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jcurtis2
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slayoo
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Add sectional and exact simulations plus aero_binned type (#426)
Co-authored-by: Sylwester Arabas <sylwester.arabas@agh.edu.pl>
1 parent 8ba1e54 commit 68e48e1

28 files changed

Lines changed: 1456 additions & 20 deletions

‎CMakeLists.txt‎

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

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!###################################################################################################
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! This file is a part of PyPartMC licensed under the GNU General Public License v3 (LICENSE file) #
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! Copyright (C) 2025 University of Illinois Urbana-Champaign #
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! Authors: https://github.com/open-atmos/PyPartMC/graphs/contributors #
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!###################################################################################################
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module PyPartMC_aero_binned
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use iso_c_binding
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use pmc_aero_binned
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implicit none
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contains
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subroutine f_aero_binned_ctor(ptr_c) bind(C)
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type(aero_binned_t), pointer :: ptr_f => null()
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type(c_ptr), intent(out) :: ptr_c
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allocate(ptr_f)
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ptr_c = c_loc(ptr_f)
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end subroutine
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subroutine f_aero_binned_dtor(ptr_c) bind(C)
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type(aero_binned_t), pointer :: ptr_f => null()
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type(c_ptr), intent(in) :: ptr_c
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call c_f_pointer(ptr_c, ptr_f)
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deallocate(ptr_f)
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end subroutine
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subroutine f_aero_binned_num_conc(ptr_c, num_conc, n_bins) bind(C)
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type(aero_binned_t), pointer :: ptr_f => null()
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type(c_ptr), intent(in) :: ptr_c
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integer(c_int), intent(in) :: n_bins
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real(c_double), intent(inout) :: num_conc(n_bins)
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call c_f_pointer(ptr_c, ptr_f)
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num_conc = ptr_f%num_conc
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end subroutine
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subroutine f_aero_binned_species_vol_conc(ptr_c, vol_conc, n_bins, i_spec) bind(C)
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type(aero_binned_t), pointer :: ptr_f => null()
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type(c_ptr), intent(in) :: ptr_c
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integer(c_int), intent(in) :: n_bins, i_spec
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real(c_double), intent(inout) :: vol_conc(n_bins)
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call c_f_pointer(ptr_c, ptr_f)
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vol_conc = ptr_f%vol_conc(:,i_spec+1)
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end subroutine
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subroutine f_aero_binned_len(ptr_c, len) bind(C)
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type(aero_binned_t), pointer :: ptr_f => null()
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type(c_ptr), intent(in) :: ptr_c
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integer(c_int), intent(out) :: len
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call c_f_pointer(ptr_c, ptr_f)
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len = size(ptr_f%num_conc)
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end subroutine
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subroutine f_aero_binned_add_aero_dist(ptr_c, bin_grid_ptr_c, aero_data_ptr_c, &
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aero_dist_ptr_c) bind(C)
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type(c_ptr), intent(in) :: ptr_c, bin_grid_ptr_c, aero_data_ptr_c, &
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aero_dist_ptr_c
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type(aero_binned_t), pointer :: ptr_f => null()
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type(aero_data_t), pointer :: aero_data_ptr_f => null()
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type(aero_dist_t), pointer :: aero_dist_ptr_f => null()
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type(bin_grid_t), pointer :: bin_grid_ptr_f => null()
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call c_f_pointer(ptr_c, ptr_f)
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call c_f_pointer(bin_grid_ptr_c, bin_grid_ptr_f)
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call c_f_pointer(aero_data_ptr_c, aero_data_ptr_f)
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call c_f_pointer(aero_dist_ptr_c, aero_dist_ptr_f)
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call aero_binned_add_aero_dist(ptr_f, bin_grid_ptr_f, &
80+
aero_data_ptr_f, aero_dist_ptr_f)
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end subroutine
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subroutine f_aero_binned_set_sizes(ptr_c, aero_data_ptr_c, bin_grid_ptr_c) bind(C)
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type(c_ptr), intent(in) :: ptr_c, bin_grid_ptr_c, aero_data_ptr_c
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type(aero_binned_t), pointer :: ptr_f => null()
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type(aero_data_t), pointer :: aero_data_ptr_f => null()
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type(bin_grid_t), pointer :: bin_grid_ptr_f => null()
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call c_f_pointer(ptr_c, ptr_f)
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call c_f_pointer(bin_grid_ptr_c, bin_grid_ptr_f)
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call c_f_pointer(aero_data_ptr_c, aero_data_ptr_f)
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call aero_binned_set_sizes(ptr_f, bin_grid_size(bin_grid_ptr_f), &
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aero_data_n_spec(aero_data_ptr_f))
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end subroutine
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end module

‎src/aero_binned.hpp‎

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/*##################################################################################################
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# This file is a part of PyPartMC licensed under the GNU General Public License v3 (LICENSE file) #
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# Copyright (C) 2025 University of Illinois Urbana-Champaign #
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# Authors: https://github.com/open-atmos/PyPartMC/graphs/contributors #
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##################################################################################################*/
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#pragma once
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#include "pmc_resource.hpp"
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#include "aero_data.hpp"
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#include "bin_grid.hpp"
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#include "aero_dist.hpp"
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#include "aero_data.hpp"
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#include "pybind11/stl.h"
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extern "C" void f_aero_binned_ctor(void *ptr) noexcept;
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extern "C" void f_aero_binned_dtor(void *ptr) noexcept;
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extern "C" void f_aero_binned_len(
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const void *ptr, int *len
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) noexcept;
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extern "C" void f_aero_binned_add_aero_dist(
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void *ptr,
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const void *aero_data,
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const void *bin_grid,
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const void *aero_dist
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) noexcept;
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extern "C" void f_aero_binned_set_sizes(
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void *ptr,
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const void *aero_data,
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const void *aero_binned
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) noexcept;
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extern "C" void f_aero_binned_num_conc(
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const void *ptr,
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double *num_conc,
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const int *len
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) noexcept;
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extern "C" void f_aero_binned_species_vol_conc(
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const void *ptr,
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double *data,
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const int *n_bins,
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const int *i_spec
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) noexcept;
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struct AeroBinned {
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PMCResource ptr;
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std::shared_ptr<AeroData> aero_data;
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AeroBinned(std::shared_ptr<AeroData> aero_data) :
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ptr(f_aero_binned_ctor, f_aero_binned_dtor),
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aero_data(aero_data)
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{
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}
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AeroBinned(std::shared_ptr<AeroData> aero_data, const BinGrid &bin_grid) :
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ptr(f_aero_binned_ctor, f_aero_binned_dtor),
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aero_data(aero_data)
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{
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f_aero_binned_set_sizes(
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ptr.f_arg_non_const(),
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aero_data->ptr.f_arg(),
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bin_grid.ptr.f_arg()
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);
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}
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static auto num_conc(const AeroBinned &self) {
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int len;
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f_aero_binned_len(
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self.ptr.f_arg(),
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&len
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);
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std::valarray<double> num_conc(len);
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f_aero_binned_num_conc(
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self.ptr.f_arg(),
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begin(num_conc),
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&len
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);
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return num_conc;
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}
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static auto vol_conc(const AeroBinned &self){
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int len;
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f_aero_binned_len(
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self.ptr.f_arg(),
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&len
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);
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int cols = len;
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int rows;
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f_aero_data_len(self.aero_data->ptr.f_arg(), &rows);
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std::valarray<std::valarray<double>> vol_conc(rows);
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std::valarray<double> vol_species(cols);
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for (int i = 0; i < rows; i++) {
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vol_conc[i] = std::valarray<double>(cols);
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f_aero_binned_species_vol_conc(self.ptr.f_arg(), begin(vol_species), &cols, &i);
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for (int j = 0; j < cols; ++j) {
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vol_conc[i][j] = vol_species[j];
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}
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}
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return vol_conc;
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}
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static void add_aero_dist(AeroBinned &self,
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const BinGrid &bin_grid, const AeroDist &aero_dist)
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{
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f_aero_binned_add_aero_dist(
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self.ptr.f_arg_non_const(),
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bin_grid.ptr.f_arg(),
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self.aero_data->ptr.f_arg(),
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aero_dist.ptr.f_arg()
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);
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}
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};
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‎src/bin_grid.F90‎

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

Lines changed: 29 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
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/*##################################################################################################
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# This file is a part of PyPartMC licensed under the GNU General Public License v3 (LICENSE file) #
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# Copyright (C) 2022 University of Illinois Urbana-Champaign #
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# Copyright (C) 2022-2025 University of Illinois Urbana-Champaign #
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# Authors: https://github.com/open-atmos/PyPartMC/graphs/contributors #
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##################################################################################################*/
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@@ -38,6 +38,12 @@ extern "C" void f_bin_grid_centers(
3838
const int *arr_size
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) noexcept;
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extern "C" void f_bin_grid_widths(
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const void *ptr,
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void *arr_data,
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const int *arr_size
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) noexcept;
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extern "C" void f_bin_grid_histogram_1d(
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const void *x_bin_grid_ptr_c,
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const void *x_data,
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7480
f_bin_grid_init(ptr.f_arg(), &n_bin, &type, &min, &max);
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}
7682

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BinGrid():
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ptr(f_bin_grid_ctor, f_bin_grid_dtor)
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{
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}
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static std::size_t __len__(const BinGrid &self) {
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int len;
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f_bin_grid_size(
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);
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return data;
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}
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static auto widths(const BinGrid &self)
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{
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int len;
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f_bin_grid_size(
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self.ptr.f_arg(),
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&len
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);
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std::valarray<double> data(len);
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f_bin_grid_widths(
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self.ptr.f_arg(),
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begin(data),
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&len
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);
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return data;
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}
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};
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std::valarray<double> histogram_1d(

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