81 supply custom rate constants to fortran (#82)

* passed mapping properly

* using the user defined reaction rates

* changing branch

* correcting usage

* adding correct config copy path

* private sources

* better naming

docker/Dockerfile.fortran-gcc

@@ -44,6 +44,6 @@ RUN cd musica/fortran/test/fetch_content_integration \
         -D CMAKE_BUILD_TYPE=Debug \
     && make
 
-RUN cp -r /musica/configs/chapman musica/fortran/test/fetch_content_integration/build
+RUN cp -r /musica/configs musica/fortran/test/fetch_content_integration/build
 
 WORKDIR musica/fortran/test/fetch_content_integration/build

docker/Dockerfile.fortran-intel

@@ -48,6 +48,6 @@ RUN cd musica/fortran/test/fetch_content_integration \
         -D CMAKE_BUILD_TYPE=Release \
     && make
 
-RUN cp -r /musica/configs/chapman musica/fortran/test/fetch_content_integration/build
+RUN cp -r /musica/configs musica/fortran/test/fetch_content_integration/build
 
 WORKDIR musica/fortran/test/fetch_content_integration/build

docker/Dockerfile.fortran-nvhpc

@@ -53,6 +53,6 @@ RUN cd musica/fortran/test/fetch_content_integration \
         -D CMAKE_BUILD_TYPE=Release \
     && make
 
-RUN cp -r /musica/configs/chapman musica/fortran/test/fetch_content_integration/build
+RUN cp -r /musica/configs musica/fortran/test/fetch_content_integration/build
 
 WORKDIR musica/fortran/test/fetch_content_integration/build

fortran/CMakeLists.txt

@@ -40,7 +40,7 @@ target_link_libraries(musica-fortran
 )
 
 target_sources(musica-fortran
-  PUBLIC
+  PRIVATE
     micm_core.F90
 )
 

fortran/micm_core.F90

@@ -3,13 +3,14 @@ module micm_core
    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
+   public :: micm_t, mapping_t
    private
 
-   type, bind(c) :: Mapping
+   type, bind(c) :: mapping_t
       character(kind=c_char, len=1) :: name(256)
       integer(c_size_t) :: index
-   end type Mapping
+      integer(c_size_t) :: string_length
+   end type mapping_t
 
    interface
       function create_micm_c(config_path, error_code) bind(C, name="create_micm")
@@ -24,14 +25,17 @@ subroutine delete_micm_c(micm) bind(C, name="delete_micm")
          type(c_ptr), intent(in) :: micm
       end subroutine delete_micm_c
 
-      subroutine micm_solve_c(micm, time_step, temperature, pressure, num_concentrations, concentrations) bind(C, name="micm_solve")
+      subroutine micm_solve_c(micm, time_step, temperature, pressure, num_concentrations, concentrations, &
+                              num_user_defined_reaction_rates, user_defined_reaction_rates) bind(C, name="micm_solve")
          import c_ptr, c_double, c_int
          type(c_ptr), value, intent(in)         :: micm
          real(kind=c_double), value, intent(in) :: time_step
          real(kind=c_double), value, intent(in) :: temperature
          real(kind=c_double), value, intent(in) :: pressure
          integer(kind=c_int), value, intent(in) :: num_concentrations
          real(kind=c_double), intent(inout)     :: concentrations(num_concentrations)
+         integer(kind=c_int), value, intent(in) :: num_user_defined_reaction_rates
+         real(kind=c_double), intent(inout)     :: user_defined_reaction_rates(num_user_defined_reaction_rates)
       end subroutine micm_solve_c
 
       function get_species_ordering(micm, array_size) bind(c, name="get_species_ordering")
@@ -50,8 +54,8 @@ end function get_user_defined_reaction_rates_ordering
    end interface
 
    type :: micm_t
-      type(Mapping), pointer   :: species_ordering(:), reaction_rates_ordering(:)
-      integer(kind=c_size_t) :: species_ordering_length, reaction_rates_ordering_length
+      type(mapping_t), pointer   :: species_ordering(:), user_defined_reaction_rates(:)
+      integer(kind=c_size_t) :: species_ordering_length, user_defined_reaction_rates_length
       type(c_ptr), private   :: ptr
    contains
       ! Solve the chemical system
@@ -76,7 +80,6 @@ function constructor(config_path, errcode)  result( this )
 
       allocate( this )
 
-      print *, "Config Path:", config_path
       n = len_trim(config_path)
       do i = 1, n
          c_config_path(i) = config_path(i:i)
@@ -92,21 +95,23 @@ function constructor(config_path, errcode)  result( this )
       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
+      mappings_ptr = get_user_defined_reaction_rates_ordering(this%ptr, this%user_defined_reaction_rates_length)
+      call c_f_pointer(mappings_ptr, this%user_defined_reaction_rates, [this%user_defined_reaction_rates_length])
    end function constructor
 
-   subroutine solve(this, time_step, temperature, pressure, num_concentrations, concentrations)
+   subroutine solve(this, time_step, temperature, pressure, num_concentrations, concentrations, &
+                     num_user_defined_reaction_rates, user_defined_reaction_rates)
       class(micm_t)                 :: this
       real(c_double), intent(in)    :: time_step
       real(c_double), intent(in)    :: temperature
       real(c_double), intent(in)    :: pressure
       integer(c_int), intent(in)    :: num_concentrations
       real(c_double), intent(inout) :: concentrations(*)
-      call micm_solve_c(this%ptr, time_step, temperature, pressure, num_concentrations, concentrations)
+      integer(c_int), intent(in)    :: num_user_defined_reaction_rates
+      real(c_double), intent(inout) :: user_defined_reaction_rates(*)
+      call micm_solve_c(this%ptr, time_step, temperature, pressure, num_concentrations, concentrations, &
+                        num_user_defined_reaction_rates, user_defined_reaction_rates)
    end subroutine solve
 
    subroutine finalize(this)

fortran/test/fetch_content_integration/test_micm_fort_api.F90

@@ -1,28 +1,42 @@
 program test_micm_fort_api
   use iso_c_binding
-  use micm_core, only: micm_t
+  use micm_core, only: micm_t, mapping_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
+  integer(c_int)                :: num_concentrations, num_user_defined_reaction_rates
+  real(c_double), dimension(5)  :: concentrations 
+  real(c_double), dimension(3)  :: user_defined_reaction_rates 
+  integer                       :: errcode, i
+  character(len=256)            :: config_path
+  type(mapping_t)               :: the_mapping
 
   time_step = 200
   temperature = 272.5
-  pressure = 101253.3
+  pressure = 101253.4
   num_concentrations = 5
   concentrations = (/ 0.75, 0.4, 0.8, 0.01, 0.02 /)
-  config_path = "chapman"
+  config_path = "configs/chapman"
+  num_user_defined_reaction_rates = 3
+  user_defined_reaction_rates = (/ 0.1, 0.2, 0.3 /)
+
 
   write(*,*) "[test micm fort api] Creating MICM solver..."
   micm => micm_t(config_path, errcode)
 
+  do i = 1, micm%species_ordering_length
+    the_mapping = micm%species_ordering(i)
+    print *, "Species Name:", the_mapping%name(:the_mapping%string_length), ", Index:", the_mapping%index
+  end do
+  do i = 1, micm%user_defined_reaction_rates_length
+    the_mapping = micm%user_defined_reaction_rates(i)
+    print *, "User Defined Reaction Rate Name:", the_mapping%name(:the_mapping%string_length), ", Index:", the_mapping%index
+  end do
+
   if (errcode /= 0) then
     write(*,*) "[test micm fort api] Failed in creating solver."
     stop 3
@@ -31,7 +45,8 @@ program test_micm_fort_api
   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)
+  call micm%solve(time_step, temperature, pressure, num_concentrations, concentrations, &
+                  num_user_defined_reaction_rates, user_defined_reaction_rates)
 
   write(*,*) "[test micm fort api] After solving, concentrations", concentrations
 

fortran/test/fetch_content_integration/test_micm_fort_api_invalid.F90

@@ -5,19 +5,9 @@ subroutine test_micm_fort_api_invalid()
   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 = "invalid_config"
 
   write(*,*) "[test micm fort api] Creating MICM solver..."

fortran/test/unit/test_musica_fortran_interface.F90

@@ -1,28 +1,42 @@
 program test_micm_fort_api
   use iso_c_binding
-  use micm_core, only: micm_t
+  use micm_core, only: micm_t, mapping_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
+  integer(c_int)                :: num_concentrations, num_user_defined_reaction_rates
+  real(c_double), dimension(5)  :: concentrations 
+  real(c_double), dimension(3)  :: user_defined_reaction_rates 
+  integer                       :: errcode, i
+  character(len=256)            :: config_path
+  type(mapping_t)                 :: the_mapping
 
   time_step = 200
   temperature = 272.5
-  pressure = 101253.3
+  pressure = 101253.4
   num_concentrations = 5
   concentrations = (/ 0.75, 0.4, 0.8, 0.01, 0.02 /)
   config_path = "configs/chapman"
+  num_user_defined_reaction_rates = 3
+  user_defined_reaction_rates = (/ 0.1, 0.2, 0.3 /)
+
 
   write(*,*) "[test micm fort api] Creating MICM solver..."
   micm => micm_t(config_path, errcode)
 
+  do i = 1, micm%species_ordering_length
+    the_mapping = micm%species_ordering(i)
+    print *, "Species Name:", the_mapping%name(:the_mapping%string_length), ", Index:", the_mapping%index
+  end do
+  do i = 1, micm%user_defined_reaction_rates_length
+    the_mapping = micm%user_defined_reaction_rates(i)
+    print *, "User Defined Reaction Rate Name:", the_mapping%name(:the_mapping%string_length), ", Index:", the_mapping%index
+  end do
+
   if (errcode /= 0) then
     write(*,*) "[test micm fort api] Failed in creating solver."
     stop 3
@@ -31,7 +45,8 @@ program test_micm_fort_api
   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)
+  call micm%solve(time_step, temperature, pressure, num_concentrations, concentrations, &
+                  num_user_defined_reaction_rates, user_defined_reaction_rates)
 
   write(*,*) "[test micm fort api] After solving, concentrations", concentrations
 

include/musica/micm.hpp

@@ -17,8 +17,9 @@ class MICM;
 
 struct Mapping
 {
-    char *name;
+    char name[256];
     size_t index;
+    size_t string_length;
 };
 
 #ifdef __cplusplus
@@ -39,12 +40,6 @@ extern "C"
 class MICM
 {
 public:
-    /// @brief Constructor
-    MICM();
-
-    /// @brief Destructor
-    ~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

src/micm/micm.cpp

@@ -40,22 +40,22 @@ void micm_solve(MICM *micm, double time_step, double temperature, double pressur
 Mapping *get_species_ordering(MICM *micm, size_t *array_size)
 {
     auto map = micm->get_species_ordering();
-    Mapping *reactionRates = new Mapping[map.size()];
+    Mapping *species_ordering = new Mapping[map.size()];
 
     // Copy data from the map to the array of structs
     size_t i = 0;
     for (const auto &entry : map)
     {
-        reactionRates[i].name = new char[entry.first.size() + 1]; // +1 for null terminator
-        std::strcpy(reactionRates[i].name, entry.first.c_str());
-        reactionRates[i].index = entry.second;
+        std::strcpy(species_ordering[i].name, entry.first.c_str());
+        species_ordering[i].index = entry.second;
+        species_ordering[i].string_length = entry.first.size();
         ++i;
     }
 
     // Set the size of the array
     *array_size = map.size();
 
-    return reactionRates;
+    return species_ordering;
 }
 
 Mapping *get_user_defined_reaction_rates_ordering(MICM *micm, size_t *array_size)
@@ -67,9 +67,9 @@ Mapping *get_user_defined_reaction_rates_ordering(MICM *micm, size_t *array_size
     size_t i = 0;
     for (const auto &entry : map)
     {
-        reactionRates[i].name = new char[entry.first.size() + 1]; // +1 for null terminator
         std::strcpy(reactionRates[i].name, entry.first.c_str());
         reactionRates[i].index = entry.second;
+        reactionRates[i].string_length = entry.first.size();
         ++i;
     }
 
@@ -79,12 +79,6 @@ Mapping *get_user_defined_reaction_rates_ordering(MICM *micm, size_t *array_size
     return reactionRates;
 }
 
-MICM::MICM() : solver_(nullptr) {}
-
-MICM::~MICM()
-{
-}
-
 int MICM::create_solver(const std::string &config_path)
 {
     int parsing_status = 0; // 0 on success, 1 on failure