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https://git.gfz-potsdam.de/naaice/iphreeqc.git
synced 2025-12-16 00:28:23 +01:00
Refactor API
This commit is contained in:
Max Luebke
parent
54136c8e0c
commit
d92ab31765
@ -14,6 +14,7 @@
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#include <map>
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#include <string>
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#include <sys/types.h>
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#include <utility>
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#include <vector>
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enum { POET_SOL = 0, POET_EXCH, POET_KIN, POET_EQUIL, POET_SURF };
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@ -33,42 +34,51 @@ public:
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this->LoadDatabase(database.c_str());
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this->RunFile(input_script.c_str());
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this->parseInitValues();
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this->parseInit();
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}
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std::vector<std::string> getInitNames() const {
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std::vector<std::string> names;
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IPhreeqcPOET(const std::string &database, const std::string &input_script,
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const std::vector<std::string> &solutionInitVector,
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std::uint32_t n_cells)
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: IPhreeqc(), n_cells(n_cells), solutionInitVector(solutionInitVector) {
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this->LoadDatabase(database.c_str());
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this->RunFile(input_script.c_str());
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for (auto &sol : this->initial_names) {
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names.insert(names.end(), sol.begin(), sol.end());
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if (n_cells > 1) {
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std::string copy_string =
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"COPY cell 1 2-" + std::to_string(n_cells) + "\n";
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}
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return names;
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}
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std::vector<std::vector<double>> getInitValues() const {
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return this->initial_concentrations;
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}
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struct PhreeqcMat {
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std::vector<std::string> names;
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std::vector<int> ids;
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std::vector<std::vector<double>> values;
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};
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std::vector<int> getSolutionIds() const { return this->solution_ids; }
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PhreeqcMat getPhreeqcMat();
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PhreeqcMat getPhreeqcMat(const std::vector<int> &ids);
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std::map<int, std::string> raw_dumps() {
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std::map<int, std::string> dumps;
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this->SetDumpStringOn(true);
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for (const auto &sol_id : this->solution_ids) {
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for (const auto &[sol_id, unused] : this->raw_initials) {
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std::string call_string = "DUMP\n -cells " + std::to_string(sol_id);
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this->RunString(call_string.c_str());
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dumps[sol_id] = this->GetDumpString();
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}
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this->SetDumpStringOn(false);
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return dumps;
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}
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using essential_names = std::array<std::vector<std::string>, 5>;
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using ModulesArray = std::array<std::uint32_t, 5>;
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ModulesArray getModuleSizes() const {
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ModulesArray module_sizes;
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for (std::uint8_t i = 0; i < 5; i++) {
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@ -79,13 +89,13 @@ public:
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}
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private:
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using essential_names = std::array<std::vector<std::string>, 5>;
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// required only for simulation
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essential_names initial_names;
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std::vector<std::vector<double>> initial_concentrations;
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std::vector<int> solution_ids;
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std::uint32_t n_cells;
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std::vector<std::string> solutionInitVector;
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void parseInitValues();
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void parseInit();
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essential_names dump_essential_names(std::size_t cell_number);
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@ -110,13 +120,15 @@ private:
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return Utilities::Rxn_find(this->PhreeqcPtr->Get_Rxn_surface_map(), n);
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}
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void resolveSolutionUseKW(
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const std::vector<IPhreeqc::SolutionMapping> &unresolved,
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std::map<int, std::pair<essential_names, std::vector<double>>>
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&mapped_values);
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using RawMap = std::map<int, std::pair<essential_names, std::vector<double>>>;
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void valuesFromModule(const std::string &module_name, int cell_number,
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essential_names &names, std::vector<double> &values);
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essential_names union_raws(const RawMap &raws);
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std::vector<std::vector<double>>
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conc_from_essentials(const RawMap &raws, const essential_names &names);
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// void valuesFromModule(const std::string &module_name, int cell_number,
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// essential_names &names, std::vector<double> &values);
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std::string subExchangeName(std::string name) {
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for (const auto &species : this->PhreeqcPtr->Get_species_list()) {
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@ -128,4 +140,6 @@ private:
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}
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return name;
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};
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RawMap raw_initials;
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};
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119
poet/src/GetSet.cpp
Normal file
119
poet/src/GetSet.cpp
Normal file
@ -0,0 +1,119 @@
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#include <IPhreeqcPOET.hpp>
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IPhreeqcPOET::essential_names
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IPhreeqcPOET::dump_essential_names(std::size_t cell_number) {
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essential_names eNames;
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// Solutions
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if (this->Get_solution(cell_number) != NULL) {
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std::vector<std::string> &eSolNames = eNames[POET_SOL];
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this->Get_solution(cell_number)->dump_essential_names(eSolNames);
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}
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// Exchange
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if (this->Get_exchange(cell_number) != NULL) {
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std::vector<std::string> &eExchNames = eNames[POET_EXCH];
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this->Get_exchange(cell_number)->dump_essential_names(eExchNames);
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}
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// Kinetics
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if (this->Get_kinetic(cell_number) != NULL) {
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std::vector<std::string> &eKinNames = eNames[POET_KIN];
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this->Get_kinetic(cell_number)->dump_essential_names(eKinNames);
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}
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// PPassemblage
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if (this->Get_equilibrium(cell_number) != NULL) {
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std::vector<std::string> &eEquNames = eNames[POET_EQUIL];
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this->Get_equilibrium(cell_number)->dump_essential_names(eEquNames);
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}
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// Surface
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if (this->Get_surface(cell_number) != NULL) {
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std::vector<std::string> &eSurfNames = eNames[POET_SURF];
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this->Get_surface(cell_number)->dump_essential_names(eSurfNames);
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}
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return eNames;
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}
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std::vector<double>
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IPhreeqcPOET::get_essential_values(std::size_t cell_number,
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const std::vector<std::string> &order) {
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std::vector<double> essentials;
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// Solutions
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if (this->Get_solution(cell_number) != NULL) {
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std::vector<double> sol_values;
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this->Get_solution(cell_number)->get_essential_values(sol_values, order);
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essentials.insert(essentials.end(), sol_values.begin(), sol_values.end());
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}
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// Exchange
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if (this->Get_exchange(cell_number) != NULL) {
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std::vector<double> exch_values;
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this->Get_exchange(cell_number)->get_essential_values(exch_values);
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essentials.insert(essentials.end(), exch_values.begin(), exch_values.end());
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}
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// Kinetics
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if (this->Get_kinetic(cell_number) != NULL) {
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std::vector<double> kin_values;
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this->Get_kinetic(cell_number)->get_essential_values(kin_values);
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essentials.insert(essentials.end(), kin_values.begin(), kin_values.end());
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}
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// PPassemblage
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if (this->Get_equilibrium(cell_number) != NULL) {
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std::vector<double> equ_values;
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this->Get_equilibrium(cell_number)->get_essential_values(equ_values);
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essentials.insert(essentials.end(), equ_values.begin(), equ_values.end());
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}
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// Surface
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if (this->Get_surface(cell_number) != NULL) {
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std::vector<double> surf_values;
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this->Get_surface(cell_number)->get_essential_values(surf_values);
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essentials.insert(essentials.end(), surf_values.begin(), surf_values.end());
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}
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return essentials;
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}
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void IPhreeqcPOET::set_essential_values(std::size_t cell_number,
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const std::vector<std::string> &order,
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std::vector<double> &values) {
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auto dump_it = values.begin();
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// Solutions
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if (this->Get_solution(cell_number) != NULL) {
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this->Get_solution(cell_number)->set_essential_values(dump_it, order);
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}
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// Exchange
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if (this->Get_exchange(cell_number) != NULL) {
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this->Get_exchange(cell_number)->set_essential_values(dump_it);
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}
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// Kinetics
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if (this->Get_kinetic(cell_number) != NULL) {
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this->Get_kinetic(cell_number)->set_essential_values(dump_it);
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}
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// PPassemblage
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if (this->Get_equilibrium(cell_number) != NULL) {
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this->Get_equilibrium(cell_number)->set_essential_values(dump_it);
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}
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// Surface
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if (this->Get_surface(cell_number) != NULL) {
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this->Get_surface(cell_number)->set_essential_values(dump_it);
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}
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}
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@ -38,57 +38,58 @@ createConcVector(const std::vector<std::string> &conc_names,
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return conc_vec;
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}
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void IPhreeqcPOET::valuesFromModule(const std::string &module_name,
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int cell_number, essential_names &names,
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std::vector<double> &values) {
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std::size_t dest_module_i = 0;
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std::vector<double> to_insert;
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if (module_name == "exchange") { // 1
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this->Get_exchange(cell_number)->dump_essential_names(names[POET_EXCH]);
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this->Get_exchange(cell_number)->get_essential_values(to_insert);
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dest_module_i = 1;
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} else if (module_name == "kinetics") { // 2
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this->Get_kinetic(cell_number)->dump_essential_names(names[POET_KIN]);
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this->Get_kinetic(cell_number)->get_essential_values(to_insert);
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dest_module_i = 2;
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} else if (module_name == "surface") { // 4
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this->Get_surface(cell_number)->dump_essential_names(names[POET_SURF]);
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this->Get_surface(cell_number)->get_essential_values(to_insert);
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dest_module_i = 4;
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}
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// void IPhreeqcPOET::valuesFromModule(const std::string &module_name,
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// int cell_number, essential_names &names,
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// std::vector<double> &values) {
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// std::size_t dest_module_i = 0;
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// std::vector<double> to_insert;
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// if (module_name == "exchange") { // 1
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// this->Get_exchange(cell_number)->dump_essential_names(names[POET_EXCH]);
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// this->Get_exchange(cell_number)->get_essential_values(to_insert);
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// dest_module_i = 1;
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// } else if (module_name == "kinetics") { // 2
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// this->Get_kinetic(cell_number)->dump_essential_names(names[POET_KIN]);
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// this->Get_kinetic(cell_number)->get_essential_values(to_insert);
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// dest_module_i = 2;
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// } else if (module_name == "surface") { // 4
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// this->Get_surface(cell_number)->dump_essential_names(names[POET_SURF]);
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// this->Get_surface(cell_number)->get_essential_values(to_insert);
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// dest_module_i = 4;
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// }
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std::size_t offset = 0;
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for (std::size_t i = 0; i < dest_module_i; i++) {
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offset += names[i].size();
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}
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// std::size_t offset = 0;
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// for (std::size_t i = 0; i < dest_module_i; i++) {
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// offset += names[i].size();
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// }
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values.insert(values.begin() + offset, to_insert.begin(), to_insert.end());
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}
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// values.insert(values.begin() + offset, to_insert.begin(), to_insert.end());
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// }
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void IPhreeqcPOET::resolveSolutionUseKW(
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const std::vector<IPhreeqc::SolutionMapping> &unresolved,
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std::map<int, std::pair<essential_names, std::vector<double>>>
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&mapped_values) {
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// void IPhreeqcPOET::resolveSolutionUseKW(
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// const std::vector<IPhreeqc::SolutionMapping> &unresolved,
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// std::map<int, std::pair<essential_names, std::vector<double>>>
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// &mapped_values) {
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for (const auto &input : unresolved) {
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if (mapped_values.find(input.module_n) != mapped_values.end()) {
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continue;
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}
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// for (const auto &input : unresolved) {
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// if (mapped_values.find(input.module_n) != mapped_values.end()) {
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// continue;
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// }
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essential_names new_conc_names;
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new_conc_names[0] = mapped_values[input.sol_n].first[0];
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// essential_names new_conc_names;
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// new_conc_names[0] = mapped_values[input.sol_n].first[0];
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const auto &curr_sol_vec = mapped_values[input.sol_n].second;
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std::vector<double> new_conc_values(
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curr_sol_vec.begin(), curr_sol_vec.begin() + new_conc_names[0].size());
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// const auto &curr_sol_vec = mapped_values[input.sol_n].second;
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// std::vector<double> new_conc_values(
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// curr_sol_vec.begin(), curr_sol_vec.begin() +
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// new_conc_names[0].size());
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valuesFromModule(input.module_name, input.module_n, new_conc_names,
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new_conc_values);
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// valuesFromModule(input.module_name, input.module_n, new_conc_names,
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// new_conc_values);
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mapped_values[input.module_n] =
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std::make_pair(new_conc_names, new_conc_values);
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}
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}
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// mapped_values[input.module_n] =
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// std::make_pair(new_conc_names, new_conc_values);
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// }
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// }
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void IPhreeqcPOET::parseInitValues() {
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@ -106,8 +107,8 @@ void IPhreeqcPOET::parseInitValues() {
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curr_conc_names, this->get_essential_values(id, curr_conc_names[0]));
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}
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const auto unresolved_modules = this->getSolutionMapping();
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resolveSolutionUseKW(unresolved_modules, init_values);
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// const auto unresolved_modules = this->getSolutionMapping();
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// resolveSolutionUseKW(unresolved_modules, init_values);
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std::vector<int> ids_to_erase;
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@ -182,122 +183,4 @@ void IPhreeqcPOET::parseInitValues() {
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// solution_only, init_values[val.sol_n].second);
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// }
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// }
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}
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IPhreeqcPOET::essential_names
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IPhreeqcPOET::dump_essential_names(std::size_t cell_number) {
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essential_names eNames;
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// Solutions
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if (this->Get_solution(cell_number) != NULL) {
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std::vector<std::string> &eSolNames = eNames[POET_SOL];
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this->Get_solution(cell_number)->dump_essential_names(eSolNames);
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}
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// Exchange
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if (this->Get_exchange(cell_number) != NULL) {
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std::vector<std::string> &eExchNames = eNames[POET_EXCH];
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this->Get_exchange(cell_number)->dump_essential_names(eExchNames);
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}
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// Kinetics
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if (this->Get_kinetic(cell_number) != NULL) {
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std::vector<std::string> &eKinNames = eNames[POET_KIN];
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this->Get_kinetic(cell_number)->dump_essential_names(eKinNames);
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}
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// PPassemblage
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if (this->Get_equilibrium(cell_number) != NULL) {
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std::vector<std::string> &eEquNames = eNames[POET_EQUIL];
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this->Get_equilibrium(cell_number)->dump_essential_names(eEquNames);
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}
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// Surface
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if (this->Get_surface(cell_number) != NULL) {
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std::vector<std::string> &eSurfNames = eNames[POET_SURF];
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this->Get_surface(cell_number)->dump_essential_names(eSurfNames);
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}
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return eNames;
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}
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std::vector<double>
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IPhreeqcPOET::get_essential_values(std::size_t cell_number,
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const std::vector<std::string> &order) {
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std::vector<double> essentials;
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// Solutions
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if (this->Get_solution(cell_number) != NULL) {
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std::vector<double> sol_values;
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this->Get_solution(cell_number)->get_essential_values(sol_values, order);
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essentials.insert(essentials.end(), sol_values.begin(), sol_values.end());
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}
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// Exchange
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if (this->Get_exchange(cell_number) != NULL) {
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std::vector<double> exch_values;
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this->Get_exchange(cell_number)->get_essential_values(exch_values);
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essentials.insert(essentials.end(), exch_values.begin(), exch_values.end());
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}
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// Kinetics
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if (this->Get_kinetic(cell_number) != NULL) {
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std::vector<double> kin_values;
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this->Get_kinetic(cell_number)->get_essential_values(kin_values);
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essentials.insert(essentials.end(), kin_values.begin(), kin_values.end());
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}
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// PPassemblage
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if (this->Get_equilibrium(cell_number) != NULL) {
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std::vector<double> equ_values;
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this->Get_equilibrium(cell_number)->get_essential_values(equ_values);
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essentials.insert(essentials.end(), equ_values.begin(), equ_values.end());
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}
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// Surface
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if (this->Get_surface(cell_number) != NULL) {
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std::vector<double> surf_values;
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this->Get_surface(cell_number)->get_essential_values(surf_values);
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essentials.insert(essentials.end(), surf_values.begin(), surf_values.end());
|
||||
}
|
||||
|
||||
return essentials;
|
||||
}
|
||||
|
||||
void IPhreeqcPOET::set_essential_values(std::size_t cell_number,
|
||||
const std::vector<std::string> &order,
|
||||
std::vector<double> &values) {
|
||||
|
||||
auto dump_it = values.begin();
|
||||
|
||||
// Solutions
|
||||
if (this->Get_solution(cell_number) != NULL) {
|
||||
this->Get_solution(cell_number)->set_essential_values(dump_it, order);
|
||||
}
|
||||
|
||||
// Exchange
|
||||
if (this->Get_exchange(cell_number) != NULL) {
|
||||
this->Get_exchange(cell_number)->set_essential_values(dump_it);
|
||||
}
|
||||
|
||||
// Kinetics
|
||||
if (this->Get_kinetic(cell_number) != NULL) {
|
||||
this->Get_kinetic(cell_number)->set_essential_values(dump_it);
|
||||
}
|
||||
|
||||
// PPassemblage
|
||||
if (this->Get_equilibrium(cell_number) != NULL) {
|
||||
this->Get_equilibrium(cell_number)->set_essential_values(dump_it);
|
||||
}
|
||||
|
||||
// Surface
|
||||
if (this->Get_surface(cell_number) != NULL) {
|
||||
this->Get_surface(cell_number)->set_essential_values(dump_it);
|
||||
}
|
||||
}
|
||||
110
poet/src/Init.cpp
Normal file
110
poet/src/Init.cpp
Normal file
@ -0,0 +1,110 @@
|
||||
#include <IPhreeqcPOET.hpp>
|
||||
|
||||
#include <algorithm>
|
||||
#include <cstddef>
|
||||
#include <tuple>
|
||||
#include <vector>
|
||||
|
||||
static inline std::vector<std::string>
|
||||
unionStringVectors(const std::vector<std::string> &a,
|
||||
const std::vector<std::string> &b) {
|
||||
std::vector<std::string> result;
|
||||
|
||||
std::set_union(a.begin(), a.end(), b.begin(), b.end(),
|
||||
std::back_inserter(result));
|
||||
|
||||
return result;
|
||||
}
|
||||
|
||||
static std::vector<double>
|
||||
createConcVector(const std::vector<std::string> &conc_names,
|
||||
const std::vector<double>::const_iterator &conc_it,
|
||||
const std::vector<std::string> &new_names) {
|
||||
std::vector<double> conc_vec;
|
||||
|
||||
for (const auto &i : new_names) {
|
||||
auto it = std::find(conc_names.begin(), conc_names.end(), i);
|
||||
|
||||
auto conc_index = std::distance(conc_names.begin(), it);
|
||||
|
||||
if (it != conc_names.end()) {
|
||||
conc_vec.push_back(*(conc_it + conc_index));
|
||||
} else {
|
||||
conc_vec.push_back(std::numeric_limits<double>::quiet_NaN());
|
||||
}
|
||||
}
|
||||
|
||||
return conc_vec;
|
||||
}
|
||||
|
||||
void IPhreeqcPOET::parseInit() {
|
||||
|
||||
std::map<int, std::pair<essential_names, std::vector<double>>> init_values;
|
||||
|
||||
for (const auto &[id, val] : this->PhreeqcPtr->Get_Rxn_solution_map()) {
|
||||
// A key less than zero indicates an internal solution
|
||||
if (id < 0) {
|
||||
continue;
|
||||
}
|
||||
|
||||
const essential_names curr_conc_names = this->dump_essential_names(id);
|
||||
|
||||
auto pair = std::make_pair(
|
||||
curr_conc_names, this->get_essential_values(id, curr_conc_names[0]));
|
||||
raw_initials[id] = pair;
|
||||
}
|
||||
}
|
||||
|
||||
IPhreeqcPOET::essential_names IPhreeqcPOET::union_raws(const RawMap &raws) {
|
||||
IPhreeqcPOET::essential_names names;
|
||||
for (const auto &[sol_id, val] : raws) {
|
||||
for (std::size_t i = 0; i < names.size(); i++) {
|
||||
names[i] = unionStringVectors(names[i], val.first[i]);
|
||||
}
|
||||
|
||||
for (auto &specie : names[POET_EXCH]) {
|
||||
specie = this->subExchangeName(specie);
|
||||
}
|
||||
}
|
||||
|
||||
return names;
|
||||
}
|
||||
|
||||
std::vector<std::vector<double>>
|
||||
IPhreeqcPOET::conc_from_essentials(const RawMap &raws,
|
||||
const essential_names &names) {
|
||||
std::vector<std::vector<double>> values;
|
||||
|
||||
for (const auto &[key, val] : raws) {
|
||||
std::vector<double> combined_conc_vec;
|
||||
|
||||
for (std::size_t i = 0, offset = 0; i < names.size(); i++) {
|
||||
std::vector<double> union_vec =
|
||||
createConcVector(val.first[i], val.second.begin() + offset, names[i]);
|
||||
|
||||
combined_conc_vec.insert(combined_conc_vec.end(), union_vec.begin(),
|
||||
union_vec.end());
|
||||
|
||||
offset += val.first[i].size();
|
||||
}
|
||||
|
||||
values.push_back(combined_conc_vec);
|
||||
}
|
||||
}
|
||||
|
||||
IPhreeqcPOET::PhreeqcMat IPhreeqcPOET::getPhreeqcMat() {
|
||||
std::vector<std::vector<double>> values;
|
||||
|
||||
const IPhreeqcPOET::essential_names names =
|
||||
this->union_raws(this->raw_initials);
|
||||
|
||||
const std::vector<std::vector<double>> conc_values =
|
||||
this->conc_from_essentials(this->raw_initials, names);
|
||||
|
||||
|
||||
std::vector<int> ids(this->raw_initials.size());
|
||||
|
||||
std::transform(this->raw_initials.begin(), this->raw_initials.end(),
|
||||
ids.begin(), [](const auto &pair) { return pair.first; });
|
||||
|
||||
}
|
||||
Loading…
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Reference in New Issue
Block a user