Merge branch 'develop' into ejh_d7

NOAA-EMC · Jan 28, 2024 · d83fcab · d83fcab
2 parents 03e35a0 + 1d2c823
commit d83fcab
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diff --git a/.github/workflows/GCC.yml b/.github/workflows/GCC.yml
@@ -26,6 +26,10 @@ jobs:
 
     steps:
 
+    - name: install-doxygen
+      run: |
+        sudo apt-get install doxygen graphviz
+        
     - name: checkout-fv3atm
       uses: actions/checkout@v3
       with:
@@ -37,7 +41,7 @@ jobs:
       uses: actions/cache@v3
       with:
         path: ${{ github.workspace }}/spack-develop
-        key: spack-${{ hashFiles('fv3atm/ci/spack.yaml') }}-gcc${{ matrix.gcc_ver }}-2
+        key: spack-${{ hashFiles('fv3atm/ci/spack.yaml') }}-gcc${{ matrix.gcc_ver }}-2-${{ matrix.cmake_opts }}-${{ matrix.mpich }}
 
     # Building dependencies takes 40+ min
     - name: spack-install
@@ -55,13 +59,6 @@ jobs:
         spack concretize |& tee ${SPACK_ENV}/log.concretize
         spack install -j2 --fail-fast
 
-    - name: cache-save
-      uses: actions/cache/save@v3
-      if: ${{ always() }}
-      with:
-        path: ${{ github.workspace }}/spack-develop
-        key: spack-${{ hashFiles('fv3atm/ci/spack.yaml') }}-gcc${{ matrix.gcc_ver }}-2
-
     - name: build-fv3atm
       run: |
         . ${GITHUB_WORKSPACE}/spack-develop/share/spack/setup-env.sh
@@ -71,13 +68,22 @@ jobs:
         git clone https://github.com/NOAA-EMC/CMakeModules
         git clone --recurse-submodules https://github.com/NOAA-PSL/stochastic_physics stochastic_physics_repo
         mkdir ${GITHUB_WORKSPACE}/build
+        sed -i 's/doc /upp_doc /' upp/docs/CMakeLists.txt
         cd ${GITHUB_WORKSPACE}/build
-        cmake ${GITHUB_WORKSPACE}/fv3atm -DBUILD_TESTING=ON ${{ matrix.cmake_opts }}
+        cmake ${GITHUB_WORKSPACE}/fv3atm -DBUILD_TESTING=ON ${{ matrix.cmake_opts }} -DENABLE_DOCS=ON
         make -j2
+        ls -l /home/runner/work/fv3atm/fv3atm/fv3atm/io
 
+    - uses: actions/upload-artifact@v3
+      with:
+        name: docs
+        path: |
+          build/docs/html
+          
     - name: debug-artifacts
       uses: actions/upload-artifact@v3
       if: ${{ failure() }}
       with:
         name: ccpp_prebuild_logs
         path: ${{ github.workspace }}/build/ccpp/ccpp_prebuild.*
+
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -1,6 +1,19 @@
+# This is the main CMake file for fv3atm.
+#
+# Dusan Jovic, Alex Richert
+cmake_minimum_required(VERSION 3.19)
+
+# Handle user build options.
+option(ENABLE_DOCS "Enable generation of doxygen-based documentation." OFF)
+
+# Determine whether or not to generate documentation.
+if(ENABLE_DOCS)
+  find_package(Doxygen REQUIRED)
+  add_subdirectory(docs)  
+endif()
+
 # Enable CI build & unit testing:
 if(BUILD_TESTING)
-  cmake_minimum_required(VERSION 3.19)
   project(fv3atm VERSION 1.0 LANGUAGES C CXX Fortran)
   include(ci/CMakeLists.txt)
 endif()

diff --git a/atmos_cubed_sphere b/atmos_cubed_sphere
diff --git a/atmos_model.F90 b/atmos_model.F90
@@ -2349,6 +2349,266 @@ subroutine assign_importdata(jdat, rc)
             endif
           endif
 
+! get surface snow area fraction: over land (if cpllnd=true and cpllnd2atm=true)
+!------------------------------------------------
+          fldname = 'inst_snow_area_fraction_lnd'
+          if (trim(impfield_name) == trim(fldname)) then
+            findex  = queryImportFields(fldname)
+            if (importFieldsValid(findex) .and. GFS_control%cpllnd .and. GFS_control%cpllnd2atm) then
+!$omp parallel do default(shared) private(i,j,nb,ix)
+              do j=jsc,jec
+                do i=isc,iec
+                  nb = Atm_block%blkno(i,j)
+                  ix = Atm_block%ixp(i,j)
+                  if (GFS_data(nb)%Sfcprop%landfrac(ix) > zero) then
+                    GFS_data(nb)%Coupling%sncovr1_lnd(ix) = datar8(i,j)
+                  endif
+                enddo
+              enddo
+              if (mpp_pe() == mpp_root_pe() .and. debug)  print *,'fv3 assign_import: get snow area fraction from land'
+            endif
+          endif
+
+! get latent heat flux: over land (if cpllnd=true and cpllnd2atm=true)
+!------------------------------------------------
+          fldname = 'inst_laten_heat_flx_lnd'
+          if (trim(impfield_name) == trim(fldname)) then
+            findex  = queryImportFields(fldname)
+            if (importFieldsValid(findex) .and. GFS_control%cpllnd .and. GFS_control%cpllnd2atm) then
+!$omp parallel do default(shared) private(i,j,nb,ix)
+              do j=jsc,jec
+                do i=isc,iec
+                  nb = Atm_block%blkno(i,j)
+                  ix = Atm_block%ixp(i,j)
+                  if (GFS_data(nb)%Sfcprop%landfrac(ix) > zero) then
+                    GFS_data(nb)%Coupling%evap_lnd(ix) = datar8(i,j)
+                  endif
+                enddo
+              enddo
+              if (mpp_pe() == mpp_root_pe() .and. debug)  print *,'fv3 assign_import: get latent heat flux from land'
+            endif
+          endif
+
+! get sensible heat flux: over land (if cpllnd=true and cpllnd2atm=true)
+!--------------------------------------------------
+          fldname = 'inst_sensi_heat_flx_lnd'
+          if (trim(impfield_name) == trim(fldname)) then
+            findex  = queryImportFields(fldname)
+            if (importFieldsValid(findex) .and. GFS_control%cpllnd .and. GFS_control%cpllnd2atm) then
+!$omp parallel do default(shared) private(i,j,nb,ix)
+              do j=jsc,jec
+                do i=isc,iec
+                  nb = Atm_block%blkno(i,j)
+                  ix = Atm_block%ixp(i,j)
+                  if (GFS_data(nb)%Sfcprop%landfrac(ix) > zero) then
+                    GFS_data(nb)%Coupling%hflx_lnd(ix) = datar8(i,j)
+                  endif
+                enddo
+              enddo
+              if (mpp_pe() == mpp_root_pe() .and. debug)  print *,'fv3 assign_import: get sensible heat flux from land'
+            endif
+          endif
+
+! get surface upward potential latent heat flux: over land (if cpllnd=true and cpllnd2atm=true)
+!------------------------------------------------
+          fldname = 'inst_potential_laten_heat_flx_lnd'
+          if (trim(impfield_name) == trim(fldname)) then
+            findex  = queryImportFields(fldname)
+            if (importFieldsValid(findex) .and. GFS_control%cpllnd .and. GFS_control%cpllnd2atm) then
+!$omp parallel do default(shared) private(i,j,nb,ix)
+              do j=jsc,jec
+                do i=isc,iec
+                  nb = Atm_block%blkno(i,j)
+                  ix = Atm_block%ixp(i,j)
+                  if (GFS_data(nb)%Sfcprop%landfrac(ix) > zero) then
+                    GFS_data(nb)%Coupling%ep_lnd(ix) = datar8(i,j)
+                  endif
+                enddo
+              enddo
+              if (mpp_pe() == mpp_root_pe() .and. debug)  print *,'fv3 assign_import: get potential latent heat flux from land'
+            endif
+          endif
+
+! get 2m air temperature: over land (if cpllnd=true and cpllnd2atm=true)
+!------------------------------------------------
+          fldname = 'inst_temp_height2m_lnd'
+          if (trim(impfield_name) == trim(fldname)) then
+            findex  = queryImportFields(fldname)
+            if (importFieldsValid(findex) .and. GFS_control%cpllnd .and. GFS_control%cpllnd2atm) then
+!$omp parallel do default(shared) private(i,j,nb,ix)
+              do j=jsc,jec
+                do i=isc,iec
+                  nb = Atm_block%blkno(i,j)
+                  ix = Atm_block%ixp(i,j)
+                  if (GFS_data(nb)%Sfcprop%landfrac(ix) > zero) then
+                    GFS_data(nb)%Coupling%t2mmp_lnd(ix) = datar8(i,j)
+                  endif
+                enddo
+              enddo
+              if (mpp_pe() == mpp_root_pe() .and. debug)  print *,'fv3 assign_import: get temperature at 2m from land'
+            endif
+          endif
+
+! get 2m specific humidity: over land (if cpllnd=true and cpllnd2atm=true)
+!------------------------------------------------
+          fldname = 'inst_spec_humid_height2m_lnd'
+          if (trim(impfield_name) == trim(fldname)) then
+            findex  = queryImportFields(fldname)
+            if (importFieldsValid(findex) .and. GFS_control%cpllnd .and. GFS_control%cpllnd2atm) then
+!$omp parallel do default(shared) private(i,j,nb,ix)
+              do j=jsc,jec
+                do i=isc,iec
+                  nb = Atm_block%blkno(i,j)
+                  ix = Atm_block%ixp(i,j)
+                  if (GFS_data(nb)%Sfcprop%landfrac(ix) > zero) then
+                    GFS_data(nb)%Coupling%q2mp_lnd(ix) = datar8(i,j)
+                  endif
+                enddo
+              enddo
+              if (mpp_pe() == mpp_root_pe() .and. debug)  print *,'fv3 assign_import: get specific humidity at 2m from land'
+            endif
+          endif
+
+! get specific humidity: over land (if cpllnd=true and cpllnd2atm=true)
+!------------------------------------------------
+          fldname = 'inst_spec_humid_lnd'
+          if (trim(impfield_name) == trim(fldname)) then
+            findex  = queryImportFields(fldname)
+            if (importFieldsValid(findex) .and. GFS_control%cpllnd .and. GFS_control%cpllnd2atm) then
+!$omp parallel do default(shared) private(i,j,nb,ix)
+              do j=jsc,jec
+                do i=isc,iec
+                  nb = Atm_block%blkno(i,j)
+                  ix = Atm_block%ixp(i,j)
+                  if (GFS_data(nb)%Sfcprop%landfrac(ix) > zero) then
+                    GFS_data(nb)%Coupling%qsurf_lnd(ix) = datar8(i,j)
+                  endif
+                enddo
+              enddo
+              if (mpp_pe() == mpp_root_pe() .and. debug)  print *,'fv3 assign_import: get specific humidity from land'
+            endif
+          endif
+
+! get upward heat flux in soil (if cpllnd=true and cpllnd2atm=true)
+!------------------------------------------------
+          fldname = 'inst_upward_heat_flux_lnd'
+          if (trim(impfield_name) == trim(fldname)) then
+            findex  = queryImportFields(fldname)
+            if (importFieldsValid(findex) .and. GFS_control%cpllnd .and. GFS_control%cpllnd2atm) then
+!$omp parallel do default(shared) private(i,j,nb,ix)
+              do j=jsc,jec
+                do i=isc,iec
+                  nb = Atm_block%blkno(i,j)
+                  ix = Atm_block%ixp(i,j)
+                  if (GFS_data(nb)%Sfcprop%landfrac(ix) > zero) then
+                    GFS_data(nb)%Coupling%gflux_lnd(ix) = datar8(i,j)
+                  endif
+                enddo
+              enddo
+              if (mpp_pe() == mpp_root_pe() .and. debug)  print *,'fv3 assign_import: get upward heat flux from land'
+            endif
+          endif
+
+! get surface runoff in soil (if cpllnd=true and cpllnd2atm=true)
+!------------------------------------------------
+          fldname = 'inst_runoff_rate_lnd'
+          if (trim(impfield_name) == trim(fldname)) then
+            findex  = queryImportFields(fldname)
+            if (importFieldsValid(findex) .and. GFS_control%cpllnd .and. GFS_control%cpllnd2atm) then
+!$omp parallel do default(shared) private(i,j,nb,ix)
+              do j=jsc,jec
+                do i=isc,iec
+                  nb = Atm_block%blkno(i,j)
+                  ix = Atm_block%ixp(i,j)
+                  if (GFS_data(nb)%Sfcprop%landfrac(ix) > zero) then
+                    GFS_data(nb)%Coupling%runoff_lnd(ix) = datar8(i,j)
+                  endif
+                enddo
+              enddo
+              if (mpp_pe() == mpp_root_pe() .and. debug)  print *,'fv3 assign_import: get surface runoff from land'
+            endif
+          endif
+
+! get subsurface runoff in soil (if cpllnd=true and cpllnd2atm=true)
+!------------------------------------------------
+          fldname = 'inst_subsurface_runoff_rate_lnd'
+          if (trim(impfield_name) == trim(fldname)) then
+            findex  = queryImportFields(fldname)
+            if (importFieldsValid(findex) .and. GFS_control%cpllnd .and. GFS_control%cpllnd2atm) then
+!$omp parallel do default(shared) private(i,j,nb,ix)
+              do j=jsc,jec
+                do i=isc,iec
+                  nb = Atm_block%blkno(i,j)
+                  ix = Atm_block%ixp(i,j)
+                  if (GFS_data(nb)%Sfcprop%landfrac(ix) > zero) then
+                    GFS_data(nb)%Coupling%drain_lnd(ix) = datar8(i,j)
+                  endif
+                enddo
+              enddo
+              if (mpp_pe() == mpp_root_pe() .and. debug)  print *,'fv3 assign_import: get subsurface runoff from land'
+            endif
+          endif
+
+! get momentum exchange coefficient (if cpllnd=true and cpllnd2atm=true)
+!------------------------------------------------
+          fldname = 'inst_drag_wind_speed_for_momentum'
+          if (trim(impfield_name) == trim(fldname)) then
+            findex  = queryImportFields(fldname)
+            if (importFieldsValid(findex) .and. GFS_control%cpllnd .and. GFS_control%cpllnd2atm) then
+!$omp parallel do default(shared) private(i,j,nb,ix)
+              do j=jsc,jec
+                do i=isc,iec
+                  nb = Atm_block%blkno(i,j)
+                  ix = Atm_block%ixp(i,j)
+                  if (GFS_data(nb)%Sfcprop%landfrac(ix) > zero) then
+                    GFS_data(nb)%Coupling%cmm_lnd(ix) = datar8(i,j)
+                  endif
+                enddo
+              enddo
+              if (mpp_pe() == mpp_root_pe() .and. debug)  print *,'fv3 assign_import: get drag wind speed for momentum from land'
+            endif
+          endif
+
+! get thermal exchange coefficient (if cpllnd=true and cpllnd2atm=true)
+!------------------------------------------------
+          fldname = 'inst_drag_mass_flux_for_heat_and_moisture'
+          if (trim(impfield_name) == trim(fldname)) then
+            findex  = queryImportFields(fldname)
+            if (importFieldsValid(findex) .and. GFS_control%cpllnd .and. GFS_control%cpllnd2atm) then
+!$omp parallel do default(shared) private(i,j,nb,ix)
+              do j=jsc,jec
+                do i=isc,iec
+                  nb = Atm_block%blkno(i,j)
+                  ix = Atm_block%ixp(i,j)
+                  if (GFS_data(nb)%Sfcprop%landfrac(ix) > zero) then
+                    GFS_data(nb)%Coupling%chh_lnd(ix) = datar8(i,j)
+                  endif
+                enddo
+              enddo
+              if (mpp_pe() == mpp_root_pe() .and. debug)  print *,'fv3 assign_import: get thermal exchange coefficient form land'
+            endif
+          endif
+
+! get function of surface roughness length and green vegetation fraction (if cpllnd=true and cpllnd2atm=true)
+!------------------------------------------------
+          fldname = 'inst_func_of_roughness_length_and_vfrac'
+          if (trim(impfield_name) == trim(fldname)) then
+            findex  = queryImportFields(fldname)
+            if (importFieldsValid(findex) .and. GFS_control%cpllnd .and. GFS_control%cpllnd2atm) then
+!$omp parallel do default(shared) private(i,j,nb,ix)
+              do j=jsc,jec
+                do i=isc,iec
+                  nb = Atm_block%blkno(i,j)
+                  ix = Atm_block%ixp(i,j)
+                  if (GFS_data(nb)%Sfcprop%landfrac(ix) > zero) then
+                    GFS_data(nb)%Coupling%zvfun_lnd(ix) = datar8(i,j)
+                  endif
+                enddo
+              enddo
+              if (mpp_pe() == mpp_root_pe() .and. debug)  print *,'fv3 assign_import: get func. of roughness length and vfrac form land'
+            endif
+          endif
+
         endif ! if (datar8(isc,jsc) > -99999.0) then
 
 !-------------------------------------------------------
@@ -3072,12 +3332,6 @@ subroutine setup_exportdata(rc)
             ! bottom layer meridional wind (v)
             case('inst_merid_wind_height_lowest')
               call block_data_copy_or_fill(datar82d, DYCORE_data(nb)%coupling%v_bot, zeror8, Atm_block, nb, rc=localrc)
-            ! bottom layer zonal wind (u) from physics
-            case('inst_zonal_wind_height_lowest_from_phys')
-              call block_data_copy_or_fill(datar82d, GFS_data(nb)%Statein%ugrs, 1, zeror8, Atm_block, nb, rc=localrc)
-            ! bottom layer meridional wind (v) from physics
-            case('inst_merid_wind_height_lowest_from_phys')
-              call block_data_copy_or_fill(datar82d, GFS_data(nb)%Statein%vgrs, 1, zeror8, Atm_block, nb, rc=localrc)
             ! surface friction velocity
             case('surface_friction_velocity')
               call block_data_copy_or_fill(datar82d, GFS_data(nb)%Sfcprop%uustar, zeror8, Atm_block, nb, rc=localrc)

diff --git a/ccpp/config/ccpp_prebuild_config.py b/ccpp/config/ccpp_prebuild_config.py
@@ -192,6 +192,7 @@
     'physics/physics/SFC_Layer/UFS/sfc_nst_post.f90',
     'physics/physics/SFC_Models/Land/RUC/lsm_ruc.F90',
     'physics/physics/SFC_Models/SeaIce/CICE/sfc_cice.f',
+    'physics/physics/SFC_Models/Land/sfc_land.F90',
     'physics/physics/SFC_Models/Land/Noah/lsm_noah.f',
     'physics/physics/SFC_Models/Land/Noahmp/noahmpdrv.F90',
     'physics/physics/SFC_Models/Lake/Flake/flake_driver.F90',
+5 −15		driver/fvGFS/atmosphere.F90
+6 −1		model/fv_arrays.F90
+21 −1		model/fv_control.F90
+3 −13		model/molecular_diffusion.F90
+7 −17		model/multi_gases.F90
+6 −2		tools/fv_grid_tools.F90
+3 −3		tools/fv_iau_mod.F90
+0 −2		tools/fv_restart.F90
+46 −13		tools/module_diag_hailcast.F90
+1 −1		tools/test_cases.F90