merge to head of escomp

.github/workflows/test.yaml

@@ -0,0 +1,18 @@
+name: build
+
+on:
+  push:
+  pull_request:
+    types: [opened, reopened]
+
+jobs:
+  test_micm_api:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        submodules: recursive
+    - name: build Docker image
+      run: docker build -t musica -f test/docker/Dockerfile.musica .
+    - name: run tests in container
+      run: docker run --name test-container -t musica bash -c 'ctest'

doc/ChangeLog

@@ -1,3 +1,56 @@
+===============================================================
+
+Tag name:atmos_phys0_02_001
+Originator(s): boulderdaze
+Date: 29 Jan 2024
+One-line Summary: Update MICM wrapper for species unit conversions
+Github PR URL: https://github.com/ESCOMP/atmospheric_physics/pull/78
+
+Purpose of changes (include the issue number and title text for each relevant GitHub issue):
+
+The main purpose of this PR is to add unit conversion functions for species concentrations
+to convert CAM-SIMA units (kg kg-1) to MICM units (mol m-3) and vise versa.
+A github action has also been added to test the new MICM-CCPP interface.
+
+This PR fixes the following NCAR/atmospheric_physics Github issues:
+
+#73 -> Update MICM wrapper for species unit conversions
+
+Code reviewed by: mattldawson, nusbaume, K20shores, peverwhee
+
+List all existing files that have been added (A), modified (M), or deleted (D),
+and describe the changes:
+
+M       musica/micm/micm.F90
+  - Added unit conversion functions for species concentrations
+M       musica/micm/micm.meta
+  - Updated the list of the entries that are added
+M       suite_musica.xml
+  - Updated the xml to add dry air density scheme
+M       utilities/state_converters.meta
+  - Updated the standard name of dry air density
+A       .github/workflows/test.yaml
+  - Added github action to automate testing
+A       test/.dockerignore
+A       test/CMakeLists.txt
+A       test/cmake/SetDefaults.cmake
+A       test/docker/Dockerfile.musica
+A       test/include/ccpp_kinds.F90
+A       test/musica/micm/CMakeLists.txt
+A       test/musica/micm/test_micm_api.F90
+  - Added docker, cmake and test files to test the new MICM-CCPP interface
+A       test/musica/micm/configs/chapman/config.json
+A       test/musica/micm/configs/chapman/reactions.json
+A       test/musica/micm/configs/chapman/species.json
+  - Moved a set of the MICM configuration to be underneath the test directory
+D       musica/micm/configs/chapman/config.json
+D       musica/micm/configs/chapman/reactions.json
+D       musica/micm/configs/chapman/species.json
+  - Deleted a set of the MICM configuration
+
+List and Describe any test failures: No known test failures.
+
+Summarize any changes to answers: Answer changes when MICM is used.
 
 ===============================================================
 

doc/NamesNotInDictionary.txt

@@ -1,7 +1,7 @@
 
 #######################
 Date/time of when script was run:
-2024-01-11 14:34:07.485725
+2024-02-07 10:29:13.957426
 #######################
 
 Non-dictionary standard names found in the following metadata files:
@@ -16,53 +16,52 @@ Non-dictionary standard names found in the following metadata files:
 
 ./atmospheric_physics/kessler/kessler.meta
 
-    - composition_dependent_specific_heat_of_dry_air_at_constant_pressure
-    - rain_mixing_ratio_wrt_dry_air
     - density_of_dry_air
+    - rain_mixing_ratio_wrt_dry_air
     - scheme_name
+    - composition_dependent_specific_heat_of_dry_air_at_constant_pressure
 
 --------------------------
 
 ./atmospheric_physics/utilities/geopotential_temp.meta
 
-    - ccpp_constituent_properties
-    - number_of_ccpp_constituents
-    - ccpp_constituents
-    - lagrangian_vertical_coordinate
     - geopotential_height_wrt_surface_at_interface
+    - ccpp_constituents
+    - number_of_ccpp_constituents
+    - ccpp_constituent_properties
 
 --------------------------
 
 ./atmospheric_physics/utilities/state_converters.meta
 
+    - dry_air_density
+    - composition_dependent_specific_heat_of_dry_air_at_constant_pressure
     - cloud_liquid_water_mixing_ratio_wrt_moist_air_and_condensed_water
-    - rain_mixing_ratio_wrt_moist_air_and_condensed_water
     - rain_mixing_ratio_wrt_dry_air
-    - composition_dependent_specific_heat_of_dry_air_at_constant_pressure
-    - density_of_dry_air
+    - rain_mixing_ratio_wrt_moist_air_and_condensed_water
 
 --------------------------
 
 ./atmospheric_physics/utilities/qneg.meta
 
+    - ccpp_constituent_minimum_values
+    - ccpp_constituents
+    - log_output_unit
+    - number_of_ccpp_constituents
     - ccpp_constituent_properties
-    - flag_for_mpi_root
     - print_qneg_warn
-    - number_of_ccpp_constituents
+    - flag_for_mpi_root
     - scheme_name
-    - log_output_unit
-    - ccpp_constituents
-    - ccpp_constituent_minimum_values
 
 --------------------------
 
 ./atmospheric_physics/utilities/physics_tendency_updaters.meta
 
-    - heating_rate
-    - tendency_of_northward_wind_due_to_model_physics
-    - tendency_of_eastward_wind_due_to_model_physics
     - tendency_of_eastward_wind
     - tendency_of_northward_wind
+    - tendency_of_eastward_wind_due_to_model_physics
+    - tendency_of_northward_wind_due_to_model_physics
+    - heating_rate
     - composition_dependent_specific_heat_of_dry_air_at_constant_pressure
 
 --------------------------
@@ -75,20 +74,21 @@ Non-dictionary standard names found in the following metadata files:
 
 ./atmospheric_physics/held_suarez/held_suarez_1994.meta
 
-    - heating_rate
+    - tendency_of_eastward_wind
+    - composition_dependent_specific_heat_of_dry_air_at_constant_pressure
     - reference_pressure_in_atmosphere_layer_normalized_by_reference_pressure
     - scheme_name
+    - heating_rate
     - composition_dependent_ratio_of_dry_air_gas_constant_to_specific_heat_of_dry_air_at_constant_pressure
-    - tendency_of_eastward_wind
-    - composition_dependent_specific_heat_of_dry_air_at_constant_pressure
     - tendency_of_northward_wind
 
 --------------------------
 
 ./atmospheric_physics/musica/micm/micm.meta
 
+    - ccpp_constituent_properties
     - log_output_unit
+    - dry_air_density
     - ccpp_constituents
-    - number_of_ccpp_constituents
 
 #######################