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unsaturated

leaching_kinetic.cpp
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			// ============================================

			// Leaching of a cement paste
			// with kinetic dissolution of C3S

			// =============================================

			// This file can be used to learn how to use ReactMiCP


			// Include ReactMiCP
			#include "reactmicp.hpp"

			#include "specmicp/adimensional/adimensional_system_solution_saver.hpp"
			#include "reactmicp/systems/saturated_react/diffusive_upscaling_stagger.hpp"
			#include "reactmicp/systems/saturated_react/kinetic_stagger.hpp"

			// Other includes that would be needed later :
			#include <Eigen/QR>

			#include "physics/laws.hpp"
			#include "utils/timer.hpp"
			#include <functional>
			#include <iostream>
			#include <fstream>


			// we use the following namespaces
			using namespace specmicp;
			using namespace reactmicp;
			using namespace reactmicp::systems;

			using namespace specmicp::reactmicp::systems::satdiff;
			using namespace reactmicp::solver;

			// We declare some functions that we will be using :

			// Database
			// ========

			// Parse and Prepare the database
			RawDatabasePtr get_database(const std::string& path_to_database);

			// Boundary and initial conditions
			// ===============================

			// Return the chemistry constraints for the inital condition
			AdimensionalSystemConstraints get_cement_initial_constraints(
			RawDatabasePtr the_database,
			const units::UnitsSet& units_set);
			// return the chemistry constraints for the boundary condition
			AdimensionalSystemConstraints get_bc_initial_constraints(
			RawDatabasePtr the_database,
			const units::UnitsSet& units_set);


			Vector initial_compo(const Vector& publi);

			void compo_from_oxyde(Vector& compo_oxyde, Vector& compo_species);

			// The mesh
			// ========

			// There is two version
			// a uniform mesh
			mesh::Mesh1DPtr get_mesh(scalar_t dx);
			// and a non uniform mesh
			mesh::Mesh1DPtr get_mesh();

			// Options
			// =======

			// Speciation solver options
			AdimensionalSystemSolverOptions get_specmicp_options();
			// Transport options
			void set_transport_options(dfpmsolver::ParabolicDriverOptions& transport_options);
			// Reactive Solver options
			void set_reactive_solver_options(reactmicp::solver::ReactiveTransportOptions& reactive_options);


			// Kinetic model and variables
			// ===========================

			// Kinetic variables
			class C3SKineticVariables : public KineticSaturatedVariablesBase
			{
			public:

			Vector amount_minerals; // concentration of C3S
			Vector predictor; // Initial amount
			Vector velocity; // dC_c3s/dt
			Vector volume_fractions;
			};

			using C3SKineticVariablesPtr = std::shared_ptr<C3SKineticVariables>;

			// The dissolution model
			class C3SDissolutionModel : public KineticModelBase
			{
			public:
			C3SDissolutionModel(RawDatabasePtr the_database, const units::UnitsSet the_units):
			m_database(the_database),
			m_units(the_units),
			id_c3s(the_database->get_id_mineral_kinetic("C3S"))
			{
			if (id_c3s == no_species)
			throw database::invalid_database("The database do not contain C3S !");

			}

			KineticSaturatedVariablesBasePtr initialize_variables(mesh::Mesh1DPtr the_mesh, scalar_t init_vol_fraction);

			//! \brief Initialize a timestep
			void initialize_timestep(scalar_t dt, KineticSaturatedVariablesBasePtr kinetic_variables) override;
			//! \brief Restart a timestep
			void restart_timestep(
			index_t node,
			const AdimensionalSystemSolution& eq_solution,
			KineticSaturatedVariablesBasePtr kinetic_variables) override;
			//! \brief Return the volume fraction of kinetic (or inert) phases
			scalar_t get_volume_fraction_kinetic(index_t node, KineticSaturatedVariablesBasePtr kinetic_variables) override;
			//! \brief Return the velocity of the total immobile kinetic concentration for component
			scalar_t get_velocity_kinetic(index_t node, index_t component, KineticSaturatedVariablesBasePtr kinetic_variables) override;

			private:
			scalar_t volume_fraction(scalar_t concentration);
			scalar_t dy_dt(scalar_t log_IAP, scalar_t Aeff);

			scalar_t m_dt {-1.0};

			RawDatabasePtr m_database;
			units::UnitsSet m_units;

			index_t id_c3s;
			};

			KineticSaturatedVariablesBasePtr C3SDissolutionModel::initialize_variables(mesh::Mesh1DPtr the_mesh, scalar_t init_vol_fraction)
			{
			C3SKineticVariablesPtr var = std::make_shared<C3SKineticVariables>();

			var->predictor.setZero(the_mesh->nb_nodes());
			var->velocity.setZero(the_mesh->nb_nodes());

			var->volume_fractions.setConstant(the_mesh->nb_nodes(), init_vol_fraction);
			var->amount_minerals.setConstant(the_mesh->nb_nodes(),
			init_vol_fraction/m_database->molar_volume_mineral_kinetic(id_c3s, m_units.length));

			var->volume_fractions(0) = 0.0;
			var->amount_minerals(0) = 0.0;

			return std::static_pointer_cast<KineticSaturatedVariablesBase>(var);
			}

			void C3SDissolutionModel::initialize_timestep(scalar_t dt, KineticSaturatedVariablesBasePtr kinetic_variables)
			{
			m_dt = dt;
			C3SKineticVariablesPtr true_kin_var = std::static_pointer_cast<C3SKineticVariables>(kinetic_variables);

			true_kin_var->predictor = true_kin_var->amount_minerals;
			true_kin_var->velocity.setZero();
			}

			void C3SDissolutionModel::restart_timestep(
			index_t node,
			const AdimensionalSystemSolution &eq_solution,
			KineticSaturatedVariablesBasePtr kinetic_variables
			)
			{
			C3SKineticVariablesPtr true_kin_var = std::static_pointer_cast<C3SKineticVariables>(kinetic_variables);

			AdimensionalSystemSolutionExtractor extr(eq_solution, m_database, m_units);
			scalar_t log_IAP = 0;
			for (index_t component: m_database->range_component())
			{
			if (m_database->nu_mineral_kinetic(id_c3s, component) == 0.0) continue;
			log_IAP += m_database->nu_mineral_kinetic(id_c3s, component)*extr.log_molality_component(component);
			}
			scalar_t tmp = 0;

			scalar_t Aeff = 0;
			scalar_t porosity = extr.porosity();
			if (porosity > 0.6)
			{
			Aeff= 14001e-4/1e-3m_database->molar_mass_mineral_kinetic(id_c3s)/m_database->molar_volume_mineral_kinetic(id_c3s)*true_kin_var->volume_fractions(node);
			tmp = 1e-6*dy_dt(log_IAP, Aeff);
			}
			true_kin_var->velocity(node) = tmp;

			tmp = true_kin_var->predictor(node) + m_dt*true_kin_var->velocity(node);
			if (tmp < 1e-20) {

			tmp =0.0;
			true_kin_var->velocity(node) = - true_kin_var->predictor(node) / m_dt;
			}

			true_kin_var->amount_minerals(node) = tmp;

			true_kin_var->volume_fractions(node) = tmp*m_database->molar_volume_mineral_kinetic(id_c3s, m_units.length);
			}

			scalar_t C3SDissolutionModel::dy_dt(scalar_t log_IAP, scalar_t Aeff)
			{
			scalar_t res = (-57.0 -std::log(10)*log_IAP)/21.5;
			scalar_t tmp_2 = std::pow(res, 3.73);
			res = - 125.3e-6Aeff(1.0 - std::exp(-tmp_2));
			return res;

			}

			scalar_t C3SDissolutionModel::get_volume_fraction_kinetic(index_t node, KineticSaturatedVariablesBasePtr kinetic_variables)
			{
			C3SKineticVariablesPtr true_kin_var = std::static_pointer_cast<C3SKineticVariables>(kinetic_variables);
			return true_kin_var->volume_fractions(node);
			}

			scalar_t C3SDissolutionModel::get_velocity_kinetic(index_t node, index_t component, KineticSaturatedVariablesBasePtr kinetic_variables)
			{
			C3SKineticVariablesPtr true_kin_var = std::static_pointer_cast<C3SKineticVariables>(kinetic_variables);
			return m_database->nu_mineral_kinetic(id_c3s, component)*true_kin_var->velocity(node);
			}

			// ==============
			// Output
			// ==============

			// Many information is generated throughout a computation and we can't save everything
			// The reactmicp runner can call a function to output the desired information
			// Here the output function is a member function for convenience
			class OutputPolicy
			{
			public:
			// Initialise the output
			// SimulationInformation contain basic information from the simulation
			OutputPolicy(const SimulationInformation& simul_info,
			mesh::Mesh1DPtr the_mesh,
			RawDatabasePtr the_database,
			units::UnitsSet the_units):
			m_mesh(the_mesh),
			m_database(the_database),
			m_units(the_units)

			{
			// Open the files
			// Save the pH
			out_c_ph.open(simul_info.complete_filepath("ph", suffix));
			// Save the total aqueous concentration of HCO3[-]
			out_c_hco3.open(simul_info.complete_filepath("c_hco3", suffix));
			// save the total solid concentration of s_ca
			out_s_ca.open(simul_info.complete_filepath("s_ca", suffix));
			// Save the volume fraction of calcite
			out_calcite.open(simul_info.complete_filepath("calcite", suffix));
			// Save the porosity
			out_poro.open(simul_info.complete_filepath("poro", suffix));
			out_kin_vol_frac.open(simul_info.complete_filepath("kin_vol_frac", suffix));
			// save useful indices from the database
			m_id_hco3 = m_database->get_id_component("HCO3[-]");
			m_id_ca = m_database->get_id_component("Ca[2+]");
			m_id_calcite = m_database->get_id_mineral("Calcite");
			}


			void output(scalar_t time, VariablesBasePtr variables)
			{
			SaturatedVariablesPtr true_var = cast_var_from_base(variables);

			out_c_ph << time;
			out_c_hco3 << time;
			out_s_ca << time;
			out_calcite << time;
			out_poro << time;
			out_kin_vol_frac << time;

			for (index_t node: m_mesh->range_nodes())
			{
			// Again AdimensionalSystemSolutionExtractor is used to obtain information about the speciation system
			AdimensionalSystemSolutionExtractor extractor(true_var ->equilibrium_solution(node), m_database, m_units);
			out_c_ph << "\t" << extractor.pH();
			out_c_hco3 << "\t" << true_var->aqueous_concentration(node, m_id_hco3);
			out_s_ca << "\t" << true_var->solid_concentration(node, m_id_ca);
			out_calcite << "\t" << extractor.volume_fraction_mineral(m_id_calcite);
			out_poro << "\t" << extractor.porosity();
			out_kin_vol_frac << "\t" << std::static_pointer_cast<C3SKineticVariables>(true_var->kinetic_variables())->volume_fractions(node);
			}
			out_c_hco3 << std::endl;
			out_c_ph << std::endl;
			out_s_ca << std::endl;
			out_calcite << std::endl;
			out_poro << std::endl;
			out_kin_vol_frac << std::endl;

			}

			private:
			mesh::Mesh1DPtr m_mesh;
			RawDatabasePtr m_database;
			units::UnitsSet m_units;

			std::string suffix { "dat" };

			std::ofstream out_c_ph;
			std::ofstream out_c_hco3;
			std::ofstream out_s_ca;
			std::ofstream out_calcite;
			std::ofstream out_poro;
			std::ofstream out_kin_vol_frac;

			index_t m_id_hco3;
			index_t m_id_ca;
			index_t m_id_calcite;
			};

			// ===================
			// MAIN
			// ===================

			int main()
			{
			// initialize eigen
			// This is needed if OpenMP is used
			Eigen::initParallel();

			// Setup the log
			// The output will be on cerr
			specmicp::logger::ErrFile::stream() = &std::cerr;
			// And only Warning and error messages will be printed
			specmicp::stdlog::ReportLevel() = specmicp::logger::Warning;

			// The database
			// -------------

			// Obtain the database
			RawDatabasePtr the_database = get_database("../data/cemdata.js");

			// SpecMiCP options
			// ----------------

			// Set the options
			AdimensionalSystemSolverOptions specmicp_options = get_specmicp_options();
			units::UnitsSet units_set = specmicp_options.units_set;


			// The mesh
			// --------

			// Obtain the mesh
			mesh::Mesh1DPtr the_mesh = get_mesh(0.0050); // uniform
			//mesh::Mesh1DPtr the_mesh = get_mesh(); // non uniform
			index_t nb_nodes = the_mesh->nb_nodes(); // just boilerplate to make things easier


			// Print the mesh
			io::print_mesh("out_carbo_mesh.dat", the_mesh, units::LengthUnit::centimeter);


			// Initial and boundary conditions
			// --------------------------------

			// Obtain the initial constraints
			// Note : the database is modified at this point
			// Only the relevant components are kept at this point
			AdimensionalSystemConstraints cement_constraints = get_cement_initial_constraints(the_database, units_set);

			// Freeze the database
			the_database->freeze_db();


			// Obtain the initial condition
			AdimensionalSystemSolution cement_solution = solve_equilibrium(
			the_database,
			cement_constraints,
			specmicp_options);

			if(not the_database->is_valid())
			throw std::runtime_error("The database has been changed during the initial condition computation");


			// Just to check that everything is ok !
			AdimensionalSystemSolutionExtractor extractor(cement_solution, the_database, units_set);
			std::cout << "Porosity : " << extractor.porosity() << std::endl;
			std::cout << "Water volume fraction " << extractor.volume_fraction_water() << std::endl;



			//return EXIT_SUCCESS;

			// Obtain the boundary conditions
			AdimensionalSystemConstraints bc_constraints = get_bc_initial_constraints(
			the_database,
			specmicp_options.units_set
			);
			AdimensionalSystemSolution bc_solution = solve_equilibrium(
			the_database,
			bc_constraints,
			specmicp_options
			);

			if(not the_database->is_valid())
			throw std::runtime_error("The database has been changed during the boundary conditions computation");


			// The constraints
			// --------------

			// Boundary condition
			// 'list_fixed_nodes' lists the node with fixed composition
			std::vector<index_t> list_fixed_nodes = {0};


			// list_constraints lists the different speciation constraints in the system
			// Note : the total concentrations are computed from the initial solution,
			// and thus different total concentrations do not constitute a reason to create different constraints
			std::vector<specmicp::AdimensionalSystemConstraints> list_constraints = {cement_constraints,
			bc_constraints};

			// index_constraints links a node to the set of constraints that will be used
			std::vector<int> index_constraints(nb_nodes, 0);
			index_constraints[0] = 1; // Boundary conditions

			// This is the list of initial composition
			std::vector<specmicp::AdimensionalSystemSolution> list_initial_composition = {cement_solution, bc_solution};
			// This list links a node to its initial conditions
			std::vector<int> index_initial_state(nb_nodes, 0);
			index_initial_state[0] = 1; // boundary condition

			// Variables
			// -----------

			// Create the main set of variables
			// They will be initialized using the list of initial composition
			satdiff::SaturatedVariablesPtr variables =
			satdiff::init_variables(the_mesh, the_database, units_set,
			list_fixed_nodes,
			list_initial_composition,
			index_initial_state);

			std::shared_ptr<C3SDissolutionModel> kinetic_model = std::make_shared<C3SDissolutionModel>(the_database, units_set);
			variables->kinetic_variables() = kinetic_model->initialize_variables(the_mesh, 0.2);

			// Staggers
			// ---------

			// This section initialize the staggers

			// The equilibrium stagger
			// - - - - - - - - - - - -

			std::shared_ptr<KineticStagger> kinetic_stagger =
			std::make_shared<satdiff::KineticStagger>(kinetic_model, list_constraints, index_constraints, specmicp_options);

			// The transport stagger
			// - - - - - - - - - - -

			std::shared_ptr<SaturatedTransportStagger> transport_stagger =
			std::make_shared<satdiff::SaturatedTransportStagger>(variables, list_fixed_nodes);
			set_transport_options(transport_stagger->options_solver());

			// The upscaling stagger
			// - - - - - - - - - - -

			CappedPowerLawParameters upscaling_param;
			upscaling_param.d_eff_0 = 2.726e-12*1e4;
			upscaling_param.cap = 1e10*1e6;
			upscaling_param.exponent = 3.32;
			upscaling_param.porosity_0 = 0.25;
			upscaling_param.porosity_res = 0.02;

			CappedPowerLaw upscaling_law(upscaling_param);

			UpscalingStaggerPtr upscaling_stagger =
			std::make_shared<DiffusiveUpscalingStagger>(upscaling_law.get_law(),the_database, units_set);

			// Solver
			// ------

			// This section initialize the reactive transport solver

			ReactiveTransportSolver solver(transport_stagger, kinetic_stagger, upscaling_stagger);
			set_reactive_solver_options(solver.get_options());
			transport_stagger->initialize(variables);
			kinetic_stagger->initialize(variables);
			upscaling_stagger->initialize(variables);


			// Some basic information about the simulation
			// First argument : the name of the simulation
			// Second argument : the output function will be called every 3600s
			SimulationInformation simul_info("kincarbo", 1800);
			simul_info.output_prefix = "out_kincarbo_";

			// Runner
			// -------

			// Create the runner : loop through the timestep
			ReactiveTransportRunner runner(solver, 0.1, 100.0, simul_info);


			// Create the output class
			OutputPolicy output_policy(simul_info, the_mesh, the_database, specmicp_options.units_set);
			// and bind it to the runner
			runner.set_output_policy(std::bind(&OutputPolicy::output, &output_policy, std::placeholders::_1, std::placeholders::_2));

			// Solve the problem
			runner.run_until(10243600, cast_var_to_base(variables));


			if(not the_database->is_valid())
			throw std::runtime_error("The database has been changed during the computation");

			AdimensionalSystemSolutionSaver saver(the_database);
			saver.save_solutions(simul_info.complete_filepath("solutions", "dat"), variables->equilibrium_solutions());

			// output information at the end of the timestep

			io::print_minerals_profile(the_database, variables, the_mesh, specmicp_options.units_set,
			simul_info.complete_filepath("profiles_end", "dat"));
			io::print_components_total_aqueous_concentration(the_database, variables,
			the_mesh, specmicp_options.units_set,
			simul_info.complete_filepath("c_profiles_end", "dat"));
			io::print_components_total_solid_concentration(the_database, variables,
			the_mesh, specmicp_options.units_set,
			simul_info.complete_filepath("s_profiles_end", "dat"));
			}


			AdimensionalSystemSolverOptions get_specmicp_options()
			{
			AdimensionalSystemSolverOptions options;


			options.solver_options.maxiter_maxstep = 100;
			options.solver_options.maxstep = 20.0;
			options.solver_options.threshold_cycling_linesearch = 1e-6;

			options.solver_options.set_tolerance(1e-8, 1e-14);
			options.solver_options.disable_condition_check();
			options.solver_options.disable_descent_direction();
			options.solver_options.enable_non_monotone_linesearch();
			options.solver_options.enable_scaling();


			options.system_options.non_ideality_tolerance = 1e-14;
			options.system_options.cutoff_total_concentration = 1e-10;

			options.units_set.length = units::LengthUnit::centimeter;

			return options;
			}

			void set_transport_options(dfpmsolver::ParabolicDriverOptions& transport_options)
			{
			transport_options.maximum_iterations = 450;
			transport_options.quasi_newton = 3;
			transport_options.residuals_tolerance = 1e-8;
			transport_options.step_tolerance = 1e-14;
			transport_options.absolute_tolerance = 1e-18;

			transport_options.alpha = 1.0;
			//transport_options.linesearch = dfpmsolver::ParabolicLinesearch::Strang;
			transport_options.sparse_solver = SparseSolver::SparseLU;
			//transport_options.sparse_solver = SparseSolver::GMRES;
			transport_options.threshold_stationary_point = 1e-4;
			}

			void set_reactive_solver_options(reactmicp::solver::ReactiveTransportOptions& reactive_options)
			{
			reactive_options.maximum_iterations = 100; //500;
			reactive_options.residuals_tolerance = 1e-2;
			reactive_options.good_enough_tolerance = 1.0;

			reactive_options.absolute_residuals_tolerance = 1e-14;
			reactive_options.implicit_upscaling = true;
			}

			RawDatabasePtr get_database(const std::string& path_to_database) {
			database::Database the_database(path_to_database);
			std::map<std::string, std::string> swapping({
			{"H[+]","HO[-]"},
			{"Si(OH)4", "SiO(OH)3[-]"},
			{"Al[3+]","Al(OH)4[-]"}
			});
			the_database.swap_components(swapping);
			the_database.remove_gas_phases();
			return the_database.get_database();

			}



			AdimensionalSystemConstraints get_cement_initial_constraints(
			RawDatabasePtr the_database,
			const units::UnitsSet& units_set)
			{

			Vector oxyde_compo(4);
			oxyde_compo << 66.98, 21.66, 7.19, 2.96;
			Vector species_compo;
			compo_from_oxyde(oxyde_compo, species_compo);

			scalar_t mult = 1e-6;
			species_compo *= 0.85e-2;
			Formulation formulation;
			formulation.mass_solution = 1.0;
			formulation.amount_minerals = {
			{"C3S", species_compo(0)},
			{"C2S", species_compo(1)},
			{"C3A", species_compo(2)},
			{"Gypsum", species_compo(3)},
			{"Calcite", species_compo(0)*1e-3}

			};
			formulation.extra_components_to_keep = {"HCO3[-]"};
			formulation.concentration_aqueous =
			{
			{"Na[+]", mult*1.0298},
			{"K[+]", mult*0.0801},
			{"Cl[-]", mult*0.0001},
			{"HO[-]", mult*1.8298}
			},
			formulation.minerals_to_keep = {
			"Portlandite",
			"CSH,jennite",
			"CSH,tobermorite",
			"SiO2(am)",
			"Calcite",
			"Al(OH)3(mic)",
			"C3AH6",
			"C3ASO_41H5_18",
			"C3ASO_84H4_32",
			"C4AH19",
			"C4AH13",
			"C2AH7_5",
			"CAH10",
			"Monosulfoaluminate",
			"Tricarboaluminate",
			"Monocarboaluminate",
			"Hemicarboaluminate",
			"Straetlingite",
			"Gypsum",
			"Ettringite",
			//"Thaumasite"
			};
			Dissolver dissolver(the_database);
			dissolver.set_units(units_set);

			AdimensionalSystemConstraints constraints;
			constraints.set_charge_keeper(1);

			constraints.total_concentrations = dissolver.dissolve(formulation);

			std::cout << constraints.total_concentrations << std::endl;

			constraints.set_saturated_system();
			constraints.set_inert_volume_fraction(0.2);

			return constraints;
			}

			AdimensionalSystemConstraints get_bc_initial_constraints(
			RawDatabasePtr the_database,
			const units::UnitsSet& units_set)
			{
			const scalar_t rho_w = laws::density_water(units::celsius(25.0), units_set.length, units_set.mass);
			const scalar_t nacl = 0.3*rho_w;
			const scalar_t kcl = 0.28*rho_w;

			Vector total_concentrations;
			total_concentrations.setZero(the_database->nb_component());
			total_concentrations(the_database->get_id_component("K[+]")) = kcl;
			total_concentrations(the_database->get_id_component("Cl[-]")) = nacl + kcl;
			total_concentrations(the_database->get_id_component("Na[+]")) = nacl;
			total_concentrations(the_database->get_id_component("SiO(OH)3[-]")) = 0.0001*rho_w;

			AdimensionalSystemConstraints constraints;
			constraints.add_fixed_activity_component(the_database->get_id_component("HO[-]"), -10.3);
			constraints.set_charge_keeper(the_database->get_id_component("HCO3[-]"));
			constraints.total_concentrations = total_concentrations;

			constraints.set_saturated_system();
			constraints.disable_surface_model();
			constraints.fixed_fugacity_cs ={};

			return constraints;
			}

			AdimensionalSystemSolution get_bc_initial_compo(
			RawDatabasePtr the_database,
			const AdimensionalSystemConstraints& constraints,
			const AdimensionalSystemSolverOptions& options
			)
			{
			Vector variables;
			AdimensionalSystemSolver solver(the_database,
			constraints,
			options);

			micpsolver::MiCPPerformance perf = solver.solve(variables, true);

			if (perf.return_code <= micpsolver::MiCPSolverReturnCode::NotConvergedYet)
			throw std::runtime_error("Failed to solve initial composition");

			std::cout << variables << std::endl;

			return solver.get_raw_solution(variables);
			}

			void compo_from_oxyde(Vector& compo_oxyde, Vector& compo_species)
			{
			constexpr double M_CaO = 56.08;
			constexpr double M_SiO2 = 60.09;
			constexpr double M_Al2O3 = 101.96;
			constexpr double M_SO3 = 80.06;

			Eigen::MatrixXd compo_in_oxyde(4, 4);
			Vector molar_mass(4);
			molar_mass << 1.0/M_CaO, 1.0/M_SiO2, 1.0/M_Al2O3, 1.0/M_SO3;
			compo_oxyde = compo_oxyde.cwiseProduct(molar_mass);
			//C3S C2S C3A Gypsum
			compo_in_oxyde << 3, 2, 3, 1, // CaO
			1, 1, 0, 0, // SiO2
			0, 0, 1, 0, // Al2O3
			0, 0, 0, 1; // SO3
			Eigen::ColPivHouseholderQR<Eigen::MatrixXd> solver(compo_in_oxyde);
			compo_species = solver.solve(compo_oxyde);

			}


			Vector initial_compo(const Vector& publi)
			{
			Matrix publi_stochio(5,5);
			publi_stochio << 1, 0, 0, 0, 0,
			9, 6, 0, 0, 0,
			3, 0, 1, 1, 0,
			3, 0, 1, 3, 0,
			0, 0, 0, 0, 1;

			Matrix cemdata_stochio(5, 5);
			cemdata_stochio << 1, 0, 0, 0, 0,
			1.0/0.6, 1.0, 0, 0, 0,
			3, 0, 1, 1, 0,
			3, 0, 1, 3, 0,
			0, 0, 0, 0, 1;

			Vector oxyde;
			Eigen::ColPivHouseholderQR<Matrix> solver(publi_stochio);
			oxyde = solver.solve(publi);

			Vector for_cemdata = cemdata_stochio*oxyde;
			return for_cemdata;
			}


			mesh::Mesh1DPtr get_mesh(scalar_t dx)
			{
			const scalar_t total_length = 0.75/2.0 + dx; //cm
			const scalar_t height = 20.0;

			index_t nb_nodes = total_length/dx + 1;

			return mesh::uniform_axisymmetric_mesh1d(nb_nodes, total_length, dx, height);
			}

			mesh::Mesh1DPtr get_mesh()
			{
			Vector radius(71);

			const scalar_t height = 20;

			radius <<
			3.751,
			3.750,
			3.745,
			3.740,
			3.735,
			3.730,
			3.720,
			3.710,
			3.700,
			3.690,
			3.680,
			3.670,
			3.660,
			3.645,
			3.630,
			3.615,
			3.600,
			3.580,
			3.560,
			3.540,
			3.520,
			3.500,
			3.475,
			3.450,
			3.425,
			3.400,
			3.375,
			3.350,
			3.325,
			3.300,
			3.275,
			3.250,
			3.225,
			3.200,
			3.175,
			3.150,
			3.125,
			3.100,
			3.050,
			3.025,
			3.000,
			2.950,
			2.900,
			2.850,
			2.800,
			2.750,
			2.700,
			2.650,
			2.600,
			2.550,
			2.500,
			2.450,
			2.400,
			2.350,
			2.300,
			2.250,
			2.200,
			2.150,
			2.100,
			2.050,
			2.000,
			1.950,
			1.900,
			1.850,
			1.800,
			1.750,
			1.700,
			1.650,
			1.600,
			1.550,
			1.500
			;
			radius = radius/10;
			return mesh::axisymmetric_mesh1d(radius, height);
			}

specmicp/examples/reactmicp/saturated_react/leaching_kinetic.cppf48b6ea5015ebin/unsaturated

leaching_kinetic.cppView Options

specmicp/examples/reactmicp/saturated_react/leaching_kinetic.cpp
f48b6ea5015ebin/unsaturated

leaching_kinetic.cpp
View Options