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refactor: Replace PhreeqcEngine instances with PhreeqcRunner for improved chemistry processing

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This commit is contained in:
Max Lübke 2024-12-04 10:34:13 +00:00
parent db7a2ad2ce
commit 6c660557fd
4 changed files with 21 additions and 34 deletions
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2
ext/iphreeqc

@ -1 +1 @@
Subproject commit 61214a01ad4cf99527f657e6a41c68282e4886c4 Subproject commit 38268b4aad03e6ce4755315f4cd690f007fa2720

14
src/Chemistry/ChemistryModule.cpp
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@ -2,6 +2,7 @@
#include "PhreeqcEngine.hpp" #include "PhreeqcEngine.hpp"
#include "PhreeqcMatrix.hpp" #include "PhreeqcMatrix.hpp"
#include "PhreeqcRunner.hpp"
#include "SurrogateModels/DHT_Wrapper.hpp" #include "SurrogateModels/DHT_Wrapper.hpp"
#include "SurrogateModels/Interpolation.hpp" #include "SurrogateModels/Interpolation.hpp"
@ -170,16 +171,9 @@ poet::ChemistryModule::ChemistryModule(
if (!is_master) { if (!is_master) {
PhreeqcMatrix pqc_mat = PhreeqcMatrix pqc_mat =
PhreeqcMatrix(chem_params.database, chem_params.pqc_script); PhreeqcMatrix(chem_params.database, chem_params.pqc_script);
for (const auto &cell_id : chem_params.pqc_ids) {
this->phreeqc_instances[cell_id] = this->pqc_runner =
std::make_unique<PhreeqcEngine>(pqc_mat, cell_id); std::make_unique<PhreeqcRunner>(pqc_mat.subset(chem_params.pqc_ids));
}
// for (std::size_t i = 0; i < chem_params.pqc_ids.size(); i++) {
// this->phreeqc_instances[chem_params.pqc_ids[i]] =
// std::make_unique<PhreeqcWrapper>(
// chem_params.database, chem_params.pqc_scripts[i],
// chem_params.pqc_sol_order, chem_params.field_header, wp_size_);
// }
} }
} }

5
src/Chemistry/ChemistryModule.hpp
View File

@ -8,10 +8,11 @@
#include "ChemistryDefs.hpp" #include "ChemistryDefs.hpp"
#include "Init/InitialList.hpp" #include "Init/InitialList.hpp"
#include "NameDouble.h"
#include "SurrogateModels/DHT_Wrapper.hpp" #include "SurrogateModels/DHT_Wrapper.hpp"
#include "SurrogateModels/Interpolation.hpp" #include "SurrogateModels/Interpolation.hpp"
#include "PhreeqcEngine.hpp" #include "PhreeqcRunner.hpp"
#include <array> #include <array>
#include <cstdint> #include <cstdint>
#include <map> #include <map>
@ -390,7 +391,7 @@ protected:
const InitialList::ChemistryInit params; const InitialList::ChemistryInit params;
std::map<int, std::unique_ptr<PhreeqcEngine>> phreeqc_instances; std::unique_ptr<PhreeqcRunner> pqc_runner;
}; };
} // namespace poet } // namespace poet

34
src/Chemistry/WorkerFunctions.cpp
View File

@ -48,13 +48,15 @@ void poet::ChemistryModule::WorkerLoop() {
case CHEM_FIELD_INIT: { case CHEM_FIELD_INIT: {
ChemBCast(&this->prop_count, 1, MPI_UINT32_T); ChemBCast(&this->prop_count, 1, MPI_UINT32_T);
if (this->ai_surrogate_enabled) { if (this->ai_surrogate_enabled) {
this->ai_surrogate_validity_vector.resize(this->n_cells); // resize statt reserve? this->ai_surrogate_validity_vector.resize(
this->n_cells); // resize statt reserve?
} }
break; break;
} }
case CHEM_AI_BCAST_VALIDITY: { case CHEM_AI_BCAST_VALIDITY: {
// Receive the index vector of valid ai surrogate predictions // Receive the index vector of valid ai surrogate predictions
MPI_Bcast(&this->ai_surrogate_validity_vector.front(), this->n_cells, MPI_INT, 0, this->group_comm); MPI_Bcast(&this->ai_surrogate_validity_vector.front(), this->n_cells,
MPI_INT, 0, this->group_comm);
break; break;
} }
case CHEM_WORK_LOOP: { case CHEM_WORK_LOOP: {
@ -187,7 +189,6 @@ void poet::ChemistryModule::WorkerDoWork(MPI_Status &probe_status,
} }
} }
phreeqc_time_start = MPI_Wtime(); phreeqc_time_start = MPI_Wtime();
WorkerRunWorkPackage(s_curr_wp, current_sim_time, dt); WorkerRunWorkPackage(s_curr_wp, current_sim_time, dt);
@ -300,28 +301,19 @@ void poet::ChemistryModule::WorkerRunWorkPackage(WorkPackage &work_package,
double dSimTime, double dSimTime,
double dTimestep) { double dTimestep) {
std::vector<std::vector<double>> inout_chem = work_package.input;
std::vector<std::size_t> to_ignore;
for (std::size_t wp_id = 0; wp_id < work_package.size; wp_id++) { for (std::size_t wp_id = 0; wp_id < work_package.size; wp_id++) {
if (work_package.mapping[wp_id] != CHEM_PQC) { if (work_package.mapping[wp_id] != CHEM_PQC) {
continue; to_ignore.push_back(wp_id);
} }
}
this->pqc_runner->run(inout_chem, dTimestep, to_ignore);
auto curr_input = work_package.input[wp_id]; for (std::size_t wp_id = 0; wp_id < work_package.size; wp_id++) {
const auto pqc_id = static_cast<int>(curr_input[0]); if (work_package.mapping[wp_id] == CHEM_PQC) {
work_package.output[wp_id] = inout_chem[wp_id];
auto &phreeqc_instance = this->phreeqc_instances[pqc_id];
work_package.output[wp_id] = work_package.input[wp_id];
curr_input.erase(std::remove_if(curr_input.begin(), curr_input.end(),
[](double d) { return std::isnan(d); }),
curr_input.end());
phreeqc_instance->runCell(curr_input, dTimestep);
std::size_t output_index = 0;
for (std::size_t i = 0; i < work_package.output[wp_id].size(); i++) {
if (!std::isnan(work_package.output[wp_id][i])) {
work_package.output[wp_id][i] = curr_input[output_index++];
}
} }
} }
} }