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rSPECMICP SpecMiCP / ReactMiCP
carbonation.cpp
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// ============================================
// Saturated carbonation of a cement past
// =============================================
// This file can be used to learn how to use ReactMiCP
// Include ReactMiCP
#include "reactmicp.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);
// Upscaling
// =========
// Upscaling is the stagger in charge of finding the porosity and transport properties
// This is a class that is dependant on the problem to solve and should be defined by the user
// The following class is an example on how to define such a class
// The Upscaling class should inherit from UpscalingStaggerBase
class CarboUspcaling: public solver::UpscalingStaggerBase
{
public:
// Initiation
// This is not call automatically so can be adjusted by the user
CarboUspcaling(RawDatabasePtr the_database,
units::UnitsSet the_units):
m_data(the_database),
m_units_set(the_units),
m_dt(HUGE_VAL)
{
}
// Initialize the stagger at the beginning of the computation
// The porosity and transport properties should be initialized here
void initialize(VariablesBasePtr var)
{
SaturatedVariablesPtr true_var = cast_var_from_base(var);
true_var->upscaling_variables().setZero();
for (index_t node=0; node<true_var->nb_nodes(); ++node)
{
upscaling_one_node(node, true_var);
}
}
// Initialize the stagger at the beginning of a timestep
// Typically do nothing but erase the "dot" variable (velocity such as the vel_porosity)
void initialize_timestep(scalar_t dt, VariablesBasePtr var)
{
SaturatedVariablesPtr true_var = cast_var_from_base(var);
m_dt = dt;
for (index_t node=1; node<true_var->nb_nodes(); ++node)
{
upscaling_one_node(node, true_var);
true_var->vel_porosity(node) = 0.0;
}
}
//! This is the main function called during a timestep
StaggerReturnCode restart_timestep(VariablesBasePtr var)
{
SaturatedVariablesPtr true_var = cast_var_from_base(var);
for (index_t node=1; node<true_var->nb_nodes(); ++node)
{
upscaling_one_node(node, true_var);
}
return StaggerReturnCode::ResidualMinimized; // This is the value that should be returned if everything is ok
}
// A function that return the diffusion coefficient when porosity is equal to 'porosity'
scalar_t coeff_diffusion_law(scalar_t porosity)
{
static constexpr scalar_t de_0 = 2.726e-12; //1e-11;
static constexpr scalar_t factor = 1e4;
static constexpr scalar_t porosity_r = 0.02;
const scalar_t ratio = ((porosity - porosity_r)/(0.25 - porosity_r));
const scalar_t d_e = factor*de_0*std::pow(ratio, 3.32);
return std::min(d_e, 1e4*1e-10);
}
// Compute the upscaling for 'node'
void upscaling_one_node(index_t node, SaturatedVariablesPtr true_var)
{
// AdimensionalSystemSolutionExtractor is the class to use to
// extract information from a SpecMiCP solution
// To obtain correct information the correct units must be used
AdimensionalSystemSolutionExtractor extractor(true_var->equilibrium_solution(node),
m_data, m_units_set);
// We can obtain the porosity very easily :
scalar_t porosity = extractor.porosity();
true_var->vel_porosity(node) += (porosity - true_var->porosity(node))/m_dt;
true_var->porosity(node) = porosity;
true_var->diffusion_coefficient(node) = coeff_diffusion_law(porosity);
}
private:
RawDatabasePtr m_data;
units::UnitsSet m_units_set;
index_t m_id_cshj;
scalar_t m_initial_sat_cshj;
scalar_t m_dt;
};
// ==============
// 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));
// 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;
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_c_hco3 << std::endl;
out_c_ph << std::endl;
out_s_ca << std::endl;
out_calcite << std::endl;
out_poro << 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;
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_specmicp.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);
// Staggers
// ---------
// This section initialize the staggers
std::shared_ptr<EquilibriumStagger> equilibrium_stagger =
std::make_shared<satdiff::EquilibriumStagger>(list_constraints, index_constraints, specmicp_options);
std::shared_ptr<SaturatedTransportStagger> transport_stagger =
std::make_shared<satdiff::SaturatedTransportStagger>(variables, list_fixed_nodes);
set_transport_options(transport_stagger->options_solver());
UpscalingStaggerPtr upscaling_stagger =
std::make_shared<CarboUspcaling>(the_database, units_set);
// Solver
// ------
// This section initialize the reactive transport solver
ReactiveTransportSolver solver(transport_stagger, equilibrium_stagger, upscaling_stagger);
set_reactive_solver_options(solver.get_options());
transport_stagger->initialize(variables);
equilibrium_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("carbo", 3600);
simul_info.output_prefix = "out_carbo_";
// 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(1.0*24*3600, cast_var_to_base(variables));
if(not the_database->is_valid())
throw std::runtime_error("The database has been changed during the computation");
// output information at the end of the timestep
io::print_minerals_profile(the_database, variables, the_mesh, 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 = 50.0;
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 = 50; //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 init_min_publi(5);
// init_min_publi << 12.9, 1.62, 0.605, 0.131, 0.001;
// Vector init_min;
// init_min = initial_compo(init_min_publi);
// std::cout << "Init min \n ---- \n" << init_min << "\n ---- \n" << std::endl;
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;
//scalar_t mult = 6.73153e-4;
//scalar_t mult = 0.001296315;
//init_min *= 6.71146e-4;
//species_compo *= 0.947e-2; // poro 0.47
//species_compo *= 1.08e-2; // poro 0.4
//species_compo *= 1.25e-2; // poro 0.3
species_compo *= 1.518e-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}
// {"Portlandite", init_min(0)},
// {"CSH,jennite", init_min(1)},
// {"Monosulfoaluminate", init_min(2)},
// {"Ettringite", init_min(3)},
// {"Calcite", init_min(4)}
};
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,am",
"C3AH6",
"C4AH13",
"C2AH8",
"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();
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);
}
//AdimensionalSystemSolution get_cement_initial_compo(
// RawDatabasePtr the_database,
// const AdimensionalSystemConstraints& constraints,
// const AdimensionalSystemSolverOptions& options
// )
//{
// AdimensionalSystemSolver solver(the_database,
// constraints,
// options);
// Vector variables;
// solver.initialise_variables(
// variables,
// 0.4,
// {
// {"HO[-]", -1.2},
// {"Al(OH)4[-]", -4},
// {"HCO3[-]", -5},
// {"Ca[2+]", -1.6}
// });
// micpsolver::MiCPPerformance perf = solver.solve(variables);
// 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,
// 3.749,
// 3.748,
// 3.747,
// 3.745,
// 3.740,
// 3.735,
// 3.730,
// 3.720,
// 3.710,
// 3.700,
// 3.675,
// 3.650,
// 3.625,
// 3.600,
// 3.575,
// 3.550,
// 3.525,
// 3.500,
// 3.475,
// 3.450,
// 3.425,
// 3.400,
// 3.375,
// 3.350,
// 3.325,
// 3.300,
// 3.250,
// 3.200,
// 3.150,
// 3.100,
// 3.050,
// 3.000,
// 2.975,
// 2.950,
// 2.925,
// 2.900,
// 2.875,
// 2.850,
// 2.825,
// 2.800,
// 2.775,
// 2.750,
// 2.700,
// 2.650;
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);
}
Event Timeline
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