Merge branch 'ufs-community:develop' into feature/cmaq54

.github/linters/.yaml-lint.yml

@@ -0,0 +1,28 @@
+---
+
+extends: default
+
+rules:
+  braces:
+    level: warning
+    max-spaces-inside: 1
+  brackets:
+    level: warning
+    max-spaces-inside: 1
+  colons:
+    level: warning
+  commas: disable
+  comments: disable
+  comments-indentation: disable
+  document-start: disable
+  empty-lines:
+    level: warning
+  hyphens:
+    level: warning
+  indentation:
+    level: warning
+    indent-sequences: consistent
+  line-length: disable
+  truthy: disable
+  trailing-spaces: disable
+

.github/pull_request_template.md

@@ -42,6 +42,7 @@ Please delete what is not needed.
   * MOM6 - 
   * NOAHMP - 
   * WW3 - 
+  * fire_behavior
   * stochastic_physics - 
 ```
 
@@ -89,6 +90,7 @@ Example:
 * MOM6:
 * NOAHMP:
 * WW3:
+* fire_behavior:
 * stochastic_physics:
 * None
 

.github/workflows/aux.yml

@@ -18,43 +18,42 @@ jobs:
     runs-on: ubuntu-20.04
 
     steps:
-    - name: Share helper id
-      run: echo -n ${{ github.run_id }} >~/id_file
+      - name: Share helper id
+        run: echo -n ${{ github.run_id }} >~/id_file
 
-    - uses: actions/cache@v2
-      with:
-        path: ~/id_file
-        key: helperid-${{ github.event.workflow_run.id }}
+      - uses: actions/cache@v4
+        with:
+          path: ~/id_file
+          key: helperid-${{ github.event.workflow_run.id }}
 
   repocheck:
     name: Repo check
     runs-on: ubuntu-20.04
 
     steps:
-    - name: Check up-to-dateness and post comment
-      run: |
-        trap 'echo "exit-code=$?" >> "$GITHUB_OUTPUT"' EXIT
-        head_sha=${{ github.event.pull_request.head.sha }}
-        head_brc=${{ github.event.pull_request.head.ref }}
-        head_url=${{ github.event.pull_request.head.repo.html_url }}
-        git clone -q -b $head_brc $head_url .
-        git checkout -q $head_sha
-        git submodule -q update --init --recursive
-        cd ${{ github.workspace }}/tests/ci
-        url=$GITHUB_API_URL/repos/$GITHUB_REPOSITORY
-        pr_number=$(curl -sS -H $app $url/pulls \
-          | jq -r '.[] | select(.head.sha == "'"$head_sha"'") | .number')
-        echo "pr_number is $pr_number"
-        pr_uid=${{ github.event.pull_request.head.repo.owner.login }}
-        echo "pr_uid is $pr_uid"
-        ./repo_check.sh
-        #comment="$(./repo_check.sh 2>/dev/null)"
-        #echo "comment is $comment"
-        #if [[ -n $comment ]]; then
-        #  curl -sS -X POST -H $app -H "Authorization: token ${{ secrets.GITHUB_TOKEN }}" \
-        #    $url/issues/$pr_number/comments -d '{"body": "'"${comment}"'"}'
-        #  echo -n "failure" >~/repocheck_file
-        #else
-        #  echo -n "success" >~/repocheck_file
-        #fi
-        
+      - name: Check up-to-dateness and post comment
+        run: |
+          trap 'echo "exit-code=$?" >> "$GITHUB_OUTPUT"' EXIT
+          head_sha=${{ github.event.pull_request.head.sha }}
+          head_brc=${{ github.event.pull_request.head.ref }}
+          head_url=${{ github.event.pull_request.head.repo.html_url }}
+          git clone -q -b $head_brc $head_url .
+          git checkout -q $head_sha
+          git submodule -q update --init --recursive
+          cd ${{ github.workspace }}/tests/ci
+          url=$GITHUB_API_URL/repos/$GITHUB_REPOSITORY
+          pr_number=$(curl -sS -H $app $url/pulls \
+            | jq -r '.[] | select(.head.sha == "'"$head_sha"'") | .number')
+          echo "pr_number is $pr_number"
+          pr_uid=${{ github.event.pull_request.head.repo.owner.login }}
+          echo "pr_uid is $pr_uid"
+          ./repo_check.sh
+          #comment="$(./repo_check.sh 2>/dev/null)"
+          #echo "comment is $comment"
+          #if [[ -n $comment ]]; then
+          #  curl -sS -X POST -H $app -H "Authorization: token ${{ secrets.GITHUB_TOKEN }}" \
+          #    $url/issues/$pr_number/comments -d '{"body": "'"${comment}"'"}'
+          #  echo -n "failure" >~/repocheck_file
+          #else
+          #  echo -n "success" >~/repocheck_file
+          #fi

.github/workflows/build_test.yml → .github/workflows/build_test._yml

@@ -16,12 +16,12 @@ jobs:
       current: ${{ steps.check.outputs.current }}
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
 
     - name: Wait for caching source
       run: sleep 30
 
-    - uses: actions/cache@v2
+    - uses: actions/cache@v4
       with:
         path: ~/id_file
         key: helperid-${{ github.run_id }}

.github/workflows/superlinter.yml

@@ -24,7 +24,7 @@ jobs:
       - name: Super-Linter
         uses: super-linter/[email protected]
         env:
-          LINTER_RULES_PATH: /
+          LINTER_RULES_PATH: '.github/linters/'
           DEFAULT_BRANCH: origin/develop
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           FILTER_REGEX_EXCLUDE: .*(tests/fv3_conf/.*|tests/ci/.*|tests/auto/.*|tests/auto-jenkins/.*|tests/opnReqTests/.*|tests/opnReqTest|tests/atparse.bash).*
@@ -33,5 +33,5 @@ jobs:
           #VALIDATE_GITHUB_ACTIONS: true
           #VALIDATE_LUA: true
           #VALIDATE_MARKDOWN: true
-          #VALIDATE_PYTHON_PYLINT: true
-          #VALIDATE_YAML: true
+          VALIDATE_PYTHON_PYLINT: true
+          VALIDATE_YAML: true

.gitmodules

@@ -46,3 +46,7 @@
   path = NOAHMP-interface/noahmp
   url = https://github.com/NOAA-EMC/noahmp
   branch = develop
+[submodule "fire_behavior"]
+  path = fire_behavior
+  url = https://github.com/NCAR/fire_behavior
+  branch = develop

CDEPS-interface/cdeps_files.cmake

@@ -41,14 +41,11 @@ list(APPEND cdeps_dshr_files
 
 list(APPEND cdeps_datm_files
   CDEPS/datm/atm_comp_nuopc.F90
-  CDEPS/datm/datm_datamode_cfsr_mod.F90
   CDEPS/datm/datm_datamode_clmncep_mod.F90
   CDEPS/datm/datm_datamode_core2_mod.F90
   CDEPS/datm/datm_datamode_cplhist_mod.F90
   CDEPS/datm/datm_datamode_era5_mod.F90
   CDEPS/datm/datm_datamode_gefs_mod.F90
-  CDEPS/datm/datm_datamode_gfs_mod.F90
-  CDEPS/datm/datm_datamode_gfs_hafs_mod.F90
   CDEPS/datm/datm_datamode_jra_mod.F90
   CDEPS/datm/datm_datamode_simple_mod.F90
 )

CMakeLists.txt

@@ -16,7 +16,7 @@ list(APPEND CMAKE_MODULE_PATH ${CMAKE_SOURCE_DIR}/CMakeModules/Modules)
 ###############################################################################
 
 # Valid applications and choices
-list(APPEND VALID_APPS ATM ATMAERO ATMAQ ATMW ATMWM ATML LND S2S S2SA S2SW S2SWA S2SWAL ATM_DS2S ATM_DS2S-PCICE HAFS HAFSW HAFS-MOM6 HAFS-MOM6W HAFS-ALL NG-GODAS)
+list(APPEND VALID_APPS ATM ATMAERO ATMAQ ATMW ATMWM ATML ATMF LND S2S S2SA S2SW S2SWA S2SWAL ATM_DS2S ATM_DS2S-PCICE HAFS HAFSW HAFS-MOM6 HAFS-MOM6W HAFS-ALL NG-GODAS)
 set(APP NONE CACHE BOOL "Application Name")
 if(NOT (APP IN_LIST VALID_APPS))
   message(FATAL_ERROR "${APP} is not a valid application.\nValid Applications are: ${VALID_APPS}")
@@ -34,6 +34,7 @@ set(STOCH_PHYS      OFF CACHE BOOL "Enable Stochastic Physics")
 set(CMEPS           OFF CACHE BOOL "Enable CMEPS")
 set(CDEPS           OFF CACHE BOOL "Enable CDEPS")
 set(NOAHMP          OFF CACHE BOOL "Enable NOAHMP")
+set(FIRE_BEHAVIOR   OFF CACHE BOOL "Enable Fire Behavior")
 
 # Configure selected application specific components
 message("")
@@ -52,6 +53,7 @@ message("STOCH_PHYS ....... ${STOCH_PHYS}")
 message("CDEPS ............ ${CDEPS}")
 message("CMEPS ............ ${CMEPS}")
 message("NOAHMP ........... ${NOAHMP}")
+message("FIRE_BEHAVIOR .... ${FIRE_BEHAVIOR}")
 
 ###############################################################################
 ### Build Options
@@ -155,7 +157,7 @@ if(FMS)
   elseif (APP MATCHES "^(S2S|S2SA|S2SW|S2SWA|S2SWAL|ATM_DS2S|ATM_DS2S-PCICE|NG-GODAS|HAFS-MOM6|HAFS-MOM6W)$")
     add_library(fms ALIAS FMS::fms_r8)
   endif()
-  if(APP MATCHES "^(ATM|ATMAERO|ATMAQ|ATMWM|ATMW|ATML|HAFS|HAFS-ALL)$")
+  if(APP MATCHES "^(ATM|ATMAERO|ATMAQ|ATMWM|ATMW|ATML|ATMF|HAFS|HAFS-ALL)$")
     if(32BIT)
       add_library(fms ALIAS FMS::fms_r4)
     else()
@@ -260,6 +262,14 @@ if(NOAHMP)
   add_subdirectory(NOAHMP-interface)
 endif()
 
+###############################################################################
+### Fire Components [FIRE_BEHAVIOR]
+###############################################################################
+if(FIRE_BEHAVIOR)
+  set(NUOPC "ON" CACHE STRING "Build fire_behavior with NUOPC cap" FORCE)
+  add_subdirectory(fire_behavior)
+endif()
+
 ###############################################################################
 ### UFS Library
 ###############################################################################
@@ -339,6 +349,12 @@ if(NOAHMP)
   list(APPEND _ufs_libs_public noahmp)
 endif()
 
+if(FIRE_BEHAVIOR)
+  add_dependencies(ufs fire_behavior_nuopc)
+  list(APPEND _ufs_defs_private FRONT_FIRE_BEHAVIOR=fire_behavior_nuopc)
+  list(APPEND _ufs_libs_public fire_behavior_nuopc)
+endif()
+
 target_compile_definitions(ufs PRIVATE "${_ufs_defs_private}")
 target_link_libraries(ufs PUBLIC "${_ufs_libs_public}")
 

MOM6-interface/mom6_files.cmake

@@ -36,6 +36,7 @@ list(APPEND mom6_src_files
   MOM6/src/core/MOM_continuity_PPM.F90
   MOM6/src/core/MOM_density_integrals.F90
   MOM6/src/core/MOM_dynamics_split_RK2.F90
+  MOM6/src/core/MOM_dynamics_split_RK2b.F90
   MOM6/src/core/MOM_dynamics_unsplit.F90
   MOM6/src/core/MOM_dynamics_unsplit_RK2.F90
   MOM6/src/core/MOM_forcing_type.F90
@@ -59,6 +60,7 @@ list(APPEND mom6_src_files
   MOM6/src/diagnostics/MOM_sum_output.F90
   MOM6/src/diagnostics/MOM_wave_speed.F90
 
+  MOM6/src/equation_of_state/MOM_EOS_base_type.F90
   MOM6/src/equation_of_state/MOM_EOS.F90
   MOM6/src/equation_of_state/MOM_EOS_Jackett06.F90
   MOM6/src/equation_of_state/MOM_EOS_Roquet_SpV.F90

build.sh

@@ -1,17 +1,10 @@
 #!/bin/bash
 set -eu
-uname_s=$(uname -s)
-if [[ ${uname_s} == Darwin ]]; then
-  UFS_MODEL_DIR=$(greadlink -f -n "${BASH_SOURCE[0]}")
-  UFS_MODEL_DIR=$(dirname "${UFS_MODEL_DIR}")
-  UFS_MODEL_DIR=$(cd "${UFS_MODEL_DIR}" && pwd -P)
-else
-  UFS_MODEL_DIR=$(readlink -f -n "${BASH_SOURCE[0]}")
-  UFS_MODEL_DIR=$(dirname "${UFS_MODEL_DIR}")
-  UFS_MODEL_DIR=$(cd "${UFS_MODEL_DIR}" && pwd -P)
-fi
-echo "UFS MODEL DIR: ${UFS_MODEL_DIR}"
+
+SCRIPT_REALPATH=$(realpath "${BASH_SOURCE[0]}")
+UFS_MODEL_DIR=$(dirname "${SCRIPT_REALPATH}")
 readonly UFS_MODEL_DIR
+echo "UFS MODEL DIR: ${UFS_MODEL_DIR}"
 
 export CC=${CC:-mpicc}
 export CXX=${CXX:-mpicxx}
@@ -26,4 +19,4 @@ for i in ${CMAKE_FLAGS}; do ARR_CMAKE_FLAGS+=("${i}") ; done
 cmake "${UFS_MODEL_DIR}" "${ARR_CMAKE_FLAGS[@]}"
 # Turn off OpenMP threading for parallel builds
 # to avoid exhausting the number of user processes
-OMP_NUM_THREADS=1 make -j "${BUILD_JOBS:-4}" "VERBOSE=${BUILD_VERBOSE:-}"
+OMP_NUM_THREADS=1 make -j "${BUILD_JOBS:-4}" "VERBOSE=${BUILD_VERBOSE:-}"

cmake/Intel.cmake

@@ -20,7 +20,8 @@ endif()
 
 if(DEBUG)
     add_definitions(-DDEBUG)
-    set(CMAKE_Fortran_FLAGS_DEBUG "${CMAKE_Fortran_FLAGS_DEBUG} -O0 -check -check noarg_temp_created -check nopointer -warn -warn noerrors -fp-stack-check -fstack-protector-all -fpe0 -debug -ftrapuv -init=snan,arrays")
+    #set(CMAKE_Fortran_FLAGS_DEBUG "${CMAKE_Fortran_FLAGS_DEBUG} -O0 -check -check noarg_temp_created -check nopointer -warn -warn noerrors -fp-stack-check -fstack-protector-all -fpe0 -debug -ftrapuv -init=snan,arrays")
+    set(CMAKE_Fortran_FLAGS_DEBUG "${CMAKE_Fortran_FLAGS_DEBUG} -O0 -check -check noarg_temp_created -warn -warn noerrors -fp-stack-check -fstack-protector-all -fpe0 -debug -ftrapuv -init=snan,arrays")
     set(CMAKE_C_FLAGS_DEBUG "${CMAKE_C_FLAGS_DEBUG} -O0 -ftrapuv")
 else()
     if(FASTER)

cmake/configure_apps.cmake

@@ -13,7 +13,7 @@
 ###############################################################################
 ### Configure Application Components
 ###############################################################################
-if(APP MATCHES "^(ATM|ATMW|ATMWM|ATMAQ|ATML)$")
+if(APP MATCHES "^(ATM|ATMW|ATMWM|ATMAQ|ATML|ATMF)$")
   set(FMS        ON  CACHE BOOL "Enable FMS"                 FORCE)
   set(FV3        ON  CACHE BOOL "Enable FV3"                 FORCE)
   set(STOCH_PHYS ON  CACHE BOOL "Enable Stochastic Physics"  FORCE)
@@ -31,6 +31,8 @@ if(APP MATCHES "^(ATM|ATMW|ATMWM|ATMAQ|ATML)$")
     set(CMEPS    ON  CACHE BOOL "Enable CMEPS"               FORCE)
     set(NOAHMP   ON  CACHE BOOL "Enable NOAHMP"              FORCE)
     message("Configuring UFS app in Atmosphere with Air Quality mode")
+  elseif(APP MATCHES "ATMF")
+    set(FIRE_BEHAVIOR ON CACHE BOOL "Enable Fire Behavior"   FORCE)
   else()
     message("Configuring UFS app in Atmosphere Only mode")
   endif()

doc/UsersGuide/source/Glossary.rst

@@ -68,7 +68,8 @@ Glossary
       Global atmospheric model based on fluid dynamics principles, including Euler's equations of motion.
 
    EMC
-      The `Environmental Modeling Center <https://www.emc.ncep.noaa.gov/emc.php>`_ is one of :term:`NCEP`'s nine centers and leads the :term:`National Weather Service <NWS>`'s modeling efforts.
+      The `Environmental Modeling Center <https://www.emc.ncep.noaa.gov/emc.php>`__ is one of :term:`NCEP`'s nine centers and leads the :term:`National Weather Service <NWS>`'s modeling efforts.
+
 
    ESMF
       `Earth System Modeling Framework <https://earthsystemmodeling.org/docs/release/latest/ESMF_usrdoc/>`__. The ESMF defines itself as "a suite of software tools for developing high-performance, multi-component Earth science modeling applications." It is a community-developed software infrastructure for building and coupling models. 

doc/UsersGuide/source/InputsOutputs.rst

@@ -1304,6 +1304,26 @@ These field section entries are described in :numref:`Table %s <FieldDescription
 
 Comments can be added to the diag_table using the hash symbol (``#``).
 
+
+Each WM component has its own ``diag_table`` with associated variables. :numref:`Table %s <diag-table-options>` contains links to the full set of options for each WM component.
+
+.. _diag-table-options:
+
+.. list-table:: * *diag_table* Options for WM Components*
+   :widths: 16 24 24
+   :header-rows: 1
+
+   * - WM Component
+     - Diag Table
+     - Source File
+   * - FV3
+     - :ref:`FV3 Variables <fv3diagtable>`
+     - `GFS_diagnostics.F90 <https://github.com/NOAA-EMC/fv3atm/blob/develop/ccpp/driver/GFS_diagnostics.F90>`_
+   * - MOM6
+     - `MOM6 Variables <https://ncar.github.io/MOM6/APIs/namespacemom__diagnostics.html>`_
+     - `MOM_diagnostics.F90 <https://github.com/NOAA-EMC/MOM6/blob/main/src/diagnostics/MOM_diagnostics.F90>`_
+
+
 A brief example of the diag_table is shown below.  ``"..."`` denotes where lines have been removed.
 
 .. _code-block-fv3-diag-table:

doc/UsersGuide/source/conf.py

@@ -92,6 +92,7 @@
                             ]
 # Ignore working links that cause a linkcheck 403 error.
 linkcheck_ignore = [r'https://agupubs\.onlinelibrary\.wiley\.com/doi/10\.1029/2020MS002260',
+                    r'https://glossary.ametsoc.org/wiki/*',
                    ]
 
 # -- Options for HTML output -------------------------------------------------

doc/UsersGuide/source/tables/fv3_diag_table.rst

@@ -0,0 +1,13 @@
+:orphan:
+
+.. _fv3diagtable:
+
+****************************
+FV3 Weather Model Variables
+****************************
+
+
+.. csv-table::
+    :file: fv3diagtable.csv
+    :widths: 10, 15
+    :header-rows: 1