Merge branch 'develop' into develop

modulefiles/gsiutils_gaea.intel.lua

@@ -0,0 +1,24 @@
+help([[
+]])
+
+prepend_path("MODULEPATH", "/ncrc/proj/epic/spack-stack/spack-stack-1.6.0/envs/gsi-addon-dev/install/modulefiles/Core")
+
+local python_ver=os.getenv("python_ver") or "3.11.6"
+local stack_intel_ver=os.getenv("stack_intel_ver") or "2023.1.0"
+local stack_cray_mpich_ver=os.getenv("stack_cray_mpich_ver") or "8.1.25"
+local cmake_ver=os.getenv("cmake_ver") or "3.23.1"
+local prod_util_ver=os.getenv("prod_util_ver") or "2.1.1"
+
+load(pathJoin("stack-intel", stack_intel_ver))
+load(pathJoin("stack-cray-mpich", stack_cray_mpich_ver))
+load(pathJoin("python", python_ver))
+load(pathJoin("cmake", cmake_ver))
+
+load("gsiutils_common")
+
+load(pathJoin("prod_util", prod_util_ver))
+
+pushenv("CFLAGS", "-xHOST")
+pushenv("FFLAGS", "-xHOST")
+
+whatis("Description: GSI utilities environment on Gaea with Intel Compilers")

modulefiles/gsiutils_jet.intel.lua

@@ -1,7 +1,7 @@
 help([[
 ]])
 
-prepend_path("MODULEPATH", "/mnt/lfs4/HFIP/hfv3gfs/role.epic/spack-stack/spack-stack-1.6.0/envs/gsi-addon-dev-rocky8/install/modulefiles/Core")
+prepend_path("MODULEPATH", "/contrib/spack-stack/spack-stack-1.6.0/envs/gsi-addon-intel/install/modulefiles/Core")
 
 local python_ver=os.getenv("python_ver") or "3.11.6"
 local stack_intel_ver=os.getenv("stack_intel_ver") or "2021.5.0"

modulefiles/gsiutils_orion.intel.lua

@@ -1,11 +1,16 @@
 help([[
 ]])
 
-prepend_path("MODULEPATH", "/work/noaa/epic/role-epic/spack-stack/orion/spack-stack-1.6.0/envs/gsi-addon-env/install/modulefiles/Core")
+-- Spack Stack installation specs
+local ss_dir="/work/noaa/epic/role-epic/spack-stack/orion"
+local ss_ver=os.getenv("stack_ver") or "1.6.0"
+local ss_env=os.getenv("stack_env") or "gsi-addon-env-rocky9"
+
+prepend_path("MODULEPATH", pathJoin(ss_dir, "spack-stack-" .. ss_ver, "envs", ss_env, "install/modulefiles/Core"))
 
 local stack_python_ver=os.getenv("python_ver") or "3.11.6"
-local stack_intel_ver=os.getenv("stack_intel_ver") or "2022.0.2"
-local stack_impi_ver=os.getenv("stack_impi_ver") or "2021.5.1"
+local stack_intel_ver=os.getenv("stack_intel_ver") or "2021.9.0"
+local stack_impi_ver=os.getenv("stack_impi_ver") or "2021.9.0"
 local cmake_ver=os.getenv("cmake_ver") or "3.23.1"
 local prod_util_ver=os.getenv("prod_util_ver") or "2.1.1"
 

src/netcdf_io/calc_analysis.fd/inc2anl.f90

@@ -1,34 +1,56 @@
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-!! module inc2anl 
+!! module inc2anl
 !!        contains subroutines for calculating analysis fields
-!!        for a given input background and increment 
+!!        for a given input background and increment
 !! Original: 2019-09-18   martin   - original module
 !!           2019-10-24   martin   - removed support for NEMSIO background but
 !!                                   allows for either NEMSIO or netCDF analysis write
 !!           2020-01-21   martin   - parallel IO support added
+!!           2024-08-12   martin   - aerosol support added
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-module inc2anl 
+module inc2anl
   implicit none
 
   private
 
   public :: gen_anl, close_files
 
-  integer, parameter :: nincv=10
+  integer, parameter :: nincv=13
   character(len=7) :: incvars_nemsio(nincv), incvars_netcdf(nincv), incvars_ncio(nincv)
-  integer, parameter :: nnciov=20
-  character(len=7) :: iovars_netcdf(nnciov)
+  integer, parameter :: nnciov=22
+  integer, parameter :: naero=14
+  integer, parameter :: naero_copy=6
+  character(len=7) :: iovars_netcdf(nnciov), iovars_aero(naero), copyvars_aero(naero_copy)
+  character(len=50) :: incvars_aero(naero)
 
   data incvars_nemsio / 'ugrd   ', 'vgrd   ', 'dpres  ', 'delz   ', 'o3mr   ',&
-                        'tmp    ', 'spfh   ', 'clwmr  ', 'icmr   ', 'pres   '/
+                        'tmp    ', 'spfh   ', 'clwmr  ', 'icmr   ', 'rwmr   ',&
+                        'snmr   ', 'grle   ', 'pres   '/
   data incvars_netcdf / 'u      ', 'v      ', 'delp   ', 'delz   ', 'o3mr   ',&
-                        'T      ', 'sphum  ', 'liq_wat', 'icmr   ', 'pres   '/
-  data incvars_ncio / 'ugrd   ', 'vgrd   ', 'dpres  ', 'delz   ', 'o3mr   ',&
-                        'tmp    ', 'spfh   ', 'clwmr  ', 'icmr   ', 'pressfc'/
+                        'T      ', 'sphum  ', 'liq_wat', 'icmr   ', 'rwmr   ',&
+                        'snmr   ', 'grle   ', 'pres   '/
+  data incvars_ncio /   'ugrd   ', 'vgrd   ', 'dpres  ', 'delz   ', 'o3mr   ',&
+                        'tmp    ', 'spfh   ', 'clwmr  ', 'icmr   ', 'rwmr   ',&
+                        'snmr   ', 'grle   ', 'pressfc'/
   data iovars_netcdf /  'grid_xt', 'grid_yt', 'pfull  ', 'phalf  ', 'clwmr  ',&
                         'delz   ', 'dpres  ', 'dzdt   ', 'grle   ', 'hgtsfc ',&
                         'icmr   ', 'o3mr   ', 'pressfc', 'rwmr   ', 'snmr   ',&
-                        'spfh   ', 'tmp    ', 'ugrd   ', 'vgrd   ', 'cld_amt'/
+                        'spfh   ', 'tmp    ', 'ugrd   ', 'vgrd   ', 'cld_amt',&
+                        'nccice ', 'nconrd '/
+  data iovars_aero / 'so4    ', 'bc1    ', 'bc2    ', 'oc1    ', 'oc2    ', &
+                     'dust1  ', 'dust2  ', 'dust3  ', 'dust4  ', 'dust5  ',&
+                     'seas1  ', 'seas2  ', 'seas3  ', 'seas4  '/
+  data incvars_aero / 'mass_fraction_of_sulfate_in_air',&
+                      'mass_fraction_of_hydrophobic_black_carbon_in_air', &
+                      'mass_fraction_of_hydrophilic_black_carbon_in_air', &
+                      'mass_fraction_of_hydrophobic_organic_carbon_in_air', &
+                      'mass_fraction_of_hydrophilic_organic_carbon_in_air', &
+                      'mass_fraction_of_dust001_in_air', 'mass_fraction_of_dust002_in_air', &
+                      'mass_fraction_of_dust003_in_air', 'mass_fraction_of_dust004_in_air', &
+                      'mass_fraction_of_dust005_in_air', 'mass_fraction_of_sea_salt001_in_air', &
+                      'mass_fraction_of_sea_salt002_in_air', 'mass_fraction_of_sea_salt003_in_air', &
+                      'mass_fraction_of_sea_salt004_in_air' /
+  data copyvars_aero / 'seas5  ', 'so2    ', 'dms    ', 'msa    ', 'pm25   ', 'pm10   ' /
 
 contains
   subroutine gen_anl
@@ -38,7 +60,7 @@ subroutine gen_anl
   !            increment, add the two together, and write out
   !            the analysis to a new file
   !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-    use vars_calc_analysis, only: mype 
+    use vars_calc_analysis, only: mype, do_aero
     implicit none
     ! variables local to this subroutine
     integer :: i, j, iincvar
@@ -68,11 +90,24 @@ subroutine gen_anl
         end if
       else
         ! otherwise just write out what is in the input to the output
-        if (mype==0) print *, 'Copying from Background ', iovars_netcdf(i) 
+        if (mype==0) print *, 'Copying from Background ', iovars_netcdf(i)
         call copy_ges_to_anl(iovars_netcdf(i))
       end if
     end do
 
+    ! if including aerosols, loop and add them
+    if (do_aero) then
+      do i=1,naero
+        if (mype==0) print *, 'Adding Increment to ', iovars_aero(i)
+        call add_aero_inc(iovars_aero(i), incvars_aero(i))
+      end do
+      ! need to handle fields that just need copied
+      do i=1,naero_copy
+        if (mype==0) print *, 'Copying from Background ', copyvars_aero(i)
+        call copy_ges_to_anl(copyvars_aero(i))
+      end do
+    end if
+
   end subroutine gen_anl
 
   subroutine close_files
@@ -157,17 +192,60 @@ subroutine copy_ges_to_anl(varname)
             end do
           end if
       end select
-    else 
+    else
       if (mype == 0) write(6,*) varname, 'not in background file, skipping...'
     end if
 
   end subroutine copy_ges_to_anl
 
+  subroutine add_aero_inc(fcstvar, incvar)
+  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+  ! subroutine add_aero_inc
+  !            generic subroutine for adding increment to background
+  !            and writing out to analysis for aerosol variables
+  !  args:
+  !       fcstvar - input string of netCDF fcst/anal var name
+  !       incvar  - input string of netCDF increment var name
+  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+    use vars_calc_analysis, only: fcstncfile, anlncfile, aero_file,&
+    nlat, nlon, nlev, anlfile, levpe, mype
+    use module_ncio, only: Dataset, read_vardata, write_vardata, &
+        open_dataset, close_dataset, has_var
+    use nemsio_module
+    implicit none
+    ! input vars
+    character(7), intent(in) :: fcstvar
+    character(50), intent(in) :: incvar
+    ! local variables
+    real, allocatable, dimension(:,:,:) :: work3d_bg
+    real, allocatable, dimension(:,:) :: work3d_inc
+    real, allocatable, dimension(:) :: work1d
+    integer :: j,jj,k,krev,iret
+    type(Dataset) :: incncfile
+    do k=1,nlev
+      if (mype == levpe(k)) then
+        ! get first guess
+        call read_vardata(fcstncfile, trim(fcstvar), work3d_bg, nslice=k, slicedim=3)
+        ! get increment
+        incncfile = open_dataset(aero_file)
+        call read_vardata(incncfile, trim(incvar), work3d_inc, nslice=k, slicedim=1)
+        ! add increment to background
+        work3d_bg(:,:,1) = work3d_bg(:,:,1) + work3d_inc(:,:)
+        ! write out analysis to file
+        call write_vardata(anlncfile, trim(fcstvar), work3d_bg, nslice=k, slicedim=3)
+      end if
+    end do
+    ! clean up and close
+    deallocate(work3d_bg, work3d_inc)
+    call close_dataset(incncfile)
+
+  end subroutine add_aero_inc
+
   subroutine add_increment(fcstvar, incvar)
   !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
   ! subroutine add_increment
   !            generic subroutine for adding increment to background
-  !            and writing out to analysis 
+  !            and writing out to analysis
   !  args:
   !       fcstvar - input string of netCDF fcst/anal var name
   !       incvar  - input string of netCDF increment var name
@@ -189,7 +267,7 @@ subroutine add_increment(fcstvar, incvar)
     real, allocatable, dimension(:) :: work1d
     integer :: j,jj,k,krev,iret
     type(Dataset) :: incncfile
-    
+
     if (has_var(fcstncfile, fcstvar)) then
       do k=1,nlev
         if (mype == levpe(k)) then
@@ -234,17 +312,17 @@ subroutine add_increment(fcstvar, incvar)
       end if
       deallocate(work3d_bg)
       call close_dataset(incncfile)
-    else 
+    else
       write(6,*) fcstvar, ' not in background file, skipping...'
     end if
-  
+
   end subroutine add_increment
 
   subroutine add_psfc_increment
   !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
   ! subroutine add_psfc_increment
   !            special case of getting surface pressure analysis from
-  !            bk5 and delp increment to get sfc pressure increment 
+  !            bk5 and delp increment to get sfc pressure increment
   !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
     use vars_calc_analysis, only: fcstncfile, anlncfile, nlat, nlon, incr_file,&
                                   use_nemsio_anl, anlfile, nlev
@@ -260,7 +338,7 @@ subroutine add_psfc_increment
     type(Dataset) :: incncfile
 
     ! get bk5 from attributes
-    call read_attribute(fcstncfile, 'bk', bk5) 
+    call read_attribute(fcstncfile, 'bk', bk5)
     ! read in delp increment to get ps increment
     incncfile = open_dataset(incr_file)
     call read_vardata(incncfile, 'delp_inc', work3d_inc)
@@ -277,7 +355,7 @@ subroutine add_psfc_increment
     ! write out to file
     if (use_nemsio_anl) then
       allocate(work1d(nlon*nlat))
-      ! now write out new psfc to NEMSIO analysis file 
+      ! now write out new psfc to NEMSIO analysis file
       work1d = reshape(work2d,(/size(work1d)/))
       call nemsio_writerecv(anlfile, 'pres', 'sfc', 1, work1d, iret=iret)
       if (iret /=0) write(6,*) 'Error with NEMSIO write sfc pressure'

src/netcdf_io/calc_analysis.fd/init_calc_analysis.f90

@@ -6,6 +6,7 @@
 !!           2019-09-25   martin   - update to allow for netCDF I/O
 !!           2019-10-24   martin   - update to support nemsio output
 !!           2020-01-17   martin   - parallel IO support added
+!!           2024-04-04   martin   - aerosol support added
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 module init_calc_analysis
   implicit none
@@ -14,20 +15,22 @@ subroutine read_nml
     !! read in namelist parameters from
     !! calc_analysis.nml file in same directory
     !! as executable
-    use vars_calc_analysis, only: anal_file, fcst_file, incr_file, use_nemsio_anl, fhr, mype, npes, jedi
+    use vars_calc_analysis, only: anal_file, fcst_file, incr_file, aero_file, use_nemsio_anl, do_aero, fhr, mype, npes, jedi
     implicit none
     ! local variables to this subroutine
     character(len=500) :: datapath = './'
     character(len=500) :: analysis_filename = 'atmanl.nc'
     character(len=500) :: firstguess_filename = 'atmges.nc'
     character(len=500) :: increment_filename = 'atminc.nc'
+    character(len=500) :: aero_inc_filename = 'aeroinc.nc'
     character(len=2) :: hrstr
     integer, parameter :: lunit = 10
     logical :: lexist = .false.
-    namelist /setup/ datapath, analysis_filename, firstguess_filename, increment_filename, fhr, use_nemsio_anl, jedi
+    namelist /setup/ datapath, analysis_filename, firstguess_filename, increment_filename, aero_inc_filename, fhr, use_nemsio_anl, do_aero, jedi
 
     fhr = 6 ! default to 6 hour cycle only
     use_nemsio_anl = .false. ! default to using netCDF for background and analysis
+    do_aero = .false. ! default to only do atm, not aero also
     jedi = .false. ! default to GSI (not JEDI)
 
     ! read in the namelist
@@ -47,16 +50,21 @@ subroutine read_nml
     anal_file = trim(adjustl(datapath)) // '/' // trim(adjustl(analysis_filename)) // '.' // hrstr 
     fcst_file = trim(adjustl(datapath)) // '/' // trim(adjustl(firstguess_filename)) // '.' // hrstr 
     incr_file = trim(adjustl(datapath)) // '/' // trim(adjustl(increment_filename)) // '.' // hrstr
+    aero_file = trim(adjustl(datapath)) // '/' // trim(adjustl(aero_inc_filename)) // '.' // hrstr
     else
     anal_file = trim(adjustl(datapath)) // '/' // trim(adjustl(analysis_filename)) 
     fcst_file = trim(adjustl(datapath)) // '/' // trim(adjustl(firstguess_filename)) 
     incr_file = trim(adjustl(datapath)) // '/' // trim(adjustl(increment_filename))
+    aero_file = trim(adjustl(datapath)) // '/' // trim(adjustl(aero_inc_filename))
     endif
 
     if (mype == 0) then
       write(6,*) 'Analysis File    = ', trim(anal_file)
       write(6,*) 'First Guess File = ', trim(fcst_file)
       write(6,*) 'Increment File   = ', trim(incr_file) 
+      if (do_aero) then
+        write(6,*) 'Aerosol Increment File   = ', trim(aero_file)
+      end if
       if (fhr > 0) write(6,*) 'Forecast Hour    = ', fhr
       write(6,*) 'Number of PEs    = ', npes
       write(6,*) 'input guess file and increment file should be in netCDF format'

src/netcdf_io/calc_analysis.fd/vars_calc_analysis.f90

@@ -6,14 +6,15 @@
 !!           2019-09-26   martin   - add support for netCDF read/write
 !!           2019-10-24   martin   - support NEMSIO output write
 !!           2020-01-17   martin   - parallel IO support added
+!!           2024-04-04   martin   - aerosol support added
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 module vars_calc_analysis
   use nemsio_module, only: nemsio_gfile
   use module_ncio, only: Dataset
   implicit none
   private
 
-  public :: anal_file, fcst_file, incr_file
+  public :: anal_file, fcst_file, incr_file, aero_file
   public :: idate, jdate
   public :: idate6, jdate6
   public :: nfday, nfhour, nfminute, nfsecondn, nfsecondd
@@ -23,14 +24,15 @@ module vars_calc_analysis
   public :: work1
   public :: nhrs_assim
   public :: use_nemsio_anl
+  public :: do_aero
   public :: fcstncfile, anlncfile, incncfile
   public :: fhrs_pe
   public :: fhr
   public :: mype, npes
   public :: levpe
   public :: jedi
 
-  character(len=500) :: anal_file, fcst_file, incr_file
+  character(len=500) :: anal_file, fcst_file, incr_file, aero_file
   integer, dimension(7) :: idate, jdate
   integer, dimension(6) :: idate6, jdate6
   integer :: nfday, nfhour, nfminute, nfsecondn, nfsecondd
@@ -40,7 +42,7 @@ module vars_calc_analysis
   type(nemsio_gfile) :: anlfile
   real, allocatable, dimension(:) :: work1
   integer :: nhrs_assim, fhr
-  logical :: use_nemsio_anl
+  logical :: use_nemsio_anl, do_aero
   type(Dataset) :: fcstncfile, anlncfile, incncfile
   integer, dimension(7) :: fhrs_pe
   integer :: mype, npes