Merge with develop

Merge remote-tracking branch 'upstream/develop' into develop
sanatcumar · Nov 14, 2023 · 815ee4f · 815ee4f
2 parents df0788d + dc0e4a6
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diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -0,0 +1,15 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html
+
+# Required
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-20.04
+  tools:
+    python: "3.9"
+
+sphinx:
+   configuration: docs/source/conf.py
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -74,7 +74,7 @@ if(CMAKE_Fortran_COMPILER_ID MATCHES "^(Intel)$")
 elseif(CMAKE_Fortran_COMPILER_ID MATCHES "^(GNU)$")
   set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -g -fbacktrace")
   if(${CMAKE_Fortran_COMPILER_VERSION} VERSION_GREATER_EQUAL 10)
-    set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -fallow-argument-mismatch -fallow-invalid-boz")
+    set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -fallow-invalid-boz")
   endif()
   set(CMAKE_Fortran_FLAGS_RELEASE "-O3")
   set(CMAKE_Fortran_FLAGS_DEBUG "-O0 -ggdb -Wall -fcheck=all")

diff --git a/VERSION b/VERSION
@@ -1 +1 @@
-1.10.0
+1.11.0
diff --git a/docs/Doxyfile.in b/docs/Doxyfile.in
@@ -854,7 +854,7 @@ WARN_LOGFILE           =
 # spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
 # Note: If this tag is empty the current directory is searched.
 
-INPUT                  = @abs_top_srcdir@/docs/user_guide.md
+INPUT                  = @abs_top_srcdir@/docs/main.md
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
@@ -1014,7 +1014,7 @@ FILTER_SOURCE_PATTERNS =
 # (index.html). This can be useful if you have a project on for instance GitHub
 # and want to reuse the introduction page also for the doxygen output.
 
-USE_MDFILE_AS_MAINPAGE = @abs_top_srcdir@/docs/sp_user_guide.md
+USE_MDFILE_AS_MAINPAGE = @abs_top_srcdir@/docs/main.md
 
 #---------------------------------------------------------------------------
 # Configuration options related to source browsing

diff --git a/docs/README.md b/docs/README.md
@@ -0,0 +1,5 @@
+For documentation see:
+
+https://ufs-community.github.io/UFS_UTILS
+
+https://noaa-emcufs-utils.readthedocs.io/en/latest
diff --git a/docs/user_guide.md → docs/main.md b/docs/user_guide.md → docs/main.md
@@ -9,6 +9,7 @@ https://github.com/ufs-community/UFS_UTILS.
 
 ## Documentation for Previous Versions of UFS_UTILS
 
+* [UFS_UTILS Version 1.11.0](ver-1.11.0/index.html)
 * [UFS_UTILS Version 1.10.0](ver-1.10.0/index.html)
 * [UFS_UTILS Version 1.9.0](ver-1.9.0/index.html)
 * [UFS_UTILS Version 1.8.0](ver-1.8.0/index.html)

diff --git a/docs/requirements.txt b/docs/requirements.txt
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -50,11 +50,10 @@
     'sphinx.ext.ifconfig',
     'sphinx.ext.viewcode',
     'sphinx.ext.githubpages',
-    'sphinx.ext.napoleon',
-    'sphinxcontrib.bibtex'
+    'sphinx.ext.napoleon'
 ]
 
-bibtex_bibfiles = ['references.bib']
+#bibtex_bibfiles = ['references.bib']
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']

diff --git a/docs/source/ufs_utils.rst b/docs/source/ufs_utils.rst
@@ -375,8 +375,13 @@ Program inputs and outputs
 
       * grid file - the "grid" file from the make_hgrid or regional_esg programs  - CRES_grid.tile#.nc - (NetCDF)
       * orography file - the orography file including the 'inland' flag record from the inland program - oro.CRES.tile#.nc (NetCDF)
-      * lake status code file - GlobalLakeStatus.dat (located in `./fix/fix_orog <https://noaa-ufs-srw-pds.s3.amazonaws.com/index.html#fix/fix_orog/>`_). See GlobalLakeStatus.txt for the defintion of each code.
-      * lake depth file - GlobalLakeDepth.dat (located in `./fix/fix_orog <https://noaa-ufs-srw-pds.s3.amazonaws.com/index.html#fix/fix_orog/>`_). See GlobalLakeDepth.txt for a description of this file.
+      * lake status code file - One of the following files. (located in `./fix/fix_orog <https://noaa-ufs-srw-pds.s3.amazonaws.com/index.html#fix/fix_orog/>`_). See GlobalLakeStatus.txt for a description of the file format.
+          * GlobalLakeStatus_MOSISp.dat
+          * GlobalLakeStatus_GLDBv3release.dat
+          * GlobalLakeStatus_VIIRS.dat
+      * lake depth file - One of the following files. (located in `./fix/fix_orog <https://noaa-ufs-srw-pds.s3.amazonaws.com/index.html#fix/fix_orog/>`_). See GlobalLakeDepth.txt for a description of this file.
+          * GlobalLakeDepth_GLDBv3release.dat
+          * GlobalLakeDepth_GLOBathy.dat
 
 **Output data:**
 

diff --git a/driver_scripts/driver_grid.hera.sh b/driver_scripts/driver_grid.hera.sh
@@ -106,10 +106,15 @@ export soil_type_src="bnu.v3.30s" #  Soil type data.
                                 # For Beijing Norm. Univ. data
                                 # 1) "bnu.v3.30s" for global 30s data.
 
+# choose dataset sources for lakefrac & lakedepth so that lake_data_srce=LakeFrac_LakeDepth; 
+# available options are 'MODISP_GLDBV3', 'MODISP_GLOBATHY', 'VIIRS_GLDBV3', 'VIIRS_GLOBATHY' & 'GLDBV3'
+export lake_data_srce=MODISP_GLDBV3 
+
 if [ $gtype = uniform ]; then
   export res=96
-  export add_lake=false        # Add lake frac and depth to orography data.
-  export lake_cutoff=0.20      # lake frac < lake_cutoff ignored when add_lake=T
+  export add_lake=true         # Add lake frac and depth to orography data.
+  export lake_cutoff=0.50      # return 0 if lake_frac <  lake_cutoff & add_lake=T
+  export binary_lake=1         # return 1 if lake_frac >= lake_cutoff & add_lake=T
 elif [ $gtype = stretch ]; then
   export res=96
   export stretch_fac=1.5       # Stretching factor for the grid

diff --git a/driver_scripts/driver_grid.jet.sh b/driver_scripts/driver_grid.jet.sh
@@ -104,10 +104,15 @@ export soil_type_src="bnu.v3.30s" # Soil type data.
                                 # 4) "statsgo.nh.30s" for NH 30s data
                                 # 5) "statsgo.30s" for global 30s data
 
+# choose dataset sources for lakefrac & lakedepth so that lake_data_srce=LakeFrac_LakeDepth; 
+# available options are 'MODISP_GLDBV3', 'MODISP_GLOBATHY', 'VIIRS_GLDBV3', 'VIIRS_GLOBATHY' & 'GLDBV3'
+export lake_data_srce=MODISP_GLDBV3 
+
 if [ $gtype = uniform ]; then
   export res=96
-  export add_lake=false        # Add lake frac and depth to orography data.
-  export lake_cutoff=0.20      # lake frac < lake_cutoff ignored when add_lake=T
+  export add_lake=true         # Add lake frac and depth to orography data.
+  export lake_cutoff=0.50      # return 0 if lake_frac <  lake_cutoff & add_lake=T
+  export binary_lake=1         # return 1 if lake_frac >= lake_cutoff & add_lake=T
 elif [ $gtype = stretch ]; then
   export res=96
   export stretch_fac=1.5       # Stretching factor for the grid

diff --git a/driver_scripts/driver_grid.orion.sh b/driver_scripts/driver_grid.orion.sh
@@ -103,10 +103,15 @@ export soil_type_src="bnu.v3.30s" #  Soil type data.
                                 # 4) "statsgo.nh.30s" for NH 30s data
                                 # 5) "statsgo.30s" for global 30s data
 
+# choose dataset sources for lakefrac & lakedepth so that lake_data_srce=LakeFrac_LakeDepth; 
+# available options are 'MODISP_GLDBV3', 'MODISP_GLOBATHY', 'VIIRS_GLDBV3', 'VIIRS_GLOBATHY' & 'GLDBV3'
+export lake_data_srce=MODISP_GLDBV3 
+
 if [ $gtype = uniform ]; then
   export res=96
-  export add_lake=false        # Add lake frac and depth to orography data.
-  export lake_cutoff=0.20      # lake frac < lake_cutoff ignored when add_lake=T
+  export add_lake=true         # Add lake frac and depth to orography data.
+  export lake_cutoff=0.50      # return 0 if lake_frac <  lake_cutoff & add_lake=T
+  export binary_lake=1         # return 1 if lake_frac >= lake_cutoff & add_lake=T
 elif [ $gtype = stretch ]; then
   export res=96
   export stretch_fac=1.5       # Stretching factor for the grid

diff --git a/driver_scripts/driver_grid.wcoss2.sh b/driver_scripts/driver_grid.wcoss2.sh
@@ -102,10 +102,15 @@ export soil_type_src="bnu.v3.30s"  # Soil type data
                                 # 4) "statsgo.nh.30s" for NH 30s data
                                 # 5) "statsgo.30s" for global 30s data
 
+# choose dataset sources for lakefrac & lakedepth so that lake_data_srce=LakeFrac_LakeDepth; 
+# available options are 'MODISP_GLDBV3', 'MODISP_GLOBATHY', 'VIIRS_GLDBV3', 'VIIRS_GLOBATHY' & 'GLDBV3'
+export lake_data_srce=MODISP_GLDBV3 
+
 if [ $gtype = uniform ]; then
   export res=96
-  export add_lake=false        # Add lake frac and depth to orography data.
-  export lake_cutoff=0.20      # lake frac < lake_cutoff ignored when add_lake=T
+  export add_lake=true         # Add lake frac and depth to orography data.
+  export lake_cutoff=0.50      # return 0 if lake_frac <  lake_cutoff & add_lake=T
+  export binary_lake=1         # return 1 if lake_frac >= lake_cutoff & add_lake=T
 elif [ $gtype = stretch ]; then
   export res=96
   export stretch_fac=1.5       # Stretching factor for the grid

diff --git a/reg_tests/cpld_gridgen/RegressionTests_hera.intel.log b/reg_tests/cpld_gridgen/RegressionTests_hera.intel.log
@@ -1,8 +1,8 @@
-Sat Apr 23 17:52:41 UTC 2022
+Thu Oct 26 17:23:32 UTC 2023
 Start Regression test
 
-Working dir = /scratch1/NCEPDEV/stmp4/Minsuk.Ji/CPLD_GRIDGEN/rt_142841/025
-Baseline dir = /scratch1/NCEPDEV/nems/role.ufsutils/ufs_utils/reg_tests/cpld_gridgen/baseline_data/025
+Working dir = /scratch1/NCEPDEV/stmp4/Denise.Worthen/CPLD_GRIDGEN/rt_198243/025
+Baseline dir = /scratch1/NCEPDEV/nems/role.ufsutils/ufs_utils/reg_tests/cpld_gridgen/baseline_data/025.new
 
 Checking test 025 results ....
 Comparing Bu.mx025_SCRIP.nc........OK
@@ -20,11 +20,26 @@ Comparing Cv.mx025_SCRIP.nc........OK
 Comparing grid_cice_NEMS_mx025.nc........OK
 Comparing kmtu_cice_NEMS_mx025.nc........OK
 Comparing mesh.mx025.nc........OK
+Comparing rect.0p25_SCRIP.nc........OK
+Comparing rect.0p5_SCRIP.nc........OK
+Comparing rect.1p0_SCRIP.nc........OK
+Comparing rect.5p0_SCRIP.nc........OK
+Comparing tripole.mx025.Bu.to.Ct.bilinear.nc........OK
+Comparing tripole.mx025.Ct.to.rect.0p25.bilinear.nc........OK
+Comparing tripole.mx025.Ct.to.rect.0p25.conserve.nc........OK
+Comparing tripole.mx025.Ct.to.rect.0p5.bilinear.nc........OK
+Comparing tripole.mx025.Ct.to.rect.0p5.conserve.nc........OK
+Comparing tripole.mx025.Ct.to.rect.1p0.bilinear.nc........OK
+Comparing tripole.mx025.Ct.to.rect.1p0.conserve.nc........OK
+Comparing tripole.mx025.Ct.to.rect.5p0.bilinear.nc........OK
+Comparing tripole.mx025.Ct.to.rect.5p0.conserve.nc........OK
+Comparing tripole.mx025.Cu.to.Ct.bilinear.nc........OK
+Comparing tripole.mx025.Cv.to.Ct.bilinear.nc........OK
 Comparing tripole.mx025.nc........OK
 
 
-Working dir = /scratch1/NCEPDEV/stmp4/Minsuk.Ji/CPLD_GRIDGEN/rt_142841/050
-Baseline dir = /scratch1/NCEPDEV/nems/role.ufsutils/ufs_utils/reg_tests/cpld_gridgen/baseline_data/050
+Working dir = /scratch1/NCEPDEV/stmp4/Denise.Worthen/CPLD_GRIDGEN/rt_198243/050
+Baseline dir = /scratch1/NCEPDEV/nems/role.ufsutils/ufs_utils/reg_tests/cpld_gridgen/baseline_data/050.new
 
 Checking test 050 results ....
 Comparing Bu.mx050_SCRIP.nc........OK
@@ -43,12 +58,24 @@ Comparing Cv.mx050_SCRIP.nc........OK
 Comparing grid_cice_NEMS_mx050.nc........OK
 Comparing kmtu_cice_NEMS_mx050.nc........OK
 Comparing mesh.mx050.nc........OK
+Comparing rect.0p5_SCRIP.nc........OK
+Comparing rect.1p0_SCRIP.nc........OK
+Comparing rect.5p0_SCRIP.nc........OK
 Comparing tripole.mx025.Ct.to.mx050.Ct.neareststod.nc........OK
+Comparing tripole.mx050.Bu.to.Ct.bilinear.nc........OK
+Comparing tripole.mx050.Ct.to.rect.0p5.bilinear.nc........OK
+Comparing tripole.mx050.Ct.to.rect.0p5.conserve.nc........OK
+Comparing tripole.mx050.Ct.to.rect.1p0.bilinear.nc........OK
+Comparing tripole.mx050.Ct.to.rect.1p0.conserve.nc........OK
+Comparing tripole.mx050.Ct.to.rect.5p0.bilinear.nc........OK
+Comparing tripole.mx050.Ct.to.rect.5p0.conserve.nc........OK
+Comparing tripole.mx050.Cu.to.Ct.bilinear.nc........OK
+Comparing tripole.mx050.Cv.to.Ct.bilinear.nc........OK
 Comparing tripole.mx050.nc........OK
 
 
-Working dir = /scratch1/NCEPDEV/stmp4/Minsuk.Ji/CPLD_GRIDGEN/rt_142841/100
-Baseline dir = /scratch1/NCEPDEV/nems/role.ufsutils/ufs_utils/reg_tests/cpld_gridgen/baseline_data/100
+Working dir = /scratch1/NCEPDEV/stmp4/Denise.Worthen/CPLD_GRIDGEN/rt_198243/100
+Baseline dir = /scratch1/NCEPDEV/nems/role.ufsutils/ufs_utils/reg_tests/cpld_gridgen/baseline_data/100.new
 
 Checking test 100 results ....
 Comparing Bu.mx100_SCRIP.nc........OK
@@ -67,10 +94,50 @@ Comparing Cv.mx100_SCRIP.nc........OK
 Comparing grid_cice_NEMS_mx100.nc........OK
 Comparing kmtu_cice_NEMS_mx100.nc........OK
 Comparing mesh.mx100.nc........OK
+Comparing rect.1p0_SCRIP.nc........OK
+Comparing rect.5p0_SCRIP.nc........OK
 Comparing tripole.mx025.Ct.to.mx100.Ct.neareststod.nc........OK
+Comparing tripole.mx100.Bu.to.Ct.bilinear.nc........OK
+Comparing tripole.mx100.Ct.to.rect.1p0.bilinear.nc........OK
+Comparing tripole.mx100.Ct.to.rect.1p0.conserve.nc........OK
+Comparing tripole.mx100.Ct.to.rect.5p0.bilinear.nc........OK
+Comparing tripole.mx100.Ct.to.rect.5p0.conserve.nc........OK
+Comparing tripole.mx100.Cu.to.Ct.bilinear.nc........OK
+Comparing tripole.mx100.Cv.to.Ct.bilinear.nc........OK
 Comparing tripole.mx100.nc........OK
 Comparing ufs.topo_edits_011818.nc........OK
 
 
+Working dir = /scratch1/NCEPDEV/stmp4/Denise.Worthen/CPLD_GRIDGEN/rt_198243/500
+Baseline dir = /scratch1/NCEPDEV/nems/role.ufsutils/ufs_utils/reg_tests/cpld_gridgen/baseline_data/500.new
+
+Checking test 500 results ....
+Comparing Bu.mx500_SCRIP.nc........OK
+Comparing C48.mx500.tile1.nc........OK
+Comparing C48.mx500.tile2.nc........OK
+Comparing C48.mx500.tile3.nc........OK
+Comparing C48.mx500.tile4.nc........OK
+Comparing C48.mx500.tile5.nc........OK
+Comparing C48.mx500.tile6.nc........OK
+Comparing Ct.mx025_SCRIP.nc........OK
+Comparing Ct.mx500_SCRIP_land.nc........OK
+Comparing Ct.mx500_SCRIP.nc........OK
+Comparing Ct.mx500.to.C48.nc........OK
+Comparing Cu.mx500_SCRIP.nc........OK
+Comparing Cv.mx500_SCRIP.nc........OK
+Comparing grid_cice_NEMS_mx500.nc........OK
+Comparing kmtu_cice_NEMS_mx500.nc........OK
+Comparing mesh.mx500.nc........OK
+Comparing rect.5p0_SCRIP.nc........OK
+Comparing tripole.mx025.Ct.to.mx500.Ct.neareststod.nc........OK
+Comparing tripole.mx500.Bu.to.Ct.bilinear.nc........OK
+Comparing tripole.mx500.Ct.to.rect.5p0.bilinear.nc........OK
+Comparing tripole.mx500.Ct.to.rect.5p0.conserve.nc........OK
+Comparing tripole.mx500.Cu.to.Ct.bilinear.nc........OK
+Comparing tripole.mx500.Cv.to.Ct.bilinear.nc........OK
+Comparing tripole.mx500.nc........OK
+
+
 REGRESSION TEST WAS SUCCESSFUL
-Sat Apr 23 17:57:15 UTC 2022
+Thu Oct 26 17:46:20 UTC 2023
+Elapsed time: 00h:24m:25s. Have a nice day!