Add enabling of CAMP for chemistry

src/aero_data.F90

@@ -36,6 +36,19 @@ subroutine f_aero_data_from_json(ptr_c) bind(C)
     call spec_file_read_aero_data(file, ptr_f)
   end subroutine
 
+  subroutine f_aero_data_from_camp(ptr_c, camp_core_ptr_c) bind(C)
+    type(aero_data_t), pointer :: ptr_f => null()
+    type(c_ptr), intent(in) :: ptr_c
+    type(c_ptr), intent(in) :: camp_core_ptr_c
+    type(camp_core_t), pointer :: camp_core_ptr_f => null()
+
+    call c_f_pointer(ptr_c, ptr_f)
+    call c_f_pointer(camp_core_ptr_c, camp_core_ptr_f)
+
+    call aero_data_initialize(ptr_f, camp_core_ptr_f)
+
+  end subroutine
+
   subroutine f_aero_data_spec_by_name(ptr_c, value, name_data, name_size) bind(C)
     type(aero_data_t), pointer :: ptr_f => null()
     type(c_ptr), intent(in) :: ptr_c

src/aero_data.hpp

@@ -8,12 +8,14 @@
 
 #include "pmc_resource.hpp"
 #include "json_resource.hpp"
+#include "camp_core.hpp"
 #include "pybind11/stl.h"
 #include "aero_data_parameters.hpp"
 
 extern "C" void f_aero_data_ctor(void *ptr) noexcept;
 extern "C" void f_aero_data_dtor(void *ptr) noexcept;
 extern "C" void f_aero_data_from_json(const void *ptr) noexcept;
+extern "C" void f_aero_data_from_camp(const void *ptr, const void *camp_core_ptr) noexcept;
 extern "C" void f_aero_data_spec_by_name(const void *ptr, int *value, const char *name_data, const int *name_size) noexcept;
 extern "C" void f_aero_data_len(const void *ptr, int *len) noexcept;
 extern "C" void f_aero_data_n_source(const void *ptr, int *len) noexcept;
@@ -38,6 +40,12 @@ extern "C" void f_aero_data_spec_name_by_index(const void *ptr, const int *i_spe
 struct AeroData {
     PMCResource ptr;
 
+    AeroData(const nlohmann::json &json, const CampCore &camp_core) :
+        ptr(f_aero_data_ctor, f_aero_data_dtor)
+    {
+        f_aero_data_from_camp(this->ptr.f_arg(), camp_core.ptr.f_arg());
+    }
+
     AeroData(const nlohmann::json &json) :
         ptr(f_aero_data_ctor, f_aero_data_dtor)
     {

src/aero_state.F90

@@ -638,4 +638,18 @@ subroutine f_aero_state_sample_particles(ptr_c, aero_state_to_ptr_c, &
 
   end subroutine
 
+  subroutine f_aero_state_initialize(ptr_c, aero_data_ptr_c, camp_core_ptr_c) bind(C)
+    type(c_ptr) :: ptr_c, aero_data_ptr_c, camp_core_ptr_c
+    type(aero_state_t), pointer :: ptr_f => null()
+    type(aero_data_t), pointer :: aero_data_ptr_f => null()
+    type(camp_core_t), pointer :: camp_core_ptr_f => null()
+
+    call c_f_pointer(ptr_c, ptr_f)
+    call c_f_pointer(aero_data_ptr_c, aero_data_ptr_f)
+    call c_f_pointer(camp_core_ptr_c, camp_core_ptr_f)
+
+    call aero_state_initialize(ptr_f, aero_data_ptr_f, camp_core_ptr_f)
+
+  end subroutine
+
 end module

src/aero_state.hpp

@@ -9,6 +9,7 @@
 #include "pmc_resource.hpp"
 #include "aero_data.hpp"
 #include "aero_dist.hpp"
+#include "camp_core.hpp"
 #include "aero_particle.hpp"
 #include "env_state.hpp"
 #include "bin_grid.hpp"
@@ -208,6 +209,12 @@ extern "C" void f_aero_state_sample_particles(
      const double *sample_prob
 ) noexcept;
 
+extern "C" void f_aero_state_initialize(
+     void *ptr_c,
+     const void *aero_data_ptr_c,
+     const void *camp_core_ptr_c
+) noexcept;
+
 template <typename arr_t, typename arg_t>
 auto pointer_vec_magic(arr_t &data_vec, const arg_t &arg) {
     std::vector<char*> pointer_vec(data_vec.size());
@@ -269,6 +276,44 @@ struct AeroState {
     {
     }
 
+    AeroState(
+        std::shared_ptr<AeroData> aero_data,
+        const double &n_part,
+        const bpstd::string_view &weight,
+        const CampCore &camp_core
+    ):
+        ptr(f_aero_state_ctor, f_aero_state_dtor),
+        aero_data(aero_data)
+    {
+        static const std::map<bpstd::string_view, char> weight_c{
+          //{"none", '-'},
+          {"flat", 'f'},
+          {"flat_source", 'F'},
+          //{"power", 'p'},
+          //{"power_source", 'P'},
+          {"nummass", 'n'},
+          {"nummass_source", 'N'},
+        };
+
+        if (weight_c.find(weight) == weight_c.end()) {
+            std::ostringstream msg;
+            msg << "unknown weighting scheme '" << weight << "', valid options are: ";
+            auto index = 0;
+            for (auto const& pair: weight_c)
+                msg << (!index++ ? "" : ", ") << pair.first;
+            throw std::runtime_error(msg.str());
+        }
+
+        f_aero_state_init(
+            ptr.f_arg(),
+            aero_data->ptr.f_arg(),
+            &n_part,
+            &weight_c.at(weight)
+        );
+        f_aero_state_initialize(ptr.f_arg_non_const(), aero_data->ptr.f_arg(),
+           camp_core.ptr.f_arg());
+    }
+
     static std::size_t __len__(const AeroState &self) {
         int len;
         f_aero_state_len(

src/camp_core.F90

@@ -20,6 +20,24 @@ subroutine f_camp_core_ctor(ptr_c) bind(C)
         ptr_c = c_loc(ptr_f)
     end subroutine
 
+    subroutine f_camp_core_initialize(ptr_c, prefix_data, prefix_size) bind(C)
+        type(camp_core_t), pointer :: ptr_f => null()
+        type(c_ptr), intent(out) :: ptr_c
+
+    character(kind=c_char), dimension(*), intent(in) :: prefix_data
+    integer(c_int), intent(in) :: prefix_size
+    character(len=prefix_size) :: prefix
+    integer :: i
+
+    do i=1, prefix_size
+       prefix(i:i) = prefix_data(i)
+    end do
+
+        ptr_f => camp_core_t(prefix)
+        call ptr_f%initialize()
+        ptr_c = c_loc(ptr_f)
+    end subroutine
+
     subroutine f_camp_core_dtor(ptr_c) bind(C)
         type(camp_core_t), pointer :: ptr_f => null()
         type(c_ptr), intent(in) :: ptr_c

src/camp_core.hpp

@@ -11,6 +11,8 @@
 
 extern "C" void f_camp_core_ctor(void *ptr) noexcept;
 extern "C" void f_camp_core_dtor(void *ptr) noexcept;
+extern "C" void f_camp_core_initialize(void *ptr, const char *prefix,
+    const int *prefix_size) noexcept;
 
 struct CampCore {
     PMCResource ptr;
@@ -19,4 +21,11 @@ struct CampCore {
         ptr(f_camp_core_ctor, f_camp_core_dtor)
     {
     }
+
+    CampCore(const std::string &config_name) :
+        ptr(f_camp_core_ctor, f_camp_core_dtor)
+    {
+        const int config_name_size = config_name.size();
+        f_camp_core_initialize(ptr.f_arg_non_const(), config_name.c_str(), &config_name_size);
+    }
 };

src/gas_data.F90

@@ -46,6 +46,16 @@ subroutine f_gas_data_from_json(ptr_c) bind(C)
         call spec_file_read_gas_data(nofile, ptr_f)
     end subroutine
 
+    subroutine f_gas_data_from_camp(ptr_c, camp_core_ptr_c) bind(C)
+        type(gas_data_t), pointer :: ptr_f => null()
+        type(c_ptr), intent(in) :: ptr_c, camp_core_ptr_c
+        type(camp_core_t), pointer :: camp_core_ptr_f => null()
+
+        call c_f_pointer(ptr_c, ptr_f)
+        call c_f_pointer(camp_core_ptr_c, camp_core_ptr_f)
+        call gas_data_initialize(ptr_f, camp_core_ptr_f)
+    end subroutine
+
     subroutine f_gas_data_spec_by_name(ptr_c, value, name_data, name_size) &
          bind(C)
       type(gas_data_t), pointer :: ptr_f => null()

src/gas_data.hpp

@@ -9,13 +9,15 @@
 #include "json_resource.hpp"
 #include "pmc_resource.hpp"
 #include "gas_data_parameters.hpp"
+#include "camp_core.hpp"
 #include "pybind11/stl.h"
 #include "pybind11_json/pybind11_json.hpp"
 
 extern "C" void f_gas_data_ctor(void *ptr) noexcept;
 extern "C" void f_gas_data_dtor(void *ptr) noexcept;
 extern "C" void f_gas_data_len(const void *ptr, int *len) noexcept;
 extern "C" void f_gas_data_from_json(const void *ptr) noexcept;
+extern "C" void f_gas_data_from_camp(const void *ptr, const void *camp_core_ptr) noexcept;
 extern "C" void f_gas_data_to_json(const void *ptr) noexcept;
 extern "C" void f_gas_data_spec_by_name(const void *ptr, int *value, const char *name_data,
     const int *name_size) noexcept;
@@ -26,6 +28,12 @@ struct GasData {
     PMCResource ptr;
     const nlohmann::json json;
 
+    GasData(const CampCore &CampCore) :
+        ptr(f_gas_data_ctor, f_gas_data_dtor)
+    {
+        f_gas_data_from_camp(this->ptr.f_arg(), CampCore.ptr.f_arg());
+    }
+
     GasData(const pybind11::tuple &tpl) :
         ptr(f_gas_data_ctor, f_gas_data_dtor),
         json(tpl)

src/photolysis.F90

@@ -6,6 +6,7 @@
 
 module PyPartMC_photolysis
     use iso_c_binding
+    use camp_camp_core
     use pmc_photolysis
     implicit none
 
@@ -19,6 +20,20 @@ subroutine f_photolysis_ctor(ptr_c) bind(C)
         ptr_c = c_loc(ptr_f)
     end subroutine
 
+    subroutine f_photolysis_create(ptr_c, camp_core_ptr_c) bind(C)
+        type(photolysis_t), pointer :: ptr_f => null()
+        type(camp_core_t), pointer :: camp_core_ptr_f => null()
+        type(c_ptr), intent(inout) :: ptr_c
+        type(c_ptr), intent(in) :: camp_core_ptr_c
+
+        call c_f_pointer(ptr_c, ptr_f)
+        call c_f_pointer(camp_core_ptr_c, camp_core_ptr_f)
+
+        ptr_f => photolysis_t(camp_core_ptr_f)
+
+        ptr_c = c_loc(ptr_f)
+   end subroutine
+
     subroutine f_photolysis_dtor(ptr_c) bind(C)
         type(photolysis_t), pointer :: ptr_f => null()
         type(c_ptr), intent(in) :: ptr_c

src/photolysis.hpp

@@ -8,15 +8,22 @@
 
 #include "json_resource.hpp"
 #include "pmc_resource.hpp"
+#include "camp_core.hpp"
 
 extern "C" void f_photolysis_ctor(void *ptr) noexcept;
 extern "C" void f_photolysis_dtor(void *ptr) noexcept;
-
+extern "C" void f_photolysis_create(const void *ptr, const void *camp_core) noexcept;
 struct Photolysis {
     PMCResource ptr;
 
     Photolysis() :
         ptr(f_photolysis_ctor, f_photolysis_dtor)
     {
     }
+
+    Photolysis(const CampCore &camp_core) :
+        ptr(f_photolysis_ctor, f_photolysis_dtor)
+    {
+        f_photolysis_create(this->ptr.f_arg(), camp_core.ptr.f_arg());
+    }
 };

src/pypartmc.cpp

@@ -104,6 +104,7 @@ PYBIND11_MODULE(_PyPartMC, m) {
              same, but without the \c _a suffix.
         )pbdoc"
     )
+        .def(py::init<const nlohmann::json&, const CampCore&>())
         .def(py::init<const nlohmann::json&>())
         .def("spec_by_name", AeroData::spec_by_name,
              "Returns the number of the species in AeroData with the given name")
@@ -229,6 +230,8 @@ PYBIND11_MODULE(_PyPartMC, m) {
         )pbdoc"
     )
         .def(py::init<std::shared_ptr<AeroData>, const double, const std::string>())
+        .def(py::init<std::shared_ptr<AeroData>, const double, const std::string,
+             const CampCore&>())
         .def("__len__", AeroState::__len__,
             "returns current number of particles")
         .def_property_readonly("total_num_conc", AeroState::total_num_conc,
@@ -307,6 +310,7 @@ PYBIND11_MODULE(_PyPartMC, m) {
             is gas_state%%mix_rat(i).
         )pbdoc"
     )
+        .def(py::init<const CampCore&>())
         .def(py::init<const py::tuple&>())
         .def("__len__", GasData::__len__,
             "returns number of gas species")
@@ -357,6 +361,7 @@ PYBIND11_MODULE(_PyPartMC, m) {
         )pbdoc"
     )
         .def(py::init<>())
+        .def(py::init<const CampCore&>())
     ;
 
     py::class_<CampCore>(m,
@@ -366,6 +371,7 @@ PYBIND11_MODULE(_PyPartMC, m) {
         )pbdoc"
     )
         .def(py::init<>())
+        .def(py::init<const std::string &>())
     ;
 
     py::class_<Scenario>(m,

src/run_part.F90

@@ -8,6 +8,8 @@ module PyPartMC_run_part
 
   use iso_c_binding
   use pmc_run_part
+  use camp_camp_core
+  use pmc_photolysis
 
   implicit none
 
@@ -61,6 +63,10 @@ subroutine f_run_part( &
     call c_f_pointer(camp_core_ptr_c, camp_core_ptr_f)
     call c_f_pointer(photolysis_ptr_c, photolysis_ptr_f)
 
+    if (run_part_opt_ptr_f%do_camp_chem) then
+       call camp_core_ptr_f%solver_initialize()
+    end if
+
     call run_part( &
       scenario_ptr_f, &
       env_state_ptr_f, &
@@ -148,6 +154,9 @@ subroutine f_run_part_timestep( &
     if (env_state_ptr_f%elapsed_time < run_part_opt_ptr_f%del_t) then
        call mosaic_init(env_state_ptr_f, aero_data_ptr_f, run_part_opt_ptr_f%del_t, &
             run_part_opt_ptr_f%do_optical)
+       if (run_part_opt_ptr_f%do_camp_chem) then
+          call camp_core_ptr_f%solver_initialize()
+       end if
        if (run_part_opt_ptr_f%t_output > 0) then
           call output_state(run_part_opt_ptr_f%output_prefix, &
                run_part_opt_ptr_f%output_type, aero_data_ptr_f, aero_state_ptr_f, gas_data_ptr_f, &
@@ -156,6 +165,7 @@ subroutine f_run_part_timestep( &
                run_part_opt_ptr_f%do_optical, run_part_opt_ptr_f%uuid)
        end if
     end if
+
     call run_part_timestep(scenario_ptr_f, env_state_ptr_f, aero_data_ptr_f, aero_state_ptr_f, &
        gas_data_ptr_f, gas_state_ptr_f, run_part_opt_ptr_f, camp_core_ptr_f, photolysis_ptr_f, &
        i_time, t_start, last_output_time, &
@@ -241,6 +251,9 @@ subroutine f_run_part_timeblock( &
     if (env_state_ptr_f%elapsed_time < run_part_opt_ptr_f%del_t) then
        call mosaic_init(env_state_ptr_f, aero_data_ptr_f, run_part_opt_ptr_f%del_t, &
             run_part_opt_ptr_f%do_optical)
+       if (run_part_opt_ptr_f%do_camp_chem) then
+          call camp_core_ptr_f%solver_initialize()
+       end if
        if (run_part_opt_ptr_f%t_output > 0) then
           call output_state(run_part_opt_ptr_f%output_prefix, &
                run_part_opt_ptr_f%output_type, aero_data_ptr_f, aero_state_ptr_f, gas_data_ptr_f, &

tests/test_photolysis.py

@@ -0,0 +1,11 @@
+import PyPartMC as ppmc
+
+
+class TestPhotolysis:
+    @staticmethod
+    def test_ctor_without_camp():
+        _ = ppmc.Photolysis()
+
+    @staticmethod
+    def test_ctor_with_camp():
+        _ = ppmc.Photolysis(ppmc.CampCore())