RRTMGP for prototype 8

.github/CODEOWNERS

@@ -0,0 +1,7 @@
+# This is a comment.
+# Each line is a file pattern followed by one or more owners.
+# Order is important; the last matching pattern takes the most
+# precedence.
+
+# The components are owned by their respective teams
+/FV3/ @noaa-emc/fv3atm-team

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,56 @@
+---
+name: Bug report
+about: Create a report to fix bugs
+title: ''
+labels: bug
+assignees: ''
+
+---
+
+## Description
+Provide a clear and concise description of what the bug is.
+Also give a description of how to fix the bug.
+
+
+### To Reproduce:
+What compilers/machines are you seeing this with?
+Give explicit steps to reproduce the behavior.
+1. do this
+2. then that
+3. then, oops, look at the bug
+
+
+## Additional context
+Add any other context about the problem here.
+Directly reference any issues or PRs in this or other repositories that this is related to, and describe how they are related. Example:
+- needs to be fixed also in noaa-emc/nems/issues/<issue_number>
+- needed for noaa-emc/fv3atm/pull/<pr_number>
+
+
+## Output
+
+**Screenshots**
+If applicable, drag and drop screenshots to help explain your problem.
+
+**output logs**
+If applicable, include relevant output logs.
+Either drag and drop the entire log file here (if a long log) or
+
+```
+paste the code here (if a short section of log)
+```
+
+## Testing:
+
+1. Have you tested the code changes? On what platforms?
+
+2. Have you run regression test in ufs-weather-model or ufs-s2s-model with code changes?
+- Will the baseline results change? 
+- If the baseline results change, is it expected? Please give brief explanation.
+
+## Dependent PRs:
+
+Directly reference any issues or PRs in this or other repositories that this is related to, and describe how they are related. Example:
+- required to support noaa-emc/GFDL_atmos_cubed_sphere/issues/<issue_number>
+- ncar/ccpp-physics/pull/<pr_number>
+- associated ufs-weather-model/pull/<pr_number>

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,32 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: enhancement
+assignees: ''
+
+---
+
+## Description
+Provide a clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+## Solution
+Add a clear and concise description of what solution you provide.
+
+## Alternatives
+If applicable, add a description of any alternative solutions or features you've considered.
+
+## Testing:
+
+1. Have you tested the code changes? On what platforms?
+2. Have you run regression test in ufs-weather-model or ufs-s2s-model with code changes?
+- Will the baseline results change?
+- If yes, please give brief explanation of your code updates on the regression test.
+
+## Dependent PRs:
+
+Directly reference any issues or PRs in this or other repositories that this is related to, and describe how they are related. Example:
+- required to support noaa-emc/GFDL_atmos_cubed_sphere/issues/<issue_number>
+- ncar/ccpp-physics/pull/<pr_number>
+- associated ufs-weather-model/pull/<pr_number>
+

.github/pull_request_template.md

@@ -0,0 +1,37 @@
+## Description
+
+(Instructions: this, and all subsequent sections of text should be removed and filled in as appropriate.)
+Provide a detailed description of what this PR does.  
+What bug does it fix, or what feature does it add?  
+Is a change of answers expected from this PR?  
+
+
+
+### Issue(s) addressed
+
+Link the issues to be closed with this PR, whether in this repository, or in another repository.
+(Remember, issues should always be created before starting work on a PR branch!)
+- fixes #<issue_number>
+- fixes noaa-emc/fv3atm/issues/<issue_number>
+
+
+
+## Testing
+
+How were these changes tested?  
+What compilers / HPCs was it tested with?  
+Are the changes covered by regression tests? (If not, why? Do new tests need to be added?)  
+Have the ufs-weather-model regression test been run? On what platform?  
+- Will the code updates change regression test baseline? If yes, why? Please show the baseline directory below.
+- Please commit the regression test log files in your ufs-weather-model branch
+
+
+## Dependencies
+
+If testing this branch requires non-default branches in other repositories, list them.
+Those branches should have matching names (ideally)
+
+Do PRs in upstream repositories need to be merged first?
+If so add the "waiting for other repos" label and list the upstream PRs
+- waiting on noaa-emc/nems/pull/<pr_number>
+- waiting on noaa-emc/fv3atm/pull/<pr_number>

.gitignore

@@ -1,4 +1,10 @@
-*.o
+*.[aox]
 *.mod
-*.a
 *.pyc
+
+*.sw[a-p]
+~
+
+build/
+install/
+

.gitmodules

@@ -1,12 +1,16 @@
 [submodule "atmos_cubed_sphere"]
-	path = atmos_cubed_sphere
-	url = https://github.com/NOAA-EMC/GFDL_atmos_cubed_sphere
-	branch = dev/emc
+  path = atmos_cubed_sphere
+  url = https://github.com/NOAA-GFDL/GFDL_atmos_cubed_sphere
+  branch = dev/emc
 [submodule "ccpp/framework"]
-	path = ccpp/framework
-	url = https://github.com/NCAR/ccpp-framework
-	branch = master
+  path = ccpp/framework
+  url = https://github.com/NCAR/ccpp-framework
+  branch = main
 [submodule "ccpp/physics"]
-	path = ccpp/physics
-	url = https://github.com/NCAR/ccpp-physics
-	branch = master
+  path = ccpp/physics
+  url = https://github.com/dustinswales/ccpp-physics
+  branch = enhanced_GP2cld_coupling_tight
+[submodule "upp"]
+  path = upp
+  url = https://github.com/NOAA-EMC/UPP
+  branch = develop

CMakeLists.txt

@@ -1,120 +1,98 @@
-if(CCPP)
-  add_definitions(-DCCPP)
-endif()
 
-add_subdirectory(cpl)
-add_subdirectory(gfsphysics)
-add_subdirectory(ipd)
-add_subdirectory(io)
+###############################################################################
+### CCPP
+###############################################################################
+
+add_subdirectory(ccpp)
 
-# fv3core library
+###############################################################################
+### fv3 dynamical core
+###############################################################################
+
+# These ifdefs need to be turned ON in the dycore.
+set(use_WRTCOMP ON)
+set(GFS_PHYS    ON)
+set(GFS_TYPES   ON)
+set(USE_GFSL63  ON)
+add_subdirectory(atmos_cubed_sphere)
+
+###############################################################################
+### fv3atm
+###############################################################################
+if(INLINE_POST)
+  set(BUILD_POSTEXEC OFF)
+  add_subdirectory(upp)
+  set(POST_SRC io/inline_post.F90 io/post_nems_routines.F90 io/post_gfs.F90 io/post_regional.F90)
+else()
+  set(POST_SRC io/inline_post_stub.F90)
+  list(APPEND _fv3atm_defs_private NO_INLINE_POST)
+endif()
 
-if(NOT CCPP)
-set(FAST_PHYSICS_SRCS_F90 atmos_cubed_sphere/model/fv_cmp.F90)
+if(NOT PARALLEL_NETCDF)
+  list(APPEND _fv3atm_defs_private NO_PARALLEL_NETCDF)
 endif()
 
-add_library(
-    fv3core
-
-    atmos_cubed_sphere/model/a2b_edge.F90
-    atmos_cubed_sphere/model/multi_gases.F90
-    atmos_cubed_sphere/model/boundary.F90
-    atmos_cubed_sphere/model/dyn_core.F90
-    atmos_cubed_sphere/model/fv_arrays.F90
-    ${FAST_PHYSICS_SRCS_F90}
-    atmos_cubed_sphere/model/fv_control.F90
-    atmos_cubed_sphere/model/fv_dynamics.F90
-    atmos_cubed_sphere/model/fv_fill.F90
-    atmos_cubed_sphere/model/fv_grid_utils.F90
-    atmos_cubed_sphere/model/fv_mapz.F90
-    atmos_cubed_sphere/model/fv_nesting.F90
-    atmos_cubed_sphere/model/fv_regional_bc.F90
-    atmos_cubed_sphere/model/fv_sg.F90
-    atmos_cubed_sphere/model/fv_tracer2d.F90
-    atmos_cubed_sphere/model/fv_update_phys.F90
-    atmos_cubed_sphere/model/sw_core.F90
-    atmos_cubed_sphere/model/tp_core.F90
-    atmos_cubed_sphere/model/nh_core.F90
-    atmos_cubed_sphere/model/nh_utils.F90
-    atmos_cubed_sphere/tools/external_ic.F90
-    atmos_cubed_sphere/tools/external_sst.F90
-    atmos_cubed_sphere/tools/fv_diagnostics.F90
-    atmos_cubed_sphere/tools/fv_eta.F90
-    atmos_cubed_sphere/tools/fv_grid_tools.F90
-    atmos_cubed_sphere/tools/fv_io.F90
-    atmos_cubed_sphere/tools/fv_mp_mod.F90
-    atmos_cubed_sphere/tools/fv_nudge.F90
-    atmos_cubed_sphere/tools/fv_treat_da_inc.F90
-    atmos_cubed_sphere/tools/fv_iau_mod.F90
-    atmos_cubed_sphere/tools/fv_restart.F90
-    atmos_cubed_sphere/tools/fv_surf_map.F90
-    atmos_cubed_sphere/tools/fv_timing.F90
-    atmos_cubed_sphere//tools/init_hydro.F90
-    atmos_cubed_sphere/tools/sim_nc_mod.F90
-    atmos_cubed_sphere/tools/sorted_index.F90
-    atmos_cubed_sphere/tools/test_cases.F90
-    atmos_cubed_sphere/driver/fvGFS/DYCORE_typedefs.F90
-    atmos_cubed_sphere/driver/fvGFS/fv_nggps_diag.F90
-    atmos_cubed_sphere/driver/fvGFS/atmosphere.F90
+add_library(fv3atm
+  atmos_model.F90
+  fv3_cap.F90
+  module_fv3_config.F90
+  module_fcst_grid_comp.F90
+  stochastic_physics/stochastic_physics_wrapper.F90
+  cpl/module_block_data.F90
+  cpl/module_cplfields.F90
+  cpl/module_cap_cpl.F90
+  io/FV3GFS_io.F90
+  io/module_write_netcdf.F90
+  io/module_fv3_io_def.F90
+  io/module_write_internal_state.F90
+  io/module_wrt_grid_comp.F90
+  ${POST_SRC}
 )
 
-set_property(SOURCE atmos_cubed_sphere/model/nh_utils.F90 APPEND_STRING PROPERTY COMPILE_FLAGS "${FAST}")
-set_property(SOURCE atmos_cubed_sphere/model/fv_mapz.F90  APPEND_STRING PROPERTY COMPILE_FLAGS "${FAST}")
+add_dependencies(fv3atm fv3 fv3ccpp stochastic_physics)
 
-target_link_libraries(fv3core PRIVATE fms)
-target_link_libraries(fv3core PRIVATE gfsphysics)
-target_link_libraries(fv3core PRIVATE ipd)
+list(APPEND _fv3atm_defs_private GFS_PHYS
+                                 INTERNAL_FILE_NML
+                                 use_WRTCOMP)
 
-target_include_directories(fv3core PRIVATE atmos_cubed_sphere ${ESMF_MOD})
+target_compile_definitions(fv3atm PRIVATE "${_fv3atm_defs_private}")
 
-# end of fv3core
+set_target_properties(fv3atm PROPERTIES Fortran_MODULE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/mod)
+target_include_directories(fv3atm INTERFACE $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/mod>
+                                            $<INSTALL_INTERFACE:mod>)
 
-###############################################################################
-### ccpp
-###############################################################################
-if(CCPP)
-  add_subdirectory(ccpp)
-  add_subdirectory(ccpp/driver)
-  add_dependencies(gfsphysics ccpp ccppphys)
-  add_dependencies(ccppdriver ccpp ccppphys)
-  add_dependencies(ccppphys ccpp)
-
-  target_include_directories(fv3core PRIVATE ${CMAKE_BINARY_DIR}/FV3/ccpp/framework/src)
-  target_include_directories(fv3core PRIVATE ${CMAKE_BINARY_DIR}/FV3/ccpp/driver)
+if(MULTI_GASES)
+  list(APPEND _fv3atm_defs_private MULTI_GASES)
 endif()
 
-set_target_properties(fv3core PROPERTIES Fortran_MODULE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/mod)
-target_include_directories(fv3core PUBLIC ${CMAKE_CURRENT_BINARY_DIR}/mod)
-
-# When specifying an out-of-tree source a binary directory must be explicitly specified.
-#add_subdirectory(../stochastic_physics stochastic_physics)
-add_subdirectory(stochastic_physics)
+target_link_libraries(fv3atm PUBLIC fv3
+                                    fv3ccpp
+                                    stochastic_physics
+                                    fms)
 
-add_library(
-    fv3cap
+target_link_libraries(fv3atm PUBLIC w3nco::w3nco_d
+                                    sp::sp_d
+                                    bacio::bacio_4
+                                    esmf)
 
-    atmos_model.F90
-    fv3_cap.F90
-    module_fv3_config.F90
-    module_fcst_grid_comp.F90
-    time_utils.F90
-)
+if(INLINE_POST)
+  target_link_libraries(fv3atm PUBLIC upp::upp)
+endif()
 
-if(CCPP)
-target_include_directories(fv3cap PRIVATE ${CMAKE_CURRENT_BINARY_DIR}/ccpp/driver/mod)
-add_dependencies(fv3cap ccppdriver ccppphys)
+if(OPENMP)
+  target_link_libraries(fv3atm PUBLIC OpenMP::OpenMP_Fortran)
 endif()
-target_include_directories(fv3cap PRIVATE ${CMAKE_CURRENT_BINARY_DIR}/stochastic_physics)
-target_compile_definitions(fv3cap PRIVATE -DESMF_VERSION_MAJOR=${ESMF_VERSION_MAJOR})
-target_include_directories(fv3cap PRIVATE ${ESMF_MOD})
-
-target_link_libraries(fv3cap PRIVATE fms)
-target_link_libraries(fv3cap PRIVATE fv3cpl)
-target_link_libraries(fv3cap PRIVATE gfsphysics)
-target_link_libraries(fv3cap PRIVATE ipd)
-target_link_libraries(fv3cap PRIVATE io)
-target_link_libraries(fv3cap PRIVATE fv3core)
-target_link_libraries(fv3cap PRIVATE stochastic_physics)
-
-set_target_properties(fv3cap PROPERTIES Fortran_MODULE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/mod)
-target_include_directories(fv3cap PUBLIC ${CMAKE_CURRENT_BINARY_DIR}/mod)
+
+###############################################################################
+### Install
+###############################################################################
+install(
+  TARGETS fv3atm
+  EXPORT fv3atm-config
+  LIBRARY DESTINATION lib
+  ARCHIVE DESTINATION lib)
+
+install(DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/mod DESTINATION ${CMAKE_INSTALL_PREFIX})
+
+install(EXPORT fv3atm-config
+  DESTINATION lib/cmake)