79 allow updates to custom rate constant parameters and mapping by na…

…me (#80)

* converting tests into python unit tests, adding analytical test

* moving configs

* moving one more config

* adding python interfade, stubbing c stuff for fortran

* passing rate constants in solve with python

* trying to fix mac build

* fine I'll add the three

* trying a python setup action

* release builds in docker files

* am annoyed

* thing

* stuff

* using most recent micm version

.github/workflows/mac.yml

@@ -29,6 +29,9 @@ jobs:
     steps:
       - uses: actions/checkout@v3
 
+      - uses: actions/setup-python@v5
+      - run: pip install -r python/requirements.txt
+
       - name: Run Cmake 
         run: cmake -S . -B build -D CMAKE_BUILD_TYPE=${{ matrix.build_type }} -D MUSICA_ENABLE_PYTHON_LIBRARY=ON
 

.github/workflows/ubuntu.yml

@@ -29,6 +29,9 @@ jobs:
     steps:
       - uses: actions/checkout@v3
 
+      - uses: actions/setup-python@v5
+      - run: pip install -r python/requirements.txt
+
       - name: Run Cmake 
         run: cmake -S . -B build -D CMAKE_BUILD_TYPE=${{ matrix.build_type }}  -D MUSICA_ENABLE_PYTHON_LIBRARY=ON
 

.github/workflows/windows.yml

@@ -25,6 +25,9 @@ jobs:
         with:
           platform: ${{ matrix.architecture }}
           version: 12.2.0 # https://github.com/egor-tensin/setup-mingw/issues/14
+
+      - uses: actions/setup-python@v5
+      - run: pip install -r python/requirements.txt
 
       - name: Run Cmake 
         run: cmake -S . -B build -G "MinGW Makefiles"  -D MUSICA_ENABLE_PYTHON_LIBRARY=ON
@@ -48,11 +51,12 @@ jobs:
     - uses: actions/checkout@v3
 
     - name: Set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       if: ${{ matrix.architecture == 'Win32' }}
       with:
         python-version: '3.x'
         architecture: x86
+    - run: pip install -r python/requirements.txt
 
     - name: Run CMake
       run: cmake -S . -B build -G "Visual Studio 16 2019" -A ${{ matrix.architecture }} -DCMAKE_BUILD_TYPE=${{ matrix.build_type }}  -D MUSICA_ENABLE_PYTHON_LIBRARY=ON
@@ -74,12 +78,14 @@ jobs:
     - uses: actions/checkout@v3
 
     - name: Set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       if: ${{ matrix.architecture == 'Win32' }}
       with:
         python-version: '3.x'
         architecture: x86
 
+    - run: pip install -r python/requirements.txt
+
     - name: Run CMake
       run: cmake -S . -B build -G "Visual Studio 17 2022" -A ${{ matrix.architecture }} -DCMAKE_BUILD_TYPE=${{ matrix.build_type }}  -D MUSICA_ENABLE_PYTHON_LIBRARY=ON
 
@@ -97,12 +103,19 @@ jobs:
 
     steps:
       - uses: actions/checkout@v3
+
       - name: Install Clang
         run: curl -fsSL -o LLVM${{ matrix.version }}.exe https://github.com/llvm/llvm-project/releases/download/llvmorg-${{ matrix.version }}.0.0/LLVM-${{ matrix.version }}.0.0-win64.exe ; 7z x LLVM${{ matrix.version }}.exe -y -o"C:/Program Files/LLVM"
+
+      - uses: actions/setup-python@v5
+      - run: pip install -r python/requirements.txt
+
       - name: Run CMake
         run: cmake -S . -B build -DCMAKE_CXX_COMPILER="C:/Program Files/LLVM/bin/clang++.exe" -DCMAKE_C_COMPILER="C:/Program Files/LLVM/bin/clang.exe" -G"MinGW Makefiles" -D MUSICA_ENABLE_PYTHON_LIBRARY=ON
+
       - name: Build
         run: cmake --build build --parallel
+
       - name: Test
         run: cd build ; ctest -j 10 -C Debug --exclude-regex "test-unicode" --output-on-failure
 
@@ -122,6 +135,9 @@ jobs:
           python-version: '3.x'
           architecture: x86
 
+      - uses: actions/setup-python@v5
+      - run: pip install -r python/requirements.txt
+
       - name: Run CMake
         run: cmake -S . -B build -G "Visual Studio 16 2019" -A ${{ matrix.architecture }} -T ClangCL  -D MUSICA_ENABLE_PYTHON_LIBRARY=ON
 

configs/analytical/config.json

@@ -0,0 +1 @@
+{"camp-files": ["species.json", "reactions.json"]}

configs/analytical/reactions.json

@@ -0,0 +1 @@
+{"camp-data": [{"type": "MECHANISM", "name": "music box interactive configuration", "reactions": [{"type": "ARRHENIUS", "A": 0.00012, "B": 7, "C" : 75, "D": 50, "E": 0.5, "reactants": {"B": {"qty": 1}}, "products": {"C": {"yield": 1}, "irr__089f1f45-4cd8-4278-83d5-d638e98e4315": {"yield": 1}}}, {"type": "ARRHENIUS", "A": 0.004, "C" : 50, "reactants": {"A": {"qty": 1}}, "products": {"B": {"yield": 1}, "irr__2a109b21-bb24-41ae-8f06-7485fd36f1a7": {"yield": 1}}}]}]}

configs/analytical/species.json

@@ -0,0 +1 @@
+{"camp-data": [{"name": "A", "type": "CHEM_SPEC"}, {"name": "B", "type": "CHEM_SPEC"}, {"name": "C", "type": "CHEM_SPEC"},  {"name": "irr__089f1f45-4cd8-4278-83d5-d638e98e4315", "type": "CHEM_SPEC"}, {"name": "irr__2a109b21-bb24-41ae-8f06-7485fd36f1a7", "type": "CHEM_SPEC"}]}

configs/chapman/config.json

@@ -3,4 +3,4 @@
     "species.json",
     "reactions.json"
   ]
-}
+}

docker/Dockerfile.fortran-intel

@@ -33,7 +33,7 @@ RUN cd musica \
              -B build \
              -D MUSICA_ENABLE_TESTS=ON \
              -D MUSICA_ENABLE_TUVX=OFF \
-             -D CMAKE_BUILD_TYPE=Debug \
+             -D CMAKE_BUILD_TYPE=Release \
     && cd build \
     && make install
 
@@ -45,7 +45,7 @@ ENV FC=ifx
 RUN cd musica/fortran/test/fetch_content_integration \
     && mkdir build && cd build \
     && cmake .. \
-        -D CMAKE_BUILD_TYPE=Debug \
+        -D CMAKE_BUILD_TYPE=Release \
     && make
 
 RUN cp -r /musica/configs/chapman musica/fortran/test/fetch_content_integration/build

docker/Dockerfile.fortran-nvhpc

@@ -38,7 +38,7 @@ RUN cd musica \
              -B build \
              -D MUSICA_ENABLE_TESTS=ON \
              -D MUSICA_ENABLE_TUVX=OFF \
-             -D CMAKE_BUILD_TYPE=Debug \
+             -D CMAKE_BUILD_TYPE=Release \
     && cd build \
     && make install
 
@@ -50,7 +50,7 @@ ENV FC=nvfortran
 RUN cd musica/fortran/test/fetch_content_integration \
     && mkdir build && cd build \
     && cmake .. \
-        -D CMAKE_BUILD_TYPE=Debug \
+        -D CMAKE_BUILD_TYPE=Release \
     && make
 
 RUN cp -r /musica/configs/chapman musica/fortran/test/fetch_content_integration/build

fortran/micm_core.F90

@@ -1,11 +1,16 @@
 module micm_core
 
-   use iso_c_binding, only: c_ptr, c_char, c_int, c_double, c_null_char
+   use iso_c_binding, only: c_ptr, c_char, c_int, c_double, c_null_char, c_size_t, c_f_pointer
    implicit none
 
    public :: micm_t
    private
 
+   type, bind(c) :: Mapping
+      character(kind=c_char, len=1) :: name(256)
+      integer(c_size_t) :: index
+   end type Mapping
+
    interface
       function create_micm_c(config_path, error_code) bind(C, name="create_micm")
          import c_ptr, c_int, c_char
@@ -28,11 +33,26 @@ subroutine micm_solve_c(micm, time_step, temperature, pressure, num_concentratio
          integer(kind=c_int), value, intent(in) :: num_concentrations
          real(kind=c_double), intent(inout)     :: concentrations(num_concentrations)
       end subroutine micm_solve_c
+
+      function get_species_ordering(micm, array_size) bind(c, name="get_species_ordering")
+         import :: c_ptr, c_size_t
+         type(c_ptr), value :: micm
+         integer(kind=c_size_t), intent(out) :: array_size
+         type(c_ptr)                         :: get_species_ordering
+      end function get_species_ordering
+
+      type(c_ptr) function get_user_defined_reaction_rates_ordering(micm, array_size) &
+         bind(c, name="get_user_defined_reaction_rates_ordering")
+         import :: c_ptr, c_size_t
+         type(c_ptr), value :: micm
+         integer(kind=c_size_t), intent(out) :: array_size
+      end function get_user_defined_reaction_rates_ordering
    end interface
 
    type :: micm_t
-      private
-      type(c_ptr) :: ptr
+      type(Mapping), pointer   :: species_ordering(:), reaction_rates_ordering(:)
+      integer(kind=c_size_t) :: species_ordering_length, reaction_rates_ordering_length
+      type(c_ptr), private   :: ptr
    contains
       ! Solve the chemical system
       procedure :: solve
@@ -52,9 +72,11 @@ function constructor(config_path, errcode)  result( this )
       integer, intent(out)          :: errcode
       character(len=1, kind=c_char) :: c_config_path(len_trim(config_path)+1)
       integer                       :: n, i
+      type(c_ptr) :: mappings_ptr
 
       allocate( this )
 
+      print *, "Config Path:", config_path
       n = len_trim(config_path)
       do i = 1, n
          c_config_path(i) = config_path(i:i)
@@ -66,6 +88,15 @@ function constructor(config_path, errcode)  result( this )
       if (errcode /= 0) then
          return
       end if
+
+      mappings_ptr = get_species_ordering(this%ptr, this%species_ordering_length)
+      call c_f_pointer(mappings_ptr, this%species_ordering, [this%species_ordering_length])
+
+      ! this%reaction_rates_ordering = get_user_defined_reaction_rates_ordering(this%ptr, this%reaction_rates_ordering_length)
+
+      ! do i = 1, this%reaction_rates_ordering_length
+      !    print *, "Reaction Rate Name:", this%reaction_rates_ordering(i)%name, ", Index:", this%reaction_rates_ordering(i)%index
+      ! end do
    end function constructor
 
    subroutine solve(this, time_step, temperature, pressure, num_concentrations, concentrations)

fortran/test/fetch_content_integration/CMakeLists.txt

@@ -11,7 +11,7 @@ include(FetchContent)
 
 FetchContent_Declare(musica-fortran
   GIT_REPOSITORY https://github.com/NCAR/musica.git
-  GIT_TAG        main
+  GIT_TAG        79-allow-updates-to-custom-rate-constant-parameters-and-mapping-by-name
 )
 
 set(MUSICA_BUILD_C_CXX_INTERFACE OFF)

fortran/test/unit/CMakeLists.txt

@@ -1,5 +1,7 @@
 include(test_util)
 
+create_standard_test_fortran(NAME musica_fortran_interface SOURCES test_musica_fortran_interface.F90)
+
 if (MUSICA_ENABLE_TUVX)
   create_standard_test_fortran(NAME connect_to_tuvx SOURCES tuvx.F90)
   if (MUSICA_ENABLE_OPENMP)

fortran/test/unit/test_musica_fortran_interface.F90

@@ -0,0 +1,40 @@
+program test_micm_fort_api
+  use iso_c_binding
+  use micm_core, only: micm_t
+
+  implicit none
+
+  type(micm_t), pointer         :: micm
+  real(c_double)                :: time_step
+  real(c_double)                :: temperature
+  real(c_double)                :: pressure
+  integer(c_int)                :: num_concentrations
+  real(c_double), dimension(5)  :: concentrations
+  integer                       :: errcode
+  character(len=7)              :: config_path
+
+  time_step = 200
+  temperature = 272.5
+  pressure = 101253.3
+  num_concentrations = 5
+  concentrations = (/ 0.75, 0.4, 0.8, 0.01, 0.02 /)
+  config_path = "configs/chapman"
+
+  write(*,*) "[test micm fort api] Creating MICM solver..."
+  micm => micm_t(config_path, errcode)
+
+  if (errcode /= 0) then
+    write(*,*) "[test micm fort api] Failed in creating solver."
+    stop 3
+  endif
+
+  write(*,*) "[test micm fort api] Initial concentrations", concentrations
+
+  write(*,*) "[test micm fort api] Solving starts..."
+  call micm%solve(time_step, temperature, pressure, num_concentrations, concentrations)
+
+  write(*,*) "[test micm fort api] After solving, concentrations", concentrations
+
+  write(*,*) "[test micm fort api] Finished."
+
+end program

include/musica/micm.hpp

@@ -2,7 +2,7 @@
  * This file contains the defintion of the MICM class, which represents a multi-component
  * reactive transport model. It also includes functions for creating and deleting MICM instances with c binding
  * Copyright (C) 2023-2024 National Center for Atmospheric Research,
- * 
+ *
  * SPDX-License-Identifier: Apache-2.0* creating solvers, and solving the model.
  */
 #pragma once
@@ -15,13 +15,22 @@
 
 class MICM;
 
+struct Mapping
+{
+    char *name;
+    size_t index;
+};
+
 #ifdef __cplusplus
-extern "C" {
+extern "C"
+{
 #endif
 
-MICM* create_micm(const char* config_path, int* error_code);
-void delete_micm(const MICM* micm);
-void micm_solve(MICM* micm, double time_step, double temperature, double pressure, int num_concentrations, double* concentrations);
+    MICM *create_micm(const char *config_path, int *error_code);
+    void delete_micm(const MICM *micm);
+    void micm_solve(MICM *micm, double time_step, double temperature, double pressure, int num_concentrations, double *concentrations, int num_custom_rate_parameters, double *custom_rate_parameters);
+    Mapping *get_species_ordering(MICM *micm, size_t *array_size);
+    Mapping *get_user_defined_reaction_rates_ordering(MICM *micm, size_t *array_size);
 
 #ifdef __cplusplus
 }
@@ -39,16 +48,19 @@ class MICM
     /// @brief Create a solver by reading and parsing configuration file
     /// @param config_path Path to configuration file or directory containing configuration file
     /// @return 0 on success, 1 on failure in parsing configuration file
-    int create_solver(const std::string& config_path);
-    
+    int create_solver(const std::string &config_path);
+
     /// @brief Solve the system
     /// @param time_step Time [s] to advance the state by
     /// @para/ @briefm temperature Temperature [K]
     /// @param pressure Pressure/ [P@brief C@param num_concentrations The number oconfiguration file
     /// @param config_path Path to configuration file or directory containing configuration file
     /// @return 0 on success, 1 on failure in parsing species' concentrations
     /// @param concentrations Species's concentrations
-    void solve(double time_step, double temperature, double pressure, int num_concentrations, double* concentrations);
+    void solve(double time_step, double temperature, double pressure, int num_concentrations, double *concentrations, int num_custom_rate_parameters, double *custom_rate_parameters);
+
+    std::map<std::string, size_t> get_species_ordering();
+    std::map<std::string, size_t> get_user_defined_reaction_rates_ordering();
 
     static constexpr size_t NUM_GRID_CELLS = 1;
 

python/CMakeLists.txt

@@ -12,7 +12,6 @@ target_link_libraries(musica_python PUBLIC musica::musica)
 
 
 if(WIN32)
-
   # makefiles on windows don't need the config directory
   if (${CMAKE_GENERATOR} MATCHES "MinGW Makefiles")
       set(PYTHON_MODULE_PATH "${CMAKE_CURRENT_BINARY_DIR}")
@@ -24,7 +23,5 @@ else()
   set(PYTHON_MODULE_PATH "${CMAKE_CURRENT_BINARY_DIR}")
 endif()
 
-add_test(NAME musica_python_test
-  WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
-  COMMAND ${CMAKE_COMMAND} -E env PYTHONPATH=${PYTHON_MODULE_PATH} 
-  ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/micm_test.py)
+
+add_subdirectory(test)

python/requirements.txt

@@ -0,0 +1 @@
+numpy

python/test/CMakeLists.txt

@@ -0,0 +1,9 @@
+add_test(NAME musica_python_chapman_test
+  WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
+  COMMAND ${CMAKE_COMMAND} -E env PYTHONPATH=${PYTHON_MODULE_PATH} 
+  ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/chapman.py)
+
+add_test(NAME musica_python_analytical_test
+  WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
+  COMMAND ${CMAKE_COMMAND} -E env PYTHONPATH=${PYTHON_MODULE_PATH} 
+  ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/analytical.py)