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https://git.gfz-potsdam.de/naaice/iphreeqc.git
synced 2025-12-16 16:44:49 +01:00
Refactor getModuleSizes method and remove commented code
This commit is contained in:
Max Lübke
Max Lübke
parent
73cb29b1bd
commit
42bcf5e446
@ -57,8 +57,7 @@ public:
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};
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PhreeqcMat getPhreeqcMat();
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PhreeqcMat getPhreeqcMat(const std::vector<int> &ids);
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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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@ -79,14 +78,7 @@ public:
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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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module_sizes[i] = this->initial_names[i].size();
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}
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return module_sizes;
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}
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ModulesArray getModuleSizes(const std::vector<int> &cell_ids);
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private:
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// required only for simulation
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@ -1,186 +0,0 @@
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#include "IPhreeqcPOET.hpp"
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#include <algorithm>
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#include <cstddef>
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#include <iterator>
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#include <string>
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#include <vector>
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static inline std::vector<std::string>
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unionStringVectors(const std::vector<std::string> &a,
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const std::vector<std::string> &b) {
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std::vector<std::string> result;
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std::set_union(a.begin(), a.end(), b.begin(), b.end(),
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std::back_inserter(result));
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return result;
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}
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static std::vector<double>
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createConcVector(const std::vector<std::string> &conc_names,
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const std::vector<double>::const_iterator &conc_it,
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const std::vector<std::string> &new_names) {
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std::vector<double> conc_vec;
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for (const auto &i : new_names) {
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auto it = std::find(conc_names.begin(), conc_names.end(), i);
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auto conc_index = std::distance(conc_names.begin(), it);
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if (it != conc_names.end()) {
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conc_vec.push_back(*(conc_it + conc_index));
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} else {
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conc_vec.push_back(std::numeric_limits<double>::quiet_NaN());
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}
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}
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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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// 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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// 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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// 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() +
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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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// 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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std::map<int, std::pair<essential_names, std::vector<double>>> init_values;
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for (const auto &[id, val] : this->PhreeqcPtr->Get_Rxn_solution_map()) {
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// A key less than zero indicates an internal solution
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if (id < 0) {
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continue;
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}
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essential_names curr_conc_names = this->dump_essential_names(id);
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init_values[id] = std::make_pair(
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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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std::vector<int> ids_to_erase;
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// loop over found initial values and erase those that are not in the ids
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for (const auto &[id, values] : init_values) {
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// find key in vector of ids
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// auto it = std::find(ids.begin(), ids.end(), id);
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// if (it == ids.end()) {
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// ids_to_erase.push_back(id);
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// continue;
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// }
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// create a union of all known concentration names
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for (std::size_t i = 0; i < 5; i++) {
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this->initial_names[i] =
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unionStringVectors(this->initial_names[i], values.first[i]);
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if (i == 1) {
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for (auto &specie : this->initial_names[i]) {
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specie = subExchangeName(specie);
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}
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}
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}
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}
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for (const auto &key : ids_to_erase) {
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init_values.erase(key);
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}
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// create a vector of the initial concentrations with NaNs for missing
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// concentrations
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for (const auto &[key, val] : init_values) {
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std::vector<double> combined_conc_vec;
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for (std::size_t i = 0, offset = 0; i < 5; i++) {
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std::vector<double> union_vec = createConcVector(
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val.first[i], val.second.begin() + offset, this->initial_names[i]);
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combined_conc_vec.insert(combined_conc_vec.end(), union_vec.begin(),
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union_vec.end());
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offset += val.first[i].size();
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}
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this->initial_concentrations.push_back(combined_conc_vec);
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this->solution_ids.push_back(key);
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}
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// const auto unresolved_modules = this->getSolutionMapping();
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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 &val : unresolved_modules) {
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// const auto &module_n = val.module_n;
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// if (init_values.find(module_n) != init_values.end()) {
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// break;
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// }
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// if (std::find(this->solution_ids.begin(), this->solution_ids.end(),
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// module_n) == this->solution_ids.end()) {
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// const int solution_index =
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// std::find(solution_ids.begin(), solution_ids.end(), val.sol_n) -
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// solution_ids.begin();
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// essential_names solution_only;
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// solution_only[0] = init_values[val.sol_n].first[0];
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// mapped_values[module_n] = std::make_pair(
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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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@ -90,21 +90,69 @@ IPhreeqcPOET::conc_from_essentials(const RawMap &raws,
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values.push_back(combined_conc_vec);
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}
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return values;
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}
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IPhreeqcPOET::PhreeqcMat IPhreeqcPOET::getPhreeqcMat() {
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std::vector<std::vector<double>> values;
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const IPhreeqcPOET::essential_names names =
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const IPhreeqcPOET::essential_names ess_names =
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this->union_raws(this->raw_initials);
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const std::vector<std::vector<double>> conc_values =
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this->conc_from_essentials(this->raw_initials, names);
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this->conc_from_essentials(this->raw_initials, ess_names);
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std::vector<std::string> conc_names;
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for (const auto &i : ess_names) {
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conc_names.insert(conc_names.end(), i.begin(), i.end());
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}
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std::vector<int> ids(this->raw_initials.size());
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std::transform(this->raw_initials.begin(), this->raw_initials.end(),
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ids.begin(), [](const auto &pair) { return pair.first; });
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return {.names = conc_names, .ids = ids, .values = conc_values};
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}
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IPhreeqcPOET::ModulesArray
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IPhreeqcPOET::getModuleSizes(const std::vector<int> &cell_ids) {
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ModulesArray module_sizes;
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RawMap raws;
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for (const auto &id : cell_ids) {
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raws[id] = this->raw_initials[id];
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}
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const IPhreeqcPOET::essential_names ess_names = this->union_raws(raws);
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std::transform(ess_names.begin(), ess_names.end(), module_sizes.begin(),
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[](const auto &mod) { return mod.size(); });
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return module_sizes;
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}
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// IPhreeqcPOET::PhreeqcMat
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// IPhreeqcPOET::getPhreeqcMat(const std::vector<int> &use_ids) {
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// std::vector<std::vector<double>> values;
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// RawMap raws;
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// for (const auto &id : use_ids) {
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// raws[id] = this->raw_initials[id];
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// }
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// const IPhreeqcPOET::essential_names ess_names = this->union_raws(raws);
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// const std::vector<std::vector<double>> conc_values =
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// this->conc_from_essentials(raws, ess_names);
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// std::vector<std::string> conc_names;
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// for (const auto &i : ess_names) {
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// conc_names.insert(conc_names.end(), i.begin(), i.end());
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// }
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// return {.names = conc_names, .ids = use_ids, .values = conc_values};
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// }
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