202101

.github/pull_request_template.md

@@ -0,0 +1,23 @@
+**Description**
+
+Include a summary of the change and which issue is fixed. Please also include
+relevant motivation and context. List any dependencies that are required for
+this change.
+
+Fixes # (issue)
+
+**How Has This Been Tested?**
+
+Please describe the tests that you ran to verify your changes. Please also note
+any relevant details for your test configuration (e.g. compiler, OS).  Include
+enough information so someone can reproduce your tests.
+
+**Checklist:**
+
+Please check all whether they apply or not
+- [ ] My code follows the style guidelines of this project
+- [ ] I have performed a self-review of my own code
+- [ ] I have commented my code, particularly in hard-to-understand areas
+- [ ] I have made corresponding changes to the documentation
+- [ ] My changes generate no new warnings
+- [ ] Any dependent changes have been merged and published in downstream modules

README.md

@@ -1,28 +1,28 @@
-This is for the FV3 dynamical core and the GFDL Microphysics for use by NCEP/EMC within GFS.
-The source in this branch reflects the codebase delivered to NCEP/EMC for use in GFS.  Updates will be forthcoming.
+# GFDL_atmos_cubed_sphere
 
+This is for the FV3 dynamical core and the GFDL Microphysics for use by NCEP/EMC within GFS.
+The source in this branch reflects the codebase used by NCEP/EMC for use in GFS and UFS.
 # Where to find information
 
-See the [FV3 documentation and references](https://www.gfdl.noaa.gov/fv3/fv3-documentation-and-references/) for more information.
+Visit the [FV3 website](https://www.gfdl.noaa.gov/fv3/) for more information. Reference material is available at [FV3 documentation and references](https://www.gfdl.noaa.gov/fv3/fv3-documentation-and-references/). 
 
 # Proper usage attribution
 
-Cite either Putman and Lin (2007) or Harris and Lin (2013) when describing a model using the FV3 dynamical core.
-Cite Chen et al (2013) and Zhou et al (2019) if using the GFDL Microphysics.
+Cite Putman and Lin (2007) and Harris and Lin (2013) when describing a model using the FV3 dynamical core.
+Cite Chen et al (2013) and Zhou et al (2019) when using the GFDL Microphysics.
 
 # What files are what
 
 The top level directory structure groups source code and input files as follow:
 
-| File/directory    | Purpose |
-| --------------    | ------- |
-| ```LICENSE.md```  | a copy of the Gnu lesser general public license, version 3. |
-| ```README.md```   | this file with basic pointers to more information |
-| ```model/```      | contains the source code for core of the FV3 dyanmical core |
-| ```model_nh/```   | contains the source code for non-hydrostatic extensions |
-| ```driver/```     | contains drivers used by different models/modeling systems |
-| ```tools/```      | contains source code of tools used within the core |
-| ```GFDL_tools/``` | contains source code of tools specific to GFDL models |
+| File/directory       | Purpose |
+| --------------       | ------- |
+| ```LICENSE.md```     | a copy of the Gnu lesser general public license, version 3. |
+| ```README.md```      | this file with basic pointers to more information |
+| ```model/```         | contains the source code for core of the FV3 dyanmical core |
+| ```driver/```        | contains drivers used by different models/modeling systems |
+| ```tools/```         | contains source code of tools used within the core |
+| ```docs/```          | contains documentation for the FV3 dynamical core |
 
 # Disclaimer
 

docs/Doxyfile

@@ -1,6 +1,6 @@
 DOXYFILE_ENCODING      = UTF-8
 PROJECT_NAME           = "FV3DYCORE"
-PROJECT_LOGO	       = image/UFSLogo.png
+PROJECT_LOGO           = image/UFSLogo.png
 CREATE_SUBDIRS         = NO
 OUTPUT_LANGUAGE        = English
 BRIEF_MEMBER_DESC      = YES
@@ -63,7 +63,7 @@ MAX_INITIALIZER_LINES  = 30
 SHOW_USED_FILES        = YES
 SHOW_FILES             = YES
 SHOW_NAMESPACES        = YES
-LAYOUT_FILE            = 
+LAYOUT_FILE            =
 CITE_BIB_FILES         =
 QUIET                  = NO
 WARNINGS               = YES
@@ -72,59 +72,62 @@ WARN_IF_DOC_ERROR      = YES
 WARN_NO_PARAMDOC       = NO
 WARN_FORMAT            = "$file:$line: $text"
 WARN_LOGFILE           =
-INPUT = 			./documentation.dox \
-				./Preface.md \
-                                ./Chapter1.md \
-                                ./Chapter2.md \
-                                ./Chapter3.md \
-                                ./Chapter4.md \
-                                ./appendixA.md \
-                                ./appendixB.md \
-                                ./appendixB1.md \
-				./appendixB2.md \
-                                ./AdvectionOperators.md \
-                                ./OverviewFV3Dycore.md \
-                                ./Links.md \
-			../model/gwdps.f \
-			../model/a2b_edge.F90 \
-			../model/boundary.F90 \
-			../model/dyn_core.F90 \
-			../model/fv_arrays.F90 \
-			../model/fv_control.F90 \
-			../model/fv_dynamics.F90 \
-			../model/fv_fill.F90 \
-			../model/fv_grid_utils.F90 \
-			../model/fv_mapz.F90 \
-			../model/fv_nesting.F90 \
-			../model/fv_regional_bc.F90 \
-			../model/fv_sg.F90 \
-			../model/fv_tracer2d.F90 \
-			../model/fv_update_phys.F90 \
-			../model/multi_gases.F90 \
-			../model/nh_core.F90 \
-			../model/nh_utils.F90 \
-			../model/sw_core.F90 \
-			../model/tp_core.F90 \
-			../tools/external_ic.F90 \
-			../tools/external_sst.F90 \
-			../tools/fv_diagnostics.F90 \
-			../tools/fv_eta.F90 \
-			../tools/fv_grid_tools.F90 \
-			../tools/fv_iau_mod.F90 \
-			../tools/fv_io.F90 \
-			../tools/fv_mp_mod.F90 \
-			../tools/fv_nudge.F90 \
-			../tools/fv_restart.F90 \
-			../tools/fv_surf_map.F90 \
-			../tools/fv_timing.F90 \
-			../tools/fv_treat_da_inc.F90 \
-			../tools/init_hydro.F90 \
-			../tools/sim_nc_mod.F90 \
-			../tools/sorted_index.F90 \
-			../tools/test_cases.F90 \			
-			../driver/fvGFS/atmosphere.F90 \
-			../driver/fvGFS/DYCORE_typedefs.F90 \
-			../driver/fvGFS/fv_nggps_diag.F90 
+INPUT =                 ./documentation.dox \
+                        ./Preface.md \
+                        ./Chapter1.md \
+                        ./Chapter2.md \
+                        ./Chapter3.md \
+                        ./Chapter4.md \
+                        ./appendixA.md \
+                        ./appendixB.md \
+                        ./appendixB1.md \
+                        ./appendixB2.md \
+                        ./AdvectionOperators.md \
+                        ./OverviewFV3Dycore.md \
+                        ./Links.md \
+                        ../model/a2b_edge.F90 \
+                        ../model/boundary.F90 \
+                        ../model/dyn_core.F90 \
+                        ../model/fv_arrays.F90 \
+                        ../model/fv_control.F90 \
+                        ../model/fv_dynamics.F90 \
+                        ../model/fv_fill.F90 \
+                        ../model/fv_grid_utils.F90 \
+                        ../model/fv_mapz.F90 \
+                        ../model/fv_nesting.F90 \
+                        ../model/fv_regional_bc.F90 \
+                        ../model/fv_sg.F90 \
+                        ../model/fv_tracer2d.F90 \
+                        ../model/fv_update_phys.F90 \
+                        ../model/multi_gases.F90 \
+                        ../model/nh_core.F90 \
+                        ../model/nh_utils.F90 \
+                        ../model/sw_core.F90 \
+                        ../model/tp_core.F90 \
+                        ../tools/coarse_grained_diagnostics.F90 \
+                        ../tools/coarse_grained_restart_files.F90 \
+                        ../tools/coarse_graining.F90 \
+                        ../tools/external_ic.F90 \
+                        ../tools/external_sst.F90 \
+                        ../tools/fv_diag_column.F90 \
+                        ../tools/fv_diagnostics.F90 \
+                        ../tools/fv_eta.F90 \
+                        ../tools/fv_grid_tools.F90 \
+                        ../tools/fv_iau_mod.F90 \
+                        ../tools/fv_io.F90 \
+                        ../tools/fv_mp_mod.F90 \
+                        ../tools/fv_nudge.F90 \
+                        ../tools/fv_restart.F90 \
+                        ../tools/fv_surf_map.F90 \
+                        ../tools/fv_timing.F90 \
+                        ../tools/fv_treat_da_inc.F90 \
+                        ../tools/init_hydro.F90 \
+                        ../tools/sim_nc_mod.F90 \
+                        ../tools/sorted_index.F90 \
+                        ../tools/test_cases.F90 \
+                        ../driver/fvGFS/atmosphere.F90 \
+                        ../driver/fvGFS/DYCORE_typedefs.F90 \
+                        ../driver/fvGFS/fv_nggps_diag.F90
 INPUT_ENCODING         = UTF-8
 FILE_PATTERNS          =
 RECURSIVE              = YES
@@ -248,7 +251,7 @@ GENERATE_AUTOGEN_DEF   = NO
 GENERATE_PERLMOD       = NO
 PERLMOD_LATEX          = NO
 PERLMOD_PRETTY         = YES
-PERLMOD_MAKEVAR_PREFIX = 
+PERLMOD_MAKEVAR_PREFIX =
 ENABLE_PREPROCESSING   = YES
 MACRO_EXPANSION        = NO
 EXPAND_ONLY_PREDEF     = NO

driver/fvGFS/DYCORE_typedefs.F90

@@ -163,6 +163,6 @@ subroutine diag_zero (Diag)
 
     class(DYCORE_diag_type)            :: Diag
 
-  end subroutine diag_zero 
+  end subroutine diag_zero
 
 end module DYCORE_typedefs