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specmicp/examples/reactmicp/equilibrium_curve.cpp
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/* =============================================================================
Copyright (c) 2014 - 2016
F. Georget <fabieng@princeton.edu> Princeton University
All rights reserved.
Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:
1. Redistributions of source code must retain the above copyright notice,
this list of conditions and the following disclaimer.
2. Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
3. Neither the name of the copyright holder nor the names of its
contributors may be used to endorse or promote products derived from this
software without specific prior written permission.
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR
ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. *
============================================================================= */
#include <iostream>
#include "utils/log.hpp"
#include "reactmicp/equilibrium_curve/chemistry.hpp"
#include "specmicp/problem_solver/dissolver.hpp"
#include "specmicp/problem_solver/formulation.hpp"
#include "reactmicp/equilibrium_curve/eqcurve_extractor.hpp"
#include "reactmicp/equilibrium_curve/eqcurve_coupler.hpp"
#include "dfpm/meshes/axisymmetric_uniform_mesh1d.hpp"
#include "dfpm/meshes/uniform_mesh1d.hpp"
#include "reactmicp/equilibrium_curve/eqcurve_solid_transport.hpp"
#include "database/database.hpp"
specmicp::Matrix test_chemistry() {
specmicp::database::Database thedatabase("../data/cemdata.yaml");
std::map<std::string, std::string> swapping ({
{"H[+]","HO[-]"},
{"Si(OH)4", "SiO(OH)3[-]"},
});
thedatabase.swap_components(swapping);
thedatabase.remove_gas_phases();
specmicp::RawDatabasePtr raw_data = thedatabase.get_database();
specmicp::Formulation formulation;
specmicp::scalar_t mult = 6.5e3;
specmicp::scalar_t m_c3s = mult*0.7;
specmicp::scalar_t m_c2s = mult*0.3;
specmicp::scalar_t wc = 0.5;
specmicp::scalar_t m_water = wc*1e-3*(
m_c3s*(3*56.08+60.08)
+ m_c2s*(2*56.06+60.08)
);
formulation.mass_solution = m_water;
formulation.amount_minerals = {
{"C3S", m_c3s},
{"C2S", m_c2s},
};
specmicp::Vector total_concentrations = specmicp::Dissolver(raw_data).dissolve(formulation);
specmicp::index_t id_h2o = thedatabase.component_label_to_id("H2O");
specmicp::index_t id_ho = thedatabase.component_label_to_id("HO[-]");
specmicp::index_t id_ca = thedatabase.component_label_to_id("Ca[2+]");
specmicp::AdimensionalSystemConstraints constraints(total_concentrations);
constraints.charge_keeper = id_ho;
specmicp::AdimensionalSystemSolverOptions options;
options.solver_options.maxstep = 10.0;
options.solver_options.max_iter = 100;
options.solver_options.maxiter_maxstep = 100;
options.solver_options.use_crashing = false;
options.solver_options.use_scaling = false;
options.solver_options.factor_descent_condition = -1;
options.solver_options.factor_gradient_search_direction = 100;
options.solver_options.projection_min_variable = 1e-9;
options.solver_options.fvectol = 1e-6;
options.solver_options.steptol = 1e-14;
options.system_options.non_ideality_tolerance = 1e-10;
specmicp::reactmicp::eqcurve::EquilibriumCurveSpeciation spec_solver(raw_data, constraints, id_ca, options);
return spec_solver.get_equilibrium_curve(0.05, -500);
}
specmicp::Matrix test_chemistry_with_al()
{
specmicp::database::Database thedatabase("../data/cemdata_specmicp.js");
std::map<std::string, std::string> swapping ({
{"H[+]","HO[-]"},
{"Si(OH)4", "SiO(OH)3[-]"},
{"Al[3+]","Al(OH)4[-]"}
});
thedatabase.swap_components(swapping);
thedatabase.remove_gas_phases();
specmicp::RawDatabasePtr raw_data = thedatabase.get_database();
specmicp::Formulation formulation;
specmicp::scalar_t mult = 6.5e3;
specmicp::scalar_t m_c3s = mult*0.6;
specmicp::scalar_t m_c2s = mult*0.2;
specmicp::scalar_t m_c3a = mult*0.10;
specmicp::scalar_t m_gypsum = mult*0.10;
specmicp::scalar_t wc = 0.8;
specmicp::scalar_t m_water = wc*1e-3*(
m_c3s*(3*56.08+60.08)
+ m_c2s*(2*56.06+60.08)
+ m_c3a*(3*56.08+101.96)
+ m_gypsum*(56.08+80.06+2*18.02)
);
formulation.mass_solution = m_water;
formulation.amount_minerals = {
{"C3S", m_c3s},
{"C2S", m_c2s},
{"C3A", m_c3a},
{"Gypsum", m_gypsum}
};
formulation.minerals_to_keep = {
"Portlandite",
"CSH,jennite",
"CSH,tobermorite",
"SiO2,am",
"Al(OH)3,am",
"Monosulfoaluminate",
"Straetlingite",
"Gypsum",
"Ettringite",
};
for (specmicp::index_t component: raw_data->range_component())
{
std::cout << raw_data->get_label_component(component) << std::endl;
}
specmicp::Vector total_concentrations = specmicp::Dissolver(raw_data).dissolve(formulation);
//specmicp::index_t id_h2o = thedatabase.component_label_to_id("H2O");
specmicp::index_t id_ho = thedatabase.component_label_to_id("HO[-]");
specmicp::index_t id_ca = thedatabase.component_label_to_id("Ca[2+]");
specmicp::AdimensionalSystemConstraints constraints(total_concentrations);
constraints.charge_keeper = id_ho;
specmicp::AdimensionalSystemSolverOptions options;
options.solver_options.maxstep = 20.0;
options.solver_options.max_iter = 100;
options.solver_options.maxiter_maxstep = 100;
options.solver_options.use_crashing = false;
options.solver_options.use_scaling = false;
options.solver_options.factor_descent_condition = -1;
options.solver_options.factor_gradient_search_direction = 100;
options.solver_options.projection_min_variable = 1e-9;
options.solver_options.fvectol = 1e-6;
options.solver_options.steptol = 1e-14;
options.system_options.non_ideality_tolerance = 1e-10;
specmicp::reactmicp::eqcurve::EquilibriumCurveSpeciation spec_solver(raw_data, constraints, id_ca, options);
return spec_solver.get_equilibrium_curve(0.05, -500.0);
}
void test_eqcurve_extractor()
{
specmicp::reactmicp::eqcurve::EquilibriumCurveExtractor extract(test_chemistry_with_al());
specmicp::index_t index = extract.find_point(111.0);
std::cout << "111.0 \t " << extract.totsolid_concentration(index) << "\t"
<< extract.totaq_concentration(index) << "\t"
<< extract.porosity(index) << "\t"
<< extract.diffusion_coefficient(index) << std::endl;
}
void test_diffeqcurve()
{
specmicp::Matrix eqcurve = test_chemistry_with_al();
eqcurve.col(0) *= 1e-6; //mol/m3 -> mol/cm3
eqcurve.col(1) *= 1e-3; //mol/kg -> mol/cm3
std::cout << eqcurve << std::endl;
specmicp::scalar_t radius = 3.5; //cm
specmicp::scalar_t height = 8.0; //cm
specmicp::scalar_t dx = 0.005;
specmicp::index_t additional_nodes = 1;
radius = radius + additional_nodes*dx;
specmicp::index_t nb_nodes =25+additional_nodes;
specmicp::mesh::Mesh1DPtr the_mesh = specmicp::mesh::axisymmetric_uniform_mesh1d(nb_nodes, radius, dx, height);
specmicp::dfpmsolver::ParabolicDriverOptions options;
options.step_tolerance = 1e-10;
options.residuals_tolerance = 1e-8;
options.quasi_newton = 1;
specmicp::reactmicp::eqcurve::EquilibriumCurveCoupler solver(eqcurve, the_mesh, options);
specmicp::scalar_t sum_0 =0;
for (specmicp::index_t node=0; node< the_mesh->nb_nodes(); ++node)
{
sum_0 += solver.solid_concentrations()(node)*the_mesh->get_volume_cell(node);
std::cout << the_mesh->get_volume_cell(node) << std::endl;
}
specmicp::scalar_t dt = 0.4;
specmicp::scalar_t total = 0;
std::cout << total << "\t" << 0.0 << "\t" << sum_0 << "\t" << 0.0 << std::endl;
specmicp::index_t k=0;
while (total < 65)
{
solver.run_step(dt);
total += dt/3600/24;
if (k % 5000 == 0)
{
specmicp::scalar_t sum =0;
for (specmicp::index_t node=0; node< the_mesh->nb_nodes(); ++node)
{
sum += solver.solid_concentrations()(node)*the_mesh->get_volume_cell(node);
}
std::cout << total << "\t" << std::sqrt(total) << "\t" << sum << "\t" << (sum_0 -sum)/(1.75929e-2) << std::endl;
}
++k;
}
//std::cout << solver.solid_concentrations() << std::endl;
}
void test_eqcurve_solid()
{
//specmicp::Matrix eq_curve = test_chemistry();
specmicp::Matrix eq_curve = test_chemistry_with_al();
eq_curve.col(0) *= 1e-6; //mol/m3 -> mol/cm3
eq_curve.col(1) *= 1e-3; //mol/kg -> mol/cm3
for (specmicp::index_t ind=1; ind<eq_curve.rows(); ++ind)
{
if (eq_curve(ind, 1) >= eq_curve(ind-1, 1))
eq_curve(ind, 1) = eq_curve(ind-1, 1);
}
std::cout << eq_curve << std::endl;
specmicp::scalar_t radius = 3.5; //cm
specmicp::scalar_t height = 8.0; //cm
specmicp::scalar_t dx = 0.005;
specmicp::index_t additional_nodes = 1;
radius = radius + additional_nodes*dx;
specmicp::index_t nb_nodes = 50+additional_nodes;
specmicp::mesh::Mesh1DPtr the_mesh = specmicp::mesh::axisymmetric_uniform_mesh1d(nb_nodes, radius, dx, height);
//specmicp::mesh::Mesh1DPtr the_mesh = specmicp::mesh::uniform_mesh1d(nb_nodes, dx, 5);
specmicp::dfpmsolver::ParabolicDriverOptions options;
options.step_tolerance = 1e-12;
options.residuals_tolerance = 1e-6;
options.sparse_solver = specmicp::SparseSolver::GMRES;
//options.linesearch = specmicp::dfpmsolver::ParabolicLinesearch::Strang;
options.alpha = 1.0;
options.quasi_newton = 1;
options.maximum_step_length = 10;
specmicp::reactmicp::eqcurve::SolidDiffusion program(the_mesh, eq_curve, {0,});
specmicp::dfpmsolver::ParabolicDriver< specmicp::reactmicp::eqcurve::SolidDiffusion> solver(program);
solver.get_options() = options;
solver.set_scaling(specmicp::Vector::Constant(program.get_neq(), 1e6));
specmicp::Vector variables(nb_nodes);
variables(0) = eq_curve(eq_curve.rows()-10, 0);
for (specmicp::index_t node=1; node<the_mesh->nb_nodes(); ++node)
{
variables(node) = eq_curve(10, 0);
}
specmicp::scalar_t sum_0 =0;
for (specmicp::index_t node=0; node< the_mesh->nb_nodes(); ++node)
{
sum_0 += variables(node)*the_mesh->get_volume_cell(node);
std::cout << the_mesh->get_volume_cell(node) << std::endl;
}
specmicp::scalar_t dt = 10.0;
specmicp::scalar_t total = 0;
std::cout << total << "\t" << 0.0 << "\t" << sum_0 << "\t" << 0.0 << std::endl;
specmicp::index_t k=0;
while (total < 50)
{
//std::cout << " ==== TIMESTEP === " << std::endl;
solver.solve_timestep(dt, variables);
for (int node=0; node<the_mesh->nb_nodes(); ++node)
if (variables(node) < 1e-6) variables(node) = 0;
//std::cout << solver.get_perfs().nb_iterations << std::endl;
total += dt/3600/24;
if (k % 5000 == 0)
{
specmicp::scalar_t sum =0;
for (specmicp::index_t node=0; node< the_mesh->nb_nodes(); ++node)
{
sum += variables(node)*the_mesh->get_volume_cell(node);
}
std::cout << total << "\t" << std::sqrt(total) << "\t" << sum << "\t" << (sum_0 -sum)/(1.75929e-2) << std::endl;
}
++k;
}
std::cout << variables << std::endl;
}
void test_interpolator()
{
specmicp::Matrix mat(5,4);
mat << 1, 1, 1, 1,
2, 1, 2, 0,
3, 1, 3, -1,
4, 1, 4, -2,
5, 1, 5, -3;
specmicp::reactmicp::eqcurve::EquilibriumCurveExtractor interpolator(mat);
std::cout << " " << interpolator.slope(0, 1) << " ?== " << 0 << std::endl;
std::cout << " " << interpolator.slope(0, 2) << " ?== " << 1 << std::endl;
std::cout << interpolator.slope(0, 3) << " ?== " << -1 << std::endl;
std::cout << interpolator.find_point(1.5) << " ? == " << 0 << std::endl;
std::cout << interpolator.find_point(3.5) << " ? == " << 2 << std::endl;
std::cout << interpolator.interpolate(2, 3.5, 2) << " ? == " << 3.5 << std::endl;
std::cout << interpolator.interpolate(2, 3.5, 3) << " ? == " << -1.5 << std::endl;
specmicp::Matrix mat2(5,4);
mat2 << 5, 1, 1, 1,
4, 1, 2, 0,
3, 1, 3, -1,
2, 1, 4, -2,
1, 1, 5, -3;
specmicp::reactmicp::eqcurve::EquilibriumCurveExtractor interpolator2(mat2);
std::cout << " " << interpolator2.slope(0, 1) << " ?== " << 0 << std::endl;
std::cout << " " << interpolator2.slope(0, 2) << " ?== " << -1 << std::endl;
std::cout << interpolator2.slope(0, 3) << " ?== " << +1 << std::endl;
std::cout << interpolator2.find_point(1.5) << " ? == " << 3 << std::endl;
std::cout << interpolator2.find_point(3.5) << " ? == " << 1 << std::endl;
std::cout << interpolator2.interpolate(1, 3.5, 2) << " ? == " << 2.5 << std::endl;
std::cout << interpolator2.interpolate(1, 3.5, 3) << " ? == " << -0.5 << std::endl;
std::cout << interpolator2.interpolate(4, 1.0, 2) << " ? == " << 5 << std::endl;
std::cout << interpolator2.interpolate(4, 1.0, 3) << " ? == " << -3 << std::endl;
}
int main()
{
specmicp::stdlog::ReportLevel() = specmicp::logger::Warning;
specmicp::logger::ErrFile::stream() = &std::cerr;
//test_chemistry();
//std::cout << test_chemistry_with_al() << std::endl;
//test_eqcurve_extractor();
test_diffeqcurve();
//test_eqcurve_solid();
//test_interpolator();
return EXIT_SUCCESS;
}
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