Merge pull request #35 from NCAR/adding_solver

Added creating solver interface

Dockerfile

@@ -9,6 +9,7 @@ RUN dnf -y update \
         lcov \
         make \
         netcdf-fortran-devel \
+        json-devel \
         valgrind \
     && dnf clean all
 
@@ -35,5 +36,5 @@ RUN cd musica \
              -D ENABLE_TESTS=ON \
     && cd build \
     && make install -j 8 
-    
+
 WORKDIR musica/build

Dockerfile.fortran

@@ -9,6 +9,7 @@ RUN apt update \
     libcurl4-openssl-dev \
     libhdf5-dev \
     m4 \
+    nlohmann-json3-dev \
     vim \
     zlib1g-dev \
     git \
@@ -44,6 +45,7 @@ RUN cd musica \
     && cmake -S . \
              -B build \
              -D ENABLE_TESTS=ON \
+             -D ENABLE_TUVX=OFF \
     && cd build \
     && make install -j 8 
 
@@ -67,4 +69,7 @@ RUN cd musica/musica-fortran/test \
     && cmake .. \
     && make
 
+RUN cd musica/musica-fortran/test \
+    && cp -r micm_config ./build/micm_config
+
 WORKDIR musica/musica-fortran/test/build

Dockerfile.mpi

@@ -18,6 +18,7 @@ RUN sudo dnf -y install \
         make \
         netcdf-fortran-devel \
         openmpi-devel \
+        json-devel \
         valgrind-openmpi \
     && dnf clean all
 

Dockerfile.mpi_openmp

@@ -17,6 +17,7 @@ RUN sudo dnf -y install \
         lcov \
         make \
         netcdf-fortran-devel \
+        json-devel \
         openmpi-devel \
         valgrind-openmpi \
     && dnf clean all

Dockerfile.openmp

@@ -17,6 +17,7 @@ RUN sudo dnf -y install \
         lcov \
         make \
         netcdf-fortran-devel \
+        json-devel \
         openmpi-devel \
         valgrind-openmpi \
     && dnf clean all

musica-fortran/CMakeLists.txt

@@ -28,7 +28,7 @@ find_package(PkgConfig REQUIRED)
 pkg_check_modules(netcdff IMPORTED_TARGET REQUIRED netcdf-fortran)
 
 # Find MUSICA package
-find_package(musica 0.3.0 REQUIRED)
+find_package(musica 0.4.0 REQUIRED)
 
 target_link_libraries(musica-fortran
  PUBLIC 

musica-fortran/src/micm/CMakeLists.txt

@@ -1,4 +1,4 @@
 target_sources(musica-fortran
   PUBLIC
-  interface.F90
+    micm_mod.F90
 )

musica-fortran/src/micm/micm_c_def.F90

@@ -0,0 +1,32 @@
+interface   
+    function create_micm_c(config_path) bind(C, name="create_micm")
+        use iso_c_binding
+        implicit none
+        type(c_ptr) :: create_micm_c
+        character(len=1, kind=C_CHAR), intent(in) :: config_path(*)
+    end function
+
+    subroutine delete_micm_c(micm_t) bind(C, name="delete_micm")
+        use iso_c_binding
+        implicit none
+        type(c_ptr), value :: micm_t
+    end subroutine
+
+    function micm_create_solver_c(micm_t) bind(C, name="micm_create_solver")
+        use iso_c_binding
+        implicit none
+        integer(c_int) :: micm_create_solver_c  ! TODO(jiwon) return value?
+        type(c_ptr), intent(in), value :: micm_t
+    end function
+
+    subroutine micm_solve_c(micm_t, temperature, pressure, time_step, concentrations, num_concentrations) bind(C, name="micm_solve")
+        use iso_c_binding
+        implicit none
+        type(c_ptr), intent(in), value :: micm_t
+        real(c_double), value :: temperature   
+        real(c_double), value :: pressure
+        real(c_double), value :: time_step
+        real(c_double), dimension(*), intent(inout) :: concentrations
+        integer(c_size_t), value, intent(in) :: num_concentrations
+    end subroutine
+end interface

musica-fortran/src/micm/micm_mod.F90

@@ -0,0 +1,60 @@
+module micm
+    use iso_c_binding
+    implicit none
+
+    private
+    public :: micm_t
+
+    include "micm_c_def.F90"
+
+    type micm_t
+        private
+        type(c_ptr) :: ptr
+    contains
+        procedure :: create_solver => micm_create_solver
+        procedure :: solve => micm_solve
+        final :: delete_micm
+    end type
+
+    interface micm_t
+        procedure create_micm
+    end interface
+
+contains
+    function create_micm(config_path)
+        type(micm_t) :: create_micm
+        character(len=*), intent(in) :: config_path
+        character(len=1, kind=C_CHAR) :: c_config_path(len_trim(config_path) + 1)
+        integer :: N, i
+
+        ! Converting Fortran string to C string
+        N = len_trim(config_path)
+        do i = 1, N
+            c_config_path(i) = config_path(i:i)
+        end do
+        c_config_path(N + 1) = C_NULL_CHAR
+
+        create_micm%ptr = create_micm_c(c_config_path)
+    end function
+
+    subroutine delete_micm(this)
+        type(micm_t) :: this
+        call delete_micm_c(this%ptr)
+    end subroutine
+
+    integer function micm_create_solver(this)
+        class(micm_t), intent(in) :: this
+        micm_create_solver = micm_create_solver_c(this%ptr)
+    end function
+
+    subroutine micm_solve(this, temperature, pressure, time_step, concentrations, num_concentrations)
+        class(micm_t), intent(in) :: this
+        real(c_double), intent(in) :: temperature
+        real(c_double), intent(in) :: pressure
+        real(c_double), intent(in) :: time_step
+        real(c_double), dimension(*), intent(inout) :: concentrations
+        integer(c_size_t), intent(in) :: num_concentrations
+        call micm_solve_c(this%ptr, temperature, pressure, time_step, concentrations, num_concentrations)
+    end subroutine
+
+end module

musica-fortran/test/CMakeLists.txt

@@ -12,10 +12,11 @@ include(FetchContent)
 
 set(USE_MUSICA OFF)
 set(USE_MUSICA_FORTRAN ON)
+set(ENABLE_TUVX OFF)
 
 FetchContent_Declare(musica 
   GIT_REPOSITORY https://github.com/NCAR/musica.git
-  GIT_TAG        bf1b77b  ## todo: jiwon update this
+  GIT_TAG        bad9756  # TODO(jiwon) - update the tag
 )
 
 FetchContent_MakeAvailable(musica)

musica-fortran/test/micm_config/mechanism.json

@@ -0,0 +1 @@
+{"camp-data": [{"name": "Chapman", "type": "MECHANISM", "reactions": [{"type": "ARRHENIUS", "reactants": {"spec_0": {}, "spec_1": {}, "spec_2": {}}, "products": {"spec_3": {"yield": 0.7}, "spec_4": {"yield": 0.6}, "spec_5": {"yield": 0.4}, "spec_6": {"yield": 0.1}}, "MUSICA name": "reaction_0", "A": 0.06307742014373313, "C": -4.580502916806157}, {"type": "ARRHENIUS", "reactants": {"spec_7": {}, "spec_8": {}}, "products": {"spec_9": {"yield": 1.4}}, "MUSICA name": "reaction_1", "A": 0.04349975747486285, "C": 0.9227077653687363}, {"type": "ARRHENIUS", "reactants": {"spec_3": {}, "spec_6": {}, "spec_8": {}}, "products": {"spec_5": {"yield": 1.2}, "spec_0": {"yield": 0.5}, "spec_7": {"yield": 0.6}, "spec_8": {"yield": 0.3}}, "MUSICA name": "reaction_2", "A": 0.06852791722073094, "C": 3.2487346324460002}, {"type": "ARRHENIUS", "reactants": {"spec_8": {}, "spec_4": {}}, "products": {"spec_9": {"yield": 0.5}, "spec_1": {"yield": 0.7}, "spec_6": {"yield": 1.1}, "spec_8": {"yield": 1.3}, "spec_4": {"yield": 1.2}, "spec_3": {"yield": 0.4}}, "MUSICA name": "reaction_3", "A": 0.25712668426775886, "C": -1.6984663902168808}, {"type": "ARRHENIUS", "reactants": {"spec_9": {}, "spec_1": {}}, "products": {"spec_5": {"yield": 0.6}}, "MUSICA name": "reaction_4", "A": 0.09981506051562195, "C": 4.434345327828195}, {"type": "ARRHENIUS", "reactants": {"spec_8": {}, "spec_1": {}, "spec_3": {}}, "products": {"spec_0": {"yield": 0.7}}, "MUSICA name": "reaction_5", "A": 0.04095822066544459, "C": -0.9768070373515956}, {"type": "ARRHENIUS", "reactants": {"spec_1": {}, "spec_7": {}}, "products": {"spec_8": {"yield": 1.1}, "spec_1": {"yield": 1.5}}, "MUSICA name": "reaction_6", "A": 0.05421274033990674, "C": -2.8281780970323145}, {"type": "ARRHENIUS", "reactants": {"spec_3": {}}, "products": {"spec_5": {"yield": 0.8}, "spec_8": {"yield": 0.6}}, "MUSICA name": "reaction_7", "A": 0.48935553510912033, "C": -4.956655119700008}, {"type": "ARRHENIUS", "reactants": {"spec_3": {}}, "products": {"spec_7": {"yield": 0.9}, "spec_3": {"yield": 1.0}, "spec_2": {"yield": 1.3}}, "MUSICA name": "reaction_8", "A": 0.18950947076801095, "C": 0.04442551245927007}, {"type": "ARRHENIUS", "reactants": {"spec_6": {}}, "products": {"spec_4": {"yield": 0.7}, "spec_9": {"yield": 0.5}, "spec_3": {"yield": 0.8}, "spec_1": {"yield": 0.6}, "spec_5": {"yield": 0.2}}, "MUSICA name": "reaction_9", "A": 0.021971337763203702, "C": -2.81627531289537}]}]}

musica-fortran/test/micm_config/species.json

@@ -0,0 +1 @@
+{"camp-data": [{"name": "spec_0", "type": "CHEM_SPEC", "absolute tolerance": 1e-12}, {"name": "spec_1", "type": "CHEM_SPEC", "absolute tolerance": 1e-12}, {"name": "spec_2", "type": "CHEM_SPEC", "absolute tolerance": 1e-12}, {"name": "spec_3", "type": "CHEM_SPEC", "absolute tolerance": 1e-12}, {"name": "spec_4", "type": "CHEM_SPEC", "absolute tolerance": 1e-12}, {"name": "spec_5", "type": "CHEM_SPEC", "absolute tolerance": 1e-12}, {"name": "spec_6", "type": "CHEM_SPEC", "absolute tolerance": 1e-12}, {"name": "spec_7", "type": "CHEM_SPEC", "absolute tolerance": 1e-12}, {"name": "spec_8", "type": "CHEM_SPEC", "absolute tolerance": 1e-12}, {"name": "spec_9", "type": "CHEM_SPEC", "absolute tolerance": 1e-12}]}

musica-fortran/test/test_musica_api.F90

@@ -1,10 +1,38 @@
-program test_musica_api
-  use iso_c_binding
-  use micm
+program test
+    use iso_c_binding
+    use micm
+    implicit none
+    type(micm_t) :: m
 
-  character(len=5, kind=c_char) :: c_filepath
-  type(c_funptr)                   :: csolver_func_pointer
-  c_filepath = 'asdf'
-  csolver_func_pointer = get_solver(c_filepath)
+    real(c_double) :: temperature      
+    real(c_double) :: pressure
+    real(c_double) :: time_step
+    real(c_double), dimension(10) :: concentrations
+    integer(c_size_t) :: num_concentrations
 
-end program test_musica_api
+    temperature = 10d0
+    pressure = 20d0
+    time_step = 1d0
+    concentrations = (/ 1d0, 2d0, 3d0, 4d0, 5d0, 6d0, 7d0, 8d0, 9d0, 10d0 /)
+    num_concentrations = 10
+
+    write(*,*) "  * [Fortran] Creating MICM"
+    m = micm_t("micm_config")
+
+    write(*,*) "  * [Fortran] Creating solver"
+    write(*,*) "  * [Fortran] Solver creating status indicates ", m%create_solver(), " (1 is success, else failure) "
+
+    write(*,*) "  * [Fortran] Initial temp", temperature
+    write(*,*) "  * [Fortran] Initial pressure", pressure
+    write(*,*) "  * [Fortran] Initial time_step", time_step
+    write(*,*) "  * [Fortran] Initial concentrations", concentrations
+    write(*,*) "  * [Fortran] Initial number of concentrations", num_concentrations
+
+    write(*,*) "  * [Fortran] Starting to solve"
+    call m%solve(temperature, pressure, time_step, concentrations, num_concentrations)
+    write(*,*) "  * [Fortran] After solving, concentrations", concentrations
+
+    write(*,*) "  * [Fortran] Calling destructor for MICM"
+    call m%delete
+
+end program

musica/CMakeLists.txt

@@ -89,7 +89,7 @@ target_sources(musica
 
 add_subdirectory(${PROJECT_SOURCE_DIR}/lib/musica-core/src ${MUSICA_LIB_DIR}/musica-core/src)
 
-# ####################
+####################
 # TUV-x
 if (ENABLE_TUVX)
   add_definitions(-DMUSICA_USE_TUVX)
@@ -122,7 +122,7 @@ if (ENABLE_TUVX)
   )
 endif()
 
-# ####################
+####################
 # MICM
 if (ENABLE_MICM)
   add_definitions(-DMUSICA_USE_MICM)
@@ -136,7 +136,7 @@ if (ENABLE_MICM)
 
   install(
     DIRECTORY 
-      ${PROJECT_SOURCE_DIR}/lib/micm/include/micm
+      ${PROJECT_SOURCE_DIR}/lib/micm/include
     DESTINATION 
       ${INSTALL_MOD_DIR}
   )

musica/include/micm/micm.hpp

@@ -0,0 +1,38 @@
+#pragma once
+
+#include <string>
+#include <vector>
+#include <cstddef>
+
+#include <micm/solver/rosenbrock.hpp>
+#include <micm/util/sparse_matrix_vector_ordering.hpp>
+#include <micm/util/vector_matrix.hpp>
+
+
+class MICM 
+{
+public:
+    MICM(const std::string& config_path);
+    ~MICM();
+
+    // TODO(jiwon): can return type indicate error?
+    int create_solver();
+    void solve(double temperature, double pressure, double time_step, double*& concentrations, size_t num_concentrations);
+
+private:
+    static constexpr size_t NUM_GRID_CELLS = 1; // TODO(jiwon)
+
+    std::string config_path_;
+
+    // TODO(jiwon) - currently hard coded
+    std::vector<double> v_concentrations_;
+
+    // TODO(jiwon) - currently hard coded
+    template <class T = double>
+    using Vector1MatrixParam = micm::VectorMatrix<T, 1>;
+    template <class T = double>
+    using Vector1SparseMatrixParam = micm::SparseMatrix<T, micm::SparseMatrixVectorOrdering<1>>;
+    typedef micm::RosenbrockSolver<Vector1MatrixParam, Vector1SparseMatrixParam> VectorRosenbrockSolver;
+    VectorRosenbrockSolver* solver_;
+};
+

musica/include/micm/micm_c.h

@@ -0,0 +1,18 @@
+#include <cstddef>
+
+#ifdef __cplusplus
+extern "C" {
+    class MICM;
+    typedef MICM Micm;
+#endif
+
+Micm* create_micm(const char* config_path);
+void delete_micm(const Micm* micm);
+int micm_create_solver(Micm* micm);
+void micm_solve(Micm* micm, double temperature, double pressure, double time_step, 
+                double* concentrations, size_t num_concentrations);
+
+#ifdef __cplusplus
+}
+#endif
+

musica/src/micm/CMakeLists.txt

@@ -1,4 +1,5 @@
 target_sources(musica
   PRIVATE
-    interface.cpp
+    micm_c_api.cpp
+    micm.cpp
 )