizontal strain = DS = (dx)(u/dx)_y + (dy)(v/dy)_x
- Units of the tension and strain are sec^-1.
-
-
- Subroutine to perform linear stability check for the Laplacian
- operator given a value for the horizontal biharmonic viscosity.
-
- Subroutine to compute the LLaplacian grid Reynolds number. Large
- Reynolds numbers indicate regions where solution may experience
- some grid noise due to lack of enough horizontal friction.
-
- Horizontal velocity field at time tau
-
- Compute Neptune velocity for c-grid.
-
- Method follows that used in MOM2 and MOM3 as implemented by
- Greg Holloway (zounds@ios.bc.ca) and Michael Eby (eby@uvic.ca)
- Coded in mom4 by Stephen.Griffies
-
- Neptune is calculated as an equilibrium streamfunction given by
- pnep = -f*snep*snep*ht and is applied through friction whereby
- the solution is damped towards the equilibrium streamfunction
- rather than being damped towards zero kinetic energy.
-
- hu = depth of B-grid velocity corner
- snep = spnep + (senep-spnep)*(0.5 + 0.5*cos(2.0*latitude))
-
- Neptune length scale snep has a value of senep at the
- equator and smoothly changes to spnep at the poles
-
- Reference:
- Holloway, G., 1992: Representing topographic stress for large
- scale ocean models, J. Phys. Oceanogr., 22, 1033-1046
-
- Eby and Holloway, 1994: Sensitivity of a large scale ocean model
- to a parameterization of topographic stress. JPO, vol. 24,
- pages 2577-2588
-
- March 2012
- Stephen.Griffies
- Algorithm updated to Eby and Holloway (1994)
-
- May 2012
- Stephen.Griffies
- upgraded to Cgrid
-
-
diff --git a/src/mom5/ocean_param/lateral/ocean_lapcst_friction.F90 b/src/mom5/ocean_param/lateral/ocean_lapcst_friction.F90
index 92d7e7f305..c5c8ebfa43 100644
--- a/src/mom5/ocean_param/lateral/ocean_lapcst_friction.F90
+++ b/src/mom5/ocean_param/lateral/ocean_lapcst_friction.F90
@@ -129,9 +129,9 @@ module ocean_lapcst_friction_mod
integer :: isd, ied, jsd, jed, isc, iec, jsc, jec, nk
character(len=256) :: version=&
- '=>Using: ocean_lapcst_friction.f90 ($Id: ocean_lapcst_friction.F90,v 1.1.2.4 2012/06/01 20:47:08 Stephen.Griffies Exp $)'
+ '=>Using: ocean_lapcst_friction.f90 ($Id: ocean_lapcst_friction.F90,v 20.0 2013/12/14 00:14:24 fms Exp $)'
character (len=128) :: tagname = &
- '$Name: mom5_siena_08jun2012_smg $'
+ '$Name: tikal $'
logical :: use_this_module = .false.
logical :: debug_this_module = .false.
diff --git a/src/mom5/ocean_param/lateral/ocean_lapcst_friction.html b/src/mom5/ocean_param/lateral/ocean_lapcst_friction.html
deleted file mode 100644
index 9303429f3d..0000000000
--- a/src/mom5/ocean_param/lateral/ocean_lapcst_friction.html
+++ /dev/null
@@ -1,265 +0,0 @@
-
-
-
-Module ocean_lapcst_friction_mod
-
-
-
-
-PUBLIC INTERFACE
-
- ~ PUBLIC ROUTINES
- ~ NAMELIST
-
-
- This module computes the thickness weighted and density weighted
- acceleration for horizontal velocity arising from horizontal
- Laplacian friction.
-
-
-
-
-
- This module computes the thickness weighted and density weighted
- time tendency for horizontal velocity arising from horizontal
- Laplacian friction.
-
- The viscosity used to determine the strength of the tendency
- can be a general function of space yet it is constant in time.
- A namelist option exists that determines this viscosity
- as a local function of the grid spacing.
-
-
- Initialize the horizontal Laplacian friction module by
- registering fields for diagnostic output and performing some
- numerical checks to see that viscosity is set appropriately.
-
-
-
-
-
-
-
-
lapcst_friction
-
-
-DESCRIPTION
-
-
- This routine computes the rho*thickness weighted time tendency for
- horizontal velocity from horizontal Laplacian friction.
-
-
-
-
-
-
-
-
lapcst_viscosity_check
-
-
-DESCRIPTION
-
-
- Perform linear stability check for the Laplacian operator
- given a value for the horizontal laplacian viscosity.
-
-
-
-
-
-
-
-
lapcst_reynolds_check
-
-
-DESCRIPTION
-
-
- Subroutine to compute the Laplacian grid Reynolds number. Large
- Reynolds numbers indicate regions where solution may experience
- some grid noise due to lack of enough horizontal friction.
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_lapcst_friction_nml
-
-
-
-
-
-use_this_module
-
-
- Must be true to use this module. Default is false.
-
-[logical]
-
-
-debug_this_module
-
-
- For debugging by printing checksums.
-
-[logical]
-
-
-alap
-
-
- This is the value for the space-time constant Laplacian viscosity.
-
-[real, units: m^2/sec]
-
-
-velocity_mix_micom
-
-
- If .true., then the viscosity is set according to a velocity scale times
- the cube of the grid spacing. It is based on an approach recommended by
- Eric Chassignet that is used in the Miami Isopycnal Model.
-
-[logical]
-
-
-vel_micom
-
-
- Velocity scale that is used for computing the MICOM viscosity.
-
-[real, units: m/sec]
-
-
-
-
-
-
-
-
-
-
-
REFERENCES
-
-
-
-
- R. J. Murray and C. J. C. Reason,
- A curvilinear version of the Bryan-Cox ocean model
- Journal of Computational Physics (2002), vol 171, pages 1--46
-
-
- S.M. Griffies, Elements of MOM (2012)
-
-
-
-
-
-
-
-
NOTES
-
-
- The numerical implementation requires no calls to mpp_update_domains.
-
-
- This scheme has been found to be faster than the Smagorinsky viscosity
- scheme. However, the algorithm here is less robust since it
- contains null modes in the terms associated with the sphericity
- of the earth. Hence, there may be flow configurations that are
- not dissipated.
-
-
- The sink from drag next to partial cells has been dropped
- from MOM4p1.
-
-
-
diff --git a/src/mom5/ocean_param/lateral/ocean_lapcst_friction.xml b/src/mom5/ocean_param/lateral/ocean_lapcst_friction.xml
deleted file mode 100644
index 7da01929e3..0000000000
--- a/src/mom5/ocean_param/lateral/ocean_lapcst_friction.xml
+++ /dev/null
@@ -1,62 +0,0 @@
-
-
- Stephen M. Griffies
-
- This module computes the thickness weighted and density weighted
- acceleration for horizontal velocity arising from horizontal
- Laplacian friction.
-
- This module computes the thickness weighted and density weighted
- time tendency for horizontal velocity arising from horizontal
- Laplacian friction.
-
- The viscosity used to determine the strength of the tendency
- can be a general function of space yet it is constant in time.
- A namelist option exists that determines this viscosity
- as a local function of the grid spacing.
-
-
- R. J. Murray and C. J. C. Reason,
- A curvilinear version of the Bryan-Cox ocean model
- Journal of Computational Physics (2002), vol 171, pages 1--46
-
- S.M. Griffies, Elements of MOM (2012)
-
- The numerical implementation requires no calls to mpp_update_domains.
-
- This scheme has been found to be faster than the Smagorinsky viscosity
- scheme. However, the algorithm here is less robust since it
- contains null modes in the terms associated with the sphericity
- of the earth. Hence, there may be flow configurations that are
- not dissipated.
-
- The sink from drag next to partial cells has been dropped
- from MOM4p1.
-
- Must be true to use this module. Default is false.
-
- For debugging by printing checksums.
-
- This is the value for the space-time constant Laplacian viscosity.
-
- If .true., then the viscosity is set according to a velocity scale times
- the cube of the grid spacing. It is based on an approach recommended by
- Eric Chassignet that is used in the Miami Isopycnal Model.
-
- Velocity scale that is used for computing the MICOM viscosity.
-
- Initialize the horizontal Laplacian friction module by
- registering fields for diagnostic output and performing some
- numerical checks to see that viscosity is set appropriately.
-
- This routine computes the rho*thickness weighted time tendency for
- horizontal velocity from horizontal Laplacian friction.
-
- Perform linear stability check for the Laplacian operator
- given a value for the horizontal laplacian viscosity.
-
- Subroutine to compute the Laplacian grid Reynolds number. Large
- Reynolds numbers indicate regions where solution may experience
- some grid noise due to lack of enough horizontal friction.
-
diff --git a/src/mom5/ocean_param/lateral/ocean_lapgen_friction.F90 b/src/mom5/ocean_param/lateral/ocean_lapgen_friction.F90
index 3b7a9f2d9f..e6ba6a6573 100644
--- a/src/mom5/ocean_param/lateral/ocean_lapgen_friction.F90
+++ b/src/mom5/ocean_param/lateral/ocean_lapgen_friction.F90
@@ -445,9 +445,9 @@ module ocean_lapgen_friction_mod
type(ocean_domain_type), pointer :: Dom => NULL()
character(len=256) :: version=&
- '=>Using: ocean_lapgen_friction.F90 ($Id: ocean_lapgen_friction.F90,v 1.1.2.4.14.1 2013/04/03 13:25:25 smg Exp $)'
+ '=>Using: ocean_lapgen_friction.F90 ($Id: ocean_lapgen_friction.F90,v 20.0 2013/12/14 00:14:26 fms Exp $)'
character (len=128) :: tagname = &
- '$Name: mom5_siena_201303_smg $'
+ '$Name: tikal $'
logical :: use_this_module = .false.
logical :: debug_this_module = .false.
@@ -1093,8 +1093,8 @@ subroutine lapgen_friction(Time, Thickness, Adv_vel, Velocity, &
usqrd = (Velocity%u(i,j,k,1,taum1)-neptune_velocity(i,j,1))**2
vsqrd = (Velocity%u(i,j,k,2,taum1)-neptune_velocity(i,j,2))**2
umagr = 1.0/(epsln + usqrd + vsqrd)
- sin2theta(i,j) = 2.0*(Velocity%u(i,j,k,1,taum1) - neptune_velocity(i,j,1))* &
- (Velocity%u(i,j,k,2,taum1) - neptune_velocity(i,j,2))*umagr
+ sin2theta(i,j) = 2.0*(Velocity%u(i,j,k,1,taum1)-neptune_velocity(i,j,1)) &
+ *(Velocity%u(i,j,k,2,taum1)-neptune_velocity(i,j,2))*umagr
cos2theta(i,j) = (usqrd-vsqrd)*umagr
endif
@@ -1370,7 +1370,7 @@ subroutine lapgen_friction(Time, Thickness, Adv_vel, Velocity, &
enddo
enddo
enddo
- call diagnose_3d_u(TIme, Grd, id_horz_lap_diss, wrk2(:,:,:))
+ call diagnose_3d_u(Time, Grd, id_horz_lap_diss, wrk2(:,:,:))
endif
call diagnose_2d_u(Time, Grd, id_viscosity_scaling, viscosity_scaling(:,:))
diff --git a/src/mom5/ocean_param/lateral/ocean_lapgen_friction.html b/src/mom5/ocean_param/lateral/ocean_lapgen_friction.html
deleted file mode 100644
index 22e6940d1c..0000000000
--- a/src/mom5/ocean_param/lateral/ocean_lapgen_friction.html
+++ /dev/null
@@ -1,883 +0,0 @@
-
-
-
-Module ocean_lapgen_friction_mod
-
-
-
-
-PUBLIC INTERFACE
-
- ~ PUBLIC ROUTINES
- ~ NAMELIST
-
-
- This module computes the thickness weighted time tendency for
- horizontal velocity arising from horizontal Laplacian friction.
-
-
-
-
-
- This module computes the thickness weighted time tendency for
- horizontal velocity arising from horizontal Laplacian friction.
- The viscosity used to determine the strength of the tendency
- can be a general function of space and time as specified by
- the Smagorinsky approach as well as a grid-scale dependent
- background viscosity. The form of the friction operator
- can be isotropic or anisotropic in the horizontal plane.
-
- Initialize the horizontal Laplacian friction module by
- registering fields for diagnostic output and performing some
- numerical checks to see that viscosity is set appropriately.
-
-
-
-
-
-
-
-
lapgen_friction
-
-
-DESCRIPTION
-
-
- This routine computes thickness weighted and density weighted
- time tendency for horizontal velocity arising from horizontal
- Laplacian friction.
-
- The algorithm is derived from a functional approach that ensures
- kinetic energy is consistenty dissipated for all flow configurations.
- The triad do-loops are expanded in order to enhance the
- ability of cache-based machines to keep most of the variables
- on-cache.
-
- Fundamental to the scheme are the rates of horizontal deformation
- horizontal tension = DT = (dy)(u/dy)_x - (dx)(v/dx)_y
- horizontal strain = DS = (dx)(u/dx)_y + (dy)(v/dy)_x
- Units of the tension and strain are sec^-1.
-
- Four tensions and four strains are computed for each velocity point,
- corresponding to the four triads surrounding the point.
- The following notation is used to distinguish the triads:
- (0,1)=northwest triad (1,1)=northeast triad,
- (0,0)=southwest triad, (1,0)=southeast triad
-
- A triad contributes when at least one of its velocities is
- not a land point. In order to obtain the correct tension
- and strain next to boundaries, tension and strain should not be
- masked with umask.
-
-
-
-
-
-
-
-
-
BDX_EU_smag
-
-
-DESCRIPTION
-
-
- Compute backwards derivative in X of a quantity defined on the east
- face of a U-cell. Slightly modified version of BDX_EU used in
- ocean_operators.F90. If input is a(i,j) then output is defined
- at (i-1/2,j).
-
- BDX_EU_smag(a) has dimensions of a*m^-3
-
-
-
-
-
-INPUT
-
-
-
-
-
a
- field defined on the east face of a U-cell
- [real, dimension(isd:ied,jsd:jed)]
-
-
-
-
-
-
-
-
-
BDY_NU_smag
-
-
-DESCRIPTION
-
-
- Compute backwards derivative in Y of a quantity defined on the north
- face of a U-cell. Slightly modified version of BDY_EU used in
- ocean_operators.F90. If input is a(i,j) then output is defined
- at (i,j-1/2)
-
- BDY_NU_smag(a) has dimensions of a*m^-3
-
-
-
-
-
-INPUT
-
-
-
-
-
a
- field defined on the north face of a U-cell
- [real, dimension(isd:ied,jsd:jed)]
-
-
-
-
-
-
-
-
-
anisotropic_ncar
-
-
-DESCRIPTION
-
-
-
- Spatially-varying anisotropic viscosity initialization
-
- This routine defines NCOM-like spatial distributions of
- viscosity coefficients F_PARA and F_PERP.
- Uses NCAR CCSM2.0 algorithm with cm^2/sec --> m^2/sec.
-
- written by: Stephen Yeager 3/2000
-
- modified by: Gokhan Danabasoglu (08/2001)
-
- port to mom4: Stephen.Griffies (9/2002)
-
- update to mom4p1 based on new tunes from NCAR
- Stephen.Griffies (7/2007)
-
-
- "A_viscosity" = F_PARA = Along = viscosity parallel to flow
- = max{0.5*visc_vel_scale(z)*A*max[dx,dy],vconst_6}
-
- where
- A = 0.425 * cos(pi*y*radian/30) + 0.575 for |y*radian| < 30
- A = 0.15 otherwise
-
- Here, A provides a horizontal variation for visc_vel_scale.
-
- "B_viscosity" = F_PERP = Across = viscosity perpendicular to flow = max( bu, bv)
-
- and
- F_PARA = min(F_PARA, AMAX_CFL),
- F_PERP = min(F_PERP, AMAX_CFL),
- F_PARA = max(F_PARA, F_PERP)
- are enforced
-
- In the above equations,
-
- bu = vconst_1 * ( 1 + vconst_2 * ( 1 + cos( 2*y + pi ) ) )
- bv = vconst_3 * beta_f * dx^3 * exp( - (vconst_4 * distance)^2 )
-
- with
- beta_f (x,y) = 2 * omega_earth* cos(ULAT(i,j)) / radius
- distance (x,y,z) = actual distance to "vconst_5" points
- west of the nearest western boundary
- dx (x,y) = DXU(i,j)
- dy (x,y) = DYU(i,j)
- visc_vel_scale (z) = vconst_7 * exp(-zt(k)/visc_vel_scale_length)
- visc_vel_scale_length = e-folding scale ( default = 1500.0e2 cm)
- y (x,y) = ULAT(i,j), latitude of "u/v" grid pts in radians
- In MOM, ULAT(radians) = xu*pi/180 with xu(i,j) the longitude of U grid points in degrees
-
- "vconst_#" are input parameters defined in namelist ocean_lapgen_friction_general_nml.
- "vconst_1", "vconst_6", and "vconst_4" have dimensions of cm^2/s,
- cm^2/s, and 1/cm, respectively. "vconst_5" is an INTEGER.
-
- NOTE: The nearest western boundary computations are done along the
- model i-grid lines. Therefore, viscosity based on these are
- only approximate in the high Northern Hemisphere when using
- generalized coordinates with coordinate pole(s) shifted onto land.
-
-
-
-
-
-
-
-
-
lapgen_viscosity_check
-
-
-DESCRIPTION
-
-
- Subroutine to perform linear stability check for the Laplacian
- operator given a value for the horizontal biharmonic viscosity.
-
-
-
-
-
-
-
-
lapgen_reynolds_check
-
-
-DESCRIPTION
-
-
- Subroutine to compute the LLaplacian grid Reynolds number. Large
- Reynolds numbers indicate regions where solution may experience
- some grid noise due to lack of enough horizontal friction.
-
-
-
-
-INPUT
-
-
-
-
-
u
- Horizontal velocity field at time tau
- [real, dimension(isd:ied,jsd:jed,nk,2)]
-
-
-
-
-
-
-
-
-
compute_neptune_velocity
-
-
-DESCRIPTION
-
-
- Compute Neptune velocity.
-
- Method follows that used in MOM2 and MOM3 as implemented by
- Greg Holloway (zounds@ios.bc.ca) and Michael Eby (eby@uvic.ca)
- Coded in mom4 by Stephen.Griffies
-
- Neptune is calculated as an equilibrium streamfunction given by
- pnep = -f*snep*snep*ht and is applied through friction whereby
- the solution is damped towards the equilibrium streamfunction
- rather than being damped towards zero kinetic energy.
-
- ht = depth of tracer cells
- snep = spnep + (senep-spnep)*(0.5 + 0.5*cos(2.0*latitude))
-
- Neptune length scale snep has a value of senep at the
- equator and smoothly changes to spnep at the poles
-
- Reference:
- Holloway, G., 1992: Representing topographic stress for large
- scale ocean models, J. Phys. Oceanogr., 22, 1033-1046
-
- Eby and Holloway, 1994: Sensitivity of a large scale ocean model
- to a parameterization of topographic stress. JPO, vol. 24,
- pages 2577-2588
-
- March 2012
- Stephen.Griffies
- Algorithm updated to Eby and Holloway (1994)
-
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_lapgen_friction_nml
-
-
-
-
-
-use_this_module
-
-
- Must be true to use this module. Default is false.
-
-[logical]
-
-
-debug_this_module
-
-
- For debugging by printing checksums.
-
-[logical]
-
-
-viscosity_scale_by_rossby
-
-
- To scale down the laplacian viscosity according to the relative scale of the
- horizontal grid and the first baroclinic Rossby radius. This is a useful
- scheme for models that resolve the Rossby radius in the lower latitudes, and so
- presumably do not wish to have much laplacian friction, whereas the higher latitudes
- need more friction. Default viscosity_scale_by_rossby=.false.
-
-[logical]
-
-
-viscosity_scale_by_rossby_power
-
-
- The power used to determine the viscosity scaling function.
- Default viscosity_scale_by_rossby_power=2.0.
-
-[real]
-
-
-divergence_damp
-
-
- To damp the divergence field.
-
-[logical]
-
-
-divergence_damp_vel_micom
-
-
- Velocity scale to set the viscosity used with divergence damping.
-
-[real, units: m/s]
-
-
-k_smag_iso
-
-
- This is the dimensionless Smagorinsky coefficient used to set the scale
- of the Smagorinsky isotropic viscosity.
-
-[real, units: dimensionless]
-
-
-k_smag_aniso
-
-
- This is the dimensionless Smagorinsky coefficient used to set the scale
- of the Smagorinsky anisotropic viscosity.
-
-[real, units: dimensionless]
-
-
-viscosity_ncar
-
-
- Anisotropic background viscosities used by NCAR.
-
-[logical]
-
-
-viscosity_ncar_2000
-
-
- Anisotropic background viscosities used by NCAR, using the
- formulation as of 2000. Default viscosity_ncar_2000=.true.
-
-[logical]
-
-
-viscosity_ncar_2007
-
-
- Anisotropic background viscosities used by NCAR, using the
- formulation as of 2007. Default viscosity_ncar_2007=.false.
-
-[logical]
-
-
-vel_micom_iso
-
-
- Velocity scale that is used for computing the MICOM isotropic viscosity.
-
-[real, units: m/sec]
-
-
-vel_micom_aniso
-
-
- Velocity scale that is used for computing the MICOM anisotropic viscosity.
-
-[real, units: m/sec]
-
-
-equatorial_zonal
-
-
- Orient the anisotropic friction within a latitudinal band according to zonal direction.
-
-[logical]
-
-
-equatorial_zonal_lat
-
-
- Latitudinal band to use the zonal friction orientation.
-
-[real]
-
-
-ncar_isotropic_off_equator
-
-
- Polewards of equatorial_zonal_lat, revert NCAR scheme to isotropic
-
-[logical]
-
-
-equatorial_no_smag
-
-
- Turn smag off within equatorial_zonal_lat region.
-
-[logical]
-
-
-eq_vel_micom_iso
-
-
- Velocity scale that is used for computing the MICOM isotropic viscosity within
- a user specified equatorial band.
-
-[real]
-
-
-eq_vel_micom_aniso
-
-
- Velocity scale that is used for computing the MICOM anisotropic viscosity within
- a user specified equatorial band.
-
-[real]
-
-
-eq_lat_micom
-
-
- Equatorial latitude band (degrees) within which the MICOM viscosity is set according
- to eq_vel_micom_iso and eq_vel_micom_aniso.
-
-[real]
-
-
-restrict_polar_visc
-
-
- For restricting the background viscosity poleward of a
- latitude. This method may be useful for coupling to an ice model
- in which case the horizontal viscosity may need to be a bit
- smaller to maintain time step constraints. This is because the
- effective friction is larger than that just within the ocean.
-
-[logical]
-
-
-restrict_polar_visc_lat
-
-
- Latitude poleward of which we restrict the viscosity.
-
-[real]
-
-
-restrict_polar_visc_ratio
-
-
- Ratio of the normal critical value that we limit the
- viscosity to be no greater than. If restrict_polar_visc_ratio=1.0
- then there is no special limitation of the viscosity beyond that
- of the one-dimensional stability constraint.
-
-[real]
-
-
-bottom_5point
-
-
- To alleviate problems with small partial cells, it is often necessary to reduce the
- operator to the traditional 5-point Laplacian at the ocean bottom. This logical
- implements this mixing. Default bottom_5point=.false.
-
-[logical]
-
-
-neptune
-
-
- Set to true for computing friction relative to Neptune barotropic velocity.
- Default neptune=.false.
-
-[logical]
-
-
-neptune_length_eq
-
-
- Length scale used to compute Neptune velocity at equator.
-
-[real, units: m]
-
-
-neptune_length_pole
-
-
- Length scale used to compute Neptune velocity at pole.
-
-[real, units: m]
-
-
-neptune_depth_min
-
-
- Minimum depth scale used for computing Neptune velocity.
- Default neptune_depth_min=100.0
-
-[real, units: m]
-
-
-neptune_smooth
-
-
- For doing a horizontal 1-2-1 smoothing on the diagnosed
- neptune velocity scale.
- Default neptune_smooth=.true.
-
-[logical]
-
-
-neptune_smooth_num
-
-
- Number of smoothing passes for neptune velocity.
- Default neptune_smooth_num=1.
-
-[integer]
-
- For NCAR viscosity algorithm.
-
-[real, units: 1/cm]
-
-
-vconst_5
-
-
- For NCAR viscosity algorithm.
-
-[integer]
-
-
-vconst_6
-
-
- For NCAR viscosity algorithm.
-
-[real, units: cm^2/sec]
-
-
-vconst_7
-
-
- For NCAR viscosity algorithm.
-
-[, units: cm/sec]
-
-
-vconst_8
-
-
- For NCAR viscosity algorithm.
-
-[, units: degrees]
-
-
-visc_vel_scale_length
-
-
- For NCAR viscosity algorithm: efolding depth for
- depth dependent background viscosity.
- Default visc_vel_scale_length=1500.e2 cm
-
-[, units: cm]
-
-
-ncar_isotropic_at_depth
-
-
- Sets the NCAR scheme to be isotropic beneath a chosen depth.
-
-[logical]
-
-
-ncar_isotropic_depth
-
-
- Sets the NCAR scheme to be isotropic beneath this chosen depth.
-
-[real, units: m]
-
-
-ncar_isotropic_at_depth_visc
-
-
- Sets the NCAR scheme to be isotropic beneath this chosen depth, with
- minimum viscosity set according to this value.
-
-[real, units: m2/sec]
-
-
-debug_ncar_A
-
-
- Sets f_perp=f_para for debugging purposes with the NCAR scheme.
-
-[logical]
-
-
-debug_ncar_B
-
-
- Sets f_para=f_perp for debugging purposes with the NCAR scheme.
-
-[logical]
-
-
-use_side_drag_friction
-
-
- For converting friction at U-cells next to walls into
- a drag law, as per Deremble et al. Use cdbot_array
- from ocean_core/ocean_bbc.F90 to compute drag force.
- Default use_side_drag_friction=.false.
-
-[logical]
-
-
-side_drag_friction_scaling
-
-
- Dimensionless scaling used for cdbot_array when setting
- side drag friction. So the effective side dragy coefficient
- is side_drag_friction_scaling*cdbot_array.
- Default side_drag_friction_scaling=1.0.
-
-[real]
-
-
-side_drag_friction_uvmag_max
-
-
- Maximum magnitude of horizontal velocity used to compute the
- side drag friction. This parameter can be useful especially
- for pressure models where the bottom cells can be quite thin
- and subject to sporadic large magnitudes. We do the same thing with
- bottom drag calculations.
- Default side_drag_friction_uvmag_max=10.0.
-
-[real, units: m/s]
-
-
-side_drag_friction_max
-
-
- Maximum magnitude of the side drag induced friction.
- This parameter can be useful especially for pressure models
- where the bottom cells can be quite thin and subject to sporadic
- large magnitudes. We do the same thing with bottom drag calculations.
- Default side_drag_friction_max=1.0.
-
-[real, units: N/m^2]
-
-
-
-
-
-
-
-
-
-
-
REFERENCES
-
-
-
-
- S.M. Griffies and R.W. Hallberg, 2000:
- Biharmonic friction with a Smagorinsky viscosity for use in large-scale
- eddy-permitting ocean models
- Monthly Weather Review, vol. 128, pages 2935-2946
-
-
- R. D. Smith and J. C. McWilliams, 2003:
- Anisotropic horizontal viscosity for ocean models,
- Ocean Modelling, vol. 5, pages 129-156.
-
-
- Maltrud and Holloway, 2008: Implementing biharmonic neptune in a
- global eddying ocean model, Ocean Modelling, vol. 21, pages 22-34.
-
-
- Deremble, Hogg, Berloff, and Dewar, 2011:
- On the application of no-slip lateral boundary conditions to coarsely
- resolved ocean models, Ocean Modelling.
-
-
- Griffies: Elements of MOM (2012)
-
-
-
-
-
-
-
-
NOTES
-
-
- The ocean model can generally run with both Laplacian and biharmonic friction
- enabled at the same time. Such has been found useful for some eddying
- ocean simulations.
-
-
-
diff --git a/src/mom5/ocean_param/lateral/ocean_lapgen_friction.xml b/src/mom5/ocean_param/lateral/ocean_lapgen_friction.xml
deleted file mode 100644
index 3d3495da77..0000000000
--- a/src/mom5/ocean_param/lateral/ocean_lapgen_friction.xml
+++ /dev/null
@@ -1,328 +0,0 @@
-
-
- S. M. Griffies
-
- This module computes the thickness weighted time tendency for
- horizontal velocity arising from horizontal Laplacian friction.
-
- This module computes the thickness weighted time tendency for
- horizontal velocity arising from horizontal Laplacian friction.
- The viscosity used to determine the strength of the tendency
- can be a general function of space and time as specified by
- the Smagorinsky approach as well as a grid-scale dependent
- background viscosity. The form of the friction operator
- can be isotropic or anisotropic in the horizontal plane.
-
- S.M. Griffies and R.W. Hallberg, 2000:
- Biharmonic friction with a Smagorinsky viscosity for use in large-scale
- eddy-permitting ocean models
- Monthly Weather Review, vol. 128, pages 2935-2946
-
- R. D. Smith and J. C. McWilliams, 2003:
- Anisotropic horizontal viscosity for ocean models,
- Ocean Modelling, vol. 5, pages 129-156.
-
- Maltrud and Holloway, 2008: Implementing biharmonic neptune in a
- global eddying ocean model, Ocean Modelling, vol. 21, pages 22-34.
-
- Deremble, Hogg, Berloff, and Dewar, 2011:
- On the application of no-slip lateral boundary conditions to coarsely
- resolved ocean models, Ocean Modelling.
-
- Griffies: Elements of MOM (2012)
-
- The ocean model can generally run with both Laplacian and biharmonic friction
- enabled at the same time. Such has been found useful for some eddying
- ocean simulations.
-
- Must be true to use this module. Default is false.
-
- For debugging by printing checksums.
-
- To scale down the laplacian viscosity according to the relative scale of the
- horizontal grid and the first baroclinic Rossby radius. This is a useful
- scheme for models that resolve the Rossby radius in the lower latitudes, and so
- presumably do not wish to have much laplacian friction, whereas the higher latitudes
- need more friction. Default viscosity_scale_by_rossby=.false.
-
- The power used to determine the viscosity scaling function.
- Default viscosity_scale_by_rossby_power=2.0.
-
- To damp the divergence field.
-
- Velocity scale to set the viscosity used with divergence damping.
-
- This is the dimensionless Smagorinsky coefficient used to set the scale
- of the Smagorinsky isotropic viscosity.
-
- This is the dimensionless Smagorinsky coefficient used to set the scale
- of the Smagorinsky anisotropic viscosity.
-
- Anisotropic background viscosities used by NCAR.
-
- Anisotropic background viscosities used by NCAR, using the
- formulation as of 2000. Default viscosity_ncar_2000=.true.
-
- Anisotropic background viscosities used by NCAR, using the
- formulation as of 2007. Default viscosity_ncar_2007=.false.
-
- Velocity scale that is used for computing the MICOM isotropic viscosity.
-
- Velocity scale that is used for computing the MICOM anisotropic viscosity.
-
- Orient the anisotropic friction within a latitudinal band according to zonal direction.
-
- Latitudinal band to use the zonal friction orientation.
-
- Polewards of equatorial_zonal_lat, revert NCAR scheme to isotropic
-
- Turn smag off within equatorial_zonal_lat region.
-
- Velocity scale that is used for computing the MICOM isotropic viscosity within
- a user specified equatorial band.
-
- Velocity scale that is used for computing the MICOM anisotropic viscosity within
- a user specified equatorial band.
-
- Equatorial latitude band (degrees) within which the MICOM viscosity is set according
- to eq_vel_micom_iso and eq_vel_micom_aniso.
-
- For restricting the background viscosity poleward of a
- latitude. This method may be useful for coupling to an ice model
- in which case the horizontal viscosity may need to be a bit
- smaller to maintain time step constraints. This is because the
- effective friction is larger than that just within the ocean.
-
- Latitude poleward of which we restrict the viscosity.
-
- Ratio of the normal critical value that we limit the
- viscosity to be no greater than. If restrict_polar_visc_ratio=1.0
- then there is no special limitation of the viscosity beyond that
- of the one-dimensional stability constraint.
-
- To alleviate problems with small partial cells, it is often necessary to reduce the
- operator to the traditional 5-point Laplacian at the ocean bottom. This logical
- implements this mixing. Default bottom_5point=.false.
-
- Set to true for computing friction relative to Neptune barotropic velocity.
- Default neptune=.false.
-
- Length scale used to compute Neptune velocity at equator.
-
- Length scale used to compute Neptune velocity at pole.
-
- Minimum depth scale used for computing Neptune velocity.
- Default neptune_depth_min=100.0
-
- For doing a horizontal 1-2-1 smoothing on the diagnosed
- neptune velocity scale.
- Default neptune_smooth=.true.
-
- Number of smoothing passes for neptune velocity.
- Default neptune_smooth_num=1.
-
- Background viscosity for NCAR algorithm.
-
- For NCAR viscosity algorithm.
-
- For NCAR viscosity algorithm.
-
- For NCAR viscosity algorithm.
-
- For NCAR viscosity algorithm.
-
- For NCAR viscosity algorithm.
-
- For NCAR viscosity algorithm.
-
- For NCAR viscosity algorithm.
-
- For NCAR viscosity algorithm: efolding depth for
- depth dependent background viscosity.
- Default visc_vel_scale_length=1500.e2 cm
-
- Sets the NCAR scheme to be isotropic beneath a chosen depth.
-
- Sets the NCAR scheme to be isotropic beneath this chosen depth.
-
- Sets the NCAR scheme to be isotropic beneath this chosen depth, with
- minimum viscosity set according to this value.
-
- Sets f_perp=f_para for debugging purposes with the NCAR scheme.
-
- Sets f_para=f_perp for debugging purposes with the NCAR scheme.
-
- For converting friction at U-cells next to walls into
- a drag law, as per Deremble et al. Use cdbot_array
- from ocean_core/ocean_bbc.F90 to compute drag force.
- Default use_side_drag_friction=.false.
-
- Dimensionless scaling used for cdbot_array when setting
- side drag friction. So the effective side dragy coefficient
- is side_drag_friction_scaling*cdbot_array.
- Default side_drag_friction_scaling=1.0.
-
- Maximum magnitude of horizontal velocity used to compute the
- side drag friction. This parameter can be useful especially
- for pressure models where the bottom cells can be quite thin
- and subject to sporadic large magnitudes. We do the same thing with
- bottom drag calculations.
- Default side_drag_friction_uvmag_max=10.0.
-
- Maximum magnitude of the side drag induced friction.
- This parameter can be useful especially for pressure models
- where the bottom cells can be quite thin and subject to sporadic
- large magnitudes. We do the same thing with bottom drag calculations.
- Default side_drag_friction_max=1.0.
-
- Initialize the horizontal Laplacian friction module by
- registering fields for diagnostic output and performing some
- numerical checks to see that viscosity is set appropriately.
-
- This routine computes thickness weighted and density weighted
- time tendency for horizontal velocity arising from horizontal
- Laplacian friction.
-
- The algorithm is derived from a functional approach that ensures
- kinetic energy is consistenty dissipated for all flow configurations.
- The triad do-loops are expanded in order to enhance the
- ability of cache-based machines to keep most of the variables
- on-cache.
-
- Fundamental to the scheme are the rates of horizontal deformation
- horizontal tension = DT = (dy)(u/dy)_x - (dx)(v/dx)_y
- horizontal strain = DS = (dx)(u/dx)_y + (dy)(v/dy)_x
- Units of the tension and strain are sec^-1.
-
- Four tensions and four strains are computed for each velocity point,
- corresponding to the four triads surrounding the point.
- The following notation is used to distinguish the triads:
- (0,1)=northwest triad (1,1)=northeast triad,
- (0,0)=southwest triad, (1,0)=southeast triad
-
- A triad contributes when at least one of its velocities is
- not a land point. In order to obtain the correct tension
- and strain next to boundaries, tension and strain should not be
- masked with umask.
-
-
- Compute backwards derivative in X of a quantity defined on the east
- face of a U-cell. Slightly modified version of BDX_EU used in
- ocean_operators.F90. If input is a(i,j) then output is defined
- at (i-1/2,j).
-
- BDX_EU_smag(a) has dimensions of a*m^-3
-
-
- field defined on the east face of a U-cell
-
- Compute backwards derivative in Y of a quantity defined on the north
- face of a U-cell. Slightly modified version of BDY_EU used in
- ocean_operators.F90. If input is a(i,j) then output is defined
- at (i,j-1/2)
-
- BDY_NU_smag(a) has dimensions of a*m^-3
-
-
- field defined on the north face of a U-cell
-
-
- Spatially-varying anisotropic viscosity initialization
-
- This routine defines NCOM-like spatial distributions of
- viscosity coefficients F_PARA and F_PERP.
- Uses NCAR CCSM2.0 algorithm with cm^2/sec --> m^2/sec.
-
- written by: Stephen Yeager 3/2000
-
- modified by: Gokhan Danabasoglu (08/2001)
-
- port to mom4: Stephen.Griffies (9/2002)
-
- update to mom4p1 based on new tunes from NCAR
- Stephen.Griffies (7/2007)
-
-
- "A_viscosity" = F_PARA = Along = viscosity parallel to flow
- = max{0.5*visc_vel_scale(z)*A*max[dx,dy],vconst_6}
-
- where
- A = 0.425 * cos(pi*y*radian/30) + 0.575 for |y*radian| < 30
- A = 0.15 otherwise
-
- Here, A provides a horizontal variation for visc_vel_scale.
-
- "B_viscosity" = F_PERP = Across = viscosity perpendicular to flow = max( bu, bv)
-
- and
- F_PARA = min(F_PARA, AMAX_CFL),
- F_PERP = min(F_PERP, AMAX_CFL),
- F_PARA = max(F_PARA, F_PERP)
- are enforced
-
- In the above equations,
-
- bu = vconst_1 * ( 1 + vconst_2 * ( 1 + cos( 2*y + pi ) ) )
- bv = vconst_3 * beta_f * dx^3 * exp( - (vconst_4 * distance)^2 )
-
- with
- beta_f (x,y) = 2 * omega_earth* cos(ULAT(i,j)) / radius
- distance (x,y,z) = actual distance to "vconst_5" points
- west of the nearest western boundary
- dx (x,y) = DXU(i,j)
- dy (x,y) = DYU(i,j)
- visc_vel_scale (z) = vconst_7 * exp(-zt(k)/visc_vel_scale_length)
- visc_vel_scale_length = e-folding scale ( default = 1500.0e2 cm)
- y (x,y) = ULAT(i,j), latitude of "u/v" grid pts in radians
- In MOM, ULAT(radians) = xu*pi/180 with xu(i,j) the longitude of U grid points in degrees
-
- "vconst_#" are input parameters defined in namelist ocean_lapgen_friction_general_nml.
- "vconst_1", "vconst_6", and "vconst_4" have dimensions of cm^2/s,
- cm^2/s, and 1/cm, respectively. "vconst_5" is an INTEGER.
-
- NOTE: The nearest western boundary computations are done along the
- model i-grid lines. Therefore, viscosity based on these are
- only approximate in the high Northern Hemisphere when using
- generalized coordinates with coordinate pole(s) shifted onto land.
-
-
- Subroutine to perform linear stability check for the Laplacian
- operator given a value for the horizontal biharmonic viscosity.
-
- Subroutine to compute the LLaplacian grid Reynolds number. Large
- Reynolds numbers indicate regions where solution may experience
- some grid noise due to lack of enough horizontal friction.
-
- Horizontal velocity field at time tau
-
- Compute Neptune velocity.
-
- Method follows that used in MOM2 and MOM3 as implemented by
- Greg Holloway (zounds@ios.bc.ca) and Michael Eby (eby@uvic.ca)
- Coded in mom4 by Stephen.Griffies
-
- Neptune is calculated as an equilibrium streamfunction given by
- pnep = -f*snep*snep*ht and is applied through friction whereby
- the solution is damped towards the equilibrium streamfunction
- rather than being damped towards zero kinetic energy.
-
- ht = depth of tracer cells
- snep = spnep + (senep-spnep)*(0.5 + 0.5*cos(2.0*latitude))
-
- Neptune length scale snep has a value of senep at the
- equator and smoothly changes to spnep at the poles
-
- Reference:
- Holloway, G., 1992: Representing topographic stress for large
- scale ocean models, J. Phys. Oceanogr., 22, 1033-1046
-
- Eby and Holloway, 1994: Sensitivity of a large scale ocean model
- to a parameterization of topographic stress. JPO, vol. 24,
- pages 2577-2588
-
- March 2012
- Stephen.Griffies
- Algorithm updated to Eby and Holloway (1994)
-
-
diff --git a/src/mom5/ocean_param/lateral/ocean_mixdownslope.F90 b/src/mom5/ocean_param/lateral/ocean_mixdownslope.F90
index f9a05c52af..d0241a18ac 100644
--- a/src/mom5/ocean_param/lateral/ocean_mixdownslope.F90
+++ b/src/mom5/ocean_param/lateral/ocean_mixdownslope.F90
@@ -191,9 +191,9 @@ module ocean_mixdownslope_mod
character(len=128) :: version=&
- '=>Using: ocean_mixdownslope.f90 ($Id: ocean_mixdownslope.F90,v 1.1.2.2 2012/05/17 13:41:45 smg Exp $)'
+ '=>Using: ocean_mixdownslope.f90 ($Id: ocean_mixdownslope.F90,v 20.0 2013/12/14 00:14:28 fms Exp $)'
character (len=128) :: tagname=&
- '$Name: mom5_siena_08jun2012_smg $'
+ '$Name: tikal $'
! number of prognostic tracers
integer :: num_prog_tracers=0
@@ -894,8 +894,16 @@ subroutine mixdownslope (Time, Thickness, T_prog, Dens, index_temp, index_salt)
enddo
enddo
- if(id_mixdownslope(nt) > 0) then
- call diagnose_3d(Time, Grd, id_mixdownslope(nt), T_prog(nt)%conversion*tend_mix(:,:,:))
+ if(id_mixdownslope(nt) > 0) then
+ wrk1(:,:,:) = 0.0
+ do k=1,nk
+ do j=jsc,jec
+ do i=isc,iec
+ wrk1(i,j,k) = tend_mix(i,j,k)*mixdownslope_mask(i,j)
+ enddo
+ enddo
+ enddo
+ call diagnose_3d(Time, Grd, id_mixdownslope(nt), wrk1(:,:,:))
endif
if(nt==index_temp) then
diff --git a/src/mom5/ocean_param/lateral/ocean_mixdownslope.html b/src/mom5/ocean_param/lateral/ocean_mixdownslope.html
deleted file mode 100644
index 494575e3ad..0000000000
--- a/src/mom5/ocean_param/lateral/ocean_mixdownslope.html
+++ /dev/null
@@ -1,294 +0,0 @@
-
-
-
-Module ocean_mixdownslope_mod
-
-
-
-
-PUBLIC INTERFACE
-
- ~ PUBLIC ROUTINES
- ~ NAMELIST
-
-
- Mixing of tracer between dense shallow parcel and
- deeper parcels downslope.
-
-
-
-
-
- Mixing of tracer properties as dense shallow parcel is discharged
- into deeper water to approach the parcel's depth of neutral buoyancy.
- This module can be characterized as a mixture of the approach from
- Campin and Goosse (1999) and slope convection.
-
- Initial set up for mixing of tracers into the abyss next to topography.
-
-
-
-
-
-
-
-
mixdownslope
-
-
-DESCRIPTION
-
-
- Compute thickness and density weighted tracer tendency [tracer*rho*m/s]
- due to exchange of tracer properties in regions where density-driven
- downslope transport is favorable.
-
- Allow for exchanges to occur over horizontally
- distant points, so long as the dense shallow parcel finds that it
- will sit on the bottom of the horizontally adjacent columns. Doing
- so requires a search algorithm, which requires some if-test logic
- as well as extended halos. Note that the halos cannot be extended
- to larger than the size of the computational domain on a processor.
- This restriction limits the extent that we can search horizontally.
-
- The rates for the exchange are functions of the topographic slope
- and the density differences between parcels.
-
- This scheme can be characterized as a slope convection based on
- logic incorporated into the overflow and overexchange schemes.
-
-
-
-
-
-
-
-
-
watermass_diag_init
-
-
-DESCRIPTION
-
-
- Initialization of watermass diagnostic output files.
-
-
-
-
-
-
-
-
watermass_diag
-
-
-DESCRIPTION
-
-
- Diagnose effects from mixdownslope on the watermass transformation.
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_mixdownslope_nml
-
-
-
-
-
-use_this_module
-
-
- For using this module. Default use_this_module=.false.
-
-[logical]
-
-
-debug_this_module
-
-
- For debugging
-
-[logical]
-
-
-do_bitwise_exact_sum
-
-
- Set true to do bitwise exact global sum. When it is false, the global
- sum will be non-bitwise_exact, but will significantly increase efficiency.
- The default value is false.
-
-[logical]
-
-
-mixdownslope_npts
-
-
- Number of horizontally distant points used in search downslope.
- Note: it is not possible to have
- mixdownslope_npts greater than or equal to the computational domain
- extents, as this would require updates across multiple processors.
- Default mixdownslope_npts=1.
-
-[integer]
-
-
-mixdownslope_frac_central
-
-
- Fraction of the central cell that participates in downslope mixing
- in any particular direction. Default mixdownslope_frac_central=0.25
-
-[real]
-
-
-mixdownslope_weight_far
-
-
- To place more weight on points further from central point. This may
- be done to enhance properties getting downslope. Default is
- mixdownslope_weight_far=.false.
-
-[logical]
-
-
-mixdownslope_width
-
-
- Width of the re-weighting function used to emphasize points further
- along in the search for exchange points. Default mixdownslope_width=1.
-
-[integer]
-
-
-read_mixdownslope_mask
-
-
- For reading in a mask that selects regions of the domain
- where mixdownslope is allowed to function (mask=1) or not
- to function (mask=0). Default read_mixdownslope_mask=.false.,
- whereby mixdownslope_mask is set to tmask(k=1).
-
-[logical]
-
-
-mixdownslope_mask_gfdl
-
-
- For modifying the mixdownslope mask based on reading in
- the GFDL regional mask. Default mixdownslope_mask_gfdl=.false.
-
-[logical]
-
-
-
-
-
-
-
-
-
-
-
REFERENCES
-
-
-
-
- Campin and Goosse (1999): Parameterization of density-driven downsloping flow
- for a coarse-resolution model in z-coordinate", Tellus 51A, pages 412-430
-
-
- S.M. Griffies: Elements of MOM (2012)
- NOAA/Geophysical Fluid Dynamics Laboratory
-
-
-
diff --git a/src/mom5/ocean_param/lateral/ocean_mixdownslope.xml b/src/mom5/ocean_param/lateral/ocean_mixdownslope.xml
deleted file mode 100644
index a76672a800..0000000000
--- a/src/mom5/ocean_param/lateral/ocean_mixdownslope.xml
+++ /dev/null
@@ -1,76 +0,0 @@
-
-
- S.M. Griffies
-
- Mixing of tracer between dense shallow parcel and
- deeper parcels downslope.
-
- Mixing of tracer properties as dense shallow parcel is discharged
- into deeper water to approach the parcel's depth of neutral buoyancy.
- This module can be characterized as a mixture of the approach from
- Campin and Goosse (1999) and slope convection.
-
- Campin and Goosse (1999): Parameterization of density-driven downsloping flow
- for a coarse-resolution model in z-coordinate", Tellus 51A, pages 412-430
-
- S.M. Griffies: Elements of MOM (2012)
- NOAA/Geophysical Fluid Dynamics Laboratory
-
- For using this module. Default use_this_module=.false.
-
- For debugging
-
- Set true to do bitwise exact global sum. When it is false, the global
- sum will be non-bitwise_exact, but will significantly increase efficiency.
- The default value is false.
-
- Number of horizontally distant points used in search downslope.
- Note: it is not possible to have
- mixdownslope_npts greater than or equal to the computational domain
- extents, as this would require updates across multiple processors.
- Default mixdownslope_npts=1.
-
- Fraction of the central cell that participates in downslope mixing
- in any particular direction. Default mixdownslope_frac_central=0.25
-
- To place more weight on points further from central point. This may
- be done to enhance properties getting downslope. Default is
- mixdownslope_weight_far=.false.
-
- Width of the re-weighting function used to emphasize points further
- along in the search for exchange points. Default mixdownslope_width=1.
-
- For reading in a mask that selects regions of the domain
- where mixdownslope is allowed to function (mask=1) or not
- to function (mask=0). Default read_mixdownslope_mask=.false.,
- whereby mixdownslope_mask is set to tmask(k=1).
-
- For modifying the mixdownslope mask based on reading in
- the GFDL regional mask. Default mixdownslope_mask_gfdl=.false.
-
- Initial set up for mixing of tracers into the abyss next to topography.
-
- Compute thickness and density weighted tracer tendency [tracer*rho*m/s]
- due to exchange of tracer properties in regions where density-driven
- downslope transport is favorable.
-
- Allow for exchanges to occur over horizontally
- distant points, so long as the dense shallow parcel finds that it
- will sit on the bottom of the horizontally adjacent columns. Doing
- so requires a search algorithm, which requires some if-test logic
- as well as extended halos. Note that the halos cannot be extended
- to larger than the size of the computational domain on a processor.
- This restriction limits the extent that we can search horizontally.
-
- The rates for the exchange are functions of the topographic slope
- and the density differences between parcels.
-
- This scheme can be characterized as a slope convection based on
- logic incorporated into the overflow and overexchange schemes.
-
-
- Initialization of watermass diagnostic output files.
-
- Diagnose effects from mixdownslope on the watermass transformation.
-
diff --git a/src/mom5/ocean_param/lateral/ocean_sigma_transport.F90 b/src/mom5/ocean_param/lateral/ocean_sigma_transport.F90
index 098929975c..cb63c75e37 100644
--- a/src/mom5/ocean_param/lateral/ocean_sigma_transport.F90
+++ b/src/mom5/ocean_param/lateral/ocean_sigma_transport.F90
@@ -342,9 +342,9 @@ module ocean_sigma_transport_mod
integer :: index_salt=-1
character(len=128) :: version=&
- '$Id: ocean_sigma_transport.F90,v 1.1.2.2 2012/05/17 13:41:45 smg Exp $'
+ '$Id: ocean_sigma_transport.F90,v 20.0 2013/12/14 00:14:30 fms Exp $'
character (len=128) :: tagname = &
- '$Name: mom5_siena_08jun2012_smg $'
+ '$Name: tikal $'
integer :: unit=6
logical :: module_is_initialized = .FALSE.
diff --git a/src/mom5/ocean_param/lateral/ocean_sigma_transport.html b/src/mom5/ocean_param/lateral/ocean_sigma_transport.html
deleted file mode 100644
index 69673c4605..0000000000
--- a/src/mom5/ocean_param/lateral/ocean_sigma_transport.html
+++ /dev/null
@@ -1,519 +0,0 @@
-
-
-
-Module ocean_sigma_transport_mod
-
-
-
-
-PUBLIC INTERFACE
-
- ~ PUBLIC ROUTINES
- ~ NAMELIST
-
-
- Thickness weighted and density weighted time tendency for
- tracer from transport within a bottom "sigma" layer.
- The advective portion of this routine is experimental,
- and has many problems. It is retained in MOM for
- exploratory use only. Also note that the advection
- contributes a lot of instability when running realistic
- simulations with pressure vertical coordinates. The
- instability mechanism is unknown.
-
-
-
-
-
- This module computes the thickness weighted and density weighted
- time tendency for tracer arising from
-
- 1. Laplacian diffusion within a bottom turbulent boundary layer.
-
- 2. Upwind advection within this layer. Advection velocities
- determined by model resolved velocity and parameterized
- downslope velocity. We use first order upwind tracer advection
- to ensure positive definite tracer transport in the sigma
- layer. As the sigma layer is a proxy for a bottom turbulent
- boundary layer, the added mixing from the first order upwind
- should be physically acceptable.
-
- CAUTION: The advective portion of this algorithm has problems
- and it retained in MOM only for research purposes. It
- is NOT supported for general use.
-
- The diffusivity used to determine the strength of the diffusion
- is generally set to be a function of the local horizontal grid
- spacing. Diffusivity is the sum of an a priori background plus
- a velocity dependent diffusivity. It is large if there is a
- a heavier parcel living adjacent within the "sigma layer" above
- a lighter parcel. It is small otherwise.
-
- The advection is set to zero if the density is not downslope
- favorable. That is, rho_{,x} * H_{,x} < 0 for downslope
- flow in the x-direction, and likewise in the y-direction.
-
- The thickness of the bottom layer can span more than a single
- bottom grid cell. This feature allows the sigma
- layer thickness to undulate in time according to the convergence
- or divergence of mass within the sigma layer.
-
-
- Initialize the sigma transport module by registering fields for
- diagnostic output and performing some numerical checks to see
- that namelist settings are appropriate.
-
-
-
-
-
-
-
-
sigma_transport
-
-
-DESCRIPTION
-
-
- This subroutine computes the thickness weighted and density
- weighted time tendency for tracer arising from transport in a
- bottom turbulent boundary layer. The result is stored in
- tracer th_tendency.
-
- NOTE: In this algorithm, we ideally wish to have advection
- velocity components on full data domain. Unfortunately,
- from ocean_advection_velocity_mod, they are only known
- on the following domains:
-
- Adv_vel%uhrho_et: (isd,ied) x (jsc,jed)
- Adv_vel%vhrho_nt: (isc,ied) x (jsd,jed).
-
- So to proceed with the sigma_transport algorithm, we
- transfer into local arrays and then update. These
- updates may be avoided (possibly), but at the price
- of much more logic in the algorithm. We choose to
- instead do the updates and have less logic. This
- decision may need to be revisited.
-
- CAUTION: The advective portion of this algorithm
- has fundamental problems. It is retained in MOM
- only for process physics research purposes. It is
- NOT recommended for use in general use.
-
-
-
-
-
-
-
-
-
ocean_sigma_transport_restart
-
-
-DESCRIPTION
-
-
- Write out restart files registered through register_restart_file
-
-
-
-
-
-
-
-
ocean_sigma_transport_end
-
-
-DESCRIPTION
-
-
- Write to restart.
-
-
-
-
-
-
-
-
advect_sigma_upwind
-
-
-DESCRIPTION
-
-
- First order upwind to advect tracers in sigma layer.
-
-
-
-
-
-
-
-
watermass_diag_init
-
-
-DESCRIPTION
-
-
- Initialization of watermass diagnostic output files.
-
-
-
-
-
-
-
-
watermass_diag
-
-
-DESCRIPTION
-
-
- Diagnose effects from sigma transport on the watermass transformation.
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_sigma_transport_nml
-
-
-
-
-
-use_this_module
-
-
- Must be true to use this module. Default is false.
-
-[logical]
-
-
-debug_this_module
-
-
- For debugging.
-
-[logical]
-
-
-sigma_diffusion_on
-
-
- For using sigma diffusion. Default is true.
-
-[logical]
-
-
-sigma_advection_on
-
-
- For using sigma advection. Default is false.
-
-[logical]
-
-
-sigma_advection_sgs_only
-
-
- In many cases, adding the resolved transport to the
- sigma-advective transport produces a tremendous level of
- noise at the bottom. The problem is that there are
- grid-scale features that may cause large jumps in whether
- the velocity should be added or not, depending on the logic
- of the scheme. For this reason, it may be prudent to remove
- the resolved velocity from that contributing to the sigma
- transport scheme. Note that its removal from sigma transport
- does not remove the contributions of the resolved velocity
- from the resolved advective transport arising from
- ocean_tracer_advect_mod. It simply removes it from the
- added transport arising in the sigma transport module.
- Default is sigma_advection_sgs_only=.true.
-
-[logical]
-
-
-sigma_advection_check
-
-
- If true, then will only include the resolved advection
- velocity in the sigma-layer if the direction of
- transport is downslope favorable for enhancing deep density.
- IF false, then will include the velocity regardless.
- This option aims to reduce the large divergences
- that occur for the case when only include the velocity
- if it is favorable for deep water getting more dense.
- Default is sigma_advection_check=.true.
-
-[logical]
-
-
-thickness_sigma_layer
-
-
- Initial thickness of the bottom sigma layer.
-
-[real, units: meter]
-
-
-thickness_sigma_min
-
-
- Minimum thickness of the bottom sigma layer.
-
-[real, units: meter]
-
-
-thickness_sigma_max
-
-
- Maximum thickness of the bottom sigma layer.
-
-[real, units: meter]
-
-
-sigma_just_in_bottom_cell
-
-
- For just having sigma layer in the bottom cell, as in mom4p0.
- This option must be .false. in order to use sigma_advection_on=.true.
- Default sigma_just_in_bottom_cell=.true.
-
-[logical]
-
-
-tmask_sigma_on
-
-
- IF .true. then masks out fluxes passing into the sigma layer, except those
- associated with sigma transport. Typically set to .false.
-
-[logical]
-
-
-sigma_diffusivity
-
-
- Sigma tracer diffusivity for use if not using micom diffusivity.
-
-[real, units: m^2/sec]
-
-
-sigma_diffusivity_ratio
-
-
- When flow along sigma surface is stable (i.e., heavy parcels are below lighter parcels)
- then sigma diffusivity is reduced by sigma_diffusivity_ratio from the case where
- heavy parcels are above lighter parcels.
-
-[real, units: dimensionless]
-
-
-tracer_mix_micom
-
-
- If .true., then the sigma diffusivity is set according to a velocity scale
- times the grid spacing.
-
-[logical]
-
-
-vel_micom
-
-
- Velocity scale that is used for computing the MICOM diffusivity.
-
-[real, units: m/sec]
-
-
-campingoose_mu
-
-
- Dissipation rate for the bottom friction. Campin and Goosse
- suggest campingoose_mu=10^-4
-
-[real, units: inverse seconds]
-
-
-campingoose_delta
-
-
- Fraction of a grid cell participating in the overflow process.
- Campin and Goosse suggest campingoose_delta=1/3.
-
-[real, units: dimensionless]
-
-
-sigma_umax
-
-
- Maximum downslope speed allowed in sigma layer.
- In some cases, the model will be unstable if sigma_umax
- is too large.
-
-[real, units: m/s]
-
-
-smooth_sigma_velocity
-
-
- To smooth the sigma advective transport velocity.
- Default is smooth_sigma_velocity=.true.
-
-[logical]
-
-
-smooth_sigma_thickness
-
-
- To smooth the sigma thickness. This may be needed especially
- for case with sigma advection, in which case the thickness
- can become noisy. Default is smooth_sigma_thickness=.true.
-
-[logical]
-
-
-sigma_velmicom
-
-
- For smoothing the sigma_thickness, use this as velocity scale to
- determine the thickness diffusivity.
- Default is smooth_velmicom = 0.2
-
-[real, units: m/s]
-
-
-
-
-
-
-
-
-
-
-
REFERENCES
-
-
-
-
- A. Beckmann and R. Doscher, 1997: A method for improved
- representation of dense water spreading over
- topography in geopotential--coordinate models
- Journal of Physical Oceanography, vol 27,
- pages 581--59.
-
-
- R. Doscher and A. Beckmann, 2000:
- Effects of a bottom boundary layer parameterization
- in a coarse-resolution model of the North Atlantic Ocean
- Journal of Atmospheric and Oceanic Technology,
- vol 17 pages 698--707
-
-
- Campin and Goosse 1999: Parameterization of density-driven downsloping
- flow for a coarse-resolution model in z-coordinate", Tellus 51A,
- pages 412-430.
-
-
-
diff --git a/src/mom5/ocean_param/lateral/ocean_sigma_transport.xml b/src/mom5/ocean_param/lateral/ocean_sigma_transport.xml
deleted file mode 100644
index 78f28c7598..0000000000
--- a/src/mom5/ocean_param/lateral/ocean_sigma_transport.xml
+++ /dev/null
@@ -1,182 +0,0 @@
-
-
- Stephen M. Griffies
-
- Thickness weighted and density weighted time tendency for
- tracer from transport within a bottom "sigma" layer.
- The advective portion of this routine is experimental,
- and has many problems. It is retained in MOM for
- exploratory use only. Also note that the advection
- contributes a lot of instability when running realistic
- simulations with pressure vertical coordinates. The
- instability mechanism is unknown.
-
- This module computes the thickness weighted and density weighted
- time tendency for tracer arising from
-
- 1. Laplacian diffusion within a bottom turbulent boundary layer.
-
- 2. Upwind advection within this layer. Advection velocities
- determined by model resolved velocity and parameterized
- downslope velocity. We use first order upwind tracer advection
- to ensure positive definite tracer transport in the sigma
- layer. As the sigma layer is a proxy for a bottom turbulent
- boundary layer, the added mixing from the first order upwind
- should be physically acceptable.
-
- CAUTION: The advective portion of this algorithm has problems
- and it retained in MOM only for research purposes. It
- is NOT supported for general use.
-
- The diffusivity used to determine the strength of the diffusion
- is generally set to be a function of the local horizontal grid
- spacing. Diffusivity is the sum of an a priori background plus
- a velocity dependent diffusivity. It is large if there is a
- a heavier parcel living adjacent within the "sigma layer" above
- a lighter parcel. It is small otherwise.
-
- The advection is set to zero if the density is not downslope
- favorable. That is, rho_{,x} * H_{,x} < 0 for downslope
- flow in the x-direction, and likewise in the y-direction.
-
- The thickness of the bottom layer can span more than a single
- bottom grid cell. This feature allows the sigma
- layer thickness to undulate in time according to the convergence
- or divergence of mass within the sigma layer.
-
-
- A. Beckmann and R. Doscher, 1997: A method for improved
- representation of dense water spreading over
- topography in geopotential--coordinate models
- Journal of Physical Oceanography, vol 27,
- pages 581--59.
-
- R. Doscher and A. Beckmann, 2000:
- Effects of a bottom boundary layer parameterization
- in a coarse-resolution model of the North Atlantic Ocean
- Journal of Atmospheric and Oceanic Technology,
- vol 17 pages 698--707
-
- Campin and Goosse 1999: Parameterization of density-driven downsloping
- flow for a coarse-resolution model in z-coordinate", Tellus 51A,
- pages 412-430.
-
- S.M. Griffies: Elements of MOM (2012)
-
- Must be true to use this module. Default is false.
-
- For debugging.
-
- For using sigma diffusion. Default is true.
-
- For using sigma advection. Default is false.
-
- In many cases, adding the resolved transport to the
- sigma-advective transport produces a tremendous level of
- noise at the bottom. The problem is that there are
- grid-scale features that may cause large jumps in whether
- the velocity should be added or not, depending on the logic
- of the scheme. For this reason, it may be prudent to remove
- the resolved velocity from that contributing to the sigma
- transport scheme. Note that its removal from sigma transport
- does not remove the contributions of the resolved velocity
- from the resolved advective transport arising from
- ocean_tracer_advect_mod. It simply removes it from the
- added transport arising in the sigma transport module.
- Default is sigma_advection_sgs_only=.true.
-
- If true, then will only include the resolved advection
- velocity in the sigma-layer if the direction of
- transport is downslope favorable for enhancing deep density.
- IF false, then will include the velocity regardless.
- This option aims to reduce the large divergences
- that occur for the case when only include the velocity
- if it is favorable for deep water getting more dense.
- Default is sigma_advection_check=.true.
-
- Initial thickness of the bottom sigma layer.
-
- Minimum thickness of the bottom sigma layer.
-
- Maximum thickness of the bottom sigma layer.
-
- For just having sigma layer in the bottom cell, as in mom4p0.
- This option must be .false. in order to use sigma_advection_on=.true.
- Default sigma_just_in_bottom_cell=.true.
-
- IF .true. then masks out fluxes passing into the sigma layer, except those
- associated with sigma transport. Typically set to .false.
-
- Sigma tracer diffusivity for use if not using micom diffusivity.
-
- When flow along sigma surface is stable (i.e., heavy parcels are below lighter parcels)
- then sigma diffusivity is reduced by sigma_diffusivity_ratio from the case where
- heavy parcels are above lighter parcels.
-
- If .true., then the sigma diffusivity is set according to a velocity scale
- times the grid spacing.
-
- Velocity scale that is used for computing the MICOM diffusivity.
-
- Dissipation rate for the bottom friction. Campin and Goosse
- suggest campingoose_mu=10^-4
-
- Fraction of a grid cell participating in the overflow process.
- Campin and Goosse suggest campingoose_delta=1/3.
-
- Maximum downslope speed allowed in sigma layer.
- In some cases, the model will be unstable if sigma_umax
- is too large.
-
- To smooth the sigma advective transport velocity.
- Default is smooth_sigma_velocity=.true.
-
- To smooth the sigma thickness. This may be needed especially
- for case with sigma advection, in which case the thickness
- can become noisy. Default is smooth_sigma_thickness=.true.
-
- For smoothing the sigma_thickness, use this as velocity scale to
- determine the thickness diffusivity.
- Default is smooth_velmicom = 0.2
-
- Initialize the sigma transport module by registering fields for
- diagnostic output and performing some numerical checks to see
- that namelist settings are appropriate.
-
- This subroutine computes the thickness weighted and density
- weighted time tendency for tracer arising from transport in a
- bottom turbulent boundary layer. The result is stored in
- tracer th_tendency.
-
- NOTE: In this algorithm, we ideally wish to have advection
- velocity components on full data domain. Unfortunately,
- from ocean_advection_velocity_mod, they are only known
- on the following domains:
-
- Adv_vel%uhrho_et: (isd,ied) x (jsc,jed)
- Adv_vel%vhrho_nt: (isc,ied) x (jsd,jed).
-
- So to proceed with the sigma_transport algorithm, we
- transfer into local arrays and then update. These
- updates may be avoided (possibly), but at the price
- of much more logic in the algorithm. We choose to
- instead do the updates and have less logic. This
- decision may need to be revisited.
-
- CAUTION: The advective portion of this algorithm
- has fundamental problems. It is retained in MOM
- only for process physics research purposes. It is
- NOT recommended for use in general use.
-
-
- Write out restart files registered through register_restart_file
-
- Write to restart.
-
- First order upwind to advect tracers in sigma layer.
-
- Initialization of watermass diagnostic output files.
-
- Diagnose effects from sigma transport on the watermass transformation.
-
diff --git a/src/mom5/ocean_param/lateral/ocean_submesoscale.F90 b/src/mom5/ocean_param/lateral/ocean_submesoscale.F90
index 94b9d3cb1b..1d20cb7686 100644
--- a/src/mom5/ocean_param/lateral/ocean_submesoscale.F90
+++ b/src/mom5/ocean_param/lateral/ocean_submesoscale.F90
@@ -352,7 +352,7 @@ module ocean_submesoscale_mod
type(ocean_domain_type), save :: Dom_flux_sub
character(len=128) :: version='$$'
-character (len=128) :: tagname = '$Name: mom5_siena_08jun2012_smg $'
+character (len=128) :: tagname = '$Name: tikal $'
#ifdef MOM_STATIC_ARRAYS
diff --git a/src/mom5/ocean_param/lateral/ocean_submesoscale.html b/src/mom5/ocean_param/lateral/ocean_submesoscale.html
deleted file mode 100644
index 7e6e7c5efa..0000000000
--- a/src/mom5/ocean_param/lateral/ocean_submesoscale.html
+++ /dev/null
@@ -1,929 +0,0 @@
-
-
-
-Module ocean_submesoscale_mod
-
-
-
-
-PUBLIC INTERFACE
-
- ~ PUBLIC ROUTINES
- ~ NAMELIST
-
-
- This module computes a streamfunction within
- the upper surface boundary layer, and applies this
- streamfunction to all tracers. It also optionally
- applies horizontal diffusion in the surface layer
- as determined by the strength of the streamfunction.
-
-
-
-
-
- This module computes a streamfunction within
- the upper surface boundary layer, and applies this
- streamfunction to all tracers. It also optionally
- applies horizontal diffusion in the surface layer
- as determined by the strength of the streamfunction.
-
- Initialization for the ocean_submesoscale module.
-
-
-
-
-
-
-
-
submeso_restrat
-
-
-DESCRIPTION
-
-
- This routine computes a thickness and density weighted time tendency
- for each tracer, arising from the effects of parameterized
- submesoscale eddies acting in the surface mixed layer.
-
-
-
-
-
-
-
-
compute_bldepth
-
-
-DESCRIPTION
-
-
- Compute the boundary layer depth and kblt.
-
-
-
-
-
-
-
-
tracer_derivs
-
-
-DESCRIPTION
-
-
- Compute the tracer derivatives, with the
- lateral derivatives computed along constant k-level.
-
-
-
-
-
-
-
-
salinity_derivs
-
-
-DESCRIPTION
-
-
- Compute the density-salinity derivatives, with lateral
- derivative computed on constant k-level.
-
-
-
-
-
-
-
-
compute_psi
-
-
-DESCRIPTION
-
-
- Compute the vector streamfunction from parameterized
- submesoscale restratification.
-
- Units of psi are m^2/sec
-
- psix is defined on north face of tracer cell for jq=0,1.
- psiy is defined on east face of tracer cell for ip=0,1.
-
- NOTE: the mpp updates for psix and psiy are treated as a
- scalar, whereas they are actually components to a pseudo-vector.
- Some further thought is required for the tripolar grid. We ignore
- this detail in the present implementation.
-
-
-
-
-
-
-
-
-
compute_psi_legacy
-
-
-DESCRIPTION
-
-
- Compute the vector streamfunction
-
- Units of psi are m^2/sec
-
- If computing skewsion tendency, then need psi at depth_zt.
- If computing advection tendency, then need psi at depth_zwt.
-
- Jan2012: This scheme has problems with the limiters and smoothers.
- These problems become particularly egregious when trying to compute
- an advective flux rather than a skew flux. This routine is
- retained only for legacy purposes.
- Stephen.Griffies
-
-
-
-
-
-
-
-
-
compute_transport
-
-
-DESCRIPTION
-
-
- Compute the mass transport from submeso.
-
- This routine is a diagnostic routine if skewsion, and
- part of the calculation of the eddy-induced velocity if
- advective approach used.
-
- Comments on the scheme:
-
- 1/ compute vertical component from convergence of horizontal, just
- as for the vertical velocity component for the Eulerian transport.
-
- 2/ wrho_bt_submeso(:,:,k=0) = 0.0 by definition
-
- 3/ expand the BDX_ET and BDY_NT operators for efficiency.
-
- 4/ mask to zero those regions where the horizontal divergence
- vanishes, as these are regions beneath the submeso boundary
- layer. Base the mask on horz divergence rather than kblt(i,j),
- since any smoothing performed to uhrho_et_submeso and vhrho_nt_submeso
- will modify the region of nonzero submesoscale advection so that
- it reaches potentially to below kblt.
-
-
-
-
-
-
-
-
-
compute_submeso_skewsion
-
-
-DESCRIPTION
-
-
- Compute tendency from submeso skewsion.
-
-
-
-
-
-
-
-
compute_flux_x
-
-
-DESCRIPTION
-
-
-
- Subroutine computes the zonal submesoscale tracer skew flux component.
-
- fx has physical dimensions (area*diffusivity*density*tracer gradient)
-
-
-
- Subroutine computes the vertical submeso tracer skew flux component.
-
- Surface and bottom boundary condition fz(k=0)=fz(k=kmt(i,j))=0
-
- fz has physical dimensions (density*diffusivity*tracer gradient)
-
-
-
-
-
-
-
-
-
compute_submeso_upwind
-
-
-DESCRIPTION
-
-
- First order upwind to compute the tendency from submeso advection.
-
- Although this method adds diffusion, some of the mixing
- is physically relevant. Absent this mixing, the submesoscale
- parameterization is incomplete. The submesoscale parameterization is,
- afterall, active only in the mixed layer, where there is lot of
- physical mixing.
-
- Use of first order upwind ensures that the tendency computed
- from submesoscale parameterization will not, in principle,
- introduce extrema. However, there remain some issues with large
- tendencies appearing near boundaries that may compromise this
- monotonicity property.
-
- Apply masks so that there is no flux leaving cell next to bottom.
-
-
-
-
-
-
-
-
-
compute_submeso_sweby
-
-
-DESCRIPTION
-
-
- Sweby scheme to compute the tendency from submeso advection.
- Algorithm taken after advect_tracer_sweby_all in the module
- ocean_tracers/ocean_tracer_advect.F90.
-
- Jan 2012: Stephen.Griffies
- This scheme has known bugs; it is not meant for general use.
-
-
-
-
-
-
-
-
-
compute_submeso_diffusion
-
-
-DESCRIPTION
-
-
- Compute tendency from submeso horizontal diffusion.
-
-
-
-
-
-
-
-
maximum_bottom_w_general
-
-
-DESCRIPTION
-
-
- Compute maximum vertical velocity from submeso.
-
-
-
-
-
-
-
-
transport_on_nrho_submeso
-
-
-DESCRIPTION
-
-
- Classify horizontal submeso mass transport according to neutral
- density classes.
-
- NOTE: This diagnostic works with transport integrated from bottom to
- a particular cell depth. To get transport_on_rho_submeso, a remapping is
- performed, rather than the binning done for transport_on_nrho_submeso_adv.
-
- This is the same algorithm as used for GM skew fluxes on rho surfaces.
-
- Caveat: Since the submeso scheme operates only in the mixed layer,
- there are difficulties mapping this transport to neutral density
- layers. The user should be mindful of the problems with this
- remapping. An alternative that may be more suitable is to use
- Ferret to remap the time mean submeso transport to the time mean
- neutral density surfaces. There are missing correlations, but for
- many purposes, the Ferret remapping may be preferable.
-
- Briefly, the Ferret command is the following:
-
- let ty_trans_nrho_submeso_new = ZAXREPLACE(TY_TRANS_SUBMESO,NEUTRAL_RHO,TY_TRANS_NRHO)
- where TY_TRANS_SUBMESO is the level-space transport
- NEUTRAL_RHO is the level space version of the neutral density
- TY_TRANS_NRHO is any density space field whose vertical coordinates
- are accessed for the remapping.
-
-
-
-
-
-
-
-
transport_on_nrho_submeso_adv
-
-
-DESCRIPTION
-
-
- Classify horizontal transport according to neutral density classes.
-
- Based on transport_on_nrho in ocean_diag/ocean_adv_diag.F90.
-
-
-
-
-
-
-
-
-
watermass_diag_init
-
-
-DESCRIPTION
-
-
- Initialization of watermass diagnostic output files.
-
-
-
-
-
-
-
-
watermass_diag
-
-
-DESCRIPTION
-
-
- Diagnose effects from submesoscale on watermass transformation.
-
-
-
-
-
-
-
-
watermass_diag_diffusion
-
-
-DESCRIPTION
-
-
- Diagnose effects from submesoscale horizontal diffusion
- on watermass transformation.
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_submesoscale_nml
-
-
-
-
-
-use_this_module=
-
-
- Must be .true. to use this module.
-
-[logical]
-
-
-debug_this_module
-
-
- For debugging purposes.
-
-[logical]
-
-
-diag_step
-
-
- Number of time steps between computing max bottom value for
- wrho_bt_submeso. Default diag_step=1200.
-
-[integer]
-
-
-submeso_skew_flux
-
-
- For computing the tendency as convergence of skew flux.
- This is the recommended method.
- Default submeso_skew_flux=.true.
-
-[logical]
-
-
-submeso_advect_flux
-
-
- For computing the tendency as convergence of advective flux.
- This approach uses either a flux limited sweby advection or
- first order upwind, both of which ensure that the resulting
- tendency will not create extrema in the tracer field.
- Default submeso_advect_flux=.false.
-
-[logical]
-
-
-submeso_advect_upwind
-
-
- For computing the tendency as convergence of a first order
- advective flux.
- Default submeso_advect_upwind=.true.
-
-[logical]
-
-
-submeso_advect_sweby
-
-
- For computing the tendency as convergence of a sweby
- advective flux. This routine is incomplete and has a bug.
- Default submeso_advect_sweby=.false.
-
-[logical]
-
-
-submeso_advect_limit
-
-
- For limiting the value of the horizontal transports
- to be less than a velocity scale set by limit_psi_velocity_scale.
- This option is not needed if limit_psi=.true.
- Default submeso_advect_limit=.false.
-
-[logical]
-
-
-submeso_advect_zero_bdy
-
-
- For removing the advective transport next to boundaries.
- This is useful since computation of the advective transport
- velocity components can be problematic next to boundaries.
- Default submeso_advect_zero_bdy=.false.
-
-[logical]
-
-
-smooth_advect_transport
-
-
- For doing a horizontal 1-2-1 smoothing on the diagnosed
- uhrho_et_submeso and vhrho_nt_submeso fields.
- Default smooth_advect_transport=.true.
-
-[logical]
-
-
-smooth_advect_transport_num
-
-
- Number of iterations for the smooothing of horizontal transport.
- Default smooth_advect_transport_num=2.
-
-[integer]
-
-
-submeso_diag_advect_transport
-
-
- For diagnosing the advective mass transport even when
- using the skew approach.
- Default submeso_diag_advect_transport=.false.
-
-[logical]
-
-
-submeso_diffusion
-
-
- For computing a horizontal diffusive flux in the boundary layer
- as determined by the strength of the vector streamfunction.
- Default submeso_diffusion=.false.
-
-[logical]
-
-
-submeso_diffusion_biharmonic
-
-
- The default submeso diffusion is Laplacian. However, one may wish to
- use a biharmonic mixing operator instead.
- Default submeso_diffusion_biharmonic=.false.
-
-[logical]
-
-
-submeso_diffusion_scale
-
-
- A dimensionless scaling to be used for scaling up or down the effects from
- horizontal diffusion in the boundary layer. Default submeso_diffusion_scale=1.0.
-
-[real, units: dimensionless]
-
-
-use_hblt_constant
-
-
- For running with a constant boundary layer depth. This for the case when
- not using a realistic mixed layer scheme. Default use_hblt_constant=.false.
-
-[logical]
-
-
-constant_hblt
-
-
- The boundary layer depth for the case when use_hblt_constant=.true.
- Default constant_hblt=100.0.
-
-[real, units: metre]
-
-
-use_hblt_equal_mld
-
-
- For using the diagnosed mld as the hblt for submeso.
- This is useful for those test models that do not have a mixed layer
- scheme enabled, such as KPP, where the mixed layer scheme provides a
- boundary layer depth. In this case, it is sensible to employ the diagnosed
- mixed layer depth for the submeso scheme. Additionally, in general it is
- more physical to use the mld than the KPP hblt as the depth over which
- the submesoscale eddies act. Hence, default use_hblt_equal_mld=.true.
-
-[logical]
-
-
-min_kblt
-
-
- The minimum number of vertical cells in the surface boundary layer
- that are required in order to compute the submesoscale streamfunction.
- Default min_kblt=4. Need at least three to fit a parabola with zero
- streamfunction at the top and bottom of the boundary layer.
-
-[integer, units: dimensionless]
-
-
-minimum_hblt
-
-
- For setting a floor to the hblt used for submesoscale scheme.
- Default minimum_hblt=0.0.
-
-[real, units: metre]
-
-
-smooth_hblt
-
-
- For smoothing on the submeso bldepth field. This is useful
- since the bldepth obtained from KPP or diagnosed mld can
- have some grid noise.
- Default smooth_hblt=.false. since this agrees with legacy.
- Note that this scheme fails to reproduce across
- processor layout, so it remains broken.
-
-[logical]
-
-
-smooth_hblt_num
-
-
- Number of iterations for the smooothing of bldepth.
- Default smooth_hblt_num=1.
-
-[integer]
-
-
-use_psi_legacy
-
-
- For computing psi using older legacy methods.
- These methods are not ideal, and can be problematic
- depending on nml settings for the limiters and smoothers.
- This option is retained only for legacy purposes.
- Default use_psi_legacy=.false.
-
-[logical]
-
-
-smooth_psi
-
-
- For doing a horizontal 1-2-1 smoothing on the
- psix_horz and psiy_horz fields.
- Default smooth_psi=.true.
-
-[logical]
-
-
-smooth_psi_num
-
-
- Number of iterations for the smooothing of psi.
- Default smooth_psi_num=2.
-
-[integer]
-
-
-limit_psi
-
-
- For limiting the magnitude of psi in order to reduce possibility of
- model crashes. Rescales the full psi to maintain vertical structure
- but to keep overall magnitude within bounds.
- Default limit_psi=.false.
-
-[logical]
-
-
-limit_psi_velocity_scale
-
-
- Velocity scale used to limit the value of psi when limit_psi=.true.
- Default limit_psi_velocity_scale=5.0
-
-[real, units: metre/sec]
-
-
-submeso_limit_flux
-
-
- For limiting the fluxes arising from submeso scheme, according to
- tmask_limit. When reach a point where tmask_limit=1.0, then set
- the submeso flux for this cell to zero.
- Default submeso_limit_flux=.true.
-
-[logical]
-
-
-coefficient_ce
-
-
- The dimensionless coefficient from the Fox-Kemper etal scheme.
- They recommend setting coefficient_ce between 0.06 and 0.08.
- Default coefficient_ce=0.07.
-
-[real, units: dimensionless]
-
-
-time_constant
-
-
- Timescale to mix momentum across the mixed layer.
- Default time_constant=86400.0 = 1day.
-
-[real, units: seconds]
-
-
-front_length_const
-
-
- Take constant horizontal length scale of submesoscale front.
- Default front_length_const=5e3.
-
-[real, units: metre]
-
-
-front_length_deform_radius
-
-
- To compute the front length using the mixed layer deformation
- radius. Default front_length_deform_radius=.true. Note,
- will have a floor on the variable front length set by the
- nml setting for front_length_const.
-
-[logical]
-
-
-
-
-
-
-
-
-
-
-
REFERENCES
-
-
-
-
- Fox-Kemper, Ferrari, and Hallberg 2008: Parameterization of
- mixed layer eddies. Part I: theory and diagnosis
- Journal of Physical Oceanography, vol. 38, pages 1145-1165.
-
-
- Fox-Kemper, Danabasoglu, Ferrari, and Hallberg 2008:
- Parameterizing submesoscale physics in global models.
- Clivar Exchanges, vol 13, no.1, Jan2008. pages 3-5.
-
-
- Fox-Kemper, Danabasoglu, Ferrari, Griffies, Hallberg,
- Holland, Peacock, Samuels, 2011: Parameterization of
- Mixed Layer Eddies. III: Global Implementation and
- Impact on Ocean Climate Simulations, Ocean Modelling,
- vol. 39, pages 61-78.
-
-
-
diff --git a/src/mom5/ocean_param/lateral/ocean_submesoscale.xml b/src/mom5/ocean_param/lateral/ocean_submesoscale.xml
deleted file mode 100644
index 13466f03fd..0000000000
--- a/src/mom5/ocean_param/lateral/ocean_submesoscale.xml
+++ /dev/null
@@ -1,316 +0,0 @@
-
-
- S. M. Griffies
-
- This module computes a streamfunction within
- the upper surface boundary layer, and applies this
- streamfunction to all tracers. It also optionally
- applies horizontal diffusion in the surface layer
- as determined by the strength of the streamfunction.
-
- This module computes a streamfunction within
- the upper surface boundary layer, and applies this
- streamfunction to all tracers. It also optionally
- applies horizontal diffusion in the surface layer
- as determined by the strength of the streamfunction.
-
- Fox-Kemper, Ferrari, and Hallberg 2008: Parameterization of
- mixed layer eddies. Part I: theory and diagnosis
- Journal of Physical Oceanography, vol. 38, pages 1145-1165.
-
- Fox-Kemper, Danabasoglu, Ferrari, and Hallberg 2008:
- Parameterizing submesoscale physics in global models.
- Clivar Exchanges, vol 13, no.1, Jan2008. pages 3-5.
-
- Fox-Kemper, Danabasoglu, Ferrari, Griffies, Hallberg,
- Holland, Peacock, Samuels, 2011: Parameterization of
- Mixed Layer Eddies. III: Global Implementation and
- Impact on Ocean Climate Simulations, Ocean Modelling,
- vol. 39, pages 61-78.
-
- Griffies, 2012: Elements of MOM
-
- Must be .true. to use this module.
-
- For debugging purposes.
-
- Number of time steps between computing max bottom value for
- wrho_bt_submeso. Default diag_step=1200.
-
- For computing the tendency as convergence of skew flux.
- This is the recommended method.
- Default submeso_skew_flux=.true.
-
- For computing the tendency as convergence of advective flux.
- This approach uses either a flux limited sweby advection or
- first order upwind, both of which ensure that the resulting
- tendency will not create extrema in the tracer field.
- Default submeso_advect_flux=.false.
-
- For computing the tendency as convergence of a first order
- advective flux.
- Default submeso_advect_upwind=.true.
-
- For computing the tendency as convergence of a sweby
- advective flux. This routine is incomplete and has a bug.
- Default submeso_advect_sweby=.false.
-
- For limiting the value of the horizontal transports
- to be less than a velocity scale set by limit_psi_velocity_scale.
- This option is not needed if limit_psi=.true.
- Default submeso_advect_limit=.false.
-
- For removing the advective transport next to boundaries.
- This is useful since computation of the advective transport
- velocity components can be problematic next to boundaries.
- Default submeso_advect_zero_bdy=.false.
-
- For doing a horizontal 1-2-1 smoothing on the diagnosed
- uhrho_et_submeso and vhrho_nt_submeso fields.
- Default smooth_advect_transport=.true.
-
- Number of iterations for the smooothing of horizontal transport.
- Default smooth_advect_transport_num=2.
-
- For diagnosing the advective mass transport even when
- using the skew approach.
- Default submeso_diag_advect_transport=.false.
-
- For computing a horizontal diffusive flux in the boundary layer
- as determined by the strength of the vector streamfunction.
- Default submeso_diffusion=.false.
-
- The default submeso diffusion is Laplacian. However, one may wish to
- use a biharmonic mixing operator instead.
- Default submeso_diffusion_biharmonic=.false.
-
- A dimensionless scaling to be used for scaling up or down the effects from
- horizontal diffusion in the boundary layer. Default submeso_diffusion_scale=1.0.
-
- For running with a constant boundary layer depth. This for the case when
- not using a realistic mixed layer scheme. Default use_hblt_constant=.false.
-
- The boundary layer depth for the case when use_hblt_constant=.true.
- Default constant_hblt=100.0.
-
- For using the diagnosed mld as the hblt for submeso.
- This is useful for those test models that do not have a mixed layer
- scheme enabled, such as KPP, where the mixed layer scheme provides a
- boundary layer depth. In this case, it is sensible to employ the diagnosed
- mixed layer depth for the submeso scheme. Additionally, in general it is
- more physical to use the mld than the KPP hblt as the depth over which
- the submesoscale eddies act. Hence, default use_hblt_equal_mld=.true.
-
- The minimum number of vertical cells in the surface boundary layer
- that are required in order to compute the submesoscale streamfunction.
- Default min_kblt=4. Need at least three to fit a parabola with zero
- streamfunction at the top and bottom of the boundary layer.
-
- For setting a floor to the hblt used for submesoscale scheme.
- Default minimum_hblt=0.0.
-
- For smoothing on the submeso bldepth field. This is useful
- since the bldepth obtained from KPP or diagnosed mld can
- have some grid noise.
- Default smooth_hblt=.false. since this agrees with legacy.
- Note that this scheme fails to reproduce across
- processor layout, so it remains broken.
-
- Number of iterations for the smooothing of bldepth.
- Default smooth_hblt_num=1.
-
- For computing psi using older legacy methods.
- These methods are not ideal, and can be problematic
- depending on nml settings for the limiters and smoothers.
- This option is retained only for legacy purposes.
- Default use_psi_legacy=.false.
-
- For doing a horizontal 1-2-1 smoothing on the
- psix_horz and psiy_horz fields.
- Default smooth_psi=.true.
-
- Number of iterations for the smooothing of psi.
- Default smooth_psi_num=2.
-
- For limiting the magnitude of psi in order to reduce possibility of
- model crashes. Rescales the full psi to maintain vertical structure
- but to keep overall magnitude within bounds.
- Default limit_psi=.false.
-
- Velocity scale used to limit the value of psi when limit_psi=.true.
- Default limit_psi_velocity_scale=5.0
-
- For limiting the fluxes arising from submeso scheme, according to
- tmask_limit. When reach a point where tmask_limit=1.0, then set
- the submeso flux for this cell to zero.
- Default submeso_limit_flux=.true.
-
- The dimensionless coefficient from the Fox-Kemper etal scheme.
- They recommend setting coefficient_ce between 0.06 and 0.08.
- Default coefficient_ce=0.07.
-
- Timescale to mix momentum across the mixed layer.
- Default time_constant=86400.0 = 1day.
-
- Take constant horizontal length scale of submesoscale front.
- Default front_length_const=5e3.
-
- To compute the front length using the mixed layer deformation
- radius. Default front_length_deform_radius=.true. Note,
- will have a floor on the variable front length set by the
- nml setting for front_length_const.
-
- Initialization for the ocean_submesoscale module.
-
- This routine computes a thickness and density weighted time tendency
- for each tracer, arising from the effects of parameterized
- submesoscale eddies acting in the surface mixed layer.
-
- Compute the boundary layer depth and kblt.
-
- Compute the tracer derivatives, with the
- lateral derivatives computed along constant k-level.
-
- Compute the density-salinity derivatives, with lateral
- derivative computed on constant k-level.
-
- Compute the vector streamfunction from parameterized
- submesoscale restratification.
-
- Units of psi are m^2/sec
-
- psix is defined on north face of tracer cell for jq=0,1.
- psiy is defined on east face of tracer cell for ip=0,1.
-
- NOTE: the mpp updates for psix and psiy are treated as a
- scalar, whereas they are actually components to a pseudo-vector.
- Some further thought is required for the tripolar grid. We ignore
- this detail in the present implementation.
-
-
- Compute the vector streamfunction
-
- Units of psi are m^2/sec
-
- If computing skewsion tendency, then need psi at depth_zt.
- If computing advection tendency, then need psi at depth_zwt.
-
- Jan2012: This scheme has problems with the limiters and smoothers.
- These problems become particularly egregious when trying to compute
- an advective flux rather than a skew flux. This routine is
- retained only for legacy purposes.
- Stephen.Griffies
-
-
- Compute the mass transport from submeso.
-
- This routine is a diagnostic routine if skewsion, and
- part of the calculation of the eddy-induced velocity if
- advective approach used.
-
- Comments on the scheme:
-
- 1/ compute vertical component from convergence of horizontal, just
- as for the vertical velocity component for the Eulerian transport.
-
- 2/ wrho_bt_submeso(:,:,k=0) = 0.0 by definition
-
- 3/ expand the BDX_ET and BDY_NT operators for efficiency.
-
- 4/ mask to zero those regions where the horizontal divergence
- vanishes, as these are regions beneath the submeso boundary
- layer. Base the mask on horz divergence rather than kblt(i,j),
- since any smoothing performed to uhrho_et_submeso and vhrho_nt_submeso
- will modify the region of nonzero submesoscale advection so that
- it reaches potentially to below kblt.
-
-
- Compute tendency from submeso skewsion.
-
-
- Subroutine computes the zonal submesoscale tracer skew flux component.
-
- fx has physical dimensions (area*diffusivity*density*tracer gradient)
-
-
-
- Subroutine computes the meridional submesoscale tracer skew flux component.
-
- fy has physical dimensions (area*diffusivity*density*tracer gradient)
-
-
-
- Subroutine computes the vertical submeso tracer skew flux component.
-
- Surface and bottom boundary condition fz(k=0)=fz(k=kmt(i,j))=0
-
- fz has physical dimensions (density*diffusivity*tracer gradient)
-
-
- First order upwind to compute the tendency from submeso advection.
-
- Although this method adds diffusion, some of the mixing
- is physically relevant. Absent this mixing, the submesoscale
- parameterization is incomplete. The submesoscale parameterization is,
- afterall, active only in the mixed layer, where there is lot of
- physical mixing.
-
- Use of first order upwind ensures that the tendency computed
- from submesoscale parameterization will not, in principle,
- introduce extrema. However, there remain some issues with large
- tendencies appearing near boundaries that may compromise this
- monotonicity property.
-
- Apply masks so that there is no flux leaving cell next to bottom.
-
-
- Sweby scheme to compute the tendency from submeso advection.
- Algorithm taken after advect_tracer_sweby_all in the module
- ocean_tracers/ocean_tracer_advect.F90.
-
- Jan 2012: Stephen.Griffies
- This scheme has known bugs; it is not meant for general use.
-
-
- Compute tendency from submeso horizontal diffusion.
-
- Compute maximum vertical velocity from submeso.
-
- Classify horizontal submeso mass transport according to neutral
- density classes.
-
- NOTE: This diagnostic works with transport integrated from bottom to
- a particular cell depth. To get transport_on_rho_submeso, a remapping is
- performed, rather than the binning done for transport_on_nrho_submeso_adv.
-
- This is the same algorithm as used for GM skew fluxes on rho surfaces.
-
- Caveat: Since the submeso scheme operates only in the mixed layer,
- there are difficulties mapping this transport to neutral density
- layers. The user should be mindful of the problems with this
- remapping. An alternative that may be more suitable is to use
- Ferret to remap the time mean submeso transport to the time mean
- neutral density surfaces. There are missing correlations, but for
- many purposes, the Ferret remapping may be preferable.
-
- Briefly, the Ferret command is the following:
-
- let ty_trans_nrho_submeso_new = ZAXREPLACE(TY_TRANS_SUBMESO,NEUTRAL_RHO,TY_TRANS_NRHO)
- where TY_TRANS_SUBMESO is the level-space transport
- NEUTRAL_RHO is the level space version of the neutral density
- TY_TRANS_NRHO is any density space field whose vertical coordinates
- are accessed for the remapping.
-
- Classify horizontal transport according to neutral density classes.
-
- Based on transport_on_nrho in ocean_diag/ocean_adv_diag.F90.
-
-
- Initialization of watermass diagnostic output files.
-
- Diagnose effects from submesoscale on watermass transformation.
-
- Diagnose effects from submesoscale horizontal diffusion
- on watermass transformation.
-
diff --git a/src/mom5/ocean_param/neutral/ocean_nphysics.F90 b/src/mom5/ocean_param/neutral/ocean_nphysics.F90
index c70d174c94..449f576c9f 100644
--- a/src/mom5/ocean_param/neutral/ocean_nphysics.F90
+++ b/src/mom5/ocean_param/neutral/ocean_nphysics.F90
@@ -97,9 +97,9 @@ module ocean_nphysics_mod
#include
character(len=128) :: version=&
- '$Id: ocean_nphysics.F90,v 1.1.2.2 2012/05/17 13:41:47 smg Exp $'
+ '$Id: ocean_nphysics.F90,v 20.0 2013/12/14 00:14:34 fms Exp $'
character (len=128) :: tagname = &
- '$Name: mom5_siena_08jun2012_smg $'
+ '$Name: tikal $'
character(len=*), parameter :: FILENAME=&
__FILE__
diff --git a/src/mom5/ocean_param/neutral/ocean_nphysics.html b/src/mom5/ocean_param/neutral/ocean_nphysics.html
deleted file mode 100644
index bbdef7dc97..0000000000
--- a/src/mom5/ocean_param/neutral/ocean_nphysics.html
+++ /dev/null
@@ -1,233 +0,0 @@
-
-
-
-Module ocean_nphysics_mod
-
-
-
-
-PUBLIC INTERFACE
-
- ~ PUBLIC ROUTINES
- ~ NAMELIST
-
-
- Must be true to use this module.
- Default use_this_module=.false.
-
-[logical]
-
-
-debug_this_module
-
-
- For printing starting and ending checksums for restarts
- Default debug_this_module=.false.
-
-[logical]
-
-
-write_a_restart
-
-
- Set true to write a restart. False setting only for rare
- cases where wish to benchmark model without measuring the cost
- of writing restarts and associated chksums.
- Default is write_a_restart=.true.
-
-[logical]
-
-
-use_nphysicsA
-
-
- For using the nphysicsA method of neutral physics, based on that
- developed in MOM4.0. This scheme is more robust and recommended for
- general use. Default use_nphysicsA=.true.
-
-[logical]
-
-
-use_nphysicsB
-
-
- For using the nphysicsB method of neutral physics. This method is
- experimental, and is not recommended for general use.
- Default use_nphysicsB=.false.
-
-[logical]
-
-
-use_nphysicsC
-
-
- For using the nphysicsC method of neutral physics. This method is
- experimental, and is not recommended for general use.
- Default use_nphysicsC=.false.
-
-[logical]
-
-
-
diff --git a/src/mom5/ocean_param/neutral/ocean_nphysics.xml b/src/mom5/ocean_param/neutral/ocean_nphysics.xml
deleted file mode 100644
index a4c8d0e3a1..0000000000
--- a/src/mom5/ocean_param/neutral/ocean_nphysics.xml
+++ /dev/null
@@ -1,44 +0,0 @@
-
-
- Stephen M. Griffies
- Tim Leslie
-
-
- Driver for ocean neutral physics.
-
- Driver for ocean neutral physics.
-
- Must be true to use this module.
- Default use_this_module=.false.
-
- For printing starting and ending checksums for restarts
- Default debug_this_module=.false.
-
- Set true to write a restart. False setting only for rare
- cases where wish to benchmark model without measuring the cost
- of writing restarts and associated chksums.
- Default is write_a_restart=.true.
-
- For using the nphysicsA method of neutral physics, based on that
- developed in MOM4.0. This scheme is more robust and recommended for
- general use. Default use_nphysicsA=.true.
-
- For using the nphysicsB method of neutral physics. This method is
- experimental, and is not recommended for general use.
- Default use_nphysicsB=.false.
-
- For using the nphysicsC method of neutral physics. This method is
- experimental, and is not recommended for general use.
- Default use_nphysicsC=.false.
-
- Initialize the neutral physics module.
-
-
- Call the relevant neutral physics scheme.
-
-
- Write to restart.
-
- Write to restart.
-
diff --git a/src/mom5/ocean_param/neutral/ocean_nphysicsA.F90 b/src/mom5/ocean_param/neutral/ocean_nphysicsA.F90
index 4dcdd52344..3bc6d49ba7 100644
--- a/src/mom5/ocean_param/neutral/ocean_nphysicsA.F90
+++ b/src/mom5/ocean_param/neutral/ocean_nphysicsA.F90
@@ -426,9 +426,9 @@ module ocean_nphysicsA_mod
integer :: neutralrho_nk
character(len=128) :: version=&
- '$Id: ocean_nphysicsA.F90,v 1.1.2.2 2012/05/17 13:41:47 smg Exp $'
+ '$Id: ocean_nphysicsA.F90,v 20.0 2013/12/14 00:14:36 fms Exp $'
character (len=128) :: tagname = &
- '$Name: mom5_siena_08jun2012_smg $'
+ '$Name: tikal $'
character(len=*), parameter :: FILENAME=&
__FILE__
diff --git a/src/mom5/ocean_param/neutral/ocean_nphysicsA.html b/src/mom5/ocean_param/neutral/ocean_nphysicsA.html
deleted file mode 100644
index 207e24bf46..0000000000
--- a/src/mom5/ocean_param/neutral/ocean_nphysicsA.html
+++ /dev/null
@@ -1,720 +0,0 @@
-
-
-
-Module ocean_nphysicsA_mod
-
-
-
-
-PUBLIC INTERFACE
-
- ~ PUBLIC ROUTINES
- ~ NAMELIST
-
-
- Thickness weighted and density weighted time tendency for tracer
- from Laplacian neutral diffusion + Laplacian GM skew-diffusion.
-
-
-
-
-
- This module computes the cell thickness weighted and density
- weighted tracer tendency from small angle Laplacian neutral diffusion
- plus Laplacian GM skew-diffusion. The algorithms are based on
- MOM4p0d methods. The fundamental differences from the ocean_nphysicsB
- methods relate to the handling of fluxes near the domain boundaries.
-
- Initialize the neutral physics module by registering fields for
- diagnostic output and performing some numerical checks to see
- that namelist settings are appropriate.
-
-
-
-
-
-
-
-
nphysicsA
-
-
-DESCRIPTION
-
-
- This function computes the thickness weighted and density weighted
- time tendency for tracer from neutral physics. Full discussion
- and details are provided by Griffies (2004).
-
- Here is a brief summary.
-
----How the neutral diffusive flux components are computed:
-
- The vertical flux component is split into diagonal (3,3) and
- off-diagonal (3,1) and (3,2) terms. The off-diagonal (3,1) and (3,2)
- terms are included explicitly in time. The main contribution from the
- (3,3) term to the time tendency is included implicitly in time
- along with the usual contribution from diapycnal processes
- (vertical mixing schemes). This is the K33_implicit term.
- This approach is necessary with high vertical resolution, as
- noted by Cox (1987). However, splitting the vertical flux into
- an implicit and explicit piece compromises the
- integrity of the vertical flux component (see Griffies et al. 1998).
- So to minimize the disparity engendered by this split, the portion of
- K33 that can be stably included explicitly in time is computed along
- with the (3,1) and (3,2) terms.
-
- All other terms in the mixing tensor are included explicitly in time
- using a forward time step as required for temporal stability of
- numerical diffusive processes.
-
- The off-diagonal terms in the horizontal flux components, and all terms
- in the vertical flux component, are tapered in regions of steep neutral
- slope according to the requirements of linear stability. MOM allows for
- choice of two tapering schemes:
-
- (a) the tanh taper of Danabasoglu and McWilliams (1995)
- (b) the quadratic scheme of Gerdes, Koberle, and Willebrand (1991)
-
- Linear stability is far less stringent on the diagonal (1,1) and (2,2)
- part of the horizontal flux. Indeed, these terms in practice need
- not be tapered in steep sloped regions. The namelist
- neutral_taper_diagonal=.false. keeps the diagnonal terms maintained
- for all neutral slopes. This approach assists in reducing numerical
- noise in regions where the physical system experiences a lot of
- diapycnal mixing anyhow.
-
----How the skew diffusive flux components are computed:
-
- The GM skew flux components are purely off-diagonal.
- They are generally tapered when neutral slope
- is large (neutral_physics_simple=.false).
- Doing so maintains a nontrivial GM slumping effect even when the
- neutral slopes are vertical. The alternative neutral_physics_simple=.true.
- is the approach used in MOM3, whereby GM effects are removed
- in steep sloped regions. neutral_physics_simple=.false. is
- less efficient, but has been seen to yield superior simulations.
-
-
-
-
-
-
-
-
-
neutral_blayer
-
-
-DESCRIPTION
-
-
- Subroutine computes the boundary layer as determined by
- 1. steep neutral slopes
- 2. depth within which typical mesoscale eddies are partially outcropped
- 3. depth within which vertical mixing scheme (e.g., kpp) computes a boundary layer
-
- Note: Only consider surface boundary layers here.
-
- Scheme originally coded for MOM4.0 by Stephen.Griffies
- with help for optimization by Russell.Fiedler@csiro.au.
-
-
-
-
-
-
-
-
-
fz_terms
-
-
-DESCRIPTION
-
-
- Subroutine computes the tracer independent pieces of the vertical
- flux component. As a result of this routine,
- Array tensor_31 = x-diffusivity*slope (m^2/sec) for fz
- Array tensor_32 = y-diffusivity*slope (m^2/sec) for fz
-
- K33 is the (3,3) term in small angle Redi diffusion tensor.
- It is broken into an explicit in time piece and implicit
- in time piece. It is weighted by density for non-Boussinesq
- and rho0 for Boussinesq.
-
- K33 has units (kg/m^3)*m^2/sec.
-
- Also will compute the squared Eady growth rate, with the maximum
- slope contributing to this growth rate set by smax.
-
-
-
-
-
-
-
-
fz_terms_diag
-
-
-DESCRIPTION
-
-
- For saving the contributions from GM and Redi separately, it is
- necessary to compute the tensor_redi component here.
-
- We do so here, reproducing some lines of code from fz_terms,
- to reduce minimize the need to impinge on the case when NOT
- using this generally expensive (memory and computational)
- diagnostic.
-
- This routine MUST be called prior to fz_terms, since we use
- tensor_31 and tensor_32 in their raw slope forms here.
-
-
-
-
-
-
-
-
-
fx_flux
-
-
-DESCRIPTION
-
-
- Subroutine computes the i-directed neutral physics tracer flux component.
- Compute this component for all tracers at level k.
-
- fx has physical dimensions (area*diffusivity*density*tracer gradient)
-
-
-
-
-
-
-
-
-
fx_flux_diag
-
-
-DESCRIPTION
-
-
- Subroutine computes the i-directed neutral physics tracer flux component
- for Redi separately from GM, in order to diagnose GM and Redi
- fluxes independent of one another.
-
- Compute this component for all tracers at level k.
-
- fx has physical dimensions (area*diffusivity*density*tracer gradient)
-
-
-
-
-
-
-
-
-
fy_flux
-
-
-DESCRIPTION
-
-
- Subroutine computes the j-directed neutral physics tracer flux component.
- Compute this component for all tracers at level k.
-
- fy has physical dimensions (area*diffusivity*density*tracer gradient)
-
-
-
-
-
-
-
-
-
fy_flux_diag
-
-
-DESCRIPTION
-
-
- Subroutine computes the j-directed neutral physics tracer flux component
- for Redi separately, in order to diagnose GM and Redi contributions
- independent of one another.
-
- Compute this component for all tracers at level k.
-
- fy has physical dimensions (area*diffusivity*density*tracer gradient)
-
-
-
-
-
-
-
-
-
fz_flux
-
-
-DESCRIPTION
-
-
- Subroutine computes the vertical neutral physics tracer flux component.
- Compute this component for all tracers at level k.
- Surface and bottom boundary condition fz(k=0)=fz(k=kmt(i,j))=0
-
- fz has physical dimensions (density*diffusivity*tracer gradient)
-
-
-
-
-
-
-
-
-
fz_flux_diag
-
-
-DESCRIPTION
-
-
- For diagnosing the GM and Redi pieces separately.
- Compute this component for all tracers at level k.
- Surface and bottom boundary condition fz(k=0)=fz(k=kmt(i,j))=0
-
- fz has physical dimensions (density*diffusivity*tracer gradient)
-
-
-
-
-
-
-
-
-
gm_velocity
-
-
-DESCRIPTION
-
-
- Subroutine computes GM eddy-induced velocity field for diagnostics.
- Compute ustar and vstar at U-cell point, and wstar at T-cell bottom.
-
- Do a two-point average rather than more democratic four-point avg
- in order to avoid having to call mpp_update domains on tensor_31 and
- tensor_32. The 0.5 factor is due to the two-point average.
-
- Note that this algorithm is ad hoc. Researchers interested in this
- field may wish to test alternatives.
-
-
-
-
-
-
-
-
slope_function_gm
-
-
-DESCRIPTION
-
-
- Function for defining effective slope in diagnostic GM velocity
- calculation. Used only for diagnostic purposes.
-
-
-
-
-
-
-
-
nphysics_diagnostics
-
-
-DESCRIPTION
-
-
- Send some diagnostics to diagnostics manager.
-
-
-
-
-
-
-
-
ocean_nphysicsA_restart
-
-
-DESCRIPTION
-
-
- Write out restart files registered through register_restart_file
-
-
-
-
-
-
-
-
ocean_nphysicsA_end
-
-
-DESCRIPTION
-
-
- Write to restart.
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_nphysicsA_nml
-
-
-
-
-
-use_this_module
-
-
- Must be true to use this module. Default is false.
-
-[logical]
-
-
-debug_this_module
-
-
- For printing starting and ending checksums for restarts
-
-[logical]
-
-
-use_gm_skew
-
-
- Must be true to use GM skewsion. Set to false if wish to
- incorporate the "GM-effect" through form drag, as in
- ocean_form_drag module. Default use_gm_skew=.true.
-
-[logical]
-
-
-diffusion_all_explicit
-
-
- To compute all contributions from neutral diffusion explicitly in time, including
- the K33 diagonal piece. This approach is available only when have small time
- steps and/or running with just a single tracer. It is for testing purposes.
-
-[logical]
-
-
-neutral_physics_simple
-
-
- If .true. then must have aredi_equal_agm=.true.. The horizontal fluxes are then
- computed as horizontal downgradient diffusive fluxes regardless the neutral slope.
- This approach precluds one from being able to have the GM-skew fluxes remain active
- in the steep sloped regions, thus shutting off their effects to reduce the slopes
- of isopycnals in convective and mixed layer regimes. It is for this reason that
- neutral_physics_simple=.false. is the recommended default in MOM.
-
-[logical]
-
-
-neutral_physics_limit
-
-
- When tracer falls outside a specified range, revert to horizontal
- diffusive fluxes at this cell. This is an ad hoc and incomplete attempt
- to maintain monotonicity with the neutral physics scheme.
- Default neutral_physics_limit=.true.
-
-[logical]
-
-
-tmask_neutral_on
-
-
- If .true. then this logical reduces the neutral fluxes to
- horizontal/vertical diffusion next to boundaries.
- This approach has been found to reduce spurious
- extrema resulting from truncation of triads used to compute
- a neutral flux component. Default tmask_neutral_on=.false.
-
-[logical]
-
-
-dm_taper
-
-
- Set to true to use the tanh tapering scheme of Danabasoglu and McWilliams.
- Default is true.
-
-[logical]
-
-
-gkw_taper
-
-
- Set to true to use the quadradic tapering scheme of Gerdes, Koberle, and Willebrand.
- Default is false.
-
-[logical]
-
-
-neutral_linear_gm_taper
-
-
- If .true. then with neutral_physics_simple=.false., will linearly taper GM
- skew fluxes towards the surface within regions of steep neutral slopes.
- This approach leads to a constant horizontal eddy-induced velocity in
- the steeply sloping regions and is recommended for realistic simulations.
-
-[logical]
-
-
-neutral_sine_taper
-
-
- If .true. then with neutral_physics_simple=.false., will apply a sine-taper
- to GM and neutral diffusive fluxes in regions where the penetration depth
- of eddies is deeper than the grid point. This method is essential for
- fine vertical resolution grids.
-
-[logical]
-
-
-turb_blayer_min
-
-
- Minimum depth of a surface turbulent boundary layer
- used in the transition of the neutral physics fluxes
- to the surface. Note that in MOM4.0,
- turb_blayer_min was always set to zero.
-
-[real]
-
-
-neutral_blayer_diagnose
-
-
- Diagnose properties of the neutral physics boundary layer, whether have
- neutral_linear_gm_taper or neutral_sine_taper true or not.
-
-[logical]
-
-
-neutral_taper_diagonal
-
-
- For cases with neutral_physics_simple=.false., then neutral_taper_diagonal=.true.
- will taper the diagonal pieces of the horizontal flux components when neutral slopes
- are steep. With neutral_taper_diagonal=.false., then the horizontal flux components will
- remain enabled for all slopes, thus producing horizontal downgradient diffusion in
- regions of vertical neutral directions.
-
-[logical, units: dimensionless]
-
-
-
-
-
-
-
-
-
-
-
REFERENCES
-
-
-
-
- S.M. Griffies, A. Gnanadesikan, R.C. Pacanowski, V. Larichev,
- J.K. Dukowicz, and R.D. Smith
- Isoneutral diffusion in a z-coordinate ocean model
- Journal of Physical Oceanography (1998) vol 28 pages 805-830
-
-
- S.M. Griffies
- The Gent-McWilliams Skew-flux
- Journal of Physical Oceanography (1998) vol 28 pages 831-841
-
-
- S.M. Griffies
- Fundamentals of Ocean Climate Models (2004)
- Princeton University Press
-
-
- S.M. Griffies, Elements of MOM (2012)
-
-
- G. Danabasoglu and J. C. McWilliams
- Sensitivity of the global ocean circulation to
- parameterizations of mesoscale tracer transports
- Journal of Climate (1995) vol 8 pages 2967--2987
-
-
- Gerdes, Koberle, and Willebrand
- The influence of numerical advection schemes on the results of ocean
- general circulation models, Climate Dynamics (1991), vol. 5,
- pages 211--226.
-
-
-
-
-
-
-
-
NOTES
-
-
- Numerical implementation of the flux components follows the triad
- approach documented in the references and implemented in MOM2 and MOM3.
- The MOM algorithm accounts for partial bottom cells and generalized
- orthogonal horizontal coordinates.
-
-
- neutral_physics_simple=.true. requires aredi_equal_agm=.true.
- neutral_physics_simple=.true. results in down-gradient
- horizontal flux components. This setting reduces the overall cost
- of the neutral physics scheme, but it is not used at GFDL
- anymore, since we favor methods whereby treatment of GM and Redi
- in the boundary layers are distinct.
-
-
- In steep slope regions, neutral diffusive fluxes are tapered to
- zero with the tanh taper of Danabasoglu and McWilliams (1995) or the
- quadratic scheme of Gerdes, Koberle, and Willebrand. However, if
- neutral_physics_simple=.false., the GM skew-diffusive fluxes
- can remain nonzero if have neutral_linear_gm_taper=.true.
-
-
-
diff --git a/src/mom5/ocean_param/neutral/ocean_nphysicsA.xml b/src/mom5/ocean_param/neutral/ocean_nphysicsA.xml
deleted file mode 100644
index d3362f4c69..0000000000
--- a/src/mom5/ocean_param/neutral/ocean_nphysicsA.xml
+++ /dev/null
@@ -1,278 +0,0 @@
-
-
- Stephen M. Griffies
- Russell Fiedler
- Tim Leslie
-
- Thickness weighted and density weighted time tendency for tracer
- from Laplacian neutral diffusion + Laplacian GM skew-diffusion.
-
- This module computes the cell thickness weighted and density
- weighted tracer tendency from small angle Laplacian neutral diffusion
- plus Laplacian GM skew-diffusion. The algorithms are based on
- MOM4p0d methods. The fundamental differences from the ocean_nphysicsB
- methods relate to the handling of fluxes near the domain boundaries.
-
- S.M. Griffies, A. Gnanadesikan, R.C. Pacanowski, V. Larichev,
- J.K. Dukowicz, and R.D. Smith
- Isoneutral diffusion in a z-coordinate ocean model
- Journal of Physical Oceanography (1998) vol 28 pages 805-830
-
- S.M. Griffies
- The Gent-McWilliams Skew-flux
- Journal of Physical Oceanography (1998) vol 28 pages 831-841
-
- S.M. Griffies
- Fundamentals of Ocean Climate Models (2004)
- Princeton University Press
-
- S.M. Griffies, Elements of MOM (2012)
-
- G. Danabasoglu and J. C. McWilliams
- Sensitivity of the global ocean circulation to
- parameterizations of mesoscale tracer transports
- Journal of Climate (1995) vol 8 pages 2967--2987
-
- Gerdes, Koberle, and Willebrand
- The influence of numerical advection schemes on the results of ocean
- general circulation models, Climate Dynamics (1991), vol. 5,
- pages 211--226.
-
- Numerical implementation of the flux components follows the triad
- approach documented in the references and implemented in MOM2 and MOM3.
- The MOM algorithm accounts for partial bottom cells and generalized
- orthogonal horizontal coordinates.
-
- neutral_physics_simple=.true. requires aredi_equal_agm=.true.
- neutral_physics_simple=.true. results in down-gradient
- horizontal flux components. This setting reduces the overall cost
- of the neutral physics scheme, but it is not used at GFDL
- anymore, since we favor methods whereby treatment of GM and Redi
- in the boundary layers are distinct.
-
- In steep slope regions, neutral diffusive fluxes are tapered to
- zero with the tanh taper of Danabasoglu and McWilliams (1995) or the
- quadratic scheme of Gerdes, Koberle, and Willebrand. However, if
- neutral_physics_simple=.false., the GM skew-diffusive fluxes
- can remain nonzero if have neutral_linear_gm_taper=.true.
-
- Must be true to use this module. Default is false.
-
- For printing starting and ending checksums for restarts
-
- Must be true to use GM skewsion. Set to false if wish to
- incorporate the "GM-effect" through form drag, as in
- ocean_form_drag module. Default use_gm_skew=.true.
-
- To compute all contributions from neutral diffusion explicitly in time, including
- the K33 diagonal piece. This approach is available only when have small time
- steps and/or running with just a single tracer. It is for testing purposes.
-
- If .true. then must have aredi_equal_agm=.true.. The horizontal fluxes are then
- computed as horizontal downgradient diffusive fluxes regardless the neutral slope.
- This approach precluds one from being able to have the GM-skew fluxes remain active
- in the steep sloped regions, thus shutting off their effects to reduce the slopes
- of isopycnals in convective and mixed layer regimes. It is for this reason that
- neutral_physics_simple=.false. is the recommended default in MOM.
-
- When tracer falls outside a specified range, revert to horizontal
- diffusive fluxes at this cell. This is an ad hoc and incomplete attempt
- to maintain monotonicity with the neutral physics scheme.
- Default neutral_physics_limit=.true.
-
- If .true. then this logical reduces the neutral fluxes to
- horizontal/vertical diffusion next to boundaries.
- This approach has been found to reduce spurious
- extrema resulting from truncation of triads used to compute
- a neutral flux component. Default tmask_neutral_on=.false.
-
- Set to true to use the tanh tapering scheme of Danabasoglu and McWilliams.
- Default is true.
-
- Set to true to use the quadradic tapering scheme of Gerdes, Koberle, and Willebrand.
- Default is false.
-
- If .true. then with neutral_physics_simple=.false., will linearly taper GM
- skew fluxes towards the surface within regions of steep neutral slopes.
- This approach leads to a constant horizontal eddy-induced velocity in
- the steeply sloping regions and is recommended for realistic simulations.
-
- If .true. then with neutral_physics_simple=.false., will apply a sine-taper
- to GM and neutral diffusive fluxes in regions where the penetration depth
- of eddies is deeper than the grid point. This method is essential for
- fine vertical resolution grids.
-
- Minimum depth of a surface turbulent boundary layer
- used in the transition of the neutral physics fluxes
- to the surface. Note that in MOM4.0,
- turb_blayer_min was always set to zero.
-
- Diagnose properties of the neutral physics boundary layer, whether have
- neutral_linear_gm_taper or neutral_sine_taper true or not.
-
- For cases with neutral_physics_simple=.false., then neutral_taper_diagonal=.true.
- will taper the diagonal pieces of the horizontal flux components when neutral slopes
- are steep. With neutral_taper_diagonal=.false., then the horizontal flux components will
- remain enabled for all slopes, thus producing horizontal downgradient diffusion in
- regions of vertical neutral directions.
-
- Initialize the neutral physics module by registering fields for
- diagnostic output and performing some numerical checks to see
- that namelist settings are appropriate.
-
- This function computes the thickness weighted and density weighted
- time tendency for tracer from neutral physics. Full discussion
- and details are provided by Griffies (2004).
-
- Here is a brief summary.
-
----How the neutral diffusive flux components are computed:
-
- The vertical flux component is split into diagonal (3,3) and
- off-diagonal (3,1) and (3,2) terms. The off-diagonal (3,1) and (3,2)
- terms are included explicitly in time. The main contribution from the
- (3,3) term to the time tendency is included implicitly in time
- along with the usual contribution from diapycnal processes
- (vertical mixing schemes). This is the K33_implicit term.
- This approach is necessary with high vertical resolution, as
- noted by Cox (1987). However, splitting the vertical flux into
- an implicit and explicit piece compromises the
- integrity of the vertical flux component (see Griffies et al. 1998).
- So to minimize the disparity engendered by this split, the portion of
- K33 that can be stably included explicitly in time is computed along
- with the (3,1) and (3,2) terms.
-
- All other terms in the mixing tensor are included explicitly in time
- using a forward time step as required for temporal stability of
- numerical diffusive processes.
-
- The off-diagonal terms in the horizontal flux components, and all terms
- in the vertical flux component, are tapered in regions of steep neutral
- slope according to the requirements of linear stability. MOM allows for
- choice of two tapering schemes:
-
- (a) the tanh taper of Danabasoglu and McWilliams (1995)
- (b) the quadratic scheme of Gerdes, Koberle, and Willebrand (1991)
-
- Linear stability is far less stringent on the diagonal (1,1) and (2,2)
- part of the horizontal flux. Indeed, these terms in practice need
- not be tapered in steep sloped regions. The namelist
- neutral_taper_diagonal=.false. keeps the diagnonal terms maintained
- for all neutral slopes. This approach assists in reducing numerical
- noise in regions where the physical system experiences a lot of
- diapycnal mixing anyhow.
-
----How the skew diffusive flux components are computed:
-
- The GM skew flux components are purely off-diagonal.
- They are generally tapered when neutral slope
- is large (neutral_physics_simple=.false).
- Doing so maintains a nontrivial GM slumping effect even when the
- neutral slopes are vertical. The alternative neutral_physics_simple=.true.
- is the approach used in MOM3, whereby GM effects are removed
- in steep sloped regions. neutral_physics_simple=.false. is
- less efficient, but has been seen to yield superior simulations.
-
-
- Subroutine computes the boundary layer as determined by
- 1. steep neutral slopes
- 2. depth within which typical mesoscale eddies are partially outcropped
- 3. depth within which vertical mixing scheme (e.g., kpp) computes a boundary layer
-
- Note: Only consider surface boundary layers here.
-
- Scheme originally coded for MOM4.0 by Stephen.Griffies
- with help for optimization by Russell.Fiedler@csiro.au.
-
-
- Subroutine computes the tracer independent pieces of the vertical
- flux component. As a result of this routine,
- Array tensor_31 = x-diffusivity*slope (m^2/sec) for fz
- Array tensor_32 = y-diffusivity*slope (m^2/sec) for fz
-
- K33 is the (3,3) term in small angle Redi diffusion tensor.
- It is broken into an explicit in time piece and implicit
- in time piece. It is weighted by density for non-Boussinesq
- and rho0 for Boussinesq.
-
- K33 has units (kg/m^3)*m^2/sec.
-
- Also will compute the squared Eady growth rate, with the maximum
- slope contributing to this growth rate set by smax.
-
- For saving the contributions from GM and Redi separately, it is
- necessary to compute the tensor_redi component here.
-
- We do so here, reproducing some lines of code from fz_terms,
- to reduce minimize the need to impinge on the case when NOT
- using this generally expensive (memory and computational)
- diagnostic.
-
- This routine MUST be called prior to fz_terms, since we use
- tensor_31 and tensor_32 in their raw slope forms here.
-
-
- Subroutine computes the i-directed neutral physics tracer flux component.
- Compute this component for all tracers at level k.
-
- fx has physical dimensions (area*diffusivity*density*tracer gradient)
-
-
- Subroutine computes the i-directed neutral physics tracer flux component
- for Redi separately from GM, in order to diagnose GM and Redi
- fluxes independent of one another.
-
- Compute this component for all tracers at level k.
-
- fx has physical dimensions (area*diffusivity*density*tracer gradient)
-
-
- Subroutine computes the j-directed neutral physics tracer flux component.
- Compute this component for all tracers at level k.
-
- fy has physical dimensions (area*diffusivity*density*tracer gradient)
-
-
- Subroutine computes the j-directed neutral physics tracer flux component
- for Redi separately, in order to diagnose GM and Redi contributions
- independent of one another.
-
- Compute this component for all tracers at level k.
-
- fy has physical dimensions (area*diffusivity*density*tracer gradient)
-
-
- Subroutine computes the vertical neutral physics tracer flux component.
- Compute this component for all tracers at level k.
- Surface and bottom boundary condition fz(k=0)=fz(k=kmt(i,j))=0
-
- fz has physical dimensions (density*diffusivity*tracer gradient)
-
-
- For diagnosing the GM and Redi pieces separately.
- Compute this component for all tracers at level k.
- Surface and bottom boundary condition fz(k=0)=fz(k=kmt(i,j))=0
-
- fz has physical dimensions (density*diffusivity*tracer gradient)
-
-
- Subroutine computes GM eddy-induced velocity field for diagnostics.
- Compute ustar and vstar at U-cell point, and wstar at T-cell bottom.
-
- Do a two-point average rather than more democratic four-point avg
- in order to avoid having to call mpp_update domains on tensor_31 and
- tensor_32. The 0.5 factor is due to the two-point average.
-
- Note that this algorithm is ad hoc. Researchers interested in this
- field may wish to test alternatives.
-
- Function for defining effective slope in diagnostic GM velocity
- calculation. Used only for diagnostic purposes.
-
- Send some diagnostics to diagnostics manager.
-
- Write out restart files registered through register_restart_file
-
- Write to restart.
-
diff --git a/src/mom5/ocean_param/neutral/ocean_nphysicsB.F90 b/src/mom5/ocean_param/neutral/ocean_nphysicsB.F90
index 244fc1b368..4b90414dc8 100644
--- a/src/mom5/ocean_param/neutral/ocean_nphysicsB.F90
+++ b/src/mom5/ocean_param/neutral/ocean_nphysicsB.F90
@@ -411,9 +411,9 @@ module ocean_nphysicsB_mod
integer :: neutralrho_nk
character(len=128) :: version=&
- '$Id: ocean_nphysicsB.F90,v 1.1.2.2 2012/05/17 13:41:47 smg Exp $'
+ '$Id: ocean_nphysicsB.F90,v 20.0 2013/12/14 00:14:38 fms Exp $'
character (len=128) :: tagname = &
- '$Name: mom5_siena_08jun2012_smg $'
+ '$Name: tikal $'
character(len=*), parameter :: FILENAME=&
__FILE__
diff --git a/src/mom5/ocean_param/neutral/ocean_nphysicsB.html b/src/mom5/ocean_param/neutral/ocean_nphysicsB.html
deleted file mode 100644
index 2713c9f11a..0000000000
--- a/src/mom5/ocean_param/neutral/ocean_nphysicsB.html
+++ /dev/null
@@ -1,678 +0,0 @@
-
-
-
-Module ocean_nphysicsB_mod
-
-
-
-
-PUBLIC INTERFACE
-
- ~ PUBLIC ROUTINES
- ~ NAMELIST
-
-
- Thickness weighted and density weighted time tendency for tracer
- from Laplacian neutral diffusion + Laplacian GM skew-diffusion.
-
-
-
-
-
- This module computes the cell thickness weighted and density
- weighted tracer tendency from small angle Laplacian neutral diffusion
- plus Laplacian GM skew-diffusion. The methods here differ from
- ocean_nphysicsA in the treatment of fluxes in the boundary
- regions. This module is experimental, and should be used with caution.
-
- Initialize the neutral physics module by registering fields for
- diagnostic output and performing some numerical checks to see
- that namelist settings are appropriate.
-
-
-
-
-
-
-
-
nphysicsB
-
-
-DESCRIPTION
-
-
- This function computes the thickness weighted and density weighted
- time tendency for tracer from neutral physics. Full discussion
- and details are provided by Griffies (2004,2005).
-
- Here is a brief summary of the temporal treatment.
-
----How the neutral diffusive flux components are computed:
-
- The vertical flux component is split into diagonal (3,3) and
- off-diagonal (3,1) and (3,2) terms. The off-diagonal (3,1) and (3,2)
- terms are included explicitly in time. The main contribution from the
- (3,3) term to the time tendency is included implicitly in time
- along with the usual contribution from diapycnal processes
- (vertical mixing schemes). This is the K33_implicit term.
- This approach is necessary with high vertical resolution, as
- noted by Cox (1987). However, splitting the vertical flux into
- an implicit and explicit piece compromises the
- integrity of the vertical flux component (see Griffies et al. 1998).
- So to minimize the disparity engendered by this split, the portion of
- K33 that can be stably included explicitly in time is computed along
- with the (3,1) and (3,2) terms.
-
- All other terms in the mixing tensor are included explicitly in time
- using a forward time step as required for temporal stability of
- numerical diffusive processes.
-
-
-
-
-
-
-
-
-
neutral_blayer
-
-
-DESCRIPTION
-
-
-
- This subroutine computes the "neutral boundary layers" based on
- the formulation of Ferrari and McWilliams (2006). See full
- details and discussion in Elements of MOM4p1 by Griffies (2009).
-
- Five vertical regions are identified by Ferrari and McWilliams:
- We simplify these regimes by melding the turbulent and transition
- regimes into an overall neutral boundary layer regime, within which
- the streamfunction is linearly tapers to zero moving towards the
- boundary. We also ignore the bottom regimes, as these are poorly
- resolved in most models, and the neutral physics fluxes are
- typically small at the bottom.
-
- (1) Surface turbulent region:
- Depth ("h" in Ferrari and McWilliams notation) dominated by
- 3d turbulent processes. This depth is taken from surf_blthick,
- as set by the KPP scheme or another mixed layer scheme.
- A minimum is set as surf_turb_thick_min and is specified
- as a nml parameter in ocean_nphysicsB_nml.
-
- In order to use a low frequency version of the boundary layer
- thickness, we damp its evolution with a damping time scale
- neutral_damping_time (days).
-
- In the code, "h_surf"= surf_turb_thick
-
- (2) Surface transition region:
- Thickness ("D" in Ferrari and McWilliams notation)
- between the turbulent surface boundary layer and the interior.
- This transition layer thickness is determined by the product of the
- neutral slope and first baroclinic Rossby radius. This specification
- is ad hoc, and more fundamental theories are welcome.
-
- In the code, "D_surf"= surf_trans_thick
-
-
- Within a "boundary layer" region set by the sum of
- surf_turb_thick plus surf_trans_thick, the eddy
- induced velocity is assumed to have zero vertical shear,
- which means the quasi-Stokes streamfunction is linear with
- depth. The neutral diffusive fluxes are reduced to horizontal
- downgradient diffusion, with "horizontal" defined according
- to surfaces of constant vertical coordinate.
-
-
- (3) Interior region:
- Where neutral diffusion and GM skew-diffusion are taken
- from their unmodified form.
-
- Only use the 31 and 32 triads for this computation since the
- 13 and 23 triads require extra slope calculations, and
- so will add lots of computational cost. It is felt that the
- 31 and 32 triads are sufficient for this calculation, in
- a similar manner that they are used for the calculation of
- the non-constant diffusivities.
-
- Scheme coded for MOM4p1 by Stephen.Griffies
- Version: March2006
- Simplified version: June2008
-
-
-
-
-
-
-
-
-
fz_terms
-
-
-DESCRIPTION
-
-
- Subroutine computes the tracer independent pieces of the vertical
- flux component. As a result of this routine,
- Array tensor_31 = x-diffusivity*slope (m^2/sec) for fz
- Array tensor_32 = y-diffusivity*slope (m^2/sec) for fz
-
- K33 is the (3,3) term in small angle Redi diffusion tensor.
- It is broken into an explicit in time piece and implicit
- in time piece. It is weighted by density for non-Boussinesq
- and rho0 for Boussinesq.
-
- K33 has units (kg/m^3)*m^2/sec.
-
- Also will compute the squared Eady growth rate, with the maximum
- slope contributing to this growth rate set by smax.
-
-
-
-
-
-
-
-
fz_terms_diag
-
-
-DESCRIPTION
-
-
- For saving the contributions from GM and Redi separately, it is
- necessary to compute the tensor_redi component here.
-
- We do so here, reproducing some lines of code from fz_terms,
- to reduce minimize the need to impinge on the case when NOT
- using this generally expensive (memory and computational)
- diagnostic.
-
- This routine MUST be called prior to fz_terms, since we use
- tensor_31 and tensor_32 in their raw slope forms here.
-
-
-
-
-
-
-
-
-
fx_flux
-
-
-DESCRIPTION
-
-
- Subroutine computes the i-directed neutral physics tracer flux component.
- Compute this component for all tracers at level k.
-
- fx has physical dimensions (area*diffusivity*density*tracer gradient)
-
-
-
-
-
-
-
-
-
fx_flux_diag
-
-
-DESCRIPTION
-
-
- Subroutine computes the i-directed neutral physics tracer flux component
- for Redi separately from GM, in order to diagnose GM and Redi
- fluxes independent of one another.
-
- Compute this component for all tracers at level k.
-
- fx has physical dimensions (area*diffusivity*density*tracer gradient)
-
-
-
-
-
-
-
-
-
fy_flux
-
-
-DESCRIPTION
-
-
- Subroutine computes the j-directed neutral physics tracer flux component.
- Compute this component for all tracers at level k.
-
- fy has physical dimensions (area*diffusivity*density*tracer gradient)
-
-
-
-
-
-
-
-
-
fy_flux_diag
-
-
-DESCRIPTION
-
-
- Subroutine computes the j-directed neutral physics tracer flux component
- for Redi separately, in order to diagnose GM and Redi contributions
- independent of one another.
-
- Compute this component for all tracers at level k.
-
- fy has physical dimensions (area*diffusivity*density*tracer gradient)
-
-
-
-
-
-
-
-
-
fz_flux
-
-
-DESCRIPTION
-
-
- Subroutine computes the vertical neutral physics tracer flux component.
- Compute this component for all tracers at level k.
- Surface and bottom boundary condition fz(k=0)=fz(k=kmt(i,j))=0
-
- fz has physical dimensions (density*diffusivity*tracer gradient)
-
-
-
-
-
-
-
-
-
fz_flux_diag
-
-
-DESCRIPTION
-
-
- For diagnosing the GM and Redi pieces separately.
- Compute this component for all tracers at level k.
- Surface and bottom boundary condition fz(k=0)=fz(k=kmt(i,j))=0
-
- fz has physical dimensions (density*diffusivity*tracer gradient)
-
-
-
-
-
-
-
-
-
nphysics_diagnostics
-
-
-DESCRIPTION
-
-
- Send some diagnostics to diagnostics manager.
-
-
-
-
-
-
-
-
neutral_chksums
-
-
-DESCRIPTION
-
-
- Write some checksums.
-
-
-
-
-
-
-
-
ocean_nphysicsB_restart
-
-
-DESCRIPTION
-
-
- Write out restart files registered through register_restart_file
-
-
-
-
-
-
-
-
ocean_nphysicsB_end
-
-
-DESCRIPTION
-
-
- Write to restart.
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_nphysicsB_nml
-
-
-
-
-
-use_this_module
-
-
- Must be true to use this module. Default is false.
-
-[logical]
-
-
-debug_this_module
-
-
- For printing starting and ending checksums for restarts
-
-[logical]
-
-
-use_gm_skew
-
-
- Must be true to use GM skewsion. Set to false if wish to
- incorporate the "GM-effect" through form drag, as in
- ocean_form_drag module. Default use_gm_skew=.true.
-
-[logical]
-
-
-diffusion_all_explicit
-
-
- To compute all contributions from neutral diffusion explicitly in time, including
- the K33 diagonal piece. This approach is available only when have small time
- steps and/or running with just a single tracer. It is for testing purposes.
-
-[logical]
-
-
-neutral_physics_limit
-
-
- When tracer falls outside a specified range, revert to horizontal
- diffusive fluxes at this cell. This is an ad hoc and incomplete attempt
- to maintain monotonicity with the neutral physics scheme.
- Default neutral_physics_limit=.true.
-
-[logical]
-
-
-tmask_neutral_on
-
-
- If .true. then this logical reduces the neutral fluxes to
- horizontal/vertical diffusion next to boundaries.
- This approach has been found to reduce spurious
- extrema resulting from truncation of triads used to compute
- a neutral flux component. Default tmask_neutral_on=.false.
-
-[logical]
-
-
-surf_turb_thick_min_k
-
-
- Minimum number of k-levels in surface turbulent boundary
- layer used in the transition of the neutral physics fluxes
- to the surface. Default surf_turb_thick_min_k = 2.
-
-[integer]
-
-
-surf_turb_thick_min
-
-
- Minimum thickness of surface turbulent boundary layer
- used in the transition of the neutral physics fluxes
- to the surface. Default surf_turb_thick_min=20m.
-
-[real]
-
-
-neutral_damping_time
-
-
- The damping time used for determining the effective surface
- boundary layer thickness from other portions of
- the model. Default neutral_damping_time=10days.
-
-[real, units: days]
-
-
-nblayer_smooth
-
-
- For smoothing the neutral blayer fields. This is useful
- when aiming to produce a smooth quasi-stokes streamfunction
- within the boundary layers. Default is nblayer_smooth=.true.
-
-[logical]
-
-
-vel_micom_smooth
-
-
- Velocity scale that is used for computing the MICOM Laplacian mixing
- coefficient used in the Laplacian smoothing of neutral blayer fields.
-
-[real, units: m/sec]
-
-
-
-
-
-
-
-
-
-
-
REFERENCES
-
-
-
-
- S.M. Griffies, A. Gnanadesikan, R.C. Pacanowski, V. Larichev,
- J.K. Dukowicz, and R.D. Smith
- Isoneutral diffusion in a z-coordinate ocean model
- Journal of Physical Oceanography (1998) vol 28 pages 805-830
-
-
- S.M. Griffies
- The Gent-McWilliams Skew-flux
- Journal of Physical Oceanography (1998) vol 28 pages 831-841
-
-
- R. Ferrari and J.C. McWilliams and Canuto and Dubovikov
- Parameterization of eddy fluxes near oceanic boundaries
- Journal of Climate (2008).
-
-
- Large etal (1997), Journal of Physical Oceanography,
- pages 2418-2447
-
-
- S.M. Griffies
- Fundamentals of Ocean Climate Models (2004)
- Princeton University Press
-
-
- S.M. Griffies, Elements of MOM (2012)
-
-
-
-
-
-
-
-
NOTES
-
-
- Revisions made for MOM4p1 in Sept 2005, Jan/Feb 2006,
- and June 2008 by Stephen.Griffies. The June 2008
- revision greatly simplified the boundary layer formulation
- from Ferrari and McWilliams, whereby the quadratic transition
- layer is eliminated, thus removing the need to match vertical
- derivatives of the streamfunction. The matching conditions
- implied by the transition zone added a tremendous amount
- of code that was not seen to be critical for the purpose
- of producing a reasonably smooth streamfunction.
-
-
- Numerical implementation of the flux components follows the triad
- approach documented in the references and implemented in MOM2 and MOM3.
- The MOM algorithm accounts for partial bottom cells and generalized
- orthogonal horizontal coordinates.
-
-
- Note: the option neutral_physics_simple is not supported in this
- module. Use nphysicA for that option.
-
-
-
diff --git a/src/mom5/ocean_param/neutral/ocean_nphysicsB.xml b/src/mom5/ocean_param/neutral/ocean_nphysicsB.xml
deleted file mode 100644
index a094227aef..0000000000
--- a/src/mom5/ocean_param/neutral/ocean_nphysicsB.xml
+++ /dev/null
@@ -1,269 +0,0 @@
-
-
- Stephen M. Griffies
- Russell Fiedler
- Tim Leslie
-
- Thickness weighted and density weighted time tendency for tracer
- from Laplacian neutral diffusion + Laplacian GM skew-diffusion.
-
- This module computes the cell thickness weighted and density
- weighted tracer tendency from small angle Laplacian neutral diffusion
- plus Laplacian GM skew-diffusion. The methods here differ from
- ocean_nphysicsA in the treatment of fluxes in the boundary
- regions. This module is experimental, and should be used with caution.
-
- S.M. Griffies, A. Gnanadesikan, R.C. Pacanowski, V. Larichev,
- J.K. Dukowicz, and R.D. Smith
- Isoneutral diffusion in a z-coordinate ocean model
- Journal of Physical Oceanography (1998) vol 28 pages 805-830
-
- S.M. Griffies
- The Gent-McWilliams Skew-flux
- Journal of Physical Oceanography (1998) vol 28 pages 831-841
-
- R. Ferrari and J.C. McWilliams and Canuto and Dubovikov
- Parameterization of eddy fluxes near oceanic boundaries
- Journal of Climate (2008).
-
- Large etal (1997), Journal of Physical Oceanography,
- pages 2418-2447
-
- S.M. Griffies
- Fundamentals of Ocean Climate Models (2004)
- Princeton University Press
-
- S.M. Griffies, Elements of MOM (2012)
-
- Revisions made for MOM4p1 in Sept 2005, Jan/Feb 2006,
- and June 2008 by Stephen.Griffies. The June 2008
- revision greatly simplified the boundary layer formulation
- from Ferrari and McWilliams, whereby the quadratic transition
- layer is eliminated, thus removing the need to match vertical
- derivatives of the streamfunction. The matching conditions
- implied by the transition zone added a tremendous amount
- of code that was not seen to be critical for the purpose
- of producing a reasonably smooth streamfunction.
-
- Numerical implementation of the flux components follows the triad
- approach documented in the references and implemented in MOM2 and MOM3.
- The MOM algorithm accounts for partial bottom cells and generalized
- orthogonal horizontal coordinates.
-
- Note: the option neutral_physics_simple is not supported in this
- module. Use nphysicA for that option.
-
- Must be true to use this module. Default is false.
-
- For printing starting and ending checksums for restarts
-
- Must be true to use GM skewsion. Set to false if wish to
- incorporate the "GM-effect" through form drag, as in
- ocean_form_drag module. Default use_gm_skew=.true.
-
- To compute all contributions from neutral diffusion explicitly in time, including
- the K33 diagonal piece. This approach is available only when have small time
- steps and/or running with just a single tracer. It is for testing purposes.
-
- When tracer falls outside a specified range, revert to horizontal
- diffusive fluxes at this cell. This is an ad hoc and incomplete attempt
- to maintain monotonicity with the neutral physics scheme.
- Default neutral_physics_limit=.true.
-
- If .true. then this logical reduces the neutral fluxes to
- horizontal/vertical diffusion next to boundaries.
- This approach has been found to reduce spurious
- extrema resulting from truncation of triads used to compute
- a neutral flux component. Default tmask_neutral_on=.false.
-
- Minimum number of k-levels in surface turbulent boundary
- layer used in the transition of the neutral physics fluxes
- to the surface. Default surf_turb_thick_min_k = 2.
-
- Minimum thickness of surface turbulent boundary layer
- used in the transition of the neutral physics fluxes
- to the surface. Default surf_turb_thick_min=20m.
-
- The damping time used for determining the effective surface
- boundary layer thickness from other portions of
- the model. Default neutral_damping_time=10days.
-
- For smoothing the neutral blayer fields. This is useful
- when aiming to produce a smooth quasi-stokes streamfunction
- within the boundary layers. Default is nblayer_smooth=.true.
-
- Velocity scale that is used for computing the MICOM Laplacian mixing
- coefficient used in the Laplacian smoothing of neutral blayer fields.
-
- Initialize the neutral physics module by registering fields for
- diagnostic output and performing some numerical checks to see
- that namelist settings are appropriate.
-
- This function computes the thickness weighted and density weighted
- time tendency for tracer from neutral physics. Full discussion
- and details are provided by Griffies (2004,2005).
-
- Here is a brief summary of the temporal treatment.
-
----How the neutral diffusive flux components are computed:
-
- The vertical flux component is split into diagonal (3,3) and
- off-diagonal (3,1) and (3,2) terms. The off-diagonal (3,1) and (3,2)
- terms are included explicitly in time. The main contribution from the
- (3,3) term to the time tendency is included implicitly in time
- along with the usual contribution from diapycnal processes
- (vertical mixing schemes). This is the K33_implicit term.
- This approach is necessary with high vertical resolution, as
- noted by Cox (1987). However, splitting the vertical flux into
- an implicit and explicit piece compromises the
- integrity of the vertical flux component (see Griffies et al. 1998).
- So to minimize the disparity engendered by this split, the portion of
- K33 that can be stably included explicitly in time is computed along
- with the (3,1) and (3,2) terms.
-
- All other terms in the mixing tensor are included explicitly in time
- using a forward time step as required for temporal stability of
- numerical diffusive processes.
-
-
-
- This subroutine computes the "neutral boundary layers" based on
- the formulation of Ferrari and McWilliams (2006). See full
- details and discussion in Elements of MOM4p1 by Griffies (2009).
-
- Five vertical regions are identified by Ferrari and McWilliams:
- We simplify these regimes by melding the turbulent and transition
- regimes into an overall neutral boundary layer regime, within which
- the streamfunction is linearly tapers to zero moving towards the
- boundary. We also ignore the bottom regimes, as these are poorly
- resolved in most models, and the neutral physics fluxes are
- typically small at the bottom.
-
- (1) Surface turbulent region:
- Depth ("h" in Ferrari and McWilliams notation) dominated by
- 3d turbulent processes. This depth is taken from surf_blthick,
- as set by the KPP scheme or another mixed layer scheme.
- A minimum is set as surf_turb_thick_min and is specified
- as a nml parameter in ocean_nphysicsB_nml.
-
- In order to use a low frequency version of the boundary layer
- thickness, we damp its evolution with a damping time scale
- neutral_damping_time (days).
-
- In the code, "h_surf"= surf_turb_thick
-
- (2) Surface transition region:
- Thickness ("D" in Ferrari and McWilliams notation)
- between the turbulent surface boundary layer and the interior.
- This transition layer thickness is determined by the product of the
- neutral slope and first baroclinic Rossby radius. This specification
- is ad hoc, and more fundamental theories are welcome.
-
- In the code, "D_surf"= surf_trans_thick
-
-
- Within a "boundary layer" region set by the sum of
- surf_turb_thick plus surf_trans_thick, the eddy
- induced velocity is assumed to have zero vertical shear,
- which means the quasi-Stokes streamfunction is linear with
- depth. The neutral diffusive fluxes are reduced to horizontal
- downgradient diffusion, with "horizontal" defined according
- to surfaces of constant vertical coordinate.
-
-
- (3) Interior region:
- Where neutral diffusion and GM skew-diffusion are taken
- from their unmodified form.
-
- Only use the 31 and 32 triads for this computation since the
- 13 and 23 triads require extra slope calculations, and
- so will add lots of computational cost. It is felt that the
- 31 and 32 triads are sufficient for this calculation, in
- a similar manner that they are used for the calculation of
- the non-constant diffusivities.
-
- Scheme coded for MOM4p1 by Stephen.Griffies
- Version: March2006
- Simplified version: June2008
-
-
- Subroutine computes the tracer independent pieces of the vertical
- flux component. As a result of this routine,
- Array tensor_31 = x-diffusivity*slope (m^2/sec) for fz
- Array tensor_32 = y-diffusivity*slope (m^2/sec) for fz
-
- K33 is the (3,3) term in small angle Redi diffusion tensor.
- It is broken into an explicit in time piece and implicit
- in time piece. It is weighted by density for non-Boussinesq
- and rho0 for Boussinesq.
-
- K33 has units (kg/m^3)*m^2/sec.
-
- Also will compute the squared Eady growth rate, with the maximum
- slope contributing to this growth rate set by smax.
-
- For saving the contributions from GM and Redi separately, it is
- necessary to compute the tensor_redi component here.
-
- We do so here, reproducing some lines of code from fz_terms,
- to reduce minimize the need to impinge on the case when NOT
- using this generally expensive (memory and computational)
- diagnostic.
-
- This routine MUST be called prior to fz_terms, since we use
- tensor_31 and tensor_32 in their raw slope forms here.
-
-
- Subroutine computes the i-directed neutral physics tracer flux component.
- Compute this component for all tracers at level k.
-
- fx has physical dimensions (area*diffusivity*density*tracer gradient)
-
-
- Subroutine computes the i-directed neutral physics tracer flux component
- for Redi separately from GM, in order to diagnose GM and Redi
- fluxes independent of one another.
-
- Compute this component for all tracers at level k.
-
- fx has physical dimensions (area*diffusivity*density*tracer gradient)
-
-
- Subroutine computes the j-directed neutral physics tracer flux component.
- Compute this component for all tracers at level k.
-
- fy has physical dimensions (area*diffusivity*density*tracer gradient)
-
-
- Subroutine computes the j-directed neutral physics tracer flux component
- for Redi separately, in order to diagnose GM and Redi contributions
- independent of one another.
-
- Compute this component for all tracers at level k.
-
- fy has physical dimensions (area*diffusivity*density*tracer gradient)
-
-
- Subroutine computes the vertical neutral physics tracer flux component.
- Compute this component for all tracers at level k.
- Surface and bottom boundary condition fz(k=0)=fz(k=kmt(i,j))=0
-
- fz has physical dimensions (density*diffusivity*tracer gradient)
-
-
- For diagnosing the GM and Redi pieces separately.
- Compute this component for all tracers at level k.
- Surface and bottom boundary condition fz(k=0)=fz(k=kmt(i,j))=0
-
- fz has physical dimensions (density*diffusivity*tracer gradient)
-
-
- Send some diagnostics to diagnostics manager.
-
- Write some checksums.
-
- Write out restart files registered through register_restart_file
-
- Write to restart.
-
diff --git a/src/mom5/ocean_param/neutral/ocean_nphysicsC.F90 b/src/mom5/ocean_param/neutral/ocean_nphysicsC.F90
index e63a497394..cb95277a83 100644
--- a/src/mom5/ocean_param/neutral/ocean_nphysicsC.F90
+++ b/src/mom5/ocean_param/neutral/ocean_nphysicsC.F90
@@ -514,9 +514,9 @@ module ocean_nphysicsC_mod
integer :: neutralrho_nk
character(len=128) :: version=&
- '$Id: ocean_nphysicsC.F90,v 1.1.2.2 2012/05/17 13:41:47 smg Exp $'
+ '$Id: ocean_nphysicsC.F90,v 20.0 2013/12/14 00:14:40 fms Exp $'
character (len=128) :: tagname = &
- '$Name: mom5_siena_08jun2012_smg $'
+ '$Name: tikal $'
character(len=*), parameter :: FILENAME=&
__FILE__
diff --git a/src/mom5/ocean_param/neutral/ocean_nphysicsC.html b/src/mom5/ocean_param/neutral/ocean_nphysicsC.html
deleted file mode 100644
index 1e94c21151..0000000000
--- a/src/mom5/ocean_param/neutral/ocean_nphysicsC.html
+++ /dev/null
@@ -1,993 +0,0 @@
-
-
-
-Module ocean_nphysicsC_mod
-
-
-
-
-PUBLIC INTERFACE
-
- ~ PUBLIC ROUTINES
- ~ NAMELIST
-
-
- Thickness weighted and density weighted time tendency for tracer
- from Laplacian neutral diffusion + Laplacian skew-diffusion.
-
-
-
-
-
- This module computes the cell thickness weighted and density
- weighted tracer tendency from small angle Laplacian neutral diffusion
- plus Laplacian skew-diffusion. The algorithms for neutral diffusion
- are based on mom4p0d methods. The algorithm for neutral skewsion
- are based on a projection onto a few of the lowest baroclinic
- modes. This module is experimental, and should be used with caution.
-
- Initialize the neutral physics module by registering fields for
- diagnostic output and performing some numerical checks to see
- that namelist settings are appropriate.
-
-
-
-
-
-
-
-
nphysicsC
-
-
-DESCRIPTION
-
-
- This function computes the thickness weighted and density weighted
- time tendency for tracer from neutral physics. Full discussion
- and details are provided by Griffies (2008).
-
- Here is a brief summary.
-
----How the neutral diffusive flux components are computed:
-
- The vertical flux component is split into diagonal (3,3) and
- off-diagonal (3,1) and (3,2) terms. The off-diagonal (3,1) and (3,2)
- terms are included explicitly in time. The main contribution from the
- (3,3) term to the time tendency is included implicitly in time
- along with the usual contribution from diapycnal processes
- (vertical mixing schemes). This is the K33_implicit term.
- This approach is necessary with high vertical resolution, as
- noted by Cox (1987). However, splitting the vertical flux into
- an implicit and explicit piece compromises the
- integrity of the vertical flux component (see Griffies et al. 1998).
- So to minimize the disparity engendered by this split, the portion of
- K33 that can be stably included explicitly in time is computed along
- with the (3,1) and (3,2) terms.
-
- All other terms in the mixing tensor are included explicitly in time
- using a forward time step as required for temporal stability of
- numerical diffusive processes.
-
- The off-diagonal terms in the horizontal flux components, and all terms
- in the vertical flux component, are tapered in regions of steep neutral
- slope according to the requirements of linear stability. MOM allows for
- choice of two tapering schemes:
-
- (a) the tanh taper of Danabasoglu and McWilliams (1995)
- (b) the quadratic scheme of Gerdes, Koberle, and Willebrand (1991)
-
- Linear stability is far less stringent on the diagonal (1,1) and (2,2)
- part of the horizontal flux. Indeed, these terms in practice need
- not be tapered in steep sloped regions.
-
----How the skew diffusive flux components are computed:
-
- The skew flux components are purely off-diagonal.
- They are computed based on a vector streamfunction which
- is built from a sum of baroclinic modes.
- It is this part of the calculation that differs from
- ocean_nphysicsA and ocean_nphysicsB.
-
-
-
-
-
-
-
-
neutral_blayer
-
-
-DESCRIPTION
-
-
- Subroutine computes the boundary layer as determined by
- 1. depth within which typical mesoscale eddies are partially outcropped
- 2. depth within which vertical mixing scheme (e.g., kpp) computes a boundary layer
-
- Determine depth over which mesoscale eddies feel the ocean
- surface. This depth is a function of the neutral slope
- and the Rossby radius. This depth is called "eddy_depth".
- The algorithm for computing this depth is taken from
- the appendix to Large etal, 1997 JPO vol 27, 2418-2447.
-
- In addition to considering mesoscale eddy lengths,
- include the possibility that the diabatic vertical
- mixing (e.g., KPP) produces a mixed layer depth that is
- deeper than the depth that mesoscale eddies feel the ocean
- surface. Include this surf_blthick in the considerations so
- to determine the depth of this generalized "boundary layer"
- and the neutral slope at the base of the boundary layer.
-
- Note: Only consider surface boundary layers here.
-
- This subroutine is a modification of that in ocean_nphysicsA.
- Here, we only compute the eddy_depth based on the
- algorithm in Large etal. We do not compute an eddy
- depth which is also a function of smax. that is, we
- remove the ocean_nphysicsA portion of the calculation
- that sits inside the neutral_linear_gm_taper if-test.
-
-
-
-
-
-
-
-
-
compute_ndiffusion
-
-
-DESCRIPTION
-
-
- Subroutine to compute the tendency from neutral diffusion.
-
-
-
-
-
-
-
-
compute_gmskewsion
-
-
-DESCRIPTION
-
-
- Subroutine to compute the tracer tendency from GM skewsion.
-
-
-
-
-
-
-
-
baroclinic_modes
-
-
-DESCRIPTION
-
-
- Subroutine computes the baroclinic wave speeds and the dimensionless
- baroclinic mode eigenfunction for the vertical velocity baroclinic
- modes. These modes vanish at the surface and the bottom. We use
- the Chelton etal WKB analytic formulae for the speeds and modes.
-
- The baroclinic modes are dimensionless, and normalized over the
- depth of the ocean, from free surface to bottom.
-
- Units of the speeds are m/sec.
-
-
-
-
-
-
-
-
-
compute_psi_modes
-
-
-DESCRIPTION
-
-
- Compute vector streamfunction as projection onto baroclinic modes.
-
- Units of psi are m^2/sec
-
- This method for computing the quasi-Stokes streamfunction
- is not generally recommended. It remains in MOM only for
- testing purposes.
-
-
-
-
-
-
-
-
-
compute_psi_bvp
-
-
-DESCRIPTION
-
-
- Compute vector streamfunction by solving a boundary value problem.
-
- psi is centered on bottom of tracer cell; for example,
- psi(k=1)=psi at bottom of tracer cell k=1.
- psi vanishes at the ocean surface: psi(k=0)=0
- and ocean bottom: psi(k=kmt)=0.
-
- psix is centred on north face of tracer cell
- psiy is centred on east face of tracer cell
-
- Solve for psi(k=1,kmt-1) using a tridiagonal solver from
- Section 2.4 of Press etal 1986.
-
- Units of psi are m^2/sec
-
-
-
-
-
-
-
-
-
fz_terms
-
-
-DESCRIPTION
-
-
- Subroutine computes the tracer independent pieces of the vertical
- flux component. As a result of this routine,
- Array tensor_31 = x-diffusivity*slope (m^2/sec) for fz
- Array tensor_32 = y-diffusivity*slope (m^2/sec) for fz
-
- K33 is the (3,3) term in small angle Redi diffusion tensor.
- It is broken into an explicit in time piece and implicit
- in time piece. It is weighted by density for non-Boussinesq
- and rho0 for Boussinesq.
-
- K33 has units (kg/m^3)*m^2/sec.
-
- Also will compute the squared Eady growth rate, with the maximum
- slope contributing to this growth rate set by smax.
-
- This routine is nearly the same as in ocean_nphysicsA, except
- for the following changes:
- 1/ the routine here removes all pieces related to GM-skewsion.
- 2/ the routine here uses Thickness%depth_zwt rather than Grd%zt.
-
-
-
-
-
-
-
-
-
fx_flux_ndiffuse
-
-
-DESCRIPTION
-
-
- Subroutine computes the zonal neutral diffusion tracer flux component.
- Compute this component for all tracers at level k.
-
- fx has physical dimensions (area*diffusivity*density*tracer gradient)
-
- This routine is the same as that in ocean_nphysicsA, except
- for the following changes:
- 1/ the routine here removes all pieces related to GM-skewsion.
- 2/ the routine here uses Thickness%depth_zwt rather than Grd%zt.
- 3/ ah_array is removed.
-
-
-
-
-
-
-
-
-
fy_flux_ndiffuse
-
-
-DESCRIPTION
-
-
- Subroutine computes the meridional neutral diffusion tracer flux component.
- Compute this component for all tracers at level k.
-
- fy has physical dimensions (area*diffusivity*density*tracer gradient)
-
- This routine is the same as that in ocean_nphysicsA, except
- for the following changes:
- 1/ the routine here removes all pieces related to GM-skewsion.
- 2/ the routine here uses Thickness%depth_zwt rather than Grd%zt.
- 3/ ah_array is removed.
-
-
-
-
-
-
-
-
-
fz_flux_ndiffuse
-
-
-DESCRIPTION
-
-
- Subroutine computes the vertical neutral diffusion tracer flux component.
- Compute this component for all tracers at level k.
- Surface and bottom boundary condition fz(k=0)=fz(k=kmt(i,j))=0
-
- fz has physical dimensions (density*diffusivity*tracer gradient)
-
- This is nearly the same as the subroutine in ocean_nphysicsA.
-
-
-
-
-
-
-
-
-
fx_flux_gm
-
-
-DESCRIPTION
-
-
- Subroutine computes the zonal GM tracer flux component.
- Compute this component for all tracers at level k.
-
- fx has physical dimensions (area*diffusivity*density*tracer gradient)
-
-
-
-
-
-
-
-
-
fy_flux_gm
-
-
-DESCRIPTION
-
-
- Subroutine computes the meridional GM tracer flux component.
- Compute this component for all tracers at level k.
-
- fy has physical dimensions (area*diffusivity*density*tracer gradient)
-
-
-
-
-
-
-
-
-
fz_flux_gm
-
-
-DESCRIPTION
-
-
- Subroutine computes the vertical GM tracer flux component.
- Compute this component for all tracers at level k.
- Surface and bottom boundary condition fz(k=0)=fz(k=kmt(i,j))=0
-
- fz has physical dimensions (density*diffusivity*tracer gradient)
-
-
-
-
-
-
-
-
-
invtri_bvp
-
-
-DESCRIPTION
-
-
- Solve the vertical diffusion equation implicitly using the
- method of inverting a tridiagonal matrix as described in
- Numerical Recipes in Fortran, The art of Scientific Computing,
- Second Edition, Press, Teukolsky, Vetterling, Flannery, 1992
- pages 42,43.
-
- enforce upsilon(k=kmt) = 0 via use of mask(k+1).
-
-
-
-
-
-
-
-
-
compute_advect_transport
-
-
-DESCRIPTION
-
-
- Diagnose advective mass transport from GM.
-
- This routine is a diagnostic routine since generically we use the
- skewsion approach for the GM scheme. However, it could form the
- basis for an advective implementation of GM, which remains to be done.
-
- Comments on the diagnostic scheme:
-
- 0/ algorithm based on a similar approach used for submeso parameterization.
-
- 1/ psiy(k) is centred at bottom of tracer cell at zonal face.
- so -(psiy(i,j,k-1)-psiy(i,j,k)) gives zonal transport through
- tracer cell k.
-
- 2/ psix(k) is centred at bottom of tracer cell at meridional face.
- so (psix(i,j,k-1)-psix(i,j,k)) gives meridional transport through
- tracer cell k.
-
- 3/ compute vertical component from convergence of horizontal, just
- as for the vertical velocity component for the Eulerian transport.
-
- 4/ wrho_bt_gm(:,:,k=0) = 0.0 by definition
- it should be diagnosed to have zero at the ocean bottom; we should
- check that this is indeed the case to verify the diagnostic algorithm.
-
- 5/ expand the BDX_ET and BDY_NT operators for efficiency.
-
-
-
-
-
-
-
-
-
ocean_nphysicsC_restart
-
-
-DESCRIPTION
-
-
- Write out restart files registered through register_restart_file
-
-
-
-
-
-
-
-
ocean_nphysicsC_end
-
-
-DESCRIPTION
-
-
- Write to restart.
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_nphysicsC_nml
-
-
-
-
-
-use_this_module
-
-
- Must be true to use this module. Default is false.
-
-[logical]
-
-
-debug_this_module
-
-
- For printing starting and ending checksums for restarts
-
-[logical]
-
-
-epsln_bv_freq
-
-
- Minimum buoyancy frequency accepted for the computation of
- baroclinic modes. Default epsln_bv_freq=1e-10. Note there
- is also a minimum drhodz set in ocean_density.F90 via the
- nml epsln_drhodz in that module. We provide yet another minimum
- here in case we need an extra regularization for the amplitude
- of the baroclinic modes.
-
-[real, units: kg/m4]
-
-
-do_neutral_diffusion
-
-
- To compute tendency from neutral diffusion.
- Default do_neutral_diffusion=.true.
-
-[logical]
-
-
-do_gm_skewsion
-
-
- To compute tendency from GM skewsion. Default do_gm_skewsion=.true.
-
-[logical]
-
-
-gm_skewsion_modes
-
-
- To compute tendency from GM skewsion using streamfunction established
- by baroclinic modes. Default gm_skewsion_modes=.false.
-
-[logical]
-
-
-gm_skewsion_bvproblem
-
-
- To compute tendency from GM skewsion using streamfunction established
- by a boundary value problem. Default gm_skewsion_bvproblem=.true.
-
-[logical]
-
-
-number_bc_modes
-
-
- The number of baroclinic modes used to construct the eddy induced
- streamfunction. Default number_bc_modes=1.
-
-[integer]
-
-
-bvp_bc_mode
-
-
- The particular baroclinic mode used to construct the BVP streamfunction.
- If bvp_bc_mode=0, then will set bc_speed=0 when computing the BVP streamfunction.
- Default bvp_bc_mode=1.
-
-[integer]
-
-
-bvp_constant_speed
-
-
- For taking a constant speed to be used for the calculation
- of the BVP streamfunction. Default bvp_constant_speed=.false.
-
-[logical]
-
-
-bvp_speed
-
-
- For setting the speed weighting the second order derivative operator
- in the BVP streamfunction method:
- c^2 = max[bvp_min_speed, (bvp_speed-c_mode)^2].
- If bvp_constant_speed, then c^2 = bvp_speed^2.
- Default bvp_speed=0.0, in which case c^2 = c_mode^2.
-
-[real, units: m/s]
-
-
-bvp_min_speed
-
-
- For setting a minimum speed for use with the calculation
- of the BVP streamfunction. We need bvp_min_speed>0 to ensure
- that the second order derivative operator contributes to the
- calculation of the streamfunction.
- Default bvp_min_speed=0.1.
-
-[real, units: m/s]
-
-
-bv_freq_smooth_vert
-
-
- To smooth the buoyancy frequency for use in
- computing the baroclinic modes. Generally this field has already
- been smooted in ocean_density_mod, but we maintain the possibility of
- further smoothing here. Default bv_freq_smooth_vert=.false.
-
-[logical]
-
-
-num_121_passes
-
-
- The number of 121 passes used to smooth buoyancy frequency when
- bv_freq_smooth_vert=.true. Default num_121_passes=1.
-
-[integer]
-
-
-min_bc_speed
-
-
- The minimum speed used for computing the baroclinic modes.
- Default min_bc_speed=1e-6
-
-[real, units: m/s]
-
-
-smooth_bc_modes
-
-
- For doing a vertical 1-2-1 smoothing on the baroclinic modes
- prior to normalization. This is useful to reduce noise.
- Default smooth_bc_modes=.false.
-
-[logical]
-
-
-smooth_psi
-
-
- For doing a horizontal 1-2-1 smoothing on the psix and psiy fields.
- This is useful to reduce noise. Default smooth_psi=.true.
-
-[logical]
-
-
-regularize_psi
-
-
- To reduce the magnitude of psi in regions of weak stratification,
- using the slope = smax_psi to set the overall scale of the max allowed
- for psi. Default regularize_psi=.true.
-
-[logical]
-
-
-smax_modes
-
-
- Maximum slope used for setting the overall scale of a modal
- contribution to the parameterized transport.
- Default smax_psi=0.1.
-
-[real]
-
-
-diffusion_all_explicit
-
-
- To compute all contributions from neutral diffusion explicitly in time, including
- the K33 diagonal piece. This approach is available only when have small time
- steps and/or running with just a single tracer. It is for testing purposes.
-
-[logical]
-
-
-neutral_physics_limit
-
-
- When tracer falls outside a specified range, revert to horizontal
- diffusive fluxes at this cell. This is an ad hoc and incomplete attempt
- to maintain monotonicity with the neutral physics scheme.
- Default neutral_physics_limit=.true.
-
-[logical]
-
-
-tmask_neutral_on
-
-
- If .true. then this logical reduces the neutral diffusive fluxes to
- horizontal/vertical diffusion next to boundaries.
- This approach has been found to reduce spurious
- extrema resulting from truncation of triads used to compute
- a neutral flux component.
- Default tmask_neutral_on=.false.
-
-[logical]
-
-
-dm_taper
-
-
- Set to true to use the tanh tapering scheme of Danabasoglu and McWilliams.
- Default is true.
-
-[logical]
-
-
-gkw_taper
-
-
- Set to true to use the quadradic tapering scheme of Gerdes, Koberle, and Willebrand.
- Default is false.
-
-[logical]
-
-
-neutral_eddy_depth
-
-
- Compute eddy_depth according to depth over which eddies feel the ocean surface.
- Default neutral_eddy_depth=.true.
-
-[logical]
-
-
-turb_blayer_min
-
-
- Minimum depth of a surface turbulent boundary layer
- used in the transition of the neutral diffusion fluxes
- to the surface. Note that in mom4p0,
- turb_blayer_min was always set to zero.
-
-[real]
-
-
-use_neutral_slopes_potrho
-
-
- To compute the neutral slopes based on globally referenced potential
- density rather than locally referenced potential density. This approach
- is meant solely for sensitivity studies; it is not meant for realistic
- simulations.
- Default use_neutral_slopes_potrho=.false.
-
-[logical]
-
-
-neutral_slopes_potrho_press
-
-
- The reference pressure used to compute neutral slopes when setting
- use_neutral_slopes_potrho=.true.
- Default neutral_slopes_potrho_press=2000.0
-
-[real, units: dbar]
-
-
-smooth_advect_transport
-
-
- For doing a horizontal 1-2-1 smoothing on the diagnosed
- uhrho_et_gm and vhrho_nt_gm fields.
- Default smooth_advect_transport=.true.
-
-[logical]
-
-
-smooth_advect_transport_num
-
-
- Number of iterations for the smooothing of horizontal transport.
- Default smooth_advect_transport_num=2.
-
-[integer]
-
-
-
-
-
-
-
-
-
-
-
REFERENCES
-
-
-
-
- S.M. Griffies, A. Gnanadesikan, R.C. Pacanowski, V. Larichev,
- J.K. Dukowicz, and R.D. Smith
- Isoneutral diffusion in a z-coordinate ocean model
- Journal of Physical Oceanography (1998) vol 28 pages 805-830
-
-
- S.M. Griffies
- The Gent-McWilliams Skew-flux
- Journal of Physical Oceanography (1998) vol 28 pages 831-841
-
-
- R. Ferrari, S.M. Griffies, A.J.G. Nurser, and G.K. Vallis
- A boundary value problem for the parameterized mesoscale eddy transport
- Ocean Modelling, Volume 32, 2010, Pages 143-156.
-
-
- S.M. Griffies
- Fundamentals of Ocean Climate Models (2004)
- Princeton University Press
-
-
- S.M. Griffies: Elements of MOM (2012)
-
-
- D.B. Chelton, R.A. deSzoeke, M.G. Schlax, K.E. Naggar, N. Siwertz
- Geographical Variability of the First Baroclinic Rossby Radius of Deformation
- Journal of Physical Oceanography (1998) vol 28 pages 433-460
-
-
- G. Danabasoglu and J. C. McWilliams
- Sensitivity of the global ocean circulation to
- parameterizations of mesoscale tracer transports
- Journal of Climate (1995) vol 8 pages 2967--2987
-
-
- Gerdes, Koberle, and Willebrand
- The influence of numerical advection schemes on the results of ocean
- general circulation models, Climate Dynamics (1991), vol. 5,
- pages 211--226.
-
-
-
-
-
-
-
-
NOTES
-
-
- Numerical implementation of the flux components follows the triad
- approach documented in the references and implemented in MOM2 and MOM3.
- The MOM algorithm accounts for partial bottom cells and generalized
- orthogonal horizontal coordinates and general vertical levels.
-
-
- In steep neutral slope regions, neutral diffusive fluxes are tapered
- to zero with the tanh taper of Danabasoglu and McWilliams (1995) or the
- quadratic scheme of Gerdes, Koberle, and Willebrand.
-
- Traditional tapering is not required for the skew fluxes computed in
- this module.
-
-
-
diff --git a/src/mom5/ocean_param/neutral/ocean_nphysicsC.xml b/src/mom5/ocean_param/neutral/ocean_nphysicsC.xml
deleted file mode 100644
index 113381a221..0000000000
--- a/src/mom5/ocean_param/neutral/ocean_nphysicsC.xml
+++ /dev/null
@@ -1,410 +0,0 @@
-
-
- Stephen M. Griffies
- Tim Leslie
-
- Thickness weighted and density weighted time tendency for tracer
- from Laplacian neutral diffusion + Laplacian skew-diffusion.
-
- This module computes the cell thickness weighted and density
- weighted tracer tendency from small angle Laplacian neutral diffusion
- plus Laplacian skew-diffusion. The algorithms for neutral diffusion
- are based on mom4p0d methods. The algorithm for neutral skewsion
- are based on a projection onto a few of the lowest baroclinic
- modes. This module is experimental, and should be used with caution.
-
- S.M. Griffies, A. Gnanadesikan, R.C. Pacanowski, V. Larichev,
- J.K. Dukowicz, and R.D. Smith
- Isoneutral diffusion in a z-coordinate ocean model
- Journal of Physical Oceanography (1998) vol 28 pages 805-830
-
- S.M. Griffies
- The Gent-McWilliams Skew-flux
- Journal of Physical Oceanography (1998) vol 28 pages 831-841
-
- R. Ferrari, S.M. Griffies, A.J.G. Nurser, and G.K. Vallis
- A boundary value problem for the parameterized mesoscale eddy transport
- Ocean Modelling, Volume 32, 2010, Pages 143-156.
-
- S.M. Griffies
- Fundamentals of Ocean Climate Models (2004)
- Princeton University Press
-
- S.M. Griffies: Elements of MOM (2012)
-
- D.B. Chelton, R.A. deSzoeke, M.G. Schlax, K.E. Naggar, N. Siwertz
- Geographical Variability of the First Baroclinic Rossby Radius of Deformation
- Journal of Physical Oceanography (1998) vol 28 pages 433-460
-
- G. Danabasoglu and J. C. McWilliams
- Sensitivity of the global ocean circulation to
- parameterizations of mesoscale tracer transports
- Journal of Climate (1995) vol 8 pages 2967--2987
-
- Gerdes, Koberle, and Willebrand
- The influence of numerical advection schemes on the results of ocean
- general circulation models, Climate Dynamics (1991), vol. 5,
- pages 211--226.
-
- Numerical implementation of the flux components follows the triad
- approach documented in the references and implemented in MOM2 and MOM3.
- The MOM algorithm accounts for partial bottom cells and generalized
- orthogonal horizontal coordinates and general vertical levels.
-
- In steep neutral slope regions, neutral diffusive fluxes are tapered
- to zero with the tanh taper of Danabasoglu and McWilliams (1995) or the
- quadratic scheme of Gerdes, Koberle, and Willebrand.
-
- Traditional tapering is not required for the skew fluxes computed in
- this module.
-
- Must be true to use this module. Default is false.
-
- For printing starting and ending checksums for restarts
-
- Minimum buoyancy frequency accepted for the computation of
- baroclinic modes. Default epsln_bv_freq=1e-10. Note there
- is also a minimum drhodz set in ocean_density.F90 via the
- nml epsln_drhodz in that module. We provide yet another minimum
- here in case we need an extra regularization for the amplitude
- of the baroclinic modes.
-
- To compute tendency from neutral diffusion.
- Default do_neutral_diffusion=.true.
-
- To compute tendency from GM skewsion. Default do_gm_skewsion=.true.
-
- To compute tendency from GM skewsion using streamfunction established
- by baroclinic modes. Default gm_skewsion_modes=.false.
-
- To compute tendency from GM skewsion using streamfunction established
- by a boundary value problem. Default gm_skewsion_bvproblem=.true.
-
- The number of baroclinic modes used to construct the eddy induced
- streamfunction. Default number_bc_modes=1.
-
- The particular baroclinic mode used to construct the BVP streamfunction.
- If bvp_bc_mode=0, then will set bc_speed=0 when computing the BVP streamfunction.
- Default bvp_bc_mode=1.
-
- For taking a constant speed to be used for the calculation
- of the BVP streamfunction. Default bvp_constant_speed=.false.
-
- For setting the speed weighting the second order derivative operator
- in the BVP streamfunction method:
- c^2 = max[bvp_min_speed, (bvp_speed-c_mode)^2].
- If bvp_constant_speed, then c^2 = bvp_speed^2.
- Default bvp_speed=0.0, in which case c^2 = c_mode^2.
-
- For setting a minimum speed for use with the calculation
- of the BVP streamfunction. We need bvp_min_speed>0 to ensure
- that the second order derivative operator contributes to the
- calculation of the streamfunction.
- Default bvp_min_speed=0.1.
-
- To smooth the buoyancy frequency for use in
- computing the baroclinic modes. Generally this field has already
- been smooted in ocean_density_mod, but we maintain the possibility of
- further smoothing here. Default bv_freq_smooth_vert=.false.
-
- The number of 121 passes used to smooth buoyancy frequency when
- bv_freq_smooth_vert=.true. Default num_121_passes=1.
-
- The minimum speed used for computing the baroclinic modes.
- Default min_bc_speed=1e-6
-
- For doing a vertical 1-2-1 smoothing on the baroclinic modes
- prior to normalization. This is useful to reduce noise.
- Default smooth_bc_modes=.false.
-
- For doing a horizontal 1-2-1 smoothing on the psix and psiy fields.
- This is useful to reduce noise. Default smooth_psi=.true.
-
- To reduce the magnitude of psi in regions of weak stratification,
- using the slope = smax_psi to set the overall scale of the max allowed
- for psi. Default regularize_psi=.true.
-
- Maximum slope used for setting the overall scale of a modal
- contribution to the parameterized transport.
- Default smax_psi=0.1.
-
- To compute all contributions from neutral diffusion explicitly in time, including
- the K33 diagonal piece. This approach is available only when have small time
- steps and/or running with just a single tracer. It is for testing purposes.
-
- When tracer falls outside a specified range, revert to horizontal
- diffusive fluxes at this cell. This is an ad hoc and incomplete attempt
- to maintain monotonicity with the neutral physics scheme.
- Default neutral_physics_limit=.true.
-
- If .true. then this logical reduces the neutral diffusive fluxes to
- horizontal/vertical diffusion next to boundaries.
- This approach has been found to reduce spurious
- extrema resulting from truncation of triads used to compute
- a neutral flux component.
- Default tmask_neutral_on=.false.
-
- Set to true to use the tanh tapering scheme of Danabasoglu and McWilliams.
- Default is true.
-
- Set to true to use the quadradic tapering scheme of Gerdes, Koberle, and Willebrand.
- Default is false.
-
- Compute eddy_depth according to depth over which eddies feel the ocean surface.
- Default neutral_eddy_depth=.true.
-
- Minimum depth of a surface turbulent boundary layer
- used in the transition of the neutral diffusion fluxes
- to the surface. Note that in mom4p0,
- turb_blayer_min was always set to zero.
-
- To compute the neutral slopes based on globally referenced potential
- density rather than locally referenced potential density. This approach
- is meant solely for sensitivity studies; it is not meant for realistic
- simulations.
- Default use_neutral_slopes_potrho=.false.
-
- The reference pressure used to compute neutral slopes when setting
- use_neutral_slopes_potrho=.true.
- Default neutral_slopes_potrho_press=2000.0
-
- For doing a horizontal 1-2-1 smoothing on the diagnosed
- uhrho_et_gm and vhrho_nt_gm fields.
- Default smooth_advect_transport=.true.
-
- Number of iterations for the smooothing of horizontal transport.
- Default smooth_advect_transport_num=2.
-
- Initialize the neutral physics module by registering fields for
- diagnostic output and performing some numerical checks to see
- that namelist settings are appropriate.
-
- This function computes the thickness weighted and density weighted
- time tendency for tracer from neutral physics. Full discussion
- and details are provided by Griffies (2008).
-
- Here is a brief summary.
-
----How the neutral diffusive flux components are computed:
-
- The vertical flux component is split into diagonal (3,3) and
- off-diagonal (3,1) and (3,2) terms. The off-diagonal (3,1) and (3,2)
- terms are included explicitly in time. The main contribution from the
- (3,3) term to the time tendency is included implicitly in time
- along with the usual contribution from diapycnal processes
- (vertical mixing schemes). This is the K33_implicit term.
- This approach is necessary with high vertical resolution, as
- noted by Cox (1987). However, splitting the vertical flux into
- an implicit and explicit piece compromises the
- integrity of the vertical flux component (see Griffies et al. 1998).
- So to minimize the disparity engendered by this split, the portion of
- K33 that can be stably included explicitly in time is computed along
- with the (3,1) and (3,2) terms.
-
- All other terms in the mixing tensor are included explicitly in time
- using a forward time step as required for temporal stability of
- numerical diffusive processes.
-
- The off-diagonal terms in the horizontal flux components, and all terms
- in the vertical flux component, are tapered in regions of steep neutral
- slope according to the requirements of linear stability. MOM allows for
- choice of two tapering schemes:
-
- (a) the tanh taper of Danabasoglu and McWilliams (1995)
- (b) the quadratic scheme of Gerdes, Koberle, and Willebrand (1991)
-
- Linear stability is far less stringent on the diagonal (1,1) and (2,2)
- part of the horizontal flux. Indeed, these terms in practice need
- not be tapered in steep sloped regions.
-
----How the skew diffusive flux components are computed:
-
- The skew flux components are purely off-diagonal.
- They are computed based on a vector streamfunction which
- is built from a sum of baroclinic modes.
- It is this part of the calculation that differs from
- ocean_nphysicsA and ocean_nphysicsB.
-
- Subroutine computes the boundary layer as determined by
- 1. depth within which typical mesoscale eddies are partially outcropped
- 2. depth within which vertical mixing scheme (e.g., kpp) computes a boundary layer
-
- Determine depth over which mesoscale eddies feel the ocean
- surface. This depth is a function of the neutral slope
- and the Rossby radius. This depth is called "eddy_depth".
- The algorithm for computing this depth is taken from
- the appendix to Large etal, 1997 JPO vol 27, 2418-2447.
-
- In addition to considering mesoscale eddy lengths,
- include the possibility that the diabatic vertical
- mixing (e.g., KPP) produces a mixed layer depth that is
- deeper than the depth that mesoscale eddies feel the ocean
- surface. Include this surf_blthick in the considerations so
- to determine the depth of this generalized "boundary layer"
- and the neutral slope at the base of the boundary layer.
-
- Note: Only consider surface boundary layers here.
-
- This subroutine is a modification of that in ocean_nphysicsA.
- Here, we only compute the eddy_depth based on the
- algorithm in Large etal. We do not compute an eddy
- depth which is also a function of smax. that is, we
- remove the ocean_nphysicsA portion of the calculation
- that sits inside the neutral_linear_gm_taper if-test.
-
-
- Subroutine to compute the tendency from neutral diffusion.
-
- Subroutine to compute the tracer tendency from GM skewsion.
-
- Subroutine computes the baroclinic wave speeds and the dimensionless
- baroclinic mode eigenfunction for the vertical velocity baroclinic
- modes. These modes vanish at the surface and the bottom. We use
- the Chelton etal WKB analytic formulae for the speeds and modes.
-
- The baroclinic modes are dimensionless, and normalized over the
- depth of the ocean, from free surface to bottom.
-
- Units of the speeds are m/sec.
-
-
- Compute vector streamfunction as projection onto baroclinic modes.
-
- Units of psi are m^2/sec
-
- This method for computing the quasi-Stokes streamfunction
- is not generally recommended. It remains in MOM only for
- testing purposes.
-
-
- Compute vector streamfunction by solving a boundary value problem.
-
- psi is centered on bottom of tracer cell; for example,
- psi(k=1)=psi at bottom of tracer cell k=1.
- psi vanishes at the ocean surface: psi(k=0)=0
- and ocean bottom: psi(k=kmt)=0.
-
- psix is centred on north face of tracer cell
- psiy is centred on east face of tracer cell
-
- Solve for psi(k=1,kmt-1) using a tridiagonal solver from
- Section 2.4 of Press etal 1986.
-
- Units of psi are m^2/sec
-
-
- Subroutine computes the tracer independent pieces of the vertical
- flux component. As a result of this routine,
- Array tensor_31 = x-diffusivity*slope (m^2/sec) for fz
- Array tensor_32 = y-diffusivity*slope (m^2/sec) for fz
-
- K33 is the (3,3) term in small angle Redi diffusion tensor.
- It is broken into an explicit in time piece and implicit
- in time piece. It is weighted by density for non-Boussinesq
- and rho0 for Boussinesq.
-
- K33 has units (kg/m^3)*m^2/sec.
-
- Also will compute the squared Eady growth rate, with the maximum
- slope contributing to this growth rate set by smax.
-
- This routine is nearly the same as in ocean_nphysicsA, except
- for the following changes:
- 1/ the routine here removes all pieces related to GM-skewsion.
- 2/ the routine here uses Thickness%depth_zwt rather than Grd%zt.
-
-
- Subroutine computes the zonal neutral diffusion tracer flux component.
- Compute this component for all tracers at level k.
-
- fx has physical dimensions (area*diffusivity*density*tracer gradient)
-
- This routine is the same as that in ocean_nphysicsA, except
- for the following changes:
- 1/ the routine here removes all pieces related to GM-skewsion.
- 2/ the routine here uses Thickness%depth_zwt rather than Grd%zt.
- 3/ ah_array is removed.
-
-
- Subroutine computes the meridional neutral diffusion tracer flux component.
- Compute this component for all tracers at level k.
-
- fy has physical dimensions (area*diffusivity*density*tracer gradient)
-
- This routine is the same as that in ocean_nphysicsA, except
- for the following changes:
- 1/ the routine here removes all pieces related to GM-skewsion.
- 2/ the routine here uses Thickness%depth_zwt rather than Grd%zt.
- 3/ ah_array is removed.
-
-
- Subroutine computes the vertical neutral diffusion tracer flux component.
- Compute this component for all tracers at level k.
- Surface and bottom boundary condition fz(k=0)=fz(k=kmt(i,j))=0
-
- fz has physical dimensions (density*diffusivity*tracer gradient)
-
- This is nearly the same as the subroutine in ocean_nphysicsA.
-
-
- Subroutine computes the zonal GM tracer flux component.
- Compute this component for all tracers at level k.
-
- fx has physical dimensions (area*diffusivity*density*tracer gradient)
-
-
- Subroutine computes the meridional GM tracer flux component.
- Compute this component for all tracers at level k.
-
- fy has physical dimensions (area*diffusivity*density*tracer gradient)
-
-
- Subroutine computes the vertical GM tracer flux component.
- Compute this component for all tracers at level k.
- Surface and bottom boundary condition fz(k=0)=fz(k=kmt(i,j))=0
-
- fz has physical dimensions (density*diffusivity*tracer gradient)
-
-
- Solve the vertical diffusion equation implicitly using the
- method of inverting a tridiagonal matrix as described in
- Numerical Recipes in Fortran, The art of Scientific Computing,
- Second Edition, Press, Teukolsky, Vetterling, Flannery, 1992
- pages 42,43.
-
- enforce upsilon(k=kmt) = 0 via use of mask(k+1).
-
-
- Diagnose advective mass transport from GM.
-
- This routine is a diagnostic routine since generically we use the
- skewsion approach for the GM scheme. However, it could form the
- basis for an advective implementation of GM, which remains to be done.
-
- Comments on the diagnostic scheme:
-
- 0/ algorithm based on a similar approach used for submeso parameterization.
-
- 1/ psiy(k) is centred at bottom of tracer cell at zonal face.
- so -(psiy(i,j,k-1)-psiy(i,j,k)) gives zonal transport through
- tracer cell k.
-
- 2/ psix(k) is centred at bottom of tracer cell at meridional face.
- so (psix(i,j,k-1)-psix(i,j,k)) gives meridional transport through
- tracer cell k.
-
- 3/ compute vertical component from convergence of horizontal, just
- as for the vertical velocity component for the Eulerian transport.
-
- 4/ wrho_bt_gm(:,:,k=0) = 0.0 by definition
- it should be diagnosed to have zero at the ocean bottom; we should
- check that this is indeed the case to verify the diagnostic algorithm.
-
- 5/ expand the BDX_ET and BDY_NT operators for efficiency.
-
-
- Write out restart files registered through register_restart_file
-
- Write to restart.
-
diff --git a/src/mom5/ocean_param/neutral/ocean_nphysics_diff.F90 b/src/mom5/ocean_param/neutral/ocean_nphysics_diff.F90
index c80f36f030..2e579f12a2 100644
--- a/src/mom5/ocean_param/neutral/ocean_nphysics_diff.F90
+++ b/src/mom5/ocean_param/neutral/ocean_nphysics_diff.F90
@@ -75,9 +75,9 @@ module ocean_nphysics_diff_mod
#include
character(len=128) :: version=&
- '$Id: ocean_nphysics_diff.F90,v 1.1.2.2 2012/05/17 13:41:47 smg Exp $'
+ '$Id: ocean_nphysics_diff.F90,v 20.0 2013/12/14 00:14:42 fms Exp $'
character (len=128) :: tagname = &
- '$Name: mom5_siena_08jun2012_smg $'
+ '$Name: tikal $'
character(len=*), parameter :: FILENAME=&
__FILE__
diff --git a/src/mom5/ocean_param/neutral/ocean_nphysics_diff.html b/src/mom5/ocean_param/neutral/ocean_nphysics_diff.html
deleted file mode 100644
index 52c331669e..0000000000
--- a/src/mom5/ocean_param/neutral/ocean_nphysics_diff.html
+++ /dev/null
@@ -1,384 +0,0 @@
-
-
-
-Module ocean_nphysics_diff_mod
-
-
-
-
-PUBLIC INTERFACE
-
- ~ PUBLIC ROUTINES
- ~ NAMELIST
-
-
- Read in the namelist parameters and ensure that valid values have been
- choosen.
- Also determine whether agm is z-dependent.
-
-
-
-
-
-
-
-
init_globals
-
-
-DESCRIPTION
-
-
- Allocate and initialise all (non-namelist) global variables in the module.
-
-
-
-
-
-
-
-
register fields
-
-
-DESCRIPTION
-
-
- Register diagnostic fields.
-
-
-
-
-
-
-
-
diffusivity_init
-
-
-DESCRIPTION
-
-
- Initialise the three diffusivity arrays.
-
-
-
-
-
-
-
-
check_stability
-
-
-DESCRIPTION
-
-
- Check the stability assumptions and print details of the limits of stability.
-
-
-
-
-
-
-
-
compute_diffusivity
-
-
-DESCRIPTION
-
-
-
-
-
-
-
-
-
-
-
compute_agm
-
-
-DESCRIPTION
-
-
- Compute the flow-dependent GM diffusivity.
-
-
-
-
-
-
-
-
compute_raw_growth_rate
-
-
-DESCRIPTION
-
-
- Compute the raw growth rate at each grid point, using either the eady
- growth rate or the baroclinicity to obtain raw_growth_rate = NS
-
-
-
-
-
-
-
-
compute_growth_rate
-
-
-DESCRIPTION
-
-
- Take the raw growth rate and convert it to a final growth rate to be
- used in the diffusivity calculations.
-
-
-
-
-
-
-
-
vertical_average
-
-
-DESCRIPTION
-
-
- Compute the vertical average of the given array between D_t and D_b,
- as specified by agm_rate_upper_depth and agm_rate_lower_depth.
-
-
-
-
-
-
-
-
compute_length
-
-
-DESCRIPTION
-
-
- Compute the flow-dependent length scale involved in the GM diffusivity
- calculations.
-
-
-
-
-
-
-
-
compute_bczone_radius
-
-
-DESCRIPTION
-
-
- Subroutine computes the radius of the baroclinic zone in a manner
- suggested by the Hadley Centre approach (Malcolm Roberts, personal
- communication).
-
- Algorithm is used in MOM3 and documented in the MOM3 Manual.
-
-
-
-
-
-
-
-
compute_aredi
-
-
-DESCRIPTION
-
-
- Compute the flow-dependent neutral (Redi) diffusivity.
-
-
-
-
-
-
-
-
apply_grid_scaling
-
-
-DESCRIPTION
-
-
- Scale the supplied array as a function of the grid length and the
- Rossby radius. The scaling factor takes a value between zero and one.
-
- Interesting values of the scaling factor are
- 1.0 if Rossby radius = 0.0
- 0.5 if Rossby radius = grid length
- -> 0 as rossby radius -> inf
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_nphysics_diff_nml
-
-
-
-
-
-
-
-
-
-
-[logical]
-
-
-
-
-
-
-
-
-
-
-
REFERENCES
-
-
-
-
- S.M. Griffies
- Fundamentals of Ocean Climate Models (FOCM) (2004)
- Princeton University Press
-
-
-
diff --git a/src/mom5/ocean_param/neutral/ocean_nphysics_diff.xml b/src/mom5/ocean_param/neutral/ocean_nphysics_diff.xml
deleted file mode 100644
index a9d9ef0fed..0000000000
--- a/src/mom5/ocean_param/neutral/ocean_nphysics_diff.xml
+++ /dev/null
@@ -1,61 +0,0 @@
-
-
- Tim Leslie
- Stephen M. Griffies
-
- Compute the neutral diffusivity in this module.
-
- This module computes the neutral diffusivity. There are many
- methods available.
-
- S.M. Griffies
- Fundamentals of Ocean Climate Models (FOCM) (2004)
- Princeton University Press
-
- S.M. Griffies, Elements of MOM (2012)
-
-
- Read in the namelist parameters and ensure that valid values have been
- choosen.
- Also determine whether agm is z-dependent.
-
- Allocate and initialise all (non-namelist) global variables in the module.
-
- Register diagnostic fields.
-
- Initialise the three diffusivity arrays.
-
- Check the stability assumptions and print details of the limits of stability.
-
-
- Compute the flow-dependent GM diffusivity.
-
- Compute the raw growth rate at each grid point, using either the eady
- growth rate or the baroclinicity to obtain raw_growth_rate = NS
-
- Take the raw growth rate and convert it to a final growth rate to be
- used in the diffusivity calculations.
-
- Compute the vertical average of the given array between D_t and D_b,
- as specified by agm_rate_upper_depth and agm_rate_lower_depth.
-
- Compute the flow-dependent length scale involved in the GM diffusivity
- calculations.
-
- Subroutine computes the radius of the baroclinic zone in a manner
- suggested by the Hadley Centre approach (Malcolm Roberts, personal
- communication).
-
- Algorithm is used in MOM3 and documented in the MOM3 Manual.
-
- Compute the flow-dependent neutral (Redi) diffusivity.
-
- Scale the supplied array as a function of the grid length and the
- Rossby radius. The scaling factor takes a value between zero and one.
-
- Interesting values of the scaling factor are
- 1.0 if Rossby radius = 0.0
- 0.5 if Rossby radius = grid length
- -> 0 as rossby radius -> inf
-
diff --git a/src/mom5/ocean_param/neutral/ocean_nphysics_flux.F90 b/src/mom5/ocean_param/neutral/ocean_nphysics_flux.F90
index 27c0646cfc..4b32d6ae58 100644
--- a/src/mom5/ocean_param/neutral/ocean_nphysics_flux.F90
+++ b/src/mom5/ocean_param/neutral/ocean_nphysics_flux.F90
@@ -88,9 +88,9 @@ module ocean_nphysics_flux_mod
#include
character(len=128) :: version=&
- '$Id: ocean_nphysics_flux.F90,v 1.1.2.2 2012/05/17 13:41:47 smg Exp $'
+ '$Id: ocean_nphysics_flux.F90,v 20.0 2013/12/14 00:14:44 fms Exp $'
character (len=128) :: tagname = &
- '$Name: mom5_siena_08jun2012_smg $'
+ '$Name: tikal $'
character(len=*), parameter :: FILENAME=&
__FILE__
diff --git a/src/mom5/ocean_param/neutral/ocean_nphysics_flux.html b/src/mom5/ocean_param/neutral/ocean_nphysics_flux.html
deleted file mode 100644
index 42c9b6e18b..0000000000
--- a/src/mom5/ocean_param/neutral/ocean_nphysics_flux.html
+++ /dev/null
@@ -1,314 +0,0 @@
-
-
-
-Module ocean_nphysics_flux_mod
-
-
-
-
-PUBLIC INTERFACE
-
- ~ PUBLIC ROUTINES
- ~ NAMELIST
-
-
- Initialise namelist variables and prepare diagnostics.
-
-
-
-
-
-
-
-
register fields
-
-
-DESCRIPTION
-
-
- Register diagnostic fields.
-
-
-
-
-
-
-
-
flux_calculations
-
-
-DESCRIPTION
-
-
- This function computes the thickness weighted tendency of tracers
- due to neutral physics as well as the implicit vertical diffusivity
- term.
-
-
-
-
-
-
-
-
compute_mass_diff
-
-
-DESCRIPTION
-
-
- Subroutine computes the vertical neutral diffusion tracer flux component.
- Compute this component for all tracers at level k.
- Surface and bottom boundary condition fz(k=0)=fz(k=kmt(i,j))=0
-
- fz has physical dimensions (density*diffusivity*tracer gradient)
-
- This is nearly the same as the subroutine in ocean_nphysicsA.
-
-
-
-
-
-
-
-
-
geometric_terms
-
-
-DESCRIPTION
-
-
- Calculate the density weighted quarter cell volumes of the triads.
-
-
-
-
-
-
-
-
compute_33_term
-
-
-DESCRIPTION
-
-
- K33 is the (3,3) term in small angle Redi diffusion tensor.
- It is broken into an explicit in time piece and implicit
- in time piece. It is weighted by density for non-Boussinesq
- and rho0 for Boussinesq.
-
- K33 has units (kg/m^3)*m^2/sec.
-
-
-
-
-
-
-
-
compute_fluxes
-
-
-DESCRIPTION
-
-
- Computes the tracer fluxes due to neutral diffusion and skew diffusion.
- Fluxes are computed at the tracer cell faces and have units of [kg*T/s].
-
-
-
-
-
-
-
-
apply_tracer_limits
-
-
-DESCRIPTION
-
-
- If the neutral_physics_limit flag is set, then the flux used in regions of large
- tracer gradients (as defined by T_prog(n)tmask_limit) are set to have purely
- horizontal diffusion, with no vertical or skew terms.
-
-
-
-
-
-
-
-
update_tendencies
-
-
-DESCRIPTION
-
-
- Update the tendency for each tracer in each cell based on the total flux
- flowing through each of the six cell faces. The tendency is calculated
- separately for the flux due to neutral diffusion and due skew diffusion.
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_nphysics_flux_nml
-
-
-
-
-
-diffusion_all_explicit
-
-
- To compute K33 explicitly in time. This setting is meant
- only for debugging tests, since in general the simulation
- will go unstable.
- Default diffusion_all_explicit=.false.
-
-[logical]
-
-
-neutral_physics_limit
-
-
- Revert to horizontal diffusion when tracer falls outside specified range.
- Default neutral_physics_limit=.true., so to keep tracers from going
- too far outside of physical range.
-
-[logical]
-
-
-
-
-
-
-
-
-
-
-
REFERENCES
-
-
-
-
- S.M. Griffies
- Fundamentals of Ocean Climate Models (FOCM) (2004)
- Princeton University Press
-
-
-
diff --git a/src/mom5/ocean_param/neutral/ocean_nphysics_flux.xml b/src/mom5/ocean_param/neutral/ocean_nphysics_flux.xml
deleted file mode 100644
index c58e8ddb42..0000000000
--- a/src/mom5/ocean_param/neutral/ocean_nphysics_flux.xml
+++ /dev/null
@@ -1,62 +0,0 @@
-
-
- Tim Leslie
- Stephen M. Griffies
-
- Compute the neutral physics fluxes.
-
- This module computes the neutral physics fluxes.
-
- S.M. Griffies
- Fundamentals of Ocean Climate Models (FOCM) (2004)
- Princeton University Press
-
- S.M. Griffies: Elements of MOM (2012)
-
- To compute K33 explicitly in time. This setting is meant
- only for debugging tests, since in general the simulation
- will go unstable.
- Default diffusion_all_explicit=.false.
-
- Revert to horizontal diffusion when tracer falls outside specified range.
- Default neutral_physics_limit=.true., so to keep tracers from going
- too far outside of physical range.
-
- Initialise namelist variables and prepare diagnostics.
-
- Register diagnostic fields.
-
- This function computes the thickness weighted tendency of tracers
- due to neutral physics as well as the implicit vertical diffusivity
- term.
-
- Subroutine computes the vertical neutral diffusion tracer flux component.
- Compute this component for all tracers at level k.
- Surface and bottom boundary condition fz(k=0)=fz(k=kmt(i,j))=0
-
- fz has physical dimensions (density*diffusivity*tracer gradient)
-
- This is nearly the same as the subroutine in ocean_nphysicsA.
-
-
- Calculate the density weighted quarter cell volumes of the triads.
-
- K33 is the (3,3) term in small angle Redi diffusion tensor.
- It is broken into an explicit in time piece and implicit
- in time piece. It is weighted by density for non-Boussinesq
- and rho0 for Boussinesq.
-
- K33 has units (kg/m^3)*m^2/sec.
-
- Computes the tracer fluxes due to neutral diffusion and skew diffusion.
- Fluxes are computed at the tracer cell faces and have units of [kg*T/s].
-
- If the neutral_physics_limit flag is set, then the flux used in regions of large
- tracer gradients (as defined by T_prog(n)tmask_limit) are set to have purely
- horizontal diffusion, with no vertical or skew terms.
-
- Update the tendency for each tracer in each cell based on the total flux
- flowing through each of the six cell faces. The tendency is calculated
- separately for the flux due to neutral diffusion and due skew diffusion.
-
diff --git a/src/mom5/ocean_param/neutral/ocean_nphysics_new.F90 b/src/mom5/ocean_param/neutral/ocean_nphysics_new.F90
index 1bcb02f54f..19707be892 100644
--- a/src/mom5/ocean_param/neutral/ocean_nphysics_new.F90
+++ b/src/mom5/ocean_param/neutral/ocean_nphysics_new.F90
@@ -110,9 +110,9 @@ module ocean_nphysics_new_mod
#include
character(len=128) :: version=&
- '$Id: ocean_nphysics_new.F90,v 1.1.2.2 2012/05/17 13:41:47 smg Exp $'
+ '$Id: ocean_nphysics_new.F90,v 20.0 2013/12/14 00:14:46 fms Exp $'
character (len=128) :: tagname = &
- '$Name: mom5_siena_08jun2012_smg $'
+ '$Name: tikal $'
character(len=*), parameter :: FILENAME=&
__FILE__
diff --git a/src/mom5/ocean_param/neutral/ocean_nphysics_new.html b/src/mom5/ocean_param/neutral/ocean_nphysics_new.html
deleted file mode 100644
index 54d4af5717..0000000000
--- a/src/mom5/ocean_param/neutral/ocean_nphysics_new.html
+++ /dev/null
@@ -1,409 +0,0 @@
-
-
-
-Module ocean_nphysics_new_mod
-
-
-
-
-PUBLIC INTERFACE
-
- ~ PUBLIC ROUTINES
- ~ NAMELIST
-
-
- Initialises diagnostics, namelists and constants.
-
-
-
-
-
-
-
-
register fields
-
-
-DESCRIPTION
-
-
- Register diagnostic fields.
-
-
-
-
-
-
-
-
neutral_physics_new
-
-
-DESCRIPTION
-
-
- This public interface computes the effects of neutral physics
- processes (neutral diffusion and neutral skew-diffusion).
-
- --Returns rossby_radius for use in lapgen_friction module.
- --Returns gm_diffusivity for use in visc_form_drag module
- --Updates the value of T_prog(n)%th_tendency with the explicit thickness
- weighted tendency due to neutral physics and also T_prog(n)%K33_implicit
- with the implicit component.
-
-
-
-
-
-
-
-
tracer_gradients
-
-
-DESCRIPTION
-
-
- Compute the tracer derivatives.
-
- G(2004) 16.58
- dTdx(i) = (T(i+1) - T(i))/dxte
- dTdT(j) = (T(j+1) - T(j))/dytn
- dTdz(k) = (T(k) - T(k+1))/dzwt
-
- Horizontal derivatives are taken along surfaces of
- constant vertical coordinate (constant k-level)
-
- This approach ensures that when neutral physics defaults to "horizontal" physics
- next to boundaries, it will do so as horizontal, defined along surfaces of constant
- s-surfaces, and so will not generate spurious extrema.
-
- Additionally, when using generalized vertical coordinates, the neutral diffusion
- slope should be computed relative to the s-surfaces. The skew diffusion slope
- should ideally be computed with respect to z-surfaces, as z-surfaces define
- available potential energy. However, when s and z surfaces are reasonably close,
- as they are in the interior for zstar and pstar vertical coordinates, then we
- choose to to dissipate thickness as defined relative to the zstar or pstar surfaces.
- This should not be such a big deal, and it is certainly easier computationally than
- worrying about computing two separate sets of slopes. More on this detail is
- discussed in "Elements of MOM".
-
- NOTE: This approach is not appropriate for sigma-models. Indeed, many assumptions
- in the neutral physics modules need to be rethought for terrain following vertical
- coordinates.
-
-
-
-
-
-
-
-
-
density_calculations
-
-
-DESCRIPTION
-
-
- This subroutine computes a number of values based on the density gradient.
-
- These are the neutral slope vector, the neutral buoyancy frequency,
- gravity wave speed, Rossby radius and boundary layer depth.
-
-
-
-
-
-
-
-
gradrho
-
-
-DESCRIPTION
-
-
- Calculate the raw density gradients. No smoothing or limiting
- applied here.
-
-
-
-
-
-
-
-
adjust_drhodz
-
-
-DESCRIPTION
-
-
- Comments about smoothing drhodz:
-
- 1/ Tests in coupled 1-degree model showed extreme sensitivity
- of MOC to smoothing. GFDL users generally do NOT smooth, hence
- the default drhodz_smooth_vert=drhodz_smooth_horz=.false.
-
- 2/ Smoothing the vertical derivative of drhodz helps
- produce a regularized (i.e., well behaved) neutral slope vector.
-
- 3/ An attempt was made to smooth dTdz and dSdz rather
- than drhodz. The resulting slope was smooth, but not as
- smooth as when acting on drhodz itself.
-
-
-
-
-
-
-
-
neutral_slopes
-
-
-DESCRIPTION
-
-
- Compute the neutral slope vector along with its magnitude.
- The neutral slope vector is defined as -grad_h(rho)/(drho/dz).
-
-
-
-
-
-
-
-
neutral_blayer
-
-
-DESCRIPTION
-
-
- Locate the vertical index of the neutral boundary layer. This layer is
- defined as the point where the magnitude of the neutral slope vector
- first drops below smax, when searching down from the surface.
-
-
-
-
-
-
-
-
ocean_nphysics_new_restart
-
-
-DESCRIPTION
-
-
- Write out the restart data for this module
-
-
-
-
-
-
-
-
ocean_nphysics_new_end
-
-
-DESCRIPTION
-
-
- Writes out the restart data.
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_nphysics_new_nml
-
-
-
-
-
-use_this_module
-
-
- Must be set .true. to use this module.
- Default use_this_module = .false.
-
-[logical]
-
-
-drhodz_smooth_vert
-
-
- For smoothing vertical density gradient before computing
- neutral slope. Exercise caution if using this option.
- Default drhodz_smooth_vert=.false.
-
-[logical]
-
-
-drhodz_smooth_horz
-
-
- For smoothing vertical density gradient before computing
- neutral slope. Exercise caution if using this option.
- Default drhodz_smooth_horz=.false.
-
-[logical]
-
-
-smax
-
-
- Slope maximum parameter for setting behaviour of neutral
- physics. Default smax=0.01.
-
-[real]
-
-
-vel_micom_smooth
-
-
- For horizontal smoothing of drhodz before computing neutral
- slopes. Default vel_micom_smooth=0.2.
-
-[real, units: m/s]
-
-
-
-
-
-
-
-
-
-
-
REFERENCES
-
-
-
-
- S.M. Griffies
- Fundamentals of Ocean Climate Models (FOCM) (2004)
- Princeton University Press
-
-
-
diff --git a/src/mom5/ocean_param/neutral/ocean_nphysics_new.xml b/src/mom5/ocean_param/neutral/ocean_nphysics_new.xml
deleted file mode 100644
index ef8f2ee012..0000000000
--- a/src/mom5/ocean_param/neutral/ocean_nphysics_new.xml
+++ /dev/null
@@ -1,109 +0,0 @@
-
-
- Tim Leslie
- Stephen M. Griffies
-
- Compute the effects of neutral physics processes
- (neutral diffusion and neutral skew-diffusion).
-
- Compute the effects of neutral physics processes
- (neutral diffusion and neutral skew-diffusion).
-
- S.M. Griffies
- Fundamentals of Ocean Climate Models (FOCM) (2004)
- Princeton University Press
-
- S.M. Griffies, Elements of MOM (2012)
-
- Must be set .true. to use this module.
- Default use_this_module = .false.
-
- For smoothing vertical density gradient before computing
- neutral slope. Exercise caution if using this option.
- Default drhodz_smooth_vert=.false.
-
- For smoothing vertical density gradient before computing
- neutral slope. Exercise caution if using this option.
- Default drhodz_smooth_horz=.false.
-
- Slope maximum parameter for setting behaviour of neutral
- physics. Default smax=0.01.
-
- For horizontal smoothing of drhodz before computing neutral
- slopes. Default vel_micom_smooth=0.2.
-
- Initialises diagnostics, namelists and constants.
-
- Register diagnostic fields.
-
- This public interface computes the effects of neutral physics
- processes (neutral diffusion and neutral skew-diffusion).
-
- --Returns rossby_radius for use in lapgen_friction module.
- --Returns gm_diffusivity for use in visc_form_drag module
- --Updates the value of T_prog(n)%th_tendency with the explicit thickness
- weighted tendency due to neutral physics and also T_prog(n)%K33_implicit
- with the implicit component.
-
- Compute the tracer derivatives.
-
- G(2004) 16.58
- dTdx(i) = (T(i+1) - T(i))/dxte
- dTdT(j) = (T(j+1) - T(j))/dytn
- dTdz(k) = (T(k) - T(k+1))/dzwt
-
- Horizontal derivatives are taken along surfaces of
- constant vertical coordinate (constant k-level)
-
- This approach ensures that when neutral physics defaults to "horizontal" physics
- next to boundaries, it will do so as horizontal, defined along surfaces of constant
- s-surfaces, and so will not generate spurious extrema.
-
- Additionally, when using generalized vertical coordinates, the neutral diffusion
- slope should be computed relative to the s-surfaces. The skew diffusion slope
- should ideally be computed with respect to z-surfaces, as z-surfaces define
- available potential energy. However, when s and z surfaces are reasonably close,
- as they are in the interior for zstar and pstar vertical coordinates, then we
- choose to to dissipate thickness as defined relative to the zstar or pstar surfaces.
- This should not be such a big deal, and it is certainly easier computationally than
- worrying about computing two separate sets of slopes. More on this detail is
- discussed in "Elements of MOM".
-
- NOTE: This approach is not appropriate for sigma-models. Indeed, many assumptions
- in the neutral physics modules need to be rethought for terrain following vertical
- coordinates.
-
-
- This subroutine computes a number of values based on the density gradient.
-
- These are the neutral slope vector, the neutral buoyancy frequency,
- gravity wave speed, Rossby radius and boundary layer depth.
-
- Calculate the raw density gradients. No smoothing or limiting
- applied here.
-
- Comments about smoothing drhodz:
-
- 1/ Tests in coupled 1-degree model showed extreme sensitivity
- of MOC to smoothing. GFDL users generally do NOT smooth, hence
- the default drhodz_smooth_vert=drhodz_smooth_horz=.false.
-
- 2/ Smoothing the vertical derivative of drhodz helps
- produce a regularized (i.e., well behaved) neutral slope vector.
-
- 3/ An attempt was made to smooth dTdz and dSdz rather
- than drhodz. The resulting slope was smooth, but not as
- smooth as when acting on drhodz itself.
-
- Compute the neutral slope vector along with its magnitude.
- The neutral slope vector is defined as -grad_h(rho)/(drho/dz).
-
- Locate the vertical index of the neutral boundary layer. This layer is
- defined as the point where the magnitude of the neutral slope vector
- first drops below smax, when searching down from the surface.
-
- Write out the restart data for this module
-
- Writes out the restart data.
-
diff --git a/src/mom5/ocean_param/neutral/ocean_nphysics_skew.F90 b/src/mom5/ocean_param/neutral/ocean_nphysics_skew.F90
index 99d53c6ccc..5e8e83910d 100644
--- a/src/mom5/ocean_param/neutral/ocean_nphysics_skew.F90
+++ b/src/mom5/ocean_param/neutral/ocean_nphysics_skew.F90
@@ -144,9 +144,9 @@ module ocean_nphysics_skew_mod
#include
character(len=128) :: version=&
- '$Id: ocean_nphysics_skew.F90,v 1.1.2.2 2012/05/17 13:41:47 smg Exp $'
+ '$Id: ocean_nphysics_skew.F90,v 20.0 2013/12/14 00:14:48 fms Exp $'
character (len=128) :: tagname = &
- '$Name: mom5_siena_08jun2012_smg $'
+ '$Name: tikal $'
character(len=*), parameter :: FILENAME=&
__FILE__
diff --git a/src/mom5/ocean_param/neutral/ocean_nphysics_skew.html b/src/mom5/ocean_param/neutral/ocean_nphysics_skew.html
deleted file mode 100644
index 2020f62e48..0000000000
--- a/src/mom5/ocean_param/neutral/ocean_nphysics_skew.html
+++ /dev/null
@@ -1,432 +0,0 @@
-
-
-
-Module ocean_nphysics_skew_mod
-
-
-
-
-PUBLIC INTERFACE
-
- ~ PUBLIC ROUTINES
- ~ NAMELIST
-
-
- Thickness weighted and density weighted time tendency for tracer
- from Laplacian neutral diffusion + Laplacian skew-diffusion.
-
-
-
-
-
- This module computes the cell thickness weighted and density
- weighted tracer tendency from small angle Laplacian neutral diffusion
- plus Laplacian skew-diffusion. The algorithms for neutral diffusion
- are based on mom4p0d methods. The algorithm for neutral skewsion
- are based on a projection onto a few of the lowest baroclinic
- modes. This module is experimental, and should be used with caution.
-
- Compute the skew tensor terms using the GM method.
-
-
-
-
-
-
-
-
compute_transport_modes
-
-
-DESCRIPTION
-
-
- Compute transport as projection onto baroclinic modes.
-
- Units of upsilon are m^2/sec
-
- Subroutine computes the baroclinic wave speeds and the dimensionless
- baroclinic mode eigenfunction for the vertical velocity baroclinic
- modes. These modes vanish at the surface and the bottom. We use
- the Chelton etal WKB analytic formulae for the speeds and modes.
-
- The baroclinic modes are dimensionless, and normalized over the
- depth of the ocean, from free surface to bottom.
-
- The speeds are m/sec.
-
-
-
-
-
-
-
-
-
do_regularize_transport
-
-
-DESCRIPTION
-
-
- regularize the transport to keep magnitude
- under control in regions of weak vertical stratification.
-
-
-
-
-
-
-
-
compute_transport_bvp
-
-
-DESCRIPTION
-
-
- Compute transport by solving a boundary value problem.
-
- psi is centered on bottom of tracer cell; for example,
- psi(k=1)=psi at bottom of tracer cell k=1.
- psi vanishes at the ocean surface: psi(k=0)=0
- and ocean bottom: psi(k=kmt)=0.
-
- We solve for psi(k=1,kmt-1) using a tridiagonal solver from
- Section 2.4 of Press etal 1986.
-
- Units of psi are m^2/sec
-
-
-
-
-
-
-
-
-
invtri_bvp
-
-
-DESCRIPTION
-
-
- Solve the vertical diffusion equation implicitly using the
- method of inverting a tridiagonal matrix as described in
- Numerical Recipes in Fortran, The art of Scientific Computing,
- Second Edition, Press, Teukolsky, Vetterling, Flannery, 1992
- pages 42,43.
-
- enforce upsilon(k=kmt) = 0 via use of mask(k+1).
-
-
-
-
-
-
-
-
-
do_smooth_transport
-
-
-DESCRIPTION
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_nphysics_skew_nml
-
-
-
-
-
-gm_transport
-
-
- To compute tendency from GM skewsion. Default gm_transport=.false.
-
-[logical]
-
-
-bc_modes_transport
-
-
- To compute tendency from GM skewsion using streamfunction established
- by baroclinic modes. Default bc_modes_transport=.false.
-
-[logical]
-
-
-bvp_transport
-
-
- To compute tendency from GM skewsion using streamfunction established
- by a boundary value problem. Default bvp_transport=.false.
-
-[logical]
-
-
-number_bc_modes
-
-
- The number of baroclinic modes used to construct the eddy induced
- streamfunction when bc_modes_transport. Default number_bc_modes=1.
-
-[integer]
-
-
-min_bc_speed
-
-
- The minimum speed used for computing the baroclinic modes.
- Default min_bc_speed=1e-6
-
-[real, units: m/s]
-
-
-regularize_transport
-
-
- To reduce the magnitude of psi in regions of weak stratification,
- using the slope = smax_psi to set the overall scale of the max allowed
- for psi. Default regularize_transport=.true.
-
-[logical]
-
-
-smax_psi
-
-
- Maximum slope used for setting the overall scale of a modal
- contribution to the parameterized transport.
- Default smax_psi=0.1.
-
-[real]
-
-
-bvp_constant_speed
-
-
- For taking a constant speed to be used for the calculation
- of the BVP streamfunction. Default bvp_constant_speed=.false.
-
-[logical]
-
-
-bvp_speed
-
-
- For setting the speed weighting the second order derivative operator
- in the BVP streamfunction method:
- c^2 = max[bvp_min_speed, (bvp_speed-c_mode)^2].
- If bvp_constant_speed, then c^2 = bvp_speed^2.
- Default bvp_speed=0.0, in which case c^2 = c_mode^2.
-
-[real, units: m/s]
-
-
-bvp_bc_mode
-
-
- The particular baroclinic mode used to construct the BVP streamfunction.
- If bvp_bc_mode=0, then will set bc_speed=0 when computing the BVP streamfunction.
- Default bvp_bc_mode=1.
-
-[integer]
-
-
-bvp_min_speed
-
-
- For setting a minimum speed for use with the calculation
- of the BVP streamfunction. We need bvp_min_speed>0 to ensure
- that the second order derivative operator contributes to the
- calculation of the streamfunction.
- Default bvp_min_speed=0.1.
-
-[real, units: m/s]
-
-
-bv_freq_smooth_vert
-
-
- To smooth the buoyancy frequency for use in
- computing the baroclinic modes. Generally this field has already
- been smooted in ocean_density_mod, but we maintain the possibility of
- further smoothing here. Default bv_freq_smooth_vert=.false.
-
-[logical]
-
-
-smooth_transport
-
-
- For doing a horizontal 1-2-1 smoothing on the psix and psiy fields.
- This is useful to reduce noise. Default smooth_psi=.true.
-
-[logical]
-
-
-
-
-
-
-
-
-
-
-
REFERENCES
-
-
-
-
- S.M. Griffies
- The Gent-McWilliams Skew-flux
- Journal of Physical Oceanography (1998) vol 28 pages 831-841
-
-
- R. Ferrari, S.M. Griffies, A.J.G. Nurser, and G.K. Vallis
- A boundary value problem for the parameterized mesoscale eddy transport
- Ocean Modelling, 2009.
-
-
- S.M. Griffies
- Fundamentals of Ocean Climate Models (2004)
- Princeton University Press
-
-
-
diff --git a/src/mom5/ocean_param/neutral/ocean_nphysics_skew.xml b/src/mom5/ocean_param/neutral/ocean_nphysics_skew.xml
deleted file mode 100644
index 734e023aff..0000000000
--- a/src/mom5/ocean_param/neutral/ocean_nphysics_skew.xml
+++ /dev/null
@@ -1,126 +0,0 @@
-
-
- Tim Leslie
- Stephen M. Griffies
-
- Thickness weighted and density weighted time tendency for tracer
- from Laplacian neutral diffusion + Laplacian skew-diffusion.
-
- This module computes the cell thickness weighted and density
- weighted tracer tendency from small angle Laplacian neutral diffusion
- plus Laplacian skew-diffusion. The algorithms for neutral diffusion
- are based on mom4p0d methods. The algorithm for neutral skewsion
- are based on a projection onto a few of the lowest baroclinic
- modes. This module is experimental, and should be used with caution.
-
- S.M. Griffies
- The Gent-McWilliams Skew-flux
- Journal of Physical Oceanography (1998) vol 28 pages 831-841
-
- R. Ferrari, S.M. Griffies, A.J.G. Nurser, and G.K. Vallis
- A boundary value problem for the parameterized mesoscale eddy transport
- Ocean Modelling, 2009.
-
- S.M. Griffies
- Fundamentals of Ocean Climate Models (2004)
- Princeton University Press
-
- S.M. Griffies: Elements of MOM (2012)
-
- To compute tendency from GM skewsion. Default gm_transport=.false.
-
- To compute tendency from GM skewsion using streamfunction established
- by baroclinic modes. Default bc_modes_transport=.false.
-
- To compute tendency from GM skewsion using streamfunction established
- by a boundary value problem. Default bvp_transport=.false.
-
- The number of baroclinic modes used to construct the eddy induced
- streamfunction when bc_modes_transport. Default number_bc_modes=1.
-
- The minimum speed used for computing the baroclinic modes.
- Default min_bc_speed=1e-6
-
- To reduce the magnitude of psi in regions of weak stratification,
- using the slope = smax_psi to set the overall scale of the max allowed
- for psi. Default regularize_transport=.true.
-
- Maximum slope used for setting the overall scale of a modal
- contribution to the parameterized transport.
- Default smax_psi=0.1.
-
- For taking a constant speed to be used for the calculation
- of the BVP streamfunction. Default bvp_constant_speed=.false.
-
- For setting the speed weighting the second order derivative operator
- in the BVP streamfunction method:
- c^2 = max[bvp_min_speed, (bvp_speed-c_mode)^2].
- If bvp_constant_speed, then c^2 = bvp_speed^2.
- Default bvp_speed=0.0, in which case c^2 = c_mode^2.
-
- The particular baroclinic mode used to construct the BVP streamfunction.
- If bvp_bc_mode=0, then will set bc_speed=0 when computing the BVP streamfunction.
- Default bvp_bc_mode=1.
-
- For setting a minimum speed for use with the calculation
- of the BVP streamfunction. We need bvp_min_speed>0 to ensure
- that the second order derivative operator contributes to the
- calculation of the streamfunction.
- Default bvp_min_speed=0.1.
-
- To smooth the buoyancy frequency for use in
- computing the baroclinic modes. Generally this field has already
- been smooted in ocean_density_mod, but we maintain the possibility of
- further smoothing here. Default bv_freq_smooth_vert=.false.
-
- For doing a horizontal 1-2-1 smoothing on the psix and psiy fields.
- This is useful to reduce noise. Default smooth_psi=.true.
-
- Initialization routine.
-
- Register diagnostic fields.
-
- Compute the skew tensor terms using the GM method.
-
- Compute transport as projection onto baroclinic modes.
-
- Units of upsilon are m^2/sec
-
- Subroutine computes the baroclinic wave speeds and the dimensionless
- baroclinic mode eigenfunction for the vertical velocity baroclinic
- modes. These modes vanish at the surface and the bottom. We use
- the Chelton etal WKB analytic formulae for the speeds and modes.
-
- The baroclinic modes are dimensionless, and normalized over the
- depth of the ocean, from free surface to bottom.
-
- The speeds are m/sec.
-
-
- regularize the transport to keep magnitude
- under control in regions of weak vertical stratification.
-
- Compute transport by solving a boundary value problem.
-
- psi is centered on bottom of tracer cell; for example,
- psi(k=1)=psi at bottom of tracer cell k=1.
- psi vanishes at the ocean surface: psi(k=0)=0
- and ocean bottom: psi(k=kmt)=0.
-
- We solve for psi(k=1,kmt-1) using a tridiagonal solver from
- Section 2.4 of Press etal 1986.
-
- Units of psi are m^2/sec
-
-
- Solve the vertical diffusion equation implicitly using the
- method of inverting a tridiagonal matrix as described in
- Numerical Recipes in Fortran, The art of Scientific Computing,
- Second Edition, Press, Teukolsky, Vetterling, Flannery, 1992
- pages 42,43.
-
- enforce upsilon(k=kmt) = 0 via use of mask(k+1).
-
-
-
diff --git a/src/mom5/ocean_param/neutral/ocean_nphysics_tensor.F90 b/src/mom5/ocean_param/neutral/ocean_nphysics_tensor.F90
index 8af4e4eeab..a7af4709b3 100644
--- a/src/mom5/ocean_param/neutral/ocean_nphysics_tensor.F90
+++ b/src/mom5/ocean_param/neutral/ocean_nphysics_tensor.F90
@@ -71,9 +71,9 @@ module ocean_nphysics_tensor_mod
#include
character(len=128) :: version=&
- '$Id: ocean_nphysics_tensor.F90,v 1.1.2.2 2012/05/17 13:41:47 smg Exp $'
+ '$Id: ocean_nphysics_tensor.F90,v 20.0 2013/12/14 00:14:50 fms Exp $'
character (len=128) :: tagname = &
- '$Name: mom5_siena_08jun2012_smg $'
+ '$Name: tikal $'
character(len=*), parameter :: FILENAME=&
__FILE__
diff --git a/src/mom5/ocean_param/neutral/ocean_nphysics_tensor.html b/src/mom5/ocean_param/neutral/ocean_nphysics_tensor.html
deleted file mode 100644
index c2f94db44e..0000000000
--- a/src/mom5/ocean_param/neutral/ocean_nphysics_tensor.html
+++ /dev/null
@@ -1,268 +0,0 @@
-
-
-
-Module ocean_nphysics_tensor_mod
-
-
-
-
-PUBLIC INTERFACE
-
- ~ PUBLIC ROUTINES
- ~ NAMELIST
-
-
- Compute the tensor components for the diffusion and skew-diffusion tensor.
-
-
-
-
-
-
-
-
sine_taper
-
-
-DESCRIPTION
-
-
- Calculate a sine taper for those points shallower than the given threshold.
-
- The depth_function gives the depth (in metres) at each (i,j,k) point.
- The threshold_depth is the depth (in metres) at each (i,j) point.
- The returned taper gives a value in the range [0, 1] at each (i,j,k) point,
- where those points at a depth below the threshold are set to 1.0 and those
- above approach 0.0 as they approach the surface according to a sine
- function.
-
-
-
-
-
-
-
-
-
diffusion_tensor
-
-
-DESCRIPTION
-
-
- Compute the components of the neutral diffusion tensor.
-
-
-
-
-
-
-
-
compute_diffusion_tapers
-
-
-DESCRIPTION
-
-
- Compute the taper functions to be applied to the components of the diffusion
- tensor.
-
-
-
-
-
-
-
-
compute_masked_tensor
-
-
-DESCRIPTION
-
-
- This function applies the boundary conditions relevent to the flags
- tmask_neutral_on and tmask_sigma_on.
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_nphysics_tensor_nml
-
-
-
-
-
-
-
-
-
-
-[logical]
-
-
-
-
-
-
-
-
-
-
-
REFERENCES
-
-
-
-
- S.M. Griffies
- The Gent-McWilliams Skew-flux
- Journal of Physical Oceanography (1998) vol 28 pages 831-841
-
-
- R. Ferrari, S.M. Griffies, A.J.G. Nurser, and G.K. Vallis
- A boundary value problem for the parameterized mesoscale eddy transport
- Ocean Modelling, 2009.
-
-
- S.M. Griffies
- Fundamentals of Ocean Climate Models (2004)
- Princeton University Press
-
-
-
diff --git a/src/mom5/ocean_param/neutral/ocean_nphysics_tensor.xml b/src/mom5/ocean_param/neutral/ocean_nphysics_tensor.xml
deleted file mode 100644
index e9a0f8e326..0000000000
--- a/src/mom5/ocean_param/neutral/ocean_nphysics_tensor.xml
+++ /dev/null
@@ -1,47 +0,0 @@
-
-
- Tim Leslie
- Stephen M. Griffies
-
-
-
- S.M. Griffies
- The Gent-McWilliams Skew-flux
- Journal of Physical Oceanography (1998) vol 28 pages 831-841
-
- R. Ferrari, S.M. Griffies, A.J.G. Nurser, and G.K. Vallis
- A boundary value problem for the parameterized mesoscale eddy transport
- Ocean Modelling, 2009.
-
- S.M. Griffies
- Fundamentals of Ocean Climate Models (2004)
- Princeton University Press
-
- S.M. Griffies: Elements of MOM (2012)
-
-
- Initialise this module.
-
- Register diagnostic fields.
-
- Compute the tensor components for the diffusion and skew-diffusion tensor.
-
- Calculate a sine taper for those points shallower than the given threshold.
-
- The depth_function gives the depth (in metres) at each (i,j,k) point.
- The threshold_depth is the depth (in metres) at each (i,j) point.
- The returned taper gives a value in the range [0, 1] at each (i,j,k) point,
- where those points at a depth below the threshold are set to 1.0 and those
- above approach 0.0 as they approach the surface according to a sine
- function.
-
-
- Compute the components of the neutral diffusion tensor.
-
- Compute the taper functions to be applied to the components of the diffusion
- tensor.
-
- This function applies the boundary conditions relevent to the flags
- tmask_neutral_on and tmask_sigma_on.
-
diff --git a/src/mom5/ocean_param/neutral/ocean_nphysics_util.F90 b/src/mom5/ocean_param/neutral/ocean_nphysics_util.F90
index 892999183a..6861b765bc 100644
--- a/src/mom5/ocean_param/neutral/ocean_nphysics_util.F90
+++ b/src/mom5/ocean_param/neutral/ocean_nphysics_util.F90
@@ -858,9 +858,9 @@ module ocean_nphysics_util_mod
!*************************************
character(len=128) :: version=&
- '$Id: ocean_nphysics_util.F90,v 1.1.2.2 2012/05/17 13:41:47 smg Exp $'
+ '$Id: ocean_nphysics_util.F90,v 20.0 2013/12/14 00:14:52 fms Exp $'
character (len=128) :: tagname = &
- '$Name: mom5_siena_08jun2012_smg $'
+ '$Name: tikal $'
character(len=*), parameter :: FILENAME=&
__FILE__
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-
-
-
-Module ocean_nphysics_util_mod
-
-
-
-
-PUBLIC INTERFACE
-
- ~ PUBLIC ROUTINES
- ~ NAMELIST
-
-
- Initialize the utility module for neutral physics.
-
-
-
-
-
-
-
-
cabbeling_thermob_init
-
-
-DESCRIPTION
-
-
- Initialize the cabbeling and thermobaricity related diagnostic
- fields and register the diagnostics to the diag manager.
-
-
-
-
-
-
-
-
ocean_nphysics_coeff_init
-
-
-DESCRIPTION
-
-
- Initialize the diffusivities used in neutral physics.
- Need to initialize them after the ocean_nphysics_util_init routine,
- since need to have the domain parameters known for passing the
- array size information into the ocean_nphysics_coeff_init routine.
-
-
-
-
-
-
-
-
tracer_derivs
-
-
-DESCRIPTION
-
-
- Compute the tracer derivatives.
-
- Horizontal derivatives are taken along surfaces of
- constant vertical coordinate (constant k-level)
-
- This approach ensures that when neutral physics defaults to "horizontal" physics
- next to boundaries, it will do so as horizontal, defined along surfaces of constant
- s-surfaces, and so will not generate spurious extrema.
-
- Additionally, when using generalized vertical coordinates, the neutral diffusion
- slope should be computed relative to the s-surfaces. The skew diffusion slope
- should ideally be computed with respect to z-surfaces, as z-surfaces define
- available potential energy. However, when s and z surfaces are reasonably close,
- as they are in the interior for zstar and pstar vertical coordinates, then we
- choose to to dissipate thickness as defined relative to the zstar or pstar surfaces.
- This should not be such a big deal, and it is certainly easier computationally than
- worrying about computing two separate sets of slopes. More on this detail is
- discussed in "Elements of MOM".
-
- NOTE: This approach is not appropriate for sigma-models. Indeed, many assumptions
- in the neutral physics modules need to be rethought for terrain following vertical
- coordinates.
-
- Vertical neutral density derivative for use in fz_terms
- and fz_flux, and for use in fx_flux and fy_flux.
- Note that the derivative at k=nk vanishes by definition
- since these derivatives are at the bottom of tracer cell.
- also note the use of -epsln_drhodz ensures the vertical
- derivative is always < 0. We also support the same
- approach used in the mom4p0d code for legacy purposes.
-
- Comments about smoothing drhodz:
-
- 1/ Tests in coupled 1-degree model showed extreme sensitivity
- of MOC to smoothing. GFDL users generally do NOT smooth, hence
- the default drhodz_smooth_vert=drhodz_smooth_horz=.false.
-
- 2/ Smoothing the vertical derivative of drhodzb and drhodzh helps
- is greatly needed for producing a regularized (i.e., well behaved)
- neutral slope vector.
-
- 3/ An attempt was made to smooth dTdz and dSdz rather
- than drhodz. The resulting slope was smooth, but not as
- smooth as when acting on drhodz itself.
-
-
-
-
-
-
-
-
-
neutral_slopes
-
-
-DESCRIPTION
-
-
- Subroutine computes the neutral slopes for the triads associated
- with the vertical flux component.
-
- Array tensor_31 initially holds the x-slope used for flux component fz.
- Array tensor_32 initially holds the y-slope used for flux component fz.
-
- In subsequent calculations, these arrays will be multipied by the
- diffusivities.
-
- No slope tapering is applied in this routine.
-
- slopes are computed over k=1,nk-1, since the slope at k=nk
- should be zero.
-
-
-
-
-
-
-
-
-
compute_eady_rate
-
-
-DESCRIPTION
-
-
- Finish computing eady growth rate.
-
-
-
-
-
-
-
-
compute_baroclinicity
-
-
-DESCRIPTION
-
-
- Finish computing baroclinicity, which is defined to be the vertically
- averaged magnitude of the horizontal density gradient.
-
-
-
-
-
-
-
-
compute_rossby_radius
-
-
-DESCRIPTION
-
-
- Subroutine computes the first baroclinic Rossby radius of deformation.
- Employ WKB approach described by Chelton et al. In particular,
- use formulae (2.2), (2.3a) and (2.3b) from their paper.
-
- Place a max and min value on the Rossby radius.
-
- Compute buoyancy frequency in terms of vertical gradient of
- locally referenced potential density. Place the reference point
- at the interface between the tracer cells, which is also where
- the vertical derivative of neutral density is located. This amounts
- to a centered difference computation similar to that used by
- Chelton et al. equation (B.4).
-
-
-
-
-
-
-
-
compute_bczone_radius
-
-
-DESCRIPTION
-
-
- Subroutine computes the radius of the baroclinic zone in a manner
- suggested by the Hadley Centre approach (Malcolm Roberts, personal
- communication).
-
- Algorithm is used in MOM3 and documented in the MOM3 Manual.
-
-
-
-
-
-
-
-
-
compute_diffusivity
-
-
-DESCRIPTION
-
-
- Subroutine computes flow dependent diffusivity.
- Allow for an added dimensionless tuning factor as well as a
- minimum and maximum diffusivity.
-
-
-
-
-
-
-
-
transport_on_nrho_gm
-
-
-DESCRIPTION
-
-
- Classify horizontal GM mass transport according to neutral density classes.
-
- NOTE: This diagnostic works with transport integrated from bottom to
- a particular cell depth. To get transport_on_nrho_gm, a remapping is
- performed, rather than the binning done for trans_rho.
-
- Code history
- 2008: algorithm based (incorrectly) on transport_on_rho
- 2009: algorithm corrected to be consistent with remapping
- used in tracer_on_rho algorithm
-
-
-
-
-
-
-
-
transport_on_rho_gm
-
-
-DESCRIPTION
-
-
- Classify horizontal GM mass transport according to potential density classes.
-
- Algorithm based on linear interpolation of function on s-surfaces to
- function on rho-surfaces.
-
- Diagnostic makes sense when potrho is monotonically increasing with
- depth, although the algorithm does not explicitly make this assumption.
-
- NOTE: This diagnostic works with transport integrated from bottom to
- a particular cell depth. To get transport_on_rho_gm, a remapping is
- performed, rather than the binning done for trans_rho.
-
- Code history
-
- 2008: algorithm based (incorrectly) on transport_on_rho
- 2009: algorithm corrected to be consistent with remapping
- used in tracer_on_rho algorithm
-
-
-
-
-
-
-
-
-
transport_on_theta_gm
-
-
-DESCRIPTION
-
-
- Classify horizontal GM mass transport according to potential temp classes.
-
- Algorithm based on linear interpolation of function on s-surfaces to
- function on rho-surfaces.
-
- Diagnostic makes sense when potential temp is monotonically increasing
- with depth, although the algorithm does not explicitly make this assumption.
-
- NOTE: This diagnostic works with transport integrated from bottom to
- a particular cell depth. To get transport_on_theta_gm, a remapping is
- performed, rather than the binning done for trans_rho.
-
- Code history
-
- 2009: algorithm based on transport_on_rho_gm
-
-
-
-
-
-
-
-
-
compute_eta_tend_gm90
-
-
-DESCRIPTION
-
-
- Diagnose contribution to global mean sea level evolution arising
- from analytic form of Gent-McWilliams scheme.
-
- This routine computes the diagnostic based on an analytic form of the
- GM90 contribution. The raw numerical form is computed inside the respective
- nphysics modules. The raw numerical form is more accurate and thus
- recomended for purposes of sea level budgets.
-
- Compute an averaged slope using tensor_31 and tensor_32.
- Then compute the neutral divergence of this slope vector, just
- as if each component of the slope was a scalar.
-
- To avoid stencil issues with bottom cells, mask to zero
- contributions from cells next to the bottom in either of the
- three directions.
-
- Send output to diagnostic manager.
-
- Subroutine history:
- Feb2010 version 1.0: Stephen.Griffies
-
-
-
-
-
-
-
-
-
cabbeling_thermob_tendency
-
-
-DESCRIPTION
-
-
- Compute tendencies from cabbeling and thermobaricity.
-
- To avoid stencil issues with bottom cells, mask to zero
- contributions from cells next to the bottom in either of the
- three directions.
-
- Set cabbeling and thermobaricity to zero in regions where
- vertical stratification is gravitationally unstable. The idea is
- that in such regions, convective mixing will wash away the impact of
- along-neutral diffusion, in which case cabbeling and thermobaricity
- are not relevant anyhow.
-
- Set the vertical stratification drho_dz to a negative number
- with lower bound on its magnitude as set by epsln_drhodz_diagnostics.
-
- Send output to diagnostic manager.
-
- Subroutine history:
- Jan2010 version 1.0: initial coding by Stephen.Griffies
- Mar2010 version 2.0: tweaks on the division by drho_dz and strat_mask
-
-
-
-
-
-
-
-
-
pressure_derivs
-
-
-DESCRIPTION
-
-
- Compute the pressure derivatives for use in thermobaricity diagnostic.
-
-
-
-
-
-
-
-
calc_gradx_gamma_scalar
-
-
-DESCRIPTION
-
-
- Subroutine computes the i-gradient along neutral surfaces
- for a scalar field. For use in the cabbeling and thermobaricity
- diagnostic. Thus, when slope is steep, the full derivative is
- tapered, rather than just the off-diagonal term.
-
- We only compute neutral i-gradient for interior regions,
- since will be setting thermobaricity and cabbeling to zero at
- top and bottom levels; do not trust the calculation at top
- and bottom boundaries due to stencil truncations.
-
- Algorithm slightly modified from ocean_nphysC calculation of
- neutral diffusion x-flux.
-
-
-
-
-
-
-
-
-
calc_grady_gamma_scalar
-
-
-DESCRIPTION
-
-
- Subroutine computes the y-gradient along neutral surfaces
- for a scalar field. For use in the cabbeling and thermobaricity
- diagnostic. Thus, when slope is steep, the full derivative is
- tapered, rather than just the off-diagonal term.
-
- We only compute neutral y-gradient for interior regions,
- since will be setting thermobaricity and cabbeling to zero at
- top and bottom levels; do not trust the calculation at top
- and bottom boundaries due to stencil truncations.
-
- Algorithm slightly modified from ocean_nphysC calculation of
- neutral diffusion y-flux.
-
-
-
-
-
-
-
-
-
watermass_diag_init
-
-
-DESCRIPTION
-
-
- Initialization of watermass diagnostic output files.
-
-
-
-
-
-
-
-
watermass_diag
-
-
-DESCRIPTION
-
-
- Diagnose effects from nphysics on the watermass transformation.
- For use with nphysicsA and nphysicsB.
-
-
-
-
-
-
-
-
watermass_diag_ndiffuse
-
-
-DESCRIPTION
-
-
-
- Diagnose watermass transformation from neutral diffusion.
- For use with the nphysicsC scheme.
-
-
-
-
-
-
-
-
-
watermass_diag_sdiffuse
-
-
-DESCRIPTION
-
-
-
- Diagnose watermass transformation from skew diffusion.
- For use with the neutral physics C scheme.
-
-
-
-
-
-
-
-
-
ocean_nphysics_util_restart
-
-
-DESCRIPTION
-
-
- Write out restart files registered through register_restart_file
-
-
-
-
-
-
-
-
ocean_nphysics_coeff_end
-
-
-DESCRIPTION
-
-
- Write to restart.
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_nphysics_util_nml
-
-
-
-
-
-debug_this_module
-
-
- For printing starting and ending checksums for restarts
-
-[logical]
-
-
-nphysics_util_zero_init
-
-
- For Time%init=.true. and wishing to ensure starting with a clean
- suite of nphysics_util fields, even if ocean_neutral.res.nc exists.
-
-[logical]
-
-
-epsln_drhodz
-
-
- For computing drhodz used in slope calculation.
- We must keep drhodz < 0 in order to maintain integrity of the
- quasi-Stokes streamfunction as well as computation of buoyancy frequency.
- Default epsln_drhodz=1e-30.
-
-[real, units: kg/m^3]
-
-
-drhodz_mom4p1
-
-
- For computing the vertical deriviative of locally referenced
- potrho as in the preferred MOM algorithm rather than the
- earlier mom4p0 approach. Default drhodz_mom4p1=.true.
-
-[logical]
-
-
-drhodz_smooth_horz
-
-
- For horizontal laplacian smoothing the vertical derivative
- of density prior to its use in computing the neutral slopes.
- This smoothing helps to produce regularized slopes.
- Note that this option breaks the integrity of the triads
- and is thus NOT generally recommended.
- Default drhodz_smooth_horz=.false.
-
-[logical]
-
-
-drhodz_smooth_vert
-
-
- For vertical 1-2-1 smoothing the vertical derivative of
- density prior to its use in computing the neutral slopes.
- This smoothing helps to produce regularized slopes.
- Note that this option breaks the integrity of the triads
- and is thus NOT generally recommended.
- Default drhodz_smooth_vert=.false.
-
-[logical]
-
-
-vel_micom_smooth
-
-
- Velocity scale that is used for computing the MICOM Laplacian mixing
- coefficient used in smoothing of drhodzb.
- Default vel_micom_smooth=0.2.
-
-[real, units: m/sec]
-
-
-num_121_passes
-
-
- For number of 1-2-1 passes through to smooth drhodz or
- eady_rate in vertical. Default num_121_passes=1.
-
-[integer]
-
-
-aredi
-
-
- Neutral diffusivity used for experiments using a constant diffusivity.
-
-[real]
-
-
-agm
-
-
- GM-skew diffusivity used for experiments using a constant diffusivity.
-
-[real]
-
-
-aredi_equal_agm
-
-
- Will set aredi_array=agm_array, over-riding any other specification
- of aredi_array. Default aredi_equal_agm=.true.
-
-[logical]
-
-
-smax
-
-
- Value of the maximum neutral direction slope above which the neutral fluxes are
- either tapered to zero or saturated. Typical value is smax=0.01 or smaller.
-
-[real]
-
-
-swidth
-
-
- Width in slope over which use tanh with dm_taper scheme to taper fluxes in
- steep sloped regions. Typical value swidth=0.1*smax
-
-[real]
-
-
-smax_grad_gamma_scalar
-
-
- For calculation of gradients of scalars along a neutral direction, then
- when abs(slope) > smax_grad_gamma_scalar, will compute the gradient using
- only the vertical scalar gradient, since the slopes are so large they are
- effectively infinite.
- Default smax_grad_gamma_scalar=.01
-
-[real]
-
-
-neutral_horz_mix_bdy
-
-
- If .true., then use a horizontal diffusivity in the neutral boundary layer.
-
-[logical]
-
-
-vel_micom_bdy
-
-
- Velocity scale that is used for computing the MICOM horizontal diffusivity
- within the neutral boundary layer.
-
-[real, units: m/sec]
-
-
-ah_bdy
-
-
- Constant horizontal diffusivity for the boundary layer.
- Default ah_bdy=0.0.
-
-[real, units: m^2/sec]
-
-
-tracer_mix_micom
-
-
- If .true., then the GM-skew diffusivity is set according to a velocity scale
- times the grid spacing.
-
-[logical]
-
-
-vel_micom
-
-
- Velocity scale that is used for computing the MICOM diffusivity.
-
-[real, units: m/sec]
-
-
-agm_lat_zones
-
-
- If true, will set agm_array as constant within two latitudinal zones.
- The idea is that one may wish to use a larger agm in the ACC than
- elsewhere.
-
-[logical]
-
-
-agm_lat_zones_boundary
-
-
- Boundary between agm in the south and north zones.
-
-[real]
-
-
-agm_lat_zones_ratio
-
-
- Ratio between the large agm used in the southern latitudinal zone
- to that used in the north.
- agm_array(north) = agm
- agm_array(south) = agm*agm_lat_zones_ratio
-
-[real]
-
-
-bryan_lewis_aredi
-
-
- Set bryan_lewis_aredi=.true. when want to have aredi a function of depth
- according to the Bryan and Lewis (1979) profile. Maintained for legacy
- purposes, and not recommended for new models.
-
-[logical]
-
-
-ahs
-
-
- ahs = adjustable parameter at the surface for bryan_lewis_aredi
-
-[real]
-
-
-ahb
-
-
- ahb = adjustable parameter at the bottom for bryan_lewis_aredi
-
-[real]
-
-
-agm_read_restart
-
-
- For those cases with agm_closure=.false. where we wish to read in
- the agm_array from restart files and keep the value from the restart.
- This approach allows us to read in a spatially dependent agm_array
- that may have been computed from another integration, but to leave
- the coefficient static in time.
- Default agm_read_restart=.false.
-
-[logical]
-
-
-agm_closure
-
-
- If .true. then will compute the GM-skew diffusivity as a function of the flow.
- The length scale is determined by the Rossby radius and the time scale is
- determined by the Eady growth rate. Diffusivities are depth independent.
-
-[logical]
-
-
-agm_closure_max
-
-
- Maximum GM diffusivity allowed when using agm_closure=.true.
-
-[real, units: m^2/sec]
-
-
-agm_closure_min
-
-
- Minimum GM diffusivity allowed when using agm_closure=.true.
-
-[real, units: m^2/sec]
-
- Upper depth where start the depth integration to compute the Eady
- growth rate and/or baroclinicity.
-
-[real, units: m]
-
-
-agm_closure_lower_depth
-
-
- Deeper depth where finish the depth integration to compute the Eady
- growth rate and/or baroclinicity.
-
-[real, units: m]
-
-
-agm_closure_n2_scale
-
-
- For computing the agm coefficient using a 3-dimensional
- scaling by (N/Nref)^2, with N=buoyancy frequency and
- Nref the buoyancy frequency at the base of the neutral
- blayer. Default agm_closure_n2_scale=.false.
-
-[logical]
-
-
-agm_closure_n2_scale_coeff
-
-
- Coefficient setting the scale for the diffusivity computed from
- agm_closure_n2_scale.
- Default agm_closure_n2_scale_coeff=1e3.
-
-[real, units: m^2/s]
-
-
-agm_closure_n2_scale_nref_cst
-
-
- For taking the reference buoyancy frequency as agm_closure_buoy_freq
- for the (N/Nref)^2 scaling.
- Default agm_closure_n2_scale_nref_cst=.false.
-
-[logical]
-
-
-agm_closure_baroclinic
-
-
- For computing the agm coefficient using only the vertically
- averaged magnitude of the horizontal density gradient
- (i.e., the "baroclinicity").
-
-[logical]
-
-
-agm_closure_buoy_freq
-
-
- For computing the agm coefficient using only the vertically
- averaged horizontal density gradient, we need to specify a
- buoyancy frequency, which is taken to be fixed over all space-time.
-
-[real, units: sec^-1]
-
-
-agm_closure_length_cap
-
-
- For setting a maximum length scale for the agm_closure calculation.
- Default agm_closure_length_cap=.false.
-
-[logical]
-
-
-agm_closure_length_max
-
-
- Maximum length scale used for computing agm_closure.
- Default agm_closure_length_max=50e3.
-
-[real, units: metre]
-
-
-agm_closure_length_fixed
-
-
- Use fixed length scale for computing agm_closure diffusivity
-
-[logical]
-
-
-agm_closure_length
-
-
- Fixed length scale for use with agm_closure_fixed_length
-
-[real, units: meter]
-
-
-agm_closure_length_rossby
-
-
- For computing the agm_closure length scale according to Rossby radius.
-
-[logical]
-
-
-rossby_radius_max
-
-
- Maximum Rossby radius used for agm_closure_length_rossby and
- the neutral_sine_taper. Default = 100e3 m.
-
-[real, units: meter]
-
-
-rossby_radius_min
-
-
- Minimum Rossby Radius used for agm_closure_length_rossby and
- the neutral_sine_taper. Default = 15e3 m.
-
-[real, units: meter]
-
-
-agm_closure_length_bczone
-
-
- For computing the agm_closure length scale according to radius of baroclinic zone.
-
-[logical]
-
-
-bczone_max_pts
-
-
- Max number of horizontal grid points for use in computing the baroclinic zone radius.
-
-[integer]
-
-
-agm_closure_bczone_crit_rate
-
-
- Critical growth rate for determining width of the baroclinic zone.
-
-[real, units: sec^-1]
-
-
-agm_closure_growth_scale
-
-
- Dimensionless scaling used to set a maximum for agm_growth.
-
-[real, units: dimensionless]
-
-
-agm_closure_eden_greatbatch
-
-
- For computing the agm_closure length scale according to minimum
- of the Rhines scale and the Rossby radius, and using 3d Eady
- growth rate.
-
-[logical]
-
-
-agm_closure_eden_gamma
-
-
- For use in regularizing the growth rate used in the eden/greatbatch approach.
- Default agm_closure_eden_gamma=200. Setting to zero removes the regularization.
-
-[real, units: dimensionless]
-
-
-agm_closure_eden_length_const
-
-
- To set the length scale for agm_closure_eden_greatbatch to constant.
- Default agm_closure_eden_length_const=.false.
-
-[logical]
-
-
-agm_closure_eden_length
-
-
- Length scale for use with agm_closure_eden_length_const=.true.
- Default agm_closure_eden_length=10e3.
-
-[real, units: metre]
-
-
-agm_closure_eady_smooth_vert
-
-
- For vertical 1-2-1 smoothing the eady_rate
- Default agm_closure_eady_smooth=.false.
-
-[logical]
-
-
-agm_closure_eady_smooth_horz
-
-
- For horizontal Laplacian smoothing of eady growth rate.
- Default agm_closure_eady_smooth_horz=.false.
-
-[logical]
-
-
-agm_closure_eady_cap
-
-
- For capping the eady growth rate to avoid huge values.
- Default agm_closure_eady_cap=.false.
-
-[logical]
-
-
-agm_closure_eady_ave_mixed
-
-
- To set the Eady growth rate to its average within mixed layer region.
- This is used to avoid spuriously large values which often appear just
- in the upper regions of the ocean mixed layer.
- Default agm_closure_eady_ave_mixed=.false.
-
-[logical]
-
-
-agm_smooth_space
-
-
- For smoothing the agm diffusivity in space when nonconstant diffusivity used.
- Default is agm_smooth_space=.false.
-
-[logical]
-
-
-agm_smooth_time
-
-
- For smoothing the agm diffusivity in time when nonconstant diffusivity used.
- Default is agm_smooth_time=.false.
-
-[logical]
-
-
-agm_damping_time
-
-
- The damping time used for time smoothing agm_array.
- Default agm_damping_time=10days.
-
-[real, units: days]
-
-
-agm_closure_grid_scaling
-
-
- For an overall scaling of the agm coefficient, according to
- the relative resolution of the grid and deformation radius.
- Default is agm_closure_grid_scaling=.false.
-
-[logical]
-
-
-agm_closure_grid_scaling_power
-
-
- Power used to scale the agm_closure diffusivity.
- Default is agm_closure_grid_scaling_power=2.0
-
-[real]
-
-
-aredi_diffusivity_grid_scaling
-
-
- For an overall scaling of the aredi coefficient, according to
- the relative resolution of the grid and deformation radius.
- This option is used only when aredi_equal_agm=.false.
- Default is aredi_diffusivity_grid_scaling=.false.
-
-[logical]
-
-
-epsln_drhodz_diagnostics
-
-
- For drhodz used in calculation of dianeutral velocity component
- from cabbeling and thermobaricity.
- Default epsln_drhodz_diagnostics=1e-7.
-
-[real, units: kg/m4]
-
-
-wdianeutral_smooth
-
-
- For smoothing the diagnosed dianeutral velocity component using a
- horizontal 1-2-1 smoother. Default is wdianeutral_smooth=.true.
-
-[logical]
-
-
-smooth_eta_tend_gm90
-
-
- For smoothing the diagnosed contribution to steric sea level
- time tendency associated with the GM90 scheme.
- Default is smooth_eta_tend_gm90=.false.
-
-[logical]
-
-
-
-
-
-
-
-
-
-
-
REFERENCES
-
-
-
-
- D.B. Chelton, R.A. deSzoeke, M.G. Schlax, K.E. Naggar, N. Siwertz
- Geographical Variability of the First Baroclinic Rossby Radius of Deformation
- Journal of Physical Oceanography (1998) vol 28 pages 433-460
-
-
- G. Danabasoglu and J. C. McWilliams
- Sensitivity of the global ocean circulation to
- parameterizations of mesoscale tracer transports
- Journal of Climate (1995) vol 8 pages 2967--2987
-
-
- Held and Larichev
- A scaling theory for horizontally homogeneous baroclinically
- unstable flow on a beta plane
- Journal of Atmospheric Sciences (1996) vol 53 pages 946-952
-
-
- M. Visbeck, J.C. Marshall, T. Haine and M. Spall
- Specification of eddy transfer coefficients in coarse resolution ocean
- circulation models
- Journal of Physical Oceanography (1997) vol 27 pages 381--402
-
-
- D. Ferreira, J. Marshall, and P. Heimbach,
- Estimating eddy stresses by fitting dynamics to observations
- using a residual-mean ocean circulation omdel and its adjoint.
- Journal of Physical Oceanography (2005) vol 35 pages 1891-1910.
-
-
- K. Eden, Eddy length scales in the North Atlantic, 2007,
- Preprint.
-
-
- K. Eden and R. Greatbatch, 2008: Towards a mesoscale eddy closure,
- Ocean Modelling, vol. 20, pages 223-239
-
-
-
-
-
-
-
-
NOTES
-
-
- Diffusivities can be determined in a number of manners
-
- TIME INDEPENDENT
-
- Various methods are available for specifying a time
- independent diffusivity, either globally uniform or
- with selections of spatial dependence.
-
- TIME DEPENDENT (as a function of the flow)
-
- Various methods are available for determining the
- diffusivity that changes in time according to the
- properties of the fluid. There are various means
- for specifying the length and time scales needed
- to set the diffusivity.
-
- LENGTH SCALES
-
- 1. First baroclinic Rossby radius (estimated as per Chelton etal).
- Equatorial Rossby radius is used within 5deg of the equator.
-
- 2. Width of the baroclinic zone, as done in the Hadley Centre
- model and documented in the MOM3 Manual.
-
- 3. Specified length scale set independent of the flow.
-
- TIME SCALE
-
- When using either of the above for the length scale,
- the time scale is determined by the Eady growth rate.
-
- COMBINED LENGTH/TIME SCALE
-
- Another option, used in the GFDL CM2.X coupled climate models,
- is to set the diffusivity proportional to the depth averaged
- absolute value of the horizontal density gradient.
-
-
-
diff --git a/src/mom5/ocean_param/neutral/ocean_nphysics_util.xml b/src/mom5/ocean_param/neutral/ocean_nphysics_util.xml
deleted file mode 100644
index 00bafcff4d..0000000000
--- a/src/mom5/ocean_param/neutral/ocean_nphysics_util.xml
+++ /dev/null
@@ -1,534 +0,0 @@
-
-
- Stephen M. Griffies
- Tim Leslie
-
- Utilities for neutral physics, including the code to compute
- space-time dependent diffusivities.
-
- Utilities for neutral physics, including the code to compute
- space-time dependent diffusivities and many diagnostics.
-
- D.B. Chelton, R.A. deSzoeke, M.G. Schlax, K.E. Naggar, N. Siwertz
- Geographical Variability of the First Baroclinic Rossby Radius of Deformation
- Journal of Physical Oceanography (1998) vol 28 pages 433-460
-
- G. Danabasoglu and J. C. McWilliams
- Sensitivity of the global ocean circulation to
- parameterizations of mesoscale tracer transports
- Journal of Climate (1995) vol 8 pages 2967--2987
-
- Held and Larichev
- A scaling theory for horizontally homogeneous baroclinically
- unstable flow on a beta plane
- Journal of Atmospheric Sciences (1996) vol 53 pages 946-952
-
- M. Visbeck, J.C. Marshall, T. Haine and M. Spall
- Specification of eddy transfer coefficients in coarse resolution ocean
- circulation models
- Journal of Physical Oceanography (1997) vol 27 pages 381--402
-
- D. Ferreira, J. Marshall, and P. Heimbach,
- Estimating eddy stresses by fitting dynamics to observations
- using a residual-mean ocean circulation omdel and its adjoint.
- Journal of Physical Oceanography (2005) vol 35 pages 1891-1910.
-
- K. Eden, Eddy length scales in the North Atlantic, 2007,
- Preprint.
-
- K. Eden and R. Greatbatch, 2008: Towards a mesoscale eddy closure,
- Ocean Modelling, vol. 20, pages 223-239
-
- Diffusivities can be determined in a number of manners
-
- TIME INDEPENDENT
-
- Various methods are available for specifying a time
- independent diffusivity, either globally uniform or
- with selections of spatial dependence.
-
- TIME DEPENDENT (as a function of the flow)
-
- Various methods are available for determining the
- diffusivity that changes in time according to the
- properties of the fluid. There are various means
- for specifying the length and time scales needed
- to set the diffusivity.
-
- LENGTH SCALES
-
- 1. First baroclinic Rossby radius (estimated as per Chelton etal).
- Equatorial Rossby radius is used within 5deg of the equator.
-
- 2. Width of the baroclinic zone, as done in the Hadley Centre
- model and documented in the MOM3 Manual.
-
- 3. Specified length scale set independent of the flow.
-
- TIME SCALE
-
- When using either of the above for the length scale,
- the time scale is determined by the Eady growth rate.
-
- COMBINED LENGTH/TIME SCALE
-
- Another option, used in the GFDL CM2.X coupled climate models,
- is to set the diffusivity proportional to the depth averaged
- absolute value of the horizontal density gradient.
-
- For printing starting and ending checksums for restarts
-
- For Time%init=.true. and wishing to ensure starting with a clean
- suite of nphysics_util fields, even if ocean_neutral.res.nc exists.
-
- For computing drhodz used in slope calculation.
- We must keep drhodz < 0 in order to maintain integrity of the
- quasi-Stokes streamfunction as well as computation of buoyancy frequency.
- Default epsln_drhodz=1e-30.
-
- For computing the vertical deriviative of locally referenced
- potrho as in the preferred MOM algorithm rather than the
- earlier mom4p0 approach. Default drhodz_mom4p1=.true.
-
- For horizontal laplacian smoothing the vertical derivative
- of density prior to its use in computing the neutral slopes.
- This smoothing helps to produce regularized slopes.
- Note that this option breaks the integrity of the triads
- and is thus NOT generally recommended.
- Default drhodz_smooth_horz=.false.
-
- For vertical 1-2-1 smoothing the vertical derivative of
- density prior to its use in computing the neutral slopes.
- This smoothing helps to produce regularized slopes.
- Note that this option breaks the integrity of the triads
- and is thus NOT generally recommended.
- Default drhodz_smooth_vert=.false.
-
- Velocity scale that is used for computing the MICOM Laplacian mixing
- coefficient used in smoothing of drhodzb.
- Default vel_micom_smooth=0.2.
-
- For number of 1-2-1 passes through to smooth drhodz or
- eady_rate in vertical. Default num_121_passes=1.
-
- Neutral diffusivity used for experiments using a constant diffusivity.
-
- GM-skew diffusivity used for experiments using a constant diffusivity.
-
- Will set aredi_array=agm_array, over-riding any other specification
- of aredi_array. Default aredi_equal_agm=.true.
-
- Value of the maximum neutral direction slope above which the neutral fluxes are
- either tapered to zero or saturated. Typical value is smax=0.01 or smaller.
-
- Width in slope over which use tanh with dm_taper scheme to taper fluxes in
- steep sloped regions. Typical value swidth=0.1*smax
-
- For calculation of gradients of scalars along a neutral direction, then
- when abs(slope) > smax_grad_gamma_scalar, will compute the gradient using
- only the vertical scalar gradient, since the slopes are so large they are
- effectively infinite.
- Default smax_grad_gamma_scalar=.01
-
- If .true., then use a horizontal diffusivity in the neutral boundary layer.
-
- Velocity scale that is used for computing the MICOM horizontal diffusivity
- within the neutral boundary layer.
-
- Constant horizontal diffusivity for the boundary layer.
- Default ah_bdy=0.0.
-
- If .true., then the GM-skew diffusivity is set according to a velocity scale
- times the grid spacing.
-
- Velocity scale that is used for computing the MICOM diffusivity.
-
- If true, will set agm_array as constant within two latitudinal zones.
- The idea is that one may wish to use a larger agm in the ACC than
- elsewhere.
-
- Boundary between agm in the south and north zones.
-
- Ratio between the large agm used in the southern latitudinal zone
- to that used in the north.
- agm_array(north) = agm
- agm_array(south) = agm*agm_lat_zones_ratio
-
- Set bryan_lewis_aredi=.true. when want to have aredi a function of depth
- according to the Bryan and Lewis (1979) profile. Maintained for legacy
- purposes, and not recommended for new models.
-
- ahs = adjustable parameter at the surface for bryan_lewis_aredi
-
- ahb = adjustable parameter at the bottom for bryan_lewis_aredi
-
- For those cases with agm_closure=.false. where we wish to read in
- the agm_array from restart files and keep the value from the restart.
- This approach allows us to read in a spatially dependent agm_array
- that may have been computed from another integration, but to leave
- the coefficient static in time.
- Default agm_read_restart=.false.
-
- If .true. then will compute the GM-skew diffusivity as a function of the flow.
- The length scale is determined by the Rossby radius and the time scale is
- determined by the Eady growth rate. Diffusivities are depth independent.
-
- Maximum GM diffusivity allowed when using agm_closure=.true.
-
- Minimum GM diffusivity allowed when using agm_closure=.true.
-
- Dimensionless tuning parameter for computing flow dependent diffusivities.
-
- Upper depth where start the depth integration to compute the Eady
- growth rate and/or baroclinicity.
-
- Deeper depth where finish the depth integration to compute the Eady
- growth rate and/or baroclinicity.
-
- For computing the agm coefficient using a 3-dimensional
- scaling by (N/Nref)^2, with N=buoyancy frequency and
- Nref the buoyancy frequency at the base of the neutral
- blayer. Default agm_closure_n2_scale=.false.
-
- Coefficient setting the scale for the diffusivity computed from
- agm_closure_n2_scale.
- Default agm_closure_n2_scale_coeff=1e3.
-
- For taking the reference buoyancy frequency as agm_closure_buoy_freq
- for the (N/Nref)^2 scaling.
- Default agm_closure_n2_scale_nref_cst=.false.
-
- For computing the agm coefficient using only the vertically
- averaged magnitude of the horizontal density gradient
- (i.e., the "baroclinicity").
-
- For computing the agm coefficient using only the vertically
- averaged horizontal density gradient, we need to specify a
- buoyancy frequency, which is taken to be fixed over all space-time.
-
- For setting a maximum length scale for the agm_closure calculation.
- Default agm_closure_length_cap=.false.
-
- Maximum length scale used for computing agm_closure.
- Default agm_closure_length_max=50e3.
-
- Use fixed length scale for computing agm_closure diffusivity
-
- Fixed length scale for use with agm_closure_fixed_length
-
- For computing the agm_closure length scale according to Rossby radius.
-
- Maximum Rossby radius used for agm_closure_length_rossby and
- the neutral_sine_taper. Default = 100e3 m.
-
- Minimum Rossby Radius used for agm_closure_length_rossby and
- the neutral_sine_taper. Default = 15e3 m.
-
- For computing the agm_closure length scale according to radius of baroclinic zone.
-
- Max number of horizontal grid points for use in computing the baroclinic zone radius.
-
- Critical growth rate for determining width of the baroclinic zone.
-
- Dimensionless scaling used to set a maximum for agm_growth.
-
- For computing the agm_closure length scale according to minimum
- of the Rhines scale and the Rossby radius, and using 3d Eady
- growth rate.
-
- For use in regularizing the growth rate used in the eden/greatbatch approach.
- Default agm_closure_eden_gamma=200. Setting to zero removes the regularization.
-
- To set the length scale for agm_closure_eden_greatbatch to constant.
- Default agm_closure_eden_length_const=.false.
-
- Length scale for use with agm_closure_eden_length_const=.true.
- Default agm_closure_eden_length=10e3.
-
- For vertical 1-2-1 smoothing the eady_rate
- Default agm_closure_eady_smooth=.false.
-
- For horizontal Laplacian smoothing of eady growth rate.
- Default agm_closure_eady_smooth_horz=.false.
-
- For capping the eady growth rate to avoid huge values.
- Default agm_closure_eady_cap=.false.
-
- To set the Eady growth rate to its average within mixed layer region.
- This is used to avoid spuriously large values which often appear just
- in the upper regions of the ocean mixed layer.
- Default agm_closure_eady_ave_mixed=.false.
-
- For smoothing the agm diffusivity in space when nonconstant diffusivity used.
- Default is agm_smooth_space=.false.
-
- For smoothing the agm diffusivity in time when nonconstant diffusivity used.
- Default is agm_smooth_time=.false.
-
- The damping time used for time smoothing agm_array.
- Default agm_damping_time=10days.
-
- For an overall scaling of the agm coefficient, according to
- the relative resolution of the grid and deformation radius.
- Default is agm_closure_grid_scaling=.false.
-
- Power used to scale the agm_closure diffusivity.
- Default is agm_closure_grid_scaling_power=2.0
-
- For an overall scaling of the aredi coefficient, according to
- the relative resolution of the grid and deformation radius.
- This option is used only when aredi_equal_agm=.false.
- Default is aredi_diffusivity_grid_scaling=.false.
-
- For drhodz used in calculation of dianeutral velocity component
- from cabbeling and thermobaricity.
- Default epsln_drhodz_diagnostics=1e-7.
-
- For smoothing the diagnosed dianeutral velocity component using a
- horizontal 1-2-1 smoother. Default is wdianeutral_smooth=.true.
-
- For smoothing the diagnosed contribution to steric sea level
- time tendency associated with the GM90 scheme.
- Default is smooth_eta_tend_gm90=.false.
-
- Initialize the utility module for neutral physics.
-
- Initialize the cabbeling and thermobaricity related diagnostic
- fields and register the diagnostics to the diag manager.
-
- Initialize the diffusivities used in neutral physics.
- Need to initialize them after the ocean_nphysics_util_init routine,
- since need to have the domain parameters known for passing the
- array size information into the ocean_nphysics_coeff_init routine.
-
- Compute the tracer derivatives.
-
- Horizontal derivatives are taken along surfaces of
- constant vertical coordinate (constant k-level)
-
- This approach ensures that when neutral physics defaults to "horizontal" physics
- next to boundaries, it will do so as horizontal, defined along surfaces of constant
- s-surfaces, and so will not generate spurious extrema.
-
- Additionally, when using generalized vertical coordinates, the neutral diffusion
- slope should be computed relative to the s-surfaces. The skew diffusion slope
- should ideally be computed with respect to z-surfaces, as z-surfaces define
- available potential energy. However, when s and z surfaces are reasonably close,
- as they are in the interior for zstar and pstar vertical coordinates, then we
- choose to to dissipate thickness as defined relative to the zstar or pstar surfaces.
- This should not be such a big deal, and it is certainly easier computationally than
- worrying about computing two separate sets of slopes. More on this detail is
- discussed in "Elements of MOM".
-
- NOTE: This approach is not appropriate for sigma-models. Indeed, many assumptions
- in the neutral physics modules need to be rethought for terrain following vertical
- coordinates.
-
- Vertical neutral density derivative for use in fz_terms
- and fz_flux, and for use in fx_flux and fy_flux.
- Note that the derivative at k=nk vanishes by definition
- since these derivatives are at the bottom of tracer cell.
- also note the use of -epsln_drhodz ensures the vertical
- derivative is always < 0. We also support the same
- approach used in the mom4p0d code for legacy purposes.
-
- Comments about smoothing drhodz:
-
- 1/ Tests in coupled 1-degree model showed extreme sensitivity
- of MOC to smoothing. GFDL users generally do NOT smooth, hence
- the default drhodz_smooth_vert=drhodz_smooth_horz=.false.
-
- 2/ Smoothing the vertical derivative of drhodzb and drhodzh helps
- is greatly needed for producing a regularized (i.e., well behaved)
- neutral slope vector.
-
- 3/ An attempt was made to smooth dTdz and dSdz rather
- than drhodz. The resulting slope was smooth, but not as
- smooth as when acting on drhodz itself.
-
-
- Subroutine computes the neutral slopes for the triads associated
- with the vertical flux component.
-
- Array tensor_31 initially holds the x-slope used for flux component fz.
- Array tensor_32 initially holds the y-slope used for flux component fz.
-
- In subsequent calculations, these arrays will be multipied by the
- diffusivities.
-
- No slope tapering is applied in this routine.
-
- slopes are computed over k=1,nk-1, since the slope at k=nk
- should be zero.
-
-
- Finish computing eady growth rate.
-
- Finish computing baroclinicity, which is defined to be the vertically
- averaged magnitude of the horizontal density gradient.
-
- Subroutine computes the first baroclinic Rossby radius of deformation.
- Employ WKB approach described by Chelton et al. In particular,
- use formulae (2.2), (2.3a) and (2.3b) from their paper.
-
- Place a max and min value on the Rossby radius.
-
- Compute buoyancy frequency in terms of vertical gradient of
- locally referenced potential density. Place the reference point
- at the interface between the tracer cells, which is also where
- the vertical derivative of neutral density is located. This amounts
- to a centered difference computation similar to that used by
- Chelton et al. equation (B.4).
-
- Subroutine computes the radius of the baroclinic zone in a manner
- suggested by the Hadley Centre approach (Malcolm Roberts, personal
- communication).
-
- Algorithm is used in MOM3 and documented in the MOM3 Manual.
-
-
- Subroutine computes flow dependent diffusivity.
- Allow for an added dimensionless tuning factor as well as a
- minimum and maximum diffusivity.
-
- Classify horizontal GM mass transport according to neutral density classes.
-
- NOTE: This diagnostic works with transport integrated from bottom to
- a particular cell depth. To get transport_on_nrho_gm, a remapping is
- performed, rather than the binning done for trans_rho.
-
- Code history
- 2008: algorithm based (incorrectly) on transport_on_rho
- 2009: algorithm corrected to be consistent with remapping
- used in tracer_on_rho algorithm
-
- Classify horizontal GM mass transport according to potential density classes.
-
- Algorithm based on linear interpolation of function on s-surfaces to
- function on rho-surfaces.
-
- Diagnostic makes sense when potrho is monotonically increasing with
- depth, although the algorithm does not explicitly make this assumption.
-
- NOTE: This diagnostic works with transport integrated from bottom to
- a particular cell depth. To get transport_on_rho_gm, a remapping is
- performed, rather than the binning done for trans_rho.
-
- Code history
-
- 2008: algorithm based (incorrectly) on transport_on_rho
- 2009: algorithm corrected to be consistent with remapping
- used in tracer_on_rho algorithm
-
-
- Classify horizontal GM mass transport according to potential temp classes.
-
- Algorithm based on linear interpolation of function on s-surfaces to
- function on rho-surfaces.
-
- Diagnostic makes sense when potential temp is monotonically increasing
- with depth, although the algorithm does not explicitly make this assumption.
-
- NOTE: This diagnostic works with transport integrated from bottom to
- a particular cell depth. To get transport_on_theta_gm, a remapping is
- performed, rather than the binning done for trans_rho.
-
- Code history
-
- 2009: algorithm based on transport_on_rho_gm
-
-
- Diagnose contribution to global mean sea level evolution arising
- from analytic form of Gent-McWilliams scheme.
-
- This routine computes the diagnostic based on an analytic form of the
- GM90 contribution. The raw numerical form is computed inside the respective
- nphysics modules. The raw numerical form is more accurate and thus
- recomended for purposes of sea level budgets.
-
- Compute an averaged slope using tensor_31 and tensor_32.
- Then compute the neutral divergence of this slope vector, just
- as if each component of the slope was a scalar.
-
- To avoid stencil issues with bottom cells, mask to zero
- contributions from cells next to the bottom in either of the
- three directions.
-
- Send output to diagnostic manager.
-
- Subroutine history:
- Feb2010 version 1.0: Stephen.Griffies
-
-
- Compute tendencies from cabbeling and thermobaricity.
-
- To avoid stencil issues with bottom cells, mask to zero
- contributions from cells next to the bottom in either of the
- three directions.
-
- Set cabbeling and thermobaricity to zero in regions where
- vertical stratification is gravitationally unstable. The idea is
- that in such regions, convective mixing will wash away the impact of
- along-neutral diffusion, in which case cabbeling and thermobaricity
- are not relevant anyhow.
-
- Set the vertical stratification drho_dz to a negative number
- with lower bound on its magnitude as set by epsln_drhodz_diagnostics.
-
- Send output to diagnostic manager.
-
- Subroutine history:
- Jan2010 version 1.0: initial coding by Stephen.Griffies
- Mar2010 version 2.0: tweaks on the division by drho_dz and strat_mask
-
-
- Compute the pressure derivatives for use in thermobaricity diagnostic.
-
- Subroutine computes the i-gradient along neutral surfaces
- for a scalar field. For use in the cabbeling and thermobaricity
- diagnostic. Thus, when slope is steep, the full derivative is
- tapered, rather than just the off-diagonal term.
-
- We only compute neutral i-gradient for interior regions,
- since will be setting thermobaricity and cabbeling to zero at
- top and bottom levels; do not trust the calculation at top
- and bottom boundaries due to stencil truncations.
-
- Algorithm slightly modified from ocean_nphysC calculation of
- neutral diffusion x-flux.
-
-
- Subroutine computes the y-gradient along neutral surfaces
- for a scalar field. For use in the cabbeling and thermobaricity
- diagnostic. Thus, when slope is steep, the full derivative is
- tapered, rather than just the off-diagonal term.
-
- We only compute neutral y-gradient for interior regions,
- since will be setting thermobaricity and cabbeling to zero at
- top and bottom levels; do not trust the calculation at top
- and bottom boundaries due to stencil truncations.
-
- Algorithm slightly modified from ocean_nphysC calculation of
- neutral diffusion y-flux.
-
-
- Initialization of watermass diagnostic output files.
-
- Diagnose effects from nphysics on the watermass transformation.
- For use with nphysicsA and nphysicsB.
-
-
- Diagnose watermass transformation from neutral diffusion.
- For use with the nphysicsC scheme.
-
-
-
- Diagnose watermass transformation from skew diffusion.
- For use with the neutral physics C scheme.
-
-
- Write out restart files registered through register_restart_file
-
- Write to restart.
-
diff --git a/src/mom5/ocean_param/neutral/ocean_nphysics_util_new.F90 b/src/mom5/ocean_param/neutral/ocean_nphysics_util_new.F90
index 806a52e23b..403ce48f4f 100644
--- a/src/mom5/ocean_param/neutral/ocean_nphysics_util_new.F90
+++ b/src/mom5/ocean_param/neutral/ocean_nphysics_util_new.F90
@@ -82,9 +82,9 @@ module ocean_nphysics_util_new_mod
#include
character(len=128) :: version=&
- '$Id: ocean_nphysics_util_new.F90,v 1.1.2.2 2012/05/17 13:41:47 smg Exp $'
+ '$Id: ocean_nphysics_util_new.F90,v 20.0 2013/12/14 00:14:54 fms Exp $'
character (len=128) :: tagname = &
- '$Name: mom5_siena_08jun2012_smg $'
+ '$Name: tikal $'
character(len=*), parameter :: FILENAME=&
__FILE__
diff --git a/src/mom5/ocean_param/neutral/ocean_nphysics_util_new.html b/src/mom5/ocean_param/neutral/ocean_nphysics_util_new.html
deleted file mode 100644
index cf2c58d217..0000000000
--- a/src/mom5/ocean_param/neutral/ocean_nphysics_util_new.html
+++ /dev/null
@@ -1,313 +0,0 @@
-
-
-
-Module ocean_nphysics_util_new_mod
-
-
-
-
-PUBLIC INTERFACE
-
- ~ PUBLIC ROUTINES
- ~ NAMELIST
-
-
- Take an array defined over the 4 quadrants centred on a tracer cell
- and shift them vertically to the four quadrants spanning the bottom
- cell face. The top and bottom half cells are set to zero.
- _____________ _____________
- | : | | : |
- | 0,0 : 1,0 | | : |
- | : ! | : |
- |-----T-----| ==> |-----T-----|
- | : ! | : |
- | 0,1 : 1,1 ! | 0,0 : 1,0 |
- |_____:_____| |_____:_____|
- | : |
- | 0,1 : 1,1 |
- | : |
- |-----o-----|
- | : |
- | : |
- |_____:_____|
-
-
-
-
-
-
-
-
stencil_centre_to_horiz
-
-
-DESCRIPTION
-
-
- Take an array defined over the 4 quadrants centred on a tracer cell
- and shift them horizontally to the four quadrants spanning the right hand
- cell face.
- _____________ _________________________
- | : | | : | : |
- | 0,0 : 1,0 | | : 0,0 | 1,0 : |
- | : ! | : | : |
- |-----T-----| ==> |-----T-----|-----o-----|
- | : ! | : | : |
- | 0,1 : 1,1 ! | : 0,1 | 1,1 : |
- |_____:_____| |_____:_____|_____:_____|
-
-
-
-
-
-
-
-
vert_smooth
-
-
-DESCRIPTION
-
-
- Apply a vertical smoothing using a weighted 3 point stencil.
-
- 1
- Stencil weights : 2
- 1
-
- Smoothing is applied to all points in the column which admit
- the full stencil (so vertical boundaries are not modified).
-
- The smoothing is applied multiple times, controlled by the namelist
- parameter num_121_passes.
-
-
-
-
-
-
-
-
horz_smooth
-
-
-DESCRIPTION
-
-
- Apply a horizontal smoothing using a weighted five point stencil.
-
- 1
- Stencil weights : 1 4 1
- 1
-
- Only active cells, as defined by the tmask, are used in the calculation.
- Operates over the COMP domain.
-
-
-
-
-
-
-
-
compute_rossby_radius
-
-
-DESCRIPTION
-
-
- Subroutine computes the first baroclinic Rossby radius of deformation.
- Employ WKB approach described by Chelton et al. In particular,
- use formulae (2.2), (2.3a) and (2.3b) from their paper.
-
-
-
-
-
-
-
-
check_init
-
-
-DESCRIPTION
-
-
- Helper function to ensure the module is initialised when calling the
- module's functions.
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_nphysics_util_new_nml
-
-
-
-
-
-num_121_passes
-
-
- For number of 1-2-1 passes through to smooth drhodz or
- eady_rate in vertical. Default num_121_passes=1.
-
-[integer]
-
-
-
-
-
-
-
-
-
-
-
REFERENCES
-
-
-
-
- D.B. Chelton, R.A. deSzoeke, M.G. Schlax, K.E. Naggar, N. Siwertz
- Geographical Variability of the First Baroclinic Rossby Radius of Deformation
- Journal of Physical Oceanography (1998) vol 28 pages 433-460
-
-
- K. Eden and R. Greatbatch, 2008: Towards a mesoscale eddy closure,
- Ocean Modelling, vol. 20, pages 223-239
-
-
- S.M. Griffies "Elements of MOM (2012) (EoM)"
-
-
- S.M. Griffies
- Fundamentals of Ocean Climate Models (2004)
- Princeton University Press
-
-
-
diff --git a/src/mom5/ocean_param/neutral/ocean_nphysics_util_new.xml b/src/mom5/ocean_param/neutral/ocean_nphysics_util_new.xml
deleted file mode 100644
index a57be93c55..0000000000
--- a/src/mom5/ocean_param/neutral/ocean_nphysics_util_new.xml
+++ /dev/null
@@ -1,88 +0,0 @@
-
-
- Tim Leslie
- Stephen M. Griffies
-
- Utilities for neutral physics modules.
-
- Utilities for neutral physics modules.
-
- D.B. Chelton, R.A. deSzoeke, M.G. Schlax, K.E. Naggar, N. Siwertz
- Geographical Variability of the First Baroclinic Rossby Radius of Deformation
- Journal of Physical Oceanography (1998) vol 28 pages 433-460
-
- K. Eden and R. Greatbatch, 2008: Towards a mesoscale eddy closure,
- Ocean Modelling, vol. 20, pages 223-239
-
- S.M. Griffies "Elements of MOM (2012) (EoM)"
-
- S.M. Griffies
- Fundamentals of Ocean Climate Models (2004)
- Princeton University Press
-
-
- For number of 1-2-1 passes through to smooth drhodz or
- eady_rate in vertical. Default num_121_passes=1.
-
- Initialise the grid indices and constants.
-
- Take an array defined over the 4 quadrants centred on a tracer cell
- and shift them vertically to the four quadrants spanning the bottom
- cell face. The top and bottom half cells are set to zero.
- _____________ _____________
- | : | | : |
- | 0,0 : 1,0 | | : |
- | : ! | : |
- |-----T-----| ==> |-----T-----|
- | : ! | : |
- | 0,1 : 1,1 ! | 0,0 : 1,0 |
- |_____:_____| |_____:_____|
- | : |
- | 0,1 : 1,1 |
- | : |
- |-----o-----|
- | : |
- | : |
- |_____:_____|
-
- Take an array defined over the 4 quadrants centred on a tracer cell
- and shift them horizontally to the four quadrants spanning the right hand
- cell face.
- _____________ _________________________
- | : | | : | : |
- | 0,0 : 1,0 | | : 0,0 | 1,0 : |
- | : ! | : | : |
- |-----T-----| ==> |-----T-----|-----o-----|
- | : ! | : | : |
- | 0,1 : 1,1 ! | : 0,1 | 1,1 : |
- |_____:_____| |_____:_____|_____:_____|
-
- Apply a vertical smoothing using a weighted 3 point stencil.
-
- 1
- Stencil weights : 2
- 1
-
- Smoothing is applied to all points in the column which admit
- the full stencil (so vertical boundaries are not modified).
-
- The smoothing is applied multiple times, controlled by the namelist
- parameter num_121_passes.
-
- Apply a horizontal smoothing using a weighted five point stencil.
-
- 1
- Stencil weights : 1 4 1
- 1
-
- Only active cells, as defined by the tmask, are used in the calculation.
- Operates over the COMP domain.
-
- Subroutine computes the first baroclinic Rossby radius of deformation.
- Employ WKB approach described by Chelton et al. In particular,
- use formulae (2.2), (2.3a) and (2.3b) from their paper.
-
- Helper function to ensure the module is initialised when calling the
- module's functions.
-
diff --git a/src/mom5/ocean_param/sources/ocean_increment_eta.F90 b/src/mom5/ocean_param/sources/ocean_increment_eta.F90
index 89942dc921..5243ef3148 100644
--- a/src/mom5/ocean_param/sources/ocean_increment_eta.F90
+++ b/src/mom5/ocean_param/sources/ocean_increment_eta.F90
@@ -94,8 +94,8 @@ module ocean_increment_eta_mod
public ocean_increment_eta_init
public ocean_increment_eta_source
-character(len=126) :: version = '$Id: ocean_increment_eta.F90,v 1.1.2.2 2012/05/17 13:41:49 smg Exp $'
-character (len=128) :: tagname = '$Name: mom5_siena_08jun2012_smg $'
+character(len=126) :: version = '$Id: ocean_increment_eta.F90,v 20.0 2013/12/14 00:15:56 fms Exp $'
+character (len=128) :: tagname = '$Name: tikal $'
! for diagnostics
logical :: used
diff --git a/src/mom5/ocean_param/sources/ocean_increment_eta.html b/src/mom5/ocean_param/sources/ocean_increment_eta.html
deleted file mode 100644
index 0848088022..0000000000
--- a/src/mom5/ocean_param/sources/ocean_increment_eta.html
+++ /dev/null
@@ -1,191 +0,0 @@
-
-
-
-Module ocean_increment_eta_mod
-
-
-
-
-PUBLIC INTERFACE
-
- ~ PUBLIC ROUTINES
- ~ NAMELIST
-
-
- Thickness weighted eta tendency [meter^2/sec^2] from increments.
-
-
-
-
-
-
- This increment module performs incremental update analysis (IUA),
- an approach used in data assimilation and forecasting to reduce
- spurious perturbations when correcting the model state.
- IUA involves restoring to analysis increments i.e. differences between model
- and analysis fields rather than actual fields (See Bloom et al., 1996).
- The user can define the period that IUA is carried out
- and also the fraction of the increment to be restored over that period.
-
- This module applies a general 2D source to eta. The sources
- can occur at any location and with any distribution in the domain
- An array of eta tendencies due to the increments is augmented through a
- call to increment_eta_source. The array of eta tendencies must be
- reset to zero between calls.
-
- The user is responsible for providing (and registering) the data on
- the model grid of values towards which the etas are being driven.
-
- This subroutine is intended to be used to initialize the increments.
- Everything in this subroutine is a user prototype, and should be replacable.
-
-
-
-
-
-
-
-
ocean_increment_eta_source
-
-
-DESCRIPTION
-
-
- This subroutine calculates thickness weighted and density weighted
- time tendencies of etas due to damping by increments.
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_increment_eta_nml
-
-
-
-
-
-use_this_module
-
-
- For using this module. Default use_this_module=.false.
-
-[logical]
-
-
-fraction_increment
-
-
- For prescribing the fraction of the increment.
- applied to the restoring period. Default fraction_increment=1.0
-
-[real]
-
-
-days_to_increment
-
-
- For specifying the amount of days to restore.
- Default days_to_increment=1
-
-[integer]
-
-
-secs_to_increment
-
-
- For specifying the amount of seconds to restore.
- Default secs_to_increment=0
-
-[integer]
-
-
-
diff --git a/src/mom5/ocean_param/sources/ocean_increment_eta.xml b/src/mom5/ocean_param/sources/ocean_increment_eta.xml
deleted file mode 100644
index 81994a9c3f..0000000000
--- a/src/mom5/ocean_param/sources/ocean_increment_eta.xml
+++ /dev/null
@@ -1,48 +0,0 @@
-
-
- Russell Fiedler
- Paul Sandery
-
- Thickness weighted eta tendency [meter^2/sec^2] from increments.
-
-
- This increment module performs incremental update analysis (IUA),
- an approach used in data assimilation and forecasting to reduce
- spurious perturbations when correcting the model state.
- IUA involves restoring to analysis increments i.e. differences between model
- and analysis fields rather than actual fields (See Bloom et al., 1996).
- The user can define the period that IUA is carried out
- and also the fraction of the increment to be restored over that period.
-
- This module applies a general 2D source to eta. The sources
- can occur at any location and with any distribution in the domain
- An array of eta tendencies due to the increments is augmented through a
- call to increment_eta_source. The array of eta tendencies must be
- reset to zero between calls.
-
- The user is responsible for providing (and registering) the data on
- the model grid of values towards which the etas are being driven.
-
- S.C. Bloom, L.L. Takacs, A.M. da Silva, and D. Ledvina
- Data Assimilation Using Incremental Analysis Updates
- Monthly Weather Review Volume 124, Issue 6 (June 1996)
- pages 1256--1271
-
- For using this module. Default use_this_module=.false.
-
- For prescribing the fraction of the increment.
- applied to the restoring period. Default fraction_increment=1.0
-
- For specifying the amount of days to restore.
- Default days_to_increment=1
-
- For specifying the amount of seconds to restore.
- Default secs_to_increment=0
-
- This subroutine is intended to be used to initialize the increments.
- Everything in this subroutine is a user prototype, and should be replacable.
-
- This subroutine calculates thickness weighted and density weighted
- time tendencies of etas due to damping by increments.
-
diff --git a/src/mom5/ocean_param/sources/ocean_increment_tracer.F90 b/src/mom5/ocean_param/sources/ocean_increment_tracer.F90
index c8d08d8513..5b0bb7644b 100644
--- a/src/mom5/ocean_param/sources/ocean_increment_tracer.F90
+++ b/src/mom5/ocean_param/sources/ocean_increment_tracer.F90
@@ -92,8 +92,8 @@ module ocean_increment_tracer_mod
public ocean_increment_tracer_init
public ocean_increment_tracer_source
-character(len=126) :: version = '$Id: ocean_increment_tracer.F90,v 1.1.2.2 2012/05/17 13:41:49 smg Exp $'
-character (len=128) :: tagname = '$Name: mom5_siena_08jun2012_smg $'
+character(len=126) :: version = '$Id: ocean_increment_tracer.F90,v 20.0 2013/12/14 00:15:58 fms Exp $'
+character (len=128) :: tagname = '$Name: tikal $'
! for diagnostics
logical :: used
diff --git a/src/mom5/ocean_param/sources/ocean_increment_tracer.html b/src/mom5/ocean_param/sources/ocean_increment_tracer.html
deleted file mode 100644
index 4dcd4bfeb6..0000000000
--- a/src/mom5/ocean_param/sources/ocean_increment_tracer.html
+++ /dev/null
@@ -1,191 +0,0 @@
-
-
-
-Module ocean_increment_tracer_mod
-
-
-
-
-PUBLIC INTERFACE
-
- ~ PUBLIC ROUTINES
- ~ NAMELIST
-
-
- Thickness weighted tracer tendency [tracer*meter/sec] from increments.
-
-
-
-
-
-
- This increment module performs incremental update analysis (IUA),
- an approach used in data assimilation and forecasting to reduce
- spurious perturbations when correcting the model state.
- IUA involves restoring to analysis increments i.e. differences between model
- and analysis fields rather than actual fields (See Bloom et al., 1996).
- The user can define the period that IUA is carried out
- and also the fraction of the increment to be restored over that period.
-
- This module applies a general 3D source to tracer. The sources
- can occur at any location and with any distribution in the domain
- An array of tracer tendencies due to the increments is augmented through a
- call to increment_tracer_source. The array of tracer tendencies must be
- reset to zero between calls.
-
- The user is responsible for providing (and registering) the data on
- the model grid of values towards which the etas are being driven.
-
- This subroutine is intended to be used to initialize the increments.
- Everything in this subroutine is a user prototype, and should be replacable.
-
-
-
-
-
-
-
-
ocean_increment_tracer_source
-
-
-DESCRIPTION
-
-
- This subroutine calculates thickness weighted and density weighted
- time tendencies of tracers due to damping by increments.
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_increment_tracer_nml
-
-
-
-
-
-use_this_module
-
-
- For using this module. Default use_this_module=.false.
-
-[logical]
-
-
-fraction_increment
-
-
- For prescribing the fraction of the increment.
- applied to the restoring period. Default fraction_increment=1.0
-
-[real]
-
-
-days_to_increment
-
-
- For specifying the amount of days to restore.
- Default days_to_increment=1
-
-[integer]
-
-
-secs_to_increment
-
-
- For specifying the amount of seconds to restore.
- Default secs_to_increment=0
-
-[integer]
-
-
-
diff --git a/src/mom5/ocean_param/sources/ocean_increment_tracer.xml b/src/mom5/ocean_param/sources/ocean_increment_tracer.xml
deleted file mode 100644
index 5ce1c058c3..0000000000
--- a/src/mom5/ocean_param/sources/ocean_increment_tracer.xml
+++ /dev/null
@@ -1,48 +0,0 @@
-
-
- Russell Fiedler
- Paul Sandery
-
- Thickness weighted tracer tendency [tracer*meter/sec] from increments.
-
-
- This increment module performs incremental update analysis (IUA),
- an approach used in data assimilation and forecasting to reduce
- spurious perturbations when correcting the model state.
- IUA involves restoring to analysis increments i.e. differences between model
- and analysis fields rather than actual fields (See Bloom et al., 1996).
- The user can define the period that IUA is carried out
- and also the fraction of the increment to be restored over that period.
-
- This module applies a general 3D source to tracer. The sources
- can occur at any location and with any distribution in the domain
- An array of tracer tendencies due to the increments is augmented through a
- call to increment_tracer_source. The array of tracer tendencies must be
- reset to zero between calls.
-
- The user is responsible for providing (and registering) the data on
- the model grid of values towards which the etas are being driven.
-
- S.C. Bloom, L.L. Takacs, A.M. da Silva, and D. Ledvina
- Data Assimilation Using Incremental Analysis Updates
- Monthly Weather Review Volume 124, Issue 6 (June 1996)
- pages 1256--1271
-
- For using this module. Default use_this_module=.false.
-
- For prescribing the fraction of the increment.
- applied to the restoring period. Default fraction_increment=1.0
-
- For specifying the amount of days to restore.
- Default days_to_increment=1
-
- For specifying the amount of seconds to restore.
- Default secs_to_increment=0
-
- This subroutine is intended to be used to initialize the increments.
- Everything in this subroutine is a user prototype, and should be replacable.
-
- This subroutine calculates thickness weighted and density weighted
- time tendencies of tracers due to damping by increments.
-
diff --git a/src/mom5/ocean_param/sources/ocean_increment_velocity.F90 b/src/mom5/ocean_param/sources/ocean_increment_velocity.F90
index 498bb5a581..76303d7374 100644
--- a/src/mom5/ocean_param/sources/ocean_increment_velocity.F90
+++ b/src/mom5/ocean_param/sources/ocean_increment_velocity.F90
@@ -93,8 +93,8 @@ module ocean_increment_velocity_mod
public ocean_increment_velocity_init
public ocean_increment_velocity_source
-character(len=126) :: version = '$Id: ocean_increment_velocity.F90,v 1.1.2.2.12.1 2012/07/27 04:47:06 smg Exp $'
-character (len=128) :: tagname = '$Name: mom5_siena_08jun2012_smg $'
+character(len=126) :: version = '$Id: ocean_increment_velocity.F90,v 20.0 2013/12/14 00:16:00 fms Exp $'
+character (len=128) :: tagname = '$Name: tikal $'
! for diagnostics
logical :: used
diff --git a/src/mom5/ocean_param/sources/ocean_increment_velocity.html b/src/mom5/ocean_param/sources/ocean_increment_velocity.html
deleted file mode 100644
index 6fba3bc8f0..0000000000
--- a/src/mom5/ocean_param/sources/ocean_increment_velocity.html
+++ /dev/null
@@ -1,191 +0,0 @@
-
-
-
-Module ocean_increment_velocity_mod
-
-
-
-
-PUBLIC INTERFACE
-
- ~ PUBLIC ROUTINES
- ~ NAMELIST
-
-
- Thickness weighted velocity tendency [meter^2/sec^2] from increments.
-
-
-
-
-
-
- This increment module performs incremental update analysis (IUA),
- an approach used in data assimilation and forecasting to reduce
- spurious perturbations when correcting the model state.
- IUA involves restoring to analysis increments i.e. differences between model
- and analysis fields rather than actual fields (See Bloom et al., 1996).
- The user can define the period that IUA is carried out
- and also the fraction of the increment to be restored over that period.
-
- This module applies a general 3D source to velocities. The sources
- can occur at any location and with any distribution in the domain
- An array of velocity tendencies due to the increments is augmented through a
- call to increment_velocity_source. The array of velocity tendencies must be
- reset to zero between calls.
-
- The user is responsible for providing (and registering) the data on
- the model grid of values towards which the velocitys are being driven.
-
- This subroutine is intended to be used to initialize the increments.
- Everything in this subroutine is a user prototype, and should be replacable.
-
-
-
-
-
-
-
-
ocean_increment_velocity_source
-
-
-DESCRIPTION
-
-
- This subroutine calculates thickness weighted and density weighted
- time tendencies of velocitys due to damping by increments.
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_increment_velocity_nml
-
-
-
-
-
-use_this_module
-
-
- For using this module. Default use_this_module=.false.
-
-[logical]
-
-
-fraction_increment
-
-
- For prescribing the fraction of the increment.
- applied to the restoring period. Default fraction_increment=1.0
-
-[real]
-
-
-days_to_increment
-
-
- For specifying the amount of days to restore.
- Default days_to_increment=1
-
-[integer]
-
-
-secs_to_increment
-
-
- For specifying the amount of seconds to restore.
- Default secs_to_increment=0
-
-[integer]
-
-
-
diff --git a/src/mom5/ocean_param/sources/ocean_increment_velocity.xml b/src/mom5/ocean_param/sources/ocean_increment_velocity.xml
deleted file mode 100644
index 1c941faa28..0000000000
--- a/src/mom5/ocean_param/sources/ocean_increment_velocity.xml
+++ /dev/null
@@ -1,48 +0,0 @@
-
-
- Russell Fiedler
- Paul Sandery
-
- Thickness weighted velocity tendency [meter^2/sec^2] from increments.
-
-
- This increment module performs incremental update analysis (IUA),
- an approach used in data assimilation and forecasting to reduce
- spurious perturbations when correcting the model state.
- IUA involves restoring to analysis increments i.e. differences between model
- and analysis fields rather than actual fields (See Bloom et al., 1996).
- The user can define the period that IUA is carried out
- and also the fraction of the increment to be restored over that period.
-
- This module applies a general 3D source to velocities. The sources
- can occur at any location and with any distribution in the domain
- An array of velocity tendencies due to the increments is augmented through a
- call to increment_velocity_source. The array of velocity tendencies must be
- reset to zero between calls.
-
- The user is responsible for providing (and registering) the data on
- the model grid of values towards which the velocitys are being driven.
-
- S.C. Bloom, L.L. Takacs, A.M. da Silva, and D. Ledvina
- Data Assimilation Using Incremental Analysis Updates
- Monthly Weather Review Volume 124, Issue 6 (June 1996)
- pages 1256--1271
-
- For using this module. Default use_this_module=.false.
-
- For prescribing the fraction of the increment.
- applied to the restoring period. Default fraction_increment=1.0
-
- For specifying the amount of days to restore.
- Default days_to_increment=1
-
- For specifying the amount of seconds to restore.
- Default secs_to_increment=0
-
- This subroutine is intended to be used to initialize the increments.
- Everything in this subroutine is a user prototype, and should be replacable.
-
- This subroutine calculates thickness weighted and density weighted
- time tendencies of velocitys due to damping by increments.
-
diff --git a/src/mom5/ocean_param/sources/ocean_momentum_source.F90 b/src/mom5/ocean_param/sources/ocean_momentum_source.F90
index 734de70f24..a9002224e1 100644
--- a/src/mom5/ocean_param/sources/ocean_momentum_source.F90
+++ b/src/mom5/ocean_param/sources/ocean_momentum_source.F90
@@ -94,9 +94,9 @@ module ocean_momentum_source_mod
integer :: id_rayleigh_drag_power=-1
character(len=128) :: version=&
- '$Id: ocean_momentum_source.F90,v 1.1.2.2 2012/05/17 13:41:49 smg Exp $'
+ '$Id: ocean_momentum_source.F90,v 20.0 2013/12/14 00:16:02 fms Exp $'
character (len=128) :: tagname = &
- '$Name: mom5_siena_08jun2012_smg $'
+ '$Name: tikal $'
integer :: isd, ied, jsd, jed, isc, iec, jsc, jec, nk
diff --git a/src/mom5/ocean_param/sources/ocean_momentum_source.html b/src/mom5/ocean_param/sources/ocean_momentum_source.html
deleted file mode 100644
index a6ff08295a..0000000000
--- a/src/mom5/ocean_param/sources/ocean_momentum_source.html
+++ /dev/null
@@ -1,259 +0,0 @@
-
-
-
-Module ocean_momentum_source_mod
-
-
-
-
-PUBLIC INTERFACE
-
- ~ PUBLIC ROUTINES
- ~ NAMELIST
-
-
- Internal momentum sources, such as sink from Rayleigh drag.
-
-
-
-
-
- Compute thickness weighted and density weighted tendency
- [velocity*(kg/m^3)*meter/sec] for velocity associated with
- momentun sources in the interior. Primary application is to
- specify Rayleigh drag (a momentum sink).
-
- Read in static Rayleigh drag dissipation times entered to the
- table "rayleigh_damp_table". The dissipation times should be
- entered in units of seconds.
-
-
-
-
-
-
-
-
on_comp_domain
-
-
-DESCRIPTION
-
-
- Determine if the point is in comp-domain for the processor.
-
-
-
-
-INPUT
-
-
-
-
-
nxl
- Integer labeling the particular point in a table.
- [integer]
-
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_momentum_source_nml
-
-
-
-
-
-use_this_module
-
-
- Needs to be true in order to use this scheme. Default is false.
-
-[logical]
-
-
-debug_this_module
-
-
- For debugging.
-
-[logical]
-
-
-verbose_init
-
-
- For verbose initialization information.
-
-[logical]
-
-
-use_rayleigh_damp_table
-
-
- For reading in Rayleigh damping times from a table.
-
-[logical]
-
-
-rayleigh_damp_exp_from_bottom
-
-
- For computing a Rayleigh damping time with largest at bottom and
- decaying towards surface.
-
-[logical]
-
-
-rayleigh_damp_exp_scale
-
-
- Exponential decay scale from bottom upwards for computing
- the Rayleigh damping time.
-
-[real, units: metre]
-
-
-rayleigh_damp_exp_max
-
-
- Damping time at the bottom for rayleigh_damp_exp_from_bottom=.true.
-
-[real, units: sec]
-
-
-
-
-
-
-
-
-
-
-
REFERENCES
-
-
-
-
- S.M. Griffies, Elements of MOM (2012)
- NOAA/Geophysical Fluid Dynamics Laboratory
-
-
-
diff --git a/src/mom5/ocean_param/sources/ocean_momentum_source.xml b/src/mom5/ocean_param/sources/ocean_momentum_source.xml
deleted file mode 100644
index c7f3a643ef..0000000000
--- a/src/mom5/ocean_param/sources/ocean_momentum_source.xml
+++ /dev/null
@@ -1,43 +0,0 @@
-
-
- S.M. Griffies
-
- Internal momentum sources, such as sink from Rayleigh drag.
-
- Compute thickness weighted and density weighted tendency
- [velocity*(kg/m^3)*meter/sec] for velocity associated with
- momentun sources in the interior. Primary application is to
- specify Rayleigh drag (a momentum sink).
-
- S.M. Griffies, Elements of MOM (2012)
- NOAA/Geophysical Fluid Dynamics Laboratory
-
- Needs to be true in order to use this scheme. Default is false.
-
- For debugging.
-
- For verbose initialization information.
-
- For reading in Rayleigh damping times from a table.
-
- For computing a Rayleigh damping time with largest at bottom and
- decaying towards surface.
-
- Exponential decay scale from bottom upwards for computing
- the Rayleigh damping time.
-
- Damping time at the bottom for rayleigh_damp_exp_from_bottom=.true.
-
- Initial set up for momentum source/sink
-
- Compute the momentum source/sink (N/m2).
-
- Read in static Rayleigh drag dissipation times entered to the
- table "rayleigh_damp_table". The dissipation times should be
- entered in units of seconds.
-
- Determine if the point is in comp-domain for the processor.
-
- Integer labeling the particular point in a table.
-
diff --git a/src/mom5/ocean_param/sources/ocean_overexchange.F90 b/src/mom5/ocean_param/sources/ocean_overexchange.F90
index 8705e26f45..5fb753bdaf 100644
--- a/src/mom5/ocean_param/sources/ocean_overexchange.F90
+++ b/src/mom5/ocean_param/sources/ocean_overexchange.F90
@@ -195,9 +195,9 @@ module ocean_overexchange_mod
character(len=128) :: version=&
- '=>Using: ocean_overexchange.f90 ($Id: ocean_overexchange.F90,v 1.1.2.2 2012/05/17 13:41:49 smg Exp $)'
+ '=>Using: ocean_overexchange.f90 ($Id: ocean_overexchange.F90,v 20.0 2013/12/14 00:16:04 fms Exp $)'
character (len=128) :: tagname=&
- '$Name: mom5_siena_08jun2012_smg $'
+ '$Name: tikal $'
! number of prognostic tracers
integer :: num_prog_tracers=0
diff --git a/src/mom5/ocean_param/sources/ocean_overexchange.html b/src/mom5/ocean_param/sources/ocean_overexchange.html
deleted file mode 100644
index fff3a4e98d..0000000000
--- a/src/mom5/ocean_param/sources/ocean_overexchange.html
+++ /dev/null
@@ -1,324 +0,0 @@
-
-
-
-Module ocean_overexchange_mod
-
-
-
-
-PUBLIC INTERFACE
-
- ~ PUBLIC ROUTINES
- ~ NAMELIST
-
-
- Exchange of tracer properties as dense shallow parcel discharged
- into deeper water to approach the depth of neutral buoyancy.
-
-
-
-
-
- Exchange of tracer properties as dense shallow parcel is discharged
- into deeper water to approach the parcel's depth of neutral buoyancy.
- This module can be characterized as a mixture of the approach from
- Campin and Goosse (1999) and and dynamically determined xlandmix.
-
- Initial set up for mixing of tracers into the abyss next to topography.
-
-
-
-
-
-
-
-
overexchange
-
-
-DESCRIPTION
-
-
- Compute thickness and density weighted tracer source [tracer*rho*m/s]
- due to exchange of tracer properties in regions where density-driven
- overflows are favorable. Allow for exchanges to occur over horizontally
- distant points, so long as the dense shallow parcel finds that it
- will sit on the bottom of the horizontally adjacent columns. Doing
- so requires a search algorithm, which requires some if-test logic
- as well as extended halos. Note that the halos cannot be extended
- to larger than the size of the computational domain on a processor.
- This restriction limits the extent that we can search horizontally.
-
- This scheme can be characterized as a dynamical xlandmix based on
- the scheme of Campin and Goosse. The rates for the exchange are
- functions of the topographic slope and the density differences
- between parcels.
-
-
-
-
-
-
-
-
-
watermass_diag_init
-
-
-DESCRIPTION
-
-
- Initialization of watermass diagnostic output files.
-
-
-
-
-
-
-
-
watermass_diag
-
-
-DESCRIPTION
-
-
- Diagnose effects from overexchange on the watermass transformation.
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_overexchange_nml
-
-
-
-
-
-use_this_module
-
-
- For using this module. Default use_this_module=.false.
-
-[logical]
-
-
-debug_this_module
-
-
- For debugging
-
-[logical]
-
-
-do_bitwise_exact_sum
-
-
- Set true to do bitwise exact global sum. When it is false, the global
- sum will be non-bitwise_exact, but will significantly increase efficiency.
- The default value is false.
-
-[logical]
-
-
-overexch_npts
-
-
- Number of points used in search for the exchange method.
- Default overexch_npts=1. Note: it is not possible to have
- overexch_npts greater than or equal to the computational domain
- extents, as this would require updates across multiple processors.
- Default overexch_npts=1.
-
-[integer]
-
-
-overexch_weight_far
-
-
- To place more weight on points further from central point. This may
- be done to enhance properties getting downslope. Default is
- overexch_weight_far=.false.
-
-[logical]
-
-
-overexch_width
-
-
- Width of the re-weighting function used to emphasize the points further
- along in the search for exchange points. Default overexch_width=1.
-
-[integer]
-
-
-overexch_stability
-
-
- Stability factor for determining the maximum overexch_flux.
- Default overexch_stability=0.25
-
-[real]
-
-
-overexch_min_thickness
-
-
- Minimum bottom cell thickness allowed for use of this scheme.
- Have found that with very thin cells, the model can become very
- unstable. Default overexch_min_thickness=4.0
-
-[real, units: metre]
-
-
-overexch_check_extrema
-
-
- Check to be sure there are no global tracer extrema formed due
- to the overexch process. Note that this approach DOES NOT
- conserve tracer, so it is not generally recommended.
- Default overexch_check_extrema=.false.
-
-[logical]
-
-
-overflow_mu
-
-
- Dissipation rate for the bottom friction. Campin and Goosse
- suggest overflow_mu=10^-4
-
-[real, units: sec^-1]
-
-
-overflow_delta
-
-
- Fraction of a grid cell participating in the overflow process.
- Campin and Goosse suggest overflow_delta=1/3.
-
-[real, units: dimensionless]
-
-
-overflow_umax
-
-
- Maximum downslope speed used for determining the exchange rate.
- Default overflow_umax=1.0.
-
-[real, units: m/s]
-
-
-
-
-
-
-
-
-
-
-
REFERENCES
-
-
-
-
- Campin and Goosse (1999): Parameterization of density-driven downsloping flow
- for a coarse-resolution model in z-coordinate", Tellus 51A, pages 412-430
-
-
- S.M. Griffies, M.J. Harrison, R. C. Pacanowski, and A. Rosati
- A Technical Guide to MOM4 (2003)
- NOAA/Geophysical Fluid Dynamics Laboratory
-
-
- S.M. Griffies, Elements of MOM (2012)
- NOAA/Geophysical Fluid Dynamics Laboratory
-
-
-
diff --git a/src/mom5/ocean_param/sources/ocean_overexchange.xml b/src/mom5/ocean_param/sources/ocean_overexchange.xml
deleted file mode 100644
index 0b24385b80..0000000000
--- a/src/mom5/ocean_param/sources/ocean_overexchange.xml
+++ /dev/null
@@ -1,87 +0,0 @@
-
-
- S.M. Griffies
-
- Exchange of tracer properties as dense shallow parcel discharged
- into deeper water to approach the depth of neutral buoyancy.
-
- Exchange of tracer properties as dense shallow parcel is discharged
- into deeper water to approach the parcel's depth of neutral buoyancy.
- This module can be characterized as a mixture of the approach from
- Campin and Goosse (1999) and and dynamically determined xlandmix.
-
- Campin and Goosse (1999): Parameterization of density-driven downsloping flow
- for a coarse-resolution model in z-coordinate", Tellus 51A, pages 412-430
-
- S.M. Griffies, M.J. Harrison, R. C. Pacanowski, and A. Rosati
- A Technical Guide to MOM4 (2003)
- NOAA/Geophysical Fluid Dynamics Laboratory
-
- S.M. Griffies, Elements of MOM (2012)
- NOAA/Geophysical Fluid Dynamics Laboratory
-
- For using this module. Default use_this_module=.false.
-
- For debugging
-
- Set true to do bitwise exact global sum. When it is false, the global
- sum will be non-bitwise_exact, but will significantly increase efficiency.
- The default value is false.
-
- Number of points used in search for the exchange method.
- Default overexch_npts=1. Note: it is not possible to have
- overexch_npts greater than or equal to the computational domain
- extents, as this would require updates across multiple processors.
- Default overexch_npts=1.
-
- To place more weight on points further from central point. This may
- be done to enhance properties getting downslope. Default is
- overexch_weight_far=.false.
-
- Width of the re-weighting function used to emphasize the points further
- along in the search for exchange points. Default overexch_width=1.
-
- Stability factor for determining the maximum overexch_flux.
- Default overexch_stability=0.25
-
- Minimum bottom cell thickness allowed for use of this scheme.
- Have found that with very thin cells, the model can become very
- unstable. Default overexch_min_thickness=4.0
-
- Check to be sure there are no global tracer extrema formed due
- to the overexch process. Note that this approach DOES NOT
- conserve tracer, so it is not generally recommended.
- Default overexch_check_extrema=.false.
-
- Dissipation rate for the bottom friction. Campin and Goosse
- suggest overflow_mu=10^-4
-
- Fraction of a grid cell participating in the overflow process.
- Campin and Goosse suggest overflow_delta=1/3.
-
- Maximum downslope speed used for determining the exchange rate.
- Default overflow_umax=1.0.
-
- Initial set up for mixing of tracers into the abyss next to topography.
-
- Compute thickness and density weighted tracer source [tracer*rho*m/s]
- due to exchange of tracer properties in regions where density-driven
- overflows are favorable. Allow for exchanges to occur over horizontally
- distant points, so long as the dense shallow parcel finds that it
- will sit on the bottom of the horizontally adjacent columns. Doing
- so requires a search algorithm, which requires some if-test logic
- as well as extended halos. Note that the halos cannot be extended
- to larger than the size of the computational domain on a processor.
- This restriction limits the extent that we can search horizontally.
-
- This scheme can be characterized as a dynamical xlandmix based on
- the scheme of Campin and Goosse. The rates for the exchange are
- functions of the topographic slope and the density differences
- between parcels.
-
-
- Initialization of watermass diagnostic output files.
-
- Diagnose effects from overexchange on the watermass transformation.
-
diff --git a/src/mom5/ocean_param/sources/ocean_overflow.F90 b/src/mom5/ocean_param/sources/ocean_overflow.F90
index 26f40e8899..7be564ed47 100644
--- a/src/mom5/ocean_param/sources/ocean_overflow.F90
+++ b/src/mom5/ocean_param/sources/ocean_overflow.F90
@@ -165,9 +165,9 @@ module ocean_overflow_mod
real :: transport_convert=1.0e-9
character(len=128) :: version=&
- '=>Using: ocean_overflow.f90 ($Id: ocean_overflow.F90,v 1.1.2.2 2012/05/17 13:41:49 smg Exp $)'
+ '=>Using: ocean_overflow.f90 ($Id: ocean_overflow.F90,v 20.0 2013/12/14 00:16:06 fms Exp $)'
character (len=128) :: tagname=&
- '$Name: mom5_siena_08jun2012_smg $'
+ '$Name: tikal $'
! number of prognostic tracers
integer :: num_prog_tracers=0
diff --git a/src/mom5/ocean_param/sources/ocean_overflow.html b/src/mom5/ocean_param/sources/ocean_overflow.html
deleted file mode 100644
index 6d8ddda0bd..0000000000
--- a/src/mom5/ocean_param/sources/ocean_overflow.html
+++ /dev/null
@@ -1,265 +0,0 @@
-
-
-
-Module ocean_overflow_mod
-
-
-
-
-PUBLIC INTERFACE
-
- ~ PUBLIC ROUTINES
- ~ NAMELIST
-
-
- Tracer source from discharging dense shallow water into the abyss
- at the parcel's depth of neutral buoyancy.
-
-
-
-
-
- Tracer source from discharging dense shallow water into the abyss
- at the parcel's depth of neutral buoyancy. Follow the approach
- of Campin and Goosse (1999), as well as modifications.
-
- Initial set up for mixing of tracers into the abyss next to topography.
-
-
-
-
-
-
-
-
overflow
-
-
-DESCRIPTION
-
-
- Compute thickness and density weighted tracer source [tracer*rho*m/s]
- due to upstream tracer advection in regions where density-driven
- overflows are favorable.
-
- The MOM implementation of the Campin and Goosse (1999)
- algorithm is detailed in MOM Elements.
-
-
-
-
-
-
-
-
-
watermass_diag_init
-
-
-DESCRIPTION
-
-
- Initialization of watermass diagnostic output files.
-
-
-
-
-
-
-
-
watermass_diag
-
-
-DESCRIPTION
-
-
- Diagnose effects from overflow on the watermass transformation.
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_overflow_nml
-
-
-
-
-
-use_this_module
-
-
- For using this module. Default is false.
-
-[logical]
-
-
-debug_this_module
-
-
- For debugging
-
-[logical]
-
-
-overflow_mu
-
-
- Dissipation rate for the bottom friction. Campin and Goosse
- suggest overflow_mu=10^-4
-
-[real, units: inverse seconds]
-
-
-overflow_delta
-
-
- Fraction of a grid cell participating in the overflow process.
- Campin and Goosse suggest overflow_delta=1/3.
-
-[real, units: dimensionless]
-
-
-overflow_umax
-
-
- Maximum downslope speed.
-
-[real, units: m/s]
-
-
-do_bitwise_exact_sum
-
-
- Set true to do bitwise exact global sum. When it is false, the global
- sum will be non-bitwise_exact, but will significantly increase efficiency.
- The default value is false.
-
-[logical]
-
-
-no_return_flow
-
-
- Set true to remove the Campin and Goose return flow "piping".
- Default no_return_flow=.false. to recover the standard approach from
- Campin and Goose.
-
-[logical]
-
-
-
-
-
-
-
-
-
-
-
REFERENCES
-
-
-
-
- Campin and Goosse (1999): Parameterization of density-driven downsloping flow
- for a coarse-resolution model in z-coordinate", Tellus 51A, pages 412-430
-
-
- S.M. Griffies, M.J. Harrison, R. C. Pacanowski, and A. Rosati
- A Technical Guide to MOM4 (2003)
- NOAA/Geophysical Fluid Dynamics Laboratory
-
-
- S.M. Griffies, Elements of MOM (2012)
- NOAA/Geophysical Fluid Dynamics Laboratory
-
-
-
diff --git a/src/mom5/ocean_param/sources/ocean_overflow.xml b/src/mom5/ocean_param/sources/ocean_overflow.xml
deleted file mode 100644
index d8e9ca3f66..0000000000
--- a/src/mom5/ocean_param/sources/ocean_overflow.xml
+++ /dev/null
@@ -1,57 +0,0 @@
-
-
- S.M. Griffies
- Michael Bates
-
- Tracer source from discharging dense shallow water into the abyss
- at the parcel's depth of neutral buoyancy.
-
- Tracer source from discharging dense shallow water into the abyss
- at the parcel's depth of neutral buoyancy. Follow the approach
- of Campin and Goosse (1999), as well as modifications.
-
- Campin and Goosse (1999): Parameterization of density-driven downsloping flow
- for a coarse-resolution model in z-coordinate", Tellus 51A, pages 412-430
-
- S.M. Griffies, M.J. Harrison, R. C. Pacanowski, and A. Rosati
- A Technical Guide to MOM4 (2003)
- NOAA/Geophysical Fluid Dynamics Laboratory
-
- S.M. Griffies, Elements of MOM (2012)
- NOAA/Geophysical Fluid Dynamics Laboratory
-
- For using this module. Default is false.
-
- For debugging
-
- Dissipation rate for the bottom friction. Campin and Goosse
- suggest overflow_mu=10^-4
-
- Fraction of a grid cell participating in the overflow process.
- Campin and Goosse suggest overflow_delta=1/3.
-
- Maximum downslope speed.
-
- Set true to do bitwise exact global sum. When it is false, the global
- sum will be non-bitwise_exact, but will significantly increase efficiency.
- The default value is false.
-
- Set true to remove the Campin and Goose return flow "piping".
- Default no_return_flow=.false. to recover the standard approach from
- Campin and Goose.
-
- Initial set up for mixing of tracers into the abyss next to topography.
-
- Compute thickness and density weighted tracer source [tracer*rho*m/s]
- due to upstream tracer advection in regions where density-driven
- overflows are favorable.
-
- The MOM implementation of the Campin and Goosse (1999)
- algorithm is detailed in MOM Elements.
-
-
- Initialization of watermass diagnostic output files.
-
- Diagnose effects from overflow on the watermass transformation.
-
diff --git a/src/mom5/ocean_param/sources/ocean_overflow_OFP.F90 b/src/mom5/ocean_param/sources/ocean_overflow_OFP.F90
index de515254ba..8f25d11105 100644
--- a/src/mom5/ocean_param/sources/ocean_overflow_OFP.F90
+++ b/src/mom5/ocean_param/sources/ocean_overflow_OFP.F90
@@ -338,9 +338,9 @@ module ocean_overflow_OFP_mod
!----------------------------------------------------------------------------------
character(len=128) :: version=&
- '=>Using: ocean_overflow_OFP.f90 ($Id: ocean_overflow_OFP.F90,v 1.1.2.2 2012/05/17 13:41:49 smg Exp $)'
+ '=>Using: ocean_overflow_OFP.f90 ($Id: ocean_overflow_OFP.F90,v 20.0 2013/12/14 00:16:08 fms Exp $)'
character (len=128) :: tagname=&
- '$Name: mom5_siena_08jun2012_smg $'
+ '$Name: tikal $'
! number of prognostic tracers
integer :: num_prog_tracers=0
@@ -1612,7 +1612,9 @@ subroutine ocean_overflow_OFP_init(Grid, Domain, Time, Dens, T_prog, Ocean_optio
!-- no update domains
+ ! integer variables
call mpp_update_domains (kmto, OFP_domain%domain2d, complete=.true.)
+ ! real variables
call mpp_update_domains (dato, OFP_domain%domain2d, complete=.false.)
call mpp_update_domains (dxto, OFP_domain%domain2d, complete=.false.)
call mpp_update_domains (dyto, OFP_domain%domain2d, complete=.false.)
diff --git a/src/mom5/ocean_param/sources/ocean_overflow_OFP.html b/src/mom5/ocean_param/sources/ocean_overflow_OFP.html
deleted file mode 100644
index c7a4dbb28d..0000000000
--- a/src/mom5/ocean_param/sources/ocean_overflow_OFP.html
+++ /dev/null
@@ -1,295 +0,0 @@
-
-
-
-Module ocean_overflow_OFP_mod
-
-
-
-
-PUBLIC INTERFACE
-
- ~ PUBLIC ROUTINES
- ~ NAMELIST
-
-
- Modeling the physical processes of deep overflow from regional seas.
-
-
-
-
-
-(1) Physics of the overflow is based on the paper
- of Briegleb, Danabasoglu and Large (2010)
-(2) Geographic input data (I and J points) for each region
- is given by user at the Field Table.
-(3) Model can compute the overflow processes for
- many places. There is no maximum number of overflows.
-(4) Maximum production lines (or regions) in this code is ten.
- To get more, code needs to be written.
-(5) Main acronyms.
- src:source, int:interior, ent:entrainment, prd:production
-
-
- Initialization of watermass diagnostic output files.
-
-
-
-
-
-
-
-
watermass_diag
-
-
-DESCRIPTION
-
-
- Diagnose effects from overflow on the watermass transformation.
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_overflow_OFP_nml
-
-
-
-
-
-use_this_module
-
-
- For using this module. Default use_this_module=.false.
-
-[logical]
-
-
-debug_this_module
-
-
- For debugging. Default is false.
-
-[logical]
-
-
-crit_Fr_geo_ofp
-
-
- Critical geostrophic Froude number.
- Set the minimum Froude number for mixing process
- between source and entrainment waters
- Default is 1.0
-
-[real]
-
-
-crit_Fr_geo_ofp
-
-
- Maximum overflow speed at the source region
- Default is 3.0 m/s
-
-[real]
-
-
-frac_exchange_src
-
-
- Areal fraction of the overflow exchange at the source region
- Default is 1.0
-
-[real]
-
-
-max_vol_trans_ofp
-
-
- Maximum volume transport of the overflow [m^3/s]
- Default is 10.e6
-
-[real]
-
-
-max_ofp_speed
-
-
- Maximum overflow speed [m^/s]
- Default is 2.0
-
-[real]
-
-
-do_mass_ofp
-
-
- Considering the mass source in the overflow process
- Default is .true.
-
-[logical]
-
-
-diag_step
-
-
- Diagnostic time step for OFP.
- Default is diag_step = -1
- The diagnostic output is saved in the ascii directory as the ascii format.
-
-[integer]
-
-
-do_entrainment_para_ofp
-
-
- Considering the parameterization of entrainment process
- in the overflow process
- Default is .true.
-
-[logical]
-
-
-
-
-
-
-
-
-
-
-
REFERENCES
-
-
-
-
- Briegleb B. P., G. Danabasoglu and W. G. Large (2010), An Overflow Parameterization
- for the ocean component of the Community Climate System Model. NCAR Technical Note,
- NCAR Boulder, CO.
-
-
- Danabasoglu G., W. G. Large and B. P. Briegleb (2010), Climate impacts of parameterized
- Nordic Sea Overflow, Journal of Geophysical Research, (submitted)
-
-
-
diff --git a/src/mom5/ocean_param/sources/ocean_overflow_OFP.xml b/src/mom5/ocean_param/sources/ocean_overflow_OFP.xml
deleted file mode 100644
index b9da2803c9..0000000000
--- a/src/mom5/ocean_param/sources/ocean_overflow_OFP.xml
+++ /dev/null
@@ -1,70 +0,0 @@
-
-
- H.-C. Lee
- S. M. Griffies
- Z. Liang
-
- Modeling the physical processes of deep overflow from regional seas.
-
-(1) Physics of the overflow is based on the paper
- of Briegleb, Danabasoglu and Large (2010)
-(2) Geographic input data (I and J points) for each region
- is given by user at the Field Table.
-(3) Model can compute the overflow processes for
- many places. There is no maximum number of overflows.
-(4) Maximum production lines (or regions) in this code is ten.
- To get more, code needs to be written.
-(5) Main acronyms.
- src:source, int:interior, ent:entrainment, prd:production
-
-
- Briegleb B. P., G. Danabasoglu and W. G. Large (2010), An Overflow Parameterization
- for the ocean component of the Community Climate System Model. NCAR Technical Note,
- NCAR Boulder, CO.
-
- Danabasoglu G., W. G. Large and B. P. Briegleb (2010), Climate impacts of parameterized
- Nordic Sea Overflow, Journal of Geophysical Research, (submitted)
-
- For using this module. Default use_this_module=.false.
-
- For debugging. Default is false.
-
- Critical geostrophic Froude number.
- Set the minimum Froude number for mixing process
- between source and entrainment waters
- Default is 1.0
-
- Maximum overflow speed at the source region
- Default is 3.0 m/s
-
- Areal fraction of the overflow exchange at the source region
- Default is 1.0
-
- Maximum volume transport of the overflow [m^3/s]
- Default is 10.e6
-
- Maximum overflow speed [m^/s]
- Default is 2.0
-
- Considering the mass source in the overflow process
- Default is .true.
-
- Diagnostic time step for OFP.
- Default is diag_step = -1
- The diagnostic output is saved in the ascii directory as the ascii format.
-
- Considering the parameterization of entrainment process
- in the overflow process
- Default is .true.
-
- Initial set up for OFP
-
- Compute overflow process
-
-
-
- Initialization of watermass diagnostic output files.
-
- Diagnose effects from overflow on the watermass transformation.
-
diff --git a/src/mom5/ocean_param/sources/ocean_rivermix.F90 b/src/mom5/ocean_param/sources/ocean_rivermix.F90
index e7e1a6e1d2..508ee525a4 100644
--- a/src/mom5/ocean_param/sources/ocean_rivermix.F90
+++ b/src/mom5/ocean_param/sources/ocean_rivermix.F90
@@ -347,9 +347,9 @@ module ocean_rivermix_mod
integer :: index_salt=-1
character(len=128) :: version=&
- '$Id: ocean_rivermix.F90,v 1.1.2.1 2012/05/15 16:05:39 smg Exp $'
+ '$Id: ocean_rivermix.F90,v 20.0 2013/12/14 00:16:10 fms Exp $'
character (len=128) :: tagname=&
- '$Name: mom5_siena_08jun2012_smg $'
+ '$Name: tikal $'
integer :: isd, ied, jsd, jed, isc, iec, jsc, jec, nk
@@ -694,9 +694,10 @@ subroutine rivermix (Time, Thickness, Dens, T_prog, river, runoff, calving, &
call diagnose_3d(Time, Grd, id_runoffmix(n), T_prog(n)%wrk1(:,:,:)*T_prog(n)%conversion)
endif
enddo
- call watermass_diag_runoff(Time, Dens, T_prog, calving, &
+ call watermass_diag_runoff(Time, Dens, T_prog, runoff, &
T_prog(index_temp)%wrk1(:,:,:),T_prog(index_salt)%wrk1(:,:,:))
+
do n=1,num_prog_tracers
T_prog(n)%wrk1(:,:,:) = 0.0
enddo
@@ -718,6 +719,7 @@ subroutine rivermix (Time, Thickness, Dens, T_prog, river, runoff, calving, &
call watermass_diag_calving(Time, Dens, T_prog, calving, &
T_prog(index_temp)%wrk1(:,:,:),T_prog(index_salt)%wrk1(:,:,:))
+
endif ! discharge_combine_runoff_calve
diff --git a/src/mom5/ocean_param/sources/ocean_rivermix.html b/src/mom5/ocean_param/sources/ocean_rivermix.html
deleted file mode 100644
index f484b6479a..0000000000
--- a/src/mom5/ocean_param/sources/ocean_rivermix.html
+++ /dev/null
@@ -1,451 +0,0 @@
-
-
-
-Module ocean_rivermix_mod
-
-
-
-
-PUBLIC INTERFACE
-
- ~ PUBLIC ROUTINES
- ~ NAMELIST
-
-
- Tracer source from discharging river with depth or
- mixing rivers with depth.
-
-
-
-
-
- Compute thickness weighted tendency [tracer*rho*meter/sec]
- associated with discharge of river tracer content
- over a user defined column of ocean points. Points are
- selected based on whether river flow into a point is nonzero.
- Contribution added to tracer source array.
-
- Initial set up for mixing of tracers at runoff points.
-
-
-
-
-
-
-
-
rivermix
-
-
-DESCRIPTION
-
-
- This subroutine computes one or all of the following:
-
- (1) Thickness weighted and rho weighted tracer source associated
- with river tracer content discharged into a vertical column of ocean
- tracer cells. This is done if river_discharge=.true.
-
- (2) Enhance vertical diffusivity at river mouths.
- This is done if river_diffuse_temp=.true. or
- river_diffuse_salt=.true.
-
- Doing one or both are useful for models with fine vertical
- resolution, where discharging river content to top cell
- is often not numerically suitable nor physically relevant.
-
-
-
-
-
-
-
-
-
river_discharge_tracer
-
-
-DESCRIPTION
-
-
- Compute thickness weighted tracer source [tracer*m/s]
- associated with the discharge of tracer from a river over
- a vertical column whose thickness is set by River_insertion_thickness
- and whose horizontal location is given by the river array.
-
- Jan 2005: converted to mass weighting for use with non-Boussinesq
- pressure-like coodinates.
-
- This subroutine is maintained for legacy purposes.
-
-
-
-
-
-
-
-
-
runoff_calving_discharge_tracer
-
-
-DESCRIPTION
-
-
- Compute thickness weighted tracer source [tracer*m/s]
- associated with the discharge of tracer from runoff or calving over
- a vertical column whose thickness is set by either runoff_insertion_thickness
- or calving_insertion_thickness, and whose horizontal location is given
- by the runoff or calving array.
-
- Jan 2005: converted to mass weighting for use with non-Boussinesq
- pressure-like coodinates.
-
- Feb 2009: now use calving_tracer_flux and runoff_tracer_flux, as the
- land model carries information about the tracer content in the
- liquid and solid runoff.
-
-
-
-
-
-
-
-
-
river_kappa
-
-
-DESCRIPTION
-
-
- This subroutine enhances the vertical diffusivity kappa over
- a vertical column whose thickness is set by river_diffusion_thickness
- and whose horizontal location is given by the rmask array.
- Note that rmask can be > 0 even if river=0 in the case when
- use virtual salt flux.
- The enhanced diffusivity is maximum at the top cell and is linearly
- interpolated to the normal diffusivity at the depth set by
- river_diffusion_thickness
-
-
-
-
-
-
-
-
watermass_diag_init
-
-
-DESCRIPTION
-
-
- Initialization of watermass diagnostic output files.
-
-
-
-
-
-
-
-
watermass_diag_river
-
-
-DESCRIPTION
-
-
- watermass diagnostics for river = runoff + calving.
-
-
-
-
-
-
-
-
watermass_diag_runoff
-
-
-DESCRIPTION
-
-
- watermass diagnostics for liquid runoff
-
-
-
-
-
-
-
-
watermass_diag_calving
-
-
-DESCRIPTION
-
-
- watermass diagnostics for solid calving.
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_rivermix_nml
-
-
-
-
-
-use_this_module
-
-
- Must be true to enable this module. Default=.true., since
- this is the only way that tracer in river water enters the ocean.
-
-[logical]
-
-
-discharge_combine_runoff_calve
-
-
- Set discharge_combine_runoff_calve=.true. to discharge combined tracer carried
- by liquid and solid runoff. This approach is sensible when ocean
- assigns a tracer content to the liquid and solid runoff fields.
- The alternative is to have a land model that provides information about
- the tracer coming into the ocean from land water, in which case it is
- preferable to set discharge_combine_runoff_calve=.false., so to do the runoff
- and calving separately.
- Default discharge_combine_runoff_calve=.true.
-
-[logical]
-
-
-river_insertion_thickness
-
-
- Thickness of the column over which to insert tracers from
- rivers. Default river_insertion_thickness=0.0 (all in top).
-
-[real, units: meter]
-
-
-runoff_insertion_thickness
-
-
- Thickness of the column over which to insert tracers carried by
- liquid runoff. Default runoff_insertion_thickness=0.0 (all in top).
-
-[real, units: meter]
-
-
-calving_insertion_thickness
-
-
- Thickness of the column over which to insert tracers carried by
- solid runoff. Default calving_insertion_thickness=0.0 (all in top).
-
-[real, units: meter]
-
-
-river_diffusion_thickness
-
-
- Thickness of the column over which to diffuse tracers from
- rivers.
-
-[real, units: meter]
-
-
-river_diffusivity
-
-
- Vertical diffusivity enhancement at river mouths which is applied
- to a depth of river_diffusion_thickness, with linear tapering to zero
- enhancement from the ocean surface to river_diffusion_thickness.
-
-[real, units: m^2/s]
-
-
-river_diffuse_temp
-
-
- Logical to determine if enhance vertical diffusion of temp at river mouths
-
-[logical]
-
-
-river_diffuse_salt
-
-
- Logical to determine if enhance vertical diffusion of salt and all other
- passive tracers at river mouths
-
-[logical]
-
-
-do_bitwise_exact_sum
-
-
- Set true to do bitwise exact global sum. When it is false, the global
- sum will be non-bitwise_exact, but will significantly increase efficiency.
- The default value is do_bitwise_exact_sum=.false.
-
-[logical]
-
-
-debug_this_module
-
-
- For debugging
-
-[logical]
-
-
-debug_all_in_top_cell
-
-
- For debugging, by placing all in top cell, regardless value of
- river_insertion_thickness.
-
-[logical]
-
-
-debug_this_module_heat
-
-
- For debugging, print global sum of heating rate by river water.
-
-[logical]
-
-
-
-
-
-
-
-
-
-
-
REFERENCES
-
-
-
-
- S.M. Griffies, M.J. Harrison, R. C. Pacanowski, and A. Rosati
- A Guide to MOM4 (2003)
- NOAA/Geophysical Fluid Dynamics Laboratory
-
-
-
-
-
-
-
-
NOTES
-
-
- Algorithm ensures total tracer is conserved. Note that volume/mass is
- modified by river water within the eta-equation using the big leap-frog.
-
-
-
diff --git a/src/mom5/ocean_param/sources/ocean_rivermix.xml b/src/mom5/ocean_param/sources/ocean_rivermix.xml
deleted file mode 100644
index 6349b44c15..0000000000
--- a/src/mom5/ocean_param/sources/ocean_rivermix.xml
+++ /dev/null
@@ -1,126 +0,0 @@
-
-
- S.M. Griffies
- M.J. Harrison
- K.W. Dixon
-
- Tracer source from discharging river with depth or
- mixing rivers with depth.
-
- Compute thickness weighted tendency [tracer*rho*meter/sec]
- associated with discharge of river tracer content
- over a user defined column of ocean points. Points are
- selected based on whether river flow into a point is nonzero.
- Contribution added to tracer source array.
-
- S.M. Griffies, M.J. Harrison, R. C. Pacanowski, and A. Rosati
- A Guide to MOM4 (2003)
- NOAA/Geophysical Fluid Dynamics Laboratory
-
- Algorithm ensures total tracer is conserved. Note that volume/mass is
- modified by river water within the eta-equation using the big leap-frog.
-
- Must be true to enable this module. Default=.true., since
- this is the only way that tracer in river water enters the ocean.
-
- Set discharge_combine_runoff_calve=.true. to discharge combined tracer carried
- by liquid and solid runoff. This approach is sensible when ocean
- assigns a tracer content to the liquid and solid runoff fields.
- The alternative is to have a land model that provides information about
- the tracer coming into the ocean from land water, in which case it is
- preferable to set discharge_combine_runoff_calve=.false., so to do the runoff
- and calving separately.
- Default discharge_combine_runoff_calve=.true.
-
- Thickness of the column over which to insert tracers from
- rivers. Default river_insertion_thickness=0.0 (all in top).
-
- Thickness of the column over which to insert tracers carried by
- liquid runoff. Default runoff_insertion_thickness=0.0 (all in top).
-
- Thickness of the column over which to insert tracers carried by
- solid runoff. Default calving_insertion_thickness=0.0 (all in top).
-
- Thickness of the column over which to diffuse tracers from
- rivers.
-
- Vertical diffusivity enhancement at river mouths which is applied
- to a depth of river_diffusion_thickness, with linear tapering to zero
- enhancement from the ocean surface to river_diffusion_thickness.
-
- Logical to determine if enhance vertical diffusion of temp at river mouths
-
- Logical to determine if enhance vertical diffusion of salt and all other
- passive tracers at river mouths
-
- Set true to do bitwise exact global sum. When it is false, the global
- sum will be non-bitwise_exact, but will significantly increase efficiency.
- The default value is do_bitwise_exact_sum=.false.
-
- For debugging
-
- For debugging, by placing all in top cell, regardless value of
- river_insertion_thickness.
-
- For debugging, print global sum of heating rate by river water.
-
- Initial set up for mixing of tracers at runoff points.
-
- This subroutine computes one or all of the following:
-
- (1) Thickness weighted and rho weighted tracer source associated
- with river tracer content discharged into a vertical column of ocean
- tracer cells. This is done if river_discharge=.true.
-
- (2) Enhance vertical diffusivity at river mouths.
- This is done if river_diffuse_temp=.true. or
- river_diffuse_salt=.true.
-
- Doing one or both are useful for models with fine vertical
- resolution, where discharging river content to top cell
- is often not numerically suitable nor physically relevant.
-
-
- Compute thickness weighted tracer source [tracer*m/s]
- associated with the discharge of tracer from a river over
- a vertical column whose thickness is set by River_insertion_thickness
- and whose horizontal location is given by the river array.
-
- Jan 2005: converted to mass weighting for use with non-Boussinesq
- pressure-like coodinates.
-
- This subroutine is maintained for legacy purposes.
-
-
- Compute thickness weighted tracer source [tracer*m/s]
- associated with the discharge of tracer from runoff or calving over
- a vertical column whose thickness is set by either runoff_insertion_thickness
- or calving_insertion_thickness, and whose horizontal location is given
- by the runoff or calving array.
-
- Jan 2005: converted to mass weighting for use with non-Boussinesq
- pressure-like coodinates.
-
- Feb 2009: now use calving_tracer_flux and runoff_tracer_flux, as the
- land model carries information about the tracer content in the
- liquid and solid runoff.
-
-
- This subroutine enhances the vertical diffusivity kappa over
- a vertical column whose thickness is set by river_diffusion_thickness
- and whose horizontal location is given by the rmask array.
- Note that rmask can be > 0 even if river=0 in the case when
- use virtual salt flux.
- The enhanced diffusivity is maximum at the top cell and is linearly
- interpolated to the normal diffusivity at the depth set by
- river_diffusion_thickness
-
- Initialization of watermass diagnostic output files.
-
- watermass diagnostics for river = runoff + calving.
-
- watermass diagnostics for liquid runoff
-
- watermass diagnostics for solid calving.
-
diff --git a/src/mom5/ocean_param/sources/ocean_riverspread.F90 b/src/mom5/ocean_param/sources/ocean_riverspread.F90
index 327e46bc3d..c77a3fd7a1 100644
--- a/src/mom5/ocean_param/sources/ocean_riverspread.F90
+++ b/src/mom5/ocean_param/sources/ocean_riverspread.F90
@@ -129,9 +129,9 @@ module ocean_riverspread_mod
logical, dimension(:), allocatable :: error_spread ! for checking that all spread points are OK.
character(len=256) :: version=&
- '$Id: ocean_riverspread.F90,v 1.1.2.2 2012/06/01 20:47:08 Stephen.Griffies Exp $)'
+ '$Id: ocean_riverspread.F90,v 20.0 2013/12/14 00:16:12 fms Exp $)'
character (len=128) :: tagname = &
- '$Name: mom5_siena_08jun2012_smg $'
+ '$Name: tikal $'
integer :: isd, ied, jsd, jed, isc, iec, jsc, jec, nk
real :: dtime
diff --git a/src/mom5/ocean_param/sources/ocean_riverspread.html b/src/mom5/ocean_param/sources/ocean_riverspread.html
deleted file mode 100644
index e727758a07..0000000000
--- a/src/mom5/ocean_param/sources/ocean_riverspread.html
+++ /dev/null
@@ -1,325 +0,0 @@
-
-
-
-Module ocean_riverspread_mod
-
-
-
-
-PUBLIC INTERFACE
-
- ~ PUBLIC ROUTINES
- ~ NAMELIST
-
-
- Spread runoff or calving horizontally over a region determined
- by a table. Also provide option to spread river runoff or calving
- through a diffusive operation.
-
-
-
-
-
- At some coastal ocean gridpoints, the runoff or calving flux contribution to
- (p-e+r) may be very large because of local insertion to ocean. Therefore,
- we may choose to spread the large river runoff over neighboring pairs
- of gridpoints. Annual mean river runoff greater than 0.05 m/day is
- considered to be very large.
- This module allows one to spread the river using two options.
- A/ by specifying river spreading table points
- B/ by performing a series of diffusion operations.
-
- Initial set up for spreading of tracers
-
- A/ Table drive approach
- (i,j) locations of points to be spread are set in data
- statements.
-
- Checks are performed to ensure that the spreading
- grid locations are valid according to model configuration.
-
- A summary of the locations of spreading points is written out.
-
- User specified inputs in "USER INPUT" section:
-
- ispread and jspread = user specified i,j grid locations of data for spreading.
-
- is, ie, js, je = user specified i,j grid locations of
- the corners of the spreading regions.
- is and ie are the east and west coord of each region,
- js and je are the south and north coord of each region.
-
- B/ Laplacian approach requires minimal setup
-
-
-
-
-
-
-
-
-
spread_river_horz
-
-
-DESCRIPTION
-
-
- Provide conservative spreading of river runoff field.
-
-
-
-
-
-
-
-
riverspread_laplacian
-
-
-DESCRIPTION
-
-
- Provide conservative spreading of river runoff field using a
- Laplacian operator.
-
-
-
-
-
-
-
-
at_least_one_in_spread_domain
-
-
-DESCRIPTION
-
-
- Function to see if at least one of the points in the spreading region
- is within the computational domain for the processor.
-
-
-
-
-INPUT
-
-
-
-
-
nsp
- Integer labeling the particular spreading region
- [integer]
-
-
-
-
-
-
-
-
-
on_comp_domain
-
-
-DESCRIPTION
-
-
- Determine if the point is in comp-domain for the processor
-
-
-
-
-
-
-
-
on_data_domain
-
-
-DESCRIPTION
-
-
- Determine if the point is in data-domain for the processor
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_riverspread_nml
-
-
-
-
-
-use_this_module
-
-
- Must be true to enable this module. Default=.false.
-
-[logical]
-
-
-debug_this_module
-
-
- For debugging. Default=.false.
-
-[logical]
-
-
-riverspread_diffusion
-
-
- For spreading river water via a Laplacian diffusion operation.
- Default=.false.
-
-[logical]
-
-
-riverspread_diffusion_passes
-
-
- Number of diffusion passes applied to the runoff/calving array.
- Default riverspread_diffusion_passes = 0.
-
-[integer]
-
-
-vel_micom_smooth
-
-
- Velocity scale that is used for computing the MICOM Laplacian mixing
- coefficient used in the Laplacian smoothing of river water.
- Default vel_micom_smooth=0.2.
-
-[real, units: m/sec]
-
-
-
-
-
-
-
-
-
-
-
NOTES
-
-
- Spreading in a 2D lat-long field is implemented in the following manner:
-
- A/ Table driven spreadging
-
- If the spreading region lives within the halo region
- (i.e., within same local_domain),
- then no added mpp communication required. However, more generally
- the spreading region can extend beyond the existing halo region.
- In this case, spread_domain
- is defined so that its halos incorporate the maximum separation
- of spreading points. New tracer and grid arrays
- are defined over this extended spread_domain. This added domain
- size will come at some computational cost, so it is advantageous
- to choose the spreading region carefully.
-
- B/ Laplacian diffusion spreading
-
- Apply Laplacian operator to the river runoff/calving array to spread
- the river water abroad from the river mouth.
-
-
-
- The current implementation of table driven spreading has not
- been tested for a spreading region that is separated by either
- a zonal cyclic condition or across the tripolar fold.
-
-
-
diff --git a/src/mom5/ocean_param/sources/ocean_riverspread.xml b/src/mom5/ocean_param/sources/ocean_riverspread.xml
deleted file mode 100644
index 516fcc9257..0000000000
--- a/src/mom5/ocean_param/sources/ocean_riverspread.xml
+++ /dev/null
@@ -1,94 +0,0 @@
-
-
- S.M. Griffies
-
- Spread runoff or calving horizontally over a region determined
- by a table. Also provide option to spread river runoff or calving
- through a diffusive operation.
-
- At some coastal ocean gridpoints, the runoff or calving flux contribution to
- (p-e+r) may be very large because of local insertion to ocean. Therefore,
- we may choose to spread the large river runoff over neighboring pairs
- of gridpoints. Annual mean river runoff greater than 0.05 m/day is
- considered to be very large.
- This module allows one to spread the river using two options.
- A/ by specifying river spreading table points
- B/ by performing a series of diffusion operations.
-
- Spreading in a 2D lat-long field is implemented in the following manner:
-
- A/ Table driven spreadging
-
- If the spreading region lives within the halo region
- (i.e., within same local_domain),
- then no added mpp communication required. However, more generally
- the spreading region can extend beyond the existing halo region.
- In this case, spread_domain
- is defined so that its halos incorporate the maximum separation
- of spreading points. New tracer and grid arrays
- are defined over this extended spread_domain. This added domain
- size will come at some computational cost, so it is advantageous
- to choose the spreading region carefully.
-
- B/ Laplacian diffusion spreading
-
- Apply Laplacian operator to the river runoff/calving array to spread
- the river water abroad from the river mouth.
-
-
- The current implementation of table driven spreading has not
- been tested for a spreading region that is separated by either
- a zonal cyclic condition or across the tripolar fold.
-
- Must be true to enable this module. Default=.false.
-
- For debugging. Default=.false.
-
- For spreading river water via a Laplacian diffusion operation.
- Default=.false.
-
- Number of diffusion passes applied to the runoff/calving array.
- Default riverspread_diffusion_passes = 0.
-
- Velocity scale that is used for computing the MICOM Laplacian mixing
- coefficient used in the Laplacian smoothing of river water.
- Default vel_micom_smooth=0.2.
-
- Initial set up for spreading of tracers
-
- A/ Table drive approach
- (i,j) locations of points to be spread are set in data
- statements.
-
- Checks are performed to ensure that the spreading
- grid locations are valid according to model configuration.
-
- A summary of the locations of spreading points is written out.
-
- User specified inputs in "USER INPUT" section:
-
- ispread and jspread = user specified i,j grid locations of data for spreading.
-
- is, ie, js, je = user specified i,j grid locations of
- the corners of the spreading regions.
- is and ie are the east and west coord of each region,
- js and je are the south and north coord of each region.
-
- B/ Laplacian approach requires minimal setup
-
-
- Provide conservative spreading of river runoff field.
-
- Provide conservative spreading of river runoff field using a
- Laplacian operator.
-
- Function to see if at least one of the points in the spreading region
- is within the computational domain for the processor.
-
- Integer labeling the particular spreading region
-
- Determine if the point is in comp-domain for the processor
-
- Determine if the point is in data-domain for the processor
-
diff --git a/src/mom5/ocean_param/sources/ocean_shortwave.F90 b/src/mom5/ocean_param/sources/ocean_shortwave.F90
index c7b86d08c0..82749b5dfd 100644
--- a/src/mom5/ocean_param/sources/ocean_shortwave.F90
+++ b/src/mom5/ocean_param/sources/ocean_shortwave.F90
@@ -57,8 +57,8 @@ module ocean_shortwave_mod
type(ocean_domain_type), pointer :: Dom => NULL()
type(ocean_grid_type), pointer :: Grd => NULL()
-character(len=128) :: version='$Id: ocean_shortwave.F90,v 1.1.2.3 2012/06/01 20:47:08 Stephen.Griffies Exp $'
-character (len=128) :: tagname = '$Name: mom5_siena_08jun2012_smg $'
+character(len=128) :: version='$Id: ocean_shortwave.F90,v 20.0 2013/12/14 00:16:14 fms Exp $'
+character (len=128) :: tagname = '$Name: tikal $'
public ocean_shortwave_init
public ocean_irradiance_init
diff --git a/src/mom5/ocean_param/sources/ocean_shortwave.html b/src/mom5/ocean_param/sources/ocean_shortwave.html
deleted file mode 100644
index e61799e15e..0000000000
--- a/src/mom5/ocean_param/sources/ocean_shortwave.html
+++ /dev/null
@@ -1,239 +0,0 @@
-
-
-
-Module ocean_shortwave_mod
-
-
-
-
-PUBLIC INTERFACE
-
- ~ PUBLIC ROUTINES
- ~ NAMELIST
-
-
-
- Initialize the irradiance diagnostic tracer.
-
-
-
-
-
-
-
-
-
sw_source
-
-
-DESCRIPTION
-
-
-
- Choose either of the GFDL, CSIRO, JERLOV or External sw_source methods.
-
-
-
-
-
-
-
-
-
sw_source_ext
-
-
-DESCRIPTION
-
-
-
- Example of a routine that applies an externally supplied shortwave
- heating rate (i.e. top minus bottom radiation flux in W/m^2). Users
- should modify this routine for their own purposes.
-
-
-
-
-
-
-
-
-
watermass_diag_init
-
-
-DESCRIPTION
-
-
- Initialization of watermass diagnostic output files.
-
-
-
-
-
-
-
-
watermass_diag
-
-
-DESCRIPTION
-
-
- Diagnose effects from shortwave heating on watermass transformation.
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_shortwave_nml
-
-
-
-
-
-use_this_module=
-
-
- Must be .true. to run with module. Default is false.
-
-[logical]
-
-
-use_shortwave_gfdl=
-
-
- Must be .true. to run with the GFDL shortwave module.
- Default is true.
-
-[logical]
-
-
-use_shortwave_csiro=
-
-
- Must be .true. to run with the CSIRO shortwave module.
- Default is false.
-
-[logical]
-
-
-
diff --git a/src/mom5/ocean_param/sources/ocean_shortwave.xml b/src/mom5/ocean_param/sources/ocean_shortwave.xml
deleted file mode 100644
index bcaaa567a9..0000000000
--- a/src/mom5/ocean_param/sources/ocean_shortwave.xml
+++ /dev/null
@@ -1,38 +0,0 @@
-
-
- S. M. Griffies
-
- This module sets up the shortwave routines.
-
- There are two shortwave routines available. The more complete one is
- from GFDL, and the streamlined and simpler one is from CSIRO.
-
- Must be .true. to run with module. Default is false.
-
- Must be .true. to run with the GFDL shortwave module.
- Default is true.
-
- Must be .true. to run with the CSIRO shortwave module.
- Default is false.
-
- Initialization for the shorwave module
-
-
- Initialize the irradiance diagnostic tracer.
-
-
-
- Choose either of the GFDL, CSIRO, JERLOV or External sw_source methods.
-
-
-
- Example of a routine that applies an externally supplied shortwave
- heating rate (i.e. top minus bottom radiation flux in W/m^2). Users
- should modify this routine for their own purposes.
-
-
- Initialization of watermass diagnostic output files.
-
- Diagnose effects from shortwave heating on watermass transformation.
-
diff --git a/src/mom5/ocean_param/sources/ocean_shortwave_csiro.F90 b/src/mom5/ocean_param/sources/ocean_shortwave_csiro.F90
index 275a86dc7e..cbdd1dc642 100644
--- a/src/mom5/ocean_param/sources/ocean_shortwave_csiro.F90
+++ b/src/mom5/ocean_param/sources/ocean_shortwave_csiro.F90
@@ -6,9 +6,6 @@ module ocean_shortwave_csiro_mod
! S.M. Griffies
!
!
-! Alexander Pletzer
-!
-!
!
! This module returns thickness and density weighted temperature
! tendency [kg/m^3 * deg C *m/sec] from penetrative shortwave heating.
@@ -125,8 +122,8 @@ module ocean_shortwave_csiro_mod
type(ocean_domain_type), pointer :: Dom => NULL()
type(ocean_grid_type), pointer :: Grd => NULL()
-character(len=128) :: version='$Id: ocean_shortwave_csiro.F90,v 1.1.2.2 2012/05/17 13:41:49 smg Exp $'
-character (len=128) :: tagname = '$Name: mom5_siena_08jun2012_smg $'
+character(len=128) :: version='$Id: ocean_shortwave_csiro.F90,v 20.0 2013/12/14 00:16:16 fms Exp $'
+character (len=128) :: tagname = '$Name: tikal $'
! F_vis is the amount of light in the shortwave verses the long wave.
! F_vis=0.54 on sunny days and F_vis=0.60 on cloudy days.
diff --git a/src/mom5/ocean_param/sources/ocean_shortwave_csiro.html b/src/mom5/ocean_param/sources/ocean_shortwave_csiro.html
deleted file mode 100644
index 4fbbca3677..0000000000
--- a/src/mom5/ocean_param/sources/ocean_shortwave_csiro.html
+++ /dev/null
@@ -1,297 +0,0 @@
-
-
-
-Module ocean_shortwave_csiro_mod
-
-
-
-
-PUBLIC INTERFACE
-
- ~ PUBLIC ROUTINES
- ~ NAMELIST
-
-
- This module returns thickness and density weighted temperature
- tendency [kg/m^3 * deg C *m/sec] from penetrative shortwave heating.
-
-
-
-
-
- Compute thickness and density weighted tendency [deg C *m/sec *kg/m^3]
- of temperature associated with penetrative shortwave heating in the upper
- ocean. Generally penetration is taken as a function of monthly optical
- properties of the upper ocean, where optical properties are read
- in from a file of climatological data.
-
- This module ussumes a simple single exponential decay law. The e-folding
- depth may vary spatially and temporaly. This routine is commonly
- used by researchers at CSIRO Marine and Atmospheric Research in
- Australia. It has been optimized for vector peformance in
- June 2003 on the Australian NEC computer.
-
- Add short wave penetrative heating to T_prog(index_temp)%th_tendency.
-
- Note that the divergence of shortwave for the first
- level "div_sw(0)" is compensating for the effect of having
- the shortwave component already included in the total
- surface tracer flux "stf(i,j,temp)"
-
-
-
-
-
-
-
-
-
sw_pen
-
-
-DESCRIPTION
-
-
- Absorbtion of shortwave radiation in the water assumes energy partitions
- represented by a single exponential:
-
- The exponentialsrepresents a parameterization of the
- attenuation coefficient for light between 300 um and 750 um in the following
- form:
-
- E(z) = E(0) * exp(z/efold))
- with z < 0 the ocean depth
-
- The "efold" s the efolding depth of the long and short
- visable and ultra violet light.
- efold will vary between 30 m in oligotrophic waters and 4 m in coastal
- regions.
-
- If the thickness of the first ocean level "dzt(1)" is 50 meters,
- then shortwave penetration does not do much. However, for finer
- vertical resolution, such as dzt(1) = 10 meters commonly used
- in ocean climate models, the effect of shortwave heating can
- be significant. This can be particularly noticable in the summer
- hemisphere.
-
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_shortwave_csiro_nml
-
-
-
-
-
-use_this_module=
-
-
- Must be .true. to run with module. Default is false.
-
-[logical]
-
-
-read_depth
-
-
- If .true. then read in e folding depth for radiation attenuation.
-
-[logical]
-
-
-sw_frac_top
-
-
- The fraction of shortwave radiation that should be incorporated into
- the sw_source array at k=1. The generic treatment in MOM is to assume
- that shortwave radiation is already contained inside the
- T_prog(index_temp)%stf field. Hence, to avoid
- double counting, sw_frac(k=0)=sw_frac_top should=0.0.
- If one removes shortwave from stf, then set sw_frac_top=1.0.
-
-[real]
-
-
-zmax_pen
-
-
- Maximum depth of penetration of shortwave radiation.
- Below this depth, shortwave penetration is exponentially
- small and so is ignored.
-
-[real, units: meter]
-
- To ensure the shortwave fraction is monotonically decreasing with depth.
-
-[logical]
-
-
-sw_pen_fixed_depths
-
-
- To compute penetration assuming fixed depths via Grd%zw(k) depths.
- This is strictly incorrect when have undulating free surface or
- generatlized vertical coordinates. This option is here for purposes
- of legacy, as this was done in MOM4.0 versions. The default is .false.
-
-[logical]
-
- Morel and Antoine (1994)
- Heating rate in the upper ocean in relation to its bio-optical state
- Journal of Physical Oceanography vol 24 pages 1652-1664
-
-
- Paulson and Simpson (1977)
- Irradiance measurements in the upper ocean
- Journal of Physical Oceanography vol 7 pages 952-956
-
-
- Rosati and Miyakoda (1988)
- A General Circulation Model for Upper Ocean Simulation
- Journal of Physical Oceanography vol 18 pages 1601-1626.
-
-
-
diff --git a/src/mom5/ocean_param/sources/ocean_shortwave_csiro.xml b/src/mom5/ocean_param/sources/ocean_shortwave_csiro.xml
deleted file mode 100644
index 8764292009..0000000000
--- a/src/mom5/ocean_param/sources/ocean_shortwave_csiro.xml
+++ /dev/null
@@ -1,104 +0,0 @@
-
-
- Russell Fiedler
- S.M. Griffies
- Alexander Pletzer
-
- This module returns thickness and density weighted temperature
- tendency [kg/m^3 * deg C *m/sec] from penetrative shortwave heating.
-
- Compute thickness and density weighted tendency [deg C *m/sec *kg/m^3]
- of temperature associated with penetrative shortwave heating in the upper
- ocean. Generally penetration is taken as a function of monthly optical
- properties of the upper ocean, where optical properties are read
- in from a file of climatological data.
-
- This module ussumes a simple single exponential decay law. The e-folding
- depth may vary spatially and temporaly. This routine is commonly
- used by researchers at CSIRO Marine and Atmospheric Research in
- Australia. It has been optimized for vector peformance in
- June 2003 on the Australian NEC computer.
-
- Jerlov (1968)
- Optical Oceanography
- Elsevier Press
-
- Morel and Antoine (1994)
- Heating rate in the upper ocean in relation to its bio-optical state
- Journal of Physical Oceanography vol 24 pages 1652-1664
-
- Paulson and Simpson (1977)
- Irradiance measurements in the upper ocean
- Journal of Physical Oceanography vol 7 pages 952-956
-
- Rosati and Miyakoda (1988)
- A General Circulation Model for Upper Ocean Simulation
- Journal of Physical Oceanography vol 18 pages 1601-1626.
-
- Must be .true. to run with module. Default is false.
-
- If .true. then read in e folding depth for radiation attenuation.
-
- The fraction of shortwave radiation that should be incorporated into
- the sw_source array at k=1. The generic treatment in MOM is to assume
- that shortwave radiation is already contained inside the
- T_prog(index_temp)%stf field. Hence, to avoid
- double counting, sw_frac(k=0)=sw_frac_top should=0.0.
- If one removes shortwave from stf, then set sw_frac_top=1.0.
-
- Maximum depth of penetration of shortwave radiation.
- Below this depth, shortwave penetration is exponentially
- small and so is ignored.
-
- Default efolding depth = 20m.
-
- To ensure the shortwave fraction is monotonically decreasing with depth.
-
- To compute penetration assuming fixed depths via Grd%zw(k) depths.
- This is strictly incorrect when have undulating free surface or
- generatlized vertical coordinates. This option is here for purposes
- of legacy, as this was done in MOM4.0 versions. The default is .false.
-
- For debugging purposes.
-
- Initialization for the shortwave module
-
- Add short wave penetrative heating to T_prog(index_temp)%th_tendency.
-
- Note that the divergence of shortwave for the first
- level "div_sw(0)" is compensating for the effect of having
- the shortwave component already included in the total
- surface tracer flux "stf(i,j,temp)"
-
-
- Absorbtion of shortwave radiation in the water assumes energy partitions
- represented by a single exponential:
-
- The exponentialsrepresents a parameterization of the
- attenuation coefficient for light between 300 um and 750 um in the following
- form:
-
- E(z) = E(0) * exp(z/efold))
- with z < 0 the ocean depth
-
- The "efold" s the efolding depth of the long and short
- visable and ultra violet light.
- efold will vary between 30 m in oligotrophic waters and 4 m in coastal
- regions.
-
- If the thickness of the first ocean level "dzt(1)" is 50 meters,
- then shortwave penetration does not do much. However, for finer
- vertical resolution, such as dzt(1) = 10 meters commonly used
- in ocean climate models, the effect of shortwave heating can
- be significant. This can be particularly noticable in the summer
- hemisphere.
-
-
- The terms contributing to sw_fk(i,j) are depth independent
-
- Simpson and Dickey (1981) and others have argued between one and
- two exponentials for light between 300 um and 750 um.
- With vertical grid resolution of 5 meters or finer
- for the upper 20 meters, a second exponential will make a difference.
-
diff --git a/src/mom5/ocean_param/sources/ocean_shortwave_gfdl.F90 b/src/mom5/ocean_param/sources/ocean_shortwave_gfdl.F90
index bc00e1439e..b9f314cdd1 100644
--- a/src/mom5/ocean_param/sources/ocean_shortwave_gfdl.F90
+++ b/src/mom5/ocean_param/sources/ocean_shortwave_gfdl.F90
@@ -214,8 +214,8 @@ module ocean_shortwave_gfdl_mod
type(ocean_domain_type), pointer :: Dom => NULL()
type(ocean_grid_type), pointer :: Grd => NULL()
-character(len=128) :: version='$Id: ocean_shortwave_gfdl.F90,v 1.1.2.3 2012/06/01 20:47:08 Stephen.Griffies Exp $'
-character (len=128) :: tagname = '$Name: mom5_siena_08jun2012_smg $'
+character(len=128) :: version='$Id: ocean_shortwave_gfdl.F90,v 20.0 2013/12/14 00:16:18 fms Exp $'
+character (len=128) :: tagname = '$Name: tikal $'
character(len=48), parameter :: mod_name = 'ocean_shortwave_gfdl_mod'
public ocean_shortwave_gfdl_init
diff --git a/src/mom5/ocean_param/sources/ocean_shortwave_gfdl.html b/src/mom5/ocean_param/sources/ocean_shortwave_gfdl.html
deleted file mode 100644
index a2666ec2c5..0000000000
--- a/src/mom5/ocean_param/sources/ocean_shortwave_gfdl.html
+++ /dev/null
@@ -1,440 +0,0 @@
-
-
-
-Module ocean_shortwave_gfdl_mod
-
-
-
-
-PUBLIC INTERFACE
-
- ~ PUBLIC ROUTINES
- ~ NAMELIST
-
-
- This module returns thickness weighted and density weighted
- temperature tendency [deg C *m/sec *kg/m^3] from penetrative
- shortwave heating.
-
-
-
-
-
- Compute thickness and density weighted tendency [deg C *m/sec *kg/m^3]
- of temperature associated with penetrative shortwave heating in the upper
- ocean. Generally penetration is taken as a function of monthly optical
- properties of the upper ocean, where optical properties are read
- in from a file of climatological data or from an ecosystem model.
-
- Presently there is account taken only of chlorophyll-a on the optical
- properties of ocean water. Other particulates can be added so to
- have a more complete picture of the ocean optical properties.
-
-
- Add short wave penetrative heating to T_prog(index_temp)%th_tendency.
-
- Note that the divergence of shortwave for the first
- level "div_sw(0)" is compensating for the effect of having
- the shortwave component already included in the total
- surface tracer flux "stf(i,j,temp)"
-
- If the shortwave penetration routine is activated but Chlorophyll
- is not being read from data, then that implies that an ecological
- model is being used to determine chlorophyll concentration.
- In this case, the shortwave penetration is calcualted using the
- algorithm of
-
- Manizza, M., C Le Quere, A. J. Watson, and E. T. Buitenhuis (2005)
- Bio-optical feedbacks among phytoplankton, upper ocean physics and
- sea-ice in a global model. Geophys. Res. Let. 32, L05603,
- doi:10.1029/2004GL020778.
-
- This algorithm assumes that all infrared light is absorbed in the
- top level. It separates visible light into equal portions of
- red and blue bands, treating separately absorption by water and
- chlorophyll.
-
- If the Chlorophyll is read from data, then we generally use the
- Morel and Antoine optics scheme. Here, we take their approach
- for computing a vertical profile based on the surface Chlorophyll.
- However, one may also wish to use the Manizza scheme with
- surface Chlorophyll data. In this case, we assume the surface
- Chlorophyll concentration is the same throughout the depth.
- This assumption is not generally good, but it does provide
- for a simple means of using Manizza etal scheme with Chlorophyll
- data. Note that GFDL scientists prefer Manizza etal for use with
- prognostic 3d models.
-
- NOTE: Determine depths to T-points and W-points.
- This code is needed in particular for GEOPOTENTIAL, since
- depth_zwt and depth_zt for this coordinate do not include
- the surface height undulations. For the shortwave calculation,
- we wish to include the depth level undulations, unless enable
- sw_morel_fixed_depths=.true.
-
-
-
-
-
-
-
-
-
sw_morel
-
-
-DESCRIPTION
-
-
- Solar shortwave energy penetrates below the ocean surface and is aborbed
- by water and organic matter (both particulate and dissolved). This
- routine estimates fraction of shortwave penetration using chlorophyll-a.
- Absorbtion of shortwave radiation in the water assumes energy partitions
- between three exponentials:
-
- The first exponential is for wavelength > 0.75 um (microns) and assumes a
- single attenuation of 0.267 m if the "zenith_angle" is 0. Presently the
- code assumes a zero zenith angle, but this could be modified easily.
-
- The second and third exponentials represent a parameterization of the
- attenuation coeficient for light between 300 um and 750 um in the following
- form:
-
- E(z) = E(0) * [V1 * exp(z/efold1) + V2 * exp(z/efold2)]
- with z < 0 the ocean depth
-
- Here, V1+V2=1 represent the partitioning between long (V1) and short (V2)
- wavelengths between 300 um and 750 um. Thoughout most of the ocean V1<0.5
- and V2>0.5. The "efold1" and "efold2" are the efolding depth of the long and short
- visable and ultra violet light. Throughout most of the ocean efold1 should not exceed 3 m
- while the efold2 will vary between 30 m in oligotrophic waters and 4 m in coastal
- regions. All of these constants are based on satellite estimates of chlorophyll a and
- taken from Morel and Antoine (JPO 1994, (24) 1652-1664).
-
- If the thickness of the first ocean level "dzt(1)" is 50 meters,
- then shortwave penetration does not do much. However, for higher
- vertical resolution, such as dzt(1) = 10 meters commonly used
- in ocean climate models, the effect of shortwave heating can
- be significant. This can be particularly noticable in the summer
- hemisphere.
-
-
-
-
-
-
-
-
-
sw_morel_mom4p0
-
-
-DESCRIPTION
-
-
- As in sw_morel, but uses the MOM4.0 algorithm to re-compute a k-level.
- The recomputation is not needed, it can be costly, and produces
- no physically significant differences. This routine is
- retained for legacy only and it is not otherwise recommended.
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_shortwave_gfdl_nml
-
-
-
-
-
-use_this_module
-
-
- Must be .true. to run with module. Default is false.
-
-[logical]
-
-
-use_sw_morel_mom4p0
-
-
- For backward compatibility with older simulations using
- MOM4.0. The new subroutine removes some confusing and unnecessary
- logic to recompute a vertical k-index. The differences
- between the old and new approach are nonzero and so will
- result in bitwise changes to the simulation, but these changes
- are deemed to be trivial. Default use_sw_morel_mom4p0=.false.
-
-[logical]
-
-
-read_chl
-
-
- If .true. then read in climatological data of chlorophyll-a.
-
-[logical]
-
-
-optics_morel_antoine
-
-
- For using the Morel and Antoine optics. This was the default in
- MOM4.0 for use with chlorophyll data. This scheme is NOT available
- in MOM4p1 for use with the prognostic biology models, since it has
- been improved by the Manizza scheme.
- Default optics_morel_antoine=.false.
-
-[logical]
-
-
-optics_manizza
-
-
- For using the Manizza optics with chlorophyll data. Note that
- when running with a prognostic biology model, GFDL scientists use the
- Manizza optics.
- Default optics_manizza=.false.
-
-[logical]
-
-
-sw_frac_top
-
-
- The fraction of shortwave radiation that should be incorporated into
- the sw_source array at k=1. The generic treatment in MOM is to assume
- that shortwave radiation is already contained inside the
- T_prog(index_temp)%stf field. Hence, to avoid
- double counting, sw_frac(k=0)=sw_frac_top should=0.0.
- If one removes shortwave from stf, then set sw_frac_top=1.0.
-
-[real]
-
-
-zmax_pen
-
-
- Maximum depth of penetration of shortwave radiation.
- Below this depth, shortwave penetration is exponentially
- small and so is ignored. This option formerly was useful,
- since computation of exponentials expensive. But with more
- modern computers, exponentials are cheap, so the default
- has been changed from 200 to 1e6, making this option irrelevant.
- But the option remains both for legacy purposes, and for those
- computers where exponentials are not cheap.
- Default zmax_pen=1e6.
-
-[real, units: meter]
-
- To ensure the shortwave fraction is monotonically decreasing with depth.
- Applied only if optics_morel=.true.
- Default enforce_sw_frac=.true.
-
-[logical]
-
-
-sw_morel_fixed_depths
-
-
- To compute penetration assuming fixed depths via Grd%zw(k) depths.
- This is strictly incorrect when have undulating free surface and/or
- generatlized vertical coordinates. This option is here for purposes
- of legacy, as this was done in MOM4.0 versions. The default is
- sw_morel_fixed_depths=.false.
-
-[logical]
-
-
-override_f_vis
-
-
- To fix the fraction of incoming shortwave assigned to the visible at 0.57.
-
-[logical]
-
-
-optics_for_uniform_chl
-
-
- To set the coefficients for optical model assuming the chlorophyll
- has a uniform distribution.
- Default optics_for_uniform_chl=.false.
-
-[logical]
-
- Morel and Antoine (1994), Heating rate in the upper ocean
- in relation to its bio-optical state.
- Journal of Physical Oceanography vol 24 pages 1652-1664
-
-
- Manizza, M., C Le Quere, A. J. Watson, and E. T. Buitenhuis (2005)
- Bio-optical feedbacks among phytoplankton, upper ocean physics and
- sea-ice in a global model. Geophys. Res. Let. 32, L05603,
- doi:10.1029/2004GL020778
-
-
- Paulson and Simpson (1977)
- Irradiance measurements in the upper ocean
- Journal of Physical Oceanography vol 7 pages 952-956
-
-
- Rosati and Miyakoda (1988)
- A General Circulation Model for Upper Ocean Simulation
- Journal of Physical Oceanography vol 18 pages 1601-1626.
-
-
-
-
-
-
-
-
NOTES
-
-
- Optimized for vector peformance by R. Fiedler (russell.fiedler@csiro.au)
- June 2003 on the Australian NEC computer.
-
-
-
diff --git a/src/mom5/ocean_param/sources/ocean_shortwave_gfdl.xml b/src/mom5/ocean_param/sources/ocean_shortwave_gfdl.xml
deleted file mode 100644
index 6141709275..0000000000
--- a/src/mom5/ocean_param/sources/ocean_shortwave_gfdl.xml
+++ /dev/null
@@ -1,197 +0,0 @@
-
-
- A. Rosati
- John P. Dunne
- S. M. Griffies
- Russell Fiedler
-
- This module returns thickness weighted and density weighted
- temperature tendency [deg C *m/sec *kg/m^3] from penetrative
- shortwave heating.
-
- Compute thickness and density weighted tendency [deg C *m/sec *kg/m^3]
- of temperature associated with penetrative shortwave heating in the upper
- ocean. Generally penetration is taken as a function of monthly optical
- properties of the upper ocean, where optical properties are read
- in from a file of climatological data or from an ecosystem model.
-
- Presently there is account taken only of chlorophyll-a on the optical
- properties of ocean water. Other particulates can be added so to
- have a more complete picture of the ocean optical properties.
-
-
- Jerlov (1968): Optical Oceanography, Elsevier Press
-
- Morel and Antoine (1994), Heating rate in the upper ocean
- in relation to its bio-optical state.
- Journal of Physical Oceanography vol 24 pages 1652-1664
-
- Manizza, M., C Le Quere, A. J. Watson, and E. T. Buitenhuis (2005)
- Bio-optical feedbacks among phytoplankton, upper ocean physics and
- sea-ice in a global model. Geophys. Res. Let. 32, L05603,
- doi:10.1029/2004GL020778
-
- Paulson and Simpson (1977)
- Irradiance measurements in the upper ocean
- Journal of Physical Oceanography vol 7 pages 952-956
-
- Rosati and Miyakoda (1988)
- A General Circulation Model for Upper Ocean Simulation
- Journal of Physical Oceanography vol 18 pages 1601-1626.
-
- Optimized for vector peformance by R. Fiedler (russell.fiedler@csiro.au)
- June 2003 on the Australian NEC computer.
-
- Must be .true. to run with module. Default is false.
-
- For backward compatibility with older simulations using
- MOM4.0. The new subroutine removes some confusing and unnecessary
- logic to recompute a vertical k-index. The differences
- between the old and new approach are nonzero and so will
- result in bitwise changes to the simulation, but these changes
- are deemed to be trivial. Default use_sw_morel_mom4p0=.false.
-
- If .true. then read in climatological data of chlorophyll-a.
-
- For using the Morel and Antoine optics. This was the default in
- MOM4.0 for use with chlorophyll data. This scheme is NOT available
- in MOM4p1 for use with the prognostic biology models, since it has
- been improved by the Manizza scheme.
- Default optics_morel_antoine=.false.
-
- For using the Manizza optics with chlorophyll data. Note that
- when running with a prognostic biology model, GFDL scientists use the
- Manizza optics.
- Default optics_manizza=.false.
-
- The fraction of shortwave radiation that should be incorporated into
- the sw_source array at k=1. The generic treatment in MOM is to assume
- that shortwave radiation is already contained inside the
- T_prog(index_temp)%stf field. Hence, to avoid
- double counting, sw_frac(k=0)=sw_frac_top should=0.0.
- If one removes shortwave from stf, then set sw_frac_top=1.0.
-
- Maximum depth of penetration of shortwave radiation.
- Below this depth, shortwave penetration is exponentially
- small and so is ignored. This option formerly was useful,
- since computation of exponentials expensive. But with more
- modern computers, exponentials are cheap, so the default
- has been changed from 200 to 1e6, making this option irrelevant.
- But the option remains both for legacy purposes, and for those
- computers where exponentials are not cheap.
- Default zmax_pen=1e6.
-
- Default concentration chl_default=0.08 roughly yields Jerlov Type 1A optics.
-
- To ensure the shortwave fraction is monotonically decreasing with depth.
- Applied only if optics_morel=.true.
- Default enforce_sw_frac=.true.
-
- To compute penetration assuming fixed depths via Grd%zw(k) depths.
- This is strictly incorrect when have undulating free surface and/or
- generatlized vertical coordinates. This option is here for purposes
- of legacy, as this was done in MOM4.0 versions. The default is
- sw_morel_fixed_depths=.false.
-
- To fix the fraction of incoming shortwave assigned to the visible at 0.57.
-
- To set the coefficients for optical model assuming the chlorophyll
- has a uniform distribution.
- Default optics_for_uniform_chl=.false.
-
- For debugging purposes.
-
- Initialization for the shorwave module
-
- Add short wave penetrative heating to T_prog(index_temp)%th_tendency.
-
- Note that the divergence of shortwave for the first
- level "div_sw(0)" is compensating for the effect of having
- the shortwave component already included in the total
- surface tracer flux "stf(i,j,temp)"
-
- If the shortwave penetration routine is activated but Chlorophyll
- is not being read from data, then that implies that an ecological
- model is being used to determine chlorophyll concentration.
- In this case, the shortwave penetration is calcualted using the
- algorithm of
-
- Manizza, M., C Le Quere, A. J. Watson, and E. T. Buitenhuis (2005)
- Bio-optical feedbacks among phytoplankton, upper ocean physics and
- sea-ice in a global model. Geophys. Res. Let. 32, L05603,
- doi:10.1029/2004GL020778.
-
- This algorithm assumes that all infrared light is absorbed in the
- top level. It separates visible light into equal portions of
- red and blue bands, treating separately absorption by water and
- chlorophyll.
-
- If the Chlorophyll is read from data, then we generally use the
- Morel and Antoine optics scheme. Here, we take their approach
- for computing a vertical profile based on the surface Chlorophyll.
- However, one may also wish to use the Manizza scheme with
- surface Chlorophyll data. In this case, we assume the surface
- Chlorophyll concentration is the same throughout the depth.
- This assumption is not generally good, but it does provide
- for a simple means of using Manizza etal scheme with Chlorophyll
- data. Note that GFDL scientists prefer Manizza etal for use with
- prognostic 3d models.
-
- NOTE: Determine depths to T-points and W-points.
- This code is needed in particular for GEOPOTENTIAL, since
- depth_zwt and depth_zt for this coordinate do not include
- the surface height undulations. For the shortwave calculation,
- we wish to include the depth level undulations, unless enable
- sw_morel_fixed_depths=.true.
-
-
- Solar shortwave energy penetrates below the ocean surface and is aborbed
- by water and organic matter (both particulate and dissolved). This
- routine estimates fraction of shortwave penetration using chlorophyll-a.
- Absorbtion of shortwave radiation in the water assumes energy partitions
- between three exponentials:
-
- The first exponential is for wavelength > 0.75 um (microns) and assumes a
- single attenuation of 0.267 m if the "zenith_angle" is 0. Presently the
- code assumes a zero zenith angle, but this could be modified easily.
-
- The second and third exponentials represent a parameterization of the
- attenuation coeficient for light between 300 um and 750 um in the following
- form:
-
- E(z) = E(0) * [V1 * exp(z/efold1) + V2 * exp(z/efold2)]
- with z < 0 the ocean depth
-
- Here, V1+V2=1 represent the partitioning between long (V1) and short (V2)
- wavelengths between 300 um and 750 um. Thoughout most of the ocean V1<0.5
- and V2>0.5. The "efold1" and "efold2" are the efolding depth of the long and short
- visable and ultra violet light. Throughout most of the ocean efold1 should not exceed 3 m
- while the efold2 will vary between 30 m in oligotrophic waters and 4 m in coastal
- regions. All of these constants are based on satellite estimates of chlorophyll a and
- taken from Morel and Antoine (JPO 1994, (24) 1652-1664).
-
- If the thickness of the first ocean level "dzt(1)" is 50 meters,
- then shortwave penetration does not do much. However, for higher
- vertical resolution, such as dzt(1) = 10 meters commonly used
- in ocean climate models, the effect of shortwave heating can
- be significant. This can be particularly noticable in the summer
- hemisphere.
-
-
- The terms contributing to sw_fk(i,j) are depth independent
- when chl is depth independent. However, we anticipate implementing
- a biological model, whereby chl will be depth dependent.
-
- Simpson and Dickey (1981) and others have argued between one and
- two exponentials for light between 300 um and 750 um.
- With vertical grid resolution of 5 meters or finer
- for the upper 20 meters, the second exponential will make a difference.
- We anticipate using such resolutions, and so have implemented both
- exponentials.
-
- As in sw_morel, but uses the MOM4.0 algorithm to re-compute a k-level.
- The recomputation is not needed, it can be costly, and produces
- no physically significant differences. This routine is
- retained for legacy only and it is not otherwise recommended.
-
diff --git a/src/mom5/ocean_param/sources/ocean_shortwave_jerlov.F90 b/src/mom5/ocean_param/sources/ocean_shortwave_jerlov.F90
index c9522449ea..ac225422eb 100644
--- a/src/mom5/ocean_param/sources/ocean_shortwave_jerlov.F90
+++ b/src/mom5/ocean_param/sources/ocean_shortwave_jerlov.F90
@@ -190,8 +190,8 @@ module ocean_shortwave_jerlov_mod
type(ocean_domain_type), pointer :: Dom => NULL()
type(ocean_grid_type), pointer :: Grd => NULL()
-character(len=128) :: version='$Id: ocean_shortwave_jerlov.F90,v 1.1.2.2 2012/05/17 13:41:49 smg Exp $'
-character (len=128) :: tagname = '$Name: mom5_siena_08jun2012_smg $'
+character(len=128) :: version='$Id: ocean_shortwave_jerlov.F90,v 20.0 2013/12/14 00:16:20 fms Exp $'
+character (len=128) :: tagname = '$Name: tikal $'
character(len=48), parameter :: mod_name = 'ocean_shortwave_jerlov_mod'
real :: rpart, rscl1, rscl2, rscl_ir
diff --git a/src/mom5/ocean_param/sources/ocean_shortwave_jerlov.html b/src/mom5/ocean_param/sources/ocean_shortwave_jerlov.html
deleted file mode 100644
index 5172f067fb..0000000000
--- a/src/mom5/ocean_param/sources/ocean_shortwave_jerlov.html
+++ /dev/null
@@ -1,342 +0,0 @@
-
-
-
-Module ocean_shortwave_jerlov_mod
-
-
-
-
-PUBLIC INTERFACE
-
- ~ PUBLIC ROUTINES
- ~ NAMELIST
-
-
- This module returns thickness and density weighted temperature
- tendency [kg/m^3 * deg C *m/sec] from penetrative shortwave heating.
-
-
-
-
-
- Compute thickness and density weighted tendency [deg C *m/sec *kg/m^3]
- of temperature associated with penetrative shortwave heating in the upper
- ocean.
-
- This module ussumes a simple double exponential decay law. The e-folding
- depth may vary spatially and temporaly.
-
- The exponentials represents a parameterization of the
- attenuation coefficient for light between 300 um and 750 um in the following
- form:
-
- E(z) = E(0) * (r1*exp(-z/efold1) + (1-r1)*exp(-z/efold2))
- with z > 0 the ocean depth
-
- The "efold" is the efolding depth of the long and short
- visable and ultra violet light.
- efold will vary between 30 m in oligotrophic waters and 4 m in coastal
- regions.
-
- If the thickness of the first ocean level "dzt(1)" is 50 meters,
- then shortwave penetration does not do much. However, for finer
- vertical resolution, such as dzt(1) = 10 meters commonly used
- in ocean climate models, the effect of shortwave heating can
- be significant. This can be particularly noticable in the summer
- hemisphere.
-
- Radiation at the bottom is set to zero, hence the remaining radiation
- at the bottom of the deepest ocean cells is totally absorbed
- by these cells. This implies, that partial cells need not to
- be considered explicitly. Radiation at tracer depth within these
- cells is not set to zero. This differs from
- ocean_shortwave_gfdl and ocean_shortwave_csiro and reduces slightly the
- bouyancy forcing to the mixing layer in the kpp-scheme, if surface mixing
- goes down to the bottom.
-
-
- Add short wave penetrative heating to T_prog(index_temp)%th_tendency.
-
- Note that the divergence of shortwave for the first
- level "div_sw(0)" is compensating for the effect of having
- the shortwave component already included in the total
- surface tracer flux "stf(i,j,temp)"
-
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_shortwave_jerlov_nml
-
-
-
-
-
-use_this_module=
-
-
- Must be .true. to run with module. Default is false.
-
-[logical]
-
-
-sw_frac_top
-
-
- The fraction of shortwave radiation that should be incorporated into
- the sw_source array at k=1. The generic treatment in MOM is to assume
- that shortwave radiation is already contained inside the
- T_prog(index_temp)%stf field. Hence, to avoid
- double counting, sw_frac(k=0)=sw_frac_top should=0.0.
- If one removes shortwave from stf, then set sw_frac_top=1.0.
-
-[real]
-
-
-f_vis_in
-
-
- F_vis is the amount of light in the shortwave versus the long wave.
- F_vis=0.54 on sunny days and F_vis=0.60 on cloudy days. With
- override_f_vis = .true. F_vis is defined from f_vis_in.
- We believe, that this effect is in the first exponential in
- Paulson and Simpson (1977). The default is f_vis_in=1., instead of .57
- but it is still possible to define this quantity.
-
-[real]
-
-
-rpart_in
-
-
- rpart_in = (0..1)
-
-[real]
-
-
-coef1_in
-
-
-
-
-[real, units: meter]
-
-
-coef2_in
-
-
-
-
-[real, units: meter]
-
-
-override_coeff
-
-
- With override_coeff = .true. rpart_in, coef1_in, coef2_in specify
- the parameters for the double exponential. The default is .false..
-
-[logical]
-
-
-override_f_vis
-
-
- With override_f_vis = .true. F_vis is defined from f_vis_in,
- otherwise it is the shortwave versus the long wave amount of light.
- The default is .true.
-
-[logical]
-
-
-zmax_pen
-
-
- Maximum depth of penetration of shortwave radiation.
- Below this depth, shortwave penetration is exponentially
- small and so is ignored.
-
-[real, units: meter]
-
- Logical switch to select a watertype. Default=.false.. The model stops, if none is selected
- and override_coeff=.false..
-
-[logical]
-
-
-enforce_sw_frac
-
-
- To ensure the shortwave fraction is monotonically decreasing with depth.
-
-[logical]
-
-
-sw_pen_fixed_depths
-
-
- To compute penetration assuming fixed depths via Grd%zw(k) depths.
- This is strictly incorrect when have undulating free surface or
- generatlized vertical coordinates. This option is here for purposes
- of legacy, as this was done in MOM4.0 versions. It saves some compute time
- if the surface elevation is small compared with the upper cells' thickness.
- The default is .false.
-
-[logical]
-
- Paulson and Simpson (1977)
- Irradiance measurements in the upper ocean
- Journal of Physical Oceanography vol 7 pages 952-956
-
-
- Rosati and Miyakoda (1988)
- A General Circulation Model for Upper Ocean Simulation
- Journal of Physical Oceanography vol 18 pages 1601-1626.
-
-
-
-
-
-
-
-
NOTES
-
-
- The efolding depth is depth independent.
-
-
- Simpson and Dickey (1981) and others have argued between one and
- two exponentials for light between 300 um and 750 um.
- With vertical grid resolution of 5 meters or finer
- for the upper 20 meters, a second exponential will make a difference.
-
-
-
diff --git a/src/mom5/ocean_param/sources/ocean_shortwave_jerlov.xml b/src/mom5/ocean_param/sources/ocean_shortwave_jerlov.xml
deleted file mode 100644
index 665a398cd0..0000000000
--- a/src/mom5/ocean_param/sources/ocean_shortwave_jerlov.xml
+++ /dev/null
@@ -1,119 +0,0 @@
-
-
- Martin Schmidt
- S.M. Griffies
-
- This module returns thickness and density weighted temperature
- tendency [kg/m^3 * deg C *m/sec] from penetrative shortwave heating.
-
- Compute thickness and density weighted tendency [deg C *m/sec *kg/m^3]
- of temperature associated with penetrative shortwave heating in the upper
- ocean.
-
- This module ussumes a simple double exponential decay law. The e-folding
- depth may vary spatially and temporaly.
-
- The exponentials represents a parameterization of the
- attenuation coefficient for light between 300 um and 750 um in the following
- form:
-
- E(z) = E(0) * (r1*exp(-z/efold1) + (1-r1)*exp(-z/efold2))
- with z > 0 the ocean depth
-
- The "efold" is the efolding depth of the long and short
- visable and ultra violet light.
- efold will vary between 30 m in oligotrophic waters and 4 m in coastal
- regions.
-
- If the thickness of the first ocean level "dzt(1)" is 50 meters,
- then shortwave penetration does not do much. However, for finer
- vertical resolution, such as dzt(1) = 10 meters commonly used
- in ocean climate models, the effect of shortwave heating can
- be significant. This can be particularly noticable in the summer
- hemisphere.
-
- Radiation at the bottom is set to zero, hence the remaining radiation
- at the bottom of the deepest ocean cells is totally absorbed
- by these cells. This implies, that partial cells need not to
- be considered explicitly. Radiation at tracer depth within these
- cells is not set to zero. This differs from
- ocean_shortwave_gfdl and ocean_shortwave_csiro and reduces slightly the
- bouyancy forcing to the mixing layer in the kpp-scheme, if surface mixing
- goes down to the bottom.
-
-
- The efolding depth is depth independent.
-
- Simpson and Dickey (1981) and others have argued between one and
- two exponentials for light between 300 um and 750 um.
- With vertical grid resolution of 5 meters or finer
- for the upper 20 meters, a second exponential will make a difference.
-
- Jerlov (1968)
- Optical Oceanography
- Elsevier Press
-
- Paulson and Simpson (1977)
- Irradiance measurements in the upper ocean
- Journal of Physical Oceanography vol 7 pages 952-956
-
- Rosati and Miyakoda (1988)
- A General Circulation Model for Upper Ocean Simulation
- Journal of Physical Oceanography vol 18 pages 1601-1626.
-
- Must be .true. to run with module. Default is false.
-
- The fraction of shortwave radiation that should be incorporated into
- the sw_source array at k=1. The generic treatment in MOM is to assume
- that shortwave radiation is already contained inside the
- T_prog(index_temp)%stf field. Hence, to avoid
- double counting, sw_frac(k=0)=sw_frac_top should=0.0.
- If one removes shortwave from stf, then set sw_frac_top=1.0.
-
- F_vis is the amount of light in the shortwave versus the long wave.
- F_vis=0.54 on sunny days and F_vis=0.60 on cloudy days. With
- override_f_vis = .true. F_vis is defined from f_vis_in.
- We believe, that this effect is in the first exponential in
- Paulson and Simpson (1977). The default is f_vis_in=1., instead of .57
- but it is still possible to define this quantity.
-
- rpart_in = (0..1)
-
-
-
- With override_coeff = .true. rpart_in, coef1_in, coef2_in specify
- the parameters for the double exponential. The default is .false..
-
- With override_f_vis = .true. F_vis is defined from f_vis_in,
- otherwise it is the shortwave versus the long wave amount of light.
- The default is .true.
-
- Maximum depth of penetration of shortwave radiation.
- Below this depth, shortwave penetration is exponentially
- small and so is ignored.
-
- Logical switch to select a watertype. Default=.false.. The model stops, if none is selected
- and override_coeff=.false..
-
- To ensure the shortwave fraction is monotonically decreasing with depth.
-
- To compute penetration assuming fixed depths via Grd%zw(k) depths.
- This is strictly incorrect when have undulating free surface or
- generatlized vertical coordinates. This option is here for purposes
- of legacy, as this was done in MOM4.0 versions. It saves some compute time
- if the surface elevation is small compared with the upper cells' thickness.
- The default is .false.
-
- For debugging purposes.
-
- Initialization for the shortwave module
-
- Add short wave penetrative heating to T_prog(index_temp)%th_tendency.
-
- Note that the divergence of shortwave for the first
- level "div_sw(0)" is compensating for the effect of having
- the shortwave component already included in the total
- surface tracer flux "stf(i,j,temp)"
-
-
diff --git a/src/mom5/ocean_param/sources/ocean_sponges_eta.F90 b/src/mom5/ocean_param/sources/ocean_sponges_eta.F90
index 5f0ea0e5a6..6b9f1162f2 100644
--- a/src/mom5/ocean_param/sources/ocean_sponges_eta.F90
+++ b/src/mom5/ocean_param/sources/ocean_sponges_eta.F90
@@ -82,8 +82,8 @@ module ocean_sponges_eta_mod
public ocean_sponges_eta_init
public sponge_eta_source
-character(len=126) :: version = '$Id: ocean_sponges_eta.F90,v 1.1.2.2 2012/05/17 13:41:49 smg Exp $'
-character (len=128) :: tagname = '$Name: mom5_siena_08jun2012_smg $'
+character(len=126) :: version = '$Id: ocean_sponges_eta.F90,v 20.0 2013/12/14 00:16:22 fms Exp $'
+character (len=128) :: tagname = '$Name: tikal $'
! for diagnostics
logical :: used
diff --git a/src/mom5/ocean_param/sources/ocean_sponges_eta.html b/src/mom5/ocean_param/sources/ocean_sponges_eta.html
deleted file mode 100644
index 8350f9fcf9..0000000000
--- a/src/mom5/ocean_param/sources/ocean_sponges_eta.html
+++ /dev/null
@@ -1,177 +0,0 @@
-
-
-
-Module ocean_sponges_eta_mod
-
-
-
-
-PUBLIC INTERFACE
-
- ~ PUBLIC ROUTINES
- ~ NAMELIST
-
-
- Weighted eta tendency [meter*meter/sec] from sponges.
-
-
-
-
-
-
- This module applies sponge to eta. The sponges
- can occur at any location and with any distribution in the domain, and
- with any time step and damping rate. Sponges occur where positive
- inverse restore times occur in the field passed to sponge_init. An
- array of eta tendencies due to the sponges is augmented through a
- call to sponge_eta_source. The array of eta tendencies must be
- reset to zero between calls.
-
- Different damping rates can be specified by making
- calls to register_sponge_rate - no sponges are applied to fields for
- which uniformly zero inverse damping rates are set with a call to
- register_sponge_rate. The value towards which a field is damped is
- set with calls to register_sponge_field; successive calls are used to
- set up linear interpolation of this restore rate.
-
- Sponge data and damping coefficients are 2 dimensional.
-
- The user is responsible for providing (and registering) the data on
- the model grid of values towards which the etas are being driven.
-
-
- This subroutine is intended to be used to initialize the sponges.
- Everything in this subroutine is a user prototype, and should be replacable.
-
-
-
-
-
-
-
-
sponge_eta_source
-
-
-DESCRIPTION
-
-
- This subroutine calculates thickness weighted and density weighted
- time tendencies due to damping by sponges or damping through adaptive
- restoring.
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_sponges_eta_nml
-
-
-
-
-
-use_this_module
-
-
- For using this module. Default use_this_module=.false.
-
-[logical]
-
-
-damp_coeff_3d
-
-
- For case when damping coefficients are full 3d field of values.
- Default damp_coeff_3d=.false., which means damping coeffs are
- 2d horizontal array.
-
-[logical]
-
-
-
diff --git a/src/mom5/ocean_param/sources/ocean_sponges_eta.xml b/src/mom5/ocean_param/sources/ocean_sponges_eta.xml
deleted file mode 100644
index a615ed28c6..0000000000
--- a/src/mom5/ocean_param/sources/ocean_sponges_eta.xml
+++ /dev/null
@@ -1,42 +0,0 @@
-
-
- Paul Sandery
-
- Weighted eta tendency [meter*meter/sec] from sponges.
-
-
- This module applies sponge to eta. The sponges
- can occur at any location and with any distribution in the domain, and
- with any time step and damping rate. Sponges occur where positive
- inverse restore times occur in the field passed to sponge_init. An
- array of eta tendencies due to the sponges is augmented through a
- call to sponge_eta_source. The array of eta tendencies must be
- reset to zero between calls.
-
- Different damping rates can be specified by making
- calls to register_sponge_rate - no sponges are applied to fields for
- which uniformly zero inverse damping rates are set with a call to
- register_sponge_rate. The value towards which a field is damped is
- set with calls to register_sponge_field; successive calls are used to
- set up linear interpolation of this restore rate.
-
- Sponge data and damping coefficients are 2 dimensional.
-
- The user is responsible for providing (and registering) the data on
- the model grid of values towards which the etas are being driven.
-
-
- For using this module. Default use_this_module=.false.
-
- For case when damping coefficients are full 3d field of values.
- Default damp_coeff_3d=.false., which means damping coeffs are
- 2d horizontal array.
-
- This subroutine is intended to be used to initialize the sponges.
- Everything in this subroutine is a user prototype, and should be replacable.
-
- This subroutine calculates thickness weighted and density weighted
- time tendencies due to damping by sponges or damping through adaptive
- restoring.
-
diff --git a/src/mom5/ocean_param/sources/ocean_sponges_tracer.F90 b/src/mom5/ocean_param/sources/ocean_sponges_tracer.F90
index e24964a078..9ce6ff315f 100644
--- a/src/mom5/ocean_param/sources/ocean_sponges_tracer.F90
+++ b/src/mom5/ocean_param/sources/ocean_sponges_tracer.F90
@@ -91,8 +91,8 @@ module ocean_sponges_tracer_mod
public ocean_sponges_tracer_init
public sponge_tracer_source
-character(len=126) :: version = '$Id: ocean_sponges_tracer.F90,v 1.1.2.3 2012/06/01 20:47:08 Stephen.Griffies Exp $'
-character (len=128) :: tagname = '$Name: mom5_siena_08jun2012_smg $'
+character(len=126) :: version = '$Id: ocean_sponges_tracer.F90,v 20.0 2013/12/14 00:16:24 fms Exp $'
+character (len=128) :: tagname = '$Name: tikal $'
! for diagnostics
logical :: used
diff --git a/src/mom5/ocean_param/sources/ocean_sponges_tracer.html b/src/mom5/ocean_param/sources/ocean_sponges_tracer.html
deleted file mode 100644
index bd1c39e096..0000000000
--- a/src/mom5/ocean_param/sources/ocean_sponges_tracer.html
+++ /dev/null
@@ -1,182 +0,0 @@
-
-
-
-Module ocean_sponges_tracer_mod
-
-
-
-
-PUBLIC INTERFACE
-
- ~ PUBLIC ROUTINES
- ~ NAMELIST
-
-
- Thickness weighted tracer tendency [tracer*meter/sec] from sponges.
-
-
-
-
-
- This module applies sponges to tracers. The sponges
- can occur at any location and with any distribution in the domain, and
- with any time step and damping rate. Sponges occur where positive
- inverse restore times occur in the field passed to sponge_init. An
- array of tracer tendencies due to the sponges is augmented through a
- call to sponge_tracer_source. The array of tracer tendencies must be
- reset to zero between calls.
-
- Different damping rates can be specified for each field by making
- calls to register_sponge_rate - no sponges are applied to fields for
- which uniformly zero inverse damping rates are set with a call to
- register_sponge_rate. The value towards which a field is damped is
- set with calls to register_sponge_field; successive calls are used to
- set up linear interpolation of this restore rate.
-
- Sponge data and damping coefficients are generally 3 dimensional.
-
- The user is responsible for providing (and registering) the data on
- the model grid of values towards which the tracers are being driven.
-
- This subroutine is intended to be used to initialize the tracer sponges.
- Everything in this subroutine is a user prototype, and should be replacable.
-
-
-
-
-
-
-
-
sponge_tracer_source
-
-
-DESCRIPTION
-
-
- This subroutine calculates thickness weighted and density weighted
- time tendencies of tracers due to damping by sponges.
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_sponges_tracer_nml
-
-
-
-
-
-use_this_module
-
-
- For using this module. Default use_this_module=.false.
-
-[logical]
-
-
-damp_coeff_3d
-
-
- For case when damping coefficients are full 3d field of values.
- Default damp_coeff_3d=.false., which means damping coeffs are
- 2d horizontal array.
-
-[logical]
-
-
-
diff --git a/src/mom5/ocean_param/sources/ocean_sponges_tracer.xml b/src/mom5/ocean_param/sources/ocean_sponges_tracer.xml
deleted file mode 100644
index 7c0f7c34b3..0000000000
--- a/src/mom5/ocean_param/sources/ocean_sponges_tracer.xml
+++ /dev/null
@@ -1,43 +0,0 @@
-
-
- Bonnie Samuels
- R.W. Hallberg
- M.J. Harrison
- P. S. Swathi
- S. M. Griffies
-
- Thickness weighted tracer tendency [tracer*meter/sec] from sponges.
-
- This module applies sponges to tracers. The sponges
- can occur at any location and with any distribution in the domain, and
- with any time step and damping rate. Sponges occur where positive
- inverse restore times occur in the field passed to sponge_init. An
- array of tracer tendencies due to the sponges is augmented through a
- call to sponge_tracer_source. The array of tracer tendencies must be
- reset to zero between calls.
-
- Different damping rates can be specified for each field by making
- calls to register_sponge_rate - no sponges are applied to fields for
- which uniformly zero inverse damping rates are set with a call to
- register_sponge_rate. The value towards which a field is damped is
- set with calls to register_sponge_field; successive calls are used to
- set up linear interpolation of this restore rate.
-
- Sponge data and damping coefficients are generally 3 dimensional.
-
- The user is responsible for providing (and registering) the data on
- the model grid of values towards which the tracers are being driven.
-
- For using this module. Default use_this_module=.false.
-
- For case when damping coefficients are full 3d field of values.
- Default damp_coeff_3d=.false., which means damping coeffs are
- 2d horizontal array.
-
- This subroutine is intended to be used to initialize the tracer sponges.
- Everything in this subroutine is a user prototype, and should be replacable.
-
- This subroutine calculates thickness weighted and density weighted
- time tendencies of tracers due to damping by sponges.
-
diff --git a/src/mom5/ocean_param/sources/ocean_sponges_velocity.F90 b/src/mom5/ocean_param/sources/ocean_sponges_velocity.F90
index 4bb40c5806..f69b282cd5 100644
--- a/src/mom5/ocean_param/sources/ocean_sponges_velocity.F90
+++ b/src/mom5/ocean_param/sources/ocean_sponges_velocity.F90
@@ -88,8 +88,8 @@ module ocean_sponges_velocity_mod
public ocean_sponges_velocity_init
public sponge_velocity_source
-character(len=126) :: version = '$Id: ocean_sponges_velocity.F90,v 1.1.2.2 2012/05/17 13:41:49 smg Exp $'
-character (len=128) :: tagname = '$Name: mom5_siena_08jun2012_smg $'
+character(len=126) :: version = '$Id: ocean_sponges_velocity.F90,v 20.0 2013/12/14 00:16:26 fms Exp $'
+character (len=128) :: tagname = '$Name: tikal $'
! for diagnostics
logical :: used
diff --git a/src/mom5/ocean_param/sources/ocean_sponges_velocity.html b/src/mom5/ocean_param/sources/ocean_sponges_velocity.html
deleted file mode 100644
index 6905daa09d..0000000000
--- a/src/mom5/ocean_param/sources/ocean_sponges_velocity.html
+++ /dev/null
@@ -1,176 +0,0 @@
-
-
-
-Module ocean_sponges_velocity_mod
-
-
-
-
-PUBLIC INTERFACE
-
- ~ PUBLIC ROUTINES
- ~ NAMELIST
-
-
- Thickness weighted velocity tendency [meter*meter/sec*sec] from sponges.
-
-
-
-
-
-
- This module applies sponges to currents. The sponges
- can occur at any location and with any distribution in the domain, and
- with any time step and damping rate. Sponges occur where positive
- inverse restore times occur in the field passed to sponge_init. An
- array of tracer tendencies due to the sponges is augmented through a
- call to sponge_tracer_source. The array of tracer tendencies must be
- reset to zero between calls.
-
- Different damping rates can be specified for each field by making
- calls to register_sponge_rate - no sponges are applied to fields for
- which uniformly zero inverse damping rates are set with a call to
- register_sponge_rate. The value towards which a field is damped is
- set with calls to register_sponge_field; successive calls are used to
- set up linear interpolation of this restore rate.
-
- Sponge data and damping coefficients are generally 3 dimensional.
-
- The user is responsible for providing (and registering) the data on
- the model grid of values towards which the currents are being driven.
-
-
- This subroutine is intended to be used to initialize the sponges.
- Everything in this subroutine is a user prototype, and should be replacable.
-
-
-
-
-
-
-
-
sponge_velocity_source
-
-
-DESCRIPTION
-
-
- This subroutine calculates thickness weighted and density weighted
- time tendencies due to damping by sponges.
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_sponges_velocity_nml
-
-
-
-
-
-use_this_module
-
-
- For using this module. Default use_this_module=.false.
-
-[logical]
-
-
-damp_coeff_3d
-
-
- For case when damping coefficients are full 3d field of values.
- Default damp_coeff_3d=.false., which means damping coeffs are
- 2d horizontal array.
-
-[logical]
-
-
-
diff --git a/src/mom5/ocean_param/sources/ocean_sponges_velocity.xml b/src/mom5/ocean_param/sources/ocean_sponges_velocity.xml
deleted file mode 100644
index 7e17eed8f1..0000000000
--- a/src/mom5/ocean_param/sources/ocean_sponges_velocity.xml
+++ /dev/null
@@ -1,41 +0,0 @@
-
-
- Paul Sandery
-
- Thickness weighted velocity tendency [meter*meter/sec*sec] from sponges.
-
-
- This module applies sponges to currents. The sponges
- can occur at any location and with any distribution in the domain, and
- with any time step and damping rate. Sponges occur where positive
- inverse restore times occur in the field passed to sponge_init. An
- array of tracer tendencies due to the sponges is augmented through a
- call to sponge_tracer_source. The array of tracer tendencies must be
- reset to zero between calls.
-
- Different damping rates can be specified for each field by making
- calls to register_sponge_rate - no sponges are applied to fields for
- which uniformly zero inverse damping rates are set with a call to
- register_sponge_rate. The value towards which a field is damped is
- set with calls to register_sponge_field; successive calls are used to
- set up linear interpolation of this restore rate.
-
- Sponge data and damping coefficients are generally 3 dimensional.
-
- The user is responsible for providing (and registering) the data on
- the model grid of values towards which the currents are being driven.
-
-
- For using this module. Default use_this_module=.false.
-
- For case when damping coefficients are full 3d field of values.
- Default damp_coeff_3d=.false., which means damping coeffs are
- 2d horizontal array.
-
- This subroutine is intended to be used to initialize the sponges.
- Everything in this subroutine is a user prototype, and should be replacable.
-
- This subroutine calculates thickness weighted and density weighted
- time tendencies due to damping by sponges.
-
diff --git a/src/mom5/ocean_param/sources/ocean_xlandinsert.F90 b/src/mom5/ocean_param/sources/ocean_xlandinsert.F90
index 83ba40f2d8..2b92c87dbc 100644
--- a/src/mom5/ocean_param/sources/ocean_xlandinsert.F90
+++ b/src/mom5/ocean_param/sources/ocean_xlandinsert.F90
@@ -187,9 +187,9 @@ module ocean_xlandinsert_mod
integer :: index_salt=-1
character(len=128) :: version=&
- '$Id: ocean_xlandinsert.F90,v 1.1.2.1 2012/05/15 16:05:39 smg Exp $'
+ '$Id: ocean_xlandinsert.F90,v 20.0 2013/12/14 00:16:28 fms Exp $'
character (len=128) :: tagname = &
- '$Name: mom5_siena_08jun2012_smg $'
+ '$Name: tikal $'
integer :: isd, ied, jsd, jed, isc, iec, jsc, jec, nk
integer :: isg, ieg, jsg, jeg
diff --git a/src/mom5/ocean_param/sources/ocean_xlandinsert.html b/src/mom5/ocean_param/sources/ocean_xlandinsert.html
deleted file mode 100644
index b9135a0b23..0000000000
--- a/src/mom5/ocean_param/sources/ocean_xlandinsert.html
+++ /dev/null
@@ -1,395 +0,0 @@
-
-
-
-Module ocean_xlandinsert_mod
-
-
-
-
-PUBLIC INTERFACE
-
- ~ PUBLIC ROUTINES
- ~ NAMELIST
-
-
- Tracer and mass source from cross-land insertion.
-
-
-
-
-
- Compute thickness and density weighted tendency [rho*tracer*meter/sec]
- of tracer associated with cross-land insertion. Also compute
- mass source from cross-land insertion.
-
- Initial set up for crossland insertion of tracers and eta
-
- Checks are performed to ensure that the crossland mixing
- grid locations are valid according to model configuration.
-
- A summary of the locations of crossland points is written out.
-
- User specified inputs in "USER INPUT" section:
-
- ixland and jxland = user specified nxland pairs of i,j grid locations
-
- kxland = user specified uppermost (ktop=kxland(n,1)) and
- deepest (kbot=kxland(n,2)) levels over which crossland
- will be done for each crossland pair. Note the for
- xlandinsert, kxland(nxl,1)=1 is required, since the
- aim is to move excess volume from one column to another.
-
- tauxland = user specified time constant (seconds) setting the rate
- of transport via upwind advection.
-
- NOTE: for ixland, jxland, and kxland pairs, values of the
- (n,1) element should be < the corresponding (n,2) value.
-
-
-
-
-
-
-
-
-
xlandinsert
-
-
-DESCRIPTION
-
-
- Compute thickness and density weighted tracer source
- [(kg/m^3)*tracer*m/s] and mass source (kg/m^3)*(m/s)
- associated with discharge of tracer from surface of a
- thick column into a set of boxes within a thin column.
-
- NOTE:
- Compute rho_dzt_x as if using a geopotential model, since the
- xlandinsert rates are typically first tuned with geopotential models.
- also, we wish to have the transport proportional to differences in
- eta_t, which for zstar and pstar are generally must larger than
- differences in dzt.
-
- Modified by Keith.Dixon (January 2004)
-
- Modified by Stephen.Griffies for general
- vertical coordinates January 2005 and August 2006.
-
-
-
-
-
-
-
-
-
xlandinsert_mass
-
-
-DESCRIPTION
-
-
- Compute the mass source (kg/m^3)*meter/sec.
-
- Note that xlandinsert has already been called, so xland_rho_dzt
- has been filled.
-
-
-
-
-
-
-
-
at_least_one_in_comp_domain
-
-
-DESCRIPTION
-
-
- Function to see if at least one of the two points in a crossland pair
- is within the computational domain for the processor.
-
-
-
-
-INPUT
-
-
-
-
-
nxl
- Integer labeling the particular xlandinsert pair
- [integer]
-
-
-
-
-
-
-
-
-
on_comp_domain
-
-
-DESCRIPTION
-
-
- Determine if the point is in comp-domain for the processor
-
-
-
-
-INPUT
-
-
-
-
-
nxl
- Integer labeling the particular xlandinsert pair
- [integer]
-
-
-
lx
- lx=1,2 labels the point within an xlandinsert pair
- [integer]
-
-
-
-
-
-
-
-
-
on_processor
-
-
-DESCRIPTION
-
-
- Determine if the point is on processor
-
-
-
-
-
-
-
-
watermass_diag_init
-
-
-DESCRIPTION
-
-
- Initialization of watermass diagnostic output files.
-
-
-
-
-
-
-
-
watermass_diag
-
-
-DESCRIPTION
-
-
- Diagnose effects from xlandinsert on watermass transformation.
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_xlandinsert_nml
-
-
-
-
-
-use_this_module
-
-
- Needs to be true in order to use this scheme. Default is false.
-
-[logical]
-
-
-verbose_init
-
-
- For verbose initialization information.
-
-[logical]
-
-
-debug_this_module
-
-
- For debugging.
-
-[logical]
-
-
-
-
-
-
-
-
-
-
-
REFERENCES
-
-
-
-
- S.M. Griffies, M.J. Harrison, R. C. Pacanowski, and A. Rosati
- A Technical Guide to MOM4 (2003)
- NOAA/Geophysical Fluid Dynamics Laboratory
-
-
-
-
-
-
-
-
NOTES
-
-
- Algorithm ensures both total tracer and total mass is conserved.
- Algorithm sets up the insertion points as in xlandmix, and
- transports between the columns as in rivermix.
-
-
- 2D domain decomposition is implemented according to following
- notions. If the two points in an xlandinsert pair live within halo
- of each other (i.e., within same local_domain),
- then no added mpp communication required. However, nore generally
- the two points live further away. In this case, xland_domain
- is defined so that its halos incorporate the maximum separation
- of xlandinsert points. New tracer, eta, and grid arrays
- are defined over this extended xland_domain. This added domain
- size will come at some computational cost, so it is advantageous
- to limit the separation between points within an xlandinsert pair.
-
-
- The current implementation of xlandinsert has not been generalized
- to allow for communication between points separated by the tripolar fold.
- The problem is in the logic used to compute xland_domain.
- There is nothing fundamental limiting a generalization of the
- logic used to generate xland_domain.
-
-
- Many of the user specified values given in USER INPUT are
- model dependent since unresolved straits can become resolved
- in finer mesh models.
-
-
- BUG FIX 30 May 2011.
- Trying to mix across the ends of the global domain results in incorrect indexing.
- Local indices need to be incremented/decremented by the global extent.
- Russell.Fiedler@csiro.au
-
-
-
diff --git a/src/mom5/ocean_param/sources/ocean_xlandinsert.xml b/src/mom5/ocean_param/sources/ocean_xlandinsert.xml
deleted file mode 100644
index da22b3a7e8..0000000000
--- a/src/mom5/ocean_param/sources/ocean_xlandinsert.xml
+++ /dev/null
@@ -1,117 +0,0 @@
-
-
- S.M. Griffies
- K.W. Dixon
- M.J. Harrison
-
- Tracer and mass source from cross-land insertion.
-
- Compute thickness and density weighted tendency [rho*tracer*meter/sec]
- of tracer associated with cross-land insertion. Also compute
- mass source from cross-land insertion.
-
- S.M. Griffies, M.J. Harrison, R. C. Pacanowski, and A. Rosati
- A Technical Guide to MOM4 (2003)
- NOAA/Geophysical Fluid Dynamics Laboratory
-
- Algorithm ensures both total tracer and total mass is conserved.
- Algorithm sets up the insertion points as in xlandmix, and
- transports between the columns as in rivermix.
-
- 2D domain decomposition is implemented according to following
- notions. If the two points in an xlandinsert pair live within halo
- of each other (i.e., within same local_domain),
- then no added mpp communication required. However, nore generally
- the two points live further away. In this case, xland_domain
- is defined so that its halos incorporate the maximum separation
- of xlandinsert points. New tracer, eta, and grid arrays
- are defined over this extended xland_domain. This added domain
- size will come at some computational cost, so it is advantageous
- to limit the separation between points within an xlandinsert pair.
-
- The current implementation of xlandinsert has not been generalized
- to allow for communication between points separated by the tripolar fold.
- The problem is in the logic used to compute xland_domain.
- There is nothing fundamental limiting a generalization of the
- logic used to generate xland_domain.
-
- Many of the user specified values given in USER INPUT are
- model dependent since unresolved straits can become resolved
- in finer mesh models.
-
- BUG FIX 30 May 2011.
- Trying to mix across the ends of the global domain results in incorrect indexing.
- Local indices need to be incremented/decremented by the global extent.
- Russell.Fiedler@csiro.au
-
- Needs to be true in order to use this scheme. Default is false.
-
- For verbose initialization information.
-
- For debugging.
-
- Initial set up for crossland insertion of tracers and eta
-
- Checks are performed to ensure that the crossland mixing
- grid locations are valid according to model configuration.
-
- A summary of the locations of crossland points is written out.
-
- User specified inputs in "USER INPUT" section:
-
- ixland and jxland = user specified nxland pairs of i,j grid locations
-
- kxland = user specified uppermost (ktop=kxland(n,1)) and
- deepest (kbot=kxland(n,2)) levels over which crossland
- will be done for each crossland pair. Note the for
- xlandinsert, kxland(nxl,1)=1 is required, since the
- aim is to move excess volume from one column to another.
-
- tauxland = user specified time constant (seconds) setting the rate
- of transport via upwind advection.
-
- NOTE: for ixland, jxland, and kxland pairs, values of the
- (n,1) element should be < the corresponding (n,2) value.
-
-
- Compute thickness and density weighted tracer source
- [(kg/m^3)*tracer*m/s] and mass source (kg/m^3)*(m/s)
- associated with discharge of tracer from surface of a
- thick column into a set of boxes within a thin column.
-
- NOTE:
- Compute rho_dzt_x as if using a geopotential model, since the
- xlandinsert rates are typically first tuned with geopotential models.
- also, we wish to have the transport proportional to differences in
- eta_t, which for zstar and pstar are generally must larger than
- differences in dzt.
-
- Modified by Keith.Dixon (January 2004)
-
- Modified by Stephen.Griffies for general
- vertical coordinates January 2005 and August 2006.
-
-
- Compute the mass source (kg/m^3)*meter/sec.
-
- Note that xlandinsert has already been called, so xland_rho_dzt
- has been filled.
-
- Function to see if at least one of the two points in a crossland pair
- is within the computational domain for the processor.
-
- Integer labeling the particular xlandinsert pair
-
- Determine if the point is in comp-domain for the processor
-
- Integer labeling the particular xlandinsert pair
-
- lx=1,2 labels the point within an xlandinsert pair
-
- Determine if the point is on processor
-
- Initialization of watermass diagnostic output files.
-
- Diagnose effects from xlandinsert on watermass transformation.
-
diff --git a/src/mom5/ocean_param/sources/ocean_xlandmix.F90 b/src/mom5/ocean_param/sources/ocean_xlandmix.F90
index 155983c61e..c70f4e661a 100644
--- a/src/mom5/ocean_param/sources/ocean_xlandmix.F90
+++ b/src/mom5/ocean_param/sources/ocean_xlandmix.F90
@@ -213,9 +213,9 @@ module ocean_xlandmix_mod
integer :: index_salt=-1
character(len=128) :: version=&
- '$Id: ocean_xlandmix.F90,v 1.1.2.2 2012/05/17 13:41:49 smg Exp $'
+ '$Id: ocean_xlandmix.F90,v 20.0 2013/12/14 00:16:30 fms Exp $'
character (len=128) :: tagname = &
- '$Name: mom5_siena_08jun2012_smg $'
+ '$Name: tikal $'
integer :: isd, ied, jsd, jed, isc, iec, jsc, jec, nk
integer :: isg, ieg, jsg, jeg
diff --git a/src/mom5/ocean_param/sources/ocean_xlandmix.html b/src/mom5/ocean_param/sources/ocean_xlandmix.html
deleted file mode 100644
index 0d4152078f..0000000000
--- a/src/mom5/ocean_param/sources/ocean_xlandmix.html
+++ /dev/null
@@ -1,493 +0,0 @@
-
-
-
-Module ocean_xlandmix_mod
-
-
-
-
-PUBLIC INTERFACE
-
- ~ PUBLIC ROUTINES
- ~ NAMELIST
-
-
- Tracer and mass source from cross-land mixing.
-
-
-
-
-
- Compute thickness weighted and density weighted tendency
- [tracer*(kg/m^3)*meter/sec] of tracer and mass associated with
- cross-land mixing of points.
-
- In particular, this module provides interaction between bodies of
- water separated by land in coarse models (e.g., Med-Atlantic).
- Interaction consists of mixing tracer and mass between water
- columns found on each side of the land barrier.
-
- To conserve total tracer when using xlandmix with k=1,
- also need to connect mass between remote bodies of water
- via xlandmix of eta.
-
- When connecting cells with k>1, we do not mix mass. This
- is ensured by making the time tendency only a function of the
- difference in tracer concentration.
-
-
- Initial set up for crossland mixing of tracers
-
- (i,j,k) locations of crossland mixing points are set via
- field table entries.
-
- Time invariant crossland mixing rates (in units of m**3/sec) are
- set via field table entries.
-
- Checks are performed to ensure that the crossland mixing
- grid locations are valid according to model configuration.
-
- A summary of the locations of crossland mixing points is written out.
-
- User specified inputs in "USER INPUT" section:
-
- ixland and jxland = user specified nxland pairs of i,j grid locations
-
- kxland = user specified uppermost (ktop=kxland(n,1)) and deepest
- (kbot=kxland(n,2)) levels over which crossland mixing will
- be done for each pair of crossland mixing points.
-
- vxland = user specified time invariant rates of crossland mixing (m3/sec)
- Equivalent to "the flow to the east = the flow to the west"
- Dynamic vxland is not available in MOM.
-
- NOTE: for ixland, jxland, and kxland pairs, values of the
- (n,1) element should be < the corresponding (n,2) value.
-
-
-
-
-
-
-
-
xlandmix
-
-
-DESCRIPTION
-
-
- Compute thickness and density weighted time tendency from
- xlandmix. Units of the tendency are tracer*(kg/m^3)*meter/sec.
-
- Logic is a bit tricky in order to allow each (i,j,k) point
- to participate in an arbitrary number of xlandmix pairs.
-
-
-
-
-
-
-
-
-
xlandmix_mass
-
-
-DESCRIPTION
-
-
- Compute the mass source kg/(m^2*sec).
- Note that xlandmix has already been called, so xland_mass has been
- filled.
-
-
-
-
-
-
-
-
xland_check
-
-
-DESCRIPTION
-
-
- Check if prescribed too much mixing
-
- In this routine the crossland mixing rate vxland(nxl) for
- the pair of points associated with index number nxl is
- converted into the fraction of the model grid boxes to be mixed
- per second, and checked. These checks ensure that the rate of
- crossland mixing requested is valid in that it can be realized
- given the timestep length and column volumes involved.
-
-
-
-
-INPUT
-
-
-
-
-
nxl
- Integer labeling the particular xlandmix pair
- [integer]
-
-
-
-
-
-INPUT/OUTPUT
-
-
-
-
-
error
- Error flag indicates whether initialization was performed successfully.
- [logical]
-
-
-
-
-
-
-
-
-
at_least_one_in_comp_domain
-
-
-DESCRIPTION
-
-
- Function to see if at least one of the two points in a crossland pair
- is within the computational domain for the processor.
-
-
-
-
-INPUT
-
-
-
-
-
nxl
- Integer labeling the particular xlandmix pair
- [integer]
-
-
-
-
-
-
-
-
-
both_in_local_domain
-
-
-DESCRIPTION
-
-
- Determine if both points in a crossland pair are within the
- local domain for the processor.
-
-
-
-
-INPUT
-
-
-
-
-
nxl
- Integer labeling the particular xlandmix pair
- [integer]
-
-
-
-
-
-
-
-
-
on_comp_domain
-
-
-DESCRIPTION
-
-
- Determine if the point is in comp-domain for the processor
-
-
-
-
-INPUT
-
-
-
-
-
nxl
- Integer labeling the particular xlandmix pair
- [integer]
-
-
-
lx
- lx=1,2 labels the point within an xlandmix pair
- [integer]
-
-
-
-
-
-
-
-
-
on_processor
-
-
-DESCRIPTION
-
-
- Determine if the point is on processor
-
-
-
-
-
-
-
-
watermass_diag_init
-
-
-DESCRIPTION
-
-
- Initialization of watermass diagnostic output files.
-
-
-
-
-
-
-
-
watermass_diag
-
-
-DESCRIPTION
-
-
- Diagnose effects from xlandmix on watermass transformation.
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_xlandmix_nml
-
-
-
-
-
-use_this_module
-
-
- Needs to be true in order to use this scheme. Default is false.
-
-[logical]
-
-
-xlandmix_kmt
-
-
- To allow xlandmixing to occur at k=kmt cell.
- Default is xlandmix_kmt=.false.
-
-[logical]
-
-
-verbose_init
-
-
- For verbose initialization information.
-
-[logical]
-
-
-
-
-
-
-
-
-
-
-
REFERENCES
-
-
-
-
- S.M. Griffies, M.J. Harrison, R. C. Pacanowski, and A. Rosati
- A Technical Guide to MOM4 (2004)
- NOAA/Geophysical Fluid Dynamics Laboratory
-
-
- S.M. Griffies: Elements of MOM (2012)
- NOAA/Geophysical Fluid Dynamics Laboratory
-
-
-
-
-
-
-
-
NOTES
-
-
- Algorithm ensures both total tracer and total mass is conserved.
-
-
- 2D domain decomposition is implemented according to following
- notions. If the two points in an xlandmix pair live within halo
- of each other (i.e., within same local_domain),
- then no added mpp communication required. However, more generally
- the two points live further away. In this case, xland_domain
- is defined so that its halos incorporate the maximum separation
- of xlandmix points. New tracer, eta, and grid arrays
- are defined over this extended xland_domain. This added domain
- size will come at some computational cost, so it is advantageous
- to limit the separation between points within an xlandmix pair.
-
-
- The current implementation of xlandmix has not been generalized
- to allow for communication between points separated by the tripolar fold.
- The problem is in the logic used to compute xland_domain.
- There is nothing fundamental limiting a generalization of the
- logic used to generate xland_domain.
-
-
- Many of the user specified values given in USER INPUT are
- model dependent since unresolved straits can become resolved
- in finer mesh models.
-
-
- Algorithm originally developed by Keith Dixon (Keith.Dixon)
- for rigid lid and full cells and one processor (i.e., MOM1).
- Algorithm extended to free surface and partial cells and 2D
- domain decomposition by S.M.Griffies (Stephen.Griffies).
- Further extensions to generalized vertical coordinates by
- Stephen.Griffies
-
-
- BUG FIX 30 May 2011.
- Trying to mix across the ends of the global domain results in incorrect indexing.
- Local indices need to be incremented/decremented by the global extent.
- Russell.Fiedler@csiro.au
-
-
-
diff --git a/src/mom5/ocean_param/sources/ocean_xlandmix.xml b/src/mom5/ocean_param/sources/ocean_xlandmix.xml
deleted file mode 100644
index 33cf44f227..0000000000
--- a/src/mom5/ocean_param/sources/ocean_xlandmix.xml
+++ /dev/null
@@ -1,150 +0,0 @@
-
-
- S.M. Griffies
- M.J. Harrison
- K. Dixon
-
- Tracer and mass source from cross-land mixing.
-
- Compute thickness weighted and density weighted tendency
- [tracer*(kg/m^3)*meter/sec] of tracer and mass associated with
- cross-land mixing of points.
-
- In particular, this module provides interaction between bodies of
- water separated by land in coarse models (e.g., Med-Atlantic).
- Interaction consists of mixing tracer and mass between water
- columns found on each side of the land barrier.
-
- To conserve total tracer when using xlandmix with k=1,
- also need to connect mass between remote bodies of water
- via xlandmix of eta.
-
- When connecting cells with k>1, we do not mix mass. This
- is ensured by making the time tendency only a function of the
- difference in tracer concentration.
-
-
- S.M. Griffies, M.J. Harrison, R. C. Pacanowski, and A. Rosati
- A Technical Guide to MOM4 (2004)
- NOAA/Geophysical Fluid Dynamics Laboratory
-
- S.M. Griffies: Elements of MOM (2012)
- NOAA/Geophysical Fluid Dynamics Laboratory
-
- Algorithm ensures both total tracer and total mass is conserved.
-
- 2D domain decomposition is implemented according to following
- notions. If the two points in an xlandmix pair live within halo
- of each other (i.e., within same local_domain),
- then no added mpp communication required. However, more generally
- the two points live further away. In this case, xland_domain
- is defined so that its halos incorporate the maximum separation
- of xlandmix points. New tracer, eta, and grid arrays
- are defined over this extended xland_domain. This added domain
- size will come at some computational cost, so it is advantageous
- to limit the separation between points within an xlandmix pair.
-
- The current implementation of xlandmix has not been generalized
- to allow for communication between points separated by the tripolar fold.
- The problem is in the logic used to compute xland_domain.
- There is nothing fundamental limiting a generalization of the
- logic used to generate xland_domain.
-
- Many of the user specified values given in USER INPUT are
- model dependent since unresolved straits can become resolved
- in finer mesh models.
-
- Algorithm originally developed by Keith Dixon (Keith.Dixon)
- for rigid lid and full cells and one processor (i.e., MOM1).
- Algorithm extended to free surface and partial cells and 2D
- domain decomposition by S.M.Griffies (Stephen.Griffies).
- Further extensions to generalized vertical coordinates by
- Stephen.Griffies
-
- BUG FIX 30 May 2011.
- Trying to mix across the ends of the global domain results in incorrect indexing.
- Local indices need to be incremented/decremented by the global extent.
- Russell.Fiedler@csiro.au
-
- Needs to be true in order to use this scheme. Default is false.
-
- To allow xlandmixing to occur at k=kmt cell.
- Default is xlandmix_kmt=.false.
-
- For verbose initialization information.
-
- Initial set up for crossland mixing of tracers
-
- (i,j,k) locations of crossland mixing points are set via
- field table entries.
-
- Time invariant crossland mixing rates (in units of m**3/sec) are
- set via field table entries.
-
- Checks are performed to ensure that the crossland mixing
- grid locations are valid according to model configuration.
-
- A summary of the locations of crossland mixing points is written out.
-
- User specified inputs in "USER INPUT" section:
-
- ixland and jxland = user specified nxland pairs of i,j grid locations
-
- kxland = user specified uppermost (ktop=kxland(n,1)) and deepest
- (kbot=kxland(n,2)) levels over which crossland mixing will
- be done for each pair of crossland mixing points.
-
- vxland = user specified time invariant rates of crossland mixing (m3/sec)
- Equivalent to "the flow to the east = the flow to the west"
- Dynamic vxland is not available in MOM.
-
- NOTE: for ixland, jxland, and kxland pairs, values of the
- (n,1) element should be < the corresponding (n,2) value.
-
- Compute thickness and density weighted time tendency from
- xlandmix. Units of the tendency are tracer*(kg/m^3)*meter/sec.
-
- Logic is a bit tricky in order to allow each (i,j,k) point
- to participate in an arbitrary number of xlandmix pairs.
-
-
- Compute the mass source kg/(m^2*sec).
- Note that xlandmix has already been called, so xland_mass has been
- filled.
-
- Check if prescribed too much mixing
-
- In this routine the crossland mixing rate vxland(nxl) for
- the pair of points associated with index number nxl is
- converted into the fraction of the model grid boxes to be mixed
- per second, and checked. These checks ensure that the rate of
- crossland mixing requested is valid in that it can be realized
- given the timestep length and column volumes involved.
-
- Integer labeling the particular xlandmix pair
-
- Error flag indicates whether initialization was performed successfully.
-
- Function to see if at least one of the two points in a crossland pair
- is within the computational domain for the processor.
-
- Integer labeling the particular xlandmix pair
-
- Determine if both points in a crossland pair are within the
- local domain for the processor.
-
- Integer labeling the particular xlandmix pair
-
- Determine if the point is in comp-domain for the processor
-
- Integer labeling the particular xlandmix pair
-
- lx=1,2 labels the point within an xlandmix pair
-
- Determine if the point is on processor
-
- Initialization of watermass diagnostic output files.
-
- Diagnose effects from xlandmix on watermass transformation.
-
diff --git a/src/mom5/ocean_param/vertical/ocean_convect.F90 b/src/mom5/ocean_param/vertical/ocean_convect.F90
index f461d26073..9802350eac 100644
--- a/src/mom5/ocean_param/vertical/ocean_convect.F90
+++ b/src/mom5/ocean_param/vertical/ocean_convect.F90
@@ -160,9 +160,9 @@ module ocean_convect_mod
integer :: isd, ied, jsd, jed, isc, iec, jsc, jec, nk
character(len=128) :: version=&
- '$Id: ocean_convect.F90,v 1.1.2.1 2012/05/15 16:06:17 smg Exp $'
+ '$Id: ocean_convect.F90,v 20.0 2013/12/14 00:16:32 fms Exp $'
character (len=128) :: tagname = &
- '$Name: mom5_siena_08jun2012_smg $'
+ '$Name: tikal $'
logical :: module_is_initialized=.FALSE.
logical :: use_this_module =.false.
diff --git a/src/mom5/ocean_param/vertical/ocean_convect.html b/src/mom5/ocean_param/vertical/ocean_convect.html
deleted file mode 100644
index 5f5e8e5738..0000000000
--- a/src/mom5/ocean_param/vertical/ocean_convect.html
+++ /dev/null
@@ -1,531 +0,0 @@
-
-
-
-Module ocean_convect_mod
-
-
-
-
-PUBLIC INTERFACE
-
- ~ PUBLIC ROUTINES
- ~ NAMELIST
-
-
- Vertically adjusts gravitationally unstable columns of ocean fluid.
-
-
-
-
-
- This module vertically adjusts gravitationally unstable columns of
- ocean fluid.
-
- Three algorithms are available:
-
- 1. Full convection from Rahmstorf. The algorithm produces a fully
- stable fluid column. Since most convection propagates downward, the
- scheme looks downward first and follows any instability (upward or
- downward) before checking the other direction. The routine mixes
- passive tracers only after the entire instability is found.
-
- 2. Full convection from Rahmstorf as optimized for vector machines
- by Russ Fiedler.
-
- 3. The Cox (1984) NCON-scheme. This scheme is recommended only
- for those wishing to maintain legacy code.
-
- 4. Legacy (pre TEOS-10) versions now supplied. In TEOS-10 we
- need to mix S_prog, fdelta first, and then compute S_A. This
- approach is not the same as mixing S_A directly.
-
-
-
- Initialize the convection module.
-
- For the full convection module, we register two fields
- for diagnostic output.
-
- ktot = number of levels convected in a vertical column
-
- kven = number of levels ventilated in a vertical column
-
- Note that ktot can in rare cases count some levels twice, if they
- get involved in two originally separate, but then
- overlapping convection areas in the water column. The field
- kven is 0 on land, 1 on ocean points with no
- convection, and any value up to nk on convecting points.
-
-
-
-
-
-
-
-
convection
-
-
-DESCRIPTION
-
-
- Subroutine calls one of the two possible convection schemes.
-
-
-
-
-
-
-
-
convection_full_scalar
-
-
-DESCRIPTION
-
-
- Subroutine to vertically adjust gravitationally unstable columns of ocean fluid.
- Produces updated values for all the tracers. Code implemented on scalar
- machines at GFDL. Has been found to be slow on vector machines. Use
- convection_full_vector for vector machines.
-
- internal variables:
-
- chk_la = logical flag to check level above kt
-
- chk_lb = logical flag to check level below kb
-
- kb = bottom level of (potential) instability
-
- kbo = bottom level of ocean
-
- kt = top level of (potential) instability
-
- la = test level above kt
-
- lb = test level below kb
-
- rl = lower level density referenced to lower level
-
- ru = upper level density referenced to lower level
-
- tmx = mixed tracer (1=temp, 2=salt, 3=fdelta, 4=other)
-
- tsm = sum of tracers (weighted by thickness) in the instability
-
- zsm = total thickness of the instability
-
- rho_salinity_mx = computed density salinity resulting from mixing of tracers.
-
-
-
-
-
-
-
-
-
convection_full_vector
-
-
-DESCRIPTION
-
-
- Subroutine to vertically adjust gravitationally unstable columns of ocean fluid.
- Produces updated values for all the tracers. Code implemented on vector
- machines at CSIRO. Has been found to be faster on these machines than
- convection_full_scalar. Answers differ, but not significantly.
-
- Code written by russell.fiedler@csiro.au
- most recently modified Aug2011
-
- internal variables:
-
- chk_la = logical flag to check level above kt
-
- chk_lb = logical flag to check level below kb
-
- kb = bottom level of (potential) instability
-
- kbo = bottom level of ocean
-
- kt = top level of (potential) instability
-
- la = test level above kt
-
- lb = test level below kb
-
- rl = lower level density referenced to lower level
-
- ru = upper level density referenced to lower level
-
- tmx = mixed tracer (1=temp, 2=salt, 3=other)
-
- tsm = sum of tracers (weighted by thickness) in the instability
-
- zsm = total thickness of the instability
-
- rho_salinity_mx = computed density salinity resulting from mixing of tracers.
-
-
-
-
-
-
-
-
-
convection_ncon
-
-
-DESCRIPTION
-
-
- "ncon" convection scheme
-
- Convectively adjust water column if gravitationally unstable.
- Based on algorithm from Mike Cox used in his code from 1984.
- Algorithm has well known problems with incomplete homogenization
- and sensitivity to the ncon parameter.
-
- Coded in mom4 for legacy purposes by Stephen.Griffies
- April 2001
-
-
-
-
-
-
-
-
-
convection_full_scalar_preteos10
-
-
-DESCRIPTION
-
-
-
- This routine is a legacy version which is consistent with using the old equation of state.
-
- Subroutine to vertically adjust gravitationally unstable columns of ocean fluid.
- Produces updated values for all the tracers. Code implemented on scalar
- machines at GFDL. Has been found to be slow on vector machines. Use
- convection_full_vector_preteos10 for vector machines.
-
- internal variables:
-
- chk_la = logical flag to check level above kt
-
- chk_lb = logical flag to check level below kb
-
- kb = bottom level of (potential) instability
-
- kbo = bottom level of ocean
-
- kt = top level of (potential) instability
-
- la = test level above kt
-
- lb = test level below kb
-
- rl = lower level density referenced to lower level
-
- ru = upper level density referenced to lower level
-
- tmx = mixed tracer (1=temp, 2=salt, 3=other)
-
- tsm = sum of tracers (weighted by thickness) in the instability
-
- zsm = total thickness of the instability
-
-
-
-
-
-
-
-
-
convection_full_vector_preteos10
-
-
-DESCRIPTION
-
-
-
- This routine is a legacy version which is consistent with using the old equation of state.
-
- Subroutine to vertically adjust gravitationally unstable columns of ocean fluid.
- Produces updated values for all the tracers. Code implemented on vector
- machines at CSIRO. Has been found to be faster on these machines than
- convection_full_scalar_preteos10. Answers differ, but not significantly.
-
- Code written by russell.fiedler@csiro.au
- most recently modified Aug2011
-
- internal variables:
-
- chk_la = logical flag to check level above kt
-
- chk_lb = logical flag to check level below kb
-
- kb = bottom level of (potential) instability
-
- kbo = bottom level of ocean
-
- kt = top level of (potential) instability
-
- la = test level above kt
-
- lb = test level below kb
-
- rl = lower level density referenced to lower level
-
- ru = upper level density referenced to lower level
-
- tmx = mixed tracer (1=temp, 2=salt, 3=other)
-
- tsm = sum of tracers (weighted by thickness) in the instability
-
- zsm = total thickness of the instability
-
-
-
-
-
-
-
-
-
convection_diag
-
-
-DESCRIPTION
-
-
- Some diagnostics for convection.
-
-
-
-
-
-
-
-
watermass_diag_init
-
-
-DESCRIPTION
-
-
- Initialization of watermass diagnostic output files.
-
-
-
-
-
-
-
-
watermass_diag
-
-
-DESCRIPTION
-
-
- Diagnose effects from convection of
- temp and salt on the watermass transformation diagnostics.
-
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_convect_nml
-
-
-
-
-
-use_this_module
-
-
- Must be true to use this module. Default is false.
-
-[logical]
-
-
-convect_ncon
-
-
- If true, will use the old NCON convection scheme from Cox.
- Retained only for legacy purposes to reproduce very old results.
-
-[logical]
-
-
-ncon
-
-
- Number of passes through the NCON-scheme.
-
-[integer]
-
-
-convect_full_scalar
-
-
- If true, will use the full convection scheme as implemented at GFDL for scalar
- machines.
-
-[logical]
-
-
-convect_full_vector
-
-
- If true, will use the full convection scheme as optimized for vector machines
- by russell.fiedler@csiro.au.
-
-[logical]
-
- Implementation of the full convection scheme is
- based on mom2/3 code by Stefan Rahmstorf
- (rahmstorf@pik-potsdam.de). But modified slightly
- for efficiency purposes in mom3.1
- by M. Eby (eby@uvic.ca) in June 2000. Notably, Eby
- eliminated goto statements.
-
-
- The Eby code was ported to mom4 by Griffies (Stephen.Griffies).
-
-
- To recover the exact same numerical values as the original
- Rahmstorf code, look for the two "Rahmstorf" comments in the code.
-
-
-
diff --git a/src/mom5/ocean_param/vertical/ocean_convect.xml b/src/mom5/ocean_param/vertical/ocean_convect.xml
deleted file mode 100644
index 0e478ec667..0000000000
--- a/src/mom5/ocean_param/vertical/ocean_convect.xml
+++ /dev/null
@@ -1,238 +0,0 @@
-
-
- Stephen M. Griffies
- R. Fiedler
-
- Vertically adjusts gravitationally unstable columns of ocean fluid.
-
- This module vertically adjusts gravitationally unstable columns of
- ocean fluid.
-
- Three algorithms are available:
-
- 1. Full convection from Rahmstorf. The algorithm produces a fully
- stable fluid column. Since most convection propagates downward, the
- scheme looks downward first and follows any instability (upward or
- downward) before checking the other direction. The routine mixes
- passive tracers only after the entire instability is found.
-
- 2. Full convection from Rahmstorf as optimized for vector machines
- by Russ Fiedler.
-
- 3. The Cox (1984) NCON-scheme. This scheme is recommended only
- for those wishing to maintain legacy code.
-
- 4. Legacy (pre TEOS-10) versions now supplied. In TEOS-10 we
- need to mix S_prog, fdelta first, and then compute S_A. This
- approach is not the same as mixing S_A directly.
-
-
- Stefan Rahmstorf (Ocean Modelling, 1993 vol 101 pages 9-11)
-
- Implementation of the full convection scheme is
- based on mom2/3 code by Stefan Rahmstorf
- (rahmstorf@pik-potsdam.de). But modified slightly
- for efficiency purposes in mom3.1
- by M. Eby (eby@uvic.ca) in June 2000. Notably, Eby
- eliminated goto statements.
-
- The Eby code was ported to mom4 by Griffies (Stephen.Griffies).
-
- To recover the exact same numerical values as the original
- Rahmstorf code, look for the two "Rahmstorf" comments in the code.
-
- Must be true to use this module. Default is false.
-
- If true, will use the old NCON convection scheme from Cox.
- Retained only for legacy purposes to reproduce very old results.
-
- Number of passes through the NCON-scheme.
-
- If true, will use the full convection scheme as implemented at GFDL for scalar
- machines.
-
- If true, will use the full convection scheme as optimized for vector machines
- by russell.fiedler@csiro.au.
-
-
- Initialize the convection module.
-
- For the full convection module, we register two fields
- for diagnostic output.
-
- ktot = number of levels convected in a vertical column
-
- kven = number of levels ventilated in a vertical column
-
- Note that ktot can in rare cases count some levels twice, if they
- get involved in two originally separate, but then
- overlapping convection areas in the water column. The field
- kven is 0 on land, 1 on ocean points with no
- convection, and any value up to nk on convecting points.
-
- Subroutine calls one of the two possible convection schemes.
-
- Subroutine to vertically adjust gravitationally unstable columns of ocean fluid.
- Produces updated values for all the tracers. Code implemented on scalar
- machines at GFDL. Has been found to be slow on vector machines. Use
- convection_full_vector for vector machines.
-
- internal variables:
-
- chk_la = logical flag to check level above kt
-
- chk_lb = logical flag to check level below kb
-
- kb = bottom level of (potential) instability
-
- kbo = bottom level of ocean
-
- kt = top level of (potential) instability
-
- la = test level above kt
-
- lb = test level below kb
-
- rl = lower level density referenced to lower level
-
- ru = upper level density referenced to lower level
-
- tmx = mixed tracer (1=temp, 2=salt, 3=fdelta, 4=other)
-
- tsm = sum of tracers (weighted by thickness) in the instability
-
- zsm = total thickness of the instability
-
- rho_salinity_mx = computed density salinity resulting from mixing of tracers.
-
-
- Subroutine to vertically adjust gravitationally unstable columns of ocean fluid.
- Produces updated values for all the tracers. Code implemented on vector
- machines at CSIRO. Has been found to be faster on these machines than
- convection_full_scalar. Answers differ, but not significantly.
-
- Code written by russell.fiedler@csiro.au
- most recently modified Aug2011
-
- internal variables:
-
- chk_la = logical flag to check level above kt
-
- chk_lb = logical flag to check level below kb
-
- kb = bottom level of (potential) instability
-
- kbo = bottom level of ocean
-
- kt = top level of (potential) instability
-
- la = test level above kt
-
- lb = test level below kb
-
- rl = lower level density referenced to lower level
-
- ru = upper level density referenced to lower level
-
- tmx = mixed tracer (1=temp, 2=salt, 3=other)
-
- tsm = sum of tracers (weighted by thickness) in the instability
-
- zsm = total thickness of the instability
-
- rho_salinity_mx = computed density salinity resulting from mixing of tracers.
-
-
- "ncon" convection scheme
-
- Convectively adjust water column if gravitationally unstable.
- Based on algorithm from Mike Cox used in his code from 1984.
- Algorithm has well known problems with incomplete homogenization
- and sensitivity to the ncon parameter.
-
- Coded in mom4 for legacy purposes by Stephen.Griffies
- April 2001
-
-
-
- This routine is a legacy version which is consistent with using the old equation of state.
-
- Subroutine to vertically adjust gravitationally unstable columns of ocean fluid.
- Produces updated values for all the tracers. Code implemented on scalar
- machines at GFDL. Has been found to be slow on vector machines. Use
- convection_full_vector_preteos10 for vector machines.
-
- internal variables:
-
- chk_la = logical flag to check level above kt
-
- chk_lb = logical flag to check level below kb
-
- kb = bottom level of (potential) instability
-
- kbo = bottom level of ocean
-
- kt = top level of (potential) instability
-
- la = test level above kt
-
- lb = test level below kb
-
- rl = lower level density referenced to lower level
-
- ru = upper level density referenced to lower level
-
- tmx = mixed tracer (1=temp, 2=salt, 3=other)
-
- tsm = sum of tracers (weighted by thickness) in the instability
-
- zsm = total thickness of the instability
-
-
-
- This routine is a legacy version which is consistent with using the old equation of state.
-
- Subroutine to vertically adjust gravitationally unstable columns of ocean fluid.
- Produces updated values for all the tracers. Code implemented on vector
- machines at CSIRO. Has been found to be faster on these machines than
- convection_full_scalar_preteos10. Answers differ, but not significantly.
-
- Code written by russell.fiedler@csiro.au
- most recently modified Aug2011
-
- internal variables:
-
- chk_la = logical flag to check level above kt
-
- chk_lb = logical flag to check level below kb
-
- kb = bottom level of (potential) instability
-
- kbo = bottom level of ocean
-
- kt = top level of (potential) instability
-
- la = test level above kt
-
- lb = test level below kb
-
- rl = lower level density referenced to lower level
-
- ru = upper level density referenced to lower level
-
- tmx = mixed tracer (1=temp, 2=salt, 3=other)
-
- tsm = sum of tracers (weighted by thickness) in the instability
-
- zsm = total thickness of the instability
-
-
- Some diagnostics for convection.
-
- Initialization of watermass diagnostic output files.
-
- Diagnose effects from convection of
- temp and salt on the watermass transformation diagnostics.
-
-
diff --git a/src/mom5/ocean_param/vertical/ocean_form_drag.F90 b/src/mom5/ocean_param/vertical/ocean_form_drag.F90
index 33be8594e5..0a571a7ca7 100644
--- a/src/mom5/ocean_param/vertical/ocean_form_drag.F90
+++ b/src/mom5/ocean_param/vertical/ocean_form_drag.F90
@@ -258,9 +258,9 @@ module ocean_form_drag_mod
character(len=128) :: version=&
- '$Id: ocean_form_drag.F90,v 1.1.2.2 2012/05/25 17:17:37 Stephen.Griffies Exp $'
+ '$Id: ocean_form_drag.F90,v 20.0 2013/12/14 00:16:34 fms Exp $'
character (len=128) :: tagname = &
- '$Name: mom5_siena_08jun2012_smg $'
+ '$Name: tikal $'
integer :: isd, ied, jsd, jed, isc, iec, jsc, jec, nk
diff --git a/src/mom5/ocean_param/vertical/ocean_form_drag.html b/src/mom5/ocean_param/vertical/ocean_form_drag.html
deleted file mode 100644
index 79033f4dc7..0000000000
--- a/src/mom5/ocean_param/vertical/ocean_form_drag.html
+++ /dev/null
@@ -1,474 +0,0 @@
-
-
-
-Module ocean_form_drag_mod
-
-
-
-
-PUBLIC INTERFACE
-
- ~ PUBLIC ROUTINES
- ~ NAMELIST
-
-
- Compute form drag as per Greatbatch and Lamb (1990) and/or
- Aiki etal (2004).
-
-
-
-
-
- Compute thickness weighted and density weighted tendency
- [velocity*(kg/m^3)*meter/sec] for velocity associated with
- parameterized form drag. Code employs the methods described
- in Greatbatch and Lamb (1990) as well as Aiki etal (2004).
-
- This scheme has not been updated for C-grid specific layout.
- However, there is little reason to expect that shifting the
- viscosity by 1/2 grid point will make sense physically for this
- scheme. Indeed, one does not expect this scheme to be relevant
- near boundaries anyhow. So use for both Bgrid and Cgrid should
- be reasonable, though with the caveat that differences will appear
- near boundaries.
-
-
- Initial set up for parameterized pressure form drag.
-
-
-
-
-
-
-
-
compute_visc_form_drag
-
-
-DESCRIPTION
-
-
- Compute vertical viscosity arising from parameterized
- form drag according to the methods from the Greatbatch TEM approach.
-
- Follow the method of Ferreira and Marshall (2006)
- for transitioning through the diabatic surface mixed layer.
- We take the surf_blthick from mixed layer schemes (e.g., KPP), and use
- this to define the region where the eddy induced velocity has
- zero vertical shear. Note that we do not introduce an additional
- transitional layer.
-
- There are four methods to compute the vertical viscosity within
- the interior, with one required to be chosen:
- 1/ form_drag_gbatch_f2overN2
- visc = kappa*(f/N)^2, with kappa=gm-diffusivity
- 2/ form_drag_gbatch_f2overNb2
- visc = kappa*(f/Nb)^2, with Nb=buoyancy freq just below surface mixed layer
- 3/ form_drag_gbatch_f2overNo2
- visc = kappa*(f/No)^2, with No=constant buoyancy freq
- 4/ form_drag_gbatch_alpha_f2
- visc = alpha*f^2, with alpha = constant (units of m^2*sec)
-
-
-
-
-
-
-
-
-
form_drag_accel
-
-
-DESCRIPTION
-
-
- Compute the rho*dz weighted acceleration from the Aiki etal
- form drag scheme.
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_form_drag_nml
-
-
-
-
-
-use_this_module
-
-
- Needs to be true in order to use this scheme. Default is false.
-
-[logical]
-
-
-debug_this_module
-
-
- For debugging.
-
-[logical]
-
-
-verbose_init
-
-
- For verbose initialization information.
-
-[logical]
-
-
-use_form_drag_gbatch
-
-
- For using the Greatbatch form drag approach, which places
- the contributions from "GM" into the momentum equation.
-
- use_form_drag_gbatch, is the traditional transformed
- Eulerian mean approach as per Greatbatch and Lamb (1990)
- and Greatbatch (1998). In this approach, we modify
- visc_cbu so that the the "GM-effects" occur through
- vertical viscosity.
-
- Since thise scheme is experimental, it is not recommended
- for general use, so we set default
- use_form_drag_gbatch=.false.
-
-[logical]
-
-
-form_drag_gbatch_surf_layer
-
-
- Logical to enable the use of a diabatic layer over which the
- eddy-induce velocity is assumed to be constant with depth.
- Default form_drag_gbatch_surf_layer=.false.
-
-[logical]
-
-
-ksurf_blayer_min
-
-
- Minimum number of vertical grid points in the surface turbulent
- boundary layer for use with form_drag_gbatch_surf_layer=.true.
- Default ksurf_blayer_min=3.
-
-[integer]
-
-
-form_drag_gbatch_alpha_f2
-
-
- For use of a vertical viscosity with the form_drag_gbatch that is
- equal to visc = form_drag_gbatch_alpha * f^2. This form of the
- vertical viscosity is used by Ferreira and Marshall, 2006.
- Default form_drag_gbatch_alpha_f2=.false.
-
-[logical]
-
-
-form_drag_gbatch_alpha
-
-
- For use of a vertical viscosity with the form_drag_gbatch that is
- equal to visc = form_drag_gbatch_alpha * f^2.
- Default form_drag_gbatch_alpha=3e8
-
-[real, units: m^2*sec]
-
-
-form_drag_gbatch_f2overN2
-
-
- To compute vertical viscosity according to visc=kappa*(f/N)**2
- with kappa=gm-diffusivity, f=Coriolis, and N=buoyancy frequency.
- This is the form suggested by Greatbatch and Lamb (1990).
- Default form_drag_gbatch_f2overN2=.false.
-
-[logical]
-
-
-form_drag_gbatch_f2overNb2
-
-
- To compute vertical viscosity according to visc=kappa*(f/Nb)**2
- with kappa=gm-diffusivity, f=Coriolis, and Nb=buoyancy frequency
- just below the diabatic mixed layer. This is the form suggested
- by Danabasoglu and Marshall (2007).
- Default form_drag_gbatch_f2overNb2=.false.
-
-[logical]
-
-
-form_drag_gbatch_f2overNo2
-
-
- To compute vertical viscosity according to visc=kappa*(f/No)**2
- with kappa=gm-diffusivity, f=Coriolis, and No=constant buoyancy
- frequency set via namelist.
- Default form_drag_gbatch_f2overNo2=.false.
-
-[logical]
-
-
-form_drag_gbatch_No
-
-
- To compute vertical viscosity according to visc=kappa*(f/No)**2
- with kappa=gm-diffusivity, f=Coriolis, and No=constant buoyancy
- frequency. Default form_drag_gbatch_No=5e-3
-
-[real, units: sec^-1]
-
-
-form_drag_gbatch_smooth_N2
-
-
- For vertically smoothing the squared buoyancy frequency for
- use in computing the vertical viscosity in the form drag
- approach. Default form_drag_gbatch_smooth_N2=.false.
-
-[logical]
-
-
-num_121_passes
-
-
- Number of 1-2-1 passes for vertically smoothing the squared
- buoyancy frequency. Default num_121_passes=1.
-
-[integer]
-
-
-visc_cbu_form_drag_max
-
-
- Maximum vertical viscosity used for the form drag contribution
- to vertical friction from the Greatbatch TEM approach.
- Default visc_cbu_form_drag_max=1m^2/sec.
-
-[real, units: m^2/sec]
-
-
-vel_form_drag_max
-
-
- For diagnostic purpuses, maximum form drag eddy induced velocity.
- Default vel_form_drag_max=1m/sec.
-
-[real, units: m/sec]
-
-
-N_squared_min
-
-
- Minimum sequared buoyancy frequency (N^2) for use in computing
- the vertical viscosity from the Greatbatch form drag scheme.
- Default N_squared_min=1e-10.
-
-[real, units: 1/sec]
-
-
-use_form_drag_aiki
-
-
- For using the Aiki form drag approach.
-
-[logical]
-
-
-cprime_aiki
-
-
- Dimensionless parameters from the Aiki etal scheme.
- Default cprime_aiki=0.3.
-
-[real, units: dimensionless]
-
-
-form_drag_aiki_scale_by_gm
-
-
- Compute a dimensionless scale function proportional to
- the GM-diffusivity, for use with the Aiki etal form
- drag scheme. Default form_drag_aiki_scale_by_gm=.false.
-
-[logical]
-
-
-form_drag_aiki_bottom_layer
-
-
- For implementing the Aiki form drag just in a selected number of
- bottom layers. Will still insist that the scheme conserves
- momentum, as a form drag scheme should do.
- Default form_drag_aiki_bottom_layer=.false.
-
-[logical]
-
-
-form_drag_aiki_bottom_klevels
-
-
- Number of klevels above the bottom that we choose to close the
- Aiki form drag scheme. Default form_drag_aiki_bottom_klevels=3.
- This should ideally be less than the minimum number of klevels
- in the model.
-
-[integer]
-
-
-form_drag_aiki_scale_by_gradH
-
-
- For scaling the coefficient used by the form drag scheme with
- the bottom slope.
-
-[logical]
-
-
-form_drag_aiki_gradH_power
-
-
- For scaling the coefficient used by the form drag scheme with
- the bottom slope raised to the power "form_drag_aiki_gradH_power".
-
-[real]
-
-
-form_drag_aiki_gradH_max
-
-
- For scaling setting the maximum of the bottom slope
- for use with scaling the form drag coefficient.
- Default form_drag_aiki_gradH_max=.05
-
-[logical]
-
-
-
-
-
-
-
-
-
-
-
REFERENCES
-
-
-
-
- Greatbatch and Lamb, 1990: On parameterizing vertical mixing of
- momentum in non eddy-resolving ocean models. Journal of
- Physical Oceanography. vol. 20, pages 1634-1637.
-
-
- Greatbatch, 1998: Exploring the relationship betwen eddy-induced
- transport velocity, vertical momentum transfer, and the isopycnal
- flux of potential vorticity. Journal of Physical Oceanography,
- vol. 28, pages 422-432.
-
-
- Aiki, Jacobson, and Yamagata, 2004: Parameterizing ocean eddy transports
- from surface to bottom. Geophysical Research Letters, vol. 31.
-
-
- Ferreira and Marshall, 2006: Formulation and implementation of
- a residual-mean ocean circulation model. Ocean Modelling,
- vol. 13, pages 86--107.
-
-
- Danabosaglu and Marshall, 2007: Effects of vertical variations of thickness
- diffusivity in an ocean general circulation model.
- Ocean Modelling, vol. 18, pages 122-141.
-
-
-
diff --git a/src/mom5/ocean_param/vertical/ocean_form_drag.xml b/src/mom5/ocean_param/vertical/ocean_form_drag.xml
deleted file mode 100644
index 006b6c52c3..0000000000
--- a/src/mom5/ocean_param/vertical/ocean_form_drag.xml
+++ /dev/null
@@ -1,172 +0,0 @@
-
-
- S.M. Griffies
-
- Compute form drag as per Greatbatch and Lamb (1990) and/or
- Aiki etal (2004).
-
- Compute thickness weighted and density weighted tendency
- [velocity*(kg/m^3)*meter/sec] for velocity associated with
- parameterized form drag. Code employs the methods described
- in Greatbatch and Lamb (1990) as well as Aiki etal (2004).
-
- This scheme has not been updated for C-grid specific layout.
- However, there is little reason to expect that shifting the
- viscosity by 1/2 grid point will make sense physically for this
- scheme. Indeed, one does not expect this scheme to be relevant
- near boundaries anyhow. So use for both Bgrid and Cgrid should
- be reasonable, though with the caveat that differences will appear
- near boundaries.
-
-
- Greatbatch and Lamb, 1990: On parameterizing vertical mixing of
- momentum in non eddy-resolving ocean models. Journal of
- Physical Oceanography. vol. 20, pages 1634-1637.
-
- Greatbatch, 1998: Exploring the relationship betwen eddy-induced
- transport velocity, vertical momentum transfer, and the isopycnal
- flux of potential vorticity. Journal of Physical Oceanography,
- vol. 28, pages 422-432.
-
- Aiki, Jacobson, and Yamagata, 2004: Parameterizing ocean eddy transports
- from surface to bottom. Geophysical Research Letters, vol. 31.
-
- Ferreira and Marshall, 2006: Formulation and implementation of
- a residual-mean ocean circulation model. Ocean Modelling,
- vol. 13, pages 86--107.
-
- Danabosaglu and Marshall, 2007: Effects of vertical variations of thickness
- diffusivity in an ocean general circulation model.
- Ocean Modelling, vol. 18, pages 122-141.
-
- Needs to be true in order to use this scheme. Default is false.
-
- For debugging.
-
- For verbose initialization information.
-
- For using the Greatbatch form drag approach, which places
- the contributions from "GM" into the momentum equation.
-
- use_form_drag_gbatch, is the traditional transformed
- Eulerian mean approach as per Greatbatch and Lamb (1990)
- and Greatbatch (1998). In this approach, we modify
- visc_cbu so that the the "GM-effects" occur through
- vertical viscosity.
-
- Since thise scheme is experimental, it is not recommended
- for general use, so we set default
- use_form_drag_gbatch=.false.
-
- Logical to enable the use of a diabatic layer over which the
- eddy-induce velocity is assumed to be constant with depth.
- Default form_drag_gbatch_surf_layer=.false.
-
- Minimum number of vertical grid points in the surface turbulent
- boundary layer for use with form_drag_gbatch_surf_layer=.true.
- Default ksurf_blayer_min=3.
-
- For use of a vertical viscosity with the form_drag_gbatch that is
- equal to visc = form_drag_gbatch_alpha * f^2. This form of the
- vertical viscosity is used by Ferreira and Marshall, 2006.
- Default form_drag_gbatch_alpha_f2=.false.
-
- For use of a vertical viscosity with the form_drag_gbatch that is
- equal to visc = form_drag_gbatch_alpha * f^2.
- Default form_drag_gbatch_alpha=3e8
-
- To compute vertical viscosity according to visc=kappa*(f/N)**2
- with kappa=gm-diffusivity, f=Coriolis, and N=buoyancy frequency.
- This is the form suggested by Greatbatch and Lamb (1990).
- Default form_drag_gbatch_f2overN2=.false.
-
- To compute vertical viscosity according to visc=kappa*(f/Nb)**2
- with kappa=gm-diffusivity, f=Coriolis, and Nb=buoyancy frequency
- just below the diabatic mixed layer. This is the form suggested
- by Danabasoglu and Marshall (2007).
- Default form_drag_gbatch_f2overNb2=.false.
-
- To compute vertical viscosity according to visc=kappa*(f/No)**2
- with kappa=gm-diffusivity, f=Coriolis, and No=constant buoyancy
- frequency set via namelist.
- Default form_drag_gbatch_f2overNo2=.false.
-
- To compute vertical viscosity according to visc=kappa*(f/No)**2
- with kappa=gm-diffusivity, f=Coriolis, and No=constant buoyancy
- frequency. Default form_drag_gbatch_No=5e-3
-
- For vertically smoothing the squared buoyancy frequency for
- use in computing the vertical viscosity in the form drag
- approach. Default form_drag_gbatch_smooth_N2=.false.
-
- Number of 1-2-1 passes for vertically smoothing the squared
- buoyancy frequency. Default num_121_passes=1.
-
- Maximum vertical viscosity used for the form drag contribution
- to vertical friction from the Greatbatch TEM approach.
- Default visc_cbu_form_drag_max=1m^2/sec.
-
- For diagnostic purpuses, maximum form drag eddy induced velocity.
- Default vel_form_drag_max=1m/sec.
-
- Minimum sequared buoyancy frequency (N^2) for use in computing
- the vertical viscosity from the Greatbatch form drag scheme.
- Default N_squared_min=1e-10.
-
- For using the Aiki form drag approach.
-
- Dimensionless parameters from the Aiki etal scheme.
- Default cprime_aiki=0.3.
-
- Compute a dimensionless scale function proportional to
- the GM-diffusivity, for use with the Aiki etal form
- drag scheme. Default form_drag_aiki_scale_by_gm=.false.
-
- For implementing the Aiki form drag just in a selected number of
- bottom layers. Will still insist that the scheme conserves
- momentum, as a form drag scheme should do.
- Default form_drag_aiki_bottom_layer=.false.
-
- Number of klevels above the bottom that we choose to close the
- Aiki form drag scheme. Default form_drag_aiki_bottom_klevels=3.
- This should ideally be less than the minimum number of klevels
- in the model.
-
- For scaling the coefficient used by the form drag scheme with
- the bottom slope.
-
- For scaling the coefficient used by the form drag scheme with
- the bottom slope raised to the power "form_drag_aiki_gradH_power".
-
- For scaling setting the maximum of the bottom slope
- for use with scaling the form drag coefficient.
- Default form_drag_aiki_gradH_max=.05
-
- Initial set up for parameterized pressure form drag.
-
- Compute vertical viscosity arising from parameterized
- form drag according to the methods from the Greatbatch TEM approach.
-
- Follow the method of Ferreira and Marshall (2006)
- for transitioning through the diabatic surface mixed layer.
- We take the surf_blthick from mixed layer schemes (e.g., KPP), and use
- this to define the region where the eddy induced velocity has
- zero vertical shear. Note that we do not introduce an additional
- transitional layer.
-
- There are four methods to compute the vertical viscosity within
- the interior, with one required to be chosen:
- 1/ form_drag_gbatch_f2overN2
- visc = kappa*(f/N)^2, with kappa=gm-diffusivity
- 2/ form_drag_gbatch_f2overNb2
- visc = kappa*(f/Nb)^2, with Nb=buoyancy freq just below surface mixed layer
- 3/ form_drag_gbatch_f2overNo2
- visc = kappa*(f/No)^2, with No=constant buoyancy freq
- 4/ form_drag_gbatch_alpha_f2
- visc = alpha*f^2, with alpha = constant (units of m^2*sec)
-
-
- Compute the rho*dz weighted acceleration from the Aiki etal
- form drag scheme.
-
diff --git a/src/mom5/ocean_param/vertical/ocean_vert_chen.F90 b/src/mom5/ocean_param/vertical/ocean_vert_chen.F90
index b04d35e8be..ff1f794780 100644
--- a/src/mom5/ocean_param/vertical/ocean_vert_chen.F90
+++ b/src/mom5/ocean_param/vertical/ocean_vert_chen.F90
@@ -188,9 +188,9 @@ module ocean_vert_chen_mod
type(ocean_grid_type), pointer :: Grd =>NULL()
character(len=256) :: version=&
- '$Id: ocean_vert_chen.F90,v 1.1.2.6 2012/05/25 17:17:37 Stephen.Griffies Exp $'
+ '$Id: ocean_vert_chen.F90,v 20.0 2013/12/14 00:16:36 fms Exp $'
character (len=128) :: tagname = &
- '$Name: mom5_siena_08jun2012_smg $'
+ '$Name: tikal $'
logical :: module_is_initialized = .FALSE.
logical :: use_this_module = .false.
diff --git a/src/mom5/ocean_param/vertical/ocean_vert_chen.html b/src/mom5/ocean_param/vertical/ocean_vert_chen.html
deleted file mode 100644
index eb1a82c320..0000000000
--- a/src/mom5/ocean_param/vertical/ocean_vert_chen.html
+++ /dev/null
@@ -1,374 +0,0 @@
-
-
-
-Module ocean_vert_chen_mod
-
-
-
-
-PUBLIC INTERFACE
-
- ~ PUBLIC ROUTINES
- ~ NAMELIST
-
-
- Initialization for the Chen vertical mixing scheme
-
- input:
- dzt = thickness of vertical levels (m)
- km = number of vertical levels
- yt = latitude of grid points (deg)
- dtts = density time step (sec)
- dtuv = internal mode time step (sec)
- error = logical to signal problems
- vmixset= logical to determine if a vertical mixing scheme was
- chosen
-
- output:
- visc_cbu_limit = visc max due to shear instability (m**2/sec)
- diff_cbt_limit = diffusivity .. (m**2/sec)
- visc_cbu_iw = visc background due to internal waves(m**2/sec)
- diff_cbt_iw = diffusivity .. (m**2/sec)
- error = true if some inconsistancy was found
-
-
-
-
-
-
-
-
-
vert_mix_chen
-
-
-DESCRIPTION
-
-
-
- --Compute interior mixing everywhere:
- interior mixing gets computed at all cell interfaces due to constant
- internal wave background activity ("visc_cbu_iw" and "diff_cbt_iw").
- Additionally, mixing can be enhanced by contribution from shear
- instability which is a function of the local Ri.
-
- --Boundary layer:
-
- (A) Boundary layer depth:
- at every gridpoint the depth of the Kraus boundary layer
- ("hbl") gets computed.
-
- (B) Boundary layer mixing:
- within the boundary layer, above hbl, vertical mixing is
- set to a maximum
-
- inputs
-
- outputs
-
- hbl = boundary layer depth (meters)
- visc_cbu = viscosity coefficient at bottom of U cells (m^2/s)
- diff_cbt = diffusion coefficient at bottom of T cells (m^2/s)
-
-
-
-
-
-
-
-
-
kraus_turner
-
-
-DESCRIPTION
-
-
-
- Calculate the Kraus mixed layer depth
-
- Note: This formulation assumes a single exponential decay in the solar
- shortwave penetration.
-
- Use smf_bgrid since this array contains the primary smf array read in from
- from the coupler in ocean_core/ocean_sbc.F90, when using the FMS coupler.
-
- real dbloc(ij_bounds) = local delta buoyancy (m/s^2)
- real ustar(ij_bounds) = surface friction velocity (m/s)
- real Bo(ij_bounds) = surface turbulent buoyancy forcing(m^2/s^3)
- real Bosol(ij_bounds) = radiative buoyancy forcing (m^2/s^3)
-
- output
- real hbl(ij_bounds) ! boundary layer depth (m)
- real mixmask(ij_bounds,nk) ! fraction of cell which resides in mixed layer
- integer kbl(ij_bounds) ! index of first grid level below hbl
-
-
-
-
-
-
-
-
-
ri_for_chen
-
-
-DESCRIPTION
-
-
- Compute Richardson number on tracer and velocity cell bottoms.
- rit = richardson number at bottom of T cells
- riu = richardson number at bottom of U cells
-
-
-
-
-
-
-
-
ocean_vert_chen_restart
-
-
-DESCRIPTION
-
-
- Write out restart files registered through register_restart_file
-
-
-
-
-
-
-
-
ocean_vert_chen_end
-
-
-DESCRIPTION
-
-
- Save the Kraus boundary layer depth to start next time step.
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_vert_chen_nml
-
-
-
-
-
-use_this_module
-
-
- Must be true to use this module. Default is false.
-
-[logical]
-
-
-debug_this_module
-
-
- For debugging. Default debug_this_module=.false.
-
-[logical]
-
-
-diff_cbt_iw
-
-
- Background vertical diffusivity. Note that if using Bryan-Lewis as a
- background diffusivity, then should set diff_cbt_iw=0.0.
-
-[real, units: m^2/sec]
-
- Maximum growth rate of kraus mixed layer
-
-[real, units: m/sec]
-
-
-
-
-
-
-
-
-
-
-
REFERENCES
-
-
-
-
- Chen, D., L.M. Rothstein and A.J. Busalacchi, 1994:
- A hybrid vertical mixing scheme and its application
- to tropical ocean models,
- J. Phys. Oceanogr., 24, 2156-2179
-
-
-
-
-
-
-
-
NOTES
-
-
- Surface fresh water contributes to surface buoyancy via conversion to
- a locally implied salt flux.
-
-
- This module typically runs with the ocean_shortwave_csiro scheme.
-
-
- Use smf_bgrid since this array contains the primary smf array read in from
- from the coupler in ocean_core/ocean_sbc.F90, when using the FMS coupler.
-
-
-
diff --git a/src/mom5/ocean_param/vertical/ocean_vert_chen.xml b/src/mom5/ocean_param/vertical/ocean_vert_chen.xml
deleted file mode 100644
index 7fbffabb26..0000000000
--- a/src/mom5/ocean_param/vertical/ocean_vert_chen.xml
+++ /dev/null
@@ -1,117 +0,0 @@
-
-
- Russell Fiedler
- S.M. Griffies
-
- Vertical viscosity and diffusivity according Chen scheme
-
- This scheme was originally developed by researchers
- at the CSIRO Marine and Atmospheric Research and
- Bureau of Meteorology, both in Australia.
-
- Chen, D., L.M. Rothstein and A.J. Busalacchi, 1994:
- A hybrid vertical mixing scheme and its application
- to tropical ocean models,
- J. Phys. Oceanogr., 24, 2156-2179
-
- Surface fresh water contributes to surface buoyancy via conversion to
- a locally implied salt flux.
-
- This module typically runs with the ocean_shortwave_csiro scheme.
-
- Use smf_bgrid since this array contains the primary smf array read in from
- from the coupler in ocean_core/ocean_sbc.F90, when using the FMS coupler.
-
- Must be true to use this module. Default is false.
-
- For debugging. Default debug_this_module=.false.
-
- Background vertical diffusivity. Note that if using Bryan-Lewis as a
- background diffusivity, then should set diff_cbt_iw=0.0.
-
- Background vertical viscosity
-
- Enhanced vertical viscosity due to shear instability
-
- Enhanced vertical diffusivity due to shear instability
-
- Bulk turblence parameter n_0
-
- Bulk turblence parameter m_0
-
- Maximum growth rate of kraus mixed layer
-
- Initialization for the Chen vertical mixing scheme
-
- input:
- dzt = thickness of vertical levels (m)
- km = number of vertical levels
- yt = latitude of grid points (deg)
- dtts = density time step (sec)
- dtuv = internal mode time step (sec)
- error = logical to signal problems
- vmixset= logical to determine if a vertical mixing scheme was
- chosen
-
- output:
- visc_cbu_limit = visc max due to shear instability (m**2/sec)
- diff_cbt_limit = diffusivity .. (m**2/sec)
- visc_cbu_iw = visc background due to internal waves(m**2/sec)
- diff_cbt_iw = diffusivity .. (m**2/sec)
- error = true if some inconsistancy was found
-
-
-
- --Compute interior mixing everywhere:
- interior mixing gets computed at all cell interfaces due to constant
- internal wave background activity ("visc_cbu_iw" and "diff_cbt_iw").
- Additionally, mixing can be enhanced by contribution from shear
- instability which is a function of the local Ri.
-
- --Boundary layer:
-
- (A) Boundary layer depth:
- at every gridpoint the depth of the Kraus boundary layer
- ("hbl") gets computed.
-
- (B) Boundary layer mixing:
- within the boundary layer, above hbl, vertical mixing is
- set to a maximum
-
- inputs
-
- outputs
-
- hbl = boundary layer depth (meters)
- visc_cbu = viscosity coefficient at bottom of U cells (m^2/s)
- diff_cbt = diffusion coefficient at bottom of T cells (m^2/s)
-
-
- Calculate the Kraus mixed layer depth
-
- Note: This formulation assumes a single exponential decay in the solar
- shortwave penetration.
-
- Use smf_bgrid since this array contains the primary smf array read in from
- from the coupler in ocean_core/ocean_sbc.F90, when using the FMS coupler.
-
- real dbloc(ij_bounds) = local delta buoyancy (m/s^2)
- real ustar(ij_bounds) = surface friction velocity (m/s)
- real Bo(ij_bounds) = surface turbulent buoyancy forcing(m^2/s^3)
- real Bosol(ij_bounds) = radiative buoyancy forcing (m^2/s^3)
-
- output
- real hbl(ij_bounds) ! boundary layer depth (m)
- real mixmask(ij_bounds,nk) ! fraction of cell which resides in mixed layer
- integer kbl(ij_bounds) ! index of first grid level below hbl
-
-
- Compute Richardson number on tracer and velocity cell bottoms.
- rit = richardson number at bottom of T cells
- riu = richardson number at bottom of U cells
-
- Write out restart files registered through register_restart_file
-
- Save the Kraus boundary layer depth to start next time step.
-
diff --git a/src/mom5/ocean_param/vertical/ocean_vert_const.F90 b/src/mom5/ocean_param/vertical/ocean_vert_const.F90
index a28056d1bb..f64a8bb81e 100644
--- a/src/mom5/ocean_param/vertical/ocean_vert_const.F90
+++ b/src/mom5/ocean_param/vertical/ocean_vert_const.F90
@@ -68,9 +68,9 @@ module ocean_vert_const_mod
integer :: isd, ied, jsd, jed, isc, iec, jsc, jec, nk
character(len=256) :: version=&
- '=>Using: const/ocean_vert_const.F90 ($Id: ocean_vert_const.F90,v 1.1.2.4 2012/06/08 20:33:56 Stephen.Griffies Exp $)'
+ '=>Using: const/ocean_vert_const.F90 ($Id: ocean_vert_const.F90,v 20.0 2013/12/14 00:16:38 fms Exp $)'
character (len=128) :: tagname = &
- '$Name: mom5_siena_08jun2012_smg $'
+ '$Name: tikal $'
integer :: index_temp
integer :: index_salt
diff --git a/src/mom5/ocean_param/vertical/ocean_vert_const.html b/src/mom5/ocean_param/vertical/ocean_vert_const.html
deleted file mode 100644
index d3cbe0b3e6..0000000000
--- a/src/mom5/ocean_param/vertical/ocean_vert_const.html
+++ /dev/null
@@ -1,181 +0,0 @@
-
-
-
-Module ocean_vert_const_mod
-
-
-
-
-PUBLIC INTERFACE
-
- ~ PUBLIC ROUTINES
- ~ NAMELIST
-
-
- Initialize the constant vertical diffusivity module.
-
-
-
-
-
-
-
-
vert_mix_const
-
-
-DESCRIPTION
-
-
- This function computes the vertical diffusivity and viscosity.
- These mixing coefficients are time independent but generally
- arbitrary functions of space.
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_vert_const_nml
-
-
-
-
-
-use_this_module
-
-
- Must be true to use this module. Default is false.
-
-[logical]
-
-
-kappa_h
-
-
- The constant vertical diffusivity. Used for cases when wanting a space-time
- independent diffusivity. The "h" is historical and stands for "heat".
-
-[real, units: m^2/sec]
-
-
-kappa_m
-
-
- The constant vertical viscosity. Used for cases when wanting a space-time
- independent viscosity.
-
-[real, units: m^2/sec]
-
-
-diff_cbt_limit
-
-
- The largest allowable vertical diffusivity. Of use for cases where vertically unstable
- columns are stabilized with a large vertical diffusivity.
-
-[real, units: m^2/sec]
-
-
-
-
-
-
-
-
-
-
-
NOTES
-
-
- The numerical implementation requires no calls to mpp_update_domains.
-
-
-
diff --git a/src/mom5/ocean_param/vertical/ocean_vert_const.xml b/src/mom5/ocean_param/vertical/ocean_vert_const.xml
deleted file mode 100644
index 0bdaeddf4c..0000000000
--- a/src/mom5/ocean_param/vertical/ocean_vert_const.xml
+++ /dev/null
@@ -1,28 +0,0 @@
-
-
- Stephen M. Griffies
-
- Compute constant vertical viscosity and diffusivity.
-
- This module computes a time independent vertical viscosity and diffusivity.
-
- The numerical implementation requires no calls to mpp_update_domains.
-
- Must be true to use this module. Default is false.
-
- The constant vertical diffusivity. Used for cases when wanting a space-time
- independent diffusivity. The "h" is historical and stands for "heat".
-
- The constant vertical viscosity. Used for cases when wanting a space-time
- independent viscosity.
-
- The largest allowable vertical diffusivity. Of use for cases where vertically unstable
- columns are stabilized with a large vertical diffusivity.
-
- Initialize the constant vertical diffusivity module.
-
- This function computes the vertical diffusivity and viscosity.
- These mixing coefficients are time independent but generally
- arbitrary functions of space.
-
diff --git a/src/mom5/ocean_param/vertical/ocean_vert_gotm.F90 b/src/mom5/ocean_param/vertical/ocean_vert_gotm.F90
index f7b1ad4a74..ba16753086 100644
--- a/src/mom5/ocean_param/vertical/ocean_vert_gotm.F90
+++ b/src/mom5/ocean_param/vertical/ocean_vert_gotm.F90
@@ -252,9 +252,9 @@ module ocean_vert_gotm_mod
type(restart_file_type), save :: Got_restart
character(len=256) :: version=&
- '$Id: ocean_vert_gotm.F90,v 1.1.2.6 2012/06/03 00:41:57 Stephen.Griffies Exp $'
+ '$Id: ocean_vert_gotm.F90,v 20.0 2013/12/14 00:16:40 fms Exp $'
character (len=128) :: tagname = &
- '$Name: mom5_siena_08jun2012_smg $'
+ '$Name: tikal $'
logical :: module_is_initialized = .FALSE.
integer :: advection_gotm_method = 1 ! internally set: 1=upwind, 2=sweby
diff --git a/src/mom5/ocean_param/vertical/ocean_vert_gotm.html b/src/mom5/ocean_param/vertical/ocean_vert_gotm.html
deleted file mode 100644
index 7fbfb7876d..0000000000
--- a/src/mom5/ocean_param/vertical/ocean_vert_gotm.html
+++ /dev/null
@@ -1,429 +0,0 @@
-
-
-
-Module ocean_vert_gotm_mod
-
-
-
-
-PUBLIC INTERFACE
-
- ~ PUBLIC ROUTINES
- ~ NAMELIST
-
-
- Vertical viscosity and diffusivity according GOTM.
-
-
-
-
-
- This module contains interfaces to initialize and invoke the
- Generalized Ocean Turbulence Model (GOTM) parameterizations.
- Full documentation of the schemes available with GOTM
- can be found at www.gotm.net.
-
- MOM is distributed with the basic routines from the 4.0
- release of GOTM. Questions about GOTM should be directed
- to the GOTM users group at www.gotm.net.
-
- This module assumes a twolevel time stepping scheme is used
- to update the turbulence scalar fields tke and diss.
-
- Presently it has only been implemented assuming Bgrid.
- So it needs to be updated for Cgrid layout.
-
- Here is a brief outline of the GOTM scheme:
-
- The non-conservative part of the tke
- equation is P+B-diss, where P=shear production,
- B=buoyancy production. The non-conservative part of
- the diss equation is a linear combination of tke,
- P, B and diss.
-
- The conservatie part of both tke and diss equations is
- 3D advection.
-
- So vertical shear and buoyancy contribute to the
- source and sinks (respectively) of tke and dissipation.
-
- The mixing coefficients are the product of a stability
- function, sqrt(tke), and turbulence length scale (the latter
- a non-linear function of tke and diss).
-
- In the hydro model (i.e., MOM), buoyancy fluxes are the
- surface boundary conditions for vertical diffusion of temp (heat
- fluxes) and salt (freshwater fluxes), which in turn determine the
- density, and thus enter GOTM via the calculation of buoyancy production.
-
- Hence, buoyancy fluxes are NOT directly required as surface boundary
- conditions for GOTM.
-
- Wind stress provides the surface boundary condition for vertical
- momentum mixing in MOM. This information then enters GOTM
- via the shear production calculation. However, wind stress
- can enter the GOTM tke equation as the surface boundary
- condition for vertical diffusion of tke (i.e. the prescribed,
- or Dirichlet, condition). This information is typically used in
- Mellor-Yamada turbulence models. An alternate no-flux (Neumann)
- condition is used in the k-e models, and so do not require wind stress.
-
- Boundary conditions for vertical diffusion of diss involve roughness,
- tke, and constants (both Neumann and Dirichlet).
-
-
- Initialization for the MOM wrapper to the GOTM vertical mixing scheme.
-
- For restarts:
-
- We use twolevel time stepping scheme to update tke and diss,
- so only need to read in the taup1_gotm value.
- call mpp_update_domains since need tke and diss in halos for
- the advection calculation.
-
- We need viscosity and diffusivity saved to restarts in order
- to update the tke and diss fields within GOTM.
-
-
-
-
-
-
-
-
-
vert_mix_gotm_bgrid
-
-
-DESCRIPTION
-
-
- This subroutine computes the vertical diffusivity and viscosity
- according to the GOTM mixing model.
-
- The tke, diss, NN, and SS arrays are computed on tracer cells.
-
- Use smf_bgrid since this array uses the primary smf array read in from
- the coupler in ocean_core/ocean_sbc.F90 when using the FMS coupler.
-
-
-
-
-
-
-
-
-
advect_gotm_compute
-
-
-DESCRIPTION
-
-
- Wrapper for advection of GOTM scalar fields tke and diss.
-
- Horizontally tke and diss are on tracer cells, so advection just as if
- they were tracers.
- Vertically they are between tracer cells. We do not average but shift
- tke and diss upward to tracer points for vertical advection. At the bottom
- tke and diss are define by the Dirichlet boundary condition.
-
- Since use a two-level time stepping scheme for tke and diss,
- it is necessary to advect these scalars with an upwind biased
- advection scheme.
-
-
-
-
-
-
-
-
-
advect_gotm_upwind
-
-
-DESCRIPTION
-
-
- First order upwind to advect GOTM scalar turbulence quantities tke and diss.
-
-
-
-
-
-
-
-
advect_gotm_sweby
-
-
-DESCRIPTION
-
-
- Sweby scheme to advect GOTM scalar turbulence quantities tke and diss.
-
-
-
-
-
-
-
-
ocean_vert_gotm_restart
-
-
-DESCRIPTION
-
-
- Write out restart files registered through register_restart_file
-
-
-
-
-
-
-
-
ocean_vert_gotm_end
-
-
-DESCRIPTION
-
-
- Save the advection term for restarting the next time step.
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_vert_gotm_nml
-
-
-
-
-
-use_this_module
-
-
- Must be true to use this module. Default is .false.
-
-[logical]
-
-
-debug_this_module
-
-
- For debugging. Default is .false.
-
-[logical]
-
-
-do_turbulence_gotm
-
-
- For debugging. If do_turbulence_gotm=.false., then
- will not invoke the GOTM scheme. Will only advect
- tke and diss using 3d advection scheme.
- Default is .true., so that will invoke GOTM scheme.
-
-[logical]
-
-
-do_advection_gotm
-
-
- For debugging. If do_advection_gotm=.false., then
- will not invoke the advection of tke and diss.
- Default is .true., so that will 3d advect tke and diss.
-
-[logical]
-
-
-write_a_restart
-
-
- Set true to write a restart. False setting only for rare
- cases where wish to benchmark model without measuring the cost
- of writing restarts and associated chksums.
- Default is write_a_restart=.true.
-
-[logical]
-
-
-advect_gotm_method
-
-
- For choosing how to advect the GOTM scalar fields tke and diss.
- Options are advect_gotm_method='upwind' (the default)
- advect_gotm_method='sweby'
-
-[character]
-
- Minimum energy dissipation. Default=1.0e-10.
-
-[real, units: m^2/s^3]
-
-
-
-
-
-
-
-
-
-
-
REFERENCES
-
-
-
-
- Burchard, H., K. Bolding and M. R. Villarreal
- GOTM, a general ocean turbulence model. Theory
- implementation and test cases.
- European Communities, EUR 18745 EN, 1999
-
-
-
diff --git a/src/mom5/ocean_param/vertical/ocean_vert_gotm.xml b/src/mom5/ocean_param/vertical/ocean_vert_gotm.xml
deleted file mode 100644
index d28024f55e..0000000000
--- a/src/mom5/ocean_param/vertical/ocean_vert_gotm.xml
+++ /dev/null
@@ -1,146 +0,0 @@
-
-
- Martin Schmidt
- Mike Herzfeld
- Russell Fiedler
- Stephen M. Griffies
-
- Vertical viscosity and diffusivity according GOTM.
-
- This module contains interfaces to initialize and invoke the
- Generalized Ocean Turbulence Model (GOTM) parameterizations.
- Full documentation of the schemes available with GOTM
- can be found at www.gotm.net.
-
- MOM is distributed with the basic routines from the 4.0
- release of GOTM. Questions about GOTM should be directed
- to the GOTM users group at www.gotm.net.
-
- This module assumes a twolevel time stepping scheme is used
- to update the turbulence scalar fields tke and diss.
-
- Presently it has only been implemented assuming Bgrid.
- So it needs to be updated for Cgrid layout.
-
- Here is a brief outline of the GOTM scheme:
-
- The non-conservative part of the tke
- equation is P+B-diss, where P=shear production,
- B=buoyancy production. The non-conservative part of
- the diss equation is a linear combination of tke,
- P, B and diss.
-
- The conservatie part of both tke and diss equations is
- 3D advection.
-
- So vertical shear and buoyancy contribute to the
- source and sinks (respectively) of tke and dissipation.
-
- The mixing coefficients are the product of a stability
- function, sqrt(tke), and turbulence length scale (the latter
- a non-linear function of tke and diss).
-
- In the hydro model (i.e., MOM), buoyancy fluxes are the
- surface boundary conditions for vertical diffusion of temp (heat
- fluxes) and salt (freshwater fluxes), which in turn determine the
- density, and thus enter GOTM via the calculation of buoyancy production.
-
- Hence, buoyancy fluxes are NOT directly required as surface boundary
- conditions for GOTM.
-
- Wind stress provides the surface boundary condition for vertical
- momentum mixing in MOM. This information then enters GOTM
- via the shear production calculation. However, wind stress
- can enter the GOTM tke equation as the surface boundary
- condition for vertical diffusion of tke (i.e. the prescribed,
- or Dirichlet, condition). This information is typically used in
- Mellor-Yamada turbulence models. An alternate no-flux (Neumann)
- condition is used in the k-e models, and so do not require wind stress.
-
- Boundary conditions for vertical diffusion of diss involve roughness,
- tke, and constants (both Neumann and Dirichlet).
-
-
- Burchard, H., K. Bolding and M. R. Villarreal
- GOTM, a general ocean turbulence model. Theory
- implementation and test cases.
- European Communities, EUR 18745 EN, 1999
-
- Must be true to use this module. Default is .false.
-
- For debugging. Default is .false.
-
- For debugging. If do_turbulence_gotm=.false., then
- will not invoke the GOTM scheme. Will only advect
- tke and diss using 3d advection scheme.
- Default is .true., so that will invoke GOTM scheme.
-
- For debugging. If do_advection_gotm=.false., then
- will not invoke the advection of tke and diss.
- Default is .true., so that will 3d advect tke and diss.
-
- Set true to write a restart. False setting only for rare
- cases where wish to benchmark model without measuring the cost
- of writing restarts and associated chksums.
- Default is write_a_restart=.true.
-
- For choosing how to advect the GOTM scalar fields tke and diss.
- Options are advect_gotm_method='upwind' (the default)
- advect_gotm_method='sweby'
-
- Background diffusivity. Default is 1.0e-5.
-
- Background viscosity. Default is 1.0e-5.
-
- Surface roughness length. Default is 1m.
-
- Bottom roughness length. Default is .002m.
-
- Minimum turbulent kinetic energy. Default=1.0e-6.
-
- Minimum energy dissipation. Default=1.0e-10.
-
- Initialization for the MOM wrapper to the GOTM vertical mixing scheme.
-
- For restarts:
-
- We use twolevel time stepping scheme to update tke and diss,
- so only need to read in the taup1_gotm value.
- call mpp_update_domains since need tke and diss in halos for
- the advection calculation.
-
- We need viscosity and diffusivity saved to restarts in order
- to update the tke and diss fields within GOTM.
-
-
- This subroutine computes the vertical diffusivity and viscosity
- according to the GOTM mixing model.
-
- The tke, diss, NN, and SS arrays are computed on tracer cells.
-
- Use smf_bgrid since this array uses the primary smf array read in from
- the coupler in ocean_core/ocean_sbc.F90 when using the FMS coupler.
-
-
- Wrapper for advection of GOTM scalar fields tke and diss.
-
- Horizontally tke and diss are on tracer cells, so advection just as if
- they were tracers.
- Vertically they are between tracer cells. We do not average but shift
- tke and diss upward to tracer points for vertical advection. At the bottom
- tke and diss are define by the Dirichlet boundary condition.
-
- Since use a two-level time stepping scheme for tke and diss,
- it is necessary to advect these scalars with an upwind biased
- advection scheme.
-
-
- First order upwind to advect GOTM scalar turbulence quantities tke and diss.
-
- Sweby scheme to advect GOTM scalar turbulence quantities tke and diss.
-
- Write out restart files registered through register_restart_file
-
- Save the advection term for restarting the next time step.
-
diff --git a/src/mom5/ocean_param/vertical/ocean_vert_kpp_mom4p0.F90 b/src/mom5/ocean_param/vertical/ocean_vert_kpp_mom4p0.F90
index b10a2cb89a..93f57c93e0 100644
--- a/src/mom5/ocean_param/vertical/ocean_vert_kpp_mom4p0.F90
+++ b/src/mom5/ocean_param/vertical/ocean_vert_kpp_mom4p0.F90
@@ -221,6 +221,7 @@ module ocean_vert_kpp_mom4p0_mod
real, dimension(isd:ied,jsd:jed) :: bfsfc ! surface buoyancy forcing (m^2/s^3)
real, dimension(isd:ied,jsd:jed) :: ws ! scalar velocity scale (m/s)
real, dimension(isd:ied,jsd:jed) :: wm ! momentum velocity scale (m/s)
+real, dimension(isd:ied,jsd:jed) :: Ustk2 ! magnitude of surface stokes drift velocity ^2 (m^2 / s^2)
real, dimension(isd:ied,jsd:jed) :: caseA ! = 1 in case A; =0 in case B
real, dimension(isd:ied,jsd:jed) :: stable ! = 1 in stable forcing; =0 in unstable
real, dimension(isd:ied,jsd:jed,3) :: dkm1 ! boundary layer diff_cbt at kbl-1 level
@@ -268,6 +269,7 @@ module ocean_vert_kpp_mom4p0_mod
real, dimension(:,:), allocatable :: bfsfc ! surface buoyancy forcing (m^2/s^3)
real, dimension(:,:), allocatable :: ws ! scalar velocity scale (m/s)
real, dimension(:,:), allocatable :: wm ! momentum velocity scale (m/s)
+real, dimension(:,:), allocatable :: Ustk2 ! Magnitude of surface stokes drift velocity ^2 (m^2/s^2)
real, dimension(:,:), allocatable :: caseA ! = 1 in case A; =0 in case B
real, dimension(:,:), allocatable :: stable ! = 1 in stable forcing; =0 in unstable
real, dimension(:,:,:), allocatable :: dkm1 ! boundary layer diff_cbt at kbl-1 level
@@ -336,6 +338,11 @@ module ocean_vert_kpp_mom4p0_mod
real :: deltaz ! delta zehat in table
real :: deltau ! delta ustar in table
real :: concv = 1.8 ! constant for pure convection (eqn. 23)
+real :: Lgam = 1.04 ! adjustment to non-gradient flux (McWilliam & Sullivan 2000)
+real :: Cw_0 = 0.15 ! eq. (13) in Smyth et al (2002)
+real :: l_smyth = 2.0 ! eq. (13) in Smyth et al (2002)
+real :: LTmax = 5.0 ! maximum Langmuir turbulence enhancement factor (langmuirfactor) allowed
+real :: Wstfac = 0.6 ! stability adjustment coefficient, eq. (13) in Smyth et al (2002)
! for vertical coordinate
integer :: vert_coordinate
@@ -399,6 +406,7 @@ module ocean_vert_kpp_mom4p0_mod
logical :: non_local_kpp = .true. ! enable/disable non-local term in KPP
logical :: smooth_blmc = .false. ! smooth boundary layer diffusitivies to remove grid scale noise
+logical :: do_langmuir = .false. ! whether or not calculate langmuir turbulence enhancement factor
logical :: coastal_tidal_mix = .false. ! add tidal speed (m/s) to Ri to increase coastal mixing
real :: sigma_tide = 3.0 ! the sigma constant in the Munk-Anderson scheme
@@ -426,9 +434,9 @@ module ocean_vert_kpp_mom4p0_mod
integer :: num_diag_tracers=0, index_frazil
character(len=256) :: version=&
- '$Id: ocean_vert_kpp_mom4p0.F90,v 1.1.2.6 2012/06/03 00:41:57 Stephen.Griffies Exp $'
+ '$Id: ocean_vert_kpp_mom4p0.F90,v 20.0 2013/12/14 00:16:42 fms Exp $'
character (len=128) :: tagname = &
- '$Name: mom5_siena_08jun2012_smg $'
+ '$Name: tikal $'
logical :: module_is_initialized = .FALSE.
@@ -437,10 +445,11 @@ module ocean_vert_kpp_mom4p0_mod
visc_cbu_limit, diff_cbt_limit, &
visc_con_limit, diff_con_limit, &
concv, Ricr, non_local_kpp, smooth_blmc, &
+ Lgam, Cw_0,l_smyth, LTmax, Wstfac, &
coastal_tidal_mix, p_tide, sigma_tide, &
int_tidal_mix, int_tide_zeta1, int_tide_zeta2, &
int_tide_min_depth, int_tide_q, int_tide_gamma, &
- wsfc_combine_runoff_calve
+ wsfc_combine_runoff_calve, do_langmuir
contains
@@ -633,6 +642,7 @@ subroutine ocean_vert_kpp_mom4p0_init (Grid, Domain, Time, Time_steps, Dens, T_p
allocate (Rib(isd:ied,jsd:jed,2)) ! Bulk Richardson number
allocate (wm(isd:ied,jsd:jed)) ! momentum turbulent velocity scales (m/s)
allocate (ws(isd:ied,jsd:jed)) ! scalar turbulent velocity scales (m/s)
+ allocate (Ustk2(isd:ied,jsd:jed)) ! Magnitude of surface stokes drift velocity ^2 (m^2/s^2)
allocate (gat1(isd:ied,jsd:jed,3))
allocate (dat1(isd:ied,jsd:jed,3))
allocate(sw_frac_hbl(isd:ied,jsd:jed))
@@ -652,6 +662,8 @@ subroutine ocean_vert_kpp_mom4p0_init (Grid, Domain, Time, Time_steps, Dens, T_p
hblt(:,:) = 0.0
hbl(:,:) = 0.0
sw_frac_hbl(:,:) = 0.0
+ Ustk2(:,:) = 0.0
+
do n = 1, num_prog_tracers
wsfc(n)%wsfc(:,:) = 0.0
enddo
@@ -945,7 +957,7 @@ end subroutine ocean_vert_kpp_mom4p0_init
!
!
subroutine vert_mix_kpp_mom4p0 (aidif, Time, Thickness, Velocity, T_prog, T_diag, Dens, &
- swflx, sw_frac_zt, pme, river, visc_cbu, diff_cbt, hblt_depth)
+ swflx, sw_frac_zt, pme, river, visc_cbu, diff_cbt, hblt_depth, do_wave)
real, intent(in) :: aidif
type(ocean_time_type), intent(in) :: Time
@@ -961,6 +973,7 @@ subroutine vert_mix_kpp_mom4p0 (aidif, Time, Thickness, Velocity, T_prog, T_diag
real, dimension(isd:,jsd:), intent(inout) :: hblt_depth
real, dimension(isd:,jsd:,:), intent(inout) :: visc_cbu
real, dimension(isd:,jsd:,:,:), intent(inout) :: diff_cbt
+ logical, intent(in) :: do_wave
real, dimension(isd:ied,jsd:jed,nk) :: dbloc1, dbsfc1
real, dimension(isd:ied,jsd:jed) :: frazil
@@ -989,6 +1002,14 @@ subroutine vert_mix_kpp_mom4p0 (aidif, Time, Thickness, Velocity, T_prog, T_diag
frazil(:,:) = 0.0
endif
+!---------assign Ustk2
+ if (do_wave) then
+ do j = jsd, jed
+ do i = isd, ied
+ Ustk2(i,j) = Velocity%ustoke(i,j)**2 + Velocity%vstoke(i,j)**2
+ enddo
+ enddo
+ endif
!-----------------------------------------------------------------------
! compute gradient Ri
@@ -1182,13 +1203,13 @@ subroutine vert_mix_kpp_mom4p0 (aidif, Time, Thickness, Velocity, T_prog, T_diag
! boundary layer mixing coefficients: diagnose new b.l. depth
!-----------------------------------------------------------------------
- call bldepth(sw_frac_zt)
+ call bldepth(sw_frac_zt, do_wave)
!-----------------------------------------------------------------------
! boundary layer diffusivities
!-----------------------------------------------------------------------
- call blmix_kpp(diff_cbt, visc_cbu)
+ call blmix_kpp(diff_cbt, visc_cbu, do_wave)
!-----------------------------------------------------------------------
! enhance diffusivity at interface kbl - 1
@@ -1445,9 +1466,10 @@ end subroutine vert_mix_kpp_mom4p0
! integer kbl(ij_bounds) ! index of first grid level below hbl
!
!
-subroutine bldepth(sw_frac_zt)
+subroutine bldepth(sw_frac_zt, do_wave)
real, intent(in), dimension(isd:,jsd:,:) :: sw_frac_zt !3-D array of shortwave fract
+ logical, intent(in) :: do_wave
real :: Ritop ! numerator of bulk Richardson Number
real :: bvsq, Vtsq
@@ -1504,7 +1526,7 @@ subroutine bldepth(sw_frac_zt)
!-----------------------------------------------------------------------
iwscale_use_hbl_eq_zt=1
- call wscale ( iwscale_use_hbl_eq_zt, Grd%zt(kl))
+ call wscale ( iwscale_use_hbl_eq_zt, Grd%zt(kl), do_wave)
do j=jsc,jec
@@ -1671,13 +1693,14 @@ end subroutine bldepth
!
!
!
-subroutine wscale(iwscale_use_hbl_eq_zt, zt_kl)
+subroutine wscale(iwscale_use_hbl_eq_zt, zt_kl, do_wave)
real, intent(in) :: zt_kl
integer, intent(in) :: iwscale_use_hbl_eq_zt
+ logical, intent(in) :: do_wave
real :: zdiff, udiff, zfrac, ufrac, fzfrac
- real :: wam, wbm, was, wbs, u3
+ real :: wam, wbm, was, wbs, u3, langmuirfactor, Cw_smyth
real :: zehat ! = zeta * ustar**3
integer :: iz, izp1, ju, jup1
integer :: i, j
@@ -1727,6 +1750,23 @@ subroutine wscale(iwscale_use_hbl_eq_zt, zt_kl)
endif
enddo
enddo
+
+!----------- if do_wave, add Langmuir turbulence enhancement factor
+
+ if (do_wave .and. do_langmuir) then
+ do j=jsc,jec
+ do i=isc,iec
+ Cw_smyth=Cw_0*(ustar(i,j)*ustar(i,j)*ustar(i,j)/(ustar(i,j)*ustar(i,j)*ustar(i,j) &
+ + Wstfac* 0.4 *bfsfc(i,j)*hbl(i,j) + epsln))**l_smyth
+ langmuirfactor=sqrt(1+Cw_smyth*Ustk2(i,j)/(ustar(i,j)*ustar(i,j) + epsln))
+ langmuirfactor = max(1.0, langmuirfactor)
+ langmuirfactor = min(LTmax, langmuirfactor)
+ ws(i,j)=ws(i,j)*langmuirfactor
+ wm(i,j)=wm(i,j)*langmuirfactor
+ enddo
+ enddo
+ endif
+
end subroutine wscale
! NAME="wscale"
@@ -2031,10 +2071,12 @@ end subroutine ddmix
!
!
!
-subroutine blmix_kpp(diff_cbt, visc_cbu)
+subroutine blmix_kpp(diff_cbt, visc_cbu, do_wave)
real, dimension(isd:ied,jsd:jed,nk,2) :: diff_cbt
real, dimension(isd:ied,jsd:jed,nk) :: visc_cbu
+ logical,intent(in) :: do_wave
+
real :: zt_kl_dummy
real :: delhat, R, dvdzup, dvdzdn
real :: viscp, difsp, diftp, visch, difsh, difth, f1
@@ -2056,7 +2098,7 @@ subroutine blmix_kpp(diff_cbt, visc_cbu)
iwscale_use_hbl_eq_zt = 0
zt_kl_dummy=0.0
- call wscale (iwscale_use_hbl_eq_zt, zt_kl_dummy)
+ call wscale (iwscale_use_hbl_eq_zt, zt_kl_dummy, do_wave)
do j=jsc,jec
do i = isc,iec
@@ -2126,7 +2168,7 @@ subroutine blmix_kpp(diff_cbt, visc_cbu)
iwscale_use_hbl_eq_zt=0
zt_kl_dummy=0.0
- call wscale(iwscale_use_hbl_eq_zt, zt_kl_dummy)
+ call wscale(iwscale_use_hbl_eq_zt, zt_kl_dummy, do_wave)
!-----------------------------------------------------------------------
! compute the dimensionless shape functions at the interfaces
@@ -2161,10 +2203,16 @@ subroutine blmix_kpp(diff_cbt, visc_cbu)
!-----------------------------------------------------------------------
! nonlocal transport term = ghats * o (eqn. 20)
+! To include Langmuir turbulence effects, multiply ghats
+! by a factor of Lgam (McWilliam & Sullivan 2001)
!-----------------------------------------------------------------------
-
- ghats(i,j,ki) = (1.-stable(i,j)) * cg &
+ if (do_wave .and. do_langmuir) then
+ ghats(i,j,ki) = Lgam * (1.-stable(i,j)) * cg &
+ / (ws(i,j) * hbl(i,j) + epsln)
+ else
+ ghats(i,j,ki) = (1.-stable(i,j)) * cg &
/ (ws(i,j) * hbl(i,j) + epsln)
+ endif
endif
enddo
enddo
@@ -2185,7 +2233,7 @@ subroutine blmix_kpp(diff_cbt, visc_cbu)
iwscale_use_hbl_eq_zt=0
zt_kl_dummy=0.0
- call wscale(iwscale_use_hbl_eq_zt, zt_kl_dummy)
+ call wscale(iwscale_use_hbl_eq_zt, zt_kl_dummy, do_wave)
do i = isc,iec
sig = Grd%zt(kbl(i,j)-1) / (hbl(i,j)+epsln)
diff --git a/src/mom5/ocean_param/vertical/ocean_vert_kpp_mom4p0.html b/src/mom5/ocean_param/vertical/ocean_vert_kpp_mom4p0.html
deleted file mode 100644
index f4e661b7ef..0000000000
--- a/src/mom5/ocean_param/vertical/ocean_vert_kpp_mom4p0.html
+++ /dev/null
@@ -1,771 +0,0 @@
-
-
-
-Module ocean_vert_kpp_mom4p0_mod
-
-
-
-
-PUBLIC INTERFACE
-
- ~ PUBLIC ROUTINES
- ~ NAMELIST
-
-
- Vertical viscosity and diffusivity according KPP using
- code from MOM4p0, which is hard-wired for full cell
- GEOPOTENTIAL vertical coordinate model. It remains part of
- MOM for legacy purposes.
-
-
-
-
-
- This module computes vertical viscosity and diffusivity according to
- the K-profile parameterization scheme of Large, McWilliams, and
- Doney (1994). It computes both local and non-local mixing.
-
- This module contains code that is hard-wired for GEOPOTENTIAL coordinates,
- and so is NOT generally recommended. It remains part of MOM for
- legacy purposes.
-
- This version of KPP has been implemented only for the Bgrid.
-
- This module also adds mixing due to barotropic tide drag
- (coastal_tide_mix) and baroclinic tides (int_tide_mix).
- The barotropic (coastal_tides) and baroclinic (int_tides) mixing
- schemes are directly analogous to those available in the
- module ocean_vert_tidal.F90. However, some of the averaging and
- smoothing operations differ, and so detailed comparisons will show
- differences. We retain the code here, in KPP, for legacy purposes.
-
- Initialization for the KPP vertical mixing scheme
-
- input:
- dzt = thickness of vertical levels (m)
- km = number of vertical levels
- yt = latitude of grid points (deg)
- jmt = number of latitudes
- dtxcel = time step accelerator as a function of level
- dtimet = forward time step for tracer diffusion (sec)
- dtimeu = forward time step for velcotiy friction (sec)
- error = logical to signal problems
- cifdef = array of character strings for listing enabled "ifdefs"
- ifdmax = size of "cifdef"
- nifdef = current number of enabled "ifdefs"
- vmixset= logical to determine if a vertical mixing scheme was
- chosen
-
- output:
- shear_instability = logical switch for shear instability mixing
- double_diffusion = logical switch for double-diffusive mixing
- visc_cbu_limit = visc max due to shear instability (m**2/sec)
- diff_cbt_limit = diffusivity .. (m**2/sec)
- visc_cbu_iw = visc background due to internal waves(m**2/sec)
- diff_cbt_iw = diffusivity .. (m**2/sec)
- visc_con_limit = visc due to convective instability (m**2/sec)
- diff_con_limit = diffusivity .. (m**2/sec)
- Vtc = non-dimensional constant used in calc. bulk Ri
- cg = constant used in calc.nonlocal transport term
- wmt = turbulent velocity scale for momentum
- wst = turbulent velocity scale for scaler
- error = true if some inconsistancy was found
-
-
-
-
-
-
-
-
-
vert_mix_kpp_mom4p0
-
-
-DESCRIPTION
-
-
- This subroutine computes the vertical diffusivity and viscosity according
- to the KPP scheme of Large etal. In brief, the scheme does the
- following:
-
- --Compute interior mixing everywhere:
- interior mixing gets computed at all cell interfaces due to constant
- internal wave background activity ("visc_cbu_iw" and "diff_cbt_iw").
- Mixing is enhanced in places of static instability (local Ri < 0).
- Additionally, mixing can be enhanced by contribution from shear
- instability which is a function of the local Ri.
-
- --Double diffusion:
- Interior mixing can be enhanced by double diffusion due to salt
- fingering and diffusive convection ("double_diffusion=.true.").
-
- --Boundary layer:
-
- (A) Boundary layer depth:
- at every gridpoint the depth of the oceanic boundary layer
- ("hbl") gets computed by evaluating bulk richardson numbers.
-
- (B) Boundary layer mixing:
- within the boundary layer, above hbl, vertical mixing is
- determined by turbulent surface fluxes, and interior mixing at
- the lower boundary, i.e. at hbl.
-
- NOTE: Use smf_bgrid since this uses the primary smf array read in from
- the coupler in ocean_core/ocean_sbc.F90 when using the FMS coupler.
-
-
-
-
-
-
-
-
-
bldepth
-
-
-DESCRIPTION
-
-
- The oceanic planetray boundary layer depth, hbl, is determined as
- the shallowest depth where the bulk richardson number is
- equal to the critical value, Ricr.
-
- Bulk Richardson numbers are evaluated by computing velocity and
- buoyancy differences between values at zt(kl) and surface
- reference values.
-
- In this configuration, the reference values are equal to the
- values in the surface layer.
- When using a very fine vertical grid, these values should be
- computed as the vertical average of velocity and buoyancy from
- the surface down to epsilon*zt(kl).
-
- When the bulk richardson number at k exceeds Ricr, hbl is
- linearly interpolated between grid levels zt(k) and zt(k-1).
-
- The water column and the surface forcing are diagnosed for
- stable/ustable forcing conditions, and where hbl is relative
- to grid points (caseA), so that conditional branches can be
- avoided in later subroutines.
-
- model
- real zt(1:nk) = vertical grid (m)
- real dzt(1:nk) = layer thicknesses (m)
-
- input
- real dbloc(ij_bounds,nk) = local delta buoyancy (m/s^2)
- real dbsfc(ij_bounds,nk) = delta buoyancy w/ respect to sfc(m/s)^2
- real ustar(ij_bounds) = surface friction velocity (m/s)
- real Bo(ij_bounds) = surface turbulent buoyancy forcing(m^2/s^3)
- real Bosol(ij_bounds) = radiative buoyancy forcing (m^2/s^3)
- real f(ij_bounds) = Coriolis parameter (1/s)
- integer jwtype(ij_bounds) = Jerlov water type (1 to 5)
-
- output
- real hbl(ij_bounds) ! boundary layer depth (m)
- real bfsfc(ij_bounds) !Bo+radiation absorbed to d=hbf*hbl(m^2/s^3)
- real stable(ij_bounds) ! =1 in stable forcing; =0 unstable
- real caseA(ij_bounds) ! =1 in case A, =0 in case B
- integer kbl(ij_bounds) ! index of first grid level below hbl
-
-
-
-
-
-
-
-
-
wscale
-
-
-DESCRIPTION
-
-
- Compute turbulent velocity scales.
- Use a 2D-lookup table for wm and ws as functions of ustar and
- zetahat (=vonk*sigma*hbl*bfsfc).
-
- Note: the lookup table is only used for unstable conditions
- (zehat <= 0), in the stable domain wm (=ws) gets computed
- directly.
-
- model
-
- input
- real sigma(ij_bounds) = normalized depth (d/hbl)
- real hbl(ij_bounds) = boundary layer depth (m)
- real ustar(ij_bounds) = surface friction velocity (m/s)
- real bfsfc(ij_bounds) = total surface buoyancy flux (m^2/s^3)
- output
- real wm(ij_bounds),ws(ij_bounds) ! turbulent velocity scales at sigma
- local
- real zehat ! = zeta * ustar**3
-
-
-
-
-
-
-
-
-
ri_iwmix
-
-
-DESCRIPTION
-
-
- Compute interior viscosity and diffusivity due
- to shear instability (dependent on a local richardson number),
- to background internal wave activity, and
- to static instability (local richardson number < 0).
-
- inputs:
-
- nk = number of vertical levels
- visc_cbu_iw = background "visc_cbu" (m**2/sec) due to internal waves
- diff_cbt_iw = background "diff_cbt" (m**2/sec) due to internal waves
- visc_cbu_limit = largest "visc_cbu" in regions of gravitational
- instability (m**2/sec)
- diff_cbt_limit = largest "diff_cbt" in regions of gravitational
- instability (m**2/sec)
-
- outputs:
-
- visc_cbu = viscosity coefficient at bottom of "u" cells (m**2/s)
- diff_cbt = diffusion coefficient at bottom of "t" cells (m**2/s)
-
-
-
-
-
-
-
-
-
ddmix
-
-
-DESCRIPTION
-
-
- Rrho dependent interior flux parameterization.
- Add double-diffusion diffusivities to Ri-mix values at blending
- interface and below. salt fingering code modified july 2003
- by stephen.griffies based on NCAR CCSM2.x
-
- inputs:
-
- nk = number of vertical levels
- real talpha(imt,km,jmw) ! d(rho)/ d(pot.temperature) (kg/m^3/C)
- real sbeta(imt,km,jmw) ! d(rho)/ d(salinity) (kg/m^3/PSU)
-
- outputs:
-
- diff_cbt = diffusion coefficient at bottom of "t" cells (m**2/s)
-
-
- local
-
- real alphaDT(imt,km,jmw) ! alpha * DT across interfaces
- real betaDS(imt,km,jmw) ! beta * DS across interfaces
-
-
-
-
-
-
-
-
-
-
blmix_kpp
-
-
-DESCRIPTION
-
-
- Mixing coefficients within boundary layer depend on surface
- forcing and the magnitude and gradient of interior mixing below
- the boundary layer ("matching").
-
- CAUTION: if mixing bottoms out at hbl = zt(nk) then
- fictitious layer at nk+1 is needed with small but finite width
- dzt(nk+1) (eg. epsln = 1.e-20).
-
- inputs:
-
- real ustar(ij_bounds) ! surface friction velocity (m/s)
- real bfsfc(ij_bounds) ! surface buoyancy forcing (m^2/s^3)
- real hbl(ij_bounds) ! boundary layer depth (m)
- real stable(ij_bounds) ! = 1 in stable forcing
- real caseA(ij_bounds) ! = 1 in case A
- integer kbl(ij_bounds) ! index of first grid level below hbl
-
- outputs:
-
- visc_cbu = viscosity coefficient at bottom of "u" cells (m**2/s)
- diff_cbt = diffusion coefficient at bottom of "t" cells (m**2/s)
-
- real dkm1(ij_bounds,3) = boundary layer diff_cbt at kbl-1 level
- real blmc(ij_bounds,nk,3) = boundary layer mixing coeff.(m**2/s)
- real ghats(ij_bounds,nk) = nonlocal scalar transport
-
- local:
-
- real gat1(ij_bounds,3)
- real dat1(ij_bounds,3)
- real sigma(ij_bounds) = normalized depth (d / hbl)
- real ws(ij_bounds), wm(ij_bounds) = turbulent velocity scales (m/s)
-
-
-
-
-
-
-
-
-
enhance
-
-
-DESCRIPTION
-
-
- Enhance the diffusivity at the kbl-.5 interface
-
- input
- integer kbl(ij_bounds) = grid above hbl
- real hbl(ij_bounds) = boundary layer depth (m)
- real dkm1(ij_bounds,3) = bl diffusivity at kbl-1 grid level
- real caseA(ij_bounds) = 1 in caseA, = 0 in case B
-
- input/output
- real ghats(ij_bounds,nk) = nonlocal transport (s/m**2)
- modified ghats at kbl(i)-1 interface
- output
- real blmc(ij_bounds,nk,3) = enhanced boundary layer mixing coefficient
-
- local
- real delta = fraction hbl lies beteen zt neighbors
-
-
-
-
-
-
-
-
-
ri_for_kpp
-
-
-DESCRIPTION
-
-
- Compute Richardson number on tracer and velocity cell bottoms.
- rit = richardson number at bottom of T cells
- riu = richardson number at bottom of U cells
-
-
-
-
-
-
-
-
watermass_diag_init
-
-
-DESCRIPTION
-
-
- Initialization of watermass diagnostic output files.
-
-
-
-
-
-
-
-
watermass_diag
-
-
-DESCRIPTION
-
-
- Diagnose effects from KPP nonlocal on the watermass transformation.
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_vert_kpp_mom4p0_nml
-
-
-
-
-
-use_this_module
-
-
- Logical switch to enable kpp diffusion. Default is false.
-
-[logical]
-
- Background vertical diffusivity. Note that if using Bryan-Lewis as a
- background diffusivity, then should set diff_cbt_iw=0.0.
-
-[real, units: m^2/sec]
-
- Enhanced vertical viscosity due to shear instability
-
-[real, units: m^2/sec]
-
-
-diff_cbt_limit
-
-
- Enhanced vertical diffusivity due to shear instability
-
-[real, units: m^2/sec]
-
-
-visc_con_limit
-
-
- Enhanced vertical viscosity in regions of convection
-
-[real, units: m^2/sec]
-
-
-diff_con_limit
-
-
- Enhanced vertical diffusivity in regions of convection
-
-[real, units: m^2/sec]
-
-
-concv
-
-
- constant for pure convection (eqn. 23 of Large etal)
-
-[real, units: dimensionless]
-
-
-Ricr
-
-
- Critical bulk Richardson number. Default from NCAR is
- 0.3, though this number has a large uncertainty and some
- find that 1.0 can be of use.
-
-[real, units: dimensionless]
-
-
-non_local_kpp
-
-
- logical switch for enabling the non-local mixing aspect of kpp.
- Default is .true. as this is what the original KPP scheme suggests.
-
-[logical]
-
-
-smooth_blmc
-
-
- Smooth boundary layer diffusitivies to remove grid scale noise.
- Such noise is apparent in the diagnosed mixed layer depth as well
- as the SST, especially when running coupled models where forcing
- has high temporal frequency.
-
-[logical]
-
-
-coastal_tidal_mix
-
-
- For adding an extra vertical shear associated with tidal mixing.
- This method has found to be of use for mixing near shelves.
-
-[logical]
-
-
-p_tide
-
-
- The p constant in the Munk-Anderson scheme
- Default p_tide=-0.25
-
-[real]
-
-
-sigma_tide
-
-
- The sigma constant in the Munk-Anderson scheme
- Default sigma_tide=3.0
-
-[real]
-
-
-int_tidal_mix
-
-
- For adding an internal tidal mixing over rough topography.
- This method has found to be of use for mixing in the rough topography in open ocean.
- Default int_tidal_mix=.false.
-
-[logical]
-
-
-int_tide_zeta1
-
-
- Shallow depth for computation of internal tide.
- Default int_tide_zeta1=300.0
-
-[real, units: metre]
-
-
-int_tide_zeta2
-
-
- Deeper depth for computation of internal tide.
- Default int_tide_zeta2=1800.0
-
-[real, units: metre]
-
-
-int_tide_min_depth
-
-
- Minimum depth for internal tide mixing to be computed.
- Default int_tide_min_depth=100.0
-
-[real, units: metre]
-
-
-int_tide_q
-
-
- Fraction of internal tide energy locally dissipated.
- Default int_tide_q=.33333
-
-[real, units: dimensionless]
-
-
-int_tide_gamma
-
-
- Dimensionless efficiency for converting energy dissipation to diffusivity.
- Default int_tide_gamma=0.2
-
-[real, units: dimensionless]
-
-
-wsfc_combine_runoff_calve
-
-
- For computing wsfc as in the mom4p0d code, where we combine
- the runoff+calving into a single field called river.
- The alternative keeps the fields separate, as would be appropriate
- for a land model that separately tracks the tracer content in the
- calving and runoff.
- Default wsfc_combine_runoff_calve=.true., as this will recover
- the previous behaviour, to the bit.
-
-[logical]
-
-
-
-
-
-
-
-
-
-
-
REFERENCES
-
-
-
-
- W.G. Large and J.C. McWilliams and S.C. Doney
- Oceanic vertical mixing: A review and a model with
- a nonlocal boundary layer parameterization
- Reviews of Geophysics (1994) vol 32 pages 363-403
-
-
- Hyun-Chul Lee, A. Rosati, and M.J. Spelman
- Barotropic tidal mixing impact in a coupled climate model:
- ocean condition and meridional overturning circulation
- in the northern Atlantic
- Ocean Modelling, vol 11, pages 464--477
-
-
-
-
-
-
-
-
NOTES
-
-
- Original numerical algorithm by Bill Large at NCAR June 6, 1994
-
-
- Equation numbers in the code refer to the Large etal paper.
-
-
- Surface fresh water contributes to surface buoyancy via conversion to
- a locally implied salt flux.
-
-
-
diff --git a/src/mom5/ocean_param/vertical/ocean_vert_kpp_mom4p0.xml b/src/mom5/ocean_param/vertical/ocean_vert_kpp_mom4p0.xml
deleted file mode 100644
index 08b9b5ff8c..0000000000
--- a/src/mom5/ocean_param/vertical/ocean_vert_kpp_mom4p0.xml
+++ /dev/null
@@ -1,349 +0,0 @@
-
-
- A. Rosati
- Bill Large
- Stephen Griffies
- M.J. Harrison
- Hyun-Chul Lee
-
- Vertical viscosity and diffusivity according KPP using
- code from MOM4p0, which is hard-wired for full cell
- GEOPOTENTIAL vertical coordinate model. It remains part of
- MOM for legacy purposes.
-
- This module computes vertical viscosity and diffusivity according to
- the K-profile parameterization scheme of Large, McWilliams, and
- Doney (1994). It computes both local and non-local mixing.
-
- This module contains code that is hard-wired for GEOPOTENTIAL coordinates,
- and so is NOT generally recommended. It remains part of MOM for
- legacy purposes.
-
- This version of KPP has been implemented only for the Bgrid.
-
- This module also adds mixing due to barotropic tide drag
- (coastal_tide_mix) and baroclinic tides (int_tide_mix).
- The barotropic (coastal_tides) and baroclinic (int_tides) mixing
- schemes are directly analogous to those available in the
- module ocean_vert_tidal.F90. However, some of the averaging and
- smoothing operations differ, and so detailed comparisons will show
- differences. We retain the code here, in KPP, for legacy purposes.
-
- W.G. Large and J.C. McWilliams and S.C. Doney
- Oceanic vertical mixing: A review and a model with
- a nonlocal boundary layer parameterization
- Reviews of Geophysics (1994) vol 32 pages 363-403
-
- Hyun-Chul Lee, A. Rosati, and M.J. Spelman
- Barotropic tidal mixing impact in a coupled climate model:
- ocean condition and meridional overturning circulation
- in the northern Atlantic
- Ocean Modelling, vol 11, pages 464--477
-
- Original numerical algorithm by Bill Large at NCAR June 6, 1994
-
- Equation numbers in the code refer to the Large etal paper.
-
- Surface fresh water contributes to surface buoyancy via conversion to
- a locally implied salt flux.
-
- Logical switch to enable kpp diffusion. Default is false.
-
- logical switch for shear instability mixing.
- Default shear_instability=.true.
-
- Logical switch for double-diffusive mixing.
- Default double_diffusion=.true.
-
- Background vertical diffusivity. Note that if using Bryan-Lewis as a
- background diffusivity, then should set diff_cbt_iw=0.0.
-
- Background vertical viscosity
-
- Enhanced vertical viscosity due to shear instability
-
- Enhanced vertical diffusivity due to shear instability
-
- Enhanced vertical viscosity in regions of convection
-
- Enhanced vertical diffusivity in regions of convection
-
- constant for pure convection (eqn. 23 of Large etal)
-
- Critical bulk Richardson number. Default from NCAR is
- 0.3, though this number has a large uncertainty and some
- find that 1.0 can be of use.
-
- logical switch for enabling the non-local mixing aspect of kpp.
- Default is .true. as this is what the original KPP scheme suggests.
-
- Smooth boundary layer diffusitivies to remove grid scale noise.
- Such noise is apparent in the diagnosed mixed layer depth as well
- as the SST, especially when running coupled models where forcing
- has high temporal frequency.
-
- For adding an extra vertical shear associated with tidal mixing.
- This method has found to be of use for mixing near shelves.
-
- The p constant in the Munk-Anderson scheme
- Default p_tide=-0.25
-
- The sigma constant in the Munk-Anderson scheme
- Default sigma_tide=3.0
-
- For adding an internal tidal mixing over rough topography.
- This method has found to be of use for mixing in the rough topography in open ocean.
- Default int_tidal_mix=.false.
-
- Shallow depth for computation of internal tide.
- Default int_tide_zeta1=300.0
-
- Deeper depth for computation of internal tide.
- Default int_tide_zeta2=1800.0
-
- Minimum depth for internal tide mixing to be computed.
- Default int_tide_min_depth=100.0
-
- Fraction of internal tide energy locally dissipated.
- Default int_tide_q=.33333
-
- Dimensionless efficiency for converting energy dissipation to diffusivity.
- Default int_tide_gamma=0.2
-
- For computing wsfc as in the mom4p0d code, where we combine
- the runoff+calving into a single field called river.
- The alternative keeps the fields separate, as would be appropriate
- for a land model that separately tracks the tracer content in the
- calving and runoff.
- Default wsfc_combine_runoff_calve=.true., as this will recover
- the previous behaviour, to the bit.
-
- Initialization for the KPP vertical mixing scheme
-
- input:
- dzt = thickness of vertical levels (m)
- km = number of vertical levels
- yt = latitude of grid points (deg)
- jmt = number of latitudes
- dtxcel = time step accelerator as a function of level
- dtimet = forward time step for tracer diffusion (sec)
- dtimeu = forward time step for velcotiy friction (sec)
- error = logical to signal problems
- cifdef = array of character strings for listing enabled "ifdefs"
- ifdmax = size of "cifdef"
- nifdef = current number of enabled "ifdefs"
- vmixset= logical to determine if a vertical mixing scheme was
- chosen
-
- output:
- shear_instability = logical switch for shear instability mixing
- double_diffusion = logical switch for double-diffusive mixing
- visc_cbu_limit = visc max due to shear instability (m**2/sec)
- diff_cbt_limit = diffusivity .. (m**2/sec)
- visc_cbu_iw = visc background due to internal waves(m**2/sec)
- diff_cbt_iw = diffusivity .. (m**2/sec)
- visc_con_limit = visc due to convective instability (m**2/sec)
- diff_con_limit = diffusivity .. (m**2/sec)
- Vtc = non-dimensional constant used in calc. bulk Ri
- cg = constant used in calc.nonlocal transport term
- wmt = turbulent velocity scale for momentum
- wst = turbulent velocity scale for scaler
- error = true if some inconsistancy was found
-
-
- This subroutine computes the vertical diffusivity and viscosity according
- to the KPP scheme of Large etal. In brief, the scheme does the
- following:
-
- --Compute interior mixing everywhere:
- interior mixing gets computed at all cell interfaces due to constant
- internal wave background activity ("visc_cbu_iw" and "diff_cbt_iw").
- Mixing is enhanced in places of static instability (local Ri < 0).
- Additionally, mixing can be enhanced by contribution from shear
- instability which is a function of the local Ri.
-
- --Double diffusion:
- Interior mixing can be enhanced by double diffusion due to salt
- fingering and diffusive convection ("double_diffusion=.true.").
-
- --Boundary layer:
-
- (A) Boundary layer depth:
- at every gridpoint the depth of the oceanic boundary layer
- ("hbl") gets computed by evaluating bulk richardson numbers.
-
- (B) Boundary layer mixing:
- within the boundary layer, above hbl, vertical mixing is
- determined by turbulent surface fluxes, and interior mixing at
- the lower boundary, i.e. at hbl.
-
- NOTE: Use smf_bgrid since this uses the primary smf array read in from
- the coupler in ocean_core/ocean_sbc.F90 when using the FMS coupler.
-
-
- The oceanic planetray boundary layer depth, hbl, is determined as
- the shallowest depth where the bulk richardson number is
- equal to the critical value, Ricr.
-
- Bulk Richardson numbers are evaluated by computing velocity and
- buoyancy differences between values at zt(kl) and surface
- reference values.
-
- In this configuration, the reference values are equal to the
- values in the surface layer.
- When using a very fine vertical grid, these values should be
- computed as the vertical average of velocity and buoyancy from
- the surface down to epsilon*zt(kl).
-
- When the bulk richardson number at k exceeds Ricr, hbl is
- linearly interpolated between grid levels zt(k) and zt(k-1).
-
- The water column and the surface forcing are diagnosed for
- stable/ustable forcing conditions, and where hbl is relative
- to grid points (caseA), so that conditional branches can be
- avoided in later subroutines.
-
- model
- real zt(1:nk) = vertical grid (m)
- real dzt(1:nk) = layer thicknesses (m)
-
- input
- real dbloc(ij_bounds,nk) = local delta buoyancy (m/s^2)
- real dbsfc(ij_bounds,nk) = delta buoyancy w/ respect to sfc(m/s)^2
- real ustar(ij_bounds) = surface friction velocity (m/s)
- real Bo(ij_bounds) = surface turbulent buoyancy forcing(m^2/s^3)
- real Bosol(ij_bounds) = radiative buoyancy forcing (m^2/s^3)
- real f(ij_bounds) = Coriolis parameter (1/s)
- integer jwtype(ij_bounds) = Jerlov water type (1 to 5)
-
- output
- real hbl(ij_bounds) ! boundary layer depth (m)
- real bfsfc(ij_bounds) !Bo+radiation absorbed to d=hbf*hbl(m^2/s^3)
- real stable(ij_bounds) ! =1 in stable forcing; =0 unstable
- real caseA(ij_bounds) ! =1 in case A, =0 in case B
- integer kbl(ij_bounds) ! index of first grid level below hbl
-
- Compute turbulent velocity scales.
- Use a 2D-lookup table for wm and ws as functions of ustar and
- zetahat (=vonk*sigma*hbl*bfsfc).
-
- Note: the lookup table is only used for unstable conditions
- (zehat <= 0), in the stable domain wm (=ws) gets computed
- directly.
-
- model
-
- input
- real sigma(ij_bounds) = normalized depth (d/hbl)
- real hbl(ij_bounds) = boundary layer depth (m)
- real ustar(ij_bounds) = surface friction velocity (m/s)
- real bfsfc(ij_bounds) = total surface buoyancy flux (m^2/s^3)
- output
- real wm(ij_bounds),ws(ij_bounds) ! turbulent velocity scales at sigma
- local
- real zehat ! = zeta * ustar**3
-
-
- Compute interior viscosity and diffusivity due
- to shear instability (dependent on a local richardson number),
- to background internal wave activity, and
- to static instability (local richardson number < 0).
-
- inputs:
-
- nk = number of vertical levels
- visc_cbu_iw = background "visc_cbu" (m**2/sec) due to internal waves
- diff_cbt_iw = background "diff_cbt" (m**2/sec) due to internal waves
- visc_cbu_limit = largest "visc_cbu" in regions of gravitational
- instability (m**2/sec)
- diff_cbt_limit = largest "diff_cbt" in regions of gravitational
- instability (m**2/sec)
-
- outputs:
-
- visc_cbu = viscosity coefficient at bottom of "u" cells (m**2/s)
- diff_cbt = diffusion coefficient at bottom of "t" cells (m**2/s)
-
- Rrho dependent interior flux parameterization.
- Add double-diffusion diffusivities to Ri-mix values at blending
- interface and below. salt fingering code modified july 2003
- by stephen.griffies based on NCAR CCSM2.x
-
- inputs:
-
- nk = number of vertical levels
- real talpha(imt,km,jmw) ! d(rho)/ d(pot.temperature) (kg/m^3/C)
- real sbeta(imt,km,jmw) ! d(rho)/ d(salinity) (kg/m^3/PSU)
-
- outputs:
-
- diff_cbt = diffusion coefficient at bottom of "t" cells (m**2/s)
-
-
- local
-
- real alphaDT(imt,km,jmw) ! alpha * DT across interfaces
- real betaDS(imt,km,jmw) ! beta * DS across interfaces
-
-
- Mixing coefficients within boundary layer depend on surface
- forcing and the magnitude and gradient of interior mixing below
- the boundary layer ("matching").
-
- CAUTION: if mixing bottoms out at hbl = zt(nk) then
- fictitious layer at nk+1 is needed with small but finite width
- dzt(nk+1) (eg. epsln = 1.e-20).
-
- inputs:
-
- real ustar(ij_bounds) ! surface friction velocity (m/s)
- real bfsfc(ij_bounds) ! surface buoyancy forcing (m^2/s^3)
- real hbl(ij_bounds) ! boundary layer depth (m)
- real stable(ij_bounds) ! = 1 in stable forcing
- real caseA(ij_bounds) ! = 1 in case A
- integer kbl(ij_bounds) ! index of first grid level below hbl
-
- outputs:
-
- visc_cbu = viscosity coefficient at bottom of "u" cells (m**2/s)
- diff_cbt = diffusion coefficient at bottom of "t" cells (m**2/s)
-
- real dkm1(ij_bounds,3) = boundary layer diff_cbt at kbl-1 level
- real blmc(ij_bounds,nk,3) = boundary layer mixing coeff.(m**2/s)
- real ghats(ij_bounds,nk) = nonlocal scalar transport
-
- local:
-
- real gat1(ij_bounds,3)
- real dat1(ij_bounds,3)
- real sigma(ij_bounds) = normalized depth (d / hbl)
- real ws(ij_bounds), wm(ij_bounds) = turbulent velocity scales (m/s)
-
-
- Enhance the diffusivity at the kbl-.5 interface
-
- input
- integer kbl(ij_bounds) = grid above hbl
- real hbl(ij_bounds) = boundary layer depth (m)
- real dkm1(ij_bounds,3) = bl diffusivity at kbl-1 grid level
- real caseA(ij_bounds) = 1 in caseA, = 0 in case B
-
- input/output
- real ghats(ij_bounds,nk) = nonlocal transport (s/m**2)
- modified ghats at kbl(i)-1 interface
- output
- real blmc(ij_bounds,nk,3) = enhanced boundary layer mixing coefficient
-
- local
- real delta = fraction hbl lies beteen zt neighbors
-
-
- Compute Richardson number on tracer and velocity cell bottoms.
- rit = richardson number at bottom of T cells
- riu = richardson number at bottom of U cells
-
- Initialization of watermass diagnostic output files.
-
- Diagnose effects from KPP nonlocal on the watermass transformation.
-
diff --git a/src/mom5/ocean_param/vertical/ocean_vert_kpp_mom4p1.F90 b/src/mom5/ocean_param/vertical/ocean_vert_kpp_mom4p1.F90
index d7d08d2d31..ab205e2456 100644
--- a/src/mom5/ocean_param/vertical/ocean_vert_kpp_mom4p1.F90
+++ b/src/mom5/ocean_param/vertical/ocean_vert_kpp_mom4p1.F90
@@ -287,6 +287,7 @@ module ocean_vert_kpp_mom4p1_mod
real, dimension(isd:ied,jsd:jed) :: bfsfc ! surface buoyancy forcing (m^2/s^3)
real, dimension(isd:ied,jsd:jed) :: ws ! scalar velocity scale (m/s)
real, dimension(isd:ied,jsd:jed) :: wm ! momentum velocity scale (m/s)
+real, dimension(isd:ied,jsd:jed) :: Ustk2 ! magnitude of surface stokes drift velocity ^2 (m^2 / s^2)
real, dimension(isd:ied,jsd:jed) :: caseA ! = 1 in case A; =0 in case B
real, dimension(isd:ied,jsd:jed) :: stable ! = 1 in stable forcing; =0 in unstable
real, dimension(isd:ied,jsd:jed,3) :: dkm1 ! boundary layer diff_cbt at kbl-1 level
@@ -324,6 +325,7 @@ module ocean_vert_kpp_mom4p1_mod
real, dimension(:,:), allocatable :: bfsfc ! surface buoyancy forcing (m^2/s^3)
real, dimension(:,:), allocatable :: ws ! scalar velocity scale (m/s)
real, dimension(:,:), allocatable :: wm ! momentum velocity scale (m/s)
+real, dimension(:,:), allocatable :: Ustk2 ! Magnitude of surface stokes drift velocity ^2 (m^2/s^2)
real, dimension(:,:), allocatable :: caseA ! = 1 in case A; =0 in case B
real, dimension(:,:), allocatable :: stable ! = 1 in stable forcing; =0 in unstable
real, dimension(:,:,:), allocatable :: dkm1 ! boundary layer diff_cbt at kbl-1 level
@@ -383,6 +385,12 @@ module ocean_vert_kpp_mom4p1_mod
real :: concv = 1.8 ! constant for pure convection (eqn. 23)
real :: concv_r ! inverse concv
real :: vtc_flag = 0.0 ! default to the older approach.
+real :: Lgam = 1.04 ! adjustment to non-gradient flux (McWilliam & Sullivan 2000)
+real :: Cw_0 = 0.15 ! eq. (13) in Smyth et al (2002)
+real :: l_smyth = 2.0 ! eq. (13) in Smyth et al (2002)
+real :: LTmax = 5.0 ! maximum Langmuir turbulence enhancement factor (langmuirfactor) allowed
+real :: Wstfac = 0.6 ! stability adjustment coefficient, eq. (13) in Smyth et al (2002)
+
! for global area normalization
real :: cellarea_r
@@ -460,6 +468,7 @@ module ocean_vert_kpp_mom4p1_mod
logical :: non_local_kpp = .true. ! enable/disable non-local term in KPP
logical :: smooth_blmc = .false. ! smooth boundary layer diffusitivies to remove grid scale noise
+logical :: do_langmuir = .false. ! whether or not calcualte langmuir turbulence enhance factor
integer, parameter :: nni = 890 ! number of values for zehat in the look up table
integer, parameter :: nnj = 480 ! number of values for ustar in the look up table
@@ -476,9 +485,9 @@ module ocean_vert_kpp_mom4p1_mod
integer :: kbl_max=2 ! helps to limit vertikal loops
character(len=256) :: version=&
- '$Id: ocean_vert_kpp_mom4p1.F90,v 1.1.2.4.4.1 2012/06/17 12:31:36 smg Exp $'
+ '$Id: ocean_vert_kpp_mom4p1.F90,v 20.0 2013/12/14 00:16:44 fms Exp $'
character (len=128) :: tagname = &
- '$Name: mom5_siena_08jun2012_smg $'
+ '$Name: tikal $'
logical :: module_is_initialized = .FALSE.
logical :: debug_this_module = .FALSE.
@@ -488,12 +497,14 @@ module ocean_vert_kpp_mom4p1_mod
visc_cbu_limit, diff_cbt_limit, &
visc_con_limit, diff_con_limit, &
concv, Ricr, non_local_kpp, smooth_blmc, &
+ Lgam, Cw_0,l_smyth, LTmax, Wstfac, &
kl_min, kbl_standard_method, debug_this_module, &
limit_with_hekman, limit_ghats, hbl_with_rit, &
radiation_large, radiation_zero, radiation_iow, &
use_sbl_bottom_flux, wsfc_combine_runoff_calve, &
- bvf_from_below, variable_vtc, use_max_shear, &
- linear_hbl, calc_visc_on_cgrid, smooth_ri_kmax_eq_kmu
+ bvf_from_below, variable_vtc, use_max_shear, &
+ linear_hbl, calc_visc_on_cgrid, smooth_ri_kmax_eq_kmu, &
+ do_langmuir
contains
@@ -743,6 +754,7 @@ subroutine ocean_vert_kpp_mom4p1_init (Grid, Domain, Time, Time_steps, Dens, T_p
allocate (Rib(isd:ied,jsd:jed,rib_dim)) ! Bulk Richardson number
allocate (wm(isd:ied,jsd:jed)) ! momentum turbulent velocity scales (m/s)
allocate (ws(isd:ied,jsd:jed)) ! scalar turbulent velocity scales (m/s)
+ allocate (Ustk2(isd:ied,jsd:jed)) ! Magnitude of surface stokes drift velocity ^2 (m^2/s^2)
allocate (gat1(isd:ied,jsd:jed,3))
allocate (dat1(isd:ied,jsd:jed,3))
allocate(sw_frac_hbl(isd:ied,jsd:jed))
@@ -756,6 +768,8 @@ subroutine ocean_vert_kpp_mom4p1_init (Grid, Domain, Time, Time_steps, Dens, T_p
hblt(:,:) = 0.0
hbl(:,:) = 0.0
sw_frac_hbl(:,:) = 0.0
+ Ustk2(:,:) = 0.0
+
do n = 1, num_prog_tracers
wsfc(n)%wsfc(:,:) = 0.0
enddo
@@ -927,7 +941,7 @@ end subroutine ocean_vert_kpp_mom4p1_init
!
!
subroutine vert_mix_kpp_mom4p1 (aidif, Time, Thickness, Velocity, T_prog, T_diag, Dens, &
- swflx, sw_frac_zt, pme, river, visc_cbu, diff_cbt, hblt_depth)
+ swflx, sw_frac_zt, pme, river, visc_cbu, diff_cbt, hblt_depth, do_wave)
real, intent(in) :: aidif
type(ocean_time_type), intent(in) :: Time
@@ -943,6 +957,8 @@ subroutine vert_mix_kpp_mom4p1 (aidif, Time, Thickness, Velocity, T_prog, T_diag
real, dimension(isd:,jsd:), intent(inout) :: hblt_depth
real, dimension(isd:,jsd:,:), intent(inout) :: visc_cbu
real, dimension(isd:,jsd:,:,:), intent(inout) :: diff_cbt
+ logical, intent(in) :: do_wave
+
real, dimension(isd:ied,jsd:jed,nk) :: dbloc1, dbsfc1
real, dimension(isd:ied,jsd:jed) :: frazil
@@ -972,6 +988,14 @@ subroutine vert_mix_kpp_mom4p1 (aidif, Time, Thickness, Velocity, T_prog, T_diag
frazil(:,:) = 0.0
endif
+!---------issign Ustk2
+ if (do_wave) then
+ do j = jsd, jed
+ do i = isd, ied
+ Ustk2(i,j) = Velocity%ustoke(i,j)**2 + Velocity%vstoke(i,j)**2
+ enddo
+ enddo
+ endif
!-----------------------------------------------------------------------
! compute gradient Ri
@@ -1181,13 +1205,13 @@ subroutine vert_mix_kpp_mom4p1 (aidif, Time, Thickness, Velocity, T_prog, T_diag
! boundary layer mixing coefficients: diagnose new b.l. depth
!-----------------------------------------------------------------------
- call bldepth(Thickness, sw_frac_zt)
+ call bldepth(Thickness, sw_frac_zt, do_wave)
!-----------------------------------------------------------------------
! boundary layer diffusivities
!-----------------------------------------------------------------------
- call blmix_kpp(Thickness, diff_cbt, visc_cbu)
+ call blmix_kpp(Thickness, diff_cbt, visc_cbu, do_wave)
call diagnose_3d(Time, Grd, id_ws, wrk1(:,:,:))
!-----------------------------------------------------------------------
@@ -1544,10 +1568,11 @@ end subroutine vert_mix_kpp_mom4p1
! integer kbl(ij_bounds) ! index of first grid level below hbl
!
!
-subroutine bldepth(Thickness, sw_frac_zt)
+subroutine bldepth(Thickness, sw_frac_zt, do_wave)
type(ocean_thickness_type), intent(in) :: Thickness
real, dimension(isd:,jsd:,:), intent(in) :: sw_frac_zt !3-D array of shortwave fract
+ logical, intent(in) :: do_wave
real :: Ritop ! numerator of bulk Richardson Number
real :: bvfr, Vtsq
@@ -1614,7 +1639,7 @@ subroutine bldepth(Thickness, sw_frac_zt)
! compute velocity scales at sigma, for hbl = zt(kl):
iwscale_use_hbl_eq_zt=1
- call wscale (iwscale_use_hbl_eq_zt, Thickness%depth_zt(:,:,kl))
+ call wscale (iwscale_use_hbl_eq_zt, Thickness%depth_zt(:,:,kl), do_wave)
do j=jsc,jec
do i=isc,iec
@@ -1716,7 +1741,7 @@ subroutine bldepth(Thickness, sw_frac_zt)
! compute velocity scales at sigma, for hbl = zt(kl):
iwscale_use_hbl_eq_zt=1
- call wscale (iwscale_use_hbl_eq_zt, Thickness%depth_zt(:,:,kl))
+ call wscale (iwscale_use_hbl_eq_zt, Thickness%depth_zt(:,:,kl), do_wave)
do j=jsc,jec
do i=isc,iec
@@ -1970,13 +1995,14 @@ end subroutine bldepth
! Speed gain was observed at the SX-6.
! Later compiler versions may do better.
!
-subroutine wscale(iwscale_use_hbl_eq_zt, zt_kl)
+subroutine wscale(iwscale_use_hbl_eq_zt, zt_kl, do_wave)
integer, intent(in) :: iwscale_use_hbl_eq_zt
real, dimension(isd:,jsd:), intent(in) :: zt_kl
+ logical, intent(in) :: do_wave
real :: zdiff, udiff, zfrac, ufrac, fzfrac
- real :: wam, wbm, was, wbs, u3
+ real :: wam, wbm, was, wbs, u3, langmuirfactor, Cw_smyth
real :: zehat ! = zeta * ustar**3
integer :: iz, izp1, ju, jup1
integer :: i, j
@@ -2070,6 +2096,22 @@ subroutine wscale(iwscale_use_hbl_eq_zt, zt_kl)
endif
+!----------- if do_wave, add Langmuir turbulence enhancement factor
+
+ if (do_wave .and. do_langmuir) then
+ do j=jsc,jec
+ do i=isc,iec
+ Cw_smyth=Cw_0*(ustar(i,j)*ustar(i,j)*ustar(i,j)/(ustar(i,j)*ustar(i,j)*ustar(i,j) &
+ + Wstfac*von_karman*bfsfc(i,j)*hbl(i,j) + epsln))**l_smyth
+ langmuirfactor=sqrt(1+Cw_smyth*Ustk2(i,j)/(ustar(i,j)*ustar(i,j) + epsln))
+ langmuirfactor = max(1.0, langmuirfactor)
+ langmuirfactor = min(LTmax, langmuirfactor)
+ ws(i,j)=ws(i,j)*langmuirfactor
+ wm(i,j)=wm(i,j)*langmuirfactor
+ enddo
+ enddo
+ endif
+
end subroutine wscale
! NAME="wscale"
@@ -2373,11 +2415,12 @@ end subroutine ddmix
!
!
!
-subroutine blmix_kpp(Thickness, diff_cbt, visc_cbu)
+subroutine blmix_kpp(Thickness, diff_cbt, visc_cbu, do_wave)
type(ocean_thickness_type), intent(in) :: Thickness
real, dimension(isd:,jsd:,:,:), intent(inout) :: diff_cbt
real, dimension(isd:,jsd:,:) , intent(inout) :: visc_cbu
+ logical, intent(in) :: do_wave
real, dimension(isd:ied,jsd:jed) :: zt_kl_dummy
@@ -2401,7 +2444,7 @@ subroutine blmix_kpp(Thickness, diff_cbt, visc_cbu)
iwscale_use_hbl_eq_zt = 0
zt_kl_dummy(:,:) = 0.0
- call wscale (iwscale_use_hbl_eq_zt, zt_kl_dummy)
+ call wscale (iwscale_use_hbl_eq_zt, zt_kl_dummy, do_wave)
do j=jsc,jec
do i = isc,iec
@@ -2472,7 +2515,7 @@ subroutine blmix_kpp(Thickness, diff_cbt, visc_cbu)
iwscale_use_hbl_eq_zt = 0
zt_kl_dummy(:,:) = 0.0
- call wscale(iwscale_use_hbl_eq_zt, zt_kl_dummy)
+ call wscale(iwscale_use_hbl_eq_zt, zt_kl_dummy, do_wave)
!-----------------------------------------------------------------------
! compute the dimensionless shape functions at the interfaces
@@ -2508,10 +2551,16 @@ subroutine blmix_kpp(Thickness, diff_cbt, visc_cbu)
!-----------------------------------------------------------------------
! nonlocal transport term = ghats * o (eqn. 20)
+! To include Langmuir turbulence effects, multiply ghats
+! by a factor of Lgam (McWilliam & Sullivan 2001)
!-----------------------------------------------------------------------
-
- ghats(i,j,ki) = (1.-stable(i,j)) * cg &
+ if (do_wave .and. do_langmuir) then
+ ghats(i,j,ki) = Lgam * (1.-stable(i,j)) * cg &
+ / (ws(i,j) * hbl(i,j) + epsln)
+ else
+ ghats(i,j,ki) = (1.-stable(i,j)) * cg &
/ (ws(i,j) * hbl(i,j) + epsln)
+ endif
endif
enddo
enddo
@@ -2534,7 +2583,7 @@ subroutine blmix_kpp(Thickness, diff_cbt, visc_cbu)
iwscale_use_hbl_eq_zt = 0
zt_kl_dummy(:,:) = 0.0
- call wscale(iwscale_use_hbl_eq_zt, zt_kl_dummy)
+ call wscale(iwscale_use_hbl_eq_zt, zt_kl_dummy, do_wave)
do j=jsc,jec
do i = isc,iec
diff --git a/src/mom5/ocean_param/vertical/ocean_vert_kpp_mom4p1.html b/src/mom5/ocean_param/vertical/ocean_vert_kpp_mom4p1.html
deleted file mode 100644
index 26eb495b23..0000000000
--- a/src/mom5/ocean_param/vertical/ocean_vert_kpp_mom4p1.html
+++ /dev/null
@@ -1,825 +0,0 @@
-
-
-
-Module ocean_vert_kpp_mom4p1_mod
-
-
-
-
-PUBLIC INTERFACE
-
- ~ PUBLIC ROUTINES
- ~ NAMELIST
-
-
- Vertical viscosity and diffusivity according KPP.
- This module has extra code options to handle regions of extremely fresh water.
- This particular version of the KPP module is frozen based on its use in MOM4p1
- at GFDL for the IPCC AR5 climate model ESM2M.
-
-
-
-
-
- This module computes vertical viscosity and diffusivity according to
- the K-profile parameterization scheme of Large, McWilliams, and
- Doney (1994). It computes both local and non-local mixing.
- The code has been updated to MOM4p1, so that vertical grid increments
- are suitable for generalized vertical coordinate models. When run
- as geopotential model, there will be some differences, since the
- MOM4.0 code (available in ocean_vert_kpp_mom4p0.F90) incorrectly
- ignored the free surface undulations affecting the top model grid
- cell thickness.
-
- This version of KPP has been implemented only for the Bgrid.
-
- Initialization for the KPP vertical mixing scheme
-
-
-
-
-
-
-
-
vert_mix_kpp_mom4p1
-
-
-DESCRIPTION
-
-
- This subroutine computes the vertical diffusivity and viscosity according
- to the KPP scheme of Large etal. In brief, the scheme does the
- following:
-
- --Compute interior mixing everywhere:
- interior mixing gets computed at all cell interfaces due to constant
- internal wave background activity ("visc_cbu_iw" and "diff_cbt_iw").
- Mixing is enhanced in places of static instability (local Ri < 0).
- Additionally, mixing can be enhanced by contribution from shear
- instability which is a function of the local Ri.
-
- --Double diffusion:
- Interior mixing can be enhanced by double diffusion due to salt
- fingering and diffusive convection ("double_diffusion=.true.").
-
- --Boundary layer:
-
- (A) Boundary layer depth:
- at every gridpoint the depth of the oceanic boundary layer
- ("hbl") gets computed by evaluating bulk richardson numbers.
-
- (B) Boundary layer mixing:
- within the boundary layer, above hbl, vertical mixing is
- determined by turbulent surface fluxes, and interior mixing at
- the lower boundary, i.e. at hbl.
-
-
-
-
-
-
-
-
-
bldepth
-
-
-DESCRIPTION
-
-
- The oceanic planetray boundary layer depth, hbl, is determined as
- the shallowest depth where the bulk richardson number is
- equal to the critical value, Ricr.
-
- Bulk Richardson numbers are evaluated by computing velocity and
- buoyancy differences between values at zt(kl) and surface
- reference values.
-
- In this configuration, the reference values are equal to the
- values in the surface layer.
- When using a very fine vertical grid, these values should be
- computed as the vertical average of velocity and buoyancy from
- the surface down to epsilon*zt(kl).
-
- When the bulk richardson number at k exceeds Ricr, hbl is
- linearly interpolated between grid levels zt(k) and zt(k-1).
-
- The water column and the surface forcing are diagnosed for
- stable/ustable forcing conditions, and where hbl is relative
- to grid points (caseA), so that conditional branches can be
- avoided in later subroutines.
-
- model
- real zt(1:nk) = vertical grid (m)
- real dzt(1:nk) = layer thicknesses (m)
-
- input
- real dbloc(ij_bounds,nk) = local delta buoyancy (m/s^2)
- real dbsfc(ij_bounds,nk) = delta buoyancy w/ respect to sfc(m/s)^2
- real ustar(ij_bounds) = surface friction velocity (m/s)
- real Bo(ij_bounds) = surface turbulent buoyancy forcing(m^2/s^3)
- real Bosol(ij_bounds) = radiative buoyancy forcing (m^2/s^3)
- real f(ij_bounds) = Coriolis parameter (1/s)
- integer jwtype(ij_bounds) = Jerlov water type (1 to 5)
-
- output
- real hbl(ij_bounds) ! boundary layer depth (m)
- real bfsfc(ij_bounds) !Bo+radiation absorbed to d=hbf*hbl(m^2/s^3)
- real stable(ij_bounds) ! =1 in stable forcing; =0 unstable
- real caseA(ij_bounds) ! =1 in case A, =0 in case B
- integer kbl(ij_bounds) ! index of first grid level below hbl
-
-
-
-
-
-
-
-
-
wscale
-
-
-DESCRIPTION
-
-
- Compute turbulent velocity scales.
- Use a 2D-lookup table for wm and ws as functions of ustar and
- zetahat (=von_karman*sigma*hbl*bfsfc).
-
- Note: the lookup table is only used for unstable conditions
- (zehat <= 0), in the stable domain wm (=ws) gets computed
- directly.
-
- model
-
- input
- real sigma(ij_bounds) = normalized depth (d/hbl)
- real hbl(ij_bounds) = boundary layer depth (m)
- real ustar(ij_bounds) = surface friction velocity (m/s)
- real bfsfc(ij_bounds) = total surface buoyancy flux (m^2/s^3)
- output
- real wm(ij_bounds),ws(ij_bounds) ! turbulent velocity scales at sigma
- local
- real zehat ! = zeta * ustar**3
-
-
-
-
-
-
-
-
-
ri_iwmix
-
-
-DESCRIPTION
-
-
- Compute interior viscosity and diffusivity due
- to shear instability (dependent on a local richardson number),
- to background internal wave activity, and
- to static instability (local richardson number < 0).
-
- inputs:
-
- nk = number of vertical levels
- visc_cbu_iw = background "visc_cbu" (m**2/sec) due to internal waves
- diff_cbt_iw = background "diff_cbt" (m**2/sec) due to internal waves
- visc_cbu_limit = largest "visc_cbu" in regions of gravitational
- instability (m**2/sec)
- diff_cbt_limit = largest "diff_cbt" in regions of gravitational
- instability (m**2/sec)
-
- outputs:
-
- visc_cbu = viscosity coefficient at bottom of "u" cells (m**2/s)
- diff_cbt = diffusion coefficient at bottom of "t" cells (m**2/s)
-
-
-
-
-
-
-
-
-
ddmix
-
-
-DESCRIPTION
-
-
- Rrho dependent interior flux parameterization.
- Add double-diffusion diffusivities to Ri-mix values at blending
- interface and below. salt fingering code modified july 2003
- by stephen.griffies based on NCAR CCSM2.x
-
- inputs:
-
- nk = number of vertical levels
- real talpha(imt,km,jmw) ! d(rho)/ d(pot.temperature) (kg/m^3/C)
- real sbeta(imt,km,jmw) ! d(rho)/ d(salinity) (kg/m^3/PSU)
-
- outputs:
-
- diff_cbt = diffusion coefficient at bottom of "t" cells (m**2/s)
-
-
- local
-
- real alphaDT(imt,km,jmw) ! alpha * DT across interfaces
- real betaDS(imt,km,jmw) ! beta * DS across interfaces
-
-
-
-
-
-
-
-
-
-
blmix_kpp
-
-
-DESCRIPTION
-
-
- Mixing coefficients within boundary layer depend on surface
- forcing and the magnitude and gradient of interior mixing below
- the boundary layer ("matching").
-
- CAUTION: if mixing bottoms out at hbl = zt(nk) then
- fictitious layer at nk+1 is needed with small but finite width
- dzt(nk+1) (eg. epsln = 1.e-20).
-
- inputs:
-
- real ustar(ij_bounds) ! surface friction velocity (m/s)
- real bfsfc(ij_bounds) ! surface buoyancy forcing (m^2/s^3)
- real hbl(ij_bounds) ! boundary layer depth (m)
- real stable(ij_bounds) ! = 1 in stable forcing
- real caseA(ij_bounds) ! = 1 in case A
- integer kbl(ij_bounds) ! index of first grid level below hbl
-
- outputs:
-
- visc_cbu = viscosity coefficient at bottom of "u" cells (m**2/s)
- diff_cbt = diffusion coefficient at bottom of "t" cells (m**2/s)
-
- real dkm1(ij_bounds,3) = boundary layer diff_cbt at kbl-1 level
- real blmc(ij_bounds,nk,3) = boundary layer mixing coeff.(m**2/s)
- real ghats(ij_bounds,nk) = nonlocal scalar transport
-
- local:
-
- real gat1(ij_bounds,3)
- real dat1(ij_bounds,3)
- real sigma(ij_bounds) = normalized depth (d / hbl)
- real ws(ij_bounds), wm(ij_bounds) = turbulent velocity scales (m/s)
-
-
-
-
-
-
-
-
-
enhance
-
-
-DESCRIPTION
-
-
- Enhance the diffusivity at the kbl-.5 interface
-
- input
- integer kbl(ij_bounds) = grid above hbl
- real hbl(ij_bounds) = boundary layer depth (m)
- real dkm1(ij_bounds,3) = bl diffusivity at kbl-1 grid level
- real caseA(ij_bounds) = 1 in caseA, = 0 in case B
-
- input/output
- real ghats(ij_bounds,nk) = nonlocal transport (s/m**2)
- modified ghats at kbl(i)-1 interface
- output
- real blmc(ij_bounds,nk,3) = enhanced boundary layer mixing coefficient
-
- local
- real delta = fraction hbl lies beteen zt neighbors
-
-
-
-
-
-
-
-
-
ri_for_kpp
-
-
-DESCRIPTION
-
-
- Compute Richardson number on tracer and velocity cell bottoms.
- rit = richardson number at bottom of T cells
- riu = richardson number at bottom of U cells
-
-
-
-
-
-
-
-
watermass_diag_init
-
-
-DESCRIPTION
-
-
- Initialization of watermass diagnostic output files.
-
-
-
-
-
-
-
-
watermass_diag
-
-
-DESCRIPTION
-
-
- Diagnose effects from KPP nonlocal on the watermass transformation.
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_vert_kpp_mom4p1_nml
-
-
-
-
-
-use_this_module
-
-
- Logical switch to enable kpp diffusion. Default is false.
-
-[logical]
-
-
-debug_this_module
-
-
- Logical switch for debugging. Default debug_this_module=.false.
-
-[logical]
-
- Background vertical diffusivity. Note that if using Bryan-Lewis as a
- background diffusivity, then should set diff_cbt_iw=0.0.
-
-[real, units: m^2/sec]
-
- Enhanced vertical viscosity due to shear instability
-
-[real, units: m^2/sec]
-
-
-diff_cbt_limit
-
-
- Enhanced vertical diffusivity due to shear instability
-
-[real, units: m^2/sec]
-
-
-visc_con_limit
-
-
- Enhanced vertical viscosity in regions of convection
-
-[real, units: m^2/sec]
-
-
-diff_con_limit
-
-
- Enhanced vertical diffusivity in regions of convection
-
-[real, units: m^2/sec]
-
-
-concv
-
-
- constant for pure convection (eqn. 23 of Large etal)
-
-[real, units: dimensionless]
-
-
-Ricr
-
-
- Critical bulk Richardson number. Default from NCAR is
- 0.3, though this number has a large uncertainty and some
- find that 1.0 can be of use.
-
-[real, units: dimensionless]
-
-
-non_local_kpp
-
-
- logical switch for enabling the non-local mixing aspect of kpp.
- Default is .true. as this is what the original KPP scheme suggests.
-
-[logical]
-
-
-smooth_blmc
-
-
- Smooth boundary layer diffusitivies to remove grid scale noise.
- Such noise is apparent in the diagnosed mixed layer depth as well
- as the SST, especially when running coupled models where forcing
- has high temporal frequency.
- Default smooth_blmc=.false.
-
- Warning: This smoother can cause some problems with ghat in regions
- of zero surface forcing. To understand details, one needs
- the paper of Large et al. Vertical diffusion has the general form
- <wx> = K(x_z - ghats)
- In the surface layer a vertical scale function ws is estimated.
- We have K ~ ws and ghats ~1/ws. If wind stress is zero the vertical
- scale ws becomes zero too. Hence, ghats is very large
- (something finite, since it is divided by ws+epsln). Now it may happen,
- that the bouyancy flux becomes negative (~ -10-30). This enables
- the nonlocal scheme. Because the mixing coefficient in the
- surface boundary layer scales with ws the corresponding
- time tendency should be of the order (1/ws * ws = finite). However,
- if smooth_blmc is enabled, it may happen, that from neighbouring
- points with different mixing depth a finite value for
- the mixing coefficient leaks in. In this case
- the tracer time tendency from the nonlocal scheme becomes huge
- and the model fails.
-
- The smoother destroys the consistency between ghats and diff_cbt.
- In most cases this should not matter, but the example shows,
- that sudden model failure is possible under otherwise
- stable and smooth conditions.
-
-
-[logical]
-
-
-kl_min
-
-
- Lower loop index for finding new kbl. Needed for use with certain
- tests of OBC, where kl_min=1 needed, whereas default in original
- implementation has kl_min=2. Default in MOM is kl_min=2.
-
-[integer]
-
-
-kbl_standard_method
-
-
- For computing kbl as in the MOM4p0d code, which is taken from
- the original NCAR scheme. If false, then will slightly modify
- the logic. The modified logic has been found necessary when running
- with as few as two grid cells in the vertical.
- Default kbl_standard_method=.true.
-
-[logical]
-
-
-limit_with_hekman
-
-
- Limiting the boundary layer depth with the Ekman depth may result in a
- shallow boundary layer. In this case the internal values of the vertical
- mixing and viscosity coefficients may be large. This results in
- unrealistically large non-local vertical mixing
- Default limit_with_hekman=.true.
-
-[logical]
-
-
-limit_ghats
-
-
- Limits the non-local vertical tracer flux to the value of the tracer
- surface flux.
- Default limit_ghats=.false.
-
-[logical]
-
-
-hbl_with_rit
-
-
- The default method for determination of the boundary layer depth may fail
- if the water column is instable (negative Richardson number) below or above
- the layer that contains the diagnosed hbl.
- With hbl_with_rit=.true. the search for the boundary layer depth is continued
- downward in this case even if the bulk Richardson number exceeds the
- critical value. This removes a lot of noise from the boundary layer depth.
- Default hbl_with_rit=.false.
-
-[logical]
-
-
-radiation_large
-
-
- Remove the shortwave radiation leaving the boundary layer to the ocean interior
- (hence, not absorbed in the boundary layer) from non-local vertical heat flux
- Default radiation_large=.false.
-
-[logical]
-
-
-radiation_zero
-
-
- Remove the all shortwave radiation from non-local vertical heat flux.
- Default radiation_zero=.false.
-
-[logical]
-
-
-radiation_iow
-
-
- Keep only the shortwave radiation absorbed between the surface and a certain level
- in non-local vertical heat flux through this level.
- Default radiation_iow=.false.
-
-[logical]
-
-
-bvf_from_below
-
-
- Use BV-freq. at the cell bottom instead of the cell top
- as in Danabasoglu et al. (2006).
- Default bvf_from_below=.false., as this will recover
- older behaviour.
-
-[logical]
-
-
-variable_vtc
-
-
- Make vtc dependent on BV-freq. as in Danabasoglu et al. (2006).
- Default variable_vtc=.false., as this will recover
- older behaviour.
-
-[logical]
-
-
-use_max_shear
-
-
- Use maximum shear instead of 4-point average
- (as in Danabasoglu et al. (2006)).
- Default use_max_shear=.false., as this will recover
- older behaviour.
-
-[logical]
-
-
-linear_hbl
-
-
- Use linear interpolation to find the position of hbl.
- If set to false, then use the quadratic interpolation
- as in Danabasoglu et al. (2006). The quadratic approach
- generally yields a slightly deeper surface boundary layer.
- Default linear_hbl=.true., as this will recover
- older behaviour.
-
-[logical]
-
-
-wsfc_combine_runoff_calve
-
-
- For computing wsfc as in the MOM4p0d code, where we combine
- the runoff+calving into a single field called river.
- The alternative keeps the fields separate, as would be appropriate
- for a land model that separately tracks the tracer content in the
- calving and runoff.
- Default wsfc_combine_runoff_calve=.true., as this will recover
- the previous behaviour, to the bit.
-
-[logical]
-
-
-smooth_ri_kmax_eq_kmu
-
-
- When smoothing the Richardson number, we do so over a vertical
- column with max k-levels set by either kmt or kmu. The proper
- approach is kmu, since we are smoothing riu. But for backwards
- compatibility, we default to smooth_ri_kmax_eq_kmu=.false.
-
-[logical]
-
-
-
-
-
-
-
-
-
-
-
REFERENCES
-
-
-
-
- W.G. Large and J.C. McWilliams and S.C. Doney
- Oceanic vertical mixing: A review and a model with
- a nonlocal boundary layer parameterization
- Reviews of Geophysics (1994) vol 32 pages 363-403
-
-
- Danabasoglu etal (2006)
- Diurnal coupling in the tropical oceans of CCSM3
- Journal of Climate (2006) vol 19 pages 2347--2365
-
-
-
-
-
-
-
-
NOTES
-
-
- Original numerical algorithm by Bill Large at NCAR June 6, 1994
-
-
- Equation numbers in the code refer to the Large etal paper.
-
-
- Surface fresh water contributes to surface buoyancy via conversion to
- a locally implied salt flux.
-
-
-
diff --git a/src/mom5/ocean_param/vertical/ocean_vert_kpp_mom4p1.xml b/src/mom5/ocean_param/vertical/ocean_vert_kpp_mom4p1.xml
deleted file mode 100644
index b79fc13ee4..0000000000
--- a/src/mom5/ocean_param/vertical/ocean_vert_kpp_mom4p1.xml
+++ /dev/null
@@ -1,372 +0,0 @@
-
-
- A. Rosati
- Martin Schmidt
- Bill Large
- Stephen Griffies
- M.J. Harrison
- Hyun-Chul Lee
-
- Vertical viscosity and diffusivity according KPP.
- This module has extra code options to handle regions of extremely fresh water.
- This particular version of the KPP module is frozen based on its use in MOM4p1
- at GFDL for the IPCC AR5 climate model ESM2M.
-
- This module computes vertical viscosity and diffusivity according to
- the K-profile parameterization scheme of Large, McWilliams, and
- Doney (1994). It computes both local and non-local mixing.
- The code has been updated to MOM4p1, so that vertical grid increments
- are suitable for generalized vertical coordinate models. When run
- as geopotential model, there will be some differences, since the
- MOM4.0 code (available in ocean_vert_kpp_mom4p0.F90) incorrectly
- ignored the free surface undulations affecting the top model grid
- cell thickness.
-
- This version of KPP has been implemented only for the Bgrid.
-
- W.G. Large and J.C. McWilliams and S.C. Doney
- Oceanic vertical mixing: A review and a model with
- a nonlocal boundary layer parameterization
- Reviews of Geophysics (1994) vol 32 pages 363-403
-
- Danabasoglu etal (2006)
- Diurnal coupling in the tropical oceans of CCSM3
- Journal of Climate (2006) vol 19 pages 2347--2365
-
- Original numerical algorithm by Bill Large at NCAR June 6, 1994
-
- Equation numbers in the code refer to the Large etal paper.
-
- Surface fresh water contributes to surface buoyancy via conversion to
- a locally implied salt flux.
-
- Logical switch to enable kpp diffusion. Default is false.
-
- Logical switch for debugging. Default debug_this_module=.false.
-
- logical switch for shear instability mixing.
- Default shear_instability=.true.
-
- Logical switch for double-diffusive mixing.
- Default double_diffusion=.true.
-
- Background vertical diffusivity. Note that if using Bryan-Lewis as a
- background diffusivity, then should set diff_cbt_iw=0.0.
-
- Background vertical viscosity
-
- Enhanced vertical viscosity due to shear instability
-
- Enhanced vertical diffusivity due to shear instability
-
- Enhanced vertical viscosity in regions of convection
-
- Enhanced vertical diffusivity in regions of convection
-
- constant for pure convection (eqn. 23 of Large etal)
-
- Critical bulk Richardson number. Default from NCAR is
- 0.3, though this number has a large uncertainty and some
- find that 1.0 can be of use.
-
- logical switch for enabling the non-local mixing aspect of kpp.
- Default is .true. as this is what the original KPP scheme suggests.
-
- Smooth boundary layer diffusitivies to remove grid scale noise.
- Such noise is apparent in the diagnosed mixed layer depth as well
- as the SST, especially when running coupled models where forcing
- has high temporal frequency.
- Default smooth_blmc=.false.
-
- Warning: This smoother can cause some problems with ghat in regions
- of zero surface forcing. To understand details, one needs
- the paper of Large et al. Vertical diffusion has the general form
- <wx> = K(x_z - ghats)
- In the surface layer a vertical scale function ws is estimated.
- We have K ~ ws and ghats ~1/ws. If wind stress is zero the vertical
- scale ws becomes zero too. Hence, ghats is very large
- (something finite, since it is divided by ws+epsln). Now it may happen,
- that the bouyancy flux becomes negative (~ -10-30). This enables
- the nonlocal scheme. Because the mixing coefficient in the
- surface boundary layer scales with ws the corresponding
- time tendency should be of the order (1/ws * ws = finite). However,
- if smooth_blmc is enabled, it may happen, that from neighbouring
- points with different mixing depth a finite value for
- the mixing coefficient leaks in. In this case
- the tracer time tendency from the nonlocal scheme becomes huge
- and the model fails.
-
- The smoother destroys the consistency between ghats and diff_cbt.
- In most cases this should not matter, but the example shows,
- that sudden model failure is possible under otherwise
- stable and smooth conditions.
-
-
- Lower loop index for finding new kbl. Needed for use with certain
- tests of OBC, where kl_min=1 needed, whereas default in original
- implementation has kl_min=2. Default in MOM is kl_min=2.
-
- For computing kbl as in the MOM4p0d code, which is taken from
- the original NCAR scheme. If false, then will slightly modify
- the logic. The modified logic has been found necessary when running
- with as few as two grid cells in the vertical.
- Default kbl_standard_method=.true.
-
- Limiting the boundary layer depth with the Ekman depth may result in a
- shallow boundary layer. In this case the internal values of the vertical
- mixing and viscosity coefficients may be large. This results in
- unrealistically large non-local vertical mixing
- Default limit_with_hekman=.true.
-
- Limits the non-local vertical tracer flux to the value of the tracer
- surface flux.
- Default limit_ghats=.false.
-
- The default method for determination of the boundary layer depth may fail
- if the water column is instable (negative Richardson number) below or above
- the layer that contains the diagnosed hbl.
- With hbl_with_rit=.true. the search for the boundary layer depth is continued
- downward in this case even if the bulk Richardson number exceeds the
- critical value. This removes a lot of noise from the boundary layer depth.
- Default hbl_with_rit=.false.
-
- Remove the shortwave radiation leaving the boundary layer to the ocean interior
- (hence, not absorbed in the boundary layer) from non-local vertical heat flux
- Default radiation_large=.false.
-
- Remove the all shortwave radiation from non-local vertical heat flux.
- Default radiation_zero=.false.
-
- Keep only the shortwave radiation absorbed between the surface and a certain level
- in non-local vertical heat flux through this level.
- Default radiation_iow=.false.
-
- Use BV-freq. at the cell bottom instead of the cell top
- as in Danabasoglu et al. (2006).
- Default bvf_from_below=.false., as this will recover
- older behaviour.
-
- Make vtc dependent on BV-freq. as in Danabasoglu et al. (2006).
- Default variable_vtc=.false., as this will recover
- older behaviour.
-
- Use maximum shear instead of 4-point average
- (as in Danabasoglu et al. (2006)).
- Default use_max_shear=.false., as this will recover
- older behaviour.
-
- Use linear interpolation to find the position of hbl.
- If set to false, then use the quadratic interpolation
- as in Danabasoglu et al. (2006). The quadratic approach
- generally yields a slightly deeper surface boundary layer.
- Default linear_hbl=.true., as this will recover
- older behaviour.
-
- For computing wsfc as in the MOM4p0d code, where we combine
- the runoff+calving into a single field called river.
- The alternative keeps the fields separate, as would be appropriate
- for a land model that separately tracks the tracer content in the
- calving and runoff.
- Default wsfc_combine_runoff_calve=.true., as this will recover
- the previous behaviour, to the bit.
-
- When smoothing the Richardson number, we do so over a vertical
- column with max k-levels set by either kmt or kmu. The proper
- approach is kmu, since we are smoothing riu. But for backwards
- compatibility, we default to smooth_ri_kmax_eq_kmu=.false.
-
- Initialization for the KPP vertical mixing scheme
-
- This subroutine computes the vertical diffusivity and viscosity according
- to the KPP scheme of Large etal. In brief, the scheme does the
- following:
-
- --Compute interior mixing everywhere:
- interior mixing gets computed at all cell interfaces due to constant
- internal wave background activity ("visc_cbu_iw" and "diff_cbt_iw").
- Mixing is enhanced in places of static instability (local Ri < 0).
- Additionally, mixing can be enhanced by contribution from shear
- instability which is a function of the local Ri.
-
- --Double diffusion:
- Interior mixing can be enhanced by double diffusion due to salt
- fingering and diffusive convection ("double_diffusion=.true.").
-
- --Boundary layer:
-
- (A) Boundary layer depth:
- at every gridpoint the depth of the oceanic boundary layer
- ("hbl") gets computed by evaluating bulk richardson numbers.
-
- (B) Boundary layer mixing:
- within the boundary layer, above hbl, vertical mixing is
- determined by turbulent surface fluxes, and interior mixing at
- the lower boundary, i.e. at hbl.
-
-
- The oceanic planetray boundary layer depth, hbl, is determined as
- the shallowest depth where the bulk richardson number is
- equal to the critical value, Ricr.
-
- Bulk Richardson numbers are evaluated by computing velocity and
- buoyancy differences between values at zt(kl) and surface
- reference values.
-
- In this configuration, the reference values are equal to the
- values in the surface layer.
- When using a very fine vertical grid, these values should be
- computed as the vertical average of velocity and buoyancy from
- the surface down to epsilon*zt(kl).
-
- When the bulk richardson number at k exceeds Ricr, hbl is
- linearly interpolated between grid levels zt(k) and zt(k-1).
-
- The water column and the surface forcing are diagnosed for
- stable/ustable forcing conditions, and where hbl is relative
- to grid points (caseA), so that conditional branches can be
- avoided in later subroutines.
-
- model
- real zt(1:nk) = vertical grid (m)
- real dzt(1:nk) = layer thicknesses (m)
-
- input
- real dbloc(ij_bounds,nk) = local delta buoyancy (m/s^2)
- real dbsfc(ij_bounds,nk) = delta buoyancy w/ respect to sfc(m/s)^2
- real ustar(ij_bounds) = surface friction velocity (m/s)
- real Bo(ij_bounds) = surface turbulent buoyancy forcing(m^2/s^3)
- real Bosol(ij_bounds) = radiative buoyancy forcing (m^2/s^3)
- real f(ij_bounds) = Coriolis parameter (1/s)
- integer jwtype(ij_bounds) = Jerlov water type (1 to 5)
-
- output
- real hbl(ij_bounds) ! boundary layer depth (m)
- real bfsfc(ij_bounds) !Bo+radiation absorbed to d=hbf*hbl(m^2/s^3)
- real stable(ij_bounds) ! =1 in stable forcing; =0 unstable
- real caseA(ij_bounds) ! =1 in case A, =0 in case B
- integer kbl(ij_bounds) ! index of first grid level below hbl
-
- Compute turbulent velocity scales.
- Use a 2D-lookup table for wm and ws as functions of ustar and
- zetahat (=von_karman*sigma*hbl*bfsfc).
-
- Note: the lookup table is only used for unstable conditions
- (zehat <= 0), in the stable domain wm (=ws) gets computed
- directly.
-
- model
-
- input
- real sigma(ij_bounds) = normalized depth (d/hbl)
- real hbl(ij_bounds) = boundary layer depth (m)
- real ustar(ij_bounds) = surface friction velocity (m/s)
- real bfsfc(ij_bounds) = total surface buoyancy flux (m^2/s^3)
- output
- real wm(ij_bounds),ws(ij_bounds) ! turbulent velocity scales at sigma
- local
- real zehat ! = zeta * ustar**3
-
-
- Compute interior viscosity and diffusivity due
- to shear instability (dependent on a local richardson number),
- to background internal wave activity, and
- to static instability (local richardson number < 0).
-
- inputs:
-
- nk = number of vertical levels
- visc_cbu_iw = background "visc_cbu" (m**2/sec) due to internal waves
- diff_cbt_iw = background "diff_cbt" (m**2/sec) due to internal waves
- visc_cbu_limit = largest "visc_cbu" in regions of gravitational
- instability (m**2/sec)
- diff_cbt_limit = largest "diff_cbt" in regions of gravitational
- instability (m**2/sec)
-
- outputs:
-
- visc_cbu = viscosity coefficient at bottom of "u" cells (m**2/s)
- diff_cbt = diffusion coefficient at bottom of "t" cells (m**2/s)
-
- Rrho dependent interior flux parameterization.
- Add double-diffusion diffusivities to Ri-mix values at blending
- interface and below. salt fingering code modified july 2003
- by stephen.griffies based on NCAR CCSM2.x
-
- inputs:
-
- nk = number of vertical levels
- real talpha(imt,km,jmw) ! d(rho)/ d(pot.temperature) (kg/m^3/C)
- real sbeta(imt,km,jmw) ! d(rho)/ d(salinity) (kg/m^3/PSU)
-
- outputs:
-
- diff_cbt = diffusion coefficient at bottom of "t" cells (m**2/s)
-
-
- local
-
- real alphaDT(imt,km,jmw) ! alpha * DT across interfaces
- real betaDS(imt,km,jmw) ! beta * DS across interfaces
-
-
- Mixing coefficients within boundary layer depend on surface
- forcing and the magnitude and gradient of interior mixing below
- the boundary layer ("matching").
-
- CAUTION: if mixing bottoms out at hbl = zt(nk) then
- fictitious layer at nk+1 is needed with small but finite width
- dzt(nk+1) (eg. epsln = 1.e-20).
-
- inputs:
-
- real ustar(ij_bounds) ! surface friction velocity (m/s)
- real bfsfc(ij_bounds) ! surface buoyancy forcing (m^2/s^3)
- real hbl(ij_bounds) ! boundary layer depth (m)
- real stable(ij_bounds) ! = 1 in stable forcing
- real caseA(ij_bounds) ! = 1 in case A
- integer kbl(ij_bounds) ! index of first grid level below hbl
-
- outputs:
-
- visc_cbu = viscosity coefficient at bottom of "u" cells (m**2/s)
- diff_cbt = diffusion coefficient at bottom of "t" cells (m**2/s)
-
- real dkm1(ij_bounds,3) = boundary layer diff_cbt at kbl-1 level
- real blmc(ij_bounds,nk,3) = boundary layer mixing coeff.(m**2/s)
- real ghats(ij_bounds,nk) = nonlocal scalar transport
-
- local:
-
- real gat1(ij_bounds,3)
- real dat1(ij_bounds,3)
- real sigma(ij_bounds) = normalized depth (d / hbl)
- real ws(ij_bounds), wm(ij_bounds) = turbulent velocity scales (m/s)
-
-
- Enhance the diffusivity at the kbl-.5 interface
-
- input
- integer kbl(ij_bounds) = grid above hbl
- real hbl(ij_bounds) = boundary layer depth (m)
- real dkm1(ij_bounds,3) = bl diffusivity at kbl-1 grid level
- real caseA(ij_bounds) = 1 in caseA, = 0 in case B
-
- input/output
- real ghats(ij_bounds,nk) = nonlocal transport (s/m**2)
- modified ghats at kbl(i)-1 interface
- output
- real blmc(ij_bounds,nk,3) = enhanced boundary layer mixing coefficient
-
- local
- real delta = fraction hbl lies beteen zt neighbors
-
-
- Compute Richardson number on tracer and velocity cell bottoms.
- rit = richardson number at bottom of T cells
- riu = richardson number at bottom of U cells
-
- Initialization of watermass diagnostic output files.
-
- Diagnose effects from KPP nonlocal on the watermass transformation.
-
diff --git a/src/mom5/ocean_param/vertical/ocean_vert_kpp_test.F90 b/src/mom5/ocean_param/vertical/ocean_vert_kpp_test.F90
index 21ade14ac5..433113dd8b 100644
--- a/src/mom5/ocean_param/vertical/ocean_vert_kpp_test.F90
+++ b/src/mom5/ocean_param/vertical/ocean_vert_kpp_test.F90
@@ -291,6 +291,7 @@ module ocean_vert_kpp_test_mod
real, dimension(isd:ied,jsd:jed) :: bfsfc ! surface buoyancy forcing (m^2/s^3)
real, dimension(isd:ied,jsd:jed) :: ws ! scalar velocity scale (m/s)
real, dimension(isd:ied,jsd:jed) :: wm ! momentum velocity scale (m/s)
+real, dimension(isd:ied,jsd:jed) :: Ustk2 ! magnitude of surface stokes drift velocity ^2 (m^2 / s^2)
real, dimension(isd:ied,jsd:jed) :: caseA ! = 1 in case A; =0 in case B
real, dimension(isd:ied,jsd:jed) :: stable ! = 1 in stable forcing; =0 in unstable
real, dimension(isd:ied,jsd:jed,3) :: dkm1 ! boundary layer diff_cbt at kbl-1 level
@@ -328,6 +329,7 @@ module ocean_vert_kpp_test_mod
real, dimension(:,:), allocatable :: bfsfc ! surface buoyancy forcing (m^2/s^3)
real, dimension(:,:), allocatable :: ws ! scalar velocity scale (m/s)
real, dimension(:,:), allocatable :: wm ! momentum velocity scale (m/s)
+real, dimension(:,:), allocatable :: Ustk2 ! Magnitude of surface stokes drift velocity ^2 (m^2/s^2)
real, dimension(:,:), allocatable :: caseA ! = 1 in case A; =0 in case B
real, dimension(:,:), allocatable :: stable ! = 1 in stable forcing; =0 in unstable
real, dimension(:,:,:), allocatable :: dkm1 ! boundary layer diff_cbt at kbl-1 level
@@ -388,6 +390,11 @@ module ocean_vert_kpp_test_mod
real :: concv = 1.8 ! constant for pure convection (eqn. 23)
real :: concv_r ! inverse concv
real :: vtc_flag = 0.0 ! default to the older approach.
+real :: Lgam = 1.04 ! adjustment to non-gradient flux (McWilliam & Sullivan 2000)
+real :: Cw_0 = 0.15 ! eq. (13) in Smyth et al (2002)
+real :: l_smyth = 2.0 ! eq. (13) in Smyth et al (2002)
+real :: LTmax = 5.0 ! maximum Langmuir turbulence enhancement factor (langmuirfactor) allowed
+real :: Wstfac = 0.6 ! stability adjustment coefficient, eq. (13) in Smyth et al (2002)
! for global area normalization
real :: cellarea_r
@@ -470,6 +477,7 @@ module ocean_vert_kpp_test_mod
logical :: non_local_kpp = .true. ! enable/disable non-local term in KPP
logical :: smooth_blmc = .false. ! smooth boundary layer diffusitivies to remove grid scale noise
+logical :: do_langmuir = .false. ! whether or not calcualate langmuir turbulence enhancement factor
integer, parameter :: nni = 890 ! number of values for zehat in the look up table
integer, parameter :: nnj = 480 ! number of values for ustar in the look up table
@@ -485,9 +493,9 @@ module ocean_vert_kpp_test_mod
integer :: num_diag_tracers=0, index_frazil
character(len=256) :: version=&
- '$Id: ocean_vert_kpp_test.F90,v 1.1.2.4 2012/05/25 12:49:59 Stephen.Griffies Exp $'
+ '$Id: ocean_vert_kpp_test.F90,v 20.0 2013/12/14 00:16:46 fms Exp $'
character (len=128) :: tagname = &
- '$Name: mom5_siena_08jun2012_smg $'
+ '$Name: tikal $'
logical :: module_is_initialized = .FALSE.
logical :: debug_this_module = .FALSE.
@@ -497,12 +505,13 @@ module ocean_vert_kpp_test_mod
visc_cbu_limit, diff_cbt_limit, &
visc_con_limit, diff_con_limit, &
concv, Ricr, non_local_kpp, smooth_blmc, &
+ Lgam, Cw_0,l_smyth, LTmax, Wstfac, &
kl_min, kbl_standard_method, debug_this_module, &
limit_with_hekman, limit_ghats, hbl_with_rit, &
radiation_large, radiation_zero, radiation_iow, &
use_sbl_bottom_flux, wsfc_combine_runoff_calve, &
- bvf_from_below, variable_vtc, use_max_shear, &
- linear_hbl, smooth_ri_kmax_eq_kmu
+ bvf_from_below, variable_vtc, use_max_shear, &
+ linear_hbl, smooth_ri_kmax_eq_kmu, do_langmuir
contains
@@ -759,6 +768,7 @@ subroutine ocean_vert_kpp_test_init (Grid, Domain, Time, Time_steps, Dens, T_pro
allocate (Rib(isd:ied,jsd:jed,rib_dim)) ! Bulk Richardson number
allocate (wm(isd:ied,jsd:jed)) ! momentum turbulent velocity scales (m/s)
allocate (ws(isd:ied,jsd:jed)) ! scalar turbulent velocity scales (m/s)
+ allocate (Ustk2(isd:ied,jsd:jed)) ! Magnitude of surface stokes drift velocity ^2 (m^2/s^2)
allocate (gat1(isd:ied,jsd:jed,3))
allocate (dat1(isd:ied,jsd:jed,3))
allocate(sw_frac_hbl(isd:ied,jsd:jed))
@@ -772,6 +782,8 @@ subroutine ocean_vert_kpp_test_init (Grid, Domain, Time, Time_steps, Dens, T_pro
hblt(:,:) = 0.0
hbl(:,:) = 0.0
sw_frac_hbl(:,:) = 0.0
+ Ustk2(:,:) = 0.0
+
do n = 1, num_prog_tracers
wsfc(n)%wsfc(:,:) = 0.0
enddo
@@ -952,9 +964,10 @@ end subroutine ocean_vert_kpp_test_init
!
!
!
-subroutine vert_mix_kpp_test (Time, Thickness, Velocity, T_prog, T_diag, Dens, &
- swflx, sw_frac_zt, pme, river, visc_cbu, visc_cbt, diff_cbt, hblt_depth)
+subroutine vert_mix_kpp_test (aidif, Time, Thickness, Velocity, T_prog, T_diag, Dens, &
+ swflx, sw_frac_zt, pme, river, visc_cbu, visc_cbt, diff_cbt, hblt_depth, do_wave)
+ real, intent(in) :: aidif
type(ocean_time_type), intent(in) :: Time
type(ocean_thickness_type), intent(in) :: Thickness
type(ocean_velocity_type), intent(in) :: Velocity
@@ -969,6 +982,7 @@ subroutine vert_mix_kpp_test (Time, Thickness, Velocity, T_prog, T_diag, Dens, &
real, dimension(isd:,jsd:,:), intent(inout) :: visc_cbu
real, dimension(isd:,jsd:,:), intent(inout) :: visc_cbt
real, dimension(isd:,jsd:,:,:), intent(inout) :: diff_cbt
+ logical, intent(in) :: do_wave
real, dimension(isd:ied,jsd:jed,nk) :: dbloc1, dbsfc1
real, dimension(isd:ied,jsd:jed) :: frazil
@@ -999,6 +1013,15 @@ subroutine vert_mix_kpp_test (Time, Thickness, Velocity, T_prog, T_diag, Dens, &
frazil(:,:) = 0.0
endif
+!---------assign Ustk2
+ if (do_wave) then
+ do j = jsd, jed
+ do i = isd, ied
+ Ustk2(i,j) = Velocity%ustoke(i,j)**2 + Velocity%vstoke(i,j)**2
+ enddo
+ enddo
+ endif
+
!-----------------------------------------------------------------------
! compute gradient Ri and dVsq
!-----------------------------------------------------------------------
@@ -1228,11 +1251,11 @@ subroutine vert_mix_kpp_test (Time, Thickness, Velocity, T_prog, T_diag, Dens, &
! boundary layer mixing coefficients: diagnose new bldepth
- call bldepth(Thickness, sw_frac_zt)
+ call bldepth(Thickness, sw_frac_zt, do_wave)
! boundary layer diffusivities
- call blmix_kpp(Thickness, diff_cbt, visc_cbt)
+ call blmix_kpp(Thickness, diff_cbt, visc_cbt, do_wave)
call diagnose_3d(Time, Grd, id_ws, wrk1(:,:,:))
@@ -1598,10 +1621,11 @@ end subroutine vert_mix_kpp_test
!
!
!
-subroutine bldepth(Thickness, sw_frac_zt)
+subroutine bldepth(Thickness, sw_frac_zt, do_wave)
type(ocean_thickness_type), intent(in) :: Thickness
real, dimension(isd:,jsd:,:), intent(in) :: sw_frac_zt !3-D array of shortwave fract
+ logical, intent(in) :: do_wave
real :: Ritop ! numerator of bulk Richardson Number
real :: bvfr, Vtsq
@@ -1668,7 +1692,7 @@ subroutine bldepth(Thickness, sw_frac_zt)
! compute velocity scales at sigma, for hbl = zt(kl):
iwscale_use_hbl_eq_zt=1
- call wscale (iwscale_use_hbl_eq_zt, Thickness%depth_zt(:,:,kl))
+ call wscale (iwscale_use_hbl_eq_zt, Thickness%depth_zt(:,:,kl), do_wave)
do j=jsc,jec
do i=isc,iec
@@ -1770,7 +1794,7 @@ subroutine bldepth(Thickness, sw_frac_zt)
! compute velocity scales at sigma, for hbl = zt(kl):
iwscale_use_hbl_eq_zt=1
- call wscale (iwscale_use_hbl_eq_zt, Thickness%depth_zt(:,:,kl))
+ call wscale (iwscale_use_hbl_eq_zt, Thickness%depth_zt(:,:,kl), do_wave)
do j=jsc,jec
do i=isc,iec
@@ -1819,7 +1843,7 @@ subroutine bldepth(Thickness, sw_frac_zt)
if(((rit(i,j,kl-1).lt.0).or.(rit(i,j,kl).lt.0)).and.hbl_with_rit) then
! Rib(i,j,ku) is not relevant, because locally unstable
- Rib(i,j,kdn) = Ricr*0.1
+ Rib(i,j,kdn) = Ricr*0.1
else
@@ -1841,8 +1865,8 @@ subroutine bldepth(Thickness, sw_frac_zt)
else
hbl(i,j) = (-b_co + sqrt(sqrt_arg)) / (c2*a_co)
endif
-
- kbl(i,j) = kl
+
+ kbl(i,j) = kl
iwet = iwet - 1
endif
@@ -2024,13 +2048,14 @@ end subroutine bldepth
!
!
!
-subroutine wscale(iwscale_use_hbl_eq_zt, zt_kl)
+subroutine wscale(iwscale_use_hbl_eq_zt, zt_kl, do_wave)
integer, intent(in) :: iwscale_use_hbl_eq_zt
real, dimension(isd:,jsd:), intent(in) :: zt_kl
+ logical, intent(in) :: do_wave
real :: zdiff, udiff, zfrac, ufrac, fzfrac
- real :: wam, wbm, was, wbs, u3
+ real :: wam, wbm, was, wbs, u3, langmuirfactor, Cw_smyth
real :: zehat ! = zeta * ustar**3
integer :: iz, izp1, ju, jup1
integer :: i, j
@@ -2124,6 +2149,22 @@ subroutine wscale(iwscale_use_hbl_eq_zt, zt_kl)
endif
+!----------- if do_wave, add Langmuir turbulence enhancement factor
+
+ if (do_wave .and. do_langmuir) then
+ do j=jsc,jec
+ do i=isc,iec
+ Cw_smyth=Cw_0*(ustar(i,j)*ustar(i,j)*ustar(i,j)/(ustar(i,j)*ustar(i,j)*ustar(i,j) &
+ + Wstfac*von_karman*bfsfc(i,j)*hbl(i,j) + epsln))**l_smyth
+ langmuirfactor=sqrt(1+Cw_smyth*Ustk2(i,j)/(ustar(i,j)*ustar(i,j) + epsln))
+ langmuirfactor = max(1.0, langmuirfactor)
+ langmuirfactor = min(LTmax, langmuirfactor)
+ ws(i,j)=ws(i,j)*langmuirfactor
+ wm(i,j)=wm(i,j)*langmuirfactor
+ enddo
+ enddo
+ endif
+
end subroutine wscale
! NAME="wscale"
@@ -2345,11 +2386,12 @@ end subroutine ddmix
!
!
!
-subroutine blmix_kpp(Thickness, diff_cbt, visc_cbt)
+subroutine blmix_kpp(Thickness, diff_cbt, visc_cbt, do_wave)
type(ocean_thickness_type), intent(in) :: Thickness
real, dimension(isd:,jsd:,:,:), intent(inout) :: diff_cbt
real, dimension(isd:,jsd:,:) , intent(inout) :: visc_cbt
+ logical, intent(in) :: do_wave
real, dimension(isd:ied,jsd:jed) :: zt_kl_dummy
@@ -2373,7 +2415,7 @@ subroutine blmix_kpp(Thickness, diff_cbt, visc_cbt)
iwscale_use_hbl_eq_zt = 0
zt_kl_dummy(:,:) = 0.0
- call wscale (iwscale_use_hbl_eq_zt, zt_kl_dummy)
+ call wscale (iwscale_use_hbl_eq_zt, zt_kl_dummy, do_wave)
do j=jsc,jec
do i = isc,iec
@@ -2443,7 +2485,7 @@ subroutine blmix_kpp(Thickness, diff_cbt, visc_cbt)
iwscale_use_hbl_eq_zt = 0
zt_kl_dummy(:,:) = 0.0
- call wscale(iwscale_use_hbl_eq_zt, zt_kl_dummy)
+ call wscale(iwscale_use_hbl_eq_zt, zt_kl_dummy, do_wave)
!-----------------------------------------------------------------------
! compute the dimensionless shape functions at the interfaces
@@ -2479,9 +2521,16 @@ subroutine blmix_kpp(Thickness, diff_cbt, visc_cbt)
!-----------------------------------------------------------------------
! nonlocal transport term = ghats * o (eqn. 20)
+! To include Langmuir turbulence effects, multiply ghats
+! by a factor of Lgam (McWilliam & Sullivan 2001)
!-----------------------------------------------------------------------
-
- ghats(i,j,ki) = (1.-stable(i,j)) * cg / (ws(i,j) * hbl(i,j) + epsln)
+ if (do_wave .and. do_langmuir) then
+ ghats(i,j,ki) = Lgam * (1.-stable(i,j)) * cg &
+ / (ws(i,j) * hbl(i,j) + epsln)
+ else
+ ghats(i,j,ki) = (1.-stable(i,j)) * cg &
+ / (ws(i,j) * hbl(i,j) + epsln)
+ endif
endif
enddo
enddo
@@ -2503,7 +2552,7 @@ subroutine blmix_kpp(Thickness, diff_cbt, visc_cbt)
iwscale_use_hbl_eq_zt = 0
zt_kl_dummy(:,:) = 0.0
- call wscale(iwscale_use_hbl_eq_zt, zt_kl_dummy)
+ call wscale(iwscale_use_hbl_eq_zt, zt_kl_dummy, do_wave)
do j=jsc,jec
do i = isc,iec
diff --git a/src/mom5/ocean_param/vertical/ocean_vert_kpp_test.html b/src/mom5/ocean_param/vertical/ocean_vert_kpp_test.html
deleted file mode 100644
index 56dcc4e2b2..0000000000
--- a/src/mom5/ocean_param/vertical/ocean_vert_kpp_test.html
+++ /dev/null
@@ -1,790 +0,0 @@
-
-
-
-Module ocean_vert_kpp_test_mod
-
-
-
-
-PUBLIC INTERFACE
-
- ~ PUBLIC ROUTINES
- ~ NAMELIST
-
-
- Vertical viscosity and diffusivity according KPP.
-
- This module has extra code options to handle regions of extremely fresh water.
-
- It also has options for both the Cgrid and Bgrid.
-
- It is undergoing further development in collaboration with NCAR scientists.
- So it will undergo significant change during 2012.
-
-
-
-
-
-
- This module computes vertical viscosity and diffusivity according to
- the K-profile parameterization scheme of Large, McWilliams, and
- Doney (1994). It computes both local and non-local mixing.
- The code has been updated to MOM4p1, so that vertical grid increments
- are suitable for generalized vertical coordinate models. When run
- as geopotential model, there will be some differences, since the
- MOM4.0 code (available in ocean_vert_kpp_mom4p0.F90) incorrectly
- ignored the free surface undulations affecting the top model grid
- cell thickness.
-
-
- Initialization for the KPP vertical mixing scheme
-
-
-
-
-
-
-
-
vert_mix_kpp_test
-
-
-DESCRIPTION
-
-
- This subroutine computes the vertical diffusivity and viscosity according
- to the KPP scheme of Large etal. In brief, the scheme does the
- following:
-
- --Compute interior mixing everywhere:
- interior mixing gets computed at all cell interfaces due to constant
- internal wave background activity ("visc_cbu_iw" and "diff_cbt_iw").
- Mixing is enhanced in places of static instability (local Ri < 0).
- Additionally, mixing can be enhanced by contribution from shear
- instability which is a function of the local Ri.
-
- --Double diffusion:
- Interior mixing can be enhanced by double diffusion due to salt
- fingering and diffusive convection ("double_diffusion=.true.").
-
- --Boundary layer:
-
- (A) Boundary layer depth:
- at every gridpoint the depth of the oceanic boundary layer
- ("hbl") gets computed by evaluating bulk richardson numbers.
-
- (B) Boundary layer mixing:
- within the boundary layer, above hbl, vertical mixing is
- determined by turbulent surface fluxes, and interior mixing at
- the lower boundary, i.e. at hbl.
-
- NOTE: Use smf_bgrid since this uses the primary smf array read in from
- the coupler in ocean_core/ocean_sbc.F90 when using the FMS coupler.
-
-
-
-
-
-
-
-
-
bldepth
-
-
-DESCRIPTION
-
-
- The oceanic planetray boundary layer depth, hbl, is determined as
- the shallowest depth where the bulk richardson number is
- equal to the critical value, Ricr.
-
- Bulk Richardson numbers are evaluated by computing velocity and
- buoyancy differences between values at zt(kl) and surface
- reference values.
-
- In this configuration, the reference values are equal to the
- values in the surface layer.
-
- When using a very fine vertical grid, these values should be
- computed as the vertical average of velocity and buoyancy from
- the surface down to epsilon*zt(kl).
-
- When the bulk richardson number at k exceeds Ricr, hbl is
- linearly interpolated between grid levels zt(k) and zt(k-1).
-
- The water column and the surface forcing are diagnosed for
- stable/ustable forcing conditions, and where hbl is relative
- to grid points (caseA), so that conditional branches can be
- avoided in later subroutines.
-
- input
- real dbloc = local delta buoyancy (m/s^2)
- real dbsfc = delta buoyancy w/ respect to sfc(m/s)^2
- real ustar = surface friction velocity (m/s)
- real Bo = surface turbulent buoyancy forcing(m^2/s^3)
- real Bosol = radiative buoyancy forcing (m^2/s^3)
- real f = Coriolis parameter (1/s)
-
- output
- real hbl ! boundary layer depth (m)
- real bfsfc !Bo+radiation absorbed to d=hbf*hbl(m^2/s^3)
- real stable ! =1 in stable forcing; =0 unstable
- real caseA ! =1 in case A, =0 in case B
- integer kbl ! index of first grid level below hbl
-
-
-
-
-
-
-
-
-
wscale
-
-
-DESCRIPTION
-
-
- Compute turbulent velocity scales.
- Use a 2D-lookup table for wm and ws as functions of ustar and
- zetahat (=von_karman*sigma*hbl*bfsfc).
-
- Note: the lookup table is only used for unstable conditions
- (zehat <= 0), in the stable domain wm (=ws) gets computed
- directly.
-
- Note: the loop has been doubled to allow NEC compilers for vectorisation.
- Speed gain was observed at the SX-6.
- Later compiler versions may do better.
-
-
- input
- real sigma = normalized depth (d/hbl)
- real hbl = boundary layer depth (m)
- real ustar = surface friction velocity (m/s)
- real bfsfc = total surface buoyancy flux (m^2/s^3)
- output
- real wm,ws ! turbulent velocity scales at sigma
- local
- real zehat ! = zeta * ustar**3
-
-
-
-
-
-
-
-
-
ri_iwmix
-
-
-DESCRIPTION
-
-
- Compute interior viscosity and diffusivity due
- to shear instability (dependent on a local richardson number),
- to background internal wave activity, and
- to static instability (local richardson number < 0).
-
- Diffusion and viscosity coefficients are on bottom
- of T-cells.
-
-
-
-
-
-
-
-
-
ddmix
-
-
-DESCRIPTION
-
-
- Rrho dependent interior flux parameterization.
- Add double-diffusion diffusivities to Ri-mix values at blending
- interface and below. salt fingering code modified july 2003
- by stephen.griffies based on NCAR CCSM2.x
-
- real talpha ! d(rho)/ d(pot.temperature) (kg/m^3/C)
- real sbeta ! d(rho)/ d(salinity) (kg/m^3/PSU)
-
- diff_cbt = diffusion coefficient at bottom of "t" cells (m**2/s)
-
- local
- real alphaDT ! alpha * DT across interfaces
- real betaDS ! beta * DS across interfaces
-
-
-
-
-
-
-
-
-
blmix_kpp
-
-
-DESCRIPTION
-
-
- Mixing coefficients within boundary layer depend on surface
- forcing and the magnitude and gradient of interior mixing below
- the boundary layer ("matching").
-
- CAUTION: if mixing bottoms out at hbl = zt(nk) then
- fictitious layer at nk+1 is needed with small but finite width
- dzt(nk+1) (eg. epsln = 1.e-20).
-
- inputs:
-
- real ustar ! surface friction velocity (m/s)
- real bfsfc ! surface buoyancy forcing (m^2/s^3)
- real hbl ! boundary layer depth (m)
- real stable ! = 1 in stable forcing
- real caseA ! = 1 in case A
- integer kbl ! index of first grid level below hbl
-
- outputs:
-
- visc_cbt = viscosity coefficient at bottom of "t" cells (m**2/s)
- diff_cbt = diffusion coefficient at bottom of "t" cells (m**2/s)
-
- real dkm1(,3) = boundary layer diff_cbt at kbl-1 level
- real blmc(,nk,3) = boundary layer mixing coeff.(m**2/s)
- real ghats(,nk) = nonlocal scalar transport
-
- local:
-
- real gat1(,3)
- real dat1(,3)
- real sigma() = normalized depth (d / hbl)
- real ws(), wm() = turbulent velocity scales (m/s)
-
-
-
-
-
-
-
-
-
enhance
-
-
-DESCRIPTION
-
-
- Enhance the diffusivity at the kbl-.5 interface
-
- input
- integer kbl = grid above hbl
- real hbl = boundary layer depth (m)
- real dkm1 = bl diffusivity at kbl-1 grid level
- real caseA = 1 in caseA, = 0 in case B
-
- input/output
- real ghats = nonlocal transport (s/m**2)
- modified ghats at kbl(i)-1 interface
- output
- real blmc = enhanced boundary layer mixing coefficient
-
- local
- real delta = fraction hbl lies beteen zt neighbors
-
-
-
-
-
-
-
-
-
watermass_diag_init
-
-
-DESCRIPTION
-
-
- Initialization of watermass diagnostic output files.
-
-
-
-
-
-
-
-
watermass_diag
-
-
-DESCRIPTION
-
-
- Diagnose effects from KPP nonlocal on the watermass transformation.
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_vert_kpp_test_nml
-
-
-
-
-
-use_this_module
-
-
- Logical switch to enable kpp diffusion. Default is false.
-
-[logical]
-
-
-debug_this_module
-
-
- Logical switch for debugging. Default debug_this_module=.false.
-
-[logical]
-
- Background vertical diffusivity. Note that if using Bryan-Lewis as a
- background diffusivity, then should set diff_cbt_iw=0.0.
-
-[real, units: m^2/sec]
-
- Enhanced vertical viscosity due to shear instability
-
-[real, units: m^2/sec]
-
-
-diff_cbt_limit
-
-
- Enhanced vertical diffusivity due to shear instability
-
-[real, units: m^2/sec]
-
-
-visc_con_limit
-
-
- Enhanced vertical viscosity in regions of convection
-
-[real, units: m^2/sec]
-
-
-diff_con_limit
-
-
- Enhanced vertical diffusivity in regions of convection
-
-[real, units: m^2/sec]
-
-
-concv
-
-
- constant for pure convection (eqn. 23 of Large etal)
-
-[real, units: dimensionless]
-
-
-Ricr
-
-
- Critical bulk Richardson number. Default from NCAR is
- 0.3, though this number has a large uncertainty and some
- find that 1.0 can be of use.
-
-[real, units: dimensionless]
-
-
-non_local_kpp
-
-
- logical switch for enabling the non-local mixing aspect of kpp.
- Default is .true. as this is what the original KPP scheme suggests.
-
-[logical]
-
-
-smooth_blmc
-
-
- Smooth boundary layer diffusitivies to remove grid scale noise.
- Such noise is apparent in the diagnosed mixed layer depth as well
- as the SST, especially when running coupled models where forcing
- has high temporal frequency.
- Default smooth_blmc=.false.
-
- Warning: This smoother can cause some problems with ghat in regions
- of zero surface forcing. To understand details, one needs
- the paper of Large et al. Vertical diffusion has the general form
- <wx> = K(x_z - ghats)
- In the surface layer a vertical scale function ws is estimated.
- We have K ~ ws and ghats ~1/ws. If wind stress is zero the vertical
- scale ws becomes zero too. Hence, ghats is very large
- (something finite, since it is divided by ws+epsln). Now it may happen,
- that the bouyancy flux becomes negative (~ -10-30). This enables
- the nonlocal scheme. Because the mixing coefficient in the
- surface boundary layer scales with ws the corresponding
- time tendency should be of the order (1/ws * ws = finite). However,
- if smooth_blmc is enabled, it may happen, that from neighbouring
- points with different mixing depth a finite value for
- the mixing coefficient leaks in. In this case
- the tracer time tendency from the nonlocal scheme becomes huge
- and the model fails.
-
- The smoother destroys the consistency between ghats and diff_cbt.
- In most cases this should not matter, but the example shows,
- that sudden model failure is possible under otherwise
- stable and smooth conditions.
-
-
-[logical]
-
-
-kl_min
-
-
- Lower loop index for finding new kbl. Needed for use with certain
- tests of OBC, where kl_min=1 needed, whereas default in original
- implementation has kl_min=2. Default in MOM is kl_min=2.
-
-[integer]
-
-
-kbl_standard_method
-
-
- For computing kbl as in the MOM4p0d code, which is taken from
- the original NCAR scheme. If false, then will slightly modify
- the logic. The modified logic has been found necessary when running
- with as few as two grid cells in the vertical.
- Default kbl_standard_method=.true.
-
-[logical]
-
-
-limit_with_hekman
-
-
- Limiting the boundary layer depth with the Ekman depth may result in a
- shallow boundary layer. In this case the internal values of the vertical
- mixing and viscosity coefficients may be large. This results in
- unrealistically large non-local vertical mixing
- Default limit_with_hekman=.true.
-
-[logical]
-
-
-limit_ghats
-
-
- Limits the non-local vertical tracer flux to the value of the tracer
- surface flux.
- Default limit_ghats=.false.
-
-[logical]
-
-
-hbl_with_rit
-
-
- The default method for determination of the boundary layer depth may fail
- if the water column is instable (negative Richardson number) below or above
- the layer that contains the diagnosed hbl.
- With hbl_with_rit=.true. the search for the boundary layer depth is continued
- downward in this case even if the bulk Richardson number exceeds the
- critical value. This removes a lot of noise from the boundary layer depth.
- Default hbl_with_rit=.false.
-
-[logical]
-
-
-radiation_large
-
-
- Remove the shortwave radiation leaving the boundary layer to the ocean interior
- (hence, not absorbed in the boundary layer) from non-local vertical heat flux
- Default radiation_large=.false.
-
-[logical]
-
-
-radiation_zero
-
-
- Remove the all shortwave radiation from non-local vertical heat flux.
- Default radiation_zero=.false.
-
-[logical]
-
-
-radiation_iow
-
-
- Keep only the shortwave radiation absorbed between the surface and a certain level
- in non-local vertical heat flux through this level.
- Default radiation_iow=.false.
-
-[logical]
-
-
-bvf_from_below
-
-
- Use BV-freq. at the cell bottom instead of the cell top
- as in Danabasoglu et al. (2006).
- Default bvf_from_below=.false., as this will recover
- older behaviour.
-
-[logical]
-
-
-variable_vtc
-
-
- Make vtc dependent on BV-freq. as in Danabasoglu et al. (2006).
- Default variable_vtc=.false., as this will recover
- older behaviour.
-
-[logical]
-
-
-use_max_shear
-
-
- Use maximum shear instead of 4-point average
- (as in Danabasoglu et al. (2006)).
- Default use_max_shear=.false., as this will recover
- legacy behaviour.
-
-[logical]
-
-
-linear_hbl
-
-
- Use linear interpolation to find the position of hbl.
- If set to false, then use the quadratic interpolation
- as in Danabasoglu et al. (2006). The quadratic approach
- generally yields a slightly deeper surface boundary layer.
- Default linear_hbl=.true., as this will recover
- older behaviour.
-
-[logical]
-
-
-wsfc_combine_runoff_calve
-
-
- For computing wsfc as in the MOM4p0d code, where we combine
- the runoff+calving into a single field called river.
- The alternative keeps the fields separate, as would be appropriate
- for a land model that separately tracks the tracer content in the
- calving and runoff.
- Default wsfc_combine_runoff_calve=.true., as this will recover
- the previous behaviour, to the bit.
-
-[logical]
-
-
-smooth_ri_kmax_eq_kmu
-
-
- When smoothing the Richardson number, we do so over a vertical
- column with max k-levels set by either kmt or kmu. The proper
- approach is kmu, since we are smoothing riu. But for backwards
- compatibility, we default to smooth_ri_kmax_eq_kmu=.false.
-
-[logical]
-
-
-
-
-
-
-
-
-
-
-
REFERENCES
-
-
-
-
- W.G. Large and J.C. McWilliams and S.C. Doney
- Oceanic vertical mixing: A review and a model with
- a nonlocal boundary layer parameterization
- Reviews of Geophysics (1994) vol 32 pages 363-403
-
-
- Danabasoglu etal (2006)
- Diurnal coupling in the tropical oceans of CCSM3
- Journal of Climate (2006) vol 19 pages 2347--2365
-
-
-
-
-
-
-
-
NOTES
-
-
- Original numerical algorithm by Bill Large at NCAR June 6, 1994
-
-
- Equation numbers in the code refer to the Large etal paper.
-
-
- Surface fresh water contributes to surface buoyancy via conversion to
- a locally implied salt flux.
-
-
-
diff --git a/src/mom5/ocean_param/vertical/ocean_vert_kpp_test.xml b/src/mom5/ocean_param/vertical/ocean_vert_kpp_test.xml
deleted file mode 100644
index 1716547fa4..0000000000
--- a/src/mom5/ocean_param/vertical/ocean_vert_kpp_test.xml
+++ /dev/null
@@ -1,356 +0,0 @@
-
-
- A. Rosati
- Martin Schmidt
- Bill Large
- Stephen Griffies
- M.J. Harrison
-
- Vertical viscosity and diffusivity according KPP.
-
- This module has extra code options to handle regions of extremely fresh water.
-
- It also has options for both the Cgrid and Bgrid.
-
- It is undergoing further development in collaboration with NCAR scientists.
- So it will undergo significant change during 2012.
-
-
- This module computes vertical viscosity and diffusivity according to
- the K-profile parameterization scheme of Large, McWilliams, and
- Doney (1994). It computes both local and non-local mixing.
- The code has been updated to MOM4p1, so that vertical grid increments
- are suitable for generalized vertical coordinate models. When run
- as geopotential model, there will be some differences, since the
- MOM4.0 code (available in ocean_vert_kpp_mom4p0.F90) incorrectly
- ignored the free surface undulations affecting the top model grid
- cell thickness.
-
-
- W.G. Large and J.C. McWilliams and S.C. Doney
- Oceanic vertical mixing: A review and a model with
- a nonlocal boundary layer parameterization
- Reviews of Geophysics (1994) vol 32 pages 363-403
-
- Danabasoglu etal (2006)
- Diurnal coupling in the tropical oceans of CCSM3
- Journal of Climate (2006) vol 19 pages 2347--2365
-
- Original numerical algorithm by Bill Large at NCAR June 6, 1994
-
- Equation numbers in the code refer to the Large etal paper.
-
- Surface fresh water contributes to surface buoyancy via conversion to
- a locally implied salt flux.
-
- Logical switch to enable kpp diffusion. Default is false.
-
- Logical switch for debugging. Default debug_this_module=.false.
-
- logical switch for shear instability mixing.
- Default shear_instability=.true.
-
- Logical switch for double-diffusive mixing.
- Default double_diffusion=.true.
-
- Background vertical diffusivity. Note that if using Bryan-Lewis as a
- background diffusivity, then should set diff_cbt_iw=0.0.
-
- Background vertical viscosity
-
- Enhanced vertical viscosity due to shear instability
-
- Enhanced vertical diffusivity due to shear instability
-
- Enhanced vertical viscosity in regions of convection
-
- Enhanced vertical diffusivity in regions of convection
-
- constant for pure convection (eqn. 23 of Large etal)
-
- Critical bulk Richardson number. Default from NCAR is
- 0.3, though this number has a large uncertainty and some
- find that 1.0 can be of use.
-
- logical switch for enabling the non-local mixing aspect of kpp.
- Default is .true. as this is what the original KPP scheme suggests.
-
- Smooth boundary layer diffusitivies to remove grid scale noise.
- Such noise is apparent in the diagnosed mixed layer depth as well
- as the SST, especially when running coupled models where forcing
- has high temporal frequency.
- Default smooth_blmc=.false.
-
- Warning: This smoother can cause some problems with ghat in regions
- of zero surface forcing. To understand details, one needs
- the paper of Large et al. Vertical diffusion has the general form
- <wx> = K(x_z - ghats)
- In the surface layer a vertical scale function ws is estimated.
- We have K ~ ws and ghats ~1/ws. If wind stress is zero the vertical
- scale ws becomes zero too. Hence, ghats is very large
- (something finite, since it is divided by ws+epsln). Now it may happen,
- that the bouyancy flux becomes negative (~ -10-30). This enables
- the nonlocal scheme. Because the mixing coefficient in the
- surface boundary layer scales with ws the corresponding
- time tendency should be of the order (1/ws * ws = finite). However,
- if smooth_blmc is enabled, it may happen, that from neighbouring
- points with different mixing depth a finite value for
- the mixing coefficient leaks in. In this case
- the tracer time tendency from the nonlocal scheme becomes huge
- and the model fails.
-
- The smoother destroys the consistency between ghats and diff_cbt.
- In most cases this should not matter, but the example shows,
- that sudden model failure is possible under otherwise
- stable and smooth conditions.
-
-
- Lower loop index for finding new kbl. Needed for use with certain
- tests of OBC, where kl_min=1 needed, whereas default in original
- implementation has kl_min=2. Default in MOM is kl_min=2.
-
- For computing kbl as in the MOM4p0d code, which is taken from
- the original NCAR scheme. If false, then will slightly modify
- the logic. The modified logic has been found necessary when running
- with as few as two grid cells in the vertical.
- Default kbl_standard_method=.true.
-
- Limiting the boundary layer depth with the Ekman depth may result in a
- shallow boundary layer. In this case the internal values of the vertical
- mixing and viscosity coefficients may be large. This results in
- unrealistically large non-local vertical mixing
- Default limit_with_hekman=.true.
-
- Limits the non-local vertical tracer flux to the value of the tracer
- surface flux.
- Default limit_ghats=.false.
-
- The default method for determination of the boundary layer depth may fail
- if the water column is instable (negative Richardson number) below or above
- the layer that contains the diagnosed hbl.
- With hbl_with_rit=.true. the search for the boundary layer depth is continued
- downward in this case even if the bulk Richardson number exceeds the
- critical value. This removes a lot of noise from the boundary layer depth.
- Default hbl_with_rit=.false.
-
- Remove the shortwave radiation leaving the boundary layer to the ocean interior
- (hence, not absorbed in the boundary layer) from non-local vertical heat flux
- Default radiation_large=.false.
-
- Remove the all shortwave radiation from non-local vertical heat flux.
- Default radiation_zero=.false.
-
- Keep only the shortwave radiation absorbed between the surface and a certain level
- in non-local vertical heat flux through this level.
- Default radiation_iow=.false.
-
- Use BV-freq. at the cell bottom instead of the cell top
- as in Danabasoglu et al. (2006).
- Default bvf_from_below=.false., as this will recover
- older behaviour.
-
- Make vtc dependent on BV-freq. as in Danabasoglu et al. (2006).
- Default variable_vtc=.false., as this will recover
- older behaviour.
-
- Use maximum shear instead of 4-point average
- (as in Danabasoglu et al. (2006)).
- Default use_max_shear=.false., as this will recover
- legacy behaviour.
-
- Use linear interpolation to find the position of hbl.
- If set to false, then use the quadratic interpolation
- as in Danabasoglu et al. (2006). The quadratic approach
- generally yields a slightly deeper surface boundary layer.
- Default linear_hbl=.true., as this will recover
- older behaviour.
-
- For computing wsfc as in the MOM4p0d code, where we combine
- the runoff+calving into a single field called river.
- The alternative keeps the fields separate, as would be appropriate
- for a land model that separately tracks the tracer content in the
- calving and runoff.
- Default wsfc_combine_runoff_calve=.true., as this will recover
- the previous behaviour, to the bit.
-
- When smoothing the Richardson number, we do so over a vertical
- column with max k-levels set by either kmt or kmu. The proper
- approach is kmu, since we are smoothing riu. But for backwards
- compatibility, we default to smooth_ri_kmax_eq_kmu=.false.
-
- Initialization for the KPP vertical mixing scheme
-
- This subroutine computes the vertical diffusivity and viscosity according
- to the KPP scheme of Large etal. In brief, the scheme does the
- following:
-
- --Compute interior mixing everywhere:
- interior mixing gets computed at all cell interfaces due to constant
- internal wave background activity ("visc_cbu_iw" and "diff_cbt_iw").
- Mixing is enhanced in places of static instability (local Ri < 0).
- Additionally, mixing can be enhanced by contribution from shear
- instability which is a function of the local Ri.
-
- --Double diffusion:
- Interior mixing can be enhanced by double diffusion due to salt
- fingering and diffusive convection ("double_diffusion=.true.").
-
- --Boundary layer:
-
- (A) Boundary layer depth:
- at every gridpoint the depth of the oceanic boundary layer
- ("hbl") gets computed by evaluating bulk richardson numbers.
-
- (B) Boundary layer mixing:
- within the boundary layer, above hbl, vertical mixing is
- determined by turbulent surface fluxes, and interior mixing at
- the lower boundary, i.e. at hbl.
-
- NOTE: Use smf_bgrid since this uses the primary smf array read in from
- the coupler in ocean_core/ocean_sbc.F90 when using the FMS coupler.
-
-
- The oceanic planetray boundary layer depth, hbl, is determined as
- the shallowest depth where the bulk richardson number is
- equal to the critical value, Ricr.
-
- Bulk Richardson numbers are evaluated by computing velocity and
- buoyancy differences between values at zt(kl) and surface
- reference values.
-
- In this configuration, the reference values are equal to the
- values in the surface layer.
-
- When using a very fine vertical grid, these values should be
- computed as the vertical average of velocity and buoyancy from
- the surface down to epsilon*zt(kl).
-
- When the bulk richardson number at k exceeds Ricr, hbl is
- linearly interpolated between grid levels zt(k) and zt(k-1).
-
- The water column and the surface forcing are diagnosed for
- stable/ustable forcing conditions, and where hbl is relative
- to grid points (caseA), so that conditional branches can be
- avoided in later subroutines.
-
- input
- real dbloc = local delta buoyancy (m/s^2)
- real dbsfc = delta buoyancy w/ respect to sfc(m/s)^2
- real ustar = surface friction velocity (m/s)
- real Bo = surface turbulent buoyancy forcing(m^2/s^3)
- real Bosol = radiative buoyancy forcing (m^2/s^3)
- real f = Coriolis parameter (1/s)
-
- output
- real hbl ! boundary layer depth (m)
- real bfsfc !Bo+radiation absorbed to d=hbf*hbl(m^2/s^3)
- real stable ! =1 in stable forcing; =0 unstable
- real caseA ! =1 in case A, =0 in case B
- integer kbl ! index of first grid level below hbl
-
-
- Compute turbulent velocity scales.
- Use a 2D-lookup table for wm and ws as functions of ustar and
- zetahat (=von_karman*sigma*hbl*bfsfc).
-
- Note: the lookup table is only used for unstable conditions
- (zehat <= 0), in the stable domain wm (=ws) gets computed
- directly.
-
- Note: the loop has been doubled to allow NEC compilers for vectorisation.
- Speed gain was observed at the SX-6.
- Later compiler versions may do better.
-
-
- input
- real sigma = normalized depth (d/hbl)
- real hbl = boundary layer depth (m)
- real ustar = surface friction velocity (m/s)
- real bfsfc = total surface buoyancy flux (m^2/s^3)
- output
- real wm,ws ! turbulent velocity scales at sigma
- local
- real zehat ! = zeta * ustar**3
-
-
- Compute interior viscosity and diffusivity due
- to shear instability (dependent on a local richardson number),
- to background internal wave activity, and
- to static instability (local richardson number < 0).
-
- Diffusion and viscosity coefficients are on bottom
- of T-cells.
-
-
- Rrho dependent interior flux parameterization.
- Add double-diffusion diffusivities to Ri-mix values at blending
- interface and below. salt fingering code modified july 2003
- by stephen.griffies based on NCAR CCSM2.x
-
- real talpha ! d(rho)/ d(pot.temperature) (kg/m^3/C)
- real sbeta ! d(rho)/ d(salinity) (kg/m^3/PSU)
-
- diff_cbt = diffusion coefficient at bottom of "t" cells (m**2/s)
-
- local
- real alphaDT ! alpha * DT across interfaces
- real betaDS ! beta * DS across interfaces
-
-
- Mixing coefficients within boundary layer depend on surface
- forcing and the magnitude and gradient of interior mixing below
- the boundary layer ("matching").
-
- CAUTION: if mixing bottoms out at hbl = zt(nk) then
- fictitious layer at nk+1 is needed with small but finite width
- dzt(nk+1) (eg. epsln = 1.e-20).
-
- inputs:
-
- real ustar ! surface friction velocity (m/s)
- real bfsfc ! surface buoyancy forcing (m^2/s^3)
- real hbl ! boundary layer depth (m)
- real stable ! = 1 in stable forcing
- real caseA ! = 1 in case A
- integer kbl ! index of first grid level below hbl
-
- outputs:
-
- visc_cbt = viscosity coefficient at bottom of "t" cells (m**2/s)
- diff_cbt = diffusion coefficient at bottom of "t" cells (m**2/s)
-
- real dkm1(,3) = boundary layer diff_cbt at kbl-1 level
- real blmc(,nk,3) = boundary layer mixing coeff.(m**2/s)
- real ghats(,nk) = nonlocal scalar transport
-
- local:
-
- real gat1(,3)
- real dat1(,3)
- real sigma() = normalized depth (d / hbl)
- real ws(), wm() = turbulent velocity scales (m/s)
-
-
- Enhance the diffusivity at the kbl-.5 interface
-
- input
- integer kbl = grid above hbl
- real hbl = boundary layer depth (m)
- real dkm1 = bl diffusivity at kbl-1 grid level
- real caseA = 1 in caseA, = 0 in case B
-
- input/output
- real ghats = nonlocal transport (s/m**2)
- modified ghats at kbl(i)-1 interface
- output
- real blmc = enhanced boundary layer mixing coefficient
-
- local
- real delta = fraction hbl lies beteen zt neighbors
-
-
- Initialization of watermass diagnostic output files.
-
- Diagnose effects from KPP nonlocal on the watermass transformation.
-
diff --git a/src/mom5/ocean_param/vertical/ocean_vert_mix.F90 b/src/mom5/ocean_param/vertical/ocean_vert_mix.F90
index 1aae09dc0a..9a457866df 100644
--- a/src/mom5/ocean_param/vertical/ocean_vert_mix.F90
+++ b/src/mom5/ocean_param/vertical/ocean_vert_mix.F90
@@ -1,10 +1,10 @@
module ocean_vert_mix_mod
#define COMP isc:iec,jsc:jec
!
-! S.M. Griffies
+! S.M. Griffies
!
!
-! A. Rosati
+! A. Rosati
!
!
!
@@ -661,9 +661,9 @@ module ocean_vert_mix_mod
real, dimension(:,:,:), allocatable :: flux_z
character(len=128) :: version = &
- '$Id: ocean_vert_mix.F90,v 1.1.2.19 2012/06/08 20:33:57 Stephen.Griffies Exp $'
+ '$Id: ocean_vert_mix.F90,v 20.0 2013/12/14 00:16:48 fms Exp $'
character (len=128) :: tagname = &
- '$Name: mom5_siena_08jun2012_smg $'
+ '$Name: tikal $'
logical :: module_is_initialized = .false.
logical :: debug_this_module = .false.
@@ -2784,7 +2784,7 @@ end subroutine watermass_diag_init
!
subroutine vert_mix_coeff(Time, Thickness, Velocity, T_prog, &
T_diag, Dens, swflx, sw_frac_zt, pme,&
- river, visc_cbu, visc_cbt, diff_cbt, hblt_depth)
+ river, visc_cbu, visc_cbt, diff_cbt, hblt_depth, do_wave)
type(ocean_time_type), intent(in) :: Time
type(ocean_thickness_type), intent(in) :: Thickness
@@ -2800,9 +2800,12 @@ subroutine vert_mix_coeff(Time, Thickness, Velocity, T_prog, &
real, dimension(isd:,jsd:,:), intent(inout) :: visc_cbt
real, dimension(isd:,jsd:,:,:), intent(inout) :: diff_cbt
real, dimension(isd:,jsd:), intent(inout) :: hblt_depth
+ logical, intent(in) :: do_wave
- integer :: i,j,k,kp1,tau
- real :: tmp
+ integer :: i,j,k,kp1,n,tau
+ real :: tmp, rescale
+ real :: dnu_dtheta_dz, dnu_dsalinity_dz, dtheta_dz, dsalinity_dz
+ real :: global_mean
tau = Time%tau
@@ -2826,7 +2829,7 @@ subroutine vert_mix_coeff(Time, Thickness, Velocity, T_prog, &
elseif(MIX_SCHEME == VERTMIX_KPP_MOM4P0) then
call mpp_clock_begin(id_clock_vert_kpp_mom4p0)
call vert_mix_kpp_mom4p0(aidif, Time, Thickness, Velocity, T_prog, T_diag, Dens, &
- swflx, sw_frac_zt, pme, river, visc_cbu, diff_cbt, hblt_depth)
+ swflx, sw_frac_zt, pme, river, visc_cbu, diff_cbt, hblt_depth, do_wave)
! since this scheme is frozen, we do not compute visc_cbt.
! for vertical reynolds diagnostics, we set
visc_cbt = visc_cbu
@@ -2835,7 +2838,7 @@ subroutine vert_mix_coeff(Time, Thickness, Velocity, T_prog, &
elseif(MIX_SCHEME == VERTMIX_KPP_MOM4P1) then
call mpp_clock_begin(id_clock_vert_kpp_mom4p1)
call vert_mix_kpp_mom4p1(aidif, Time, Thickness, Velocity, T_prog, T_diag, Dens, &
- swflx, sw_frac_zt, pme, river, visc_cbu, diff_cbt, hblt_depth)
+ swflx, sw_frac_zt, pme, river, visc_cbu, diff_cbt, hblt_depth, do_wave)
! since this scheme is frozen, we do not compute visc_cbt.
! for vertical reynolds diagnostics, we set
visc_cbt = visc_cbu
@@ -2843,8 +2846,8 @@ subroutine vert_mix_coeff(Time, Thickness, Velocity, T_prog, &
elseif(MIX_SCHEME == VERTMIX_KPP_TEST) then
call mpp_clock_begin(id_clock_vert_kpp_test)
- call vert_mix_kpp_test(Time, Thickness, Velocity, T_prog, T_diag, Dens, &
- swflx, sw_frac_zt, pme, river, visc_cbu, visc_cbt, diff_cbt, hblt_depth)
+ call vert_mix_kpp_test(aidif, Time, Thickness, Velocity, T_prog, T_diag, Dens, &
+ swflx, sw_frac_zt, pme, river, visc_cbu, visc_cbt, diff_cbt, hblt_depth, do_wave)
call mpp_clock_end(id_clock_vert_kpp_test)
elseif(MIX_SCHEME == VERTMIX_PP) then
diff --git a/src/mom5/ocean_param/vertical/ocean_vert_mix.html b/src/mom5/ocean_param/vertical/ocean_vert_mix.html
deleted file mode 100644
index d2e137eef7..0000000000
--- a/src/mom5/ocean_param/vertical/ocean_vert_mix.html
+++ /dev/null
@@ -1,1084 +0,0 @@
-
-
-
-Module ocean_vert_mix_mod
-
-
-
-
-PUBLIC INTERFACE
-
- ~ PUBLIC ROUTINES
- ~ NAMELIST
-
-
- This module does the following:
-
- --computes the vertical mixing coefficients for tracer and velocity,
- --computes thickness weighted and density weighted
- time tendency for tracer due to vertical diffusion processes,
- --computes the thickness weighted and density weighted
- acceleration for velocity due to vertical friction processes.
-
- Account is taken of the differences between Bgrid and Cgrid
- implementations of MOM.
-
-
- Initialization for the vertical mixing module.
-
-
-
-
-
-
-
-
diff_cbt_table_init
-
-
-DESCRIPTION
-
-
- Read in static diffusivities that have been entered to the diff_cbt_table.
-
-
-
-
-
-
-
-
bryan_lewis_init
-
-
-DESCRIPTION
-
-
- Initialize the Bryan-Lewis static background diffusivities.
-
-
-
-
-
-
-
-
hwf_init
-
-
-DESCRIPTION
-
-
- Initialize the HWF static background diffusivity.
-
- Two forms are available:
-
- 1/ Depth dependent form, meant to emulate the Bryan-Lewis approach.
- This form is not generally used at GFDL.
-
- 2/ Depth independent form motivated by use in the CM2G isopycnal
- ocean climate model at GFDL.
-
-
-
-
-
-
-
-
-
diff_cbt_tanh_init
-
-
-DESCRIPTION
-
-
- Initialize the tanh background diffusivity.
-
-
-
-
-
-
-
-
vert_friction_init
-
-
-DESCRIPTION
-
-
- Initialize vertical friction portion of ocean_vert_mix_mod
-
-
-
-
-
-
-
-
watermass_diag_init
-
-
-DESCRIPTION
-
-
- Initialization of watermass diagnostic output files.
- Also determine the logical compute_watermass_diag.
-
-
-
-
-
-
-
-
vert_mix_coeff
-
-
-DESCRIPTION
-
-
- This subroutine calls the relevant scheme to compute vertical
- diffusivity and vertical viscosity. Background values are
- also incorporated here.
-
-
-
-
-
-
-
-
vert_diffuse
-
-
-DESCRIPTION
-
-
- This subroutine computes the thickness weighted and density
- weighted time tendency for tracer associated with vertical diffusion
- based on explicit time update of the vertical diffusion equation.
-
- MOM only supports aidif==0.0 or aidif==1.0.
- MOM does not support cases with 0.0 < aidif < 1.0.
-
- The watermass diagnostics have not been ported to this subroutine
- since aidif=0 is rarely used, even in idealized studies.
-
-
-
-
-
-
-
-
-
vert_diffuse_implicit
-
-
-DESCRIPTION
-
-
- Contributions to thickness weighted and density weighted time
- tendency from time-implicit vertical diffusion.
-
-
-
-
-
-
-
-
vert_friction_bgrid
-
-
-DESCRIPTION
-
-
- This subroutine computes the thickness weighted and density weighted
- acceleration (kg/m^3)*(m^2/s^2) associated with vertical friction.
-
- Assumes here that the horizontal grid is B-grid.
-
- For aidif=1.0, this module does nothing since all vertical friction
- is in this case handled implicitly in time, and this is computed
- elswewhere.
-
- MOM only supports aidif==0.0 or aidif==1.0.
- MOM does not support cases with 0.0 < aidif < 1.0.
-
- Note that smf and bmf have units (kg/m^3)*(m^2/s^2)
- So the vertical diffusive fluxes must be in these units
- too. For this purpose, we multiply the viscosity by
- rho0. This is an approximation consistent with the
- Boussinesq approximation. For non-Boussinesq, we
- should be using the in situ rho. But to the level of
- accuracy that we know the vertical viscosity, and to
- the extent that the ocean density is close to rho0,
- our use of rho0 for the non-Boussinesq case is of
- minor consequence for vertical friction calculation.
-
- Note: the form drag contribution to vertical viscosity
- must be handled within aidif=1.0 implicit vertical
- mixing. It is ignored in this routine, as its
- contribution would generally cause the model to be
- unstable.
-
- Note: if try to merge this routine with vert_friction_cgrid
- some machines and compilers will change bits by the mere
- introduction of extra if-test logic into the calculation.
- So we define the separate routines to maintain bit-wise
- agreement with older results, with bit-wise agreement a
- useful means to check for errors as the model evolves.
-
-
-
-
-
-
-
-
-
vert_friction_cgrid
-
-
-DESCRIPTION
-
-
- This subroutine computes the thickness weighted and density weighted
- acceleration (kg/m^3)*(m^2/s^2) associated with vertical friction.
- Assumes horizontal grid is C-grid.
-
- For aidif=1.0, this module does nothing since all vertical friction
- is instead handled implicitly in time, and this is computed in the
- velocity module.
-
- MOM only supports aidif==0.0 or aidif==1.0.
- MOM does not support cases with 0.0 < aidif < 1.0.
-
- Note that smf and bmf have units (kg/m^3)*(m^2/s^2)
- So the vertical diffusive fluxes must be in these units
- too. For this purpose, we multiply the viscosity by
- rho0. This is an approximation consistent with the
- Boussinesq approximation. For non-Boussinesq, we
- should be using the in situ rho. But to the level of
- accuracy that we know the vertical viscosity, and to
- the extent that the ocean density is close to rho0,
- our use of rho0 for the non-Boussinesq case is of
- minor consequence for vertical friction calculation.
-
- Note: use visc_cbt for both C-grid velocity components,
- even though the velocity components sit at different
- sides of the tracer cell. This choice is for simplicity.
- It also acknowledges that the alternative of introducing
- distinct visc_cbt_u and visc_cbt_v would presume knowledge
- of subgrid scale features that we really do not have.
- So again, visc_cbt is used for both u,v C-grid velocity
- components.
-
- Note: the form drag contribution to vertical viscosity
- must be handled within aidif=1.0 implicit vertical
- mixing. It is ignored in this routine, as its
- contribution would generally cause the model to be
- unstable.
-
- Note: if try to merge this routine with vert_friction_cgrid
- some machines and compilers will change bits by the mere
- introduction of extra if-test logic into the calculation.
- So we define the separate routines to maintain bit-wise
- agreement with older results, with bit-wise agreement a
- useful means to check for errors as the model evolves.
-
-
-
-
-
-
-
-
-
vert_friction_implicit_bgrid
-
-
-DESCRIPTION
-
-
- Contributions to thickness weighted and density weighted acceleration
- from implicit vertical friction.
-
- Assume that the horizontal grid is B-grid.
-
- Note that smf and bmf have units N/m^2. These are the natural units
- for surface stress. To include these stresses as boundary terms in the
- call to invtri, it is necessary to use vertical viscosities with units
- (kg/m^3)*(m2^/s) = N/m^2. This is achieved by multiplying visc_cbu
- by rho0 when sent to invtri. For depth-like vertical coordinates, this
- is cancelled exactly by the rho0 in rho_dzu. For pressure-like
- vertical coordinates, the rho0*visc_cbu introduces a negligible
- change in the vertical viscosity that is well within uncertainty
- in this coefficient.
-
- Include visc_cbu_form_drag to each of the velocity components
- vertical friction.
-
- Note: if try to merge this routine with vert_friction_cgrid
- some machines and compilers will change bits by the mere
- introduction of extra if-test logic into the calculation.
- So we define the separate routines to maintain bit-wise
- agreement with older results, with bit-wise agreement a
- useful means to check for errors as the model evolves.
-
-
-
-
-
-
-
-
-
vert_friction_implicit_cgrid
-
-
-DESCRIPTION
-
-
- Contributions to thickness weighted and density weighted acceleration
- from implicit vertical friction.
-
- Assume that the horizontal grid is C-grid.
-
- Note that smf and bmf have units N/m^2. These are the natural units
- for surface stress. To include these stresses as boundary terms in the
- call to invtri, it is necessary to use vertical viscosities with units
- (kg/m^3)*(m2^/s) = N/m^2. This is achieved by multiplying visc_cbu
- by rho0 when sent to invtri. For depth-like vertical coordinates, this
- is cancelled exactly by the rho0 in rho_dzu. For pressure-like
- vertical coordinates, the rho0*visc_cbu introduces a negligible
- change in the vertical viscosity that is well within uncertainty
- in this coefficient.
-
- Include visc_cbu_form_drag to each of the velocity components
- vertical friction.
-
- Note: if try to merge this routine with vert_friction_cgrid
- some machines and compilers will change bits by the mere
- introduction of extra if-test logic into the calculation.
- So we define the separate routines to maintain bit-wise
- agreement with older results, with bit-wise agreement a
- useful means to check for errors as the model evolves.
-
- Note: use visc_cbt for both C-grid velocity components,
- even though the velocity components sit at different
- sides of the tracer cell. This choice is for simplicity.
- It also acknowledges that the alternative of introducing
- distinct visc_cbt_u and visc_cbt_v would presume knowledge
- of subgrid scale features that we really do not have.
- So again, visc_cbt is used for both u,v C-grid velocity
- components.
-
-
-
-
-
-
-
-
-
on_comp_domain
-
-
-DESCRIPTION
-
-
- Determine if the point is in comp-domain for the processor.
-
-
-
-
-
-
-
-
invcosh
-
-
-DESCRIPTION
-
-
- Inverse cosh function. Argument must be >=1.
-
-
-
-
-
-
-
-
vmix_min_dissipation
-
-
-DESCRIPTION
-
-
- Impose a floor to the dissipation arising from vertical tracer diffusion.
-
-
-
-
-
-
-
-
watermass_diag
-
-
-DESCRIPTION
-
-
- Diagnose watermass transformation diagnostics for
- --sbc
- --bbc
- --vmix = diff_cbt + K33-implicit neutral diffusion
- Estimations of the contributions from diff_cbt alone, and
- from K33-implicit alone, are computed in vert_diffuse_watermass_diag.
-
- The diagnostic for vdiffuse computes all processes in one
- invtri call, which is actually how the model prognostically
- updates tracers from vertical diffusion.
-
- The sum of the sbc + bbc + vmix should equal to the
- full vdiffuse diagnostic, so that, for example,
-
- neut_rho_vdiffuse = neut_rho_sbc + neut_rho_bbc + neut_rho_vmix
-
- Additionally, we should have
-
- neut_rho_vmix = neut_rho_diff_cbt + neut_rho_k33
-
- with the terms neut_rho_diff_cbt and neut_rho_k33 computed
- in routine vert_diffuse_watermass_diag.
-
- watermass_diag is called prior to implicit update of the tracer
- fields, so that the initial taup1 value contains only explicit
- in-time tendencies. The incremental tendencies are diagnosed
- in this routine by various calls to invtri using same methods
- as for the prognostic calculation.
-
- This routine requires the logical compute_watermass_diag=.true.,
- which is determined inside watermass_diag_init.
-
-
-
-
-
-
-
-
-
vert_diffuse_implicit_diag
-
-
-DESCRIPTION
-
-
- Diagnose contributions from time-implicit vertical diffusion.
-
- We perform the diagnostics using the taup1 value of the tracer
- concentration, obtained after performing the invtri step.
- The fluxes are diagnosed as if we are performing an explicit-time
- update, but using the taup1 values of the tracer concentrations.
-
- This diagnostic suffers from time truncation errors relative to the
- prognostic calculation, since the prognostic time update is performed using
- an invtri calculation. However, the errors are small. The alternative
- method, which is to separate the combined invtri step into individual
- physical mixing processes is not an option, since this step is not equivalent
- algorithmically to the single invtri mixing step.
- It is for this reason that we perform the diagnostic step using this
- "explicit flux computed with time-implicit computed concentration" approach.
-
- In contrast to the interior mixing, the boundary fluxes can be diagnostically
- split from the invtri step, as these fluxes are determined prior to the
- vert_diffuse_implicit routine. Hence, the boundary flux contributions can
- be diagnosed either by calling an invtri step passing just the stf and btf
- terms, or by using the even simpler methods in this subroutine.
-
-
-
-
-
-
-
-
-
vert_diffuse_watermass_diag
-
-
-DESCRIPTION
-
-
- Diagnose contributions from time-implicit vertical diffusion
- acting on watermasses from diff_cbt and k33.
-
- We perform the diagnostics using the taup1 value of the tracer
- concentration, obtained after performing the invtri step.
- The fluxes are diagnosed as if we are performing an explicit-time
- update, but using the taup1 values of the tracer concentrations.
-
- This diagnostic suffers from time truncation errors relative to the
- prognostic calculation, since the prognostic time update is performed using
- an invtri calculation. However, the errors are small. The alternative
- method, which is to separate the combined invtri step into individual
- physical mixing processes is not an option, since this step is not equivalent
- algorithmically to the single invtri mixing step.
- It is for this reason that we perform the diagnostic step using this
- "explicit flux computed with time-implicit computed concentration" approach.
-
-
-
-
-
-
-
-
-
ocean_vert_mix_restart
-
-
-DESCRIPTION
-
-
- Write out restart files registered through register_restart_file
-
-
-
-
-
-
-
-
ocean_vert_mix_end
-
-
-DESCRIPTION
-
-
- Chen Scheme requires output of Krauss mixed layer for
- reproducible results.
-
- GOTM requires fields for advection tendency.
-
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_vert_mix_nml
-
-
-
-
-
-debug_this_module
-
-
- For debugging purposes.
-
-[logical]
-
-
-aidif
-
-
- aidif=1 for implicit in time solution of the vertical mixing equation.
- aidif=0 for explicit in time solution of the vertical mixing equation.
- semi-implicit method with 0 < aidif < 1 is not fully supported in MOM.
-
-[real]
-
-
-use_explicit_vert_diffuse
-
-
- Must be true to use time-explicit vertical tracer diffusion.
-
-[logical]
-
-
-verbose_init
-
-
- For verbose writes during initialization.
-
-[logical]
-
-
-vert_mix_scheme
-
-
- To determine the vertical mixing scheme:
- "const", "kpp", "kpp_mom4p0","kpp_mom4p1", "chen", "pp", or "gotm".
-
-[character]
-
-
-vert_diff_back_via_max
-
-
- If .true. then include a static background diffusivity
- via the max function, as used in mom4p0d. The alternative
- is via simply adding the background to the diffusivity
- obtained via other approaches. This option remains for
- legacy. Default is vert_diff_back_via_max=.true.
-
-[logical]
-
-
-vert_visc_back
-
-
- If .true. then include a static depth dependent vertical
- viscosity which is used only if running w/ constant
- vertical viscosity scheme. Standard application is when
- have a model with fine vertical resolution, yet no mixed
- layer scheme. Wind stress must be spread deeper than the
- top cell, or the model may go unstable, or at the least it
- will produce spuriously large vertical shears.
-
-[logical]
-
-
-visc_cbu_back_max
-
-
- For use in setting background vertical viscosity.
-
-[real, units: m^2/sec]
-
-
-visc_cbu_back_min
-
-
- For use in setting background vertical viscosity.
-
-[real, units: m^2/sec]
-
-
-visc_cbu_back_zmid
-
-
- Mid-point of tanh function used to define background vertical viscosity.
-
-[real, units: m]
-
-
-visc_cbu_back_zwid
-
-
- Width of tanh function used to define background vertical viscosity.
-
-[real, units: m]
-
- For use in setting background vertical diffusivity.
- Default diff_cbt_tanh_max=1e-3.
-
-[real, units: m^2/sec]
-
-
-diff_cbt_tanh_min
-
-
- For use in setting background vertical diffusivity.
- Default diff_cbt_tanh_min=2e-5.
-
-[real, units: m^2/sec]
-
-
-diff_cbt_tanh_zmid
-
-
- Mid-point of tanh function used to define background vertical diffusivity.
- Default diff_cbt_tanh_zmid=150.0.
-
-[real, units: m]
-
-
-diff_cbt_tanh_zwid
-
-
- Width of tanh function used to define background vertical diffusivity.
- Default diff_cbt_tanh_zwid=30.0.
-
-[real, units: m]
-
-
-hwf_diffusivity
-
-
- 3D background diffusivity which gets smaller in equatorial region.
- Based on the work of Henyey etal (1986).
- This scheme should NOT be used if Bryan-Lewis is used.
- Default hwf_diffusivity=.false.
-
-[logical]
-
-
-hwf_diffusivity_3d
-
-
- 3D background diffusivity which gets smaller in equatorial region.
- Based on the work of Henyey etal (1986).
- This form has not been used much at GFDL, with preference given to
- a simpler two-dimensional (depth independent) form assessed with the
- default hwf_diffusivity_3d=.false.
-
-[logical]
-
-
-hwf_depth_transition
-
-
- Depth of transition for hwf scheme. The HWF method actually has
- no depth dependence. But we include the atan depth dependency
- from Bryan-Lewis, for those cases where we wish to replace
- Bryan-Lewis with the HWF scheme. To get the usual Bryan-Lewis
- transition, set hwf_depth_transition=2500.0. However, since
- we often use hwf in the presence of tide mixing, we do not wish to
- have any depth dependence, in which case the default is
- hwf_depth_transition=2500.0e4.
-
-[real, units: m]
-
-
-hwf_min_diffusivity
-
-
- Minimum diffusivity for the HWF scheme.
- Default hwf_min_diffusivity=2e-6.
-
-[real, units: m^2/sec]
-
-
-hwf_30_diffusivity
-
-
- Diffusivity at 30deg latitude for the HWF scheme.
- Default hwf_30_diffusivity=2e-5.
-
-[real, units: m^2/sec]
-
-
-hwf_N0_2Omega
-
-
- Ratio of the typical Buoyancy frequency to
- twice the earth's rotation period.
- Default hwf_N0_2Omega=20.0.
-
-[real, units: dimensionless]
-
-
-bryan_lewis_diffusivity
-
-
- If .true. then add a Bryan-Lewis background to the
- diffusivity. This background is a time-independent function
- of depth. This diffusivity is NOT used when have
- use_pp_vert_mix_coeff=.true.
- This scheme should NOT be used if HWF is used.
-
-[logical]
-
-
-bryan_lewis_lat_depend
-
-
- If .true. then allow for Bryan-Lewis background to be different
- outside of a tropical band than inside the band.
-
-[logical]
-
-
-bryan_lewis_lat_transition
-
-
- North/South latitude where transition from Bryan-Lewis values
- in the tropic to those in the higher latitudes.
-
-[real]
-
-
-afkph_90, dfkph_90, sfkph_90, zfkph_90
-
-
- Parameters setting the Bryan-Lewis vertical diffusivity profile.
- When use bryan_lewis_lat_depend, these are the values used in the pole.
-
-[real, units: dimensionless]
-
-
-afkph_00, dfkph_00, sfkph_00, zfkph_00
-
-
- Parameters setting the Bryan-Lewis vertical diffusivity profile in the tropics.
- When use bryan_lewis_lat_depend=.true. , these are the values used in the tropics.
- When use bryan_lewis_lat_depend=.false., these are the values used globally.
-
-[real, units: dimensionless]
-
-
-use_diff_cbt_table
-
-
- If .true., then read in a table that specifies (i,j,ktop-->kbottom)
- and the diffusivity. This method is useful when aiming to mix vertically
- at points where do cross-land insertion or where may wish to enhance
- mixing at river mouths.
-
-[logical]
-
-
-linear_taper_diff_cbt_table
-
-
- If .true., then linear taper the diff_cbt_table value from
- so that it gets smaller with depth.
-
-[logical]
-
-
-vmix_rescale_nonbouss
-
-
- To rescale the vertical mixing coefficients by rho0/rho
- in order to bring the effects from vertical diffusion
- in a non-Boussinesq model more in line with that from a
- Boussinesq model.
- Default vmix_rescale_nonbouss=.false.
-
-[logical]
-
-
-vmix_set_min_dissipation
-
-
- To set a minimum dissipation rate. This scheme will compute the
- dissipation from the full diffusivity. If the resulting dissipation
- is smaller than a specified dissipation, then the diffusivity will
- be locally increased so that the min dissipation is maintained.
- Default vmix_set_min_dissipation=.false.
-
-[logical]
-
-
-vmix_min_diss_const
-
-
- Minimum dissipation rate as a constant.
- Default vmix_min_diss_const=1e-7.
-
-[real, units: W/m^3]
-
-
-vmix_min_diss_bvfreq_scale
-
-
- Scaling use to set the minimum dissipation rate as determined by the
- local stratification.
- Default vmix_min_diss_bvfreq_scale=6e-4.
-
-[real, units: J/m^3]
-
-
-vmix_min_diss_flux_ri_max
-
-
- Maximum flux Richardson number for computation of diffusivity from dissipation.
- Default vmix_min_diss_flux_ri_max=0.2.
-
-[real, units: dimensionless]
-
-
-
-
-
-
-
-
-
-
-
REFERENCES
-
-
-
-
- Kirk Bryan and L.J. Lewis
- A water mass model of the world ocean
- Journal of Geophysical Research (1979) vol 84, pages 2503--2517
-
-
- Elements of MOM (2012)
- S.M. Griffies
-
-
- Henyey, F.S., J. Wright, and S.M. Flatte, 1986: Energy and
- action flow through the internal wave field: an eikonal approach.
- Journal of Geophysical Research, {\bf 91}, Issue C7, 8487--8496.
-
-
-
-
-
-
-
-
NOTES
-
-
- The Bryan-Lewis vertical diffusivity is small in the upper ocean and
- increases with depth according to an inverse tangent profile. The default
- values are from roughly 0.05e-5 m^2/sec to roughly 1.0e-4 m^2/sec.
- Latitudinally dependent Bryan-Lewis values are available.
-
-
-
diff --git a/src/mom5/ocean_param/vertical/ocean_vert_mix.xml b/src/mom5/ocean_param/vertical/ocean_vert_mix.xml
deleted file mode 100644
index fa85381c77..0000000000
--- a/src/mom5/ocean_param/vertical/ocean_vert_mix.xml
+++ /dev/null
@@ -1,438 +0,0 @@
-
-
- S.M. Griffies
- A. Rosati
-
- Time tendency from vertical mixing
-
- This module does the following:
-
- --computes the vertical mixing coefficients for tracer and velocity,
- --computes thickness weighted and density weighted
- time tendency for tracer due to vertical diffusion processes,
- --computes the thickness weighted and density weighted
- acceleration for velocity due to vertical friction processes.
-
- Account is taken of the differences between Bgrid and Cgrid
- implementations of MOM.
-
-
- Kirk Bryan and L.J. Lewis
- A water mass model of the world ocean
- Journal of Geophysical Research (1979) vol 84, pages 2503--2517
-
- Elements of MOM (2012)
- S.M. Griffies
-
- Henyey, F.S., J. Wright, and S.M. Flatte, 1986: Energy and
- action flow through the internal wave field: an eikonal approach.
- Journal of Geophysical Research, {\bf 91}, Issue C7, 8487--8496.
-
- The Bryan-Lewis vertical diffusivity is small in the upper ocean and
- increases with depth according to an inverse tangent profile. The default
- values are from roughly 0.05e-5 m^2/sec to roughly 1.0e-4 m^2/sec.
- Latitudinally dependent Bryan-Lewis values are available.
-
- For debugging purposes.
-
- aidif=1 for implicit in time solution of the vertical mixing equation.
- aidif=0 for explicit in time solution of the vertical mixing equation.
- semi-implicit method with 0 < aidif < 1 is not fully supported in MOM.
-
- Must be true to use time-explicit vertical tracer diffusion.
-
- For verbose writes during initialization.
-
- To determine the vertical mixing scheme:
- "const", "kpp", "kpp_mom4p0","kpp_mom4p1", "chen", "pp", or "gotm".
-
- If .true. then include a static background diffusivity
- via the max function, as used in mom4p0d. The alternative
- is via simply adding the background to the diffusivity
- obtained via other approaches. This option remains for
- legacy. Default is vert_diff_back_via_max=.true.
-
- If .true. then include a static depth dependent vertical
- viscosity which is used only if running w/ constant
- vertical viscosity scheme. Standard application is when
- have a model with fine vertical resolution, yet no mixed
- layer scheme. Wind stress must be spread deeper than the
- top cell, or the model may go unstable, or at the least it
- will produce spuriously large vertical shears.
-
- For use in setting background vertical viscosity.
-
- For use in setting background vertical viscosity.
-
- Mid-point of tanh function used to define background vertical viscosity.
-
- Width of tanh function used to define background vertical viscosity.
-
- For enabling tanh background vertical diffusivity profile.
- Default diff_cbt_tanh=.false.
-
- For use in setting background vertical diffusivity.
- Default diff_cbt_tanh_max=1e-3.
-
- For use in setting background vertical diffusivity.
- Default diff_cbt_tanh_min=2e-5.
-
- Mid-point of tanh function used to define background vertical diffusivity.
- Default diff_cbt_tanh_zmid=150.0.
-
- Width of tanh function used to define background vertical diffusivity.
- Default diff_cbt_tanh_zwid=30.0.
-
- 3D background diffusivity which gets smaller in equatorial region.
- Based on the work of Henyey etal (1986).
- This scheme should NOT be used if Bryan-Lewis is used.
- Default hwf_diffusivity=.false.
-
- 3D background diffusivity which gets smaller in equatorial region.
- Based on the work of Henyey etal (1986).
- This form has not been used much at GFDL, with preference given to
- a simpler two-dimensional (depth independent) form assessed with the
- default hwf_diffusivity_3d=.false.
-
- Depth of transition for hwf scheme. The HWF method actually has
- no depth dependence. But we include the atan depth dependency
- from Bryan-Lewis, for those cases where we wish to replace
- Bryan-Lewis with the HWF scheme. To get the usual Bryan-Lewis
- transition, set hwf_depth_transition=2500.0. However, since
- we often use hwf in the presence of tide mixing, we do not wish to
- have any depth dependence, in which case the default is
- hwf_depth_transition=2500.0e4.
-
- Minimum diffusivity for the HWF scheme.
- Default hwf_min_diffusivity=2e-6.
-
- Diffusivity at 30deg latitude for the HWF scheme.
- Default hwf_30_diffusivity=2e-5.
-
- Ratio of the typical Buoyancy frequency to
- twice the earth's rotation period.
- Default hwf_N0_2Omega=20.0.
-
- If .true. then add a Bryan-Lewis background to the
- diffusivity. This background is a time-independent function
- of depth. This diffusivity is NOT used when have
- use_pp_vert_mix_coeff=.true.
- This scheme should NOT be used if HWF is used.
-
- If .true. then allow for Bryan-Lewis background to be different
- outside of a tropical band than inside the band.
-
- North/South latitude where transition from Bryan-Lewis values
- in the tropic to those in the higher latitudes.
-
- Parameters setting the Bryan-Lewis vertical diffusivity profile.
- When use bryan_lewis_lat_depend, these are the values used in the pole.
-
- Parameters setting the Bryan-Lewis vertical diffusivity profile in the tropics.
- When use bryan_lewis_lat_depend=.true. , these are the values used in the tropics.
- When use bryan_lewis_lat_depend=.false., these are the values used globally.
-
- If .true., then read in a table that specifies (i,j,ktop-->kbottom)
- and the diffusivity. This method is useful when aiming to mix vertically
- at points where do cross-land insertion or where may wish to enhance
- mixing at river mouths.
-
- If .true., then linear taper the diff_cbt_table value from
- so that it gets smaller with depth.
-
- To rescale the vertical mixing coefficients by rho0/rho
- in order to bring the effects from vertical diffusion
- in a non-Boussinesq model more in line with that from a
- Boussinesq model.
- Default vmix_rescale_nonbouss=.false.
-
- To set a minimum dissipation rate. This scheme will compute the
- dissipation from the full diffusivity. If the resulting dissipation
- is smaller than a specified dissipation, then the diffusivity will
- be locally increased so that the min dissipation is maintained.
- Default vmix_set_min_dissipation=.false.
-
- Minimum dissipation rate as a constant.
- Default vmix_min_diss_const=1e-7.
-
- Scaling use to set the minimum dissipation rate as determined by the
- local stratification.
- Default vmix_min_diss_bvfreq_scale=6e-4.
-
- Maximum flux Richardson number for computation of diffusivity from dissipation.
- Default vmix_min_diss_flux_ri_max=0.2.
-
- Initialization for the vertical mixing module.
-
- Read in static diffusivities that have been entered to the diff_cbt_table.
-
- Initialize the Bryan-Lewis static background diffusivities.
-
- Initialize the HWF static background diffusivity.
-
- Two forms are available:
-
- 1/ Depth dependent form, meant to emulate the Bryan-Lewis approach.
- This form is not generally used at GFDL.
-
- 2/ Depth independent form motivated by use in the CM2G isopycnal
- ocean climate model at GFDL.
-
-
- Initialize the tanh background diffusivity.
-
- Initialize vertical friction portion of ocean_vert_mix_mod
-
- Initialization of watermass diagnostic output files.
- Also determine the logical compute_watermass_diag.
-
- This subroutine calls the relevant scheme to compute vertical
- diffusivity and vertical viscosity. Background values are
- also incorporated here.
-
- This subroutine computes the thickness weighted and density
- weighted time tendency for tracer associated with vertical diffusion
- based on explicit time update of the vertical diffusion equation.
-
- MOM only supports aidif==0.0 or aidif==1.0.
- MOM does not support cases with 0.0 < aidif < 1.0.
-
- The watermass diagnostics have not been ported to this subroutine
- since aidif=0 is rarely used, even in idealized studies.
-
-
- Contributions to thickness weighted and density weighted time
- tendency from time-implicit vertical diffusion.
-
- This subroutine computes the thickness weighted and density weighted
- acceleration (kg/m^3)*(m^2/s^2) associated with vertical friction.
-
- Assumes here that the horizontal grid is B-grid.
-
- For aidif=1.0, this module does nothing since all vertical friction
- is in this case handled implicitly in time, and this is computed
- elswewhere.
-
- MOM only supports aidif==0.0 or aidif==1.0.
- MOM does not support cases with 0.0 < aidif < 1.0.
-
- Note that smf and bmf have units (kg/m^3)*(m^2/s^2)
- So the vertical diffusive fluxes must be in these units
- too. For this purpose, we multiply the viscosity by
- rho0. This is an approximation consistent with the
- Boussinesq approximation. For non-Boussinesq, we
- should be using the in situ rho. But to the level of
- accuracy that we know the vertical viscosity, and to
- the extent that the ocean density is close to rho0,
- our use of rho0 for the non-Boussinesq case is of
- minor consequence for vertical friction calculation.
-
- Note: the form drag contribution to vertical viscosity
- must be handled within aidif=1.0 implicit vertical
- mixing. It is ignored in this routine, as its
- contribution would generally cause the model to be
- unstable.
-
- Note: if try to merge this routine with vert_friction_cgrid
- some machines and compilers will change bits by the mere
- introduction of extra if-test logic into the calculation.
- So we define the separate routines to maintain bit-wise
- agreement with older results, with bit-wise agreement a
- useful means to check for errors as the model evolves.
-
-
- This subroutine computes the thickness weighted and density weighted
- acceleration (kg/m^3)*(m^2/s^2) associated with vertical friction.
- Assumes horizontal grid is C-grid.
-
- For aidif=1.0, this module does nothing since all vertical friction
- is instead handled implicitly in time, and this is computed in the
- velocity module.
-
- MOM only supports aidif==0.0 or aidif==1.0.
- MOM does not support cases with 0.0 < aidif < 1.0.
-
- Note that smf and bmf have units (kg/m^3)*(m^2/s^2)
- So the vertical diffusive fluxes must be in these units
- too. For this purpose, we multiply the viscosity by
- rho0. This is an approximation consistent with the
- Boussinesq approximation. For non-Boussinesq, we
- should be using the in situ rho. But to the level of
- accuracy that we know the vertical viscosity, and to
- the extent that the ocean density is close to rho0,
- our use of rho0 for the non-Boussinesq case is of
- minor consequence for vertical friction calculation.
-
- Note: use visc_cbt for both C-grid velocity components,
- even though the velocity components sit at different
- sides of the tracer cell. This choice is for simplicity.
- It also acknowledges that the alternative of introducing
- distinct visc_cbt_u and visc_cbt_v would presume knowledge
- of subgrid scale features that we really do not have.
- So again, visc_cbt is used for both u,v C-grid velocity
- components.
-
- Note: the form drag contribution to vertical viscosity
- must be handled within aidif=1.0 implicit vertical
- mixing. It is ignored in this routine, as its
- contribution would generally cause the model to be
- unstable.
-
- Note: if try to merge this routine with vert_friction_cgrid
- some machines and compilers will change bits by the mere
- introduction of extra if-test logic into the calculation.
- So we define the separate routines to maintain bit-wise
- agreement with older results, with bit-wise agreement a
- useful means to check for errors as the model evolves.
-
-
- Contributions to thickness weighted and density weighted acceleration
- from implicit vertical friction.
-
- Assume that the horizontal grid is B-grid.
-
- Note that smf and bmf have units N/m^2. These are the natural units
- for surface stress. To include these stresses as boundary terms in the
- call to invtri, it is necessary to use vertical viscosities with units
- (kg/m^3)*(m2^/s) = N/m^2. This is achieved by multiplying visc_cbu
- by rho0 when sent to invtri. For depth-like vertical coordinates, this
- is cancelled exactly by the rho0 in rho_dzu. For pressure-like
- vertical coordinates, the rho0*visc_cbu introduces a negligible
- change in the vertical viscosity that is well within uncertainty
- in this coefficient.
-
- Include visc_cbu_form_drag to each of the velocity components
- vertical friction.
-
- Note: if try to merge this routine with vert_friction_cgrid
- some machines and compilers will change bits by the mere
- introduction of extra if-test logic into the calculation.
- So we define the separate routines to maintain bit-wise
- agreement with older results, with bit-wise agreement a
- useful means to check for errors as the model evolves.
-
-
- Contributions to thickness weighted and density weighted acceleration
- from implicit vertical friction.
-
- Assume that the horizontal grid is C-grid.
-
- Note that smf and bmf have units N/m^2. These are the natural units
- for surface stress. To include these stresses as boundary terms in the
- call to invtri, it is necessary to use vertical viscosities with units
- (kg/m^3)*(m2^/s) = N/m^2. This is achieved by multiplying visc_cbu
- by rho0 when sent to invtri. For depth-like vertical coordinates, this
- is cancelled exactly by the rho0 in rho_dzu. For pressure-like
- vertical coordinates, the rho0*visc_cbu introduces a negligible
- change in the vertical viscosity that is well within uncertainty
- in this coefficient.
-
- Include visc_cbu_form_drag to each of the velocity components
- vertical friction.
-
- Note: if try to merge this routine with vert_friction_cgrid
- some machines and compilers will change bits by the mere
- introduction of extra if-test logic into the calculation.
- So we define the separate routines to maintain bit-wise
- agreement with older results, with bit-wise agreement a
- useful means to check for errors as the model evolves.
-
- Note: use visc_cbt for both C-grid velocity components,
- even though the velocity components sit at different
- sides of the tracer cell. This choice is for simplicity.
- It also acknowledges that the alternative of introducing
- distinct visc_cbt_u and visc_cbt_v would presume knowledge
- of subgrid scale features that we really do not have.
- So again, visc_cbt is used for both u,v C-grid velocity
- components.
-
-
- Determine if the point is in comp-domain for the processor.
-
- Inverse cosh function. Argument must be >=1.
-
- Impose a floor to the dissipation arising from vertical tracer diffusion.
-
- Diagnose watermass transformation diagnostics for
- --sbc
- --bbc
- --vmix = diff_cbt + K33-implicit neutral diffusion
- Estimations of the contributions from diff_cbt alone, and
- from K33-implicit alone, are computed in vert_diffuse_watermass_diag.
-
- The diagnostic for vdiffuse computes all processes in one
- invtri call, which is actually how the model prognostically
- updates tracers from vertical diffusion.
-
- The sum of the sbc + bbc + vmix should equal to the
- full vdiffuse diagnostic, so that, for example,
-
- neut_rho_vdiffuse = neut_rho_sbc + neut_rho_bbc + neut_rho_vmix
-
- Additionally, we should have
-
- neut_rho_vmix = neut_rho_diff_cbt + neut_rho_k33
-
- with the terms neut_rho_diff_cbt and neut_rho_k33 computed
- in routine vert_diffuse_watermass_diag.
-
- watermass_diag is called prior to implicit update of the tracer
- fields, so that the initial taup1 value contains only explicit
- in-time tendencies. The incremental tendencies are diagnosed
- in this routine by various calls to invtri using same methods
- as for the prognostic calculation.
-
- This routine requires the logical compute_watermass_diag=.true.,
- which is determined inside watermass_diag_init.
-
-
- Diagnose contributions from time-implicit vertical diffusion.
-
- We perform the diagnostics using the taup1 value of the tracer
- concentration, obtained after performing the invtri step.
- The fluxes are diagnosed as if we are performing an explicit-time
- update, but using the taup1 values of the tracer concentrations.
-
- This diagnostic suffers from time truncation errors relative to the
- prognostic calculation, since the prognostic time update is performed using
- an invtri calculation. However, the errors are small. The alternative
- method, which is to separate the combined invtri step into individual
- physical mixing processes is not an option, since this step is not equivalent
- algorithmically to the single invtri mixing step.
- It is for this reason that we perform the diagnostic step using this
- "explicit flux computed with time-implicit computed concentration" approach.
-
- In contrast to the interior mixing, the boundary fluxes can be diagnostically
- split from the invtri step, as these fluxes are determined prior to the
- vert_diffuse_implicit routine. Hence, the boundary flux contributions can
- be diagnosed either by calling an invtri step passing just the stf and btf
- terms, or by using the even simpler methods in this subroutine.
-
-
- Diagnose contributions from time-implicit vertical diffusion
- acting on watermasses from diff_cbt and k33.
-
- We perform the diagnostics using the taup1 value of the tracer
- concentration, obtained after performing the invtri step.
- The fluxes are diagnosed as if we are performing an explicit-time
- update, but using the taup1 values of the tracer concentrations.
-
- This diagnostic suffers from time truncation errors relative to the
- prognostic calculation, since the prognostic time update is performed using
- an invtri calculation. However, the errors are small. The alternative
- method, which is to separate the combined invtri step into individual
- physical mixing processes is not an option, since this step is not equivalent
- algorithmically to the single invtri mixing step.
- It is for this reason that we perform the diagnostic step using this
- "explicit flux computed with time-implicit computed concentration" approach.
-
-
- Write out restart files registered through register_restart_file
-
- Chen Scheme requires output of Krauss mixed layer for
- reproducible results.
-
- GOTM requires fields for advection tendency.
-
-
diff --git a/src/mom5/ocean_param/vertical/ocean_vert_pp.F90 b/src/mom5/ocean_param/vertical/ocean_vert_pp.F90
index 88a2746f0a..cd48bbf737 100644
--- a/src/mom5/ocean_param/vertical/ocean_vert_pp.F90
+++ b/src/mom5/ocean_param/vertical/ocean_vert_pp.F90
@@ -97,10 +97,10 @@ module ocean_vert_pp_mod
integer :: horz_grid
character(len=128) :: version = &
- '$Id: ocean_vert_pp.F90,v 1.1.2.4 2012/06/03 00:41:57 Stephen.Griffies Exp $'
+ '$Id: ocean_vert_pp.F90,v 20.0 2013/12/14 00:16:50 fms Exp $'
character (len=128) :: tagname = &
- '$Name: mom5_siena_08jun2012_smg $'
+ '$Name: tikal $'
! for diagnostics
integer :: id_diff_cbt_pp= -1
diff --git a/src/mom5/ocean_param/vertical/ocean_vert_pp.html b/src/mom5/ocean_param/vertical/ocean_vert_pp.html
deleted file mode 100644
index 7ca2f7be93..0000000000
--- a/src/mom5/ocean_param/vertical/ocean_vert_pp.html
+++ /dev/null
@@ -1,283 +0,0 @@
-
-
-
-Module ocean_vert_pp_mod
-
-
-
-
-PUBLIC INTERFACE
-
- ~ PUBLIC ROUTINES
- ~ NAMELIST
-
-
- Vertical viscosity and diffusivity according Pacanowski and Philander (1981)
-
-
-
-
-
- This module computes vertical viscosity and diffusivity according to
- Pacanowski and Philander (1981). This scheme is most effective for
- studies of the tropical circulation. It computes the vertical mixing
- coefficient based on the Richardson number.
-
- Initialization for the Pacanowski/Philander vertical mixing scheme
-
- input:
-
- dzt = thickness of vertical levels (m)
-
- nk = number of vertical levels
-
- yt = latitude of grid points (deg)
-
- nj = number of latitudes
-
- error = logical to signal problems
-
- output:
-
- wndmix = min value for mixing at surface to simulate high freq
-
- wind mixing (if absent in forcing). (m^2/sec)
-
- fricmx = maximum mixing (m^2/sec)
-
- diff_cbt_back_pp = background "diff_cbt" (m^2/sec)
-
- visc_cbu_back_pp = background "visc_cbu" (m^2/sec)
-
- diff_cbt_limit = largest "diff_cbt" (m^2/sec)
-
- visc_cbu_limit = largest "visc_cbu" (m^2/sec)
-
- error = true if some inconsistency was found
-
-
-
-
-
-
-
-
-
vert_mix_pp
-
-
-DESCRIPTION
-
-
- This subroutine computes the vertical diffusivity and viscosity
- according to the Pacanowski and Philander scheme. Mixing coefficients
- are space and time dependent.
-
- inputs:
-
- nk = number of vertical levels
- grav = gravity (m/sec^2)
- fricmx = max viscosity (m^2/sec)
- wndmix = min viscosity at bottom of 1st level to simulate
- missing high frequency windstress components (m^2/sec)
- visc_cbu_back_pp = background "visc_cbu" (m^2/sec)
- diff_cbt_back_pp = background "diff_cbt" (m^2/sec)
- visc_cbu_limit = largest "visc_cbu" in regions of gravitational
- instability (m^2/sec)
- diff_cbt_limit = largest "diff_cbt" in regions of gravitational
- instability (m^2/sec)
- riu = richardson number at bottom of U cells
- rit = richardson number at bottom of T cells
-
- outputs:
-
- visc_cbu = viscosity at bottom of U cells (m^2/s)
- visc_cbt = viscosity at bottom of T cells (m^2/s)
- diff_cbt = diffusion at bottom of T cells (m^2/s)
-
-
-
-
-
-
-
-
-
ri_for_pp
-
-
-DESCRIPTION
-
-
- Compute richardson number for the pp scheme
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_vert_pp_nml
-
-
-
-
-
-use_this_module
-
-
- Must be true to use this module. Default is false.
-
-[logical]
-
-
-wndmix
-
-
- Minimum viscosity at bottom of 1st level to simulate
- missing high frequency windstress components.
-
-[real, units: m^2/sec]
-
-
-fricmx
-
-
- Maximum mixing
-
-[real, units: m^2/sec]
-
-
-diff_cbt_back_pp
-
-
- Space-time independent background vertical diffusivity
- thought to be that arising from internal waves. Note that
- if using Bryan-Lewis background diffusivity, then should
- set diff_cbt_back_pp=0.0.
-
-[real, units: m^2/sec]
-
- R.C. Pacanowski and G. Philander
- Parametrization of vertical mixing in numerical models of the tropical ocean
- Journal of Physical Oceanography (1981) vol 11, pages 1442--1451
-
-
-
-
-
-
-
-
NOTES
-
-
- This parameterization was designed for equatorial models
- and may not do a good job in mid or high latitudes. Simulations
- in these regions (where vertical shear is small) are improved with
- the addition of solar short wave penetration into the ocean which
- reduces buoyancy and enhances vertical mixing.
-
-
-
diff --git a/src/mom5/ocean_param/vertical/ocean_vert_pp.xml b/src/mom5/ocean_param/vertical/ocean_vert_pp.xml
deleted file mode 100644
index 51f88e3c89..0000000000
--- a/src/mom5/ocean_param/vertical/ocean_vert_pp.xml
+++ /dev/null
@@ -1,98 +0,0 @@
-
-
- Stephen Griffies
-
- Vertical viscosity and diffusivity according Pacanowski and Philander (1981)
-
- This module computes vertical viscosity and diffusivity according to
- Pacanowski and Philander (1981). This scheme is most effective for
- studies of the tropical circulation. It computes the vertical mixing
- coefficient based on the Richardson number.
-
- R.C. Pacanowski and G. Philander
- Parametrization of vertical mixing in numerical models of the tropical ocean
- Journal of Physical Oceanography (1981) vol 11, pages 1442--1451
-
- This parameterization was designed for equatorial models
- and may not do a good job in mid or high latitudes. Simulations
- in these regions (where vertical shear is small) are improved with
- the addition of solar short wave penetration into the ocean which
- reduces buoyancy and enhances vertical mixing.
-
- Must be true to use this module. Default is false.
-
- Minimum viscosity at bottom of 1st level to simulate
- missing high frequency windstress components.
-
- Maximum mixing
-
- Space-time independent background vertical diffusivity
- thought to be that arising from internal waves. Note that
- if using Bryan-Lewis background diffusivity, then should
- set diff_cbt_back_pp=0.0.
-
- Background vertical viscosity
-
- Initialization for the Pacanowski/Philander vertical mixing scheme
-
- input:
-
- dzt = thickness of vertical levels (m)
-
- nk = number of vertical levels
-
- yt = latitude of grid points (deg)
-
- nj = number of latitudes
-
- error = logical to signal problems
-
- output:
-
- wndmix = min value for mixing at surface to simulate high freq
-
- wind mixing (if absent in forcing). (m^2/sec)
-
- fricmx = maximum mixing (m^2/sec)
-
- diff_cbt_back_pp = background "diff_cbt" (m^2/sec)
-
- visc_cbu_back_pp = background "visc_cbu" (m^2/sec)
-
- diff_cbt_limit = largest "diff_cbt" (m^2/sec)
-
- visc_cbu_limit = largest "visc_cbu" (m^2/sec)
-
- error = true if some inconsistency was found
-
-
- This subroutine computes the vertical diffusivity and viscosity
- according to the Pacanowski and Philander scheme. Mixing coefficients
- are space and time dependent.
-
- inputs:
-
- nk = number of vertical levels
- grav = gravity (m/sec^2)
- fricmx = max viscosity (m^2/sec)
- wndmix = min viscosity at bottom of 1st level to simulate
- missing high frequency windstress components (m^2/sec)
- visc_cbu_back_pp = background "visc_cbu" (m^2/sec)
- diff_cbt_back_pp = background "diff_cbt" (m^2/sec)
- visc_cbu_limit = largest "visc_cbu" in regions of gravitational
- instability (m^2/sec)
- diff_cbt_limit = largest "diff_cbt" in regions of gravitational
- instability (m^2/sec)
- riu = richardson number at bottom of U cells
- rit = richardson number at bottom of T cells
-
- outputs:
-
- visc_cbu = viscosity at bottom of U cells (m^2/s)
- visc_cbt = viscosity at bottom of T cells (m^2/s)
- diff_cbt = diffusion at bottom of T cells (m^2/s)
-
-
- Compute richardson number for the pp scheme
-
diff --git a/src/mom5/ocean_param/vertical/ocean_vert_tidal.F90 b/src/mom5/ocean_param/vertical/ocean_vert_tidal.F90
index 6caf12c91a..28fe3a7b32 100644
--- a/src/mom5/ocean_param/vertical/ocean_vert_tidal.F90
+++ b/src/mom5/ocean_param/vertical/ocean_vert_tidal.F90
@@ -409,7 +409,7 @@ module ocean_vert_tidal_mod
type(ocean_grid_type), pointer :: Grd => NULL()
character(len=128) :: version='$$'
-character (len=128) :: tagname = '$Name: mom5_siena_08jun2012_smg $'
+character (len=128) :: tagname = '$Name: tikal $'
public vert_mix_tidal
public ocean_vert_tidal_init
diff --git a/src/mom5/ocean_param/vertical/ocean_vert_tidal.html b/src/mom5/ocean_param/vertical/ocean_vert_tidal.html
deleted file mode 100644
index 4e873a68e3..0000000000
--- a/src/mom5/ocean_param/vertical/ocean_vert_tidal.html
+++ /dev/null
@@ -1,852 +0,0 @@
-
-
-
-Module ocean_vert_tidal_mod
-
-
-
-
-PUBLIC INTERFACE
-
- ~ PUBLIC ROUTINES
- ~ NAMELIST
-
-
- This module computes a vertical diffusivity and vertical
- viscosity deduced from barotropic and baroclinic tidal
- dissipation. Assume Prandtl number unity.
-
-
-
-
-
- This module computes a vertical diffusivity and vertical
- viscosity deduced from barotropic and baroclinic tidal
- dissipation. For the baroclinic dissipation, we follow
- Simmons etal, and for the barotropic dissipation we follow
- Lee etal. Assume Prandtl number unity.
-
- This code is more general than that in the ocean_vert_kpp_mom4p0_mod.
- The KPP_mom4p0 code remains part of MOM for legacy purposes.
-
- Initialization for the ocean_vert_tidal module.
-
-
-
-
-
-
-
-
vert_mix_tidal
-
-
-DESCRIPTION
-
-
- This subroutine computes vertical tracer diffusivity and viscosity
- based on one or both of the following dissipation mechanisms:
-
- 1. internal wave breaking as parameterized by Simmons etal.
-
- 2. barotropic tides feeling the bottom drag, as parameterized by
- Lee etal.
-
-
-
-
-
-
-
-
-
compute_bvfreq
-
-
-DESCRIPTION
-
-
- This subroutine computes the absolute value of rho*N^2 and abs of
- N^2, with N^2 the squared Brunt-Vaisala (or buoyancy) frequency.
-
-
-
-
-
-
-
-
-
vert_mix_wave
-
-
-DESCRIPTION
-
-
- This subroutine computes dia-surface tracer diffusivity based on the
- methods of Simmons et al., which consider dissipation from breaking
- internal gravity waves and their conversion into local dia-surface
- mixing, which is parameterized as diffusion.
-
- Also compute a prototype parameterization of mixing due to
- breaking leewaves from Nikurashin.
-
- We assume a unit Prandtl number.
-
- Note that if umask(i,j,k) is 1.0, then so is
- tmask(i,j,k), tmask(i+1,j,k), tmask(i,j+1,k), and tmask(i+1,j+1,k).
- So there is no need to compute the "active_cells" when doing the
- space average to go from t-cell to u-cell to compute visc_cbu.
-
-
-
-
-
-
-
-
-
vert_mix_drag_bgrid
-
-
-DESCRIPTION
-
-
- This subroutine computes dia-surface tracer diffusivity based on the
- methods of Lee etal., which consider the dissipation from barotropic tides
- rubbing against the ocean bottom.
-
- We assume B-grid layout for the velocity
-
- We assume a unit Prandtl number, so compute the viscosity as a four-point
- average of the diffusivity.
-
- We perform various averages here in order to smooth Richardson number.
-
- 1. compute Richardson number on U-cell by averaging bvfreq from T-cell
- 2. average U-cell Richardson number to then get T-cell diffusivity
- 3. average T-cell diffusivity to get U-cell viscosity.
-
- Note that if umask(i,j,k)==1.0, then so is tmask(i,j,k), tmask(i+1,j,k),
- tmask(i,j+1,k), and tmask(i+1,j+1,k). So there is no need to compute
- active_cells when averaging from T-cell to U-cell.
-
-
-
-
-
-
-
-
-
vert_mix_drag_cgrid
-
-
-DESCRIPTION
-
-
- This subroutine computes dia-surface tracer diffusivity based on the
- methods of Lee etal., which consider the dissipation from barotropic tides
- rubbing against the ocean bottom.
-
- We assume a unit Prandtl number, so compute the viscosity as a four-point
- average of the diffusivity.
-
- We assume C-grid layout for the velocity, which renders slight
- distinctions for the calculation of Richardson number. Otherwise, the
- calculations are the same as the Bgrid. We introduce this separate
- routine, however, to enable easier bitwise agreement with older
- model results. Also, further development of this scheme may lead
- to more distinctions from the Bgrid.
-
-
-
-
-
-
-
-
-
compute_bvfreq_legacy
-
-
-DESCRIPTION
-
-
- This subroutine computes the absolute value of rho*N^2 and abs of
- N^2, with N^2 the squared Brunt-Vaisala (or buoyancy) frequency.
-
- This routine employs a legacy approach, which is not recommended.
- It remains solely to allow exact reproduction of older results.
-
-
-
-
-
-
-
-
-
vert_mix_wave_legacy
-
-
-DESCRIPTION
-
-
-
- Legacy routine maintained only to exactly reproduce older results.
- It is not recommended for new experiments, as it uses some obsolete
- methods.
-
- This subroutine computes dia-surface tracer diffusivity based on the
- methods of Simmons etal., which consider the dissipation from breaking
- internal gravity waves and their conversion into local dia-surface
- diffusion.
-
- We assume a unit Prandtl number, so compute the viscosity as a four-point
- average of the diffusivity.
-
- Note that if umask(i,j,k) is 1.0, then so is
- tmask(i,j,k), tmask(i+1,j,k), tmask(i,j+1,k), and tmask(i+1,j+1,k).
- So there is no need to compute the "active_cells" when doing the
- space average to go from t-cell to u-cell to compute viscosity.
-
-
-
-
-
-
-
-
-
vert_mix_drag_legacy
-
-
-DESCRIPTION
-
-
-
- Legacy routine maintained only to exactly reproduce older results.
- It is not recommended for new experiments, as it uses some obsolete
- methods.
-
- This subroutine computes dia-surface tracer diffusivity based on the
- methods of Lee etal., which consider the dissipation from barotropic tides
- rubbing against the ocean bottom.
-
- We assume a unit Prandtl number, so compute the viscosity as a four-point
- average of the diffusivity.
-
- We perform various averages here in order to smooth Richardson number.
-
- 1. compute Richardson number on U-cell by averaging bvfreq from T-cell
- 2. average U-cell Richardson number to then get T-cell diffusivity
- 3. average T-cell diffusivity to get U-cell viscosity.
-
- Note that if umask(i,j,k)==1.0, then so is tmask(i,j,k), tmask(i+1,j,k),
- tmask(i,j+1,k), and tmask(i+1,j+1,k). So there is no need to compute
- active_cells when averaging from T-cell to U-cell.
-
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_vert_tidal_nml
-
-
-
-
-
-use_this_module=
-
-
- Must be .true. to use this module. Default is false.
-
-[logical]
-
-
-debug_this_module
-
-
- For debugging purposes.
-
-[logical]
-
-
-use_wave_dissipation=
-
-
- Set to .true. for using the Simmons etal scheme for
- obtaining a diffusivity and viscosity based on internal
- wave breaking. This is a general form of the KPP
- scheme "int_tidal_mix".
- Default use_wave_dissipation=.false.
-
-[logical]
-
-
-use_drag_dissipation=
-
-
- Set to .true. for using the Lee etal scheme for
- obtaining a diffusivity and viscosity based on drag
- of barotropic tides on bottom. This is a general
- form of the KPP scheme "coastal_tidal_mix".
- Default use_drag_dissipation=.false.
-
-[logical]
-
-
-use_leewave_dissipation=
-
-
- Set to .true. for using a prototype Nikurashin scheme for
- obtaining a diffusivity and viscosity based on breaking
- leewaves. This scheme is not related to tides, but it
- is incorporated to the baroclinic tide parameterization scheme
- as a prototype. It will be placed into ts own module when
- the parameterization matures.
- Default use_leewave_dissipation=.false.
-
-[logical]
-
-
-read_leewave_dissipation
-
-
- If .true. then read in leewave dissipation from a file.
- Default read_leewave_dissipation=.false.
-
-[logical]
-
-
-read_wave_dissipation
-
-
- If .true. then read in wave dissipation computed from
- Jayne and St.Laurent (2001) tide model (or another model).
- Default read_wave_dissipation=.false.
-
-[logical]
-
-
-fixed_wave_dissipation
-
-
- If .true. then fix the wave dissipation from that
- read in by the tide model, such as Jayne and St.Laurent (2001).
- This power dissipation will be employed
- for computing wave induced mixing.
- Default fixed_wave_dissipation=.false.
-
-[logical]
-
-
-read_roughness
-
-
- If .true. then read in bottom roughness amplitude h,
- where roughness_length = kappa*h^2, with kappa a
- representative roughness wavelength and h a
- representative topographic amplitude. This information is
- used for the Simmons etal wave dissipation parameterization.
-
-[logical]
-
-
-reading_roughness_length
-
-
- If .true., then the field in the roughness file is
- roughness_length = kappa*h^2, with kappa a
- representative roughness wavelength and h a
- representative topographic amplitude. This information is
- used for the Simmons etal wave dissipation parameterization.
- Default reading_roughness_length=.false.
-
-[logical]
-
-
-reading_roughness_amp
-
-
- If .true., then the field in the roughness file is
- roughness_amp=h, where roughness_length=kappa*h^2.
- This information is used for the Simmons etal wave
- dissipation parameterization.
- Default reading_roughness_amp=.false.
-
-[logical]
-
-
-default_roughness_length
-
-
- Default value for kappa*h^2 = roughness length for use
- in the absence of a roughness length dataset. MOM default
- is default_roughness_length=25.0m.
-
-[real, units: m]
-
-
-read_tide_speed
-
-
- If .true. then read in tidal speed (m/s) from a tidal model.
- This information is used for the computing the energy dissipation
- from tides.
- scheme.
-
-[logical]
-
-
-tide_speed_data_on_t_grid
-
-
- To set the input tide speed data on T-grid, set to true.
- Otherwise, set to false.
- Default tide_speed_data_on_t_grid=.true.
-
-[logical]
-
-
-roughness_scale
-
-
- Scale for the roughness that characterizes the roughness
- affecting the tidal dissipation process. Used for setting
- roughness_length via roughness_length = kappa*h^2, with
- kappa = 2pi/(roughness_scale) and h=topography amplitude.
- Default roughness_scale=1e4 as in Jayne and St. Laurent (2001)
-
-[real, units: m]
-
-
-default_tide_speed
-
-
- Default value for tidal speed for use in the absence of a
- value from a tidal model.
-
-[real, units: m/s]
-
-
-speed_min
-
-
- For the drag scheme, we set the diffusivity as well as the
- Richardson number to zero if the tide speed is less than
- speed_min. This serves two purposes: 1/ to reduce overflows
- in some of the diagnostics; 2/ to set the drag induced diffusivity
- to zero in regions where the tide speed is small. Default
- speed_min=5e-3m/s.
-
-[real, units: m/s]
-
-
-shelf_depth_cutoff
-
-
- For use in defining a mask for the Simmons scheme, with depths
- shallower than shelf_depth_cutoff removed from the scheme.
- shelf_depth_cutoff=1000m in Simmons etal.
- Default shelf_depth_cutoff=-1000m so there is no cutoff.
-
-[real, units: m]
-
-
-decay_scale
-
-
- In the Simmons etal vertical profile function, the exponential decay
- scale is determined by this parameter. Default = 500m as in Simmons
- etal (2004). This vertical profile determines how to deposit the
- internal wave energy within a vertical column.
-
-[real, units: m]
-
-
-tidal_diss_efficiency
-
-
- Fraction of barotropic tidal energy that is dissipated locally, as
- opposed to that which propagates away. Default=1/3 as in
- Simmons etal (2004).
-
-[real, units: dimensionless]
-
-
-mixing_efficiency
-
-
- Fraction of energy that is dissipated which is converted into dianeutral
- diffusion of tracer. Default=0.2 based on Osborn (1980).
-
-[real, units: dimensionless]
-
-
-mixing_efficiency_n2depend
-
-
- Allow for mixing efficiency to be a function of
- N^2/(N^2+Omega^2), which is close to unity except in
- regions where N is very small.
- Default mixing_efficiency_n2depend=.false.
-
-[logical]
-
-
-wave_energy_flux_max
-
-
- The maximum mechanical energy from internal tides that is
- provided for mixing. Default wave_energy_flux_max=0.1Watt/m^2.
-
-[real, units: W/m2]
-
-
-wave_diffusivity_monotonic
-
-
- Enforce a monotonic decay of the wave dissipation diffusivity,
- with largest values near bottom and smaller as move to shallower
- water. This behaviour is not guaranteed in general, since the
- division by the buoyancy frequency can give non-monotone diffusivities.
- Default wave_diffusivity_monotonic=.true.
-
-[logical]
-
-
-munk_anderson_p
-
-
- The p constant in the Munk-Anderson scheme employed by Lee etal.
- This parameter is minus the "p_tide" parameter in the KPP schemes.
- Default munk_anderson_p=0.25
-
-[real, units: dimensionless]
-
-
-munk_anderson_sigma
-
-
- The sigma constant in the Munk-Anderson scheme employed by Lee etal.
- This parameter is called "sigma_tide" in the KPP schemes.
- Default munk_anderson_sigma=3.0
-
-[real, units: dimensionless]
-
-
-drag_dissipation_use_cdbot
-
-
- For using the cdbot_array computed from ocean_bbc.F90 module.
- Default drag_dissipation_use_cdbot=.false., as this is consistent
- with earlier simulations.
-
-[logical]
-
-
-bottom_drag_cd
-
-
- Bottom drag coefficient from Lee etal. Default bottom_drag_cd=2.4e-3
-
-[real, units: dimensionless]
-
-
-background_diffusivity
-
-
- Background vertical diffusivity not accounted for by the tidal schemes
- nor any other scheme such as KPP. Default=0.1e-4.
-
-[real, units: m^2/s]
-
-
-background_viscosity
-
-
- Background vertical viscosity not accounted for by the tidal schemes
- nor any other scheme such as KPP. Default=0.1e-4.
-
-[real, units: m^2/s]
-
-
-max_wave_diffusivity
-
-
- Maximum tracer diffusivity deduced from the wave dissipation
- scheme from Simmons etal. Default = 5.e-3 m^2/sec.
-
-[real, units: m^2/s]
-
-
-max_drag_diffusivity
-
-
- Maximum tracer diffusivity deduced from the drag dissipation scheme
- from Lee etal. Default = 5.e-3 m^2/sec.
-
-[real, units: m^2/s]
-
-
-drag_dissipation_efold
-
-
- For setting an efolding whereby the drag dissipation diffusivity
- exponentially decreases as move upward in the water column.
- There are good reasons to set this logical to true, as the scheme
- can produce unreasonably large diffusivities far from the bottom, if
- there are tides in the deep ocean.
- Default drag_dissipation_efold=.true.
-
-[logical]
-
-
-drag_dissipation_tide_period
-
-
- Characteristic tide period for use in computing efolding depth for
- the tide drag scheme. Default = 12*60*60 = 12hours for semi-diurnal tide.
-
-[real, units: s]
-
-
-drag_mask_deep
-
-
- For masking out the deep ocean regions for the drag dissipation
- scheme. This scheme is meant to apply only in shallow shelves,
- so it is physically relevant to mask it out. We apply a mask as
- determined by the ratio of the frictional tide depth scale and the
- total ocean depth.
- Default drag_mask_deep=.true.
-
-[logical]
-
-
-drag_mask_deep_ratio
-
-
- For determining the drag dissipation mask.
- The mask = 0 in regions where
- tide_depth/total_depth < drag_mask_deep_ratio
- Default drag_mask_deep_ratio=0.1
-
-[real]
-
-
-smooth_ri_drag_cgrid
-
-
- For smoothing the raw C-grid Richardson number computed for
- the drag scheme on the Cgrid. Default smooth_ri_drag_cgrid=.true.
-
-[logical]
-
-
-use_legacy_methods
-
-
- To compute all mixing coefficients using legacy methods.
- There are good reasons to prefer the newer approaches, which motivates
- setting the default use_legacy_methods=.false.
-
-[logical]
-
-
-drhodz_min
-
-
- Minimum absolute value for the drhodz used to compute N^2 and rhoN2.
- This value is needed in order to regularize the diffusivity computed
- from the tide mixing schemes. Default is drhodz_min=1e-10, which
- is much smaller than the (N^2)min = 10^-8 sec^-2 used by Simmons
- etal. There is some sensitivity to the choice of drhodz_min, with
- larger values leading to reduced deep diffusivities, due to the
- N^-2 dependence in the diffusivity calculation.
-
-[real, units: kg/m^3]
-
-
-smooth_bvfreq_bottom
-
-
- For smoothing the buoyancy frequency at the bottom.
- Default smooth_bvfreq_bottom=.true.
-
-[logical]
-
-
-vel_micom_smooth
-
-
- Velocity scale that is used for computing the MICOM Laplacian mixing
- coefficient used in the Laplacian smoothing of diffusivities.
- Default vel_micom_smooth=0.2.
-
-[real, units: m/sec]
-
-
-smooth_rho_N2
-
-
- For smoothing the rho_N2 field via a 1-2-1 filter in
- vertical. This is useful to produce smoother diffusivities.
- Default is smooth_rho_N2=.true.
-
-[logical]
-
-
-num_121_passes
-
-
- Number of passes of 1-2-1 filter in vertical for
- smoothing the rho_N2 field. Default num_121_passes=1.
-
-[integer]
-
-
-
-
-
-
-
-
-
-
-
REFERENCES
-
-
-
-
- Simmons, Jayne, St. Laurent, and Weaver, 2004:
- Tidally driven mixing in a numerical model of the ocean
- general circulation. Ocean Modelling, vol. 6,
- pages 245-263.
-
-
- Jayne and St. Laurent, 2001:
- Parameterizing tidal dissipation over rough topography.
- Geophysical Research Letters, vol. 28, pages 811-814.
-
-
- Hyun-Chul Lee, A. Rosati, and M.J. Spelman, 2006:
- Barotropic tidal mixing effects in a coupled climate model:
- ocean conditions in the northern Atlantic
- Ocean Modelling, vol 11, pages 464--477
-
-
- Osborn, T.R., 1980: Estimates of the local rate of vertical diffusion
- from dissipation measurements. JPO, vol. 10, pages 83-89.
-
-
- Munk and Anderson, 1948: Notes on a theory of the thermocline.
- Journal of Marine Research, vol 3. pages 276-295.
-
-
-
diff --git a/src/mom5/ocean_param/vertical/ocean_vert_tidal.xml b/src/mom5/ocean_param/vertical/ocean_vert_tidal.xml
deleted file mode 100644
index 02cb84e533..0000000000
--- a/src/mom5/ocean_param/vertical/ocean_vert_tidal.xml
+++ /dev/null
@@ -1,350 +0,0 @@
-
-
- S. M. Griffies
- Harper Simmons
- Hyun-Chul Lee
-
- This module computes a vertical diffusivity and vertical
- viscosity deduced from barotropic and baroclinic tidal
- dissipation. Assume Prandtl number unity.
-
- This module computes a vertical diffusivity and vertical
- viscosity deduced from barotropic and baroclinic tidal
- dissipation. For the baroclinic dissipation, we follow
- Simmons etal, and for the barotropic dissipation we follow
- Lee etal. Assume Prandtl number unity.
-
- This code is more general than that in the ocean_vert_kpp_mom4p0_mod.
- The KPP_mom4p0 code remains part of MOM for legacy purposes.
-
- Simmons, Jayne, St. Laurent, and Weaver, 2004:
- Tidally driven mixing in a numerical model of the ocean
- general circulation. Ocean Modelling, vol. 6,
- pages 245-263.
-
- Jayne and St. Laurent, 2001:
- Parameterizing tidal dissipation over rough topography.
- Geophysical Research Letters, vol. 28, pages 811-814.
-
- Hyun-Chul Lee, A. Rosati, and M.J. Spelman, 2006:
- Barotropic tidal mixing effects in a coupled climate model:
- ocean conditions in the northern Atlantic
- Ocean Modelling, vol 11, pages 464--477
-
- Osborn, T.R., 1980: Estimates of the local rate of vertical diffusion
- from dissipation measurements. JPO, vol. 10, pages 83-89.
-
- Munk and Anderson, 1948: Notes on a theory of the thermocline.
- Journal of Marine Research, vol 3. pages 276-295.
-
- S.M. Griffies, Elements of MOM (2012)
-
- Must be .true. to use this module. Default is false.
-
- For debugging purposes.
-
- Set to .true. for using the Simmons etal scheme for
- obtaining a diffusivity and viscosity based on internal
- wave breaking. This is a general form of the KPP
- scheme "int_tidal_mix".
- Default use_wave_dissipation=.false.
-
- Set to .true. for using the Lee etal scheme for
- obtaining a diffusivity and viscosity based on drag
- of barotropic tides on bottom. This is a general
- form of the KPP scheme "coastal_tidal_mix".
- Default use_drag_dissipation=.false.
-
- Set to .true. for using a prototype Nikurashin scheme for
- obtaining a diffusivity and viscosity based on breaking
- leewaves. This scheme is not related to tides, but it
- is incorporated to the baroclinic tide parameterization scheme
- as a prototype. It will be placed into ts own module when
- the parameterization matures.
- Default use_leewave_dissipation=.false.
-
- If .true. then read in leewave dissipation from a file.
- Default read_leewave_dissipation=.false.
-
- If .true. then read in wave dissipation computed from
- Jayne and St.Laurent (2001) tide model (or another model).
- Default read_wave_dissipation=.false.
-
- If .true. then fix the wave dissipation from that
- read in by the tide model, such as Jayne and St.Laurent (2001).
- This power dissipation will be employed
- for computing wave induced mixing.
- Default fixed_wave_dissipation=.false.
-
- If .true. then read in bottom roughness amplitude h,
- where roughness_length = kappa*h^2, with kappa a
- representative roughness wavelength and h a
- representative topographic amplitude. This information is
- used for the Simmons etal wave dissipation parameterization.
-
- If .true., then the field in the roughness file is
- roughness_length = kappa*h^2, with kappa a
- representative roughness wavelength and h a
- representative topographic amplitude. This information is
- used for the Simmons etal wave dissipation parameterization.
- Default reading_roughness_length=.false.
-
- If .true., then the field in the roughness file is
- roughness_amp=h, where roughness_length=kappa*h^2.
- This information is used for the Simmons etal wave
- dissipation parameterization.
- Default reading_roughness_amp=.false.
-
- Default value for kappa*h^2 = roughness length for use
- in the absence of a roughness length dataset. MOM default
- is default_roughness_length=25.0m.
-
- If .true. then read in tidal speed (m/s) from a tidal model.
- This information is used for the computing the energy dissipation
- from tides.
- scheme.
-
- To set the input tide speed data on T-grid, set to true.
- Otherwise, set to false.
- Default tide_speed_data_on_t_grid=.true.
-
- Scale for the roughness that characterizes the roughness
- affecting the tidal dissipation process. Used for setting
- roughness_length via roughness_length = kappa*h^2, with
- kappa = 2pi/(roughness_scale) and h=topography amplitude.
- Default roughness_scale=1e4 as in Jayne and St. Laurent (2001)
-
- Default value for tidal speed for use in the absence of a
- value from a tidal model.
-
- For the drag scheme, we set the diffusivity as well as the
- Richardson number to zero if the tide speed is less than
- speed_min. This serves two purposes: 1/ to reduce overflows
- in some of the diagnostics; 2/ to set the drag induced diffusivity
- to zero in regions where the tide speed is small. Default
- speed_min=5e-3m/s.
-
- For use in defining a mask for the Simmons scheme, with depths
- shallower than shelf_depth_cutoff removed from the scheme.
- shelf_depth_cutoff=1000m in Simmons etal.
- Default shelf_depth_cutoff=-1000m so there is no cutoff.
-
- In the Simmons etal vertical profile function, the exponential decay
- scale is determined by this parameter. Default = 500m as in Simmons
- etal (2004). This vertical profile determines how to deposit the
- internal wave energy within a vertical column.
-
- Fraction of barotropic tidal energy that is dissipated locally, as
- opposed to that which propagates away. Default=1/3 as in
- Simmons etal (2004).
-
- Fraction of energy that is dissipated which is converted into dianeutral
- diffusion of tracer. Default=0.2 based on Osborn (1980).
-
- Allow for mixing efficiency to be a function of
- N^2/(N^2+Omega^2), which is close to unity except in
- regions where N is very small.
- Default mixing_efficiency_n2depend=.false.
-
- The maximum mechanical energy from internal tides that is
- provided for mixing. Default wave_energy_flux_max=0.1Watt/m^2.
-
- Enforce a monotonic decay of the wave dissipation diffusivity,
- with largest values near bottom and smaller as move to shallower
- water. This behaviour is not guaranteed in general, since the
- division by the buoyancy frequency can give non-monotone diffusivities.
- Default wave_diffusivity_monotonic=.true.
-
- The p constant in the Munk-Anderson scheme employed by Lee etal.
- This parameter is minus the "p_tide" parameter in the KPP schemes.
- Default munk_anderson_p=0.25
-
- The sigma constant in the Munk-Anderson scheme employed by Lee etal.
- This parameter is called "sigma_tide" in the KPP schemes.
- Default munk_anderson_sigma=3.0
-
- For using the cdbot_array computed from ocean_bbc.F90 module.
- Default drag_dissipation_use_cdbot=.false., as this is consistent
- with earlier simulations.
-
- Bottom drag coefficient from Lee etal. Default bottom_drag_cd=2.4e-3
-
- Background vertical diffusivity not accounted for by the tidal schemes
- nor any other scheme such as KPP. Default=0.1e-4.
-
- Background vertical viscosity not accounted for by the tidal schemes
- nor any other scheme such as KPP. Default=0.1e-4.
-
- Maximum tracer diffusivity deduced from the wave dissipation
- scheme from Simmons etal. Default = 5.e-3 m^2/sec.
-
- Maximum tracer diffusivity deduced from the drag dissipation scheme
- from Lee etal. Default = 5.e-3 m^2/sec.
-
- For setting an efolding whereby the drag dissipation diffusivity
- exponentially decreases as move upward in the water column.
- There are good reasons to set this logical to true, as the scheme
- can produce unreasonably large diffusivities far from the bottom, if
- there are tides in the deep ocean.
- Default drag_dissipation_efold=.true.
-
- Characteristic tide period for use in computing efolding depth for
- the tide drag scheme. Default = 12*60*60 = 12hours for semi-diurnal tide.
-
- For masking out the deep ocean regions for the drag dissipation
- scheme. This scheme is meant to apply only in shallow shelves,
- so it is physically relevant to mask it out. We apply a mask as
- determined by the ratio of the frictional tide depth scale and the
- total ocean depth.
- Default drag_mask_deep=.true.
-
- For determining the drag dissipation mask.
- The mask = 0 in regions where
- tide_depth/total_depth < drag_mask_deep_ratio
- Default drag_mask_deep_ratio=0.1
-
- For smoothing the raw C-grid Richardson number computed for
- the drag scheme on the Cgrid. Default smooth_ri_drag_cgrid=.true.
-
- To compute all mixing coefficients using legacy methods.
- There are good reasons to prefer the newer approaches, which motivates
- setting the default use_legacy_methods=.false.
-
- Minimum absolute value for the drhodz used to compute N^2 and rhoN2.
- This value is needed in order to regularize the diffusivity computed
- from the tide mixing schemes. Default is drhodz_min=1e-10, which
- is much smaller than the (N^2)min = 10^-8 sec^-2 used by Simmons
- etal. There is some sensitivity to the choice of drhodz_min, with
- larger values leading to reduced deep diffusivities, due to the
- N^-2 dependence in the diffusivity calculation.
-
- For smoothing the buoyancy frequency at the bottom.
- Default smooth_bvfreq_bottom=.true.
-
- Velocity scale that is used for computing the MICOM Laplacian mixing
- coefficient used in the Laplacian smoothing of diffusivities.
- Default vel_micom_smooth=0.2.
-
- For smoothing the rho_N2 field via a 1-2-1 filter in
- vertical. This is useful to produce smoother diffusivities.
- Default is smooth_rho_N2=.true.
-
- Number of passes of 1-2-1 filter in vertical for
- smoothing the rho_N2 field. Default num_121_passes=1.
-
- Initialization for the ocean_vert_tidal module.
-
- This subroutine computes vertical tracer diffusivity and viscosity
- based on one or both of the following dissipation mechanisms:
-
- 1. internal wave breaking as parameterized by Simmons etal.
-
- 2. barotropic tides feeling the bottom drag, as parameterized by
- Lee etal.
-
-
- This subroutine computes the absolute value of rho*N^2 and abs of
- N^2, with N^2 the squared Brunt-Vaisala (or buoyancy) frequency.
-
-
- This subroutine computes dia-surface tracer diffusivity based on the
- methods of Simmons et al., which consider dissipation from breaking
- internal gravity waves and their conversion into local dia-surface
- mixing, which is parameterized as diffusion.
-
- Also compute a prototype parameterization of mixing due to
- breaking leewaves from Nikurashin.
-
- We assume a unit Prandtl number.
-
- Note that if umask(i,j,k) is 1.0, then so is
- tmask(i,j,k), tmask(i+1,j,k), tmask(i,j+1,k), and tmask(i+1,j+1,k).
- So there is no need to compute the "active_cells" when doing the
- space average to go from t-cell to u-cell to compute visc_cbu.
-
-
- This subroutine computes dia-surface tracer diffusivity based on the
- methods of Lee etal., which consider the dissipation from barotropic tides
- rubbing against the ocean bottom.
-
- We assume B-grid layout for the velocity
-
- We assume a unit Prandtl number, so compute the viscosity as a four-point
- average of the diffusivity.
-
- We perform various averages here in order to smooth Richardson number.
-
- 1. compute Richardson number on U-cell by averaging bvfreq from T-cell
- 2. average U-cell Richardson number to then get T-cell diffusivity
- 3. average T-cell diffusivity to get U-cell viscosity.
-
- Note that if umask(i,j,k)==1.0, then so is tmask(i,j,k), tmask(i+1,j,k),
- tmask(i,j+1,k), and tmask(i+1,j+1,k). So there is no need to compute
- active_cells when averaging from T-cell to U-cell.
-
-
- This subroutine computes dia-surface tracer diffusivity based on the
- methods of Lee etal., which consider the dissipation from barotropic tides
- rubbing against the ocean bottom.
-
- We assume a unit Prandtl number, so compute the viscosity as a four-point
- average of the diffusivity.
-
- We assume C-grid layout for the velocity, which renders slight
- distinctions for the calculation of Richardson number. Otherwise, the
- calculations are the same as the Bgrid. We introduce this separate
- routine, however, to enable easier bitwise agreement with older
- model results. Also, further development of this scheme may lead
- to more distinctions from the Bgrid.
-
-
- This subroutine computes the absolute value of rho*N^2 and abs of
- N^2, with N^2 the squared Brunt-Vaisala (or buoyancy) frequency.
-
- This routine employs a legacy approach, which is not recommended.
- It remains solely to allow exact reproduction of older results.
-
-
-
- Legacy routine maintained only to exactly reproduce older results.
- It is not recommended for new experiments, as it uses some obsolete
- methods.
-
- This subroutine computes dia-surface tracer diffusivity based on the
- methods of Simmons etal., which consider the dissipation from breaking
- internal gravity waves and their conversion into local dia-surface
- diffusion.
-
- We assume a unit Prandtl number, so compute the viscosity as a four-point
- average of the diffusivity.
-
- Note that if umask(i,j,k) is 1.0, then so is
- tmask(i,j,k), tmask(i+1,j,k), tmask(i,j+1,k), and tmask(i+1,j+1,k).
- So there is no need to compute the "active_cells" when doing the
- space average to go from t-cell to u-cell to compute viscosity.
-
-
-
- Legacy routine maintained only to exactly reproduce older results.
- It is not recommended for new experiments, as it uses some obsolete
- methods.
-
- This subroutine computes dia-surface tracer diffusivity based on the
- methods of Lee etal., which consider the dissipation from barotropic tides
- rubbing against the ocean bottom.
-
- We assume a unit Prandtl number, so compute the viscosity as a four-point
- average of the diffusivity.
-
- We perform various averages here in order to smooth Richardson number.
-
- 1. compute Richardson number on U-cell by averaging bvfreq from T-cell
- 2. average U-cell Richardson number to then get T-cell diffusivity
- 3. average T-cell diffusivity to get U-cell viscosity.
-
- Note that if umask(i,j,k)==1.0, then so is tmask(i,j,k), tmask(i+1,j,k),
- tmask(i,j+1,k), and tmask(i+1,j+1,k). So there is no need to compute
- active_cells when averaging from T-cell to U-cell.
-
-
diff --git a/src/mom5/ocean_param/vertical/ocean_vert_tidal_test.F90 b/src/mom5/ocean_param/vertical/ocean_vert_tidal_test.F90
new file mode 100644
index 0000000000..00bd2ad64a
--- /dev/null
+++ b/src/mom5/ocean_param/vertical/ocean_vert_tidal_test.F90
@@ -0,0 +1,2529 @@
+module ocean_vert_tidal_test_mod
+!
+! S. M. Griffies
+!
+!
+! Harper Simmons
+!
+!
+! Hyun-Chul Lee
+!
+!
+!
+! This module computes a vertical diffusivity and vertical
+! viscosity deduced from barotropic and baroclinic tidal
+! dissipation. Assume Prandtl number unity.
+!
+!
+!
+! This module computes a vertical diffusivity and vertical
+! viscosity deduced from barotropic and baroclinic tidal
+! dissipation. For the baroclinic dissipation, we follow
+! Simmons etal, and for the barotropic dissipation we follow
+! Lee etal. Assume Prandtl number unity.
+!
+! This code is more general than that in the ocean_vert_kpp_mom4p0_mod.
+! The KPP_mom4p0 code remains part of MOM for legacy purposes.
+!
+! There are some testing routines in this module that remain exploratory
+! at GFDL.
+!
+!
+!
+!
+!
+!
+! Simmons, Jayne, St. Laurent, and Weaver, 2004:
+! Tidally driven mixing in a numerical model of the ocean
+! general circulation. Ocean Modelling, vol. 6,
+! pages 245-263.
+!
+!
+!
+! Jayne and St. Laurent, 2001:
+! Parameterizing tidal dissipation over rough topography.
+! Geophysical Research Letters, vol. 28, pages 811-814.
+!
+!
+!
+! Hyun-Chul Lee, A. Rosati, and M.J. Spelman, 2006:
+! Barotropic tidal mixing effects in a coupled climate model:
+! ocean conditions in the northern Atlantic
+! Ocean Modelling, vol 11, pages 464--477
+!
+!
+!
+! Osborn, T.R., 1980: Estimates of the local rate of vertical diffusion
+! from dissipation measurements. JPO, vol. 10, pages 83-89.
+!
+!
+!
+! Munk and Anderson, 1948: Notes on a theory of the thermocline.
+! Journal of Marine Research, vol 3. pages 276-295.
+!
+!
+!
+! S.M. Griffies, Elements of MOM (2012)
+!
+!
+!
+!
+!
+!
+! Must be .true. to use this module. Default is false.
+!
+!
+! For debugging purposes.
+!
+!
+!
+! Set to .true. for using the Simmons etal scheme for
+! obtaining a diffusivity and viscosity based on internal
+! wave breaking. This is a general form of the KPP
+! scheme "int_tidal_mix".
+! Default use_wave_dissipation=.false.
+!
+!
+! Set to .true. for using the Lee etal scheme for
+! obtaining a diffusivity and viscosity based on drag
+! of barotropic tides on bottom. This is a general
+! form of the KPP scheme "coastal_tidal_mix".
+! Default use_drag_dissipation=.false.
+!
+!
+! Set to .true. for using a prototype Nikurashin scheme for
+! obtaining a diffusivity and viscosity based on breaking
+! leewaves. This scheme is not related to tides, but it
+! is incorporated to the baroclinic tide parameterization scheme
+! as a prototype. It will be placed into ts own module when
+! the parameterization matures.
+! Default use_leewave_dissipation=.false.
+!
+!
+!
+! If .true. then read in leewave dissipation from a file.
+! Default read_leewave_dissipation=.false.
+!
+!
+!
+! If .true. then read in wave dissipation computed from
+! Jayne and St.Laurent (2001) tide model (or another model).
+! Default read_wave_dissipation=.false.
+!
+!
+! If .true. then fix the wave dissipation from that
+! read in by the tide model, such as Jayne and St.Laurent (2001).
+! This power dissipation will be employed
+! for computing wave induced mixing.
+! Default fixed_wave_dissipation=.false.
+!
+!
+!
+! If .true. then read in bottom roughness amplitude h,
+! where roughness_length = kappa*h^2, with kappa a
+! representative roughness wavelength and h a
+! representative topographic amplitude. This information is
+! used for the Simmons etal wave dissipation parameterization.
+!
+!
+! If .true., then the field in the roughness file is
+! roughness_length = kappa*h^2, with kappa a
+! representative roughness wavelength and h a
+! representative topographic amplitude. This information is
+! used for the Simmons etal wave dissipation parameterization.
+! Default reading_roughness_length=.false.
+!
+!
+! If .true., then the field in the roughness file is
+! roughness_amp=h, where roughness_length=kappa*h^2.
+! This information is used for the Simmons etal wave
+! dissipation parameterization.
+! Default reading_roughness_amp=.false.
+!
+!
+! Default value for kappa*h^2 = roughness length for use
+! in the absence of a roughness length dataset. MOM default
+! is default_roughness_length=25.0m.
+!
+!
+!
+! If .true. then read in tidal speed (m/s) from a tidal model.
+! This information is used for the computing the energy dissipation
+! from tides.
+! scheme.
+!
+!
+! To set the input tide speed data on T-grid, set to true.
+! Otherwise, set to false.
+! Default tide_speed_data_on_t_grid=.true.
+!
+!
+!
+! Scale for the roughness that characterizes the roughness
+! affecting the tidal dissipation process. Used for setting
+! roughness_length via roughness_length = kappa*h^2, with
+! kappa = 2pi/(roughness_scale) and h=topography amplitude.
+! Default roughness_scale=1e4 as in Jayne and St. Laurent (2001)
+!
+!
+! Default value for tidal speed for use in the absence of a
+! value from a tidal model.
+!
+!
+! For the drag scheme, we set the diffusivity as well as the
+! Richardson number to zero if the tide speed is less than
+! speed_min. This serves two purposes: 1/ to reduce overflows
+! in some of the diagnostics; 2/ to set the drag induced diffusivity
+! to zero in regions where the tide speed is small. Default
+! speed_min=5e-3m/s.
+!
+!
+!
+! For use in defining a mask for the Simmons scheme, with depths
+! shallower than shelf_depth_cutoff removed from the scheme.
+! shelf_depth_cutoff=1000m in Simmons etal.
+! Default shelf_depth_cutoff=-1000m so there is no cutoff.
+!
+!
+!
+! In the Simmons etal vertical profile function, the exponential decay
+! scale is determined by this parameter. Default = 500m as in Simmons
+! etal (2004). This vertical profile determines how to deposit the
+! internal wave energy within a vertical column.
+!
+!
+!
+! Fraction of barotropic tidal energy that is dissipated locally, as
+! opposed to that which propagates away. Default=1/3 as in
+! Simmons etal (2004).
+!
+!
+!
+! Fraction of energy that is dissipated which is converted into dianeutral
+! diffusion of tracer. Default=0.2 based on Osborn (1980).
+!
+!
+! Allow for mixing efficiency to be a function of
+! N^2/(N^2+Omega^2), which is close to unity except in
+! regions where N is very small.
+! Default mixing_efficiency_n2depend=.false.
+!
+!
+!
+! The maximum mechanical energy from internal tides that is
+! provided for mixing. Default wave_energy_flux_max=0.1Watt/m^2.
+!
+!
+!
+! Enforce a monotonic decay of the wave dissipation diffusivity,
+! with largest values near bottom and smaller as move to shallower
+! water. This behaviour is not guaranteed in general, since the
+! division by the buoyancy frequency can give non-monotone diffusivities.
+! Default wave_diffusivity_monotonic=.true.
+!
+!
+!
+! The p constant in the Munk-Anderson scheme employed by Lee etal.
+! This parameter is minus the "p_tide" parameter in the KPP schemes.
+! Default munk_anderson_p=0.25
+!
+!
+! The sigma constant in the Munk-Anderson scheme employed by Lee etal.
+! This parameter is called "sigma_tide" in the KPP schemes.
+! Default munk_anderson_sigma=3.0
+!
+!
+! For using the cdbot_array computed from ocean_bbc.F90 module.
+! Default drag_dissipation_use_cdbot=.false., as this is consistent
+! with earlier simulations.
+!
+!
+! Bottom drag coefficient from Lee etal. Default bottom_drag_cd=2.4e-3
+!
+!
+!
+! Background vertical diffusivity not accounted for by the tidal schemes
+! nor any other scheme such as KPP. Default=0.1e-4.
+!
+!
+! Background vertical viscosity not accounted for by the tidal schemes
+! nor any other scheme such as KPP. Default=0.1e-4.
+!
+!
+! Maximum tracer diffusivity deduced from the wave dissipation
+! scheme from Simmons etal. Default = 5.e-3 m^2/sec.
+!
+!
+!
+! Maximum tracer diffusivity deduced from the drag dissipation scheme
+! from Lee etal. Default = 5.e-3 m^2/sec.
+!
+!
+! For setting an efolding whereby the drag dissipation diffusivity
+! exponentially decreases as move upward in the water column.
+! There are good reasons to set this logical to true, as the scheme
+! can produce unreasonably large diffusivities far from the bottom, if
+! there are tides in the deep ocean.
+! Default drag_dissipation_efold=.true.
+!
+!
+! Characteristic tide period for use in computing efolding depth for
+! the tide drag scheme. Default = 12*60*60 = 12hours for semi-diurnal tide.
+!
+!
+! For masking out the deep ocean regions for the drag dissipation
+! scheme. This scheme is meant to apply only in shallow shelves,
+! so it is physically relevant to mask it out. We apply a mask as
+! determined by the ratio of the frictional tide depth scale and the
+! total ocean depth.
+! Default drag_mask_deep=.true.
+!
+!
+! For determining the drag dissipation mask.
+! The mask = 0 in regions where
+! tide_depth/total_depth < drag_mask_deep_ratio
+! Default drag_mask_deep_ratio=0.1
+!
+!
+! For smoothing the raw C-grid Richardson number computed for
+! the drag scheme on the Cgrid. Default smooth_ri_drag_cgrid=.true.
+!
+!
+!
+! To compute all mixing coefficients using legacy methods.
+! There are good reasons to prefer the newer approaches, which motivates
+! setting the default use_legacy_methods=.false.
+!
+!
+! Minimum absolute value for the drhodz used to compute N^2 and rhoN2.
+! This value is needed in order to regularize the diffusivity computed
+! from the tide mixing schemes. Default is drhodz_min=1e-10, which
+! is much smaller than the (N^2)min = 10^-8 sec^-2 used by Simmons
+! etal. There is some sensitivity to the choice of drhodz_min, with
+! larger values leading to reduced deep diffusivities, due to the
+! N^-2 dependence in the diffusivity calculation.
+!
+!
+! For smoothing the buoyancy frequency at the bottom.
+! Default smooth_bvfreq_bottom=.true.
+!
+!
+! Velocity scale that is used for computing the MICOM Laplacian mixing
+! coefficient used in the Laplacian smoothing of diffusivities.
+! Default vel_micom_smooth=0.2.
+!
+!
+!
+! For smoothing the rho_N2 field via a 1-2-1 filter in
+! vertical. This is useful to produce smoother diffusivities.
+! Default is smooth_rho_N2=.true.
+!
+!
+! Number of passes of 1-2-1 filter in vertical for
+! smoothing the rho_N2 field. Default num_121_passes=1.
+!
+!
+!
+! for reproduce legacy results with constant cdbot.
+! To reproduce the previous results, set;
+! drag_dissipation_use_cdbot=.false., repro_legacy_const_cdbot=.true.
+! If drag_dissipation_use_cdbot=.true., then results are reproduciable.
+! Default repro_legacy_const_cdbot= .false.
+!
+!
+!
+
+!
+
+use constants_mod, only: pi, epsln
+use diag_manager_mod, only: register_diag_field, register_static_field, send_data
+use fms_mod, only: write_version_number, open_namelist_file, close_file, check_nml_error
+use fms_mod, only: stdout, stdlog, read_data, NOTE, FATAL, WARNING
+use mpp_domains_mod, only: mpp_update_domains
+use mpp_mod, only: input_nml_file, mpp_error
+
+use ocean_domains_mod, only: get_local_indices
+use ocean_operators_mod, only: LAP_T
+use ocean_parameters_mod, only: MOM_BGRID, MOM_CGRID
+use ocean_parameters_mod, only: missing_value, onehalf, onefourth
+use ocean_parameters_mod, only: von_karman, rho0, rho0r, omega_earth, grav
+use ocean_types_mod, only: ocean_time_type, ocean_domain_type, ocean_grid_type, ocean_options_type
+use ocean_types_mod, only: ocean_prog_tracer_type, ocean_thickness_type, ocean_density_type, ocean_velocity_type
+use ocean_workspace_mod, only: wrk1, wrk2, wrk3, wrk1_2d
+
+implicit none
+
+private
+
+! for diagnostics
+integer :: id_tide_speed_wave =-1
+integer :: id_tide_speed_drag =-1
+integer :: id_tide_speed_mask =-1
+integer :: id_tide_rescspeed_mask=-1
+integer :: id_tide_deepspeed_mask=-1
+integer :: id_roughness_length =-1
+integer :: id_roughness_amp =-1
+integer :: id_roughness_klevel =-1
+integer :: id_energy_flux =-1
+integer :: id_power_waves =-1
+integer :: id_leewave_dissipation=-1
+integer :: id_power_diss_wave =-1
+integer :: id_power_diss_drag =-1
+integer :: id_power_diss_tides =-1
+integer :: id_power_diss_leewave =-1
+integer :: id_rinumber_drag =-1
+integer :: id_drag_dissipation =-1
+integer :: id_bvfreq_bottom =-1
+integer :: id_mix_efficiency =-1
+integer :: id_bvfreq =-1
+integer :: id_diff_cbt_wave =-1
+integer :: id_diff_cbt_drag =-1
+integer :: id_diff_cbt_leewave =-1
+integer :: id_diff_cbt_tides =-1
+integer :: id_visc_cbt_wave =-1
+integer :: id_visc_cbt_drag =-1
+integer :: id_visc_cbt_leewave =-1
+integer :: id_visc_cbt_tides =-1
+integer :: id_visc_cbu_wave =-1
+integer :: id_visc_cbu_leewave =-1
+integer :: id_visc_cbu_drag =-1
+integer :: id_visc_cbu_tides =-1
+integer :: id_drag_diss_efold =-1
+integer :: id_tide_diff_cbt_back =-1
+integer :: id_tide_visc_cbu_back =-1
+logical :: used
+
+#include
+
+real, private, dimension(:,:), allocatable :: smooth_lap !2D array of micom diffusivities (m^2/sec) for smoothing
+real, private, dimension(:,:), allocatable :: roughness_amp ! roughness amplitude (m) from topography
+real, private, dimension(:,:), allocatable :: roughness_length ! roughness length (m) from topography
+real, private, dimension(:,:), allocatable :: wave_dissipation ! wave dissipation (W/m2) from tide model
+real, private, dimension(:,:), allocatable :: leewave_dissipation ! leewave dissipation (W/m2)
+real, private, dimension(:,:), allocatable :: tide_speed_t ! T-cell speed (m/s) from barotropic tide model
+real, private, dimension(:,:), allocatable :: tide_speed_u ! U-cell speed (m/s) from barotropic tide model
+real, private, dimension(:,:), allocatable :: tide_speed_mask ! U-cell mask for rescaled speed, only for legacy
+real, private, dimension(:,:), allocatable :: tide_rescspeed_mask ! U-cell mask for rescaled speed
+real, private, dimension(:,:), allocatable :: tide_deepspeed_mask ! U-cell mask for deep ocean region
+real, private, dimension(:,:), allocatable :: rescaled_speed_u ! U-cell speed (m/s) for Lee etal calculation of Ri
+real, private, dimension(:,:), allocatable :: rescaled_speed_t ! T-cell speed (m/s) for Lee etal calculation of Ri
+real, private, dimension(:,:), allocatable :: efold_depth_r ! T-cell inverse efold depth (1/m) for Lee etal
+real, private, dimension(:,:), allocatable :: energy_flux ! energy flux (W/m^2) out of ext-tide to int-tide
+real, private, dimension(:,:), allocatable :: wave_term ! static term in wave energy flux calculation
+real, private, dimension(:,:), allocatable :: bvfreq_bottom ! buoyancy frequency (sec^-1) at ocean bottom
+
+real, private, dimension(:,:,:), allocatable :: mix_efficiency ! dimensionless mixing efficiency
+real, private, dimension(:,:,:), allocatable :: bvfreq ! buoyancy frequency (sec^-1)
+real, private, dimension(:,:,:), allocatable :: rho_N2 ! rho*squared buoyancy frequency (kg/m^3)*(sec^-2)
+real, private, dimension(:,:,:), allocatable :: drhodT ! partial rho / partial temperature
+real, private, dimension(:,:,:), allocatable :: drhodS ! partial rho / partial salinity
+real, private, dimension(:,:,:), allocatable :: diff_drag ! diffusivity (m^2/sec) from drag mixing scheme
+real, private, dimension(:,:,:), allocatable :: diff_wave ! diffusivity (m^2/sec) from wave mixing scheme
+real, private, dimension(:,:,:), allocatable :: diff_leewave ! diffusivity (m^2/sec) from leewave mixing scheme
+real, private, dimension(:,:), allocatable :: tmask_deep ! nonzero for points deeper than shelf_depth_cutoff
+
+type(ocean_domain_type), pointer :: Dom => NULL()
+type(ocean_grid_type), pointer :: Grd => NULL()
+
+character(len=128) :: version='$$'
+character (len=128) :: tagname = '$Name: tikal $'
+
+public vert_mix_tidal_test
+public ocean_vert_tidal_test_init
+
+private vert_mix_wave
+private vert_mix_drag_bgrid
+private vert_mix_drag_cgrid
+private vert_mix_drag_legacy
+private compute_bvfreq
+
+integer :: index_temp=-1
+integer :: index_salt=-1
+
+! for Bgrid or Cgrid
+integer :: horz_grid
+
+real :: p5rho0
+real :: decay_scale_inv
+real :: sqrt_cd
+real :: von_karman_inv
+real :: dtime
+real :: roughness_kappa
+real :: omega_earth2
+
+logical :: module_is_initialized = .false.
+
+! nml parameters
+
+logical :: use_this_module = .false.
+logical :: use_legacy_methods = .false.
+logical :: debug_this_module = .false.
+logical :: use_wave_dissipation = .false.
+logical :: use_drag_dissipation = .false.
+logical :: use_leewave_dissipation = .false.
+logical :: read_roughness = .false.
+logical :: read_wave_dissipation = .false.
+logical :: read_leewave_dissipation = .false.
+logical :: reading_roughness_amp = .false.
+logical :: reading_roughness_length = .false.
+logical :: read_tide_speed = .false.
+logical :: wave_diffusivity_monotonic = .true.
+logical :: tide_speed_data_on_t_grid = .true.
+logical :: fixed_wave_dissipation = .false.
+logical :: mixing_efficiency_n2depend = .false.
+logical :: drag_dissipation_efold = .true.
+logical :: smooth_bvfreq_bottom = .true.
+logical :: drag_mask_deep = .true.
+logical :: smooth_ri_drag_cgrid = .true.
+
+logical :: smooth_rho_N2 = .true. ! for smoothing the rho_N2 field in vertical with 1-2-1
+integer :: num_121_passes = 1 ! number of 1-2-1 passes
+
+real :: drag_mask_deep_ratio = 0.1
+real :: roughness_scale = 85e3 ! (metre)
+real :: default_roughness_length = 25.0 ! (metre)
+real :: default_tide_speed = .01 ! (m/s)
+real :: shelf_depth_cutoff = -1000.0 ! (metre)
+real :: decay_scale = 500.0 ! (metre)
+real :: tidal_diss_efficiency = 0.33333 ! (dimensionless) from Simmons etal
+real :: mixing_efficiency = 0.2 ! (dimensionless) from Osborne
+real :: munk_anderson_p = 0.25 ! (dimensionless) from Munk and Anderson
+real :: munk_anderson_sigma = 3.0 ! (dimensionless) from Munk and Anderson
+real :: bottom_drag_cd = 2.4e-3 ! (dimensionless) bottom drag from Lee etal
+real :: background_diffusivity = 0.1e-4 ! (m^2/sec)
+real :: background_viscosity = 0.1e-4 ! (m^2/sec)
+real :: max_wave_diffusivity = 5.0e-3 ! (m^2/sec)
+real :: max_drag_diffusivity = 5.0e-3 ! (m^2/sec)
+real :: drhodz_min = 1.e-10 ! (kg/m^4) minimum abs(drhodz) used to compute N^2
+real :: speed_min = 5.e-3 ! (m/s) below which set a mask=0 for drag mixing diffusivity
+real :: wave_energy_flux_max = 0.1 ! (W/m^2)
+real :: drag_dissipation_tide_period = 43200. ! seconds
+real :: vel_micom_smooth = 0.2 ! m/sec for smoothing
+logical :: drag_dissipation_use_cdbot = .false. ! for using cdbot_array from ocean_bbc
+logical :: repro_legacy_const_cdbot = .false. ! for reproduce legacy results with constant cdbot
+
+
+namelist /ocean_vert_tidal_test_nml/ use_this_module, use_legacy_methods, debug_this_module, &
+ use_wave_dissipation, use_drag_dissipation, &
+ read_roughness, read_tide_speed, &
+ default_roughness_length, default_tide_speed, &
+ shelf_depth_cutoff, decay_scale, roughness_scale, &
+ tidal_diss_efficiency, mixing_efficiency, &
+ mixing_efficiency_n2depend, &
+ munk_anderson_p, munk_anderson_sigma, &
+ drag_dissipation_efold, drag_dissipation_tide_period, &
+ drag_mask_deep, drag_mask_deep_ratio, &
+ bottom_drag_cd, drhodz_min, speed_min, &
+ background_diffusivity, background_viscosity, &
+ max_wave_diffusivity, max_drag_diffusivity, &
+ smooth_bvfreq_bottom, vel_micom_smooth, &
+ smooth_rho_N2, num_121_passes, wave_diffusivity_monotonic, &
+ tide_speed_data_on_t_grid, &
+ reading_roughness_amp, reading_roughness_length, &
+ read_wave_dissipation, fixed_wave_dissipation, &
+ wave_energy_flux_max, &
+ use_leewave_dissipation, read_leewave_dissipation, &
+ drag_dissipation_use_cdbot, repro_legacy_const_cdbot
+
+contains
+
+
+!#######################################################################
+!
+!
+!
+! Initialization for the ocean_vert_tidal module.
+!
+ subroutine ocean_vert_tidal_test_init(Grid, Domain, Time, T_prog, Velocity, Ocean_options, dtime_t, vert_mix_scheme, hor_grid)
+
+ type(ocean_grid_type), intent(in), target :: Grid
+ type(ocean_domain_type), intent(in), target :: Domain
+ type(ocean_time_type), intent(in) :: Time
+ type(ocean_prog_tracer_type), intent(in) :: T_prog(:)
+ type(ocean_velocity_type), intent(in) :: Velocity
+ type(ocean_options_type), intent(inout) :: Ocean_options
+ real, intent(in) :: dtime_t
+ character(len=10), intent(in) :: vert_mix_scheme
+ integer, intent(in) :: hor_grid
+
+ real :: active_cells, temporary
+ integer :: unit, io_status, ierr
+ integer :: i,j,n
+ integer :: roughness_has_been_read=0
+
+ integer :: stdoutunit,stdlogunit
+ stdoutunit=stdout();stdlogunit=stdlog()
+
+ if ( module_is_initialized ) then
+ call mpp_error(FATAL,&
+ '==>Error from ocean_vert_tidal_test_mod (ocean_vert_tidal_test_init) module already initialized')
+ endif
+
+ module_is_initialized = .TRUE.
+
+ call write_version_number( version, tagname )
+
+#ifdef INTERNAL_FILE_NML
+read (input_nml_file, nml=ocean_vert_tidal_test_nml, iostat=io_status)
+!ierr = check_nml_error(io_status,'ocean_vert_tidal_test_nml')
+#else
+ unit = open_namelist_file()
+ read(unit, ocean_vert_tidal_test_nml,iostat=io_status)
+! ierr = check_nml_error(io_status, 'ocean_vert_tidal_test_nml')
+ call close_file(unit)
+#endif
+ write (stdoutunit,'(/)')
+ write (stdoutunit,ocean_vert_tidal_test_nml)
+ write (stdlogunit,ocean_vert_tidal_test_nml)
+
+ Dom => Domain
+ Grd => Grid
+ dtime = dtime_t
+
+#ifndef MOM_STATIC_ARRAYS
+ call get_local_indices(Domain, isd, ied, jsd, jed, isc, iec, jsc, jec)
+ nk = Grid%nk
+#endif
+
+ if(use_this_module) then
+ call mpp_error(NOTE, '==>Note: USING ocean_vert_tidal_test_mod')
+ else
+ call mpp_error(NOTE, '==>Note: NOT using ocean_vert_tidal_test_mod')
+ Ocean_options%tidal_wave_mix = 'Did NOT use tidal wave mixing option for vertical mixing.'
+ Ocean_options%tidal_drag_mix = 'Did NOT use tidal drag mixing option for vertical mixing.'
+ return
+ endif
+
+ decay_scale_inv = 1.0/decay_scale
+ p5rho0 = 0.5*rho0
+ sqrt_cd = sqrt(bottom_drag_cd)
+ von_karman_inv = 1.0/von_karman
+ roughness_kappa = 2.0*pi/roughness_scale
+ omega_earth2 = omega_earth**2
+ horz_grid = hor_grid
+
+ do n=1, size(T_prog(:))
+ if (T_prog(n)%name == 'temp') index_temp = n
+ if (T_prog(n)%name == 'salt') index_salt = n
+ enddo
+
+ ! allocate arrays needed for buoyancy frequency
+ allocate (mix_efficiency(isd:ied,jsd:jed,nk))
+ allocate (bvfreq_bottom(isd:ied,jsd:jed))
+ allocate (bvfreq(isd:ied,jsd:jed,nk))
+ allocate (rho_N2(isd:ied,jsd:jed,nk))
+ allocate (drhodT(isd:ied,jsd:jed,nk))
+ allocate (drhodS(isd:ied,jsd:jed,nk))
+ allocate (diff_drag(isd:ied,jsd:jed,nk))
+ allocate (diff_wave(isd:ied,jsd:jed,nk))
+ allocate (diff_leewave(isd:ied,jsd:jed,nk))
+ allocate (tmask_deep(isd:ied,jsd:jed))
+ mix_efficiency = 0.0
+ bvfreq_bottom = 0.0
+ bvfreq = 0.0
+ rho_N2 = 0.0
+ drhodT = 0.0
+ drhodS = 0.0
+ diff_drag = 0.0
+ diff_wave = 0.0
+ diff_leewave = 0.0
+ tmask_deep(:,:) = Grd%tmask(:,:,1)
+
+ allocate (smooth_lap(isd:ied,jsd:jed))
+ allocate (wave_term(isd:ied,jsd:jed))
+ allocate (energy_flux(isd:ied,jsd:jed))
+ allocate (wave_dissipation(isd:ied,jsd:jed))
+ allocate (leewave_dissipation(isd:ied,jsd:jed))
+ allocate (roughness_length(isd:ied,jsd:jed))
+ allocate (roughness_amp(isd:ied,jsd:jed))
+ allocate (tide_speed_t(isd:ied,jsd:jed))
+ allocate (tide_speed_u(isd:ied,jsd:jed))
+ allocate (tide_speed_mask(isd:ied,jsd:jed))
+ allocate (tide_rescspeed_mask(isd:ied,jsd:jed))
+ allocate (tide_deepspeed_mask(isd:ied,jsd:jed))
+ allocate (rescaled_speed_u(isd:ied,jsd:jed))
+ allocate (rescaled_speed_t(isd:ied,jsd:jed))
+ allocate (efold_depth_r(isd:ied,jsd:jed))
+ smooth_lap(:,:) = Grd%tmask(:,:,1)*vel_micom_smooth*2.0*Grd%dxt(:,:)*Grd%dyt(:,:)/(Grd%dxt(:,:)+Grd%dyt(:,:))
+ roughness_length(:,:) = Grd%tmask(:,:,1)*default_roughness_length
+ roughness_amp(:,:) = sqrt(Grd%tmask(:,:,1)/roughness_kappa)
+ tide_speed_t(:,:) = Grd%tmask(:,:,1)*default_tide_speed
+ tide_speed_u(:,:) = Grd%umask(:,:,1)*default_tide_speed
+ tide_speed_mask(:,:) = 0.0
+ tide_rescspeed_mask(:,:) = 0.0
+ tide_deepspeed_mask(:,:) = 0.0
+ rescaled_speed_u(:,:) = 0.0
+ rescaled_speed_t(:,:) = 0.0
+ efold_depth_r(:,:) = 0.0
+ wave_term(:,:) = 0.0
+ energy_flux(:,:) = 0.0
+ wave_dissipation(:,:) = 0.0
+ leewave_dissipation(:,:) = 0.0
+
+ if(use_wave_dissipation) then
+ write (stdoutunit,'(a)') &
+ 'Using Simmons etal scheme to compute dia-surface diffusivity and viscosity based on internal wave breaking.'
+ Ocean_options%tidal_wave_mix = 'Used tidal wave mixing option for vertical mixing.'
+ else
+ write(stdoutunit,'(a)') 'NOT using Simmons etal scheme for dia-surface diffusivity and viscosity.'
+ Ocean_options%tidal_wave_mix = 'Did NOT use tidal wave mixing option for vertical mixing.'
+ endif
+
+ if(use_drag_dissipation) then
+ write (stdoutunit,'(a)') &
+ 'Using Lee etal scheme to compute dia-surface diffusivity and viscosity based on barotropic tide drag on bottom.'
+ Ocean_options%tidal_drag_mix = 'Used tidal drag mixing option for vertical mixing.'
+ if(vert_mix_scheme == 'kpp_mom4p0') then
+ write (stdoutunit,'(a)') &
+ '===>WARNING: Using kpp_mom4p0, where Lee etal scheme can be enabled. Be sure not to double count!!!'
+ endif
+ else
+ write(stdoutunit,'(a)') 'NOT using Lee etal scheme from ocean_vert_tidal_test_mod for dia-surface mixing.'
+ Ocean_options%tidal_drag_mix = 'Did NOT use tidal drag mixing option for vertical mixing.'
+ endif
+
+ if(use_leewave_dissipation) then
+ write (stdoutunit,'(a)') &
+ 'Using prototype for Nikurashin scheme to compute dia-surface diff and visc from breaking leewaves.'
+ Ocean_options%leewave_mix = 'Using prototype for leewave mixing option for vertical mixing.'
+ else
+ write(stdoutunit,'(a)') 'NOT using Nikurashin scheme for dia-surface diffusivity and viscosity.'
+ Ocean_options%leewave_mix = 'Did NOT use prototype breaking leewave paramaterization of vertical mixing.'
+ endif
+
+ if(.not. use_drag_dissipation .and. .not. use_wave_dissipation) then
+ call mpp_error(WARNING, &
+ '==>ocean_vert_tidal_test: No dissipation mechanism is set to determine dia-surface mixing.')
+ endif
+
+ if(.not. use_wave_dissipation .and. use_leewave_dissipation) then
+ call mpp_error(WARNING, &
+ '==>ocean_vert_tidal_test: The prototype leewave mixing scheme must run with use_wave_dissipation=.true.')
+ endif
+
+ ! read in topographic amplitude ("h" in "kappa*h^2" from Simmons etal 2004) on T-grid
+ if(read_roughness) then
+ if(reading_roughness_length) then
+ roughness_has_been_read=roughness_has_been_read+1
+ call read_data('INPUT/roughness_length.nc','roughness_length', roughness_length, Domain%domain2d)
+ write (stdoutunit,*) '==>ocean_vert_tidal_test_mod: Completed read of topographic roughness length on T-grid.'
+ call mpp_update_domains(roughness_length(:,:), Dom%domain2d)
+ roughness_amp(:,:) = sqrt(roughness_length(:,:)/roughness_kappa)
+ endif
+ if(reading_roughness_amp) then
+ roughness_has_been_read=roughness_has_been_read+1
+ call read_data('INPUT/roughness_amp.nc','roughness_amp', roughness_amp, Domain%domain2d)
+ write (stdoutunit,*) '==>ocean_vert_tidal_test_mod: Completed read of topographic roughness amplitude on T-grid.'
+ call mpp_update_domains(roughness_amp(:,:), Dom%domain2d)
+ roughness_length(:,:) = roughness_kappa*roughness_amp(:,:)*roughness_amp(:,:)
+ endif
+ if(roughness_has_been_read > 1) then
+ call mpp_error(FATAL, &
+ '==>ocean_vert_tidal_test_mod: Read in both roughness_amp & roughness_length. Check to be sure what you wish.')
+ endif
+ if(roughness_has_been_read==0) then
+ call mpp_error(FATAL, &
+ '==>ocean_vert_tidal_test_mod: To read roughness, reading_roughness_amp or reading_roughness_length must be true.')
+ endif
+ else
+ write(stdoutunit,'(a)') &
+ '==>Note: NOT reading topographic roughness_length for ocean_vert_tidal_test_mod.'
+ endif
+
+ if(read_wave_dissipation) then
+ call read_data('INPUT/wave_dissipation.nc','wave_dissipation', wave_dissipation, Domain%domain2d)
+ write (stdoutunit,*) '==>ocean_vert_tidal_test_mod: Completed read of wave dissipation (W/m^2) on T-grid.'
+ call mpp_update_domains(wave_dissipation(:,:), Dom%domain2d)
+ else
+ write(stdoutunit,'(a)') &
+ '==>Note: NOT reading wave dissipation for ocean_vert_tidal_test_mod.'
+ endif
+
+ if(read_leewave_dissipation) then
+ call read_data('INPUT/leewave_dissipation.nc','leewave_dissipation', leewave_dissipation, Domain%domain2d)
+ write (stdoutunit,*) '==>ocean_vert_tidal_test_mod: Completed read of leewave dissipation (W/m^2) on T-grid.'
+ call mpp_update_domains(leewave_dissipation(:,:), Dom%domain2d)
+ else
+ write(stdoutunit,'(a)') &
+ '==>Note: NOT reading leewave dissipation for ocean_vert_tidal_test_mod.'
+ endif
+
+ ! read tidal speed (m/s) from a tide model, such as the
+ ! Global Inverse Solution TPX06.0 created by OSU.
+ if(read_tide_speed) then
+ if(tide_speed_data_on_t_grid) then
+ call read_data('INPUT/tideamp.nc','tideamp', tide_speed_t, Domain%domain2d)
+ write (stdoutunit,*) '==>ocean_vert_tidal_test_mod: Completed read of tide_speed on T-grid.'
+ call mpp_update_domains(tide_speed_t(:,:), Dom%domain2d)
+ else
+ call read_data('INPUT/tideamp.nc','tideamp', tide_speed_u, Domain%domain2d)
+ write (stdoutunit,*) '==>ocean_vert_tidal_test_mod: Completed read of tide_speed on U-grid.'
+ call mpp_update_domains(tide_speed_u(:,:), Dom%domain2d)
+ endif
+ else
+ write(stdoutunit,'(a)') &
+ '==>Note: NOT reading tide_speed for ocean_vert_tidal_test_mod.'
+ call mpp_error(NOTE, &
+ '==>ocean_vert_tidal_test_mod: Setting tide_speed to default value.')
+ endif
+
+ ! map tide speed onto U-cell by 4-point average
+ if(tide_speed_data_on_t_grid) then
+ do j=jsc,jec
+ do i=isc,iec
+ tide_speed_u(i,j) = onefourth*Grd%umask(i,j,1) &
+ *(tide_speed_t(i,j) + tide_speed_t(i+1,j) &
+ +tide_speed_t(i,j+1) + tide_speed_t(i+1,j+1))
+ enddo
+ enddo
+ call mpp_update_domains(tide_speed_u(:,:), Dom%domain2d)
+ endif
+
+
+
+ ! note for the bottom drag coefficient
+ if(drag_dissipation_use_cdbot) then
+
+ write(stdoutunit,'(a)') &
+ '==>Note from ocean_vert_tidal_test: using cdbot_array(i,j) for tide drag_dissipation scheme.'
+
+ else !if(drag_dissipation_use_cdbot)
+
+ write(stdoutunit,'(a)') &
+ '==>Note from ocean_vert_tidal_test: using constant bottom drag coefficient for tide drag_dissipation scheme.'
+
+ do j=jsd,jed
+ do i=isd,ied
+ rescaled_speed_u(i,j) = sqrt_cd*von_karman_inv*tide_speed_u(i,j)
+ rescaled_speed_t(i,j) = sqrt_cd*von_karman_inv*tide_speed_t(i,j)
+ tide_rescspeed_mask(i,j) = 0.0
+ if(rescaled_speed_u(i,j) > speed_min) then
+ tide_rescspeed_mask(i,j) = 1.0
+ endif
+ enddo
+ enddo
+
+ call mpp_update_domains(tide_rescspeed_mask(:,:), Dom%domain2d)
+
+
+ ! compute efolding depth scale for use in Lee etal scheme.
+ ! efold depth set as rescaled_speed/(radial tide frequency).
+ ! Choose default radial tide frequency as 2pi/12hrs for semi-diurnal tide.
+ ! let this efolding hold whether using Bgrid or Cgrid.
+ wrk1_2d(:,:) = 0.0
+ do j=jsc,jec
+ do i=isc,iec
+ active_cells = Grd%umask(i,j,1) + Grd%umask(i-1,j,1) &
+ + Grd%umask(i,j-1,1) + Grd%umask(i-1,j-1,1) + epsln
+ temporary = (rescaled_speed_u(i,j) + rescaled_speed_u(i-1,j) + &
+ rescaled_speed_u(i,j-1) + rescaled_speed_u(i-1,j-1))/active_cells
+ wrk1_2d(i,j) = Grd%tmask(i,j,1)*temporary*drag_dissipation_tide_period/(2.0*pi)
+ efold_depth_r(i,j) = Grd%tmask(i,j,1)/(wrk1_2d(i,j) + epsln)
+ enddo
+ enddo
+
+ endif !if(drag_dissipation_use_cdbot)
+
+
+ ! mask out the deep ocean regions for the drag scheme.
+ if(drag_mask_deep .and. .not. use_legacy_methods) then
+ ! only to reproduce the previous results with const cdbot
+ if (repro_legacy_const_cdbot .and. .not. drag_dissipation_use_cdbot) then
+ do j=jsc,jec
+ do i=isc,iec
+ if(Grd%tmask(i,j,1) == 1.0) then
+ temporary = wrk1_2d(i,j)/(epsln+Grd%ht(i,j))
+ if(temporary > drag_mask_deep_ratio) then
+ tide_deepspeed_mask(i,j) = 1.0
+ else
+ tide_deepspeed_mask(i,j) = 0.0
+ endif
+ endif
+ enddo
+ enddo
+ else
+ do j=jsc,jec
+ do i=isc,iec
+ if(Grd%tmask(i,j,1) == 1.0) then
+ if(Grd%ht(i,j) <= shelf_depth_cutoff) tide_deepspeed_mask(i,j) = 1.0
+ endif
+ enddo
+ enddo
+ endif
+ else
+ tide_deepspeed_mask(:,:) = 1.0
+ endif
+
+ call mpp_update_domains(tide_deepspeed_mask(:,:), Dom%domain2d)
+
+
+
+
+ if(use_legacy_methods) then
+
+ if(drag_dissipation_use_cdbot) then
+ write(stdoutunit,'(a)') &
+ '==>Note from ocean_vert_tidal_test: using cdbot_array(i,j) for tide drag_dissipation scheme.'
+ do j=jsd,jed
+ do i=isd,ied
+ rescaled_speed_u(i,j) = sqrt(Velocity%cdbot_array(i,j))*von_karman_inv*tide_speed_u(i,j)
+ rescaled_speed_t(i,j) = sqrt(Velocity%cdbot_array(i,j))*von_karman_inv*tide_speed_t(i,j)
+ tide_speed_mask(i,j) = 0.0
+ if(rescaled_speed_u(i,j) > speed_min) then
+ tide_speed_mask(i,j) = 1.0
+ endif
+ enddo
+ enddo
+ else
+ write(stdoutunit,'(a)') &
+ '==>Note from ocean_vert_tidal_test: using constant bottom drag coefficient for tide drag_dissipation scheme.'
+
+ do j=jsd,jed
+ do i=isd,ied
+ rescaled_speed_u(i,j) = sqrt_cd*von_karman_inv*tide_speed_u(i,j)
+ rescaled_speed_t(i,j) = sqrt_cd*von_karman_inv*tide_speed_t(i,j)
+ tide_speed_mask(i,j) = 0.0
+ if(rescaled_speed_u(i,j) > speed_min) then
+ tide_speed_mask(i,j) = 1.0
+ endif
+ enddo
+ enddo
+ endif !if(drag_dissipation_use_cdbot)
+
+ endif !if(use_legacy_methods)
+
+
+ ! compute static piece of the energy flux on T-grid for wave diffusivity
+ do j=jsd,jed
+ do i=isd,ied
+ wave_term(i,j) = Grd%tmask(i,j,1)*p5rho0*roughness_length(i,j)*tide_speed_t(i,j)**2
+ enddo
+ enddo
+
+
+
+ ! diagnostics
+
+ id_tide_diff_cbt_back = -1
+ id_tide_diff_cbt_back = register_static_field ('ocean_model', 'tide_diff_cbt_back', &
+ Grid%tracer_axes(1:3), 'static background diff_cbt set in tide module',&
+ 'm^2/s',missing_value=missing_value, range=(/-10.0,1e6/))
+ if (id_tide_diff_cbt_back > 0) then
+ wrk1(:,:,:) = background_diffusivity*Grid%tmask(:,:,:)
+ used = send_data (id_tide_diff_cbt_back, wrk1(isc:iec,jsc:jec,:), &
+ Time%model_time, rmask=Grid%tmask(isc:iec,jsc:jec,:))
+ endif
+
+ id_tide_visc_cbu_back = -1
+ id_tide_visc_cbu_back = register_static_field ('ocean_model', 'tide_visc_cbu_back', &
+ Grid%vel_axes_wu(1:3), 'static background visc_cbu set in tide module',&
+ 'm^2/s',missing_value=missing_value, range=(/-10.0,1e6/))
+ if (id_tide_visc_cbu_back > 0) then
+ wrk1(:,:,:) = background_viscosity*Grid%umask(:,:,:)
+ used = send_data (id_tide_visc_cbu_back, wrk1(isc:iec,jsc:jec,:), &
+ Time%model_time, rmask=Grid%umask(isc:iec,jsc:jec,:))
+ endif
+
+ ! e-folding depth for drag dissipation scheme
+ id_drag_diss_efold = register_static_field ('ocean_model', 'drag_diss_efold',&
+ Grid%tracer_axes(1:2), 'e-folding depth for drag dissipation scheme', &
+ 'm', missing_value=missing_value, range=(/-1.0,1e10/))
+
+ id_tide_rescspeed_mask = register_diag_field ('ocean_model', 'tide_rescspeed_mask', &
+ Grid%vel_axes_uv(1:2), Time%model_time, 'mask based on tide_speed_drag for barotropic drag mixing', &
+ 'dimensionless', missing_value=missing_value, range=(/-1e1,1e1/))
+
+ id_tide_deepspeed_mask = register_diag_field ('ocean_model', 'tide_deepspeed_mask', &
+ Grid%vel_axes_uv(1:2), Time%model_time, 'mask based on tide_speed_drag for deep ocean region', &
+ 'dimensionless', missing_value=missing_value, range=(/-1e1,1e1/))
+
+ if(.not. drag_dissipation_use_cdbot) then
+ if (id_tide_rescspeed_mask > 0) then
+ used = send_data (id_tide_rescspeed_mask, tide_rescspeed_mask(:,:), &
+ Time%model_time, rmask=Grd%umask(:,:,1), &
+ is_in=isc, js_in=jsc, ie_in=iec, je_in=jec)
+ endif
+ if (id_drag_diss_efold > 0) then
+ used = send_data (id_drag_diss_efold, wrk1_2d(:,:), &
+ Time%model_time, rmask=Grd%tmask(:,:,1), &
+ is_in=isc, js_in=jsc, ie_in=iec, je_in=jec)
+ endif
+ endif !if(drag_dissipation_use_cdbot)
+
+ if (id_tide_deepspeed_mask > 0) then
+ used = send_data (id_tide_deepspeed_mask, tide_deepspeed_mask(:,:), &
+ Time%model_time, rmask=Grd%umask(:,:,1), &
+ is_in=isc, js_in=jsc, ie_in=iec, je_in=jec)
+ endif
+
+ ! static input of leewave breaking from Nikurashin
+ id_leewave_dissipation = register_static_field ('ocean_model', 'leewave_dissipation',&
+ Grid%tracer_axes(1:2), 'specified energy flux input from breaking leewaves', &
+ 'W/m^2', missing_value=missing_value, range=(/-1e1,1e15/))
+ if (id_leewave_dissipation > 0) then
+ used = send_data (id_leewave_dissipation, leewave_dissipation(:,:),&
+ Time%model_time, rmask=Grd%tmask(:,:,1), &
+ is_in=isc, js_in=jsc, ie_in=iec, je_in=jec)
+ endif
+
+ ! tide speed for breaking internal wave dissipation scheme
+ id_tide_speed_wave = register_static_field ('ocean_model', 'tide_speed_wave', &
+ Grid%tracer_axes(1:2), 'tide speed from tide model for breaking internal wave mixing scheme',&
+ 'm/s', missing_value=missing_value, range=(/-1e1,1e9/))
+ if (id_tide_speed_wave > 0) then
+ used = send_data (id_tide_speed_wave, tide_speed_t(:,:), &
+ Time%model_time, rmask=Grd%tmask(:,:,1), &
+ is_in=isc, js_in=jsc, ie_in=iec, je_in=jec)
+ endif
+
+ ! tide speed scale for barotropic bottom drag dissipation scheme
+ id_tide_speed_drag = register_static_field ('ocean_model', 'tide_speed_drag', &
+ Grid%vel_axes_uv(1:2), 'tide speed from tide model for barotropic drag mixing scheme',&
+ 'm/s', missing_value=missing_value, range=(/-1e1,1e9/))
+ if (id_tide_speed_drag > 0) then
+ used = send_data (id_tide_speed_drag, rescaled_speed_u(:,:), &
+ Time%model_time, rmask=Grd%umask(:,:,1), &
+ is_in=isc, js_in=jsc, ie_in=iec, je_in=jec)
+ endif
+
+ id_roughness_amp = register_static_field ('ocean_model', 'roughness_amp', &
+ Grid%tracer_axes(1:2), 'roughness amplitude for breaking internal wave mixing scheme',&
+ 'metre', missing_value=missing_value, range=(/-1e1,1e9/))
+ if (id_roughness_amp > 0) then
+ used = send_data (id_roughness_amp, roughness_amp(:,:), &
+ Time%model_time, rmask=Grd%tmask(:,:,1), &
+ is_in=isc, js_in=jsc, ie_in=iec, je_in=jec)
+ endif
+
+ ! static roughness length
+ id_roughness_length = register_static_field ('ocean_model', 'roughness_length', &
+ Grid%tracer_axes(1:2), 'roughness length for breaking internal wave mixing scheme',&
+ 'metre', missing_value=missing_value, range=(/-1e1,1e9/))
+ if (id_roughness_length > 0) then
+ used = send_data (id_roughness_length, roughness_length(:,:), &
+ Time%model_time, rmask=Grd%tmask(:,:,1), &
+ is_in=isc, js_in=jsc, ie_in=iec, je_in=jec)
+ endif
+
+
+ id_roughness_klevel = register_diag_field ('ocean_model', 'roughness_klevel', &
+ Grid%tracer_axes(1:2), Time%model_time, &
+ 'klevel at top of the bottom layer defined by roughness amplitude for internal tide mixing',&
+ 'dimensionless', missing_value=missing_value, range=(/-1.0,1.e10/))
+ id_energy_flux = register_diag_field ('ocean_model', 'energy_flux', &
+ Grid%tracer_axes(1:2), Time%model_time, &
+ 'energy flux out of barotropic tides for use w/ internal tide mixing',&
+ 'W/m^2', missing_value=missing_value, range=(/-1e9,1e9/))
+ id_power_waves = register_diag_field ('ocean_model', 'power_waves', &
+ Grid%tracer_axes(1:2), Time%model_time, 'power from barotropic tides to internal tides', &
+ 'Watt', missing_value=missing_value, range=(/-1e15,1e15/))
+
+ id_power_diss_leewave = register_diag_field ('ocean_model', 'power_diss_leewave', &
+ Grid%tracer_axes(1:3), Time%model_time, 'power dissipation from mixing due to breaking leewaves',&
+ 'W/m^2', missing_value=missing_value, range=(/-1e15,1e15/))
+ id_power_diss_wave = register_diag_field ('ocean_model', 'power_diss_wave', &
+ Grid%tracer_axes(1:3), Time%model_time, 'power dissipation from internal wave induced mixing', &
+ 'W/m^2', missing_value=missing_value, range=(/-1e15,1e15/))
+ id_power_diss_drag = register_diag_field ('ocean_model', 'power_diss_drag', &
+ Grid%tracer_axes(1:3), Time%model_time, 'power dissipation from barotropic tide drag', &
+ 'W/m^2', missing_value=missing_value, range=(/-1e15,1e15/))
+ id_power_diss_tides = register_diag_field ('ocean_model', 'power_diss_tides',&
+ Grid%tracer_axes(1:3), Time%model_time, &
+ 'power dissipation from barotropic tide drag and baroclinic wave drag', &
+ 'W/m^2', missing_value=missing_value, range=(/-1e15,1e15/), &
+ standard_name='tendency_of_ocean_potential_energy_content_due_to_tides')
+
+ id_mix_efficiency = register_diag_field ('ocean_model', 'mix_efficiency', &
+ Grid%tracer_axes(1:3), Time%model_time, 'efficiency of internal wave dissipation going to mix tracer',&
+ 'dimensionless', missing_value=missing_value, range=(/-1e5,1e5/))
+ id_bvfreq_bottom = register_diag_field ('ocean_model', 'bvfreq_bottom', &
+ Grid%tracer_axes(1:2), Time%model_time, 'absolute Brunt-Vaisala freq at ocean bottom', &
+ 's^-1', missing_value=missing_value, range=(/-1e1,1e9/))
+ id_bvfreq = register_diag_field ('ocean_model', 'bvfreq', &
+ Grid%tracer_axes(1:3), Time%model_time, 'absolute Brunt-Vaisala freq at tracer cell bottom', &
+ 's^-1', missing_value=missing_value, range=(/-1e1,1e9/))
+ id_rinumber_drag = register_diag_field ('ocean_model', 'rinumber_drag', &
+ Grid%tracer_axes(1:3), Time%model_time, 'Richardson number from Lee etal', &
+ 'dimensionless', missing_value=missing_value, range=(/-1e1,1e18/))
+ id_diff_cbt_wave = register_diag_field ('ocean_model', 'diff_cbt_wave', &
+ Grid%tracer_axes(1:3), Time%model_time, 'diffusivity from breaking internal wave dissipation', &
+ 'm^2/sec', missing_value=missing_value, range=(/-1.0,1e6/))
+ id_diff_cbt_leewave = register_diag_field ('ocean_model', 'diff_cbt_leewave', &
+ Grid%tracer_axes(1:3), Time%model_time, 'diffusivity from breaking leewaves', &
+ 'm^2/sec', missing_value=missing_value, range=(/-1.0,1e6/))
+ id_diff_cbt_drag = register_diag_field ('ocean_model', 'diff_cbt_drag', &
+ Grid%tracer_axes(1:3), Time%model_time, 'diffusivity from drag of barotropic tides on bottom', &
+ 'm^2/sec', missing_value=missing_value, range=(/-1.0,1e6/))
+
+ id_visc_cbt_wave = register_diag_field ('ocean_model', 'visc_cbt_wave', &
+ Grid%tracer_axes(1:3), Time%model_time, 'viscosity from breaking internal wave dissipation', &
+ 'm^2/sec', missing_value=missing_value, range=(/-1.0,1e6/))
+ id_visc_cbt_leewave = register_diag_field ('ocean_model', 'visc_cbt_leewave', &
+ Grid%tracer_axes(1:3), Time%model_time, 'viscosity from breaking leewaves', &
+ 'm^2/sec', missing_value=missing_value, range=(/-1.0,1e6/))
+ id_visc_cbt_drag = register_diag_field ('ocean_model', 'visc_cbt_drag', &
+ Grid%tracer_axes(1:3), Time%model_time, 'viscosity from drag of barotropic tides on bottom', &
+ 'm^2/sec', missing_value=missing_value, range=(/-1.0,1e6/))
+
+ id_visc_cbu_wave = register_diag_field ('ocean_model', 'visc_cbu_wave', &
+ Grid%vel_axes_uv(1:3), Time%model_time, 'viscosity from breaking internal wave dissipation', &
+ 'm^2/sec', missing_value=missing_value, range=(/-1.0,1e6/))
+ id_visc_cbu_leewave = register_diag_field ('ocean_model', 'visc_cbu_leewave', &
+ Grid%vel_axes_uv(1:3), Time%model_time, 'viscosity from breaking leewaves ', &
+ 'm^2/sec', missing_value=missing_value, range=(/-1.0,1e6/))
+ id_visc_cbu_drag = register_diag_field ('ocean_model', 'visc_cbu_drag', &
+ Grid%vel_axes_uv(1:3), Time%model_time, 'viscosity from drag of barotropic tides on bottom', &
+ 'm^2/sec', missing_value=missing_value, range=(/-1.0,1e6/))
+ id_diff_cbt_tides = register_diag_field ('ocean_model', 'diff_cbt_tides', &
+ Grid%tracer_axes(1:3), Time%model_time, 'diffusivity from drag of barotropic tides on bottom + wave drag',&
+ 'm^2/sec', missing_value=missing_value, range=(/-1.0,1e6/), &
+ standard_name='ocean_vertical_tracer_diffusivity_due_to_tides')
+ id_visc_cbt_tides = register_diag_field ('ocean_model', 'visc_cbt_tides', &
+ Grid%tracer_axes(1:3), Time%model_time, 'viscosity from drag of barotropic tides on bottom + wave drag',&
+ 'm^2/sec', missing_value=missing_value, range=(/-1.0,1e6/), &
+ standard_name='ocean_vertical_tracer_diffusivity_due_to_tides')
+
+ id_visc_cbu_tides = register_diag_field ('ocean_model', 'visc_cbu_tides', &
+ Grid%vel_axes_uv(1:3), Time%model_time, 'viscosity from drag of barotropic tides on bottom + wave drag',&
+ 'm^2/sec', missing_value=missing_value, range=(/-1.0,1e6/), &
+ standard_name='ocean_vertical_momentum_diffusivity_due_to_tides')
+
+
+end subroutine ocean_vert_tidal_test_init
+! NAME="ocean_vert_tidal_test_init"
+
+
+!#######################################################################
+!
+!
+!
+! This subroutine computes vertical tracer diffusivity and viscosity
+! based on one or both of the following dissipation mechanisms:
+!
+! 1. internal wave breaking as parameterized by Simmons etal.
+!
+! 2. barotropic tides feeling the bottom drag, as parameterized by
+! Lee etal.
+!
+!
+!
+ subroutine vert_mix_tidal_test(Time, Thickness, Velocity, T_prog, Dens, diff_cbt, visc_cbu, visc_cbt, &
+ diff_cbt_wave, diff_cbt_leewave, diff_cbt_drag)
+
+ type(ocean_time_type), intent(in) :: Time
+ type(ocean_thickness_type), intent(in) :: Thickness
+ type(ocean_velocity_type), intent(in) :: Velocity
+ type(ocean_prog_tracer_type), intent(in) :: T_prog(:)
+ type(ocean_density_type), intent(in) :: Dens
+ real, dimension(isd:,jsd:,:,:), intent(inout) :: diff_cbt
+ real, dimension(isd:,jsd:,:), intent(inout) :: visc_cbu
+ real, dimension(isd:,jsd:,:), intent(inout) :: visc_cbt
+ real, dimension(isd:,jsd:,:), intent(inout) :: diff_cbt_wave
+ real, dimension(isd:,jsd:,:), intent(inout) :: diff_cbt_leewave
+ real, dimension(isd:,jsd:,:), intent(inout) :: diff_cbt_drag
+
+ integer :: i, j, k, kp1
+ real :: tmp
+
+ if(.not. use_this_module) return
+
+ if(use_legacy_methods) then
+
+ call compute_bvfreq_legacy(Time, Thickness, T_prog, Dens)
+ if(use_wave_dissipation) then
+ call vert_mix_wave_legacy(Time, Thickness, diff_cbt, visc_cbu, visc_cbt, diff_cbt_wave)
+ endif
+ if(use_drag_dissipation) then
+ call vert_mix_drag_legacy(Time, Thickness, diff_cbt, visc_cbu, visc_cbt, diff_cbt_drag)
+ endif
+ diff_cbt_leewave(:,:,:) = 0.0
+ diff_leewave(:,:,:) = 0.0
+
+ else
+
+ call compute_bvfreq(Time, Thickness, T_prog, Dens)
+ if(use_wave_dissipation) then
+ call vert_mix_wave(Time, Thickness, Dens, diff_cbt, visc_cbu, visc_cbt, diff_cbt_wave, diff_cbt_leewave)
+ endif
+ if(use_drag_dissipation .and. horz_grid == MOM_BGRID) then
+ call vert_mix_drag_bgrid(Time, Thickness, Velocity, diff_cbt, visc_cbu, visc_cbt, diff_cbt_drag)
+ endif
+ if(use_drag_dissipation .and. horz_grid == MOM_CGRID) then
+ call vert_mix_drag_cgrid(Time, Thickness, Velocity, diff_cbt, visc_cbu, visc_cbt, diff_cbt_drag)
+ endif
+
+ endif
+
+ ! add the background diffusivity and viscosity
+ do k=1,nk
+ kp1 = min(k+1,nk)
+ do j=jsc,jec
+ do i=isc,iec
+ diff_cbt(i,j,k,1) = Grd%tmask(i,j,kp1)*(diff_cbt(i,j,k,1) + background_diffusivity)
+ diff_cbt(i,j,k,2) = Grd%tmask(i,j,kp1)*(diff_cbt(i,j,k,2) + background_diffusivity)
+ visc_cbt(i,j,k) = Grd%tmask(i,j,kp1)*(visc_cbt(i,j,k) + background_viscosity)
+ visc_cbu(i,j,k) = Grd%umask(i,j,kp1)*(visc_cbu(i,j,k) + background_viscosity)
+ enddo
+ enddo
+ enddo
+
+ ! compute power dissipated by mixing against stratification
+ if(id_power_diss_wave > 0 .or. id_power_diss_drag > 0 .or. &
+ id_power_diss_tides > 0 .or. id_power_diss_leewave > 0 ) then
+ wrk1(:,:,:) = 0.0
+ wrk2(:,:,:) = 0.0
+ wrk3(:,:,:) = 0.0
+ do k=1,nk
+ do j=jsc,jec
+ do i=isc,iec
+ tmp = Thickness%dzt(i,j,k)*rho_N2(i,j,k)*Grd%tmask(i,j,k)
+ wrk1(i,j,k) = tmp*diff_wave(i,j,k)
+ wrk2(i,j,k) = tmp*diff_drag(i,j,k)
+ wrk3(i,j,k) = tmp*diff_leewave(i,j,k)
+ enddo
+ enddo
+ enddo
+ if (id_power_diss_wave > 0) then
+ used = send_data (id_power_diss_wave, wrk1(:,:,:), &
+ Time%model_time, rmask=Grd%tmask(:,:,:), &
+ is_in=isc, js_in=jsc, ks_in=1, ie_in=iec, je_in=jec, ke_in=nk)
+ endif
+ if (id_power_diss_drag > 0) then
+ used = send_data (id_power_diss_drag, wrk2(:,:,:), &
+ Time%model_time, rmask=Grd%tmask(:,:,:), &
+ is_in=isc, js_in=jsc, ks_in=1, ie_in=iec, je_in=jec, ke_in=nk)
+ endif
+ if (id_power_diss_leewave > 0) then
+ used = send_data (id_power_diss_leewave, wrk3(:,:,:), &
+ Time%model_time, rmask=Grd%tmask(:,:,:), &
+ is_in=isc, js_in=jsc, ks_in=1, ie_in=iec, je_in=jec, ke_in=nk)
+ endif
+ if (id_power_diss_tides > 0) then
+ used = send_data (id_power_diss_tides, wrk1(:,:,:)+wrk2(:,:,:),&
+ Time%model_time, rmask=Grd%tmask(:,:,:), &
+ is_in=isc, js_in=jsc, ks_in=1, ie_in=iec, je_in=jec, ke_in=nk)
+ endif
+ endif
+
+ if (id_diff_cbt_tides > 0) then
+ used = send_data (id_diff_cbt_tides, diff_cbt_wave(:,:,:)+diff_cbt_drag(:,:,:),&
+ Time%model_time, rmask=Grd%tmask(:,:,:), &
+ is_in=isc, js_in=jsc, ks_in=1, ie_in=iec, je_in=jec, ke_in=nk)
+ endif
+
+ ! recall unit Prandtl number
+ if (id_visc_cbt_tides > 0) then
+ used = send_data (id_visc_cbt_tides, diff_cbt_wave(:,:,:)+diff_cbt_drag(:,:,:),&
+ Time%model_time, rmask=Grd%tmask(:,:,:), &
+ is_in=isc, js_in=jsc, ks_in=1, ie_in=iec, je_in=jec, ke_in=nk)
+ endif
+
+ if (id_visc_cbu_tides > 0) then
+ wrk1=0.0
+ do k=1,nk-1
+ kp1=k+1
+ do j=jsc,jec
+ do i=isc,iec
+ wrk1(i,j,k) = Grd%umask(i,j,kp1)*onefourth &
+ *(diff_cbt_wave(i,j,k) +diff_cbt_wave(i+1,j,k) &
+ +diff_cbt_wave(i,j+1,k)+diff_cbt_wave(i+1,j+1,k)&
+ +diff_cbt_drag(i,j,k) +diff_cbt_drag(i+1,j,k) &
+ +diff_cbt_drag(i,j+1,k)+diff_cbt_drag(i+1,j+1,k))
+ enddo
+ enddo
+ enddo
+ used = send_data (id_visc_cbu_tides, wrk1(:,:,:), &
+ Time%model_time, rmask=Grd%umask(:,:,:), &
+ is_in=isc, js_in=jsc, ks_in=1, ie_in=iec, je_in=jec, ke_in=nk)
+ endif
+
+
+end subroutine vert_mix_tidal_test
+! NAME="vert_mix_tidal_test"
+
+
+
+!#######################################################################
+!
+!
+!
+! This subroutine computes the absolute value of rho*N^2 and abs of
+! N^2, with N^2 the squared Brunt-Vaisala (or buoyancy) frequency.
+!
+!
+!
+ subroutine compute_bvfreq(Time, Thickness, T_prog, Dens)
+
+ type(ocean_time_type), intent(in) :: Time
+ type(ocean_thickness_type), intent(in) :: Thickness
+ type(ocean_prog_tracer_type), intent(in) :: T_prog(:)
+ type(ocean_density_type), intent(in) :: Dens
+
+ real :: rho_inv, drhodz, bottom
+ real :: tmp, rho_N2_prev, rho_tmp
+ integer :: i, j, k, m, kp1, kbot
+ integer :: tau
+ real, dimension(isd:ied,jsd:jed) :: roughness_klevel
+
+ tau = Time%tau
+ wrk1(:,:,:) = 0.0
+ wrk2(:,:,:) = 0.0
+ bvfreq_bottom(:,:) = 0.0
+
+
+ ! absolute(rho*N^2) computed from ocean_density module calculation.
+ ! use the value at T-cell centre as this produces a smoother and
+ ! better behaved bvfreq near the bottom, than does drhodz_wt.
+ do k=1,nk
+ do j=jsd,jed
+ do i=isd,ied
+ rho_N2(i,j,k) = max(0.0,-grav*Dens%drhodz_zt(i,j,k)*Grd%tmask(i,j,k))
+ enddo
+ enddo
+ enddo
+
+ ! smooth rho_N2 in the vertical using a 1-2-1 filter
+ if (smooth_rho_N2) then
+ do m=1,num_121_passes
+ do j=jsd,jed
+ do i=isd,ied
+ rho_N2_prev = onefourth*rho_N2(i,j,1)
+ kbot=Grd%kmt(i,j)
+ if (kbot>3) then
+ do k=2,kbot-2
+ tmp = rho_N2(i,j,k)
+ rho_N2(i,j,k) = rho_N2_prev + onehalf*rho_N2(i,j,k) + onefourth*rho_N2(i,j,k+1)
+ rho_N2_prev = onefourth*tmp
+ enddo
+ endif
+ enddo
+ enddo
+ enddo
+ endif
+
+ ! compute absolute value of buoyancy frequency,
+ ! using rho0r as an approximation to 1/rho.
+ do k=1,nk
+ do j=jsd,jed
+ do i=isd,ied
+ bvfreq(i,j,k) = sqrt(rho0r*rho_N2(i,j,k))
+ enddo
+ enddo
+ enddo
+
+ ! determine k-level at top of the bottom roughness boundary layer
+ wrk1_2d(:,:) = 0.0
+ do j=jsd,jed
+ do i=isd,ied
+ kbot = Grd%kmt(i,j)
+ roughness_klevel(:,:) = kbot
+ if(kbot > 1) then
+ bottom = Thickness%depth_zwt(i,j,kbot)
+ kloop: do k=kbot,1,-1
+ tmp = Thickness%depth_zwt(i,j,k) + roughness_amp(i,j)
+ if(tmp <= bottom) then
+ wrk1_2d(i,j) = k
+ roughness_klevel(i,j) = k
+ exit kloop
+ endif
+ enddo kloop
+ endif
+ enddo
+ enddo
+
+
+ ! set bvfreq in bottom equal to value at kmt-1
+ do j=jsd,jed
+ do i=isd,ied
+ bvfreq_bottom(i,j) = 0.0
+ if(Grd%kmt(i,j) > 1) then
+ kbot=Grd%kmt(i,j)-1
+ bvfreq_bottom(i,j) = bvfreq(i,j,kbot)
+ endif
+ enddo
+ enddo
+
+ ! horizontal laplacian smoothing on the bottom bvfreq
+ if(smooth_bvfreq_bottom) then
+ bvfreq_bottom(:,:) = bvfreq_bottom(:,:) + dtime*LAP_T(bvfreq_bottom(:,:),smooth_lap(:,:))
+ call mpp_update_domains(bvfreq_bottom(:,:), Dom%domain2d)
+ endif
+
+
+ ! diagnostics
+
+ if (id_roughness_klevel > 0) then
+ used = send_data (id_roughness_klevel, wrk1_2d(:,:),&
+ Time%model_time, rmask=Grd%tmask(:,:,1), &
+ is_in=isc, js_in=jsc, ie_in=iec, je_in=jec)
+ endif
+ if (id_bvfreq_bottom > 0) then
+ used = send_data (id_bvfreq_bottom, bvfreq_bottom(:,:),&
+ Time%model_time, rmask=Grd%tmask(:,:,1), &
+ is_in=isc, js_in=jsc, ie_in=iec, je_in=jec)
+ endif
+ if (id_bvfreq > 0) then
+ used = send_data (id_bvfreq, bvfreq(:,:,:), &
+ Time%model_time, rmask=Grd%tmask(:,:,:), &
+ is_in=isc, js_in=jsc, ks_in=1, ie_in=iec, je_in=jec, ke_in=nk)
+ endif
+
+
+end subroutine compute_bvfreq
+! NAME="compute_bvfreq"
+
+
+
+!#######################################################################
+!
+!
+!
+! This subroutine computes dia-surface tracer diffusivity based on the
+! methods of Simmons et al., which consider dissipation from breaking
+! internal gravity waves and their conversion into local dia-surface
+! mixing, which is parameterized as diffusion.
+!
+! Also compute a prototype parameterization of mixing due to
+! breaking leewaves from Nikurashin.
+!
+! We assume a unit Prandtl number.
+!
+! Note that if umask(i,j,k) is 1.0, then so is
+! tmask(i,j,k), tmask(i+1,j,k), tmask(i,j+1,k), and tmask(i+1,j+1,k).
+! So there is no need to compute the "active_cells" when doing the
+! space average to go from t-cell to u-cell to compute visc_cbu.
+!
+!
+!
+ subroutine vert_mix_wave(Time, Thickness, Dens, diff_cbt, visc_cbu, visc_cbt, diff_cbt_wave, diff_cbt_leewave)
+
+ type(ocean_time_type), intent(in) :: Time
+ type(ocean_thickness_type), intent(in) :: Thickness
+ type(ocean_density_type), intent(in) :: Dens
+ real, dimension(isd:,jsd:,:,:), intent(inout) :: diff_cbt
+ real, dimension(isd:,jsd:,:), intent(inout) :: visc_cbu
+ real, dimension(isd:,jsd:,:), intent(inout) :: visc_cbt
+ real, dimension(isd:,jsd:,:), intent(inout) :: diff_cbt_wave
+ real, dimension(isd:,jsd:,:), intent(inout) :: diff_cbt_leewave
+
+ integer :: i, j, k, kbot, kp1, tau
+ real :: deposition, factor, tmp, rho_tmp
+
+ tau = Time%tau
+ diff_wave(:,:,:) = 0.0 ! diffusivity from wave scheme
+ diff_leewave(:,:,:) = 0.0 ! diffusivity from leewave scheme
+ wrk1(:,:,:) = 0.0 ! viscosity from wave scheme
+ wrk2(:,:,:) = 0.0 ! mix_efficiency / rho_N2
+
+ ! compute mask for regions that are deemed too shallow for this scheme
+ do j=jsd,jed
+ do i=isd,ied
+ kbot=Grd%kmt(i,j)
+ tmask_deep(i,j) = 0.0
+ if(kbot > 1) then
+ if(Thickness%depth_zwt(i,j,kbot) > shelf_depth_cutoff) tmask_deep(i,j) = 1.0
+ endif
+ enddo
+ enddo
+
+ ! energy flux array (W/m2) (Simmons etal equation (1))
+ if(fixed_wave_dissipation) then
+ do j=jsd,jed
+ do i=isd,ied
+ energy_flux(i,j) = min(wave_energy_flux_max, wave_dissipation(i,j)*tmask_deep(i,j))
+ enddo
+ enddo
+ else
+ do j=jsd,jed
+ do i=isd,ied
+ energy_flux(i,j) = min(wave_energy_flux_max, wave_term(i,j)*bvfreq_bottom(i,j)*tmask_deep(i,j))
+ enddo
+ enddo
+ endif
+
+ ! compute mixing efficiency function
+ if(mixing_efficiency_n2depend) then
+ do k=1,nk
+ do j=jsd,jed
+ do i=isd,ied
+ rho_tmp = Dens%rho(i,j,k,tau) + epsln
+ mix_efficiency(i,j,k) = mixing_efficiency*Grd%tmask(i,j,k) &
+ *rho_N2(i,j,k)/(rho_N2(i,j,k) + rho_tmp*omega_earth2)
+ wrk2(i,j,k) = mixing_efficiency*Grd%tmask(i,j,k) &
+ /(rho_N2(i,j,k) + rho_tmp*omega_earth2)
+ enddo
+ enddo
+ enddo
+ else
+ do k=1,nk
+ do j=jsd,jed
+ do i=isd,ied
+ mix_efficiency(i,j,k) = mixing_efficiency*Grd%tmask(i,j,k)
+ wrk2(i,j,k) = mixing_efficiency*Grd%tmask(i,j,k) &
+ /(rho_N2(i,j,k) + epsln)
+ enddo
+ enddo
+ enddo
+ endif
+
+
+ ! diffusivity calculation (Simmons etal equation (3))
+ do j=jsd,jed
+ do i=isd,ied
+
+ kbot=Grd%kmt(i,j)
+ if(kbot > 1) then
+
+ ! normalization of vertical structure function.
+ ! Ensure it integrates to unity on the discrete grid.
+ ! "factor" approx decay_scale_inv/(exp[(H+eta)*decay_scale_inv]-1.0)
+ factor = 0.0
+ do k=1,kbot-1
+ factor = factor + Thickness%dzt(i,j,k)*exp(decay_scale_inv*Thickness%depth_zwt(i,j,k))
+ enddo
+ factor = 1.0/factor
+
+ do k=1,kbot-1
+ deposition = factor*exp(decay_scale_inv*Thickness%depth_zwt(i,j,k))
+ tmp = Grd%tmask(i,j,k+1)*wrk2(i,j,k)*tidal_diss_efficiency*deposition
+ diff_wave(i,j,k) = tmp*energy_flux(i,j)
+ diff_leewave(i,j,k) = tmp*leewave_dissipation(i,j)
+ diff_wave(i,j,k) = min(diff_wave(i,j,k),max_wave_diffusivity)
+ diff_leewave(i,j,k) = min(diff_leewave(i,j,k),max_wave_diffusivity)
+ enddo
+
+ endif
+
+ enddo
+ enddo
+
+
+ ! ensure diffusivity monotonically decreases as move upward in column.
+ ! recall that diff_wave(i,j,k) is the diffusivity at the bottom of cell-k,
+ ! where diff_wave(i,j,kbot)=0.0 by definition. This prompts the kbot-2,1,-1
+ ! loop limits.
+ if(wave_diffusivity_monotonic) then
+ do j=jsd,jed
+ do i=isd,ied
+ kbot=Grd%kmt(i,j)
+ if(kbot > 1) then
+ do k=kbot-2,1,-1
+ diff_wave(i,j,k) = min(diff_wave(i,j,k),diff_wave(i,j,k+1))
+ diff_leewave(i,j,k) = min(diff_leewave(i,j,k),diff_leewave(i,j,k+1))
+ enddo
+ endif
+ enddo
+ enddo
+ endif
+
+ ! add wave induced diffusivity and viscosity to diff_cbt and visc_cbu
+ wrk1(:,:,:) = 0.0
+ wrk2(:,:,:) = 0.0
+ do k=1,nk-1
+ kp1=k+1
+ do j=jsc,jec
+ do i=isc,iec
+ diff_cbt_wave(i,j,k) = diff_wave(i,j,k)
+ diff_cbt_leewave(i,j,k) = diff_leewave(i,j,k)
+ diff_cbt(i,j,k,1) = diff_cbt(i,j,k,1) + diff_wave(i,j,k) + diff_leewave(i,j,k)
+ diff_cbt(i,j,k,2) = diff_cbt(i,j,k,2) + diff_wave(i,j,k) + diff_leewave(i,j,k)
+ visc_cbt(i,j,k) = visc_cbt(i,j,k) + diff_wave(i,j,k) + diff_leewave(i,j,k)
+ wrk1(i,j,k) = Grd%umask(i,j,kp1)*onefourth &
+ *(diff_wave(i,j,k) +diff_wave(i+1,j,k) &
+ +diff_wave(i,j+1,k) +diff_wave(i+1,j+1,k))
+ wrk2(i,j,k) = Grd%umask(i,j,kp1)*onefourth &
+ *(diff_leewave(i,j,k) +diff_leewave(i+1,j,k) &
+ +diff_leewave(i,j+1,k)+diff_leewave(i+1,j+1,k))
+ visc_cbu(i,j,k) = visc_cbu(i,j,k) + wrk1(i,j,k) + wrk2(i,j,k)
+ enddo
+ enddo
+ enddo
+
+
+ ! send some diagnostics
+
+ if (id_mix_efficiency > 0) then
+ used = send_data (id_mix_efficiency, mix_efficiency(:,:,:),&
+ Time%model_time, rmask=Grd%tmask(:,:,:), &
+ is_in=isc, js_in=jsc, ks_in=1, ie_in=iec, je_in=jec, ke_in=nk)
+ endif
+ if (id_energy_flux > 0) then
+ used = send_data (id_energy_flux, energy_flux(:,:), &
+ Time%model_time, rmask=Grd%tmask(:,:,1), &
+ is_in=isc, js_in=jsc, ie_in=iec, je_in=jec)
+ endif
+ if (id_power_waves > 0) then
+ used = send_data (id_power_waves, Grd%dat(:,:)*energy_flux(:,:), &
+ Time%model_time, rmask=Grd%tmask(:,:,1), &
+ is_in=isc, js_in=jsc, ie_in=iec, je_in=jec)
+ endif
+ if (id_diff_cbt_wave > 0) then
+ used = send_data (id_diff_cbt_wave, diff_wave(:,:,:), &
+ Time%model_time, rmask=Grd%tmask(:,:,:), &
+ is_in=isc, js_in=jsc, ks_in=1, ie_in=iec, je_in=jec, ke_in=nk)
+ endif
+ if (id_diff_cbt_leewave > 0) then
+ used = send_data (id_diff_cbt_leewave, diff_leewave(:,:,:), &
+ Time%model_time, rmask=Grd%tmask(:,:,:), &
+ is_in=isc, js_in=jsc, ks_in=1, ie_in=iec, je_in=jec, ke_in=nk)
+ endif
+ if (id_visc_cbt_wave > 0) then
+ used = send_data (id_visc_cbt_wave, diff_wave(:,:,:), &
+ Time%model_time, rmask=Grd%tmask(:,:,:), &
+ is_in=isc, js_in=jsc, ks_in=1, ie_in=iec, je_in=jec, ke_in=nk)
+ endif
+ if (id_visc_cbt_leewave > 0) then
+ used = send_data (id_visc_cbt_leewave, diff_leewave(:,:,:), &
+ Time%model_time, rmask=Grd%tmask(:,:,:), &
+ is_in=isc, js_in=jsc, ks_in=1, ie_in=iec, je_in=jec, ke_in=nk)
+ endif
+ if (id_visc_cbu_wave > 0) then
+ used = send_data (id_visc_cbu_wave, wrk1(:,:,:), &
+ Time%model_time, rmask=Grd%umask(:,:,:), &
+ is_in=isc, js_in=jsc, ks_in=1, ie_in=iec, je_in=jec, ke_in=nk)
+ endif
+ if (id_visc_cbu_leewave > 0) then
+ used = send_data (id_visc_cbu_leewave, wrk2(:,:,:), &
+ Time%model_time, rmask=Grd%umask(:,:,:), &
+ is_in=isc, js_in=jsc, ks_in=1, ie_in=iec, je_in=jec, ke_in=nk)
+ endif
+
+
+end subroutine vert_mix_wave
+! NAME="vert_mix_wave"
+
+
+!#######################################################################
+!
+!
+!
+! This subroutine computes dia-surface tracer diffusivity based on the
+! methods of Lee etal., which consider the dissipation from barotropic tides
+! rubbing against the ocean bottom.
+!
+! We assume B-grid layout for the velocity
+!
+! We assume a unit Prandtl number, so compute the viscosity as a four-point
+! average of the diffusivity.
+!
+! We perform various averages here in order to smooth Richardson number.
+!
+! 1. compute Richardson number on U-cell by averaging bvfreq from T-cell
+! 2. average U-cell Richardson number to then get T-cell diffusivity
+! 3. average T-cell diffusivity to get U-cell viscosity.
+!
+! Note that if umask(i,j,k)==1.0, then so is tmask(i,j,k), tmask(i+1,j,k),
+! tmask(i,j+1,k), and tmask(i+1,j+1,k). So there is no need to compute
+! active_cells when averaging from T-cell to U-cell.
+!
+!
+!
+ subroutine vert_mix_drag_bgrid(Time, Thickness, Velocity, diff_cbt, visc_cbu, visc_cbt, diff_cbt_drag)
+
+ type(ocean_time_type), intent(in) :: Time
+ type(ocean_thickness_type), intent(in) :: Thickness
+ type(ocean_velocity_type), intent(in) :: Velocity
+ real, dimension(isd:,jsd:,:,:), intent(inout) :: diff_cbt
+ real, dimension(isd:,jsd:,:), intent(inout) :: visc_cbu
+ real, dimension(isd:,jsd:,:), intent(inout) :: visc_cbt
+ real, dimension(isd:,jsd:,:), intent(inout) :: diff_cbt_drag
+
+ integer :: i, j, k, kbot, kp1
+ real :: height, bottom, efold
+ real :: bvfreq_u, speedr, active_cells, temporary
+
+ integer :: stdoutunit,stdlogunit
+ stdoutunit=stdout();stdlogunit=stdlog()
+
+ wrk1(:,:,:) =0.0 ! Richardson number on U-cell
+ wrk2(:,:,:) =0.0 ! Richardson number on T-cell
+ wrk3(:,:,:) =0.0 ! viscosity from drag scheme
+ diff_drag(:,:,:) =0.0 ! diffusivity from drag scheme
+
+
+ ! speed scale for tides rubbing against bottom
+ ! (defined following eq. (3) in Lee etal)
+ if(drag_dissipation_use_cdbot) then
+ do j=jsd,jed
+ do i=isd,ied
+ rescaled_speed_u(i,j) = sqrt(Velocity%cdbot_array(i,j))*von_karman_inv*tide_speed_u(i,j)
+ rescaled_speed_t(i,j) = sqrt(Velocity%cdbot_array(i,j))*von_karman_inv*tide_speed_t(i,j)
+ tide_rescspeed_mask(i,j) = 0.0
+ if(rescaled_speed_u(i,j) > speed_min) then
+ tide_rescspeed_mask(i,j) = 1.0
+ endif
+ enddo
+ enddo
+
+
+ ! compute efolding depth scale for use in Lee etal scheme.
+ ! efold depth set as rescaled_speed/(radial tide frequency).
+ ! Choose default radial tide frequency as 2pi/12hrs for semi-diurnal tide.
+ ! let this efolding hold whether using Bgrid or Cgrid.
+ wrk1_2d(:,:) = 0.0
+ do j=jsc,jec
+ do i=isc,iec
+ active_cells = Grd%umask(i,j,1) + Grd%umask(i-1,j,1) &
+ + Grd%umask(i,j-1,1) + Grd%umask(i-1,j-1,1) + epsln
+ temporary = (rescaled_speed_u(i,j) + rescaled_speed_u(i-1,j) + &
+ rescaled_speed_u(i,j-1) + rescaled_speed_u(i-1,j-1))/active_cells
+ wrk1_2d(i,j) = Grd%tmask(i,j,1)*temporary*drag_dissipation_tide_period/(2.0*pi)
+ efold_depth_r(i,j) = Grd%tmask(i,j,1)/(wrk1_2d(i,j) + epsln)
+ enddo
+ enddo
+
+ endif ! if(drag_dissipation_use_cdbot)
+
+
+ ! Richardson number on U-cell.
+ ! perform a 4-point average of T-cell bvfreq
+ ! and then divide by the U-cell tidal speed term.
+ ! tide_speed_mask is useful to reduce overflows
+ ! in later calculation of the diffusivity.
+
+
+if(drag_mask_deep .and. .not. use_legacy_methods) then
+! only to reproduce the previous results with const cdbot
+! tide_deepspeed_mask(i,j) is the same as tide_speed_mask(i,j) of the previous
+ do j=jsd,jed-1
+ do i=isd,ied-1
+ kbot=Grd%kmu(i,j)
+ if(kbot>1) then
+ bottom = Thickness%depth_zwu(i,j,kbot)
+ speedr = tide_deepspeed_mask(i,j)/(epsln+rescaled_speed_u(i,j))
+ do k=1,kbot-1
+ kp1=k+1
+ height = bottom-Thickness%depth_zwu(i,j,k)
+ bvfreq_u = onefourth*(bvfreq(i,j,k)+bvfreq(i+1,j,k)+bvfreq(i,j+1,k)+bvfreq(i+1,j+1,k))
+ wrk1(i,j,k) = 2.0*Grd%umask(i,j,kp1)*(bvfreq_u*height*speedr)**2
+ enddo
+ endif
+ enddo
+ enddo
+else
+ do j=jsd,jed-1
+ do i=isd,ied-1
+ kbot=Grd%kmu(i,j)
+ if(kbot>1) then
+ bottom = Thickness%depth_zwu(i,j,kbot)
+ speedr = tide_rescspeed_mask(i,j)*tide_deepspeed_mask(i,j)/(epsln+rescaled_speed_u(i,j))
+ do k=1,kbot-1
+ kp1=k+1
+ height = bottom-Thickness%depth_zwu(i,j,k)
+ bvfreq_u = onefourth*(bvfreq(i,j,k)+bvfreq(i+1,j,k)+bvfreq(i,j+1,k)+bvfreq(i+1,j+1,k))
+ wrk1(i,j,k) = 2.0*Grd%umask(i,j,kp1)*(bvfreq_u*height*speedr)**2
+ enddo
+ endif
+ enddo
+ enddo
+endif
+
+ ! Richardson number on bottom of T-cells.
+ ! need active_cells for averaging operation.
+ do k=1,nk-1
+ do j=jsc,jec
+ do i=isc,iec
+ active_cells = Grd%umask(i,j,k) + Grd%umask(i-1,j,k) &
+ + Grd%umask(i,j-1,k) + Grd%umask(i-1,j-1,k) + epsln
+ wrk2(i,j,k) = (wrk1(i,j,k) + wrk1(i-1,j,k) + wrk1(i,j-1,k) + wrk1(i-1,j-1,k))/active_cells
+ enddo
+ enddo
+ enddo
+
+
+ ! compute drag induced diffusivity
+ ! (Lee etal equations (1), (2), and (3))
+ ! Multiply by tide_speed_mask so to zero out
+ ! regions with tiny tide speeds, which are regions
+ ! where we do not wish to have any enhanced mixing
+ ! arising from the barotropic tide mixing parameterization
+ ! anyhow.
+
+if(drag_mask_deep .and. .not. use_legacy_methods) then
+! only to reproduce the previous results with const cdbot
+! tide_deepspeed_mask(i,j) is the same as tide_speed_mask(i,j) of the previous
+ do k=1,nk-1
+ kp1=k+1
+ do j=jsc,jec
+ do i=isc,iec
+ diff_drag(i,j,k) = Grd%tmask(i,j,kp1)*tide_deepspeed_mask(i,j) &
+ *max_drag_diffusivity*(1.0 + munk_anderson_sigma*wrk2(i,j,k))**(-munk_anderson_p)
+ enddo
+ enddo
+ enddo
+
+else
+ do k=1,nk-1
+ kp1=k+1
+ do j=jsc,jec
+ do i=isc,iec
+ diff_drag(i,j,k) = Grd%tmask(i,j,kp1)*tide_rescspeed_mask(i,j)*tide_deepspeed_mask(i,j) &
+ *max_drag_diffusivity*(1.0 + munk_anderson_sigma*wrk2(i,j,k))**(-munk_anderson_p)
+ enddo
+ enddo
+ enddo
+endif
+
+
+ if(drag_dissipation_efold) then
+ do j=jsc,jec
+ do i=isc,iec
+ kbot=Grd%kmt(i,j)
+ if(kbot>1) then
+ bottom = Thickness%depth_zwt(i,j,kbot)
+ do k=1,kbot-1
+ kp1=k+1
+ height = bottom-Thickness%depth_zwt(i,j,k)
+ diff_drag(i,j,k) = diff_drag(i,j,k)*exp(-height*efold_depth_r(i,j))
+ enddo
+ endif
+ enddo
+ enddo
+ endif
+
+ call mpp_update_domains(diff_drag(:,:,:), Dom%domain2d)
+
+
+ ! add drag induced diffusivity and viscosity to diff_cbt and visc_cbu.
+ ! average t-cell diffusivities to get u-cell viscosity.
+ do k=1,nk-1
+ kp1=k+1
+ do j=jsc,jec
+ do i=isc,iec
+ diff_cbt_drag(i,j,k) = diff_drag(i,j,k)
+ diff_cbt(i,j,k,1) = diff_cbt(i,j,k,1) + diff_drag(i,j,k)
+ diff_cbt(i,j,k,2) = diff_cbt(i,j,k,2) + diff_drag(i,j,k)
+ visc_cbt(i,j,k) = visc_cbt(i,j,k) + diff_drag(i,j,k)
+ wrk3(i,j,k) = Grd%umask(i,j,kp1)*onefourth &
+ *(diff_drag(i,j,k) +diff_drag(i+1,j,k) &
+ +diff_drag(i,j+1,k)+diff_drag(i+1,j+1,k))
+ visc_cbu(i,j,k) = visc_cbu(i,j,k) + wrk3(i,j,k)
+ enddo
+ enddo
+ enddo
+
+
+ if (id_rinumber_drag > 0) then
+ used = send_data (id_rinumber_drag, wrk2(:,:,:),&
+ Time%model_time, rmask=Grd%tmask(:,:,:), &
+ is_in=isc, js_in=jsc, ks_in=1, ie_in=iec, je_in=jec, ke_in=nk)
+ endif
+ if (id_diff_cbt_drag > 0) then
+ used = send_data (id_diff_cbt_drag, diff_drag(:,:,:), &
+ Time%model_time, rmask=Grd%tmask(:,:,:), &
+ is_in=isc, js_in=jsc, ks_in=1, ie_in=iec, je_in=jec, ke_in=nk)
+ endif
+ if (id_visc_cbu_drag > 0) then
+ used = send_data (id_visc_cbu_drag, wrk3(:,:,:), &
+ Time%model_time, rmask=Grd%umask(:,:,:), &
+ is_in=isc, js_in=jsc, ks_in=1, ie_in=iec, je_in=jec, ke_in=nk)
+ endif
+
+if(drag_dissipation_use_cdbot) then
+ if (id_tide_rescspeed_mask > 0) then
+ used = send_data (id_tide_rescspeed_mask, tide_rescspeed_mask(:,:), &
+ Time%model_time, rmask=Grd%umask(:,:,1), &
+ is_in=isc, js_in=jsc, ie_in=iec, je_in=jec)
+ endif
+ if (id_drag_diss_efold > 0) then
+ used = send_data (id_drag_diss_efold, wrk1_2d(:,:), &
+ Time%model_time, rmask=Grd%tmask(:,:,1), &
+ is_in=isc, js_in=jsc, ie_in=iec, je_in=jec)
+ endif
+endif !if(drag_dissipation_use_cdbot)
+
+
+end subroutine vert_mix_drag_bgrid
+! NAME="vert_mix_drag_bgrid"
+
+
+!#######################################################################
+!
+!
+!
+! This subroutine computes dia-surface tracer diffusivity based on the
+! methods of Lee etal., which consider the dissipation from barotropic tides
+! rubbing against the ocean bottom.
+!
+! We assume a unit Prandtl number, so compute the viscosity as a four-point
+! average of the diffusivity.
+!
+! We assume C-grid layout for the velocity, which renders slight
+! distinctions for the calculation of Richardson number. Otherwise, the
+! calculations are the same as the Bgrid. We introduce this separate
+! routine, however, to enable easier bitwise agreement with older
+! model results. Also, further development of this scheme may lead
+! to more distinctions from the Bgrid.
+!
+!
+!
+ subroutine vert_mix_drag_cgrid(Time, Thickness, Velocity, diff_cbt, visc_cbu, visc_cbt, diff_cbt_drag)
+
+ type(ocean_time_type), intent(in) :: Time
+ type(ocean_thickness_type), intent(in) :: Thickness
+ type(ocean_velocity_type), intent(in) :: Velocity
+ real, dimension(isd:,jsd:,:,:), intent(inout) :: diff_cbt
+ real, dimension(isd:,jsd:,:), intent(inout) :: visc_cbu
+ real, dimension(isd:,jsd:,:), intent(inout) :: visc_cbt
+ real, dimension(isd:,jsd:,:), intent(inout) :: diff_cbt_drag
+
+ integer :: i, j, k, kbot, kp1
+ real :: height, bottom, efold
+ real :: bvfreq_u, speedr, active_cells, temporary
+
+ integer :: stdoutunit,stdlogunit
+ stdoutunit=stdout();stdlogunit=stdlog()
+
+ wrk1(:,:,:) = 0.0 ! raw Richardson number on T-cell
+ wrk2(:,:,:) = 0.0 ! smoothed Richardson number on T-cell
+ wrk3(:,:,:) = 0.0 ! visc_cbu from drag scheme
+ diff_drag(:,:,:) = 0.0 ! diffusivity from drag scheme
+
+
+ ! speed scale for tides rubbing against bottom
+ ! (defined following eq. (3) in Lee etal)
+
+ if(drag_dissipation_use_cdbot) then
+ do j=jsd,jed
+ do i=isd,ied
+ rescaled_speed_u(i,j) = sqrt(Velocity%cdbot_array(i,j))*von_karman_inv*tide_speed_u(i,j)
+ rescaled_speed_t(i,j) = sqrt(Velocity%cdbot_array(i,j))*von_karman_inv*tide_speed_t(i,j)
+ tide_rescspeed_mask(i,j) = 0.0
+ if(rescaled_speed_u(i,j) > speed_min) then
+ tide_rescspeed_mask(i,j) = 1.0
+ endif
+ enddo
+ enddo
+! call mpp_update_domains(tide_rescspeed_mask(:,:), Dom%domain2d)
+
+ ! compute efolding depth scale for use in Lee etal scheme.
+ ! efold depth set as rescaled_speed/(radial tide frequency).
+ ! Choose default radial tide frequency as 2pi/12hrs for semi-diurnal tide.
+ ! let this efolding hold whether using Bgrid or Cgrid.
+
+ wrk1_2d(:,:) = 0.0
+ do j=jsc,jec
+ do i=isc,iec
+ active_cells = Grd%umask(i,j,1) + Grd%umask(i-1,j,1) &
+ + Grd%umask(i,j-1,1) + Grd%umask(i-1,j-1,1) + epsln
+ temporary = (rescaled_speed_u(i,j) + rescaled_speed_u(i-1,j) + &
+ rescaled_speed_u(i,j-1) + rescaled_speed_u(i-1,j-1))/active_cells
+ wrk1_2d(i,j) = Grd%tmask(i,j,1)*temporary*drag_dissipation_tide_period/(2.0*pi)
+ efold_depth_r(i,j) = Grd%tmask(i,j,1)/(wrk1_2d(i,j) + epsln)
+ enddo
+ enddo
+
+
+ endif !if(drag_dissipation_use_cdbot)
+
+ ! Richardson number on T-cell.
+if(drag_mask_deep .and. .not. use_legacy_methods) then
+! only to reproduce the previous results with const cdbot
+! tide_deepspeed_mask(i,j) is the same as tide_speed_mask(i,j) of the previous
+ do j=jsd,jed
+ do i=isd,ied
+ kbot=Grd%kmt(i,j)
+ if(kbot>1) then
+ bottom = Thickness%depth_zwt(i,j,kbot)
+ speedr = tide_deepspeed_mask(i,j)/(epsln+rescaled_speed_t(i,j))
+ do k=1,kbot-1
+ kp1=k+1
+ height = bottom-Thickness%depth_zwt(i,j,k)
+ wrk1(i,j,k) = 2.0*Grd%tmask(i,j,kp1)*(bvfreq(i,j,k)*height*speedr)**2
+ wrk2(i,j,k) = wrk1(i,j,k)
+ enddo
+ endif
+ enddo
+ enddo
+else
+ do j=jsd,jed
+ do i=isd,ied
+ kbot=Grd%kmt(i,j)
+ if(kbot>1) then
+ bottom = Thickness%depth_zwt(i,j,kbot)
+ speedr = tide_rescspeed_mask(i,j)*tide_deepspeed_mask(i,j)/(epsln+rescaled_speed_t(i,j))
+ do k=1,kbot-1
+ kp1=k+1
+ height = bottom-Thickness%depth_zwt(i,j,k)
+ wrk1(i,j,k) = 2.0*Grd%tmask(i,j,kp1)*(bvfreq(i,j,k)*height*speedr)**2
+ wrk2(i,j,k) = wrk1(i,j,k)
+ enddo
+ endif
+ enddo
+ enddo
+endif
+
+
+ ! perform 9point average to smooth, and to be more consistent
+ ! with the Bgrid approach.
+ ! need active_cells for averaging operation.
+ if(smooth_ri_drag_cgrid) then
+ do k=1,nk-1
+ do j=jsc,jec
+ do i=isc,iec
+ active_cells = Grd%tmask(i-1,j-1,k) + Grd%tmask(i,j-1,k) + Grd%tmask(i+1,j-1,k) &
+ + Grd%tmask(i,j-1,k) + Grd%tmask(i,j,k) + Grd%tmask(i+1,j,k) &
+ + Grd%tmask(i-1,j+1,k) + Grd%tmask(i,j+1,k) + Grd%tmask(i+1,j+1,k) &
+ + epsln
+ wrk2(i,j,k) = ( wrk1(i-1,j-1,k) + wrk1(i,j-1,k) + wrk1(i+1,j-1,k) &
+ + wrk1(i,j-1,k) + wrk1(i,j,k) + wrk1(i+1,j,k) &
+ + wrk1(i-1,j+1,k) + wrk1(i,j+1,k) + wrk1(i+1,j+1,k)) / active_cells
+ enddo
+ enddo
+ enddo
+ endif
+
+
+ ! compute drag induced diffusivity
+ ! (Lee etal equations (1), (2), and (3))
+ ! Multiply by tide_speed_mask so to zero out
+ ! regions with tiny tide speeds, which are regions
+ ! where we do not wish to have any enhanced mixing
+ ! arising from the barotropic tide mixing parameterization
+ ! anyhow.
+
+if(drag_mask_deep .and. .not. use_legacy_methods) then
+! only to reproduce the previous results with const cdbot
+! tide_deepspeed_mask(i,j) is the same as tide_speed_mask(i,j) of the previous
+ do k=1,nk-1
+ kp1=k+1
+ do j=jsc,jec
+ do i=isc,iec
+ diff_drag(i,j,k) = Grd%tmask(i,j,kp1)*tide_deepspeed_mask(i,j) &
+ *max_drag_diffusivity*(1.0 + munk_anderson_sigma*wrk2(i,j,k))**(-munk_anderson_p)
+ enddo
+ enddo
+ enddo
+
+else
+ do k=1,nk-1
+ kp1=k+1
+ do j=jsc,jec
+ do i=isc,iec
+ diff_drag(i,j,k) = Grd%tmask(i,j,kp1)*tide_rescspeed_mask(i,j)*tide_deepspeed_mask(i,j) &
+ *max_drag_diffusivity*(1.0 + munk_anderson_sigma*wrk2(i,j,k))**(-munk_anderson_p)
+ enddo
+ enddo
+ enddo
+endif
+
+ if(drag_dissipation_efold) then
+ do j=jsc,jec
+ do i=isc,iec
+ kbot=Grd%kmt(i,j)
+ if(kbot>1) then
+ bottom = Thickness%depth_zwt(i,j,kbot)
+ do k=1,kbot-1
+ kp1=k+1
+ height = bottom-Thickness%depth_zwt(i,j,k)
+ diff_drag(i,j,k) = diff_drag(i,j,k)*exp(-height*efold_depth_r(i,j))
+ enddo
+ endif
+ enddo
+ enddo
+ endif
+
+ call mpp_update_domains(diff_drag(:,:,:), Dom%domain2d)
+
+
+ ! add drag induced diffusivity and viscosity to diff_cbt and visc_cbu.
+ ! average t-cell diffusivities to get u-cell viscosity.
+ do k=1,nk-1
+ kp1=k+1
+ do j=jsc,jec
+ do i=isc,iec
+ diff_cbt_drag(i,j,k) = diff_drag(i,j,k)
+ diff_cbt(i,j,k,1) = diff_cbt(i,j,k,1) + diff_drag(i,j,k)
+ diff_cbt(i,j,k,2) = diff_cbt(i,j,k,2) + diff_drag(i,j,k)
+ visc_cbt(i,j,k) = visc_cbt(i,j,k) + diff_drag(i,j,k)
+ wrk3(i,j,k) = Grd%umask(i,j,kp1)*onefourth &
+ *(diff_drag(i,j,k) +diff_drag(i+1,j,k) &
+ +diff_drag(i,j+1,k)+diff_drag(i+1,j+1,k))
+ visc_cbu(i,j,k) = visc_cbu(i,j,k) + wrk3(i,j,k)
+ enddo
+ enddo
+ enddo
+
+
+ if (id_rinumber_drag > 0) then
+ used = send_data (id_rinumber_drag, wrk2(:,:,:),&
+ Time%model_time, rmask=Grd%tmask(:,:,:), &
+ is_in=isc, js_in=jsc, ks_in=1, ie_in=iec, je_in=jec, ke_in=nk)
+ endif
+ if (id_diff_cbt_drag > 0) then
+ used = send_data (id_diff_cbt_drag, diff_drag(:,:,:), &
+ Time%model_time, rmask=Grd%tmask(:,:,:), &
+ is_in=isc, js_in=jsc, ks_in=1, ie_in=iec, je_in=jec, ke_in=nk)
+ endif
+ if (id_visc_cbu_drag > 0) then
+ used = send_data (id_visc_cbu_drag, wrk3(:,:,:), &
+ Time%model_time, rmask=Grd%umask(:,:,:), &
+ is_in=isc, js_in=jsc, ks_in=1, ie_in=iec, je_in=jec, ke_in=nk)
+ endif
+
+if(drag_dissipation_use_cdbot) then
+ if (id_tide_rescspeed_mask > 0) then
+ used = send_data (id_tide_rescspeed_mask, tide_rescspeed_mask(:,:), &
+ Time%model_time, rmask=Grd%umask(:,:,1), &
+ is_in=isc, js_in=jsc, ie_in=iec, je_in=jec)
+ endif
+ if (id_drag_diss_efold > 0) then
+ used = send_data (id_drag_diss_efold, wrk1_2d(:,:), &
+ Time%model_time, rmask=Grd%tmask(:,:,1), &
+ is_in=isc, js_in=jsc, ie_in=iec, je_in=jec)
+ endif
+endif !if(drag_dissipation_use_cdbot)
+
+
+end subroutine vert_mix_drag_cgrid
+! NAME="vert_mix_drag_cgrid"
+
+
+!#######################################################################
+!
+!
+!
+! This subroutine computes the absolute value of rho*N^2 and abs of
+! N^2, with N^2 the squared Brunt-Vaisala (or buoyancy) frequency.
+!
+! This routine employs a legacy approach, which is not recommended.
+! It remains solely to allow exact reproduction of older results.
+!
+!
+!
+ subroutine compute_bvfreq_legacy(Time, Thickness, T_prog, Dens)
+
+ type(ocean_time_type), intent(in) :: Time
+ type(ocean_thickness_type), intent(in) :: Thickness
+ type(ocean_prog_tracer_type), intent(in) :: T_prog(:)
+ type(ocean_density_type), intent(in) :: Dens
+
+ real :: rho_inv, drhodz
+ real :: tmp, rho_N2_prev, rho_tmp
+ integer :: i, j, k, m, kp1, kbot
+ integer :: tau
+
+ tau = Time%tau
+ wrk1(:,:,:) = 0.0
+ wrk2(:,:,:) = 0.0
+
+ ! partial derivatives of density wrt to temperature and salinity
+ do k=1,nk
+ do j=jsd,jed
+ do i=isd,ied
+ drhodT(i,j,k) = Dens%drhodT(i,j,k)
+ drhodS(i,j,k) = Dens%drhodS(i,j,k)
+ enddo
+ enddo
+ enddo
+
+
+ ! vertical derivative of temperature and salinity at bottom of tracer cells
+ do k=1,nk
+ kp1=min(k+1,nk)
+ do j=jsd,jed
+ do i=isd,ied
+ tmp = Grd%tmask(i,j,kp1)/Thickness%dzwt(i,j,k)
+ wrk1(i,j,k) = tmp*(T_prog(index_temp)%field(i,j,k,tau)-T_prog(index_temp)%field(i,j,kp1,tau))
+ wrk2(i,j,k) = tmp*(Dens%rho_salinity(i,j,k,tau)-Dens%rho_salinity(i,j,kp1,tau))
+ enddo
+ enddo
+ enddo
+
+ ! absolute(rho*N^2) computed from vertical derivative of "neutral density"
+ do k=1,nk
+ kp1 = min(k+1,nk)
+ do j=jsd,jed
+ do i=isd,ied
+ drhodz = onehalf*( (drhodT(i,j,k)+drhodT(i,j,kp1))*wrk1(i,j,k) &
+ +(drhodS(i,j,k)+drhodS(i,j,kp1))*wrk2(i,j,k) )
+ drhodz = min(drhodz,-drhodz_min)*Grd%tmask(i,j,kp1)
+ rho_N2(i,j,k) = -grav*drhodz
+ enddo
+ enddo
+ enddo
+
+ ! smooth rho_N2 in the vertical using a 1-2-1 filter
+ if (smooth_rho_N2) then
+ do m=1,num_121_passes
+ do j=jsd,jed
+ do i=isd,ied
+ rho_N2_prev = onefourth*rho_N2(i,j,1)
+ kbot=Grd%kmt(i,j)
+ if (kbot>3) then
+ do k=2,kbot-2
+ tmp = rho_N2(i,j,k)
+ rho_N2(i,j,k) = rho_N2_prev + onehalf*rho_N2(i,j,k) + onefourth*rho_N2(i,j,k+1)
+ rho_N2_prev = onefourth*tmp
+ enddo
+ endif
+ enddo
+ enddo
+ enddo
+ endif
+
+ ! compute buoyancy frequency
+ do k=1,nk
+ kp1 = min(k+1,nk)
+ do j=jsd,jed
+ do i=isd,ied
+ rho_inv = 2.0/(epsln + Dens%rho(i,j,k,tau) + Dens%rho(i,j,kp1,tau))
+ bvfreq(i,j,k) = sqrt(rho_inv*rho_N2(i,j,k))
+ enddo
+ enddo
+ enddo
+
+ ! bvfreq at the bottom.
+ ! set kbot=kmt-1 rather than kbot=kmt, since N^2=0
+ ! at bottom of bottom-most tracer cell, by definition.
+ do j=jsd,jed
+ do i=isd,ied
+ bvfreq_bottom(i,j) = 0.0
+ if(Grd%kmt(i,j) > 1) then
+ kbot=Grd%kmt(i,j)-1
+ bvfreq_bottom(i,j) = bvfreq(i,j,kbot)
+ endif
+ enddo
+ enddo
+
+ ! horizontal laplacian smoothing on the bottom bvfreq to reduce noise
+ if(smooth_bvfreq_bottom) then
+ bvfreq_bottom(:,:) = bvfreq_bottom(:,:) + dtime*LAP_T(bvfreq_bottom(:,:),smooth_lap(:,:))
+ call mpp_update_domains(bvfreq_bottom(:,:), Dom%domain2d)
+ endif
+
+ ! compute mixing efficiency
+ mix_efficiency(:,:,:) = mixing_efficiency
+ if(mixing_efficiency_n2depend) then
+ do k=1,nk
+ do j=jsd,jed
+ do i=isd,ied
+ rho_tmp = Dens%rho(i,j,k,tau) + epsln
+ mix_efficiency(i,j,k) = mixing_efficiency*rho_N2(i,j,k)/(rho_N2(i,j,k) + rho_tmp*omega_earth2)
+ enddo
+ enddo
+ enddo
+ endif
+
+ if (id_bvfreq_bottom > 0) then
+ used = send_data (id_bvfreq_bottom, bvfreq_bottom(:,:),&
+ Time%model_time, rmask=Grd%tmask(:,:,1), &
+ is_in=isc, js_in=jsc, ie_in=iec, je_in=jec)
+ endif
+ if (id_bvfreq > 0) then
+ used = send_data (id_bvfreq, bvfreq(:,:,:), &
+ Time%model_time, rmask=Grd%tmask(:,:,:), &
+ is_in=isc, js_in=jsc, ks_in=1, ie_in=iec, je_in=jec, ke_in=nk)
+ endif
+ if (id_mix_efficiency > 0) then
+ used = send_data (id_mix_efficiency, mix_efficiency(:,:,:),&
+ Time%model_time, rmask=Grd%tmask(:,:,:), &
+ is_in=isc, js_in=jsc, ks_in=1, ie_in=iec, je_in=jec, ke_in=nk)
+ endif
+
+end subroutine compute_bvfreq_legacy
+! NAME="compute_bvfreq_legacy"
+
+
+!#######################################################################
+!
+!
+!
+!
+! Legacy routine maintained only to exactly reproduce older results.
+! It is not recommended for new experiments, as it uses some obsolete
+! methods.
+!
+! This subroutine computes dia-surface tracer diffusivity based on the
+! methods of Simmons etal., which consider the dissipation from breaking
+! internal gravity waves and their conversion into local dia-surface
+! diffusion.
+!
+! We assume a unit Prandtl number, so compute the viscosity as a four-point
+! average of the diffusivity.
+!
+! Note that if umask(i,j,k) is 1.0, then so is
+! tmask(i,j,k), tmask(i+1,j,k), tmask(i,j+1,k), and tmask(i+1,j+1,k).
+! So there is no need to compute the "active_cells" when doing the
+! space average to go from t-cell to u-cell to compute viscosity.
+!
+!
+!
+ subroutine vert_mix_wave_legacy(Time, Thickness, diff_cbt, visc_cbu, visc_cbt, diff_cbt_wave)
+
+ type(ocean_time_type), intent(in) :: Time
+ type(ocean_thickness_type), intent(in) :: Thickness
+ real, dimension(isd:,jsd:,:,:), intent(inout) :: diff_cbt
+ real, dimension(isd:,jsd:,:), intent(inout) :: visc_cbu
+ real, dimension(isd:,jsd:,:), intent(inout) :: visc_cbt
+ real, dimension(isd:,jsd:,:), intent(inout) :: diff_cbt_wave
+
+ integer :: i, j, k, kbot, kp1
+ real :: deposition, factor
+
+ diff_wave(:,:,:) = 0.0 ! diffusivity from wave scheme
+ wrk1(:,:,:) = 0.0 ! viscosity from wave scheme
+
+ ! compute mask for regions that are too shallow for this scheme
+ do j=jsd,jed
+ do i=isd,ied
+ kbot=Grd%kmt(i,j)
+ tmask_deep(i,j) = 0.0
+ if(kbot > 1) then
+ if(Thickness%depth_zwt(i,j,kbot) > shelf_depth_cutoff) tmask_deep(i,j) = 1.0
+ endif
+ enddo
+ enddo
+
+ ! compute the wave energy flux array (W/m2) and save for diagnostics
+ ! (Simmons etal equation (1))
+ if(fixed_wave_dissipation) then
+ do j=jsd,jed
+ do i=isd,ied
+ energy_flux(i,j) = min(wave_energy_flux_max, wave_dissipation(i,j)*tmask_deep(i,j))
+ enddo
+ enddo
+ else
+ do j=jsd,jed
+ do i=isd,ied
+ energy_flux(i,j) = min(wave_energy_flux_max, wave_term(i,j)*bvfreq_bottom(i,j)*tmask_deep(i,j))
+ enddo
+ enddo
+ endif
+
+ ! compute wave induced diffusivity
+ ! (Simmons etal equation (3))
+ do j=jsd,jed
+ do i=isd,ied
+ kbot=Grd%kmt(i,j)
+ if(kbot > 1) then
+
+ ! normalization of vertical structure function...ensure it
+ ! integrates to unity on the discrete grid.
+ factor = 0.0
+ do k=1,kbot-1
+ factor = factor + Thickness%dzt(i,j,k)*exp(decay_scale_inv*Thickness%depth_zwt(i,j,k))
+ enddo
+ factor = 1.0/factor
+
+ ! calculate diffusivity
+ do k=1,kbot-1
+ deposition = factor*exp(decay_scale_inv*Thickness%depth_zwt(i,j,k))
+ diff_wave(i,j,k) = Grd%tmask(i,j,k+1)*mix_efficiency(i,j,k)*tidal_diss_efficiency &
+ *energy_flux(i,j)*deposition/(epsln+rho_N2(i,j,k))
+ diff_wave(i,j,k) = min(diff_wave(i,j,k),max_wave_diffusivity)
+ enddo
+
+ endif
+ enddo
+ enddo
+
+ ! ensure diffusivity monotonically decreases as move upward in column.
+ ! recall that diff_wave(i,j,k) is the diffusivity at the bottom of cell-k,
+ ! where diff_wave(i,j,kbot)=0.0 by definition. This prompts the kbot-2,1,-1
+ ! loop limits.
+ if(wave_diffusivity_monotonic) then
+ do j=jsd,jed
+ do i=isd,ied
+ kbot=Grd%kmt(i,j)
+ if(kbot > 1) then
+ do k=kbot-2,1,-1
+ diff_wave(i,j,k) = min(diff_wave(i,j,k),diff_wave(i,j,k+1))
+ enddo
+ endif
+ enddo
+ enddo
+ endif
+
+ ! add wave induced diffusivity and viscosity to diff_cbt and visc_cbu
+ do k=1,nk-1
+ kp1=k+1
+ do j=jsc,jec
+ do i=isc,iec
+ diff_cbt_wave(i,j,k) = diff_wave(i,j,k)
+ diff_cbt(i,j,k,1) = diff_cbt(i,j,k,1) + diff_wave(i,j,k)
+ diff_cbt(i,j,k,2) = diff_cbt(i,j,k,2) + diff_wave(i,j,k)
+ visc_cbt(i,j,k) = visc_cbt(i,j,k) + diff_wave(i,j,k)
+ wrk1(i,j,k) = Grd%umask(i,j,kp1)*onefourth &
+ *(diff_wave(i,j,k) +diff_wave(i+1,j,k) &
+ +diff_wave(i,j+1,k)+diff_wave(i+1,j+1,k))
+ visc_cbu(i,j,k) = visc_cbu(i,j,k) + wrk1(i,j,k)
+ enddo
+ enddo
+ enddo
+
+ if (id_energy_flux > 0) then
+ used = send_data (id_energy_flux, energy_flux(:,:), &
+ Time%model_time, rmask=Grd%tmask(:,:,1), &
+ is_in=isc, js_in=jsc, ie_in=iec, je_in=jec)
+ endif
+ if (id_power_waves > 0) then
+ used = send_data (id_power_waves, Grd%dat(:,:)*energy_flux(:,:), &
+ Time%model_time, rmask=Grd%tmask(:,:,1), &
+ is_in=isc, js_in=jsc, ie_in=iec, je_in=jec)
+ endif
+ if (id_diff_cbt_wave > 0) then
+ used = send_data (id_diff_cbt_wave, diff_wave(:,:,:), &
+ Time%model_time, rmask=Grd%tmask(:,:,:), &
+ is_in=isc, js_in=jsc, ks_in=1, ie_in=iec, je_in=jec, ke_in=nk)
+ endif
+ if (id_visc_cbt_wave > 0) then
+ used = send_data (id_visc_cbt_wave, diff_wave(:,:,:), &
+ Time%model_time, rmask=Grd%tmask(:,:,:), &
+ is_in=isc, js_in=jsc, ks_in=1, ie_in=iec, je_in=jec, ke_in=nk)
+ endif
+ if (id_visc_cbu_wave > 0) then
+ used = send_data (id_visc_cbu_wave, wrk1(:,:,:), &
+ Time%model_time, rmask=Grd%umask(:,:,:), &
+ is_in=isc, js_in=jsc, ks_in=1, ie_in=iec, je_in=jec, ke_in=nk)
+ endif
+
+
+end subroutine vert_mix_wave_legacy
+! NAME="vert_mix_wave_legacy"
+
+
+
+!#######################################################################
+!
+!
+!
+!
+! Legacy routine maintained only to exactly reproduce older results.
+! It is not recommended for new experiments, as it uses some obsolete
+! methods.
+!
+! This subroutine computes dia-surface tracer diffusivity based on the
+! methods of Lee etal., which consider the dissipation from barotropic tides
+! rubbing against the ocean bottom.
+!
+! We assume a unit Prandtl number, so compute the viscosity as a four-point
+! average of the diffusivity.
+!
+! We perform various averages here in order to smooth Richardson number.
+!
+! 1. compute Richardson number on U-cell by averaging bvfreq from T-cell
+! 2. average U-cell Richardson number to then get T-cell diffusivity
+! 3. average T-cell diffusivity to get U-cell viscosity.
+!
+! Note that if umask(i,j,k)==1.0, then so is tmask(i,j,k), tmask(i+1,j,k),
+! tmask(i,j+1,k), and tmask(i+1,j+1,k). So there is no need to compute
+! active_cells when averaging from T-cell to U-cell.
+!
+!
+!
+ subroutine vert_mix_drag_legacy(Time, Thickness, diff_cbt, visc_cbu, visc_cbt, diff_cbt_drag)
+
+ type(ocean_time_type), intent(in) :: Time
+ type(ocean_thickness_type), intent(in) :: Thickness
+
+ real, dimension(isd:,jsd:,:,:), intent(inout) :: diff_cbt
+ real, dimension(isd:,jsd:,:), intent(inout) :: visc_cbu
+ real, dimension(isd:,jsd:,:), intent(inout) :: visc_cbt
+ real, dimension(isd:,jsd:,:), intent(inout) :: diff_cbt_drag
+
+ integer :: i, j, k, kbot, kp1
+ real :: height, bottom, bvfreq_u, speedr, active_cells
+
+ wrk1(:,:,:) =0.0 ! Richardson number on U-cell
+ wrk2(:,:,:) =0.0 ! Richardson number on T-cell
+ wrk3(:,:,:) =0.0 ! viscosity from drag scheme
+ diff_drag(:,:,:) =0.0 ! diffusivity from drag scheme
+
+ ! Richardson number on U-cell.
+ ! perform a 4-point average of T-cell bvfreq
+ ! and then divide by the U-cell tidal speed term.
+ ! tide_speed_mask is useful to reduce overflows
+ ! in later calculation of the diffusivity.
+ do j=jsd,jed-1
+ do i=isd,ied-1
+ kbot=Grd%kmu(i,j)
+ if(kbot>1) then
+ bottom = Thickness%depth_zwu(i,j,kbot)
+ speedr = tide_speed_mask(i,j)/(epsln+rescaled_speed_u(i,j))
+ do k=1,kbot-1
+ kp1=k+1
+ height = bottom-Thickness%depth_zwu(i,j,k)
+ bvfreq_u = onefourth*(bvfreq(i,j,k)+bvfreq(i+1,j,k)+bvfreq(i,j+1,k)+bvfreq(i+1,j+1,k))
+ wrk1(i,j,k) = 2.0*Grd%umask(i,j,kp1)*(bvfreq_u*height*speedr)**2
+ enddo
+ endif
+ enddo
+ enddo
+
+ ! Richardson number on bottom of T-cells.
+ ! need active_cells for averaging operation.
+ do k=1,nk-1
+ do j=jsc,jec
+ do i=isc,iec
+ active_cells = Grd%umask(i,j,k) + Grd%umask(i-1,j,k) &
+ + Grd%umask(i,j-1,k) + Grd%umask(i-1,j-1,k) + epsln
+ wrk2(i,j,k) = (wrk1(i,j,k) + wrk1(i-1,j,k) + wrk1(i,j-1,k) + wrk1(i-1,j-1,k))/active_cells
+ enddo
+ enddo
+ enddo
+
+ ! compute drag induced diffusivity
+ ! (Lee etal equations (1), (2), and (3))
+ ! Multiply by tide_speed_mask so to zero out
+ ! regions with tiny tide speeds, which are regions
+ ! where we do not wish to have any enhanced mixing
+ ! arising from the barotropic tide mixing parameterization
+ ! anyhow.
+ do k=1,nk-1
+ kp1=k+1
+ do j=jsc,jec
+ do i=isc,iec
+ diff_drag(i,j,k) = Grd%tmask(i,j,kp1)*tide_speed_mask(i,j)*max_drag_diffusivity &
+ *(1.0 + munk_anderson_sigma*wrk2(i,j,k))**(-munk_anderson_p)
+ enddo
+ enddo
+ enddo
+ call mpp_update_domains(diff_drag(:,:,:), Dom%domain2d)
+
+
+ ! add drag induced diffusivity and viscosity to diff_cbt and visc_cbu.
+ ! average t-cell diffusivities to get u-cell viscosity.
+ do k=1,nk-1
+ kp1=k+1
+ do j=jsc,jec
+ do i=isc,iec
+ diff_cbt_drag(i,j,k) = diff_drag(i,j,k)
+ diff_cbt(i,j,k,1) = diff_cbt(i,j,k,1) + diff_drag(i,j,k)
+ diff_cbt(i,j,k,2) = diff_cbt(i,j,k,2) + diff_drag(i,j,k)
+ visc_cbt(i,j,k) = visc_cbt(i,j,k) + diff_drag(i,j,k)
+ wrk3(i,j,k) = Grd%umask(i,j,kp1)*onefourth &
+ *(diff_drag(i,j,k) +diff_drag(i+1,j,k) &
+ +diff_drag(i,j+1,k)+diff_drag(i+1,j+1,k))
+ visc_cbu(i,j,k) = visc_cbu(i,j,k) + wrk3(i,j,k)
+ enddo
+ enddo
+ enddo
+
+
+ if (id_rinumber_drag > 0) then
+ used = send_data (id_rinumber_drag, wrk2(:,:,:),&
+ Time%model_time, rmask=Grd%tmask(:,:,:), &
+ is_in=isc, js_in=jsc, ks_in=1, ie_in=iec, je_in=jec, ke_in=nk)
+ endif
+ if (id_diff_cbt_drag > 0) then
+ used = send_data (id_diff_cbt_drag, diff_drag(:,:,:), &
+ Time%model_time, rmask=Grd%tmask(:,:,:), &
+ is_in=isc, js_in=jsc, ks_in=1, ie_in=iec, je_in=jec, ke_in=nk)
+ endif
+ if (id_visc_cbt_drag > 0) then
+ used = send_data (id_visc_cbt_drag, diff_drag(:,:,:), &
+ Time%model_time, rmask=Grd%tmask(:,:,:), &
+ is_in=isc, js_in=jsc, ks_in=1, ie_in=iec, je_in=jec, ke_in=nk)
+ endif
+ if (id_visc_cbu_drag > 0) then
+ used = send_data (id_visc_cbu_drag, wrk3(:,:,:), &
+ Time%model_time, rmask=Grd%umask(:,:,:), &
+ is_in=isc, js_in=jsc, ks_in=1, ie_in=iec, je_in=jec, ke_in=nk)
+ endif
+
+end subroutine vert_mix_drag_legacy
+! NAME="vert_mix_drag_legacy"
+
+
+end module ocean_vert_tidal_test_mod
diff --git a/src/mom5/ocean_param/vertical/ocean_vert_util.html b/src/mom5/ocean_param/vertical/ocean_vert_util.html
deleted file mode 100644
index f5ca06838e..0000000000
--- a/src/mom5/ocean_param/vertical/ocean_vert_util.html
+++ /dev/null
@@ -1,218 +0,0 @@
-
-
-
-Module ocean_vert_util_mod
-
-
-
-
-PUBLIC INTERFACE
-
- ~ PUBLIC ROUTINES
- ~ NAMELIST
-
-
-
- Compute Richardson number assuming horizontal B-grid layout.
-
- Richardson number rit is centered at T-cell.
- Richardson number riu is centered at U-cell.
-
- This calculation differs from that in ocean_vert_kpp_mom4p1
- since here we compute N^2 using locally referenced potential density,
- as done for tide mixing scheme and as done in ri_for_cgrid. Other
- features of the calculation, such as the horizontal averaging,
- agree with ocean_vert_kpp_mom4p1.
-
-
-
-
-
-
-
-
-
ri_for_cgrid
-
-
-DESCRIPTION
-
-
-
- Compute Richardson number assuming horizontal C-grid layout.
-
- Richardson number rit is centered at T-cell.
- Richardson number riu is set equal to rit, as there is no
- separate "U-cell" when working with a Cgrid.
-
- This calculation differs from that in ocean_vert_kpp_mom4p1
- since here we compute N^2 using locally referenced potential density,
- as done for tide mixing scheme and as done in ri_for_cgrid.
-
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_tracer_util_nml
-
-
-
-
-
-debug_this_module
-
-
- For debugging purposes.
-
-[logical]
-
-
-smooth_n2
-
-
- For vertical smoothing the N2 calculation for Richardson number.
- Default smooth_n2 = .true.
-
-[logical]
-
-
-num_n2_smooth
-
-
- For vertical smoothing N2 for Richardson number.
- Default num_n2_smooth = 1.
-
-[integer]
-
-
-
diff --git a/src/mom5/ocean_param/vertical/ocean_vert_util.xml b/src/mom5/ocean_param/vertical/ocean_vert_util.xml
deleted file mode 100644
index 3ea877b2ab..0000000000
--- a/src/mom5/ocean_param/vertical/ocean_vert_util.xml
+++ /dev/null
@@ -1,50 +0,0 @@
-
-
- S. M. Griffies
-
- This module contains routines for use in vertical mixing.
-
- Routines for vertical mixing schemes.
-
- For debugging purposes.
-
- For vertical smoothing the N2 calculation for Richardson number.
- Default smooth_n2 = .true.
-
- For vertical smoothing N2 for Richardson number.
- Default num_n2_smooth = 1.
-
- For vertical smoothing richardson number.
- Default smooth_ri_number = .true.
-
- For vertical smoothing richardson number.
- Default num_ri_smooth = 1.
-
- Initialize vertical mixing utilities.
-
-
- Compute Richardson number assuming horizontal B-grid layout.
-
- Richardson number rit is centered at T-cell.
- Richardson number riu is centered at U-cell.
-
- This calculation differs from that in ocean_vert_kpp_mom4p1
- since here we compute N^2 using locally referenced potential density,
- as done for tide mixing scheme and as done in ri_for_cgrid. Other
- features of the calculation, such as the horizontal averaging,
- agree with ocean_vert_kpp_mom4p1.
-
-
-
- Compute Richardson number assuming horizontal C-grid layout.
-
- Richardson number rit is centered at T-cell.
- Richardson number riu is set equal to rit, as there is no
- separate "U-cell" when working with a Cgrid.
-
- This calculation differs from that in ocean_vert_kpp_mom4p1
- since here we compute N^2 using locally referenced potential density,
- as done for tide mixing scheme and as done in ri_for_cgrid.
-
-
diff --git a/src/mom5/ocean_tracers/ocean_age_tracer.F90 b/src/mom5/ocean_tracers/ocean_age_tracer.F90
index 7cbbe23724..4f11ad7559 100644
--- a/src/mom5/ocean_tracers/ocean_age_tracer.F90
+++ b/src/mom5/ocean_tracers/ocean_age_tracer.F90
@@ -32,7 +32,7 @@ module ocean_age_tracer_mod !{
!
!
!
-! $Id: ocean_age_tracer.F90,v 1.1.2.1 2012/05/15 16:48:03 smg Exp $
+! $Id: ocean_age_tracer.F90,v 20.0 2013/12/14 00:16:58 fms Exp $
!
!
diff --git a/src/mom5/ocean_tracers/ocean_age_tracer.html b/src/mom5/ocean_tracers/ocean_age_tracer.html
deleted file mode 100644
index adb07ebd41..0000000000
--- a/src/mom5/ocean_tracers/ocean_age_tracer.html
+++ /dev/null
@@ -1,286 +0,0 @@
-
-
-
-Module ocean_age_tracer_mod
-
-
-
-
-PUBLIC INTERFACE
-
- ~ PUBLIC ROUTINES
-
-
- This module will perform the necessary operations to handle
- a series of ocean age tracers. The following types are allowed:
-
- normal: the age of the designated surface area is fixed at
- 0, while all other grid points increase in age.
- Therefore, the resultant age is the length of time
- since that water has been in contact with the
- designated area of surface. (This is the default type.)
-
- Note that the tracer "concentration" known as "age" is
- in units of years, hence the multiplier "secs_in_year_r"
- applied to t_prog(index)%source. This multiplier IS NOT
- needed for any other terms, since they all have units with
- meter/sec, and this is multiplied by dtime(secs) when
- time stepping.
-
-
- Finish up calculations for the tracer packages,
- possibly writing out non-field restart information
-
-
-
-
-
-
-
-
ocean_age_tracer_init
-
-
-DESCRIPTION
-
-
- Set up any extra fields needed by the tracer packages
-
- Save pointers to various "types", such as Grid and Domains.
-
-
-
-
-
-
-
-
ocean_age_tracer_source
-
-
-DESCRIPTION
-
-
- Calculate the source arrays for the tracer packages
-
-
-
-
-
-
-
-
ocean_age_tracer_start
-
-
-DESCRIPTION
-
-
- Start the ocean age tracer package
-
- Age tracer surface area specification
-
- wlon : western longitude of surface age
- region
- elon : eastern longitude of surface age
- region
- slat : southern latitude of surface age
- region
- nlat : northern latitude of surface age
- region
- coastal_only : if true, then only apply the changes in
- coastal boxes
- t_mask : logical array controlling whether to apply
- the following inhibitions and depletions to
- each month (true means set the masks,
- false means use the defaults everywhere)
-
-
- To set the surface areas, a number of namelists are read,
- each containing the above values. You may specify up to
- num_region rectangles bounded by (wlon,elon,nlat,slat).
- Any grid box whose center is in one of these rectangles will
- be considered to be part of the surface area where the
- age is reset to zero every time-step.
-
- These masks may be time-dependent by specifying t_mask.
- For any month that t_mask is true (1=Jan), the rectangular
- regions will be set, otherwise they will be skipped.
-
- nlat may not equal slat, and wlon may not equal elon
-
- If slat > nlat, then nothing will be done for that rectangle
-
- The initial surface area is empty, with the default rectangle
- setting the surface area to be empty
-
- More than num_regions rectangles may be used to specify
- the area by using more than one namelist
-
-
-
-
-
-
-
-
ocean_age_tracer_tracer
-
-
-DESCRIPTION
-
-
- Subroutine to do calculations needed every time-step after
- the continuity equation has been integrated
-
-
-
-
-
-
-
-
set_array
-
-
-DESCRIPTION
-
-
- Set up an array covering the model domain with a user-specified
- value, in user-specified regions. There are a given number of
- 2-d regions specified by the values slat, nlat, wlon and elon.
- The longitudes are for a cyclic domain, and if wlon and elon
- are on opposite sides of the cut, the correct thing will
- be done. Elon is considered to be east of wlon, so if elon is
- less than wlon, then the region east of elon to the cut will be
- filled, and the region from the cut to wlon will be filled.
-
- After setting up the array in this routine, it may prove useful
- to allow fine-tuning the settings via an array in a namelist.
-
- Arguments:
- Input:
- num_regions number of user-specified regions which will be filled
- wlon 1-d array of western (starting) longitudes for the
- rectangular regions
- elon 1-d array of eastern (ending) longitudes for the
- rectangular regions
- slat 1-d array of southern (starting) latitudes for the
- rectangular regions
- nlat 1-d array of northern (ending) latitudes for the
- rectangular regions
- Note: if slat >= nlat, then nothing is done
- for that region
- set_value the value to assign to array in the user-specified
- regions
- unset_value the value to assign to array outside of the
- user-specified regions
- name character variable used in informative messages
- coastal_only true to limit changes only to coastal points (i.e.,
- at least one bordering point is land)
-
- Output:
- array 2-d array which will contain the set- and unset-
- values. The array is assumed to have a border
- one unit wide on all edges, ala MOM. A cyclic
- boundary condition will be set if requested.
-
- This module computes the heating of seawater due to
- frazil ice formation.
-
-
-
-
-
- Frazil can generally form at any vertical level, although
- it is common for climate models to assume it is formed
- only at k=1. In this case, pressure is assumed to be
- atmospheric for purposes of computing the freezing
- temperature of seawater.
-
- The freezing temperature of seawater is computed one of two
- possible ways:
-
- (1) simple way uses a linear function of salinity
- and assumes zero (i.e. atmospheric) pressure,
-
- tfreeze(deg C) = a1*salinity(psu)
- with a1 = -0.054
-
- (2) accurate way uses a nonlinear function of
- salinity(psu) and gauge pressure(dbar), where
- gauge pressure=absolute pressure - 10.1325 dbar.
-
- tfreeze (deg C) = tf_num/tf_den
- tf_num = a0 + s*(a1 + sqrt(s)*(a2 + sqrt(s)*a3)) + p*(a4 + p*(a5 + s*a6))
- tf_dem = b0 + p*(b1 + p*b2) + s*s*sqrt(s)*b3
-
- check value : fp_theta(35,200,'air-sat') = -2.076426227617581 deg C
- fp_theta(35,200,'air-free') = -2.074408175943127 deg C
-
- This method results in a more accurate freezing
- temperature than the simpler approach. It is also
- important for ice-shelf modelling to include a
- pressure dependence when the shelf penetrates
- into the water column.
-
-
- Initialization code for the frazil diagnostic tracer.
-
-
-
-
-
-
-
-
compute_frazil_heating
-
-
-DESCRIPTION
-
-
- Compute ocean heating due to formation of frazil-ice (Joules/m^2)
-
- Note that "frazil_factor" accounts for possibly different time
- stepping used in ocean model and the sea ice model. With MOM
- using a leap-frog, and the GFDL ocean model SIS using forward,
- then frazil_factor=0.5. If use recommended tendency=twolevel
- in MOM, then frazil_factor=1.0
-
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_frazil_nml
-
-
-
-
-
-use_this_module
-
-
- If true, then compute frazil heating.
-
-[logical]
-
-
-debug_this_module
-
-
- For debugging this module
-
-[logical]
-
-
-frazil_factor
-
-
- This factor accounts for possibly different time stepping used
- in the sea ice model relative to the ocean model. If sea-ice
- and ocean use same time stepping schemes, then frazil_factor=1.0.
- If sea-ice uses a twolevel scheme and ocean a threelevel leap-frog,
- then frazil_factor=0.5. Default is 1.0 since the GFDL sea ice model
- SIS uses a two-level time stepping scheme and MOM defaults to
- a staggered two-level scheme.
-
-[real, units: dimensionless]
-
-
-freezing_temp_simple
-
-
- To use the simplified freezing point temperature of seawater,
- as used in MOM4.0.
-
-[logical]
-
-
-freezing_temp_accurate_preteos10
-
-
- To use the accurate freezing point temperature of seawater,
- which is a nonlinear function of salinity and pressure.
-
-[logical]
-
-
-freezing_temp_accurate_teos10
-
-
- To use the accurate freezing point temperature of seawater
- according to TEOS-10, which is a nonlinear function of
- salinity and pressure.
- This equation is recommended for use with ice-shelf modelling.
-
-[logical]
-
-
-frazil_only_in_surface
-
-
- For typical case where compute frazil heating only in
- the surface grid cell. Will assume the gauge
- pressure is zero in this case when computing freezing
- temperature.
-
-[logical]
-
-
-
-
-
-
-
-
-
-
-
REFERENCES
-
-
-
-
- IOC, SCOR and IAPSO, 2010: The international thermodynamic equation of
- seawater - 2010: Calculation and use of thermodynamic properties.
- Intergovernmental Oceanographic Commission, Manuals and Guides No. 56,
- UNESCO (English), 196 pp. Available from http://www.TEOS-10.org.
- See sections 3.33 and 3.34 of this TEOS-10 Manual.
-
-
- "Updated algorithms for density, potential temperature,
- conservative temperature and freezing temperature of
- seawater", Jackett, McDougall, Feistel, Wright, and Griffies
- Journal of Atmospheric and Oceanic Technology, in press 2005.
-
- This module setups various passive tracer configurations.
- Some idealized initial conditions are provided.
-
- These tracers are used for various idealized purposes,
- such as tracing water mass transports, testing
- advection schemes, etc.
-
- These passive tracers are always initialized within
- this module with an idealized profile.
- No preprocessing step is required. To define a common initial condition
- for all passive tracers use the namelist "ocean_passive_nml"
-
- This setting can be overwritten for each tracer by the namelist feature of the tracer field_table.
- For example
-
- "namelists","ocean_mod","ocean_passive/patch"
- restore = f
- init_condition = temp_sq_init
-
- init_condition is one of :: 'level', 'wall','patch', 'patch_'klevel, with "klevel" an integer
- for the k-level that will place the patch.
- 'exponential', 'shelfbowl', 'rho_surface', 'temp_sq_init', 'salt_sq_init'
- Default is 'patch'
-
- With rho_surface' a density surface can be selected, the density value
- is defined in the field table namelist, for example
-
- init_surface = 1025
-
- However, if an initial file exists for a passive tracer,
- then ocean_tracer_mod will overwrite the passive tracer
- with the tracer concentration in the initial file. In this
- way, we can, for example, initialize a passive tracer with
- some profile that is not readily determined via a simple
- algorithmic procedure.
-
- If restoring of a passive tracer to its initial value is enabled by
- setting in the field table
-
- restore = t
-
- the initial field is used only to find the grid cells where to restore the
- passive tracer to the initial tracer field. Restoring is done where the tracer
- concentration exceeds 0.00001. The inital value of passive tracers with restoring
- is always set to '1'. With the field_table namelist
-
- init_value = some_real
-
- this can be changed to another but also constant value.
-
- All passive tracers in this module are dimensionless and are
- treated the same internally to this module. However, they can
- generally have different initial conditions and can use
- different advection schemes. Indeed, one motivation for
- developing this module is to test advection schemes, with
- the same initial condition used for each of the tracers,
- but different advection schemes. In this way we can readily
- determine the difference between advection schemes on various
- profiles within MOM.
-
- Sample passive tracers are setup here. The user can modify
- code in a straightforward manner to change the number of
- passive tracers and/or the initial profiles.
-
-
- Initialize the indices for passive tracer fields.
- This routine is called by ocean_model.F90.
-
-
-
-
-
-
-
-
passive_tracer_init
-
-
-DESCRIPTION
-
-
- Initialize profiles for the passive tracers.
- This routine is called by ocean_tracer.F90.
-
-
-
-
-
-
-
-
ocean_passive_tracer_init
-
-
-DESCRIPTION
-
-
- Initialize restoring to initial values for the passive tracers.
-
- or
- Initialize profiles for the passive tracers which are tagged with
- specific values of the temperature field or potential density field.
-
- or
- Initialize profiles for the passive tracers which are defined
- as the temperature or salinity squared. These tracers are used
- for diagnosing the level of spurious mixing associated with
- PSOM advection.
-
-
-
-
-
-
-
-
surface_init
-
-
-DESCRIPTION
-
-
- Initialize passive tracer according to a particular iso-surface.
-
-
-
-
-
-
-
-
layer_init
-
-
-DESCRIPTION
-
-
-
- Initialize tracer inside a depth layer to have a value, and
- zero outside the layer.
-
-
-
-
-
-
-
-
-
wall_init
-
-
-DESCRIPTION
-
-
-
- Initialize tracer inside an (i,k) wall to have a value, and
- zero outside the wall.
-
-
-
-
-
-
-
-
-
patch_init
-
-
-DESCRIPTION
-
-
-
- Initialize tracer with simple shapes based on vertical layer:
- Level k=1, square pill box
- Level k=2, circular pill box (cylinder)
- Level k=3, circular cone
- Level k=4, cosine bell
- Level k=5, Gaussian bell
- Levels k>5, square patch based on i,j coordinates (original "patch").
-
-
-
-
-
-
-
-
-
patch_init_klevel
-
-
-DESCRIPTION
-
-
- Initialize tracer with gaussian patch or constant on a level,
- both on a single k-level
-
-
-
-
-
-
-
-
exponential_init
-
-
-DESCRIPTION
-
-
-
- Initialize tracer with a vertical exponential profile.
-
-
-
-
-
-
-
-
-
shelfbowl_init
-
-
-DESCRIPTION
-
-
-
- Initialize tracer as in the shelfbowl topography of use for studying
- idealized overflow problems, as in Winton etal (1998).
-
-
-
-
-
-
-
-
-
update_tracer_passive
-
-
-DESCRIPTION
-
-
- Update the squared tracer.
- Restore passive tracers.
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_passive_nml
-
-
-
-
-
-debug_this_module
-
-
- For debugging the module.
-
-[logical]
-
-
-common_init_condition
-
-
- Default for the tracer initial conditions.
-
- Options are the following:
- common_init_condition='level'
- common_init_condition='wall'
- common_init_condition='patch'
- common_init_condition='patch_'klevel, with "klevel" an integer
- for the k-level that will place the patch.
- common_init_condition='exponential'
- common_init_condition='shelfbowl'
- common_init_condition='rho_surface'
- common_init_condition='temp_sq_init'
- common_init_condition='salt_sq_init'
- Default=common_init_condition='patch'
-
-[character]
-
-
-layer_value
-
-
- Value of tracer concentration within the layer.
- Default=1.0.
-
-[real]
-
-
-layer_ztop
-
-
- Depth at the top of the tracer layer.
-
-[real]
-
-
-layer_zbot
-
-
- Depth at the bottom of the tracer layer.
-
-[real]
-
-
-patch_init_klevel_gaussian
-
-
- To initialize on the klevel with a gaussian region.
- Default=patch_init_klevel_gaussian=.false.
-
-[logical]
-
-
-wall_value
-
-
- Value of tracer concentration within the wall.
- Default=1.0.
-
-[real]
-
-
-wall_ratio_south
-
-
- Ratio of the full j-range, northward of which
- we place the wall.
-
-[real]
-
-
-wall_ratio_north
-
-
- Ratio of the full j-range, southward of which
- we place the wall.
-
-[real]
-
-
-patch_value
-
-
- Value of the tracer concentration within a patch.
- Default=1.0.
-
-[real]
-
-
-patch_ztop
-
-
- Depth at the top of the tracer patch.
-
-[real]
-
-
-patch_zbot
-
-
- Depth at the bottom of the tracer patch.
-
-[real]
-
-
-patch_ratio1
-
-
- For setting position of tracer patch.
-
-[real]
-
-
-patch_ratio2
-
-
- For setting position of tracer patch.
-
-[real]
-
-
-efold_depth
-
-
- The efolding depth used for exponential tracer profile.
- Default=1000.0.
-
-[real, units: metre]
-
-
-exponential_value
-
-
- The tracer value at zero depth when choosing the exponential profile.
- Default=1.0.
-
-[real, units: dimensionless]
-
-
- This module is a superset of the ocean age tracer module. It may
- be used to reproduce the age tracer, but it can also do much
- more. Unlike the ocean age tracer module, here you may specify
- a 3-d field by specifying a series of "rectangular prisms".
- The grid cells which occupy this field may vary with time due
- to the variations in the thickness of the surface layer.
-
- You may also specify a 3-d field by choosing one of three mixed-layers
- (KPP, density-derived or buoyancy-derived). You may also specify a
- region based on a a range of a prognostic or diagnostic ocean
- tracer (such as all points with a temperature of 10-20 degrees).
-
- You may specify either the mixed-layer method or the tracer range along
- with the geographic specification. If multiple methods are used, then
- the resultant field is the intersection of the two methods. In fact, the
- geographic method is always in use, and defaults to the whole ocean.
-
- There is an option of using the inverse of any method. This is sometimes
- easier to use than explicitly specifying the inverse. For instance,
- to get the temperatures outside of the range 10-20 degrees, one could
- specify the 10-20 degree range and set <swap> to true, or, specify two
- different regions, one less than 10 degrees and one greater than 20 degrees.
-
- By default, the values inside the specified region are set to a
- specified value each time-step (default is 0), and outside of this region
- the field is integrated over time in units of years (integrand is
- 1/(365.25*86400) by default, but this value can be changed. The inner region
- can be forced to be 0 (or the user-specified inner value) at each time-step
- (the default), or it can be restored to this value at a user-specified
- rate (given in days), or, it can be left alone (not integrated or set to
- any value).
-
- Finally, since we are just integrating a specified field by a constant value
- (by default), it is simple to make that field a simple function of another
- tracer. This is the final option. You may specify a prognostic or diagnostic
- variable to be the integrand, and have it scaled by a constant. One case
- which has been done is to integrate irradiance in the mixed-layer.
-
- This module is split into several different modules. This particular module
- is the only one called from outside, and it makes appropriate calls to
- the other modules to implement its features. This was done so that it would
- be easier to expand the features of the ocean residency, without cluttering
- the code too much. Ideally, this could all be done with classes, but there
- is currently no support for classes in Fortran (pre-F2003). The current
- modules are:
-
- ocean_residency.F90 This module, the control center, and also does the
- integrations and resetting in the inner regions.
- ocean_residency_meta.F90 Has specifications of the ocean_residency type
- and other utility routines. This is separate
- to stop circular references
- ocean_residency_ml.F90 Handles setting mixed-layer masks
- ocean_residency_range.F90 Handles setting the masks for the tracer ranges
- ocean_residency_integrand.F90 Handles setting the integrand to a non-constant
- value
-
- field_table namelist inputs:
-
- The following 6 arrays specify the bounds of boxes, the intersection of which
- will define the region where the integrand is set to restore_region_value. ALl arrays
- must have the same number of elements. If none are specified, then no region will
- be used, unless swap is true, which is a quick way of selecting the entire ocean.
- This may be useful when one really wants to use one of the other methods of selecting,
- such as mixed layer depth, or tracer range.
-
- Longitudes will be shifted to lie in the range 0-360 degrees. If the eastern side is
- greater than the western, then the selected region will consist of those grid cells from
- the eastern value to 360, and 0 to the western value. If the northern value is less than
- the southern value, or if the top depth is greater than the bottom depth, then
- an error occurs, and the model stops.
-
- Three special cases exist for the depth (which currently must be in meters).
- If the bottom value is less than or equal to zero, then the top box is selected.
- If the top value is greater than the maximum depth, then the bottom box is selected.
- If the top value is negative, then grid cells within "the absolute value of the top value"
- from the bottom are selected.
-
- Note that the geographic specification is used for all residency tracers, so either
- values for these 6 arrays must be given so as to select a region, or else swap must
- be set to true and no arrays given.
-
- east_bnd: array of boundary points of the eastern side of the box,
- in degrees longitude (default: NULL)
- north_bnd: array of boundary points of the northern side of the box,
- in degrees latitude (default: NULL)
- south_bnd: array of boundary points of the southern side of the box,
- in degrees latitude (default: NULL)
- west_bnd: array of boundary points of the western side of the box,
- in degrees longitude (default: NULL)
- top_bnd: array of boundary points of the top side of the box,
- in meters (default: NULL)
- bottom_bnd: array of boundary points of the bottom side of the box,
- in meters (default: NULL)
-
- swap: if true, then select the inverse of the specified geographic region,
- otherwise, just use the specified region (default: false)
- restore: restoring value for values in the defined regions
- negative => do nothing, 0 => force to integrate_region_value,
- positive => time scale in days to force to integrate_region_value
- (default: 0.0)
- restore_region_value: value to set the mask to for grid cells within
- the specified region (default: 0.0)
- integrate_region_value: value to set the mask to for grid cells outside
- the specified region (default: secs_in_year_r)
- swap_module: if true, then select the inverse of the region from the specified module,
- otherwise, just use the specified region (default: false)
- module_name: if set, then it will be used to select the alternate
- method of selecting the region (default: ' ' -- only geographic
- selection is used)
-
- For the following arrays, see the different extra modules for required and
- possible values for the module selected.
-
- params: an array of real parameters which may be used for the method
- being used for selection (default: NULL)
- flags: an array of real parameters which may be used for the method
- being used for selection (default: NULL)
- strings: an array of real parameters which may be used for the method
- being used for selection (default: NULL)
-
- For the following arrays, see the different extra modules for required and
- possible values for the module selected to specify the integrand.
- int_module_name: if set, then the name of the module used to set
- the integrand (default: ' ' -- integrate time, in years)
- int_params: an array of real parameters which may be used for the integrand
- (default: NULL)
- int_flags: an array of real parameters which may be used for the integrand
- (default: NULL)
- int_strings: an array of real parameters which may be used for the integrand
- (default: NULL)
-
-----------------------------------------------------------------------------------------
-
- Sample field table entries:
- ---------------------------
-
- "tracer_packages","ocean_mod","ocean_residency"
- names = age_surface, age_bottom_inv, kppbl_nil, kppbl_14d, kppbl_frc, kppbl_irr_14d, temp_15_20
- horizontal-advection-scheme = mdppm
- vertical-advection-scheme = mdppm
- units = yr
- min_tracer_limit=0.0
- /
-
- This is the same as the old age tracer with all surface
- values forced to zero
-
- "namelists","ocean_mod","ocean_residency/age_surface"
- south_bnd = -90.0
- north_bnd = 90.0
- west_bnd = 0.0
- east_bnd = 360.0
- top_bnd = 0.0
- bottom_bnd = 0.0
- /
-
- This integrates the age in the bottom box and forces to
- zero everywhere else (note that swap is true)
-
- "namelists","ocean_mod","ocean_residency/age_bottom_inv"
- south_bnd = -90.0
- north_bnd = 90.0
- west_bnd = 0.0
- east_bnd = 360.0
- top_bnd = 10000.0
- bottom_bnd = 10000.0
- swap = t
- /
-
- This integrates the age of the water in the KPP
- boundary layer, but lets the age outside of this region
- keep its value until it again mixes with the boundary layer.
- The module_name is set, and strings is set to pick the
- type of mixed layer desired
- (note that the global geographic area is explicitly specified,
- and that the restoring time scale is negative)
-
- "namelists","ocean_mod","ocean_residency/kppbl_nil"
- south_bnd = -90.0
- north_bnd = 90.0
- west_bnd = 0.0
- east_bnd = 360.0
- top_bnd = 0.0
- bottom_bnd = 10000.0
- restore = -1.0
- module_name = ocean_residency_ml
- strings = kpp_bl
- swap_module = t
- /
-
- This is the same as above, but forces the age outside
- the boundary layer to 0 with a 14 day time scale
- (note that the global geographic region is specified by
- setting swap to true, also note the value of restore)
-
- "namelists","ocean_mod","ocean_residency/kppbl_14d"
- swap = t
- restore = 14.0
- module_name = ocean_residency_ml
- strings = kpp_bl
- swap_module = t
- /
-
- This is the same as above, but forces age to zero outside
- the boundary layer (note that restore did not need to
- be explicitly specified, as the default is zero)
-
- "namelists","ocean_mod","ocean_residency/kppbl_frc"
- swap = t
- restore = 0.0
- module_name = ocean_residency_ml
- strings = kpp_bl
- swap_module = t
- /
-
- The following integrates irradiance in the boundary
- layer (note that the units needed to be changed for
- netCDF output purposes)
-
- "prog_tracers","ocean_mod","residency_kppbl_irr_14d"
- units = W-yr/m^2
- /
-
- "namelists","ocean_mod","ocean_residency/kppbl_irr_14d"
- swap = t
- restore = 14.0
- module_name = ocean_residency_ml
- strings = kpp_bl
- swap_module = t
- int_module_name = ocean_residency_integrand
- int_strings = irr
- /
-
- This specifies the region as the area with
- a temperature range of between 15 and 20 degrees
- (note that the params holds the variable
- range)
-
- "namelists","ocean_mod","ocean_residency/temp_15_20"
- swap = t
- module_name = ocean_residency_range
- strings = tracer_range, temp
- params = 15.0, 20.0
- /
-
-
- Set up any extra fields needed by the tracer packages
-
-
-
-
-
-
-
-
ocean_residency_source
-
-
-DESCRIPTION
-
-
- Calculate the source arrays for the tracer packages
-
-
-
-
-
-
-
-
ocean_residency_start
-
-
-DESCRIPTION
-
-
- Start the ocean residency package
-
- Residency surface area specification
-
- west_bnd : western longitude of residency region
- east_bnd : eastern longitude of residency region
- south_bnd : southern latitude of residency region
- north_bnd : northern latitude of residency region
- top_bnd : top depth of residency region
- bottom_bnd : bottom depth of residency region
-
- To set the volumes, a number of namelists are read,
- each containing the above values. You may specify up to
- num_geog_region rectangular cubes bounded by
- (west_bnd, east_bnd, north_bnd, south_bnd, top_bnd, bottom_bnd).
- Any grid box whose center is in one of these volumes will
- be considered to be part of the volume where the
- residency is reset to zero every time-step.
-
- north_bnd may not equal south_bnd, and west_bnd may not equal east_bnd
-
- top_depth may equal bottom_depth. In that case, then whatever vertical
- box contains that depth will define the vertical range for the box
-
- If south_bnd > north_bnd, then nothing will be done for that rectangle
-
- The initial surface area is empty, with the default rectangle
- setting the surface area to be empty
-
- More than num_geog_regions rectanglar volumes may be used to specify
- the volume by using more than one namelist
-
-
-
-
-
-
-
-
ocean_residency_tracer
-
-
-DESCRIPTION
-
-
- Subroutine to do calculations needed every time-step after
- the continuity equation has been integrated
-
- This module contains the subroutines to set up fields other
- than reciprocal time over which to integrate.
-
- To use this module, in the field table namelist, you must do the following:
-
- 1) set "module_name_int" to "ocean_residency_integrand"
- 2) "int_strings" should have one or two values, the first is
- the name of a prognostic or diagnostic variable to use as the integrand,
- and if the second value is given and is "average", then the array is assumed
- to be defined at the top of the grid cells, and the average of the top
- and bottom will be used for each grid cell (top of bottommost grid cell),
- otherwise the value at each level will be used
- 3) "int_params" may be set to a single value to scale the integrand,
- at most one value may be set
- 4) no "int_flags" should be set
-
- For an overview of the ocean residency modules, see ocean_residency.F90.
-
-
- Set the selected integrand field to be used in the "integrate_region"
- as defined in ocean_residency.F90. The selected prognostic
- or diagnostic variable will be multiplied by the residency mask
- (which is usually either 1 or 0, but is not so required) and a
- user-selected scale factor (default of 1). The variable may be either
- the average of the surrounding points ( C(k) = (C(k) + C(k+1))/2 )
- or just the same indexical value.
-
- This module contains the meta definitions, subroutines and functions
- to use in the ocean residency package. These routines are used by all
- of the ocean residency modules and need to be defined in a separate
- module so that there are no circular references between the modules.
-
- For an overview of the ocean residency modules, see ocean_residency.F90.
-
-
- Return an array of instances which have the given module_name
- This is used by modules, such as the mixed layer module, to obtain
- a list of instances which use that module. Then, the module
- needs only to loop over those instance to perform its required tasks.
-
-
-
-
-
-
-
-
ocean_residency_set_region_2d
-
-
-DESCRIPTION
-
-
- Given a 2-d field of depths, determine the grid cells which fall inside (above) and
- outside of that range, then set the mask appropriately, as to whether
- we are interested in those points inside (swap=false) or outside (swap=true) of the region.
-
- Note: if the output array is not initialized, then it is assumed that it is already
- filled with a region, and the resulting region will be the intersection of the
- existing region and the newly specified region.
-
- Arguments:
-
- Input:
-
- isd: low dimension of first index
- ied: high dimension of first index
- jsd: low dimension of second index
- jed: high dimension of second index
- nk: dimension of third index
- control: array of depths that specifies the region
- depth_zwt: depth of bottom of grid cell
- restore_region_value: if supplied, the value to assign to array in the user-specified
- regions (default: 0.0)
- integrate_region_value: if supplied, the value to assign to array outside of the
- user-specified regions (default: secs_in_year_r)
- swap: if supplied and true then change the invert the defined region (default: true)
- initialize: if supplied and true, then initialize the region to the integrate_region_value (default: false)
- caller: if supplied, use for traceback of error messages (default: fm_default_caller)
-
- Input/Output:
- array: 3-d array which will contain the restore_region- and integrate_region-
- values.
-
-
-
-
-
-
-
-
-
ocean_residency_set_region_geog
-
-
-DESCRIPTION
-
-
- Set up an array covering the model domain with a user-specified
- value, in user-specified regions. There are a given number of
- 3-d regions specified by the values south_bnd, north_bnd, west_bnd,
- east_bnd, top_bnd and bottom_bnd.
- The longitudes are for a cyclic domain, and if west_bnd and east_bnd
- are on opposite sides of the cut, the correct thing will
- be done. east_bnd is considered to be east of west_bnd, so if east_bnd is
- less than west_bnd, then the region east of east_bnd to the cut will be
- filled, and the region from the cut to west_bnd will be filled.
-
- If the bottom bound is less than or equal to zero, then the top model box
- will be chosen. If the top bound is greater than or equal to the maximum
- model depth, then the bottom box will be chosed. Otherwise, if the grid
- cell center depth falls between top bound and bottom bound, then those cells
- shall be chosen.
-
- For longitude and latitude, if the grid cell center lies within the
- rectabgle defined by (west_bnd,south_bnd) and (east_bnd,north_bnd), then
- the whole grid cell is inside the region.
-
- Arrays of coordinates may be specified for irregular regions.
- The final region is the union of the multiple sets
- of coordinates. If swap is true, then the inverse of the defined
- region will be set.
-
- Note: if the output array is not initialized, then it is assumed that it is already
- filled with a region, and the resulting region will be the intersection of the
- existing region and the newly specified region.
-
- Arguments:
-
- Input:
-
- isd: low dimension of first index
- ied: high dimension of first index
- jsd: low dimension of second index
- jed: high dimension of second index
- nk: dimension of third index
- grid_xt: array of coordinates in the x-direction (typically longitude)
- grid_yt: array of coordinates in the y-direction (typically latitude)
- max_depth: maximum depth of the model
- depth_zt: depth of center of grid cell
- depth_zwt: depth of bottom of grid cell
- num_geog_regions: number of user-specified regions which will be filled
- west_bnd_in: 1-d array of western (starting) longitudes for the regions
- east_bnd_in: 1-d array of eastern (ending) longitudes for the regions
- south_bnd: 1-d array of southern (starting) latitudes for the regions
- north_bnd: 1-d array of northern (ending) latitudes for the regions
- top_bnd: 1-d array of southern (starting) depths for the regions
- bottom_bnd: 1-d array of northern (ending) depths for the regions
- Note: if south_bnd >= north_bnd, then nothing is done
- for that region
- kmt: array of indices for bottom grid cells
- name: character variable used in informative messages
- restore_region_value: if supplied, the value to assign to array in the user-specified
- regions (default: 0.0)
- integrate_region_value: if supplied, the value to assign to array outside of the
- user-specified regions (default: secs_in_year_r)
- swap: if supplied and true then change the invert the defined region (default: true)
-
- Input/Output:
- array: 3-d array which will contain the restore_region- and integrate_region-
- values.
-
-
-
-
-
-
-
-
ocean_residency_set_region_3d
-
-
-DESCRIPTION
-
-
- Set up an array where the a grid box is in the region if the value
- of the specified property (temperature, say) is within the given bounds.
- Multiple values for the range may be given, and the resulting mask
- will be the union of the multiple regions. If swap is true, then the
- inverse of the selected region will be set.
-
- Note: if the output array is not initialized, then it is assumed that it is already
- filled with a region, and the resulting region will be the intersection of the
- existing region and the newly specified region.
-
- Arguments:
-
- Input:
-
- isd: low dimension of first index
- ied: high dimension of first index
- jsd: low dimension of second index
- jed: high dimension of second index
- nk: dimension of third index
- num_geog_regions: number of user-specified regions which will be filled
- bounds: 1-d array of pairs of bounding values. The first value in
- the pair must be less than the second value
- kmt: array of indices for bottom grid cells
- name: character variable used in informative messages
- restore_region_value: if supplied, the value to assign to array in the user-specified
- regions (default: 0.0)
- integrate_region_value: if supplied, the value to assign to array outside of the
- user-specified regions (default: secs_in_year_r)
- swap: if supplied and true then change the invert the defined region (default: true)
- initialize: if supplied and true, then initialize the region to the integrate_region_value (default: false)
- caller: if supplied, use for traceback of error messages (default: fm_default_caller)
-
- Input/Output:
- array: 3-d array which will contain the restore_region- and integrate_region-
- values.
-
- This module handles the case where the specified region is determined
- by a 2-d array of depths, typically mixed layer depths.
-
- To use this module, in the field table namelist, you must do the following:
-
- 1) set "module_name" to "ocean_residency_ml"
- 2) "strings" should have one value: one of "kpp_bl", "mld_buoyancy", or
- "mld_potrho"
- 3) no "params" should be set
- 4) no "flags" should be set
-
- Currently, the following mixed layers are supported:
-
- kpp_bl: KPP mixed layer
- mld_buoyancy: mixed layer defined by a change in buoyancy
- (mld in diagnostic output)
- mld_potrho: mixed layer defined by a change in potential density
- (depth_of_potrho in diagnostic output)
-
- There should be no "params" or "flags" set, and only one element of
- "strings".
-
- For an overview of the ocean residency modules, see ocean_residency.F90.
-
-
- Calculate the mask for the mixed layer.
-
- Arguments:
-
- Input:
-
- isd: low dimension of first index
- ied: high dimension of first index
- jsd: low dimension of second index
- jed: high dimension of second index
- nk: dimension of third index
- T_prog: array of ocean prognostic types
- T_diag: array of ocean diagnostic types
- Time: ocean time type
- Thickness: ocean thickness type
- Dens: ocean density type
- depth_zwt: depth of bottom of grid cell
- hblt_depth: array of depths of KPP boundary layer
-
-
-
-
-
-
-
-
ocean_residency_ml_start
-
-
-DESCRIPTION
-
-
- Start the ocean residency mixed layer package
-
-
- This module handles the case where the specified region is determined
- from a range of another tracer. Any tracer, either prognostic or
- diagnostic, may be used. The tracer field, mutiplied by an optional
- scaling factor, will be multiplied by the current value in residency
- mask array.
-
- To use this module, in the field table namelist, you must do the following:
-
- 1) set "module_name" to "ocean_residency_range"
- 2) "strings" should have two values, the first is "tracer_range", and the
- second to the name of a prognostic or diagnostic variable
- 3) set "params" to pairs of points defining the range of the variable
- to select. For each pair of values, the first value must be less than
- the second value. The grid cells will satisfy the union of all of the
- grid cells which satisfy
- "low value" < "cell value" <= "high value"
- for at least one pair of points
- 4) no "flags" should be set
-
- Any prognostic or diagnostic variable may be used. If you wish to allow
- another variable to be used, you can just create a diagnostic variable
- for it.
-
- For an overview of the ocean residency modules, see ocean_residency.F90.
-
-
- Calculate the mask for the tracer range(s)
-
- Arguments:
-
- Input:
-
- isd: low dimension of first index
- ied: high dimension of first index
- jsd: low dimension of second index
- jed: high dimension of second index
- nk: dimension of third index
- taum1: tau-1 time level index
- T_prog: array of ocean prognostic types
- T_diag: array of ocean diagnostic types
- grid_kmt: indices of the bottom grid cell
-
-
-
-
-
-
-
-
ocean_residency_range_start
-
-
-DESCRIPTION
-
-
- Start the ocean residency tracer range package
-
-
- Setup the temperature and salinity tracer fields.
- Convert between potential temperature and conservative temperature.
-
-
-
-
-
-
- This routine sets up the temperature and salinity tracer fields.
- It also performs a converstion between potential temperature and
- conservative temperature, with the conversion valid over most
- large-scale oceanographically relevant ranges.
-
- 0psu <= salinity <= 40 psu
-
- -3C <= theta <= 40C (theta=conservative temperature or potential temperature)
-
- 0dbar <= pressure <= 8000dbar
-
- Input variables are the following:
-
- salinity
-
- potential temperature (theta) in deg C
- OR
- conservative temperature (theta) in deg C
-
-
- Reinitialize the temperature/salinity fields with internally generated
- idealized profile.
-
- This routine can be called at any time within a model integration.
- The main application is to allow for there to be a nontrivial
- Thickness established, and then to reinitialize the temperature
- and salinity to be functions of the depth_st array. When
- s=zstar, this approach will produce a flat initialization in
- zstar space, but nontrivial initialization in depth space.
-
- User can customize a profile.
-
- One example given here assumes profile is a function of depth_st,
- with the assumption that s=geopotential OR s=zstar.
- To use this approach with pressure coordinate, need to alter the
- reinit_ts_with_ideal_efold value, since depth_st is in MKS, not dbar.
-
-
-
-
-
-
-
-
-
contemp_from_pottemp_field
-
-
-DESCRIPTION
-
-
-
- Compute conservative temperature for all grid points.
- Input is potential temperature (C) and salinity(psu or g/kg).
-
- contemp = potential_enthalpy(s,theta)/cp_ocean
-
-
-
-
-
-
-
-
-
contemp_from_pottemp_level
-
-
-DESCRIPTION
-
-
-
- Compute conservative temperature for one k-level.
- Input is potential temperature (C) and salinity(psu or g/kg).
-
- contemp = potential_enthalpy(s,theta)/cp_ocean
-
-
-
-
-
-
-
-
-
contemp_from_pottemp_point
-
-
-DESCRIPTION
-
-
-
- Compute conservative temperature for one grid point.
- Input is potential temperature (C) and salinity(psu or g/kg).
-
- contemp = potential_enthalpy(s,theta)/cp_ocean
-
-
-
-
-
-
-
-
-
pottemp_from_contemp_field
-
-
-DESCRIPTION
-
-
-
- Compute potential temperature from conservative temperature
- for all grid points. Perform one extra iteration to get
- precision to near computer precision.
-
- Input is salinity (psu) and conservative temperature (C).
-
- Use wrk1, wrk2, and wrk3 so to not take 3-d arrays from stack.
-
-
-
-
-
-
-
-
-
pottemp_from_contemp_level
-
-
-DESCRIPTION
-
-
-
- Compute potential temperature from conservative temperature
- over a k-level. Perform one extra iteration to get
- precision to near computer precision.
-
- Input is salinity (psu) and conservative temperature (C).
-
-
-
-
-
-
-
-
-
pottemp_from_contemp_point
-
-
-DESCRIPTION
-
-
-
- Compute potential temperature from conservative temperature at a point.
- Perform one extra iteration to get precision to near computer precision.
-
- Input is salinity (psu) and conservative temperature (C).
-
-
-
-
-
-
-
-
-
dentropy_dtheta_field
-
-
-DESCRIPTION
-
-
-
- d(entropy)/d(pottemp) at each grid point from twice differentiating
- the Gibbs potential in Feistel (2003), Prog. Ocean. 58, 43-114.
- (pressure=0 since use potential temperature)
-
- salinity : salinity (psu)
- theta : potential temperature (deg C, ITS-90)
- dentropy_dtheta : d(entropy)/d(pottemp) J/(kg degC^2)
-
- check value: dentropy_dtheta(35,20) = 13.63256369213874
-
-
-
-
-
-
-
-
-
dentropy_dtheta_level
-
-
-DESCRIPTION
-
-
-
- d(entropy)/d(pottemp) at k-level from twice differentiating
- the Gibbs potential in Feistel (2003), Prog. Ocean. 58, 43-114.
- (pressure=0 since use potential temperature)
-
- salinity : salinity (psu)
- theta : potential temperature (deg C, ITS-90)
- dentropy_dtheta : d(entropy)/d(pottemp) J/(kg degC^2)
-
- check value: dentropy_dtheta(35,20) = 13.63256369213874
-
-
-
-
-
-
-
-
-
dentropy_dtheta_point
-
-
-DESCRIPTION
-
-
-
- d(entropy)/d(pottemp) at an (i,j,k) point from twice differentiating
- the Gibbs potential in Feistel (2003), Prog. Ocean. 58, 43-114.
- (pressure=0 since use potential temperature)
-
- salinity : salinity (psu)
- theta : potential temperature (deg C, ITS-90)
- dentropy_dtheta : d(entropy)/d(pottemp) J/(kg degC^2)
-
- check value: dentropy_dtheta(35,20) = 13.63256369213874
-
-
-
-
-
-
-
-
-
tempsalt_check_range
-
-
-DESCRIPTION
-
-
-
- Check to see that temperature and salinity are within preset
- range. If outside of the range, then bring the model down.
-
- This check is particularly useful to ensure that the equation
- of state is evaluated with physically sensible values of temp
- and salinity.
-
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_tempsalt_nml
-
-
-
-
-
-teos10
-
-
- For choosing whether to use the TEOS-10 equation of state.
- This usage requires conservative temperature as the temperature variable,
- and two salinity variables: Preformed Salinity and Absolute Salinity
- anomaly. Default teos10=.false.
-
-[logical]
-
-
-temperature_variable
-
-
- For choosing the temperature variable used in the model.
- Choices are 'conservative_temp' and 'potential_temp'.
- Since conservative temperature is more accurate, it is the default.
-
-[character]
-
-
-pottemp_equal_contemp
-
-
- For certain idealized cases where the difference between potential
- temperature and conservative temperature is irrelevant. Default=.false.
-
-[logical]
-
-
-pottemp_2nd_iteration
-
-
- For taking extra iteration in computation of potential temperature
- from conservative temperature and salinity. Default is true.
-
-[logical]
-
-
-reinit_ts_with_ideal
-
-
- For setting up an ideal temperature and salinity profile
- that is generated in the model. This profile can be
- generated after the model has already been running, hence
- the name "reinit" for "reinitialize."
-
-[logical]
-
-
-reinit_ts_with_ideal_efold
-
-
- For setting efolding of reinitialized temp and salinity profile.
- Default reinit_ts_with_ideal_efold=1000.
-
-[real, units: metre]
-
-
-reinit_ts_with_ideal_tvalue
-
-
- For setting the reinitialized temperature value using the
- ideal profile. Default reinit_ts_with_ideal_tvalue = 10.0
-
-[real, units: C]
-
-
-reinit_ts_with_ideal_svalue
-
-
- For setting the reinitialized temperature value using the
- ideal profile. Default reinit_ts_with_ideal_svalue = 30.0
-
-[real, units: psu]
-
-
-t_min
-
-
- Minimum potential/conservative temperature below which we gracefully bring down the model.
-
-[real, units: deg C]
-
-
-t_max
-
-
- Maximum potential/conservative temperature above which we gracefully bring down the model.
-
-[real, units: deg C]
-
-
-s_min
-
-
- Minimum salinity below which we gracefully bring down the model.
-
-[real, units: ppt]
-
-
-s_max
-
-
- Maximum salinity below which we gracefully bring down the model.
-
-[real, units: ppt]
-
-
-t_min_limit
-
-
- Minimum potential/conservative temperature below which will employ upwind advection
- instead of quicker, and horizontal diffusion instead of neutral physics.
-
-[real, units: deg C]
-
-
-t_max_limit
-
-
- Maximum potential/conservative temperature above which will employ upwind advection
- instead of quicker, and horizontal diffusion instead of neutral physics.
-
-[real, units: deg C]
-
-
-s_min_limit
-
-
- Minimum salinity below which will employ upwind advection instead
- of quicker, and horizontal diffusion instead of neutral physics.
-
-[real, units: psu]
-
-
-s_max_limit
-
-
- Maximum salinity below which will employ upwind advection instead
- of quicker, and horizontal diffusion instead of neutral physics.
-
-[real, units: psu]
-
-
-debug_this_module
-
-
- For debugging the module.
-
-[logical]
-
-
-
-
-
-
-
-
-
-
-
REFERENCES
-
-
-
-
- Feistel (2003)
- A new extended Gibbs thermodynamic potential of seawater
- Progress in Oceanography. vol 58, pages 43-114.
-
-
- Jackett, McDougall, Feistel, Wright, and Griffies (2005)
- Algorithms for density, potential temperature,
- conservative temperature, and freezing temperature of
- seawater. Journal of Atmospheric and Oceanic
- Technology, 2005 submitted.
-
- Currently this module only works for the ocean model,
- but it could be extended (or generalized) to work with other
- models.
-
- This module consists of eight subroutines, three are called as
- the model is intialized, four are called every time-step, and
- one is called at model ending. The subroutines are called in
- the following order.
-
- These routines are called once at model startup in the
- ocean_tracer_init routine:
-
- ocean_tpm_init: This routine saves pointers to "global" model
- structures, such as Grid and Domain. Also this
- routine will call specified routines to set default
- values for each tracer for such things as advection
- scheme, tracer name, etc.
-
- ocean_tpm_flux_init: this routine initalizes field elements
- relating to the ocean-atmosphere gas fluxes
-
- ocean_tpm_start: This routine calls specified routines to
- allocate appropriate storage for the tracer packages,
- perform pre-processing and initialization (possibly
- from extra restart information) and set parameters,
- either via namelist or via the field manager.
-
- These routines are called each time-step from
- update_ocean_tracer (one before integration and one after):
-
- ocean_tpm_sbc: Calls specified routines to handle surface
- coundary condition calculations. Some or all of
- this functionality may be moved into a new, generalized
- boundary condition manager.
-
- ocean_tpm_bbc: Calls specified routines to handle bottom
- coundary condition calculations.
-
- ocean_tpm_source: Calls specified routines to calculate the
- source array for each tracer in the tracer packages.
-
- ocean_tpm_tracer: For those packages which need to do
- post-processing after the continuity equation has
- been integrated, calls may be placed here. This
- could be for global, annual means, for instance.
-
- This routine is called once at the end of the run from
- ocean_tracer_end:
-
- ocean_tpm_end: Call routines to finish up any loose ends, such
- as saving extra restart fields.
-
- The following routines are called in relation to tying in to
- the FMS coupler to calculate fluxes for the additional
- tracers:
-
- ocean_tpm_init_sfc: Allocate arrays for the accumulation of
- data to be used by the coupler
-
- ocean_tpm_sum_sfc: Accumulate data for the coupler
-
- ocean_tpm_avg_sfc: Take the time-mean of the fields for the coupler
-
- ocean_tpm_zero_sfc: Zero out the fields for the coupler to allow
- for accumulation for the next time period
-
- ocean_tpm_sfc_end: Save out fields for the restart.
-
-
- Initialization code for prognostic tracers, returning a pointer to
- the T_prog array.
-
-
-
-
-
-
-
-
ocean_diag_tracer_init
-
-
-DESCRIPTION
-
-
- Initialization code for diagnostic tracers, returning a pointer to the T_diag array
-
-
-
-
-
-
-
-
update_ocean_tracer
-
-
-DESCRIPTION
-
-
- Update value of tracer concentration to time taup1.
-
- Note that T_prog(n)%source is added at the very end
- of the time step, after the rho_dzt factor has been
- divided.
-
-
-
-
-
-
-
-
update_advection_only
-
-
-DESCRIPTION
-
-
-
- Redo tracer updates for those that use only advection--nothing else.
- This method is useful for testing advection schemes.
-
- T_prog(n)%use_only_advection==.true. ignores all boundary forcing
- and sources, so if T_prog(n)%stf or pme, rivers, sources
- are nonzero, tracer diagnostics will spuriously indicate
- non-conservation.
-
- Assume for these tests that
- (1) vertical advection is done fully explictly in time
- (2) pme, rivers, stf, btf, and other sources are zero
- (3) do not use advect_sweby_all
-
-
-
-
-
-
-
-
-
ocean_tracer_restart
-
-
-DESCRIPTION
-
-
- Write out restart files registered through register_restart_file
-
-
-
-
-
-
-
-
ocean_tracer_end
-
-
-DESCRIPTION
-
-
- Write ocean tracer restarts
-
-
-
-
-
-
-
-
compute_tmask_limit
-
-
-DESCRIPTION
-
-
- Provide for possibility that quicker advection reverts to
- first order upwind when tracer is outside a specified range.
- Likewise, may wish to revert neutral physics to horizontal diffusion.
-
- For this purpose, we define a mask which is set to unity where
- fluxes revert to first order upwind advection
- (if using quicker) and horizontal diffusion (if using neutral).
-
- This method is very ad hoc. What is preferred for advection is to use
- a monotonic scheme, such as mdfl_sweby or mdppm. For neutral physics,
- no analogous monotonic scheme has been implemented. Such could be
- useful, especially for passive tracers. In the meantime, tmask_limit
- provides a very rough limiter for neutral physics to help keep tracers
- within specified bounds.
-
-
-
-
-
-
-
-
-
remap_s_to_depth
-
-
-DESCRIPTION
-
-
-
- Remap in the vertical from s-coordinate to depth and then send to
- diagnostic manager.
-
- This routine is mostly of use for terrain following vertical
- coordinates, which generally deviate a lot from depth or pressure
- coordinates. The zstar and pstar coordinates are very similar
- to z or pressure, so there is no need to do the remapping for
- purposes of visualization.
-
- The routine needs to be made more general and faster.
- It also has been found to be problematic, so it is NOT
- recommended. It remains here as a template for a better algorithm.
- Remapping methods in Ferret are much better.
-
- Use rho_dzt weighting to account for nonBoussinesq.
-
- Author: Stephen.Griffies
-
-
-
-
-
-
-
-
-
remap_depth_to_s
-
-
-DESCRIPTION
-
-
-
- Remap in the vertical from depth to s-coordinate. This routine is
- used for initializing terrain following coordinate models given an
- initial tracer field generated assuming depth-like vertical coordinate.
-
- This routine is of use for terrain following vertical coordinates,
- which generally deviate a lot from z, zstar, pressure, or pstar
- coordinates.
-
- Algorithm is very rudimentary and can be made better.
-
- Author: Stephen.Griffies
-
-
-
-
-
-
-
-
-
inflow_nboundary_init
-
-
-DESCRIPTION
-
-
- Initialize the mask, temp, and salt values at the northern boundary
- where we are specifying values for an inflow boundary condition.
-
-
-
-
-
-
-
-
-
ocean_tracer_diagnostics_init
-
-
-DESCRIPTION
-
-
- Do some initialization required for diagnostics.
- Density must already be initialized for this routine to be used.
- Hence, this routine is called from ocean_model.F90.
-
-
-
-
-
-
-
-
send_tracer_diagnostics
-
-
-DESCRIPTION
-
-
-
- For sending some tracer diagnostics
-
-
-
-
-
-
-
-
-
watermass_diag
-
-
-DESCRIPTION
-
-
- Diagnose effects from interior ocean vertical mixing of
- temp and salt on the watermass transformation diagnostics.
-
- This routine is called prior to implicit update of the tracer
- fields, so that taup1 value contains only explicit in-time
- tendencies. The implicit in-time tendencies are diagnosed
- in this routine by various calls to invtri using same methods
- as for the prognostic calculation.
-
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_tracer_nml
-
-
-
-
-
-zero_tendency
-
-
- If true, then will freeze the tracer fields.
-
-[logical]
-
-
-zero_tracer_source
-
-
- To remove the T_prog%source contribution to tracer
- evolution. For debugging purposes. Default
- zero_tracer_source=.false.
-
-[logical]
-
-
-limit_age_tracer
-
-
- Limit the values of age tracer to be less than
- total run time and greater than zero.
- Default limit_age_tracer=.false.
-
-[logical]
-
-
-age_tracer_max_init
-
-
- Initial maximum age tracer. This nml provides the ability to
- start an integration with an age tracer that is not initialized
- to zero, say if we took an age tracer from another spin-up.
- Default age_tracer_max_init=0.0.
-
-[real, units: years]
-
-
-remap_depth_to_s_init
-
-
- For remapping initial tracer distributions, generally determined
- according to depth vertical coordinates using the mom preprocessing
- schemes, onto s-coordinates. This method is of use for initializing
- terrain following coordinate simulations with mom.
-
-[logical]
-
-
-frazil_heating_before_vphysics
-
-
- For computing frazil heating before the implicit vertical physics
- (which includes boundary fluxes), and before vertical convection.
- This is the order that CM2.0 and CM2.1 performed their calculations
- of frazil. It is arguable that one should NOT do frazil until the
- end of a time step, after vertical physics and after surface
- boundary fluxes.
- Default frazil_heating_before_vphysics=.false.
-
-[logical]
-
-
-frazil_heating_after_vphysics
-
-
- For computing frazil heating after the implicit vertical physics
- (which includes boundary fluxes), and after vertical convection.
- This is the recommended method.
- Default frazil_heating_after_vphysics=.false.
-
-[logical]
-
-
-tmask_limit_ts_same
-
-
- tmask_limit is derived separately for the tracers. However,
- it may be appropriate to have the mask be the same for temp
- and salinity, in which case the neutral physics fluxes are
- self-consistent. But for some cases, such as when running with
- linear eos, may not wish to have the temp and salinity coupled
- when computing the mask.
-
-[logical]
-
-
-compute_tmask_limit_on
-
-
- For updating the tmaks_limit array. This calculation is
- recommended for the following physics and advection schemes:
- 1/ quicker advection
- 2/ neutral physics
- 3/ submesoscale closure.
- The default is compute_tmask_limit_on=.true., but if none
- of the above schemes is used, then some time savings can be
- realized by setting compute_tmask_limit_on=.false.
-
-[logical]
-
-
-debug_this_module
-
-
- For debugging the tracer module
-
-[logical]
-
-
-write_a_restart
-
-
- Set true to write a restart. False setting only for rare
- cases where wish to benchmark model without measuring the cost
- of writing restarts and associated chksums.
- Default is write_a_restart=.true.
-
-[logical]
-
-
-interpolate_tprog_to_pbott
-
-
- To linear interpolate the initial conditions for prognostic
- tracers to the partial bottom cells. Default
- interpolate_tprog_to_pbott=.true.
-
-[logical]
-
-
-interpolate_tdiag_to_pbott
-
-
- To linear interpolate the initial conditions for diagnostic
- tracers to the partial bottom cells. Default
- interpolate_tdiag_to_pbott=.false.
-
-[logical]
-
-
-inflow_nboundary
-
-
- For adding an inflow transport from the northern boundary
- which brings in temp and salinity according to inflow data
- files. Default is inflow_nboundary=.false.
-
-[logical]
-
-
-ocean_tpm_debug
-
-
- For debugging ocean tracer package manager.
-
-[logical]
-
-
-use_tempsalt_check_range
-
-
- To call a check to see that temperature and salinity
- are within their pre-selected range.
- Default use_tempsalt_check_range=.false. since this
- check may incur some cost that users should be aware of.
-
-[logical]
-
-
-
-
-
-
-
-
-
-
-
REFERENCES
-
-
-
-
- R.C. Pacanowski and S.M. Griffies
- The MOM3 Manual (1999)
-
-
- S.M. Griffies, M.J. Harrison, R.C. Pacanowski, and A. Rosati
- A Technical Guide to MOM4 (2004)
-
-
- S.M. Griffies, Fundamentals of ocean climate models (2004)
-
- Initialize the main tracer advection diagnostics.
-
-
-
-
-
-
-
-
watermass_diag_init
-
-
-DESCRIPTION
-
-
- Initialize the watermass diagnostics.
-
-
-
-
-
-
-
-
gyre_overturn_diagnose_init
-
-
-DESCRIPTION
-
-
- Initialize diagnostics and fields for gyre/overturning.
-
- March 2012 for faster approach:
- russell.fiedler@csiro.au
-
- Some reorganization
- Stephen.Griffies
-
-
-
-
-
-
-
-
-
quicker_init
-
-
-DESCRIPTION
-
-
- Initialize quicker specific fields.
-
-
-
-
-
-
-
-
fourth_sixth_init
-
-
-DESCRIPTION
-
-
- Initialize the fourth order and sixth order advection fields.
-
-
-
-
-
-
-
-
mdfl_init
-
-
-DESCRIPTION
-
-
- Initialize mdfl and dst_linear specific fields.
-
-
-
-
-
-
-
-
mdppm_init
-
-
-DESCRIPTION
-
-
- Initialize mdppm specific fields.
-
-
-
-
-
-
-
-
mdmdt_init
-
-
-DESCRIPTION
-
-
- Initialize mdmdt specific fields.
-
-
-
-
-
-
-
-
psom_init
-
-
-DESCRIPTION
-
-
- Read restart or initialize moments for prather advection
-
-
-
-
-
-
-
-
horz_advect_tracer
-
-
-DESCRIPTION
-
-
- Compute horizontal advection of tracers
-
-
-
-
-
-
-
-
vert_advect_tracer
-
-
-DESCRIPTION
-
-
- Compute vertical advection of tracers for case
- with advect_sweby_all=.false.
-
-
-
-
-
-
-
-
horz_advect_tracer_upwind
-
-
-DESCRIPTION
-
-
- Compute horizontal advection of tracers from first order upwind.
- This scheme is positive definite but very diffusive.
-
-
-
-
-
-
-
-
horz_advect_tracer_2nd_order
-
-
-DESCRIPTION
-
-
- Compute horizontal advection of tracers from second order
- centered differences.
-
-
-
-
-
-
-
-
horz_advect_tracer_4th_order
-
-
-DESCRIPTION
-
-
- Compute horizontal advection of tracers from fourth order centered
- differences.
-
- WARNING: This code does NOT account for non-uniform grids.
-
-
-
-
-
-
-
-
-
horz_advect_tracer_6th_order
-
-
-DESCRIPTION
-
-
- Compute horizontal advection of tracers from sixth order centered
- differences.
-
- WARNING: this code does NOT account for non-uniform grids.
-
-
-
-
-
-
-
-
-
horz_advect_tracer_quicker
-
-
-DESCRIPTION
-
-
- Compute horizontal advection of tracers from quicker.
-
-
-
-
-
-
-
-
horz_advect_tracer_quickmom3
-
-
-DESCRIPTION
-
-
- Compute horizontal advection of tracers from quicker using MOM3 masking.
- This method has proven useful for reproducing MOM3 results with later MOM.
-
-
-
-
-
-
-
-
vert_advect_tracer_upwind
-
-
-DESCRIPTION
-
-
- Compute vertical advection of tracers from first order upwind.
- This scheme is positive definite, but very diffusive.
-
-
-
-
-
-
-
-
vert_advect_tracer_2nd_order
-
-
-DESCRIPTION
-
-
- Compute vertical advection of tracers from second order centered
- differences.
-
-
-
-
-
-
-
-
vert_advect_tracer_4th_order
-
-
-DESCRIPTION
-
-
- Compute vertical advection of tracers from fourth order centered
- differences. NOTE: this code does not account for non-uniform grids.
-
-
-
-
-
-
-
-
vert_advect_tracer_6th_order
-
-
-DESCRIPTION
-
-
- Compute vertical advection of tracers from sixth order centered
- differences. NOTE: this code does not account for non-uniform grids.
-
-
-
-
-
-
-
-
vert_advect_tracer_quicker
-
-
-DESCRIPTION
-
-
- Compute vertical advection of tracers from quicker.
-
-
-
-
-
-
-
-
vert_advect_tracer_quickmom3
-
-
-DESCRIPTION
-
-
- Compute vertical advection of tracers from quicker using MOM3 masking.
- This method has proven useful for reproducing MOM3 results with later MOM.
-
-
-
-
-
-
-
-
advect_tracer_mdfl_sup_b
-
-
-DESCRIPTION
-
-
--------
- NOTE: This is legacy code. It may exhibit problems with limiters
- that are improperly implemented in the case of generalized vertical level
- coordinates of MOM. Under certain circumstances, the resulting tracer
- concentration can exhibit non-monotonic behaviour (i.e., produce extrema).
-
- Sept 2011
- Stephen.Griffies
- Alistair.Adcroft
--------
-
- Compute tendency due to 3D advection of tracers using a
- multi-dimensional flux-limited method. This method differs from
- other MOM advection methods in the following ways:
-
- 1) Horizontal and vertical advection are combined
- 2) Calculations of the three coordinates (Z, X, Y) are performed sequentially as updates
- to the tracer, so that the advection components for X and Y depend on Z and Z,Y
- respectively. This helps limit the flux.
- 3) During the update for each direction, the 2nd order Super-B flux limiter is applied.
- 4) Flux divergence is included within the calculation to also help limit the flux:
- - During the update for each direction, the divergence in each direction is added.
- - During the overall tendency calculated, the divergence in all three directions
- is removed.
- 5) All fluxes are functions of the tracer field at the taum1 time step. This
- means that this method is ideally suited for the twolevel time stepping scheme,
- in which "taum1=tau", thus enabling twice the tracer time step available for the
- threelevel scheme.
-
-The calculation proceeds as follows:
-
- IMPORTANT NOTE: If this scheme is used at all, it must be used as the option for BOTH
- horizontal and vertical advection. In the the tracer tendency, it is applied as the
- horizontal term, but applies to vertical as well, for which case the vertical term in
- the tracer tendency equation is set to zero.
-
- This scheme was ported to mom4 from the MIT-GCM by John Dunne and Alistair Adcroft
- during Summer 2003
-
-
-
-
-
-
-
-
-
advect_tracer_mdfl_sweby_test
-
-
-DESCRIPTION
-
-
- Compute tendency due to 3D advection of tracers using a multi-dimensional flux-limited
- method. This method differs from other methods in the following ways:
-
- 1) Horizontal and vertical advection are combined
- 2) Calculations of the three coordinates (Z, X, Y) are performed sequentially as updates
- to the tracer, so that the advection components for X and Y depend on Z and Z,Y
- respectively... This helps limit the flux.
- 3) During the update for each direction, the 3rd order Sweby flux limiter is applied.
- 4) Flux divergence is included within the calculation to also help limit the flux:
- - During the update for each direction, the divergence in each direction is added.
- - During the overall tendency calculated, the divergence in all three directions
- is removed.
- 5) All fluxes are functions of the tracer field at the taum1 time step. This
- means that this method is ideally suited for the twolevel time stepping scheme,
- in which "taum1=tau", thus enabling twice the tracer time step available for the
- threelevel scheme.
-
- The calculation proceeds as follows:
-
- IMPORTANT NOTE: If this scheme is used at all, it must be used as the option for BOTH
- horizontal and vertical advection. In the tracer tendency, it is applied as the
- horizontal term, but applies to vertical as well, for which case the vertical term in
- the tracer tendency equation is set to zero.
-
- This scheme was ported to mom4 from the MIT-GCM by John Dunne and Alistair Adcroft
- during Summer 2003
-
- Griffies: 5/27/04
- Optimized by filling 3d arrays prior to sending for mpp_update_domains
-
- 07/11/2007 by Stephen.Griffies
- When the nonlinear limiters are removed (sweby_limiter=0.0),
- this scheme reduces to a linear direct space-time method
- (ADVECT_DST_LINEAR).
-
- This is a test version of the mdfl_sweby scheme. It is not supported for
- general use.
-
-
-
-
-
-
-
-
-
advect_tracer_mdfl_sweby
-
-
-DESCRIPTION
-
-
-
--------
- NOTE: This is a legacy version of the advect_tracer_mdfl_sweby routine.
- This version may have problems with limiters that are improperly implemented
- in the case of generalized vertical level coordinates of MOM. Consequently,
- under certain circumstances, the resulting tracer concentration can
- exhibit non-monotonic behaviour (i.e., produce extrema).
- This routine was used in various GFDL model configurations.
-
- Sept 2011
- Stephen.Griffies
- Alistair.Adcroft
--------
-
- Compute tendency due to 3D advection of tracers using a multi-dimensional flux-limited
- method. This method differs from other methods in the following ways:
-
- 1) Horizontal and vertical advection are combined
- 2) Calculations of the three coordinates (Z, X, Y) are performed sequentially as updates
- to the tracer, so that the advection components for X and Y depend on Z and Z,Y
- respectively... This helps limit the flux.
- 3) During the update for each direction, the 3rd order Sweby flux limiter is applied.
- 4) Flux divergence is included within the calculation to also help limit the flux:
- - During the update for each direction, the divergence in each direction is added.
- - During the overall tendency calculated, the divergence in all three directions
- is removed.
- 5) All fluxes are functions of the tracer field at the taum1 time step. This
- means that this method is ideally suited for the twolevel time stepping scheme,
- in which "taum1=tau", thus enabling twice the tracer time step available for the
- threelevel scheme.
-
- The calculation proceeds as follows:
-
- IMPORTANT NOTE: If this scheme is used at all, it must be used as the option for BOTH
- horizontal and vertical advection. In the tracer tendency, it is applied as the
- horizontal term, but applies to vertical as well, for which case the vertical term in
- the tracer tendency equation is set to zero.
-
- This scheme was ported to mom4 from the MIT-GCM by John Dunne and Alistair Adcroft
- during Summer 2003
-
- Griffies: 5/27/04
- Optimized by filling 3d arrays prior to sending for mpp_update_domains
-
- 07/11/2007 by Stephen.Griffies
- When the nonlinear limiters are removed (sweby_limiter=0.0),
- this scheme reduces to a linear direct space-time method
- (ADVECT_DST_LINEAR).
-
-
-
-
-
-
-
-
-
advect_tracer_sweby_all
-
-
-DESCRIPTION
-
-
-
--------
- NOTE: This is routine suffers from the same problems as the
- advect_tracer_mdfl_sweby routine. Namely, it has problems
- with limiters that are improperly implemented in the case of generalized
- vertical level coordinates of MOM. Consequently,
- under certain circumstances, the resulting tracer concentration can
- exhibit non-monotonic behaviour (i.e., produce extrema).
- This routine was used in various GFDL model configurations. It is retained
- solely to provide bitwise reproducing those earlier configurations.
-
- Sept 2011
- Stephen.Griffies
- Alistair.Adcroft
--------
-
- Sweby scheme optimized by doing all tracers at once, so
- can send larger packet to mpp_update_domains.
-
- This scheme is available ONLY when advecting all tracers with the
- sweby scheme.
-
- This scheme CANNOT be called from compute_adv_diss.
-
- Stephen.Griffies
- June 2004
-
-
-
-
-
-
-
-
-
advect_tracer_psom
-
-
-DESCRIPTION
-
-
-
- Compute advective tendency of dzt*rho*tracer concentration using
- Prather's second order moment method (SOM):
-
- Prather, M. J.,"Numerical Advection by Conservation of Second-Order Moments"
- JGR, Vol 91, NO. D6, p 6671-6681, May 20, 1986
-
- Merryfield and Holloway (2003), "Application of an accurate advection
- algorithm to sea-ice modelling". Ocean Modelling, Vol 5, p 1-15.
-
- MOM 3 code by M. Hofmann and M. A. M. Maqueda
- Ported to mom4p0 by Ronald.Pacanowski
- Ported to mom4p1 by Stephen.Griffies
-
- The preferred limiters are taken from Merryfield and Holloway,
- and generalized by Bill Merryfield for non-constant grid spacing.
-
- IMPORTANT NOTE: This scheme must be used for BOTH horizontal and
- vertical advection. In the tracer tendency, it is applied as the
- horizontal term, but applies to vertical as well, for which case the
- vertical term in the tracer tendency equation is set to zero.
-
- NOTE: When using psom_limit_prather=.true., the tracer has a lower
- bound of zero. So this limiter IS NOT appropriate for temperature
- when measured in degrees C. The preferred, and default, limiter
- is from Merryfield and Holloway.
-
-
-
-
-
-
-
-
-
psom_x
-
-
-DESCRIPTION
-
-
- Compute i-advective flux using Prather's SOM.
-
-
-
-
-
-
-
-
psom_y
-
-
-DESCRIPTION
-
-
- Computes j-advective flux using Prather's SOM.
-
-
-
-
-
-
-
-
psom_z
-
-
-DESCRIPTION
-
-
- Computes k-advective flux using Prather's SOM.
-
-
-
-
-
-
-
-
advect_tracer_mdppm_test
-
-
-DESCRIPTION
-
-
-
- Compute advective tendency of dzt*rho*tracer concentration using
- multi-dimensional piecewise parabolic method.
-
- Controlling parameters:
- Tracer%ppm_hlimiter=0 -> No limiting in the horizontal
- ppm_hlimiter=1 -> Full constraint (Colella and Woodward, 1984)
- ppm_hlimiter=2 -> Improved full constraint (Lin, 2004)
- ppm_hlimiter=3 -> Huynh limiter (Huynh, 1996)
-
- ppm_vlimiter=* -> as for ppm_hlimit but for the vertical
-
- Coded by Alistair.Adcroft
- Jan/Feb 2006
-
- Updated with controlling parameters, April 2006
-
- This is an unsupported test version of the MDPPM scheme. It is not
- meant for general use.
-
-
-
-
-
-
-
-
-
advect_tracer_mdppm
-
-
-DESCRIPTION
-
-
-
--------
- NOTE: This is routine may suffer from same problems as the
- advect_tracer_mdfl_sweby routine. Namely, it has problems
- with limiters that are improperly implemented in the case of generalized
- vertical level coordinates of MOM. Consequently,
- under certain circumstances, the resulting tracer concentration can
- exhibit non-monotonic behaviour (i.e., produce extrema).
-
- Sept 2011
- Stephen.Griffies
- Alistair.Adcroft
--------
-
- Compute advective tendency of dzt*rho*tracer concentration using
- multi-dimensional piecewise parabolic method.
-
- Controlling parameters:
- Tracer%ppm_hlimiter=0 -> No limiting in the horizontal
- ppm_hlimiter=1 -> Full constraint (Colella and Woodward, 1984)
- ppm_hlimiter=2 -> Improved full constraint (Lin, 2004)
- ppm_hlimiter=3 -> Huynh limiter (Huynh, 1996)
-
- ppm_vlimiter=* -> as for ppm_hlimit but for the vertical
-
- Coded by Alistair.Adcroft
- Jan/Feb 2006
-
- Updated with controlling parameters, April 2006
-
-
-
-
-
-
-
-
-
ppm_limit_cw84
-
-
-DESCRIPTION
-
-
-
- Kernel to limit the edge values for PPM following Colella and Woodward, 1984
-
- Coded by Alistair.Adcroft
- Apr 2006
-
-
-
-
-
-
-
-
-
ppm_limit_ifc
-
-
-DESCRIPTION
-
-
-
- Kernel to limit the edge values for PPM using the Improved Full Constraint
- (IFC) of Lin, 2004.
-
- Coded by Alistair.Adcroft
- Apr 2006
-
-
-
-
-
-
-
-
-
ppm_limit_sh
-
-
-DESCRIPTION
-
-
-
- Kernel to limit the edge values for PPM following the monotonicity-
- preserving approach of Suresh and Huynh, 1997.
-
- Coded by Alistair.Adcroft
- Apr 2006
-
-
-
-
-
-NOTE
-
-
- About efficiency: ppm_limit_sh() is not as efficient as it would be if
- we wrote a s/r for each direction. The pre-calculation of d1m, d1p, d1mm and
- d1pp duplicates operations and would be much faster if d1m was replaced
- by d1p(i+1). However, in order to re-use this limiter for the all directions
- (to simplify debugging) I have opted for the less efficient form for now. - AJA
-
-
-
-
-
-
-
-
advect_tracer_mdmdt_test
-
-
-DESCRIPTION
-
-
-
- Compute advective tendency of dzt*rho*tracer concentration using
- multi-dimensional piecewise parabolic method.
-
- Controlling parameters:
- Tracer%mdt_scheme=0 -> 7th order FV, unlimited (Daru & Tenaud, 2004)
- mdt_scheme=1 -> 7th order FV, TVD limiter
- mdt_scheme=2 -> 7th order FV, MP limiter
- mdt_scheme=3 -> 7th order MP, 4th order TVD, FCT combination (Adcroft, 2011)
-
- Coded by Alistair.Adcroft
- Aug/Sep 2011
-
- This code is unsupported test code, which is not meant for general use.
-
-
-
-
-
-
-
-
-
gyre_overturn_diagnose
-
-
-DESCRIPTION
-
-
- Diagnose tracer transport according to zonal mean and
- deviations from zonal mean.
-
- We allow for the use of a basin mask so that the zonal means
- are performed over the global domain and each of five other
- basins. If no basin mask is read, then assume global domain
- used to define the zonal means.
-
- []=zonal mean; *=deviation from zonal mean
-
- V = rho_dzt dxt T, with rho=rho0 for Boussinesq
-
- int [V T] = total advective
- int [V][T] = overturning
- int V* T* = gyre
-
- This routine is much faster than the older routine gyre_overturn_diagnose_old.
-
- In this version, we compute partial zonal sums locally and then perform
- a "global" sum over a restricted set of pes.
- This approach results in slightly different answers at the
- REAL(8) level. However, differences should be negligible for diagnostic
- purposes at the REAL(4) level.
-
- We require no global arrays here, and redundant computation is eliminated.
-
- Note that if advect_sweby_all is used we cannot do this calculation since we
- don not have flux_y, except for the last tracer computed.
- The zonal mean could be computed within the routine or flux_y itself could
- be stored in a 3D arrays.
-
- original approach
- Stephen.Griffies
- May 2007
-
- optimization by removing global arrays
- russell.fiedler@csiro.au
- March 2012
-
-
-
-
-
-
-
-
-
watermass_diag
-
-
-DESCRIPTION
-
-
- Compute watermass diagnostics associated with resolved flow
- advection of temperature and salinity.
-
-
-
-
-
-
-
-
compute_adv_diss
-
-
-DESCRIPTION
-
-
-
- Compute the dissipation due to advection truncation errors.
- This diagnostic requires computation of advection operator acting
- on the squared tracer concentration.
-
- NOTE: This scheme isolates the dissipation from trucation errors
- in advection ONLY for the following vertical coordinates:
- 1/ geopotential: for all k-levels, except for k=1
- (due to undulating surface height)
- 2/ pressure: for all k-levels, except for k=kmt
- (due to undulating bottom pressure)
-
- NOTE: For the Quicker advection scheme, we assume the preferred
- two_level time scheme is used here, so that taum1=tau.
-
- NOTE: If PSOM is used for temp or salt, then we MUST also enable
- a new passive tracer in the field table, with name
- passive_temp_sq and passive_salt_sq. This extra tracer is
- used for diagnostics alone, and is required due to the extra
- moment fields used for computing the PSOM tendency.
- If PSOM is used for another tracer besides temp or salt, then
- some extra code needs to be written inside ocean_passive.F90,
- emulating the work done for temp and salt.
-
-
-
-
-
-
-
-
-
get_tracer_stats
-
-
-DESCRIPTION
-
-
- Compute the upper/lower values of a 3D field, returning values via arguments
-
-
-
-
-
-
-
-
tracer_stats
-
-
-DESCRIPTION
-
-
- Check the upper/lower values of a 3D field fall between speficied bounds
- reporting points that fall outside. Bring model down uncleanly if bounds are
- exceeded.
-
- NOTE: This is a debugging tool and not for normal use.
-
-
-
-
-
-
-
-
-
ocean_tracer_advect_restart
-
-
-DESCRIPTION
-
-
- Write out restart files registered through register_restart_file
-
-
-
-
-
-
-
-
ocean_tracer_advect_end
-
-
-DESCRIPTION
-
-
- Write the PSOM moments for restarts.
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&ocean_tracer_advect_nml
-
-
-
-
-
-limit_with_upwind
-
-
- If true, will compute tracer fluxes entering a cell using upwind
- if the tracer value is outside a specified range. Implemented
- only for quick at this time. This is an ad hoc and incomplete attempt
- to maintain monotonicity with the quicker scheme.
-
-[logical]
-
-
-advect_sweby_all
-
-
- For running all tracers with sweby, thereby utilizing a bitwise same
- routine that reorganizes loops and can be faster for certain configurations.
- Default advect_sweby_all=.false.
-
-[logical]
-
-
-zero_tracer_advect_horz
-
-
- For debugging. Set to .true. to turn off horizontal advection.
-
-[logical]
-
-
-zero_tracer_advect_vert
-
-
- For debugging. Set to .true. to turn off vertical advection.
-
-[logical]
-
-
-psom_limit_prather
-
-
- For running with the original Prather limiter for the PSOM scheme.
- The limiter is positive definite, but not monotonic. This limiter
- is NOT recommended for most applications. The default is
- psom_limit_prather=.false., since we prefer to use the limiter
- from Merryfield and Holloway (2003).
-
-[logical]
-
-
-debug_this_module
-
-
- For debugging
-
-[logical]
-
-
-write_a_restart
-
-
- Set true to write a restart. False setting only for rare
- cases where wish to benchmark model without measuring the cost
- of writing restarts and associated chksums.
- Default is write_a_restart=.true.
-
-[logical]
-
-
-read_basin_mask
-
-
- For reading in a mask that selects regions of the domain
- for performing gyre and overturning diagnostics.
- The basin-mask convention used at GFDL has
- Southern=1.0,Atlantic=2.0,Pacific=3.0,Arctic=4.0,Indian=5.0
- Default read_basin_mask=.false., whereby basin_mask
- is set to tmask(k=1).
-
-[logical]
-
-
-
-
-
-
-
-
-
-
-
REFERENCES
-
-
-
-
- S.-J. Lin
- A "Vertically Lagrangian" Finite-Volume Dynamical Core for Global Models
- Month. Weather Rev. (2004) 132, 2293-2307
- (Appendix B)
-
-
- H.T. Huynh
- Schemes and Constraints for advection
- 15th Intern. Conf. on Numeric. Meth. in Fluid Mech., Springer (1997)
-
-
- Colella P. and P.R. Woodward
- The piecewise parabloic method (PPM) for gasdynamical simulations
- J. Comput. Phys. (1984) 54, 174-201
-
-
- A. Suresh and H.T. Huynh
- Accurate Monotonicity-Preserving Schemes with Runge-Kutta Time Splitting
- J. Comput. Phys. (1997) 136, 83-99
-
-
- V. Daru and C. Tenaud
- High order one-step monotonicity-preserving schemes for unsteady
- compressible flow calculations.
- J. Comp. Phys. (2004) 193, 563-594
-
- Prather, M. J.,"Numerical Advection by Conservation of Second-Order Moments"
- JGR, Vol 91, NO. D6, p 6671-6681, May 20, 1986
-
-
- Merryfield and Holloway (2003), "Application of an accurate advection
- algorithm to sea-ice modelling". Ocean Modelling, Vol 5, p 1-15.
-
-
- Hundsdorder and Trompert (1994), "Method of lines and
- direct discretization: a comparison for linear
- advection", Applied Numerical Mathematics,
- pages 469--490.
-
-
- Sweby (1984): "High-resolution schemes using flux
- limiters for hyperbolic conservation laws",
- SIAM Journal of Numerical Analysis, vol. 21
- pages 995-1011.
-
- Transport Matrix Method, for use in finding an approximate steady
- state of tracers.
-
- Ported to MOM4p0d by Samar Khatiwala spk@ldeo.columbia.edu
- June-July 2007
-
- Ported to MOM4p1 by Stephen.Griffies
- July 2007
-
- Some code clean-up; increased conformity to tracer module standard
- jes.13JUN08
-
- further code cleanup by Richard.Slater Jan2009.
-
- **Preliminary testing only.
-
- This module saves out the components of the explicit and implicit
- transport matrix. spk uses the output from the transport matrix module
- to assemble the actual transport matrix with his matlab code.
-
- In conjunction with the Newton-Krylov (NK) solver, the transport matrix
- is used to do an accelerated forward model in an iterative manner
- which allows the NK solver to reach solution convergence with greater
- efficiency.
-
- To create the transport matrix building blocks, passive, prognostic
- "tracers" are simulated. These "tracers" are, in practice, dye
- tracers initialized to 1 at one or more grid points and initialized
- to 0 elsewhere. Since the "area of influence" of
- a tracer at a particular grid point is determined by the advection scheme,
- it becomes more practical to introduce a number of dye tracers at other
- grid points, such that the "tracers" are staggered and will have
- non-overlapping areas of influence. These non-overlapping regions are
- called by spk, "tiles". The total number of dye tracers
- needed is independent of the horizontal grid resolution, but
- rather dependent upon the advection scheme's area of influence, i.e.
- the total number of grid points contained in a "tile". For a
- simple linear advection scheme, the number of tracers needed is about
- 10 x (number of vertical levels).
- spk has some special matlab code that generates the initial condition
- for the "tracers", given the grid_spec of the model.
-
- The behavior of the tracers' advection and diffusion is averaged over
- time (which the user may specify) and is saved out as a component
- of the later-to-be-assembled transport matrix.
-
- To run the transport_matrix module, an initial condition
- must be created by spk.
-
- Include the transport_matrix field_table and diag_table entries
- for the xml. Examples of these follow.
-
- Sample field table.
- -------------------------------------------------
- "tracer_packages","ocean_mod","transport_matrix"
-
- names = '01', '02', '03'
- horizontal-advection-scheme = mdfl_sweby
- vertical-advection-scheme = mdfl_sweby
- /
-
- --------------------------------------------------
-
- Sample diag table entry: enter as many "tracers" as you need
- with the naming convention exp_tm_# and imp_tm_#
- where # is a string as given abaove in "names"
- --------------------------------------------------
-"transport_matrix","exp_tm_01", "exp_tm_01" ,"ocean_transport_matrix","all",.false.,"none",1
-"transport_matrix","imp_tm_01", "imp_tm_01" ,"ocean_transport_matrix","all",.false.,"none",1
-"transport_matrix","exp_tm_02", "exp_tm_02" ,"ocean_transport_matrix","all",.false.,"none",1
-"transport_matrix","imp_tm_02", "imp_tm_02" ,"ocean_transport_matrix","all",.false.,"none",1
-"transport_matrix","exp_tm_03", "exp_tm_03" ,"ocean_transport_matrix","all",.false.,"none",1
-"transport_matrix","imp_tm_03", "imp_tm_03" ,"ocean_transport_matrix","all",.false.,"none",1
- --------------------------------------------------
-
-
- SPK NOTES:
- 1) The calling sequence is as follows:
- Top level driver (e.g., ocean_solo)
- -> S/R ocean_model_init(Ocean, Time_init, Time_in, Time_step_ocean, ensemble_ocean)
- Time%init = Time_in .eq. Time_init
- Time%Time_init = Time_init
- Time%Time_step = Time_step_ocean
- Time%model_time = Time_in
- Time%itt = 0
- -> S/R ocean_prog_tracer_init
- -> S/R ocean_tpm_init
- -> S/R transport_matrix_init
- -> S/R ocean_tpm_start
- -> S/R transport_matrix_start
- Start time stepping loop
- do nc=1, num_cpld_calls
- do no=1, num_ocean_calls
- ocean_seg_start = ( no .eq. 1 )
- ocean_seg_end = ( no .eq. num_ocean_calls )
- -> S/R update_ocean_model(Ice_ocean_boundary, Ocean_sfc, &
- ocean_seg_start, ocean_seg_end, num_ocean_calls)
- Time%model_time = Time%model_time + Time%Time_step
- Time%itt = Time%itt+1
- -> S/R ocean_tracer, S/R update_ocean_tracer
- do explicit transport
- -> S/R transport_matrix_store_explicit
- (accumulate explicit matrix and reset tracer field to initial condition)
- do implicit transport
- -> S/R ocean_tpm_tracer
- -> S/R transport_matrix_store_implicit
- (accumulate implicit matrix and reset tracer field to initial condition)
- -> S/R transport_matrix_write(.FALSE.) (time average and write matrices)
- Time = Time + Time_step_ocean
- enddo
- enddo
- -> S/R ocean_model_end
- -> S/R ocean_tpm_end
- -> S/R transport_matrix_end
- -> S/R transport_matrix_write(.TRUE.)
- (time average and write matrices for multi year runs)
-
- 2) Time counters are incremented BEFORE calling S/R update_ocean_tracer, so the first time
- transport_matrix_store_explicit is called, itt (and hence myIter) will be 1.
- The namelist parameter matrixStoreStartIter indicating the iteration number to begin
- accumulating matrices at should be RELATIVE to the current model run start (unlike
- in the MIT GCM where it refers to an absolute counter.
- I am not entirely certain this is handled correctly below. Things might be off by
- 1 time step.
-
-
-
-
- Idealized wave model for delivering wave number and wave height
- for coupled current-wave action on sediment.
-
-
-
-
-
- This idealized wave model delivers wave number and wave height
- for calculation of the coupled current-wave action on sediment.
- Swell is not included in this model.
-
- All fields are defined at tracer grid, for later use in sediment dynamics
- in such modules as ocean_shared/generic_tracers/generic_ERGOM.F90
-
- Returns .true. if the wave model is initialised
-
-
-
-
-
-
-
-
PUBLIC ROUTINES
-
-
-
-
-
ocean_wave_init
-
-
-DESCRIPTION
-
-
- Initialize the wave module
-
-
-
-
-
-
-
-
ocean_wave_model
-
-
-DESCRIPTION
-
-
- time step the wave model
-
-
-
-
-
-
-
-
ocean_wave_prop
-
-
-DESCRIPTION
-
-
- wave propagation
-
-
-
-
-
-
-
-
ocean_wave_diag
-
-
-DESCRIPTION
-
-
- wave diagnostics
-
-
-
-
-
-
-
-
ocean_wave_filter
-
-
-DESCRIPTION
-
-
- wave filter
-
-
-
-
-
-
-
-
read_wave
-
-
-DESCRIPTION
-
-
- Read wave restart information.
-
-
-
-
-
-
-
-
ocean_wave_restart
-
-
-DESCRIPTION
-
-
- Save wave restart information.
-
-
-
-
-
-
-
-
ocean_wave_end
-
-
-DESCRIPTION
-
-
- Write out external mode fields to restart file.
-
-
-
-
-
-
-
-
wave_chksum
-
-
-DESCRIPTION
-
-
- Compute checksum for external mode fields.
-
-
-
-
-
-
-
-
wave_model_is_initialised
-
use ocean_wave_mod, only: wave_model_is_initialised if (wave_model_is_initialised() ) then
-
-
-DESCRIPTION
-
-
- This function returns .true. if the wave model is initialised
- It is needed, because the wave model may be initialised after some module that requires a wave model
-
-
-
-
-INPUT
-
-
-
-
-
- No inputs needed.
- []
-
-
-
-
-
-OUTPUT
-
-
-
-
-
- This function returns a logical.
- [logical]
-
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&
-
-
-
-
-
-
-
-
-
-
-
-
-
REFERENCES
-
-
-
-
- P.C. Liu, D.J. Schwab and J.R. Bennett,
- Journ. of Phys. Oceanography 14, 1514 (1984).
- D.J. Schwab, J.R. Bennett, P.C. Liu and M.A. Donelan,
- Journ. of Geophysical Research 89 (C3), 3586 (1984).
-
-
- Hughes, S. A. 1984. "TMA Shallow-Water Spectrum:
- Description and Application," Technical Report CERC-84-7,
- US Army Engineer Waterways Experiment Station, Vicksburg, Miss.
-
- This module contains the generic version of BLING.
- It is designed so that both GFDL Ocean models, GOLD and MOM, can use it.
-
- WARNING: although the core components of the model (PO4, Fed, DOP, O2)
- have been quite well tested, the other components should be viewed as
- developmental at this point. There may still be some bugs, particularly
- in the CaCO3 burial scheme. EDG June 4, 2009
-
-
-
-
-
-
- Biogeochemistry with Light, Iron, Nutrient and Gas (BLING) includes an
- implicit ecological model of growth limitation by light,
- temperature, phosphate and iron, along with dissolved organic
- phosphorus and O2 pools.
- Food web processing in the euphotic zone and remineralization/
- dissolution through the ocean interior are handled as in Dunne et al.
- (2005). O2 equilibria and gas exchange follow OCMIP2 protocols.
- Additional functionality comes from an optional carbon cycle that is
- non-interactive, i.e. does not change the core BLING behaviour, as
- well as tracers for radiocarbon (14c), a decomposition of carbon
- components by gas exchange and remineralization (carbon_pre), and a
- decomposition of phosphate as preformed and remineralized (po4_pre).
-
- This subroutine:
- Adds all the BLING Tracers to the list of generic Tracers passed
- to it via utility subroutine g_tracer_add(). Adds all the parameters
- used by this module via utility subroutine g_tracer_add_param().
- Allocates all work arrays used in the module.
-
-
-
-
-INPUT
-
-
-
-
-
tracer_list
- Pointer to the head of generic tracer list.
- [type(g_tracer_type), pointer]
- Some tracer fields could be modified after values are obtained from the
- coupler. This subroutine is the place for specific tracer manipulations.
- BLING currently does not use this.
-
-
-
-
-INPUT
-
-
-
-
-
tracer_list
- Pointer to the head of generic tracer list.
- [type(g_tracer_type), pointer]
- Some tracers could have bottom fluxes and reservoirs.
- This subroutine is the place for specific tracer manipulations.
- BLING currently does not use this.
-
-
-
-
-INPUT
-
-
-
-
-
tracer_list
- Pointer to the head of generic tracer list.
- [type(g_tracer_type), pointer]
-
-
-
dt
- Time step increment
- [real]
-
-
-
tau
- Time step index to be used for %field
- [integer]
- This is the subroutine to contain most of the biogeochemistry for calculating the
- interaction of tracers with each other and with outside forcings.
-
-
-
-
-INPUT
-
-
-
-
-
tracer_list
- Pointer to the head of generic tracer list.
- [type(g_tracer_type), pointer]
-
-
-
ilb,jlb
- Lower bounds of x and y extents of input arrays on data domain
- [integer]
-
-
-
Temp
- Ocean temperature
- [real, dimension(ilb:,jlb:,:)]
- Ocean density
- [real, dimension(ilb:,jlb:,:,:)]
-
-
-
tau
- Time step index of %field
- [integer]
-
-
-
-
-
-
-
-
-
generic_BLING_end
-
-call generic_BLING_end
-
-
-
-DESCRIPTION
-
-
- Deallocate all work arrays
-
-
-
-
-
-
-
-
-
-
-
-
NAMELIST
-
-
-&generic_bling_nml
-
-
-
-
-
-do_14c
-
-
- If true, then simulate radiocarbon. Includes 2 prognostic tracers, DI14C
- and DO14C. Requires that do_carbon = .true. Note that 14C is not taken up
- by CaCO3 at the current time, but cycles only through the soft tissue.
- This is a mistake that will be fixed later.
-
-[logical]
-
-
-do_carbon
-
-
- If true, then simulate the carbon cycle based on strict stoichiometry
- of C:P. Includes 1 prognostic tracer, DIC.
-
-[logical]
-
-
-do_carbon_pre
-
-
- If true, then simulate the carbon cycle based on strict stoichiometry
- of C:P. Includes 3 prognostic tracers, DIC, ALK and ALK_pre. Requires
- that do_carbon = .true.
-
-[logical]
-
-
-do_po4_pre
-
-
- If true, then simulate preformed PO4, a useful theoretical construct
- equal to PO4 in the surface layer and subject only to passive transport
- everywhere else. 1 prognostic tracer, PO4_pre.
-
-[logical]
-
-
-bury_caco3
-
-
- If true, then allow CaCO3 to be buried in sediments as a function
- of sinking CaCO3 flux and bottom water saturation state, and allow
- a river input of alkalinity to compensate. Caution: this will cause
- the alkalinity to have a long term drift, which will produce a long
- term drift in the carbon cycle. Should be considered highly
- experimental at this point. Requires that do_carbon=.true.
-
-[logical]
-
-
-use_bling_chl
-
-
- If true, names the BLING diagnostic chlorophyll field 'chl'. Thus,
- if read_chl=.false. in the shortwave namelist, BLING chlorophyll will
- be used to calculate sw absorption. Set this to false in order to
- have the chlorophyll field named chl_b, preventing conflict with the
- TOPAZ chlorophyll field, so that the two modules can run
- simultaneously.
-
-[logical]
-
-
-
-
-
-
-
-
-
-
-
REFERENCES
-
-
-
-
- This model is available for public use.
- The current version is BLING.0. The version number refers to the core
- model behaviour; additional tracers exist in different iterations of the
- module. In publications it should be referenced as:
- Galbraith, E.D., Gnanadesikan, A., Dunne, J. and Hiscock, M. 2009.
- Regional impacts of iron-light colimitation in a global
- biogeochemical model. Biogeosciences Discussions, 6, 1-47.
-
- All parameter values are as described in this paper.
- Note that this reference is only for the core model components, and
- does not include any of the additional functionalities, which remain
- undocumented. Please contact Eric Galbraith (eric.galbraith@mcgill.ca)
- for more information.
-