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set_mineral_kinetic.cpp
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Sun, Sep 8, 18:47

set_mineral_kinetic.cpp
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#include "catch.hpp"
#include <iostream>
#include "utils/log.hpp"
#include "specmicp/adimensional/adimensional_system.hpp"
#include "micpsolver/micpsolver.hpp"
#include "specmicp/adimensional/adimensional_system_solver.hpp"
#include "specmicp/problem_solver/formulation.hpp"
#include "specmicp/problem_solver/dissolver.hpp"
#include "specmicp/adimensional/adimensional_system_solution_extractor.hpp"
#include "specmicp/adimensional/adimensional_system_solution_saver.hpp"
#include "database/database.hpp"
specmicp::RawDatabasePtr get_test_database_set_kinetic()
{
specmicp::database::Database thedatabase(TEST_CEMDATA_PATH);
std::map<std::string, std::string> swapping ({
{"H[+]","HO[-]"},
});
thedatabase.swap_components(swapping);
std::vector<std::string> to_keep = {"HO[-]", "Ca[2+]", "HCO3[-]"};
thedatabase.keep_only_components(to_keep);
thedatabase.remove_half_cell_reactions(std::vector<std::string>({"H2O", "HO[-]",})) ;
return thedatabase.get_database();
}
using namespace specmicp;
TEST_CASE("Set a mineral to be governed by kinetics", "[adimensional],[solver],[modificator],[kinetics]") {
specmicp::logger::ErrFile::stream() = &std::cerr;
specmicp::stdlog::ReportLevel() = specmicp::logger::Error;
SECTION("Set kinetics") {
specmicp::RawDatabasePtr thedatabase = get_test_database_set_kinetic();
auto id_h2o = database::DataContainer::water_index();
auto id_oh = thedatabase->get_id_component("HO[-]");
auto id_ca = thedatabase->get_id_component("Ca[2+]");
auto id_hco3 = thedatabase->get_id_component("HCO3[-]");
auto id_ch = thedatabase->get_id_mineral("Portlandite");
auto id_calcite_eq = thedatabase->get_id_mineral("Calcite");
Vector total_concentration = Vector::Zero(thedatabase->nb_component());
total_concentration(id_h2o) = 0.03;
total_concentration(id_oh) = 0.015;
total_concentration(id_ca) = 0.01;
total_concentration(id_hco3) = 0.005;
specmicp::Vector x;
specmicp::AdimensionalSystemConstraints constraints(total_concentration);
specmicp::AdimensionalSystemSolver solver(thedatabase, constraints);
solver.initialise_variables(x, 0.8, -2.0);
//x(solver.dof_surface()) = -HUGE_VAL;
solver.get_options().units_set.length = specmicp::units::LengthUnit::centimeter;
solver.get_options().solver_options.maxstep = 10.0;
solver.get_options().solver_options.maxiter_maxstep = 100;
solver.get_options().solver_options.use_crashing = false;
solver.get_options().solver_options.use_scaling = true;
solver.get_options().solver_options.disable_descent_direction();
solver.get_options().solver_options.factor_gradient_search_direction = 100;
solver.solve(x);
AdimensionalSystemSolution solution = solver.get_raw_solution(x);
AdimensionalSystemSolutionExtractor extr(solution, thedatabase, solver.get_options().units_set);
scalar_t volume_fraction_calcite = extr.volume_fraction_mineral(id_calcite_eq);
AdimensionalSystemSolutionModificator modor(solution, thedatabase, solver.get_options().units_set);
std::vector<index_t> to_kinetic {id_calcite_eq};
Vector vol_fracs = modor.set_minerals_kinetics(to_kinetic);
CHECK(vol_fracs(0) == volume_fraction_calcite);
CHECK(thedatabase->get_id_mineral_kinetic("Calcite") != no_species);
CHECK(thedatabase->get_id_mineral("Calcite") == no_species);
CHECK(thedatabase->get_id_mineral_kinetic("Calcite") == to_kinetic[0]);
}
}

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