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feat: add with_h0_o0 and with_redox parameters to ChemistryModule and related classes

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This commit is contained in:
Max Lübke 2024-12-19 08:59:56 +01:00
parent e5588a2ee9
commit 6ab404eefd
5 changed files with 21 additions and 1 deletions
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3
src/Chemistry/ChemistryModule.cpp
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@ -171,7 +171,8 @@ poet::ChemistryModule::ChemistryModule(
if (!is_master) {
PhreeqcMatrix pqc_mat =
PhreeqcMatrix(chem_params.database, chem_params.pqc_script);
PhreeqcMatrix(chem_params.database, chem_params.pqc_script,
chem_params.with_h0_o0, chem_params.with_redox);
this->pqc_runner =
std::make_unique<PhreeqcRunner>(pqc_mat.subset(chem_params.pqc_ids));

2
src/Init/ChemistryInit.cpp
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@ -69,6 +69,8 @@ InitialList::ChemistryInit InitialList::getChemistryInit() const {
chem_init.database = database;
chem_init.pqc_script = pqc_script;
chem_init.pqc_ids = pqc_ids;
chem_init.with_h0_o0 = with_h0_o0;
chem_init.with_redox = with_redox;
// chem_init.pqc_scripts = pqc_scripts;
// chem_init.pqc_ids = pqc_ids;

3
src/Init/GridInit.cpp
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@ -186,6 +186,9 @@ PhreeqcMatrix InitialList::prepareGrid(const Rcpp::List &grid_input,
grid_input[GRID_MEMBER_STR(GridMembers::PQC_WITH_REDOX)])
: false;
this->with_h0_o0 = include_h0_o0;
this->with_redox = with_redox;
PhreeqcMatrix pqc_mat =
PhreeqcMatrix(database, script, include_h0_o0, with_redox);

8
src/Init/InitialList.cpp
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@ -57,6 +57,10 @@ void InitialList::importList(const Rcpp::List &setup, bool minimal) {
Rcpp::as<std::string>(setup[static_cast<int>(ExportList::CHEM_DATABASE)]);
this->pqc_script = Rcpp::as<std::string>(
setup[static_cast<int>(ExportList::CHEM_PQC_SCRIPT)]);
this->with_h0_o0 =
Rcpp::as<bool>(setup[static_cast<int>(ExportList::CHEM_PQC_WITH_H0_O0)]);
this->with_redox =
Rcpp::as<bool>(setup[static_cast<int>(ExportList::CHEM_PQC_WITH_REDOX)]);
this->field_header = Rcpp::as<std::vector<std::string>>(
setup[static_cast<int>(ExportList::CHEM_FIELD_HEADER)]);
this->pqc_ids = Rcpp::as<std::vector<int>>(
@ -113,6 +117,10 @@ Rcpp::List InitialList::exportList() {
out[static_cast<int>(ExportList::CHEM_DATABASE)] = Rcpp::wrap(this->database);
out[static_cast<int>(ExportList::CHEM_PQC_SCRIPT)] =
Rcpp::wrap(this->pqc_script);
out[static_cast<int>(ExportList::CHEM_PQC_WITH_H0_O0)] =
Rcpp::wrap(this->with_h0_o0);
out[static_cast<int>(ExportList::CHEM_PQC_WITH_REDOX)] =
Rcpp::wrap(this->with_redox);
out[static_cast<int>(ExportList::CHEM_FIELD_HEADER)] =
Rcpp::wrap(this->field_header);
out[static_cast<int>(ExportList::CHEM_PQC_IDS)] = Rcpp::wrap(this->pqc_ids);

6
src/Init/InitialList.hpp
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@ -52,6 +52,8 @@ private:
DIFFU_ALPHA_Y,
CHEM_DATABASE,
CHEM_PQC_SCRIPT,
CHEM_PQC_WITH_H0_O0,
CHEM_PQC_WITH_REDOX,
CHEM_PQC_IDS,
CHEM_FIELD_HEADER,
// CHEM_PQC_SCRIPTS,
@ -190,6 +192,8 @@ private:
std::string database;
std::string pqc_script;
bool with_h0_o0{false};
bool with_redox{false};
// std::vector<std::string> pqc_scripts;
std::vector<int> pqc_ids;
@ -220,6 +224,8 @@ public:
std::string database;
std::string pqc_script;
bool with_h0_o0;
bool with_redox;
std::vector<int> pqc_ids;
// std::map<int, std::string> pqc_input;