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Revert "feat: make output of H(0) and O(0) optional"

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This reverts commit bdb5ce944fd001cb36c8369d8c792f2f4a54c7be.
This commit is contained in:
Max Lübke 2024-12-20 08:35:00 +01:00
parent 5664153cf9
commit a718c3efaf
5 changed files with 34 additions and 91 deletions
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12
src/Init/DiffusionInit.cpp
View File

@ -3,6 +3,7 @@
// Rcpp include
#include <map>
#include <set>
#include "DataStructures/Field.hpp"
#include "InitialList.hpp"
@ -14,6 +15,7 @@
#include <Rinternals.h>
#include <cstddef>
#include <cstdint>
#include <memory>
#include <stdexcept>
#include <string>
#include <utility>
@ -24,9 +26,9 @@ namespace poet {
enum SEXP_TYPE { SEXP_IS_LIST, SEXP_IS_VEC };
const std::map<std::uint8_t, std::string> tug_side_mapping = {
{tug::BC_SIDE_RIGHT, "E"},
{tug::BC_SIDE_LEFT, "W"},
{tug::BC_SIDE_TOP, "N"},
{tug::BC_SIDE_RIGHT , "E"},
{tug::BC_SIDE_LEFT , "W"},
{tug::BC_SIDE_TOP , "N"},
{tug::BC_SIDE_BOTTOM, "S"}};
static std::vector<TugType> colMajToRowMaj(const Rcpp::NumericVector &vec,
@ -164,8 +166,8 @@ InitialList::resolveBoundaries(const Rcpp::List &boundaries_list,
if (boundaries_list.containsElementNamed(side.second.c_str())) {
const Rcpp::List mapping = boundaries_list[side.second];
const Rcpp::IntegerVector cells = mapping["cell"]; // MDL 2024-06-13
const Rcpp::IntegerVector values = mapping["sol_id"]; // MDL
const Rcpp::IntegerVector cells = mapping["cell"]; // MDL 2024-06-13
const Rcpp::IntegerVector values = mapping["sol_id"]; // MDL
const Rcpp::CharacterVector type_str = mapping["type"];
if (cells.size() != values.size()) {

75
src/Init/GridInit.cpp
View File

@ -15,42 +15,6 @@
namespace poet {
// static Rcpp::NumericMatrix pqcMatToR(const PhreeqcMatrix &phreeqc, RInside
// &R) {
// PhreeqcMatrix::STLExport phreeqc_mat = phreeqc.get();
// // PhreeqcInit::PhreeqcMat phreeqc_mat = phreeqc->getPhreeqcMat();
// // add "id" to the front of the column names
// const std::size_t ncols = phreeqc_mat.names.size();
// const std::size_t nrows = phreeqc_mat.values.size();
// phreeqc_mat.names.insert(phreeqc_mat.names.begin(), "ID");
// Rcpp::NumericMatrix mat(nrows, ncols + 1);
// for (std::size_t i = 0; i < nrows; i++) {
// mat(i, 0) = phreeqc_mat.ids[i];
// for (std::size_t j = 0; j < ncols; ++j) {
// mat(i, j + 1) = phreeqc_mat.values[i][j];
// }
// }
// Rcpp::colnames(mat) = Rcpp::wrap(phreeqc_mat.names);
// return mat;
// }
// static inline Rcpp::List matToGrid(RInside &R, const Rcpp::NumericMatrix
// &mat,
// const Rcpp::NumericMatrix &grid) {
// Rcpp::Function pqc_to_grid_R("pqc_to_grid");
// return pqc_to_grid_R(mat, grid);
// }
static inline std::map<int, std::string>
replaceRawKeywordIDs(std::map<int, std::string> raws) {
for (auto &raw : raws) {
@ -64,26 +28,6 @@ replaceRawKeywordIDs(std::map<int, std::string> raws) {
return raws;
}
// static inline uint32_t getSolutionCount(std::unique_ptr<PhreeqcInit>
// &phreeqc,
// const Rcpp::List &initial_grid) {
// PhreeqcInit::ModulesArray mod_array;
// Rcpp::Function unique_R("unique");
// std::vector<int> row_ids =
// Rcpp::as<std::vector<int>>(unique_R(initial_grid["ID"]));
// // std::vector<std::uint32_t> sizes_vec(sizes.begin(), sizes.end());
// // Rcpp::Function modify_sizes("modify_module_sizes");
// // sizes_vec = Rcpp::as<std::vector<std::uint32_t>>(
// // modify_sizes(sizes_vec, phreeqc_mat, initial_grid));
// // std::copy(sizes_vec.begin(), sizes_vec.end(), sizes.begin());
// return phreeqc->getModuleSizes(row_ids)[POET_SOL];
// }
static std::string readFile(const std::string &path) {
std::string string_rpath(PATH_MAX, '\0');
@ -121,8 +65,7 @@ static Rcpp::List expandGrid(const PhreeqcMatrix &pqc_mat,
return Rcpp::Function("pqc_to_grid")(pqc_mat_R, grid_def);
}
PhreeqcMatrix InitialList::prepareGrid(const Rcpp::List &grid_input,
bool include_h0_o0) {
PhreeqcMatrix InitialList::prepareGrid(const Rcpp::List &grid_input) {
// parse input values
std::string script;
std::string database;
@ -186,11 +129,23 @@ 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;
bool with_h0_o0 =
grid_input.containsElementNamed(
GRID_MEMBER_STR(GridMembers::PQC_WITH_H0_O0))
? Rcpp::as<bool>(
grid_input[GRID_MEMBER_STR(GridMembers::PQC_WITH_H0_O0)])
: false;
if (with_h0_o0 && !with_redox) {
throw std::runtime_error(
"Output of H(0) and O(0) can only be used with redox.");
}
this->with_h0_o0 = with_h0_o0;
this->with_redox = with_redox;
PhreeqcMatrix pqc_mat =
PhreeqcMatrix(database, script, include_h0_o0, with_redox);
PhreeqcMatrix(database, script, with_h0_o0, with_redox);
this->transport_names = pqc_mat.getSolutionNames();

11
src/Init/InitialList.cpp
View File

@ -10,9 +10,8 @@
#include <vector>
namespace poet {
void InitialList::initializeFromList(const Rcpp::List &setup,
bool include_h0_o0) {
PhreeqcMatrix phreeqc = prepareGrid(setup[grid_key], include_h0_o0);
void InitialList::initializeFromList(const Rcpp::List &setup) {
PhreeqcMatrix phreeqc = prepareGrid(setup[grid_key]);
initDiffusion(setup[diffusion_key], phreeqc);
initChemistry(setup[chemistry_key]);
}
@ -89,8 +88,7 @@ void InitialList::importList(const Rcpp::List &setup, bool minimal) {
this->chem_hooks =
Rcpp::as<Rcpp::List>(setup[static_cast<int>(ExportList::CHEM_HOOKS)]);
this->ai_surrogate_input_script = Rcpp::as<std::string>(
setup[static_cast<int>(ExportList::AI_SURROGATE_INPUT_SCRIPT)]);
this->ai_surrogate_input_script = Rcpp::as<std::string>(setup[static_cast<int>(ExportList::AI_SURROGATE_INPUT_SCRIPT)]);
}
Rcpp::List InitialList::exportList() {
@ -142,8 +140,7 @@ Rcpp::List InitialList::exportList() {
out[static_cast<int>(ExportList::CHEM_INTERP_SPECIES)] =
Rcpp::wrap(this->interp_species);
out[static_cast<int>(ExportList::CHEM_HOOKS)] = this->chem_hooks;
out[static_cast<int>(ExportList::AI_SURROGATE_INPUT_SCRIPT)] =
this->ai_surrogate_input_script;
out[static_cast<int>(ExportList::AI_SURROGATE_INPUT_SCRIPT)] = this->ai_surrogate_input_script;
return out;
}

22
src/Init/InitialList.hpp
View File

@ -26,9 +26,9 @@ using TugType = double;
class InitialList {
public:
InitialList(RInside &R) : R(R) {};
InitialList(RInside &R) : R(R){};
void initializeFromList(const Rcpp::List &setup, bool include_h0_o0 = false);
void initializeFromList(const Rcpp::List &setup);
void importList(const Rcpp::List &setup, bool minimal = false);
Rcpp::List exportList();
@ -56,14 +56,6 @@ private:
CHEM_PQC_WITH_REDOX,
CHEM_PQC_IDS,
CHEM_FIELD_HEADER,
// CHEM_PQC_SCRIPTS,
// CHEM_PQC_SOLUTIONS,
// CHEM_PQC_SOLUTION_PRIMARY,
// CHEM_PQC_EXCHANGER,
// CHEM_PQC_KINETICS,
// CHEM_PQC_EQUILIBRIUM,
// CHEM_PQC_SURFACE_COMPS,
// CHEM_PQC_SURFACE_CHARGES,
CHEM_DHT_SPECIES,
CHEM_INTERP_SPECIES,
CHEM_HOOKS,
@ -78,6 +70,7 @@ private:
PQC_SCRIPT_STRING,
PQC_SCRIPT_FILE,
PQC_WITH_REDOX,
PQC_WITH_H0_O0,
PQC_DB_STRING,
PQC_DB_FILE,
GRID_DEF,
@ -91,9 +84,10 @@ private:
static_cast<std::size_t>(InitialList::GridMembers::ENUM_SIZE);
static constexpr std::array<const char *, size_GridMembers>
GridMembersString = {"pqc_in_string", "pqc_in_file", "pqc_with_redox",
"pqc_db_string", "pqc_db_file", "grid_def",
"grid_size", "constant_cells", "porosity"};
GridMembersString = {"pqc_in_string", "pqc_in_file", "pqc_with_redox",
"pqc_wth_h0_o0", "pqc_db_string", "pqc_db_file",
"grid_def", "grid_size", "constant_cells",
"porosity"};
constexpr const char *GRID_MEMBER_STR(GridMembers member) const {
return GridMembersString[static_cast<std::size_t>(member)];
@ -101,7 +95,7 @@ private:
// std::unique_ptr<PhreeqcMatrix> pqc_mat;
PhreeqcMatrix prepareGrid(const Rcpp::List &grid_input, bool include_h0_o0);
PhreeqcMatrix prepareGrid(const Rcpp::List &grid_input);
std::uint8_t dim{0};

5
src/initializer.cpp
View File

@ -40,11 +40,6 @@ int main(int argc, char **argv) {
bool asQS{false};
app.add_flag("-q, --qs", asQS, "Save output as .qs")->default_val(false);
bool includeH0O0{false};
app.add_flag("--include-h0-o0", includeH0O0,
"Include H(0) and O(0) in the output")
->default_val(false);
CLI11_PARSE(app, argc, argv);
// source the input script