Add sectional and exact simulations plus aero_binned type

CMakeLists.txt

@@ -50,10 +50,11 @@ add_definitions("-DSUNDIALS_INT64_T=1")
 
 set(PyPartMC_sources 
   pypartmc.cpp json_resource.cpp spec_file_pypartmc.cpp sys.cpp
+  run_sect.F90 run_sect_opt.F90 run_exact.F90 run_exact_opt.F90 aero_binned.F90
   run_part.F90 run_part_opt.F90 util.F90 aero_data.F90 aero_state.F90 env_state.F90 gas_data.F90 
   gas_state.F90 scenario.F90 condense.F90 aero_particle.F90 bin_grid.F90
   camp_core.F90 photolysis.F90 aero_mode.F90 aero_dist.F90 bin_grid.cpp condense.cpp run_part.cpp
-  scenario.cpp util.cpp output.cpp output.F90 rand.cpp rand.F90
+  run_sect.cpp run_exact.cpp scenario.cpp util.cpp output.cpp output.F90 rand.cpp rand.F90
 )
 add_prefix(src/ PyPartMC_sources)
 

src/aero_binned.F90

@@ -0,0 +1,99 @@
+!###################################################################################################
+! This file is a part of PyPartMC licensed under the GNU General Public License v3 (LICENSE file)  #
+! Copyright (C) 2025 University of Illinois Urbana-Champaign                                       #
+! Authors: https://github.com/open-atmos/PyPartMC/graphs/contributors                              #
+!###################################################################################################
+
+module PyPartMC_aero_binned
+  use iso_c_binding
+  use pmc_aero_binned
+  implicit none
+
+  contains
+
+  subroutine f_aero_binned_ctor(ptr_c) bind(C)
+    type(aero_binned_t), pointer :: ptr_f => null()
+    type(c_ptr), intent(out) :: ptr_c
+
+    allocate(ptr_f)
+    ptr_c = c_loc(ptr_f)
+  end subroutine
+
+  subroutine f_aero_binned_dtor(ptr_c) bind(C)
+    type(aero_binned_t), pointer :: ptr_f => null()
+    type(c_ptr), intent(in) :: ptr_c
+
+    call c_f_pointer(ptr_c, ptr_f)
+    deallocate(ptr_f)
+  end subroutine
+
+  subroutine f_aero_binned_num_conc(ptr_c, num_conc, n_bins) bind(C)
+    type(aero_binned_t), pointer :: ptr_f => null()
+    type(c_ptr), intent(in) :: ptr_c
+    integer(c_int), intent(in) :: n_bins
+    real(c_double), intent(inout) :: num_conc(n_bins)
+
+    call c_f_pointer(ptr_c, ptr_f)
+
+    num_conc = ptr_f%num_conc
+
+  end subroutine
+
+  subroutine f_aero_binned_species_vol_conc(ptr_c, vol_conc, n_bins, i_spec) bind(C)
+    type(aero_binned_t), pointer :: ptr_f => null()
+    type(c_ptr), intent(in) :: ptr_c
+    integer(c_int), intent(in) :: n_bins, i_spec
+    real(c_double), intent(inout) :: vol_conc(n_bins)
+
+    call c_f_pointer(ptr_c, ptr_f)
+
+    vol_conc = ptr_f%vol_conc(:,i_spec+1)
+
+  end subroutine
+
+  subroutine f_aero_binned_len(ptr_c, len) bind(C)
+    type(aero_binned_t), pointer :: ptr_f => null()
+    type(c_ptr), intent(in) :: ptr_c
+    integer(c_int), intent(out) :: len
+
+    call c_f_pointer(ptr_c, ptr_f)
+
+    len = size(ptr_f%num_conc)
+
+  end subroutine
+
+  subroutine f_aero_binned_add_aero_dist(ptr_c, bin_grid_ptr_c, aero_data_ptr_c, &
+       aero_dist_ptr_c) bind(C)
+    type(c_ptr), intent(in) :: ptr_c, bin_grid_ptr_c, aero_data_ptr_c, &
+        aero_dist_ptr_c
+    type(aero_binned_t), pointer :: ptr_f => null()
+    type(aero_data_t), pointer :: aero_data_ptr_f => null()
+    type(aero_dist_t), pointer :: aero_dist_ptr_f => null()
+    type(bin_grid_t), pointer :: bin_grid_ptr_f => null()
+
+    call c_f_pointer(ptr_c, ptr_f)
+    call c_f_pointer(bin_grid_ptr_c, bin_grid_ptr_f)
+    call c_f_pointer(aero_data_ptr_c, aero_data_ptr_f)
+    call c_f_pointer(aero_dist_ptr_c, aero_dist_ptr_f)
+
+    call aero_binned_add_aero_dist(ptr_f, bin_grid_ptr_f, &
+         aero_data_ptr_f, aero_dist_ptr_f)
+
+  end subroutine
+
+  subroutine f_aero_binned_set_sizes(ptr_c, aero_data_ptr_c, bin_grid_ptr_c) bind(C)
+    type(c_ptr), intent(in) :: ptr_c, bin_grid_ptr_c, aero_data_ptr_c
+    type(aero_binned_t), pointer :: ptr_f => null()
+    type(aero_data_t), pointer :: aero_data_ptr_f => null()
+    type(bin_grid_t), pointer :: bin_grid_ptr_f => null()
+
+    call c_f_pointer(ptr_c, ptr_f)
+    call c_f_pointer(bin_grid_ptr_c, bin_grid_ptr_f)
+    call c_f_pointer(aero_data_ptr_c, aero_data_ptr_f)
+
+    call aero_binned_set_sizes(ptr_f, bin_grid_size(bin_grid_ptr_f), &
+         aero_data_n_spec(aero_data_ptr_f))
+
+  end subroutine
+
+end module

src/aero_binned.hpp

@@ -0,0 +1,119 @@
+/*##################################################################################################
+# This file is a part of PyPartMC licensed under the GNU General Public License v3 (LICENSE file)  #
+# Copyright (C) 2025 University of Illinois Urbana-Champaign                                       #
+# Authors: https://github.com/open-atmos/PyPartMC/graphs/contributors                              #
+##################################################################################################*/
+
+#pragma once
+
+#include "pmc_resource.hpp"
+#include "aero_data.hpp"
+#include "bin_grid.hpp"
+#include "aero_dist.hpp"
+#include "aero_data.hpp"
+#include "pybind11/stl.h"
+
+extern "C" void f_aero_binned_ctor(void *ptr) noexcept;
+extern "C" void f_aero_binned_dtor(void *ptr) noexcept;
+extern "C" void f_aero_binned_len(
+    const void *ptr, int *len
+) noexcept;
+extern "C" void f_aero_binned_add_aero_dist(
+    void *ptr,
+    const void *aero_data,
+    const void *bin_grid,
+    const void *aero_dist
+) noexcept;
+extern "C" void f_aero_binned_set_sizes(
+    void *ptr,
+    const void *aero_data,
+    const void *aero_binned
+) noexcept;
+extern "C" void f_aero_binned_num_conc(
+    const void *ptr,
+    double *num_conc,
+    const int *len
+) noexcept;
+extern "C" void f_aero_binned_species_vol_conc(
+    const void *ptr,
+    double *data,
+    const int *n_bins,
+    const int *i_spec
+) noexcept;
+
+struct AeroBinned {
+    PMCResource ptr;
+    std::shared_ptr<AeroData> aero_data;
+    AeroBinned(std::shared_ptr<AeroData> aero_data) : 
+        ptr(f_aero_binned_ctor, f_aero_binned_dtor),
+        aero_data(aero_data)
+    {
+    }
+
+    AeroBinned(std::shared_ptr<AeroData> aero_data, const BinGrid &bin_grid) : 
+        ptr(f_aero_binned_ctor, f_aero_binned_dtor),
+        aero_data(aero_data)
+    {
+        f_aero_binned_set_sizes(
+            ptr.f_arg_non_const(),
+            aero_data->ptr.f_arg(),
+            bin_grid.ptr.f_arg()
+        );
+    }
+
+    static auto num_conc(const AeroBinned &self) {
+        int len;
+        f_aero_binned_len(
+            self.ptr.f_arg(),
+            &len
+        );
+        std::valarray<double> num_conc(len);
+
+        f_aero_binned_num_conc(
+            self.ptr.f_arg(),
+            begin(num_conc),
+            &len
+        );
+
+        return num_conc;
+    }
+
+    static auto vol_conc(const AeroBinned &self){
+
+        int len;
+        f_aero_binned_len(
+            self.ptr.f_arg(),
+            &len
+        );
+
+        int cols = len;
+        int rows;
+        f_aero_data_len(self.aero_data->ptr.f_arg(), &rows);
+
+        std::valarray<std::valarray<double>> vol_conc(rows);
+        std::valarray<double> vol_species(cols);
+        for (int i = 0; i < rows; i++) {
+           vol_conc[i] = std::valarray<double>(cols);
+           f_aero_binned_species_vol_conc(self.ptr.f_arg(), begin(vol_species), &cols, &i);
+           for (int j = 0; j < cols; ++j) {
+                vol_conc[i][j] = vol_species[j];
+           } 
+       }
+
+       return vol_conc;
+
+    }
+
+    static void add_aero_dist(AeroBinned &self, 
+         const BinGrid &bin_grid, const AeroDist &aero_dist)
+    {
+         f_aero_binned_add_aero_dist(
+             self.ptr.f_arg_non_const(),
+             bin_grid.ptr.f_arg(),
+             self.aero_data->ptr.f_arg(),
+             aero_dist.ptr.f_arg()
+         );
+    }
+
+};
+

src/bin_grid.F90

@@ -1,6 +1,6 @@
 !###################################################################################################
 ! This file is a part of PyPartMC licensed under the GNU General Public License v3 (LICENSE file)  #
-! Copyright (C) 2022 University of Illinois Urbana-Champaign                                       #
+! Copyright (C) 2022-2025 University of Illinois Urbana-Champaign                                  #
 ! Authors: https://github.com/open-atmos/PyPartMC/graphs/contributors                              #
 !###################################################################################################
 
@@ -70,6 +70,16 @@ subroutine f_bin_grid_centers(ptr_c, arr_data, arr_size) bind(C)
     arr_data = bin_grid%centers
   end subroutine
 
+  subroutine f_bin_grid_widths(ptr_c, arr_data, arr_size) bind(C)
+    type(c_ptr), intent(in) :: ptr_c
+    type(bin_grid_t), pointer :: bin_grid => null()
+    integer(c_int), intent(in) :: arr_size
+    real(c_double), dimension(arr_size), intent(out) :: arr_data
+
+    call c_f_pointer(ptr_c, bin_grid)
+    arr_data = bin_grid%widths
+  end subroutine
+
   subroutine f_bin_grid_histogram_1d(x_bin_grid_ptr_c, x_data, weight_data, &
        arr_size, output_data, bin_grid_size) bind(C)
 

src/bin_grid.hpp

@@ -1,6 +1,6 @@
 /*##################################################################################################
 # This file is a part of PyPartMC licensed under the GNU General Public License v3 (LICENSE file)  #
-# Copyright (C) 2022 University of Illinois Urbana-Champaign                                       #
+# Copyright (C) 2022-2025 University of Illinois Urbana-Champaign                                  #
 # Authors: https://github.com/open-atmos/PyPartMC/graphs/contributors                              #
 ##################################################################################################*/
 
@@ -38,6 +38,12 @@ extern "C" void f_bin_grid_centers(
     const int *arr_size
 ) noexcept;
 
+extern "C" void f_bin_grid_widths(
+    const void *ptr,
+    void *arr_data,
+    const int *arr_size
+) noexcept;
+
 extern "C" void f_bin_grid_histogram_1d(
     const void *x_bin_grid_ptr_c,
     const void *x_data,
@@ -74,6 +80,11 @@ struct BinGrid {
         f_bin_grid_init(ptr.f_arg(), &n_bin, &type, &min, &max);
     }
 
+    BinGrid():
+        ptr(f_bin_grid_ctor, f_bin_grid_dtor)
+    {
+    }
+
     static std::size_t __len__(const BinGrid &self) {
         int len;
         f_bin_grid_size(
@@ -115,6 +126,23 @@ struct BinGrid {
         );
         return data;
     }
+
+    static auto widths(const BinGrid &self)
+    {
+        int len;
+        f_bin_grid_size(
+            self.ptr.f_arg(),
+            &len
+        );
+        std::valarray<double> data(len);
+        f_bin_grid_widths(
+            self.ptr.f_arg(),
+            begin(data),
+            &len
+        );
+        return data;
+    }
+
 };
 
 std::valarray<double> histogram_1d(