set up micm api test

.github/workflows/test.yaml

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+name: build
+
+on: [push, pull_request]
+
+jobs:
+  build_test_connections:
+    runs-on: ubuntu-latest
+    if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name
+    steps:
+    - uses: actions/checkout@v3
+      with:
+        submodules: recursive
+    - name: build Docker image
+      run: docker build -t musica -f docker/Dockerfile.musica .
+    - name: run tests in container
+      run: docker run --name test-container -t musica bash -c 'ctest'

CMakeLists.txt

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+cmake_minimum_required(VERSION 3.21)
+
+project(
+  atmosphericphysics
+  VERSION 0.0.0
+  LANGUAGES Fortran C CXX
+)
+
+set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH};${CMAKE_CURRENT_LIST_DIR}/cmake)
+set(CMAKE_USER_MAKE_RULES_OVERRIDE ${CMAKE_MODULE_PATH}/SetDefaults.cmake)
+set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR})
+
+# --------------------------------------------------------------------------------
+# NOTE: If 'ENABLE_MICM_TEST' on, this is not a stand-alone cmake project anymore. 
+#       MICM CCPP wrapper needs MUSICA library and ccpp-framework/src.
+#       To 'ENABLE_MICM_TEST', you either build a cmake project through
+#       'docker/Dockerfile.musica' or follow the build instructions in the file.
+#       The following '$ENV' variables are set by the docker file.
+# --------------------------------------------------------------------------------
+option(ENABLE_MICM_TEST "Build the micm test" OFF)
+
+if (ENABLE_MICM_TEST)
+  set(MUSICA_VERSION $ENV{MUSICA_VERSION})
+  set(MICM_SRC_PATH ${CMAKE_SOURCE_DIR}/musica/micm)
+  set(CCPP_SRC_PATH ${CMAKE_SOURCE_DIR}/$ENV{CCPP_SRC_PATH})
+  set(CCPP_TEST_SRC_PATH ${CMAKE_SOURCE_DIR}/test/include)
+
+  add_subdirectory(test/musica/micm)
+
+  enable_testing()
+endif()

cmake/SetDefaults.cmake

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+# Overwrite the init values choosen by CMake
+if (CMAKE_Fortran_COMPILER_ID MATCHES "GNU")
+  set(CMAKE_Fortran_FLAGS_DEBUG_INIT "-g")
+endif()

cmake/atmosphericphysicsConfig.cmake.in

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+@PACKAGE_INIT@
+
+include("${CMAKE_CURRENT_LIST_DIR}/@PROJECT_NAME@_Exports.cmake")
+
+check_required_components("@PROJECT_NAME@")

cmake/cmake_uninstall.cmake.in

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+# https://gitlab.kitware.com/cmake/community/-/wikis/FAQ#can-i-do-make-uninstall-with-cmake
+
+if(NOT EXISTS "@CMAKE_BINARY_DIR@/install_manifest.txt")
+  message(FATAL_ERROR "Cannot find install manifest: @CMAKE_BINARY_DIR@/install_manifest.txt")
+endif()
+
+file(READ "@CMAKE_BINARY_DIR@/install_manifest.txt" files)
+string(REGEX REPLACE "\n" ";" files "${files}")
+foreach(file ${files})
+  message(STATUS "Uninstalling $ENV{DESTDIR}${file}")
+  if(IS_SYMLINK "$ENV{DESTDIR}${file}" OR EXISTS "$ENV{DESTDIR}${file}")
+    exec_program(
+      "@CMAKE_COMMAND@" ARGS "-E remove \"$ENV{DESTDIR}${file}\""
+      OUTPUT_VARIABLE rm_out
+      RETURN_VALUE rm_retval
+      )
+    if(NOT "${rm_retval}" STREQUAL 0)
+      message(FATAL_ERROR "Problem when removing $ENV{DESTDIR}${file}")
+    endif()
+  else(IS_SYMLINK "$ENV{DESTDIR}${file}" OR EXISTS "$ENV{DESTDIR}${file}")
+    message(STATUS "File $ENV{DESTDIR}${file} does not exist.")
+  endif()
+endforeach()
+
+set(uninstall_dirs "@INSTALL_PREFIX@;@cmake_config_install_location@")
+
+foreach(dir IN LISTS uninstall_dirs)
+  message(STATUS "Uninstalling ${dir}")
+  exec_program(
+    "@CMAKE_COMMAND@" ARGS "-E remove_directory ${dir}"
+    OUTPUT_VARIABLE rm_out
+    RETURN_VALUE rm_retval
+    )
+  if(NOT "${rm_retval}" STREQUAL 0)
+    message(FATAL_ERROR "Problem when removing ${dir}")
+  endif()
+endforeach()

docker/Dockerfile.musica

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+FROM ubuntu:22.04
+
+RUN apt update \
+    && apt -y install \
+    cmake \
+    cmake-curses-gui \
+    curl \
+    libcurl4-openssl-dev \
+    libhdf5-dev \
+    m4 \
+    nlohmann-json3-dev \
+    vim \
+    zlib1g-dev \
+    git \
+    lcov \
+    make \
+    libnetcdff-dev \
+    valgrind \
+    gcc \
+    gfortran \
+    g++ \
+    tree \
+    && apt clean
+
+ENV FC=gfortran
+ENV FFLAGS="-I/usr/include/"
+
+RUN curl -LO https://github.com/jacobwilliams/json-fortran/archive/8.2.0.tar.gz \
+    && tar -zxvf 8.2.0.tar.gz \
+    && cd json-fortran-8.2.0 \
+    && mkdir build \
+    && cd build \
+    && cmake -D SKIP_DOC_GEN:BOOL=TRUE .. \
+    && make install
+
+ENV JSON_FORTRAN_HOME="/usr/local/jsonfortran-gnu-8.2.0"
+
+# Install MUSICA (MUSICA-C)
+RUN git clone --depth 1 https://github.com/NCAR/musica.git
+RUN cd musica \
+    && cmake \
+        -S . \
+        -B build \
+        -D USE_MUSICA=ON \
+        -D USE_MUSICA_FORTRAN=OFF \
+        -D MAKE_MUSICA_FORTRAN_INSTALLABLE=ON \
+        -D ENABLE_TESTS=OFF \
+        -D ENABLE_TUVX=OFF \
+    && cd build \
+    && make install -j 8
+
+RUN ln -s /usr/local/musica-0.5.0/lib/libmusica.a /usr/local/lib/libmusica.a
+ENV MUSICA_VERSION="0.5.0"
+
+COPY . atmospheric_physics
+
+RUN cd atmospheric_physics \
+    && mkdir lib \
+    && cd lib \
+    && git clone -b add_const_interface --depth 1 https://github.com/peverwhee/ccpp-framework.git
+ENV CCPP_SRC_PATH="lib/ccpp-framework/src"
+
+RUN cd atmospheric_physics \
+    && cmake -S. \
+             -B build \
+             -D ENABLE_MICM_TEST=ON \
+    && cmake --build ./build
+
+RUN cd atmospheric_physics \
+    && cp -r test/musica/micm/configs/chapman ./build/chapman
+
+WORKDIR atmospheric_physics/build

test/include/ccpp_kinds.F90

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+module ccpp_kinds
+
+  use ISO_FORTRAN_ENV, only: kind_phys => REAL64
+
+  implicit none
+  private
+
+  public kind_phys
+
+  end module ccpp_kinds

test/musica/micm/CMakeLists.txt

@@ -0,0 +1,54 @@
+find_package(PkgConfig REQUIRED)
+pkg_check_modules(netcdff IMPORTED_TARGET REQUIRED netcdf-fortran)
+
+find_package(musica ${MUSICA_VERSION} REQUIRED)
+message(STATUS "  MUSICA version ${MUSICA_VERSION}")
+
+include(FetchContent)
+
+FetchContent_Declare(musica
+  GIT_REPOSITORY https://github.com/NCAR/musica.git
+  GIT_TAG        main
+)
+
+set(USE_MUSICA OFF)
+set(USE_MUSICA_FORTRAN ON)
+set(MAKE_MUSICA_FORTRAN_INSTALLABLE OFF)
+set(ENABLE_TUVX OFF)
+set(ENABLE_TESTS OFF)
+
+FetchContent_MakeAvailable(musica)
+
+# ---------------------------------------------------------
+# Create a test for MICM CCPP wrapper
+# ---------------------------------------------------------
+
+add_executable(test_micm_api test_micm_api.F90)
+
+target_sources(test_micm_api
+  PUBLIC
+    ${MICM_SRC_PATH}/micm.F90
+    ${CCPP_SRC_PATH}/ccpp_api.F90
+    ${CCPP_SRC_PATH}/ccpp_constituent_prop_mod.F90
+    ${CCPP_SRC_PATH}/ccpp_hash_table.F90
+    ${CCPP_SRC_PATH}/ccpp_hashable.F90
+    ${CCPP_SRC_PATH}/ccpp_types.F90
+    ${CCPP_TEST_SRC_PATH}/ccpp_kinds.F90
+)
+
+target_link_libraries(test_micm_api
+  PRIVATE
+    musica::musica-fortran
+)
+
+set_target_properties(test_micm_api
+  PROPERTIES
+  LINKER_LANGUAGE Fortran)
+
+include(CTest)
+
+add_test(
+  NAME test_micm_api
+  COMMAND $<TARGET_FILE:test_micm_api>
+  WORKING_DIRECTORY ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}
+)

test/musica/micm/test_micm_api.F90

@@ -0,0 +1,122 @@
+subroutine test_micm_ccpp_api()
+  use iso_c_binding
+  use micm
+  use ccpp_kinds,                only: kind_phys
+  use ccpp_constituent_prop_mod, only: ccpp_constituent_prop_ptr_t
+  use ccpp_constituent_prop_mod, only: ccpp_constituent_properties_t
+
+  implicit none
+
+  real(kind_phys)                                     :: time_step             ! s
+  real(kind_phys),                   dimension(2,1)   :: temperature           ! K
+  real(kind_phys),                   dimension(2,1)   :: pressure              ! Pa
+  real(kind_phys),                   dimension(2,1)   :: dry_air_density       ! kg m-3
+  type(ccpp_constituent_prop_ptr_t), dimension(5)     :: constituent_props_ptr
+  real(kind_phys),                   dimension(5)     :: molar_mass_arr        ! kg mol-1
+  real(kind_phys),                   dimension(2,1,5) :: constituents          ! kg kg-1
+  integer                                             :: iulog
+  integer                                             :: errcode
+  character(len=512)                                  :: errmsg
+
+  ! local variables
+  type(ccpp_constituent_properties_t), dimension(5), target   :: constituent_props
+  type(ccpp_constituent_properties_t), pointer                :: const_prop
+  integer                                                     :: i
+
+  time_step = 60._kind_phys
+
+  temperature(1,1) = 206.6374207_kind_phys
+  temperature(2,1) = 206.6374207_kind_phys
+
+  pressure(1,1) = 6152.049805_kind_phys
+  pressure(2,1) = 6152.049805_kind_phys
+
+  dry_air_density(1,1) = 3.580_kind_phys
+  dry_air_density(2,1) = 3.580_kind_phys
+
+  molar_mass_arr = (/ 200._kind_phys, 200._kind_phys, 200._kind_phys, 200._kind_phys, 200._kind_phys /)
+
+  constituents(1,1,1:5) = (/ 0.75_kind_phys, 8.1e-6_kind_phys, 2.42e-17_kind_phys, &
+                          1.15e-5_kind_phys, 6.61e-9_kind_phys /)
+  constituents(2,1,1:5) = (/ 0.75_kind_phys, 8.1e-6_kind_phys, 2.42e-17_kind_phys, &
+                          1.15e-5_kind_phys, 6.61e-9_kind_phys /)
+
+  iulog = 6
+
+  call constituent_props(1)%instantiate( &
+    std_name="water_vapor_mixing_ratio",      &
+    long_name="water_vapor_mixing_ratio",     &
+    units="kg kg-1",                          &
+    default_value=0._kind_phys,               &
+    vertical_dim="vertical_layer_dimension",  &
+    advected=.true.,                          &
+    molar_mass=molar_mass_arr(1),             &
+    errcode=errcode, errmsg=errmsg)
+  call constituent_props(2)%instantiate( &
+    std_name="water_vapor_mixing_ratio_a",    &
+    long_name="water_vapor_mixing_ratio",     &
+    units="kg kg-1",                          &
+    default_value=0._kind_phys,               &
+    vertical_dim="vertical_layer_dimension",  &
+    advected=.true.,                          &
+    molar_mass=molar_mass_arr(2),             &
+    errcode=errcode, errmsg=errmsg)
+  call constituent_props(3)%instantiate( &
+    std_name="water_vapor_mixing_ratio_b",    &
+    long_name="water_vapor_mixing_ratio",     &
+    units="kg kg-1",                          &
+    default_value=0._kind_phys,               &
+    vertical_dim="vertical_layer_dimension",  &
+    advected=.true.,                          &
+    molar_mass=molar_mass_arr(3),             &
+    errcode=errcode, errmsg=errmsg)
+  call constituent_props(4)%instantiate( &
+    std_name="water_vapor_mixing_ratio_c",    &
+    long_name="water_vapor_mixing_ratio",     &
+    units="kg kg-1",                          &
+    default_value=0._kind_phys,               &
+    vertical_dim="vertical_layer_dimension",  &
+    advected=.true.,                          &
+    molar_mass=molar_mass_arr(4),             &
+    errcode=errcode, errmsg=errmsg)
+  call constituent_props(5)%instantiate( &
+    std_name="water_vapor_mixing_ratio_d",    &
+    long_name="water_vapor_mixing_ratio",     &
+    units="kg kg-1",                          &
+    default_value=0._kind_phys,               &
+    vertical_dim="vertical_layer_dimension",  &
+    advected=.true.,                          &
+    molar_mass=molar_mass_arr(5),             &
+    errcode=errcode, errmsg=errmsg)
+
+  do i = 1, 5
+    const_prop => constituent_props(i)
+    call constituent_props_ptr(i)%set(const_prop, errcode, errmsg)
+  end do
+
+  call micm_init("chapman", iulog, errcode, errmsg)
+
+  write(*,*) "    -- Initial time_step", time_step
+  write(*,*) "    -- Initial temp", temperature
+  write(*,*) "    -- Initial pressure", pressure
+  write(*,*) "    -- Initial concentrations", constituents
+
+  if (errcode == 0) then
+    call micm_run(time_step, temperature, pressure, dry_air_density, constituent_props_ptr, &
+                constituents, iulog, errcode, errmsg)
+
+    write(*,*) "    -- After solving, conentrations", constituents
+  else
+    write(*,*) "    -- Exiting due to the error in creating solver"
+    stop 3
+  endif
+
+  write(*,*) "    -- Completed solving"
+  call micm_final(iulog, errcode, errmsg)
+
+end subroutine test_micm_ccpp_api
+
+program run_test_micm_ccpp
+implicit none
+  call test_micm_ccpp_api()
+end program