merge dev

.github/workflows/fortran_unit_tests.yml

@@ -0,0 +1,73 @@
+name: Fortran Unit Tests
+
+on:
+  push:
+    branches:
+      - development
+      - main
+  pull_request:
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref || github.run_id }}
+  cancel-in-progress: true
+
+jobs:
+  gcc-toolchain:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        version: [12, 13, 14]
+    env:
+      CC: gcc-${{ matrix.version }}
+      CXX: g++-${{ matrix.version }}
+      FC: gfortran-${{ matrix.version }}
+    steps:
+      - name: Checkout cam-sima
+        uses: actions/checkout@v4
+
+      - name: Build pFUnit
+        run: |
+          git clone --depth 1 --branch v4.10.0 https://github.com/Goddard-Fortran-Ecosystem/pFUnit.git
+          cd pFUnit
+          cmake -B./build -S.
+          cd build
+          make install
+
+      - name: Build cam-sima
+        run: |
+          cmake \
+            -DCMAKE_PREFIX_PATH=/home/runner/work/CAM-SIMA/CAM-SIMA/pFUnit/build/installed \
+            -DCAM_SIMA_ENABLE_CODE_COVERAGE=ON \
+            -B./build \
+            -S./test/unit/fortran
+          cd build
+          make
+      
+      - name: Run fortran unit tests
+        run: |
+          cd build && ctest -V --output-on-failure --output-junit test_results.xml
+
+      - name: Upload unit test results
+        uses: actions/upload-artifact@v4
+        with:
+          name: unit-test-results-${{ env.FC }}
+          path: build/test_results.xml
+
+      - name: Setup GCov
+        run: |
+          python3 -m venv venv
+          source venv/bin/activate
+          pip3 install gcovr
+
+      - name: Run Gcov
+        run: |
+          source venv/bin/activate
+          cd build
+          gcovr --gcov-executable gcov-${{ matrix.version }} -r .. --filter '\.\./src' --html cam_sima_code_coverage.html --txt
+
+      - name: Upload code coverage results
+        uses: actions/upload-artifact@v4
+        with:
+          name: code-coverage-results-${{ env.FC }}
+          path: build/cam_sima_code_coverage.html

.github/workflows/python_unit_tests.yml

@@ -1,6 +1,7 @@
 name: Python Unit Tests
 
 on:
+  workflow_dispatch:
   pull_request:
     types: [opened, synchronize, reopened]
   push:
@@ -16,12 +17,12 @@ jobs:
   #a PR is either opened or synced (i.e. additional commits are pushed
   #to branch involved in PR).
   python_unit_tests:
-    if: github.event_name == 'pull_request' || github.repository == 'ESCOMP/CAM-SIMA'
+    if: github.event_name == 'pull_request' || github.repository == 'ESCOMP/CAM-SIMA' || github.event_name == 'workflow_dispatch'
     runs-on: ubuntu-latest
     strategy:
       matrix:
         #All of these python versions will be used to run tests:
-        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12", "3.13"]
       fail-fast: false
     steps:
     # Acquire github action routines:
@@ -56,4 +57,4 @@ jobs:
         pytest src/data --doctest-modules
 
         # Run all python unit tests:
-        pytest test/unit
+        pytest test/unit/python

.gitignore

@@ -5,7 +5,7 @@ buildnmlc
 # Ignore test output
 test/include/*.mod
 test/include/*.o
-test/unit/tmp
+test/unit/python/tmp
 test/system/*.log
 test/system/cime-tests.o*
 test_driver_*.sh

.gitmodules

@@ -20,7 +20,7 @@
 [submodule "ncar-physics"]
         path          = src/physics/ncar_ccpp
 	url           = https://github.com/ESCOMP/atmospheric_physics
-	fxtag         = 60b71f3fd9f10b362caf64afffce12de10854d4d
+	fxtag         = 252b500a93c89f36ece7d8ba08fd8eb025279eaa
         fxrequired    = AlwaysRequired
         fxDONOTUSEurl = https://github.com/ESCOMP/atmospheric_physics
 [submodule "ccs_config"]

cime_config/atm_in_paramgen.py

@@ -1495,11 +1495,16 @@ def write(self, output_path):
                 # Write all variables within that group (sorted alphabetically):
                 for var in sorted(self._data[nml_group], key=var_sort_key):
                     #Extract variable value(s):
-                    val = self._data[nml_group][var]["values"].strip()
+                    val = self._data[nml_group][var]["values"]
 
-                    #If no value is set then move to the next variable:
+                    #Raise error if no value found:
                     if val is None:
-                        continue
+                        emsg = f"Namelist entry '{var}' is missing a "
+                        emsg += "valid/default 'value' element."
+                        raise AtmInParamGenError(emsg)
+                    else:
+                        #If value found then strip white space:
+                        val = val.strip()
                     #End if
 
                     #Extract variable type:

cime_config/buildlib

@@ -105,7 +105,8 @@ def _build_cam():
                  os.path.join(atm_root, "src", "history", "buffers", "src"),
                  os.path.join(atm_root, "src", "history", "buffers", "src", "hash"),
                  os.path.join(atm_root, "src", "history", "buffers", "src", "util"),
-                 os.path.join(atm_root, "src", "utils")]
+                 os.path.join(atm_root, "src", "utils"),
+                 os.path.join(atm_root, "src", "core_utils")]
         for path in phys_dirs:
             if path not in paths:
                 paths.append(path)

cime_config/cam_autogen.py

@@ -132,7 +132,7 @@ def _find_scheme_source(source_dirs, metadata_file_name):
     doctests:
 
     1.  Check that the function can correctly find source and namelist files:
-    >>> _find_scheme_source([os.path.join(_CAM_ROOT_DIR, "test", "unit", "sample_files", \
+    >>> _find_scheme_source([os.path.join(_CAM_ROOT_DIR, "test", "unit", "python", "sample_files", \
                             "autogen_files")], "two_scheme_banana") # doctest: +ELLIPSIS
     ('...two_scheme_banana.F90', '...two_scheme_banana_namelist.xml')
 

cime_config/testdefs/testlist_cam.xml

@@ -43,6 +43,15 @@
       <option name="comment">Test for Moist Held-Suarez (TJ2016) physics (physics_after_coupler group)</option>
     </options>
   </test>
+  <test compset="FPHYStest" grid="ne3pg3_ne3pg3_mg37" name="SMS_Ln2" testmods="cam/outfrq_zm_derecho">
+    <machines>
+      <machine name="derecho" compiler="gnu" category="aux_sima"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:10:00</option>
+      <option name="comment">Test for Zhang McFarlane physics</option>
+    </options>
+  </test>
 
   <!-- Derecho dycore tests -->
   <test compset="FKESSLER" grid="mpasa480_mpasa480" name="SMS_Ln9" testmods="cam/outfrq_kessler_mpas_derecho">

cime_config/testdefs/testmods_dirs/cam/outfrq_kessler_derecho/shell_commands

@@ -1 +1 @@
- ./xmlchange CAM_CONFIG_OPTS="--dyn none --physics-suites kessler"
+ ./xmlchange CAM_CONFIG_OPTS="--dyn none --physics-suites kessler_test"

cime_config/testdefs/testmods_dirs/cam/outfrq_zm_derecho/shell_commands

@@ -0,0 +1 @@
+ ./xmlchange CAM_CONFIG_OPTS="--dyn none --physics-suites zhang_mcfarlane"

cime_config/testdefs/testmods_dirs/cam/outfrq_zm_derecho/user_nl_cam

@@ -0,0 +1,16 @@
+ncdata='/glade/campaign/cesm/community/amwg/sima_baselines/cam_sima_test_snapshots/cam_ne3pg3_ZM_snapshot_derecho_gnu_before_c20250116.nc'
+ncdata_check='/glade/campaign/cesm/community/amwg/sima_baselines/cam_sima_test_snapshots/cam_ne3pg3_ZM_snapshot_derecho_gnu_after_c20250116.nc'
+debug_output=0
+pver=32
+zmconv_momcd=.7D0
+zmconv_momcu=.7D0
+zmconv_num_cin=1
+hist_add_inst_fields;h1: ZMDT, ZMDQ, CAPE, FREQZM, CMFMC_DP, ZMMU, ZMMD, DLFZM, PCONVT, PCONVB, ZMFLXPRC, ZMFLXSNW
+hist_add_inst_fields;h1: ZMNTPRPD, ZMNTSNPD, ZMEIHEAT, PRECCDZM, PRECZ
+hist_add_inst_fields;h1: ZMUPGU, ZMUPGD, ZMVPGU, ZMVPGD, ZMICUU, ZMICUD, ZMICVU, ZMICVD
+hist_add_inst_fields;h1: EVAPTZM, FZSNTZM, EVSNTZM, EVAPQZM
+hist_add_inst_fields;h1: ZMMTU, ZMMTV, ZMMTT
+hist_add_inst_fields;h1: ZMDLIQ, ZMDICE
+hist_output_frequency;h1: 1*nstep
+hist_precision;h1: REAL64
+hist_max_frames;h1: 1

src/core_utils/CMakeLists.txt

@@ -0,0 +1,9 @@
+set(CORE_UTILS_SRC string_core_utils.F90)
+
+# core_utils is not integrated into the CMake build of any top level
+# project yet and this CMake is for testing purposes only.
+# Making a change to this project's CMake will not impact the build of
+# a parent project at this time.
+add_library(core_utils ${CORE_UTILS_SRC})
+target_include_directories(core_utils PUBLIC ${CMAKE_CURRENT_BINARY_DIR})
+

src/core_utils/string_core_utils.F90

@@ -0,0 +1,162 @@
+module string_core_utils
+
+    implicit none
+    private
+
+    public :: core_to_str                ! Convert integer to left justified string
+    public :: core_int_date_to_yyyymmdd  ! Convert encoded date integer to "yyyy-mm-dd" format
+    public :: core_int_seconds_to_hhmmss ! Convert integer seconds past midnight to "hh:mm:ss" format
+    public :: core_stringify             ! Convert one or more values of any intrinsic data types to a character string for pretty printing
+
+CONTAINS
+
+    character(len=10) pure function core_to_str(n)
+        ! return default integer as a left justified string
+
+        integer, intent(in) :: n
+
+        write(core_to_str,'(i0)') n
+
+    end function core_to_str
+
+    character(len=10) pure function core_int_date_to_yyyymmdd (date)
+        ! Undefined behavior if date <= 0
+
+        ! Input arguments
+        integer, intent(in) :: date
+
+        ! Local variables
+        integer :: year    ! year of yyyy-mm-dd
+        integer :: month   ! month of yyyy-mm-dd
+        integer :: day     ! day of yyyy-mm-dd
+
+        year  = date / 10000
+        month = (date - year*10000) / 100
+        day   = date - year*10000 - month*100
+
+        write(core_int_date_to_yyyymmdd, '(i4.4,A,i2.2,A,i2.2)') &
+                                           year,'-',month,'-',day
+
+    end function core_int_date_to_yyyymmdd
+
+    character(len=8) pure function core_int_seconds_to_hhmmss (seconds)
+        ! Undefined behavior if seconds outside [0, 86400]
+
+        ! Input arguments
+        integer, intent(in) :: seconds
+
+        ! Local variables
+        integer :: hours     ! hours of hh:mm:ss
+        integer :: minutes   ! minutes of hh:mm:ss
+        integer :: secs      ! seconds of hh:mm:ss
+
+        hours   = seconds / 3600
+        minutes = (seconds - hours*3600) / 60
+        secs    = (seconds - hours*3600 - minutes*60)
+
+        write(core_int_seconds_to_hhmmss,'(i2.2,A,i2.2,A,i2.2)') &
+                                        hours,':',minutes,':',secs
+
+    end function core_int_seconds_to_hhmmss
+
+    !> Convert one or more values of any intrinsic data types to a character string for pretty printing.
+    !> If `value` contains more than one element, the elements will be stringified, delimited by `separator`, then concatenated.
+    !> If `value` contains exactly one element, the element will be stringified without using `separator`.
+    !> If `value` contains zero element or is of unsupported data types, an empty character string is produced.
+    !> If `separator` is not supplied, it defaults to `, ` (i.e., a comma and a space).
+    !> (KCW, 2024-02-04)
+    pure function core_stringify(value, separator)
+        use, intrinsic :: iso_fortran_env, only: int32, int64, real32, real64
+
+        class(*), intent(in) :: value(:)
+        character(*), optional, intent(in) :: separator
+        character(:), allocatable :: core_stringify
+
+        integer, parameter :: sizelimit = 1024
+
+        character(:), allocatable :: buffer, delimiter, format
+        integer :: i, n, offset
+
+        if (present(separator)) then
+            delimiter = separator
+        else
+            delimiter = ', '
+        end if
+
+        n = min(size(value), sizelimit)
+
+        if (n == 0) then
+            core_stringify = ''
+            return
+        end if
+
+        select type (value)
+            type is (character(*))
+                allocate(character(len(value) * n + len(delimiter) * (n - 1)) :: buffer)
+
+                buffer(:) = ''
+                offset = 0
+
+                do i = 1, n
+                    if (len(delimiter) > 0 .and. i > 1) then
+                        buffer(offset + 1:offset + len(delimiter)) = delimiter
+                        offset = offset + len(delimiter)
+                    end if
+
+                    if (len_trim(adjustl(value(i))) > 0) then
+                        buffer(offset + 1:offset + len_trim(adjustl(value(i)))) = trim(adjustl(value(i)))
+                        offset = offset + len_trim(adjustl(value(i)))
+                    end if
+                end do
+            type is (integer(int32))
+                allocate(character(11 * n + len(delimiter) * (n - 1)) :: buffer)
+                allocate(character(17 + len(delimiter) + floor(log10(real(n))) + 1) :: format)
+
+                write(format, '(a, i0, 3a)') '(ss, ', n, '(i0, :, "', delimiter, '"))'
+                write(buffer, format) value
+            type is (integer(int64))
+                allocate(character(20 * n + len(delimiter) * (n - 1)) :: buffer)
+                allocate(character(17 + len(delimiter) + floor(log10(real(n))) + 1) :: format)
+
+                write(format, '(a, i0, 3a)') '(ss, ', n, '(i0, :, "', delimiter, '"))'
+                write(buffer, format) value
+            type is (logical)
+                allocate(character(1 * n + len(delimiter) * (n - 1)) :: buffer)
+                allocate(character(13 + len(delimiter) + floor(log10(real(n))) + 1) :: format)
+
+                write(format, '(a, i0, 3a)') '(', n, '(l1, :, "', delimiter, '"))'
+                write(buffer, format) value
+            type is (real(real32))
+                allocate(character(13 * n + len(delimiter) * (n - 1)) :: buffer)
+
+                if (maxval(abs(value)) < 1.0e5_real32) then
+                    allocate(character(20 + len(delimiter) + floor(log10(real(n))) + 1) :: format)
+                    write(format, '(a, i0, 3a)') '(ss, ', n, '(f13.6, :, "', delimiter, '"))'
+                else
+                    allocate(character(23 + len(delimiter) + floor(log10(real(n))) + 1) :: format)
+                    write(format, '(a, i0, 3a)') '(ss, ', n, '(es13.6e2, :, "', delimiter, '"))'
+                end if
+
+                write(buffer, format) value
+            type is (real(real64))
+                allocate(character(13 * n + len(delimiter) * (n - 1)) :: buffer)
+
+                if (maxval(abs(value)) < 1.0e5_real64) then
+                    allocate(character(20 + len(delimiter) + floor(log10(real(n))) + 1) :: format)
+                    write(format, '(a, i0, 3a)') '(ss, ', n, '(f13.6, :, "', delimiter, '"))'
+                else
+                    allocate(character(23 + len(delimiter) + floor(log10(real(n))) + 1) :: format)
+                    write(format, '(a, i0, 3a)') '(ss, ', n, '(es13.6e2, :, "', delimiter, '"))'
+                end if
+
+                write(buffer, format) value
+            class default
+            core_stringify = ''
+                return
+        end select
+
+        core_stringify = trim(buffer)
+
+    end function core_stringify
+
+end module string_core_utils

src/data/physconst.meta

@@ -25,7 +25,7 @@
   dimensions = ()
   protected = True
 [ cpliq ]
-  standard_name = specific_heat_of_liquid_water_at_20c
+  standard_name = specific_heat_of_liquid_water_at_constant_pressure
   long_name = Specific heat of fresh H2O
   units = J kg-1 K-1
   type = real | kind = kind_phys

src/data/ref_pres.meta

@@ -35,7 +35,7 @@
   dimensions = ()
   protected = True
 [ trop_cloud_top_lev ]
-  standard_name = index_of_pressure_at_troposhere_cloud_top
+  standard_name = vertical_layer_index_of_troposphere_cloud_top
   units = index
   type = integer
   dimensions = ()
@@ -65,7 +65,7 @@
   dimensions = ()
   protected = True
 [ nbot_molec ]
-  standard_name = index_of_pressure_at_bottom_of_molecular_diffusion
+  standard_name = vertical_layer_index_at_bottom_of_molecular_diffusion
   units = index
   type = integer
   dimensions = ()