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kinetics.cpp
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/*-------------------------------------------------------
- Module : tests/
- File : kinetics.cpp
- Author : Fabien Georget
Copyright (c) 2014, Fabien 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:
* Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
* 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.
* Neither the name of the Princeton University 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 OWNER 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 "common.hpp"
#include "specmicp/reduced_system_solver.hpp"
#include "database.hpp"
//#include "database/database.hpp"
#include <iostream>
#include <iomanip>
#include "utils/log.hpp"
#include "odeint/runge_kutta_step.hpp"
#include "specmicp/equilibrium_data.hpp"
const double Mc3s = 228.3;
const double Vmc3s = 73e-6;
using specmicp::index_t;
using specmicp::scalar_t;
class RateComputer
{
EIGEN_MAKE_ALIGNED_OPERATOR_NEW
public:
static constexpr double m_c3s0 = 500;
const double R0 = 2.5e-6;
RateComputer():
m_database("../data/cemdata_specmicp.js")
{
std::shared_ptr<specmicp::database::DataContainer> data = m_database.get_database();
std::map<std::string, std::string> swapping ({
{"H[+]","HO[-]"},
{"Si(OH)4", "SiO(OH)3[-]"}
});
m_database.swap_components(swapping);
std::vector<index_t> to_keep = {0, 1,
m_database.safe_label_to_id("Ca[2+]", m_database.get_database()->labels_basis),
m_database.safe_label_to_id("SiO(OH)3[-]", m_database.get_database()->labels_basis)
};
m_database.keep_only_components(to_keep);
m_equilvar.resize(data->nb_component+data->nb_mineral);
m_equilvar(0) = 1.0;
m_equilvar.block(1, 0, data->nb_component-1, 1).setConstant(-7);
m_equilvar.block(data->nb_component, 0, data->nb_mineral, 1).setConstant(0.);
m_totconc = Eigen::VectorXd(data->nb_component);
m_totconc0 = Eigen::VectorXd(data->nb_component);
m_totconc << 1.0/data->molar_mass_basis(0), 1e-7, 1e-6, 2e-6;
m_totconc0 << 1.0/data->molar_mass_basis(0), 1e-7, 1e-6, 2e-6;
id_c3s = m_database.mineral_kinetic_label_to_id("C3S");
id_ch = m_database.mineral_label_to_id("Portlandite");
id_csht = m_database.mineral_label_to_id("CSH,tobermorite");
id_cshj = m_database.mineral_label_to_id("CSH,jennite");
id_ca = m_database.component_label_to_id("Ca[2+]");
n_particle = 3*Vmc3s*m_c3s0/(Mc3s*4*M_PI*std::pow(R0, 3.0));
}
void update_totconc(double mc3s)
{
std::shared_ptr<specmicp::database::DataContainer> data = m_database.get_database();
double xi = (m_c3s0 - mc3s)/Mc3s;
std::cout << "xi : " << xi << std::endl;
//std::cout <<xi*data->nu_mineral_kinetic.row(id_c3s).transpose() << std::endl;
m_totconc.noalias() = m_totconc0 + xi*data->nu_mineral_kinetic.row(id_c3s).transpose();
}
double compute_logiap()
{
return m_current_solution.logIAP_kinetic(id_c3s);
}
double compute_rate(double mc3s, double logiap)
{
double radius = std::pow((Vmc3s*mc3s*3)/(Mc3s*n_particle*4*M_PI), 1.0/3.0);
double surf = (3*Vmc3s/(Mc3s*radius));
std::cout << n_particle << "\t" << radius << "\t" << surf << std::endl;
return std::min((surf*mc3s)*Mc3s*1e-6*(2.1*logiap+35.7), -1e-6);
}
void get_rate(double _, double mc3s, double& rate)
{
//std::cout << m_totconc << std::endl;
update_totconc(mc3s);
//std::cout << m_totconc << std::endl;
compute_equilibrium();
rate = compute_rate(mc3s, compute_logiap());
}
double get_ca()
{
return m_current_solution.molality_component(id_ca);
}
double get_ch()
{
return m_current_solution.mass_mineral(id_ch);
}
double get_csht()
{
return m_current_solution.mass_mineral(id_csht);
}
double get_cshj()
{
return m_current_solution.mass_mineral(id_cshj);
}
double get_pH()
{
return m_current_solution.pH();
}
void compute_equilibrium()
{
specmicp::ReducedSystemSolver solver(m_database.get_database(), m_totconc);
solver.get_options().solver_options.maxstep = 50;
solver.get_options().system_options.charge_keeper = 1;
specmicp::micpsolver::MiCPPerformance perf = solver.solve(m_equilvar);
if (perf.return_code != specmicp::micpsolver::MiCPSolverReturnCode::ResidualMinimized)
{
std::cout << "Failed to solve the system ! Err code " << (int) perf.return_code << std::endl;
}
m_current_solution = solver.get_solution(m_equilvar);
}
Eigen::VectorXd get_vars() {return m_equilvar;}
private:
Eigen::VectorXd m_equilvar;
Eigen::VectorXd m_totconc0;
Eigen::VectorXd m_totconc;
specmicp::database::Database m_database;
specmicp::EquilibriumState m_current_solution;
int id_c3s;
int id_ch;
int id_csht;
int id_cshj;
int id_ca;
double n_particle;
};
void by_hand()
{
RateComputer rate;
double y = RateComputer::m_c3s0-0.05;
double dydx;
rate.get_rate(0, y, dydx);
std::cout << std::setprecision(6);
specmicp::odeint::rhs_f<1> rhs = std::bind(std::mem_fn(&RateComputer::get_rate),
rate,
std::placeholders::_1,
std::placeholders::_2,
std::placeholders::_3);
specmicp::odeint::CashKarpStep<1> driver = specmicp::odeint::get_cash_karp_step<1>(rhs);
//specmicp::odeint::DormandPrinceStep<1> driver = specmicp::odeint::get_dormand_prince_step<1>(rhs);
specmicp::odeint::StepLength stepl(1.0);
double x = 0.0;
int cnt = 0;
while (y > 1e-2)
//while (cnt < 10)
{
driver.rk_step(y, dydx, x, stepl);
cnt +=1;
stepl.get_next();
driver.get_rhs(x, y, dydx);
rate.update_totconc(y); // shouldn't be needed
rate.compute_equilibrium();
std::cout << x << "\t" << y << "\t" << rate.compute_logiap()
<< "\t" << rate.get_pH() << "\t" << rate.get_ca() << "\t" << rate.get_ch()
<< "\t" << rate.get_csht() << "\t" << rate.get_cshj() << std::endl;
}
// Eigen::VectorXd equil = rate.get_vars() ;
// y+= 0.00001;
// rate.get_rate(0, y, dydx);
// Eigen::VectorXd equil2 = rate.get_vars();
// std::cout << equil2 - equil << std::endl;
//std::cout << "logiap : " << rate.compute_logiap() << " - rate : " << rate.compute_rate(rate.compute_logiap()) << std::endl;
}
/////// using the new solver
///
#include "specmicp/kinetics/kinetic_model.hpp"
#include "specmicp/kinetics/kinetic_variables.hpp"
#include "specmicp/kinetics/kinetic_system_solver.hpp"
class C3SDissolution: public specmicp::kinetics::KineticModel
{
public:
static constexpr scalar_t R0 = 2.5e-6;
C3SDissolution(specmicp::RawDatabasePtr data, scalar_t n_c3s0)
{
specmicp::Database db(data);
add_equation(db.mineral_kinetic_label_to_id("C3S"));
m_n_c3s0 = n_c3s0;
n_particle = 3.0/(4.0*M_PI*std::pow(R0, 3.0))*Vmc3s*n_c3s0;
}
void compute_rate(
scalar_t _,
const specmicp::Vector& y,
specmicp::kinetics::KineticVariables& variables,
specmicp::Vector& dydt
)
{
specmicp::Vector y_temp = y;
//specmicp::odeint::set_non_negative<Eigen::Dynamic>(y_temp);
//std::cout << "y_temp : " << y_temp << std::endl;
dydt.resizeLike(y);
double radius = R0*std::pow((y_temp(0)/m_n_c3s0), 1.0/3.0);
if (radius < 0.0 or not std::isfinite(radius)) radius = 0.0;
double surf = n_particle*4*M_PI*radius*radius;
//std::cout << n_particle << "\t" << radius << "\t" << surf << std::endl;
dydt(0) = 1e-9*std::min(surf*(2.1*variables.equilibrium_state().logIAP_kinetic(index_species(0)) +35.7), -1e-6);
}
private:
double m_n_c3s0;
double n_particle;
};
void using_kinetic_solver()
{
specmicp::Database the_database("../data/cemdata_specmicp.js");
std::shared_ptr<specmicp::database::DataContainer> data = the_database.get_database();
std::map<std::string, std::string> swapping ({
{"H[+]","HO[-]"},
{"Si(OH)4", "SiO(OH)3[-]"}
});
the_database.swap_components(swapping);
std::vector<index_t> to_keep = {0, 1,
the_database.safe_label_to_id("Ca[2+]", the_database.get_database()->labels_basis),
the_database.safe_label_to_id("SiO(OH)3[-]", the_database.get_database()->labels_basis)
};
the_database.keep_only_components(to_keep);
specmicp::Vector totconc(data->nb_component);
totconc(the_database.component_label_to_id("H2O")) = 1.0/data->molar_mass_basis_si(0);
totconc(the_database.component_label_to_id("HO[-]")) = 1e-7;
totconc(the_database.component_label_to_id("Ca[2+]")) = 1e-4;
totconc(the_database.component_label_to_id("SiO(OH)3[-]")) =2e-4;
specmicp::ReducedSystemSolver first_solver(data, totconc);
specmicp::Vector minerals(1);
minerals << 1e-3*(500/Mc3s);
std::cout << "Start : " << minerals(0) << std::endl;
specmicp::Vector equilvar;
equilvar.resize(data->nb_component+data->nb_mineral);
equilvar(0) = 1.0;
equilvar.block(1, 0, data->nb_component-1, 1).setConstant(-7);
equilvar.block(data->nb_component, 0, data->nb_mineral, 1).setConstant(0.);
first_solver.solve(equilvar);
specmicp::Vector second_conc(data->nb_aqueous);
second_conc.setZero();
specmicp::Vector loggamma(data->nb_component+data->nb_aqueous);
loggamma.setZero();
specmicp::EquilibriumState equilsolution = first_solver.get_solution(equilvar);
std::cout << equilvar << std::endl;
std::cout << "Initialization finished " << std::endl;
std::shared_ptr<specmicp::kinetics::KineticModel> model = std::make_shared<C3SDissolution>(data, minerals(0));
specmicp::kinetics::KineticSystemSolver solver(model, totconc, minerals, equilsolution);
solver.get_options().speciation_options.solver_options.maxstep = 50;
solver.get_options().speciation_options.solver_options.use_scaling = true;
solver.get_options().speciation_options.solver_options.fvectol = 1e-8;
solver.get_options().speciation_options.system_options.charge_keeper = the_database.component_label_to_id("HO[-]");
solver.get_options().speciation_options.solver_options.non_monotone_linesearch = true;
solver.get_options().speciation_options.solver_options.projection_min_variable = 1e-8;
//solver.get_options().speciation_options.solver_options.threshold_cycling_linesearch = 1.0;
//solver.get_options().speciation_options.conservation_water = false;
solver.get_options().rk_options.non_negativity = true;
solver.solve(1000.0, 100000.0);
// solver.solve(1.0, 2000.0);
// solver.solve(1.0, 2000.0);
std::cout << "Solution : " << solver.variables().moles_mineral(0) << std::endl;
std::cout << "flux : " << std::endl << solver.variables().rate_components() << std::endl;
solver.variables().reset_rate();
solver.solve(solver.current_dt(), 100000.0);
// solver.solve(1.0, 2000.0);
// solver.solve(1.0, 2000.0);
std::cout << "Solution : " << solver.variables().moles_mineral(0) << std::endl;
std::cout << "flux : " << std::endl << solver.variables().rate_components() << std::endl;
solver.variables().reset_rate();
solver.solve(solver.current_dt(), 100000.0);
// solver.solve(1.0, 2000.0);
// solver.solve(1.0, 2000.0);
std::cout << "Solution : " << solver.variables().moles_mineral(0) << std::endl;
std::cout << "flux : " << std::endl << solver.variables().rate_components() << std::endl;
solver.variables().reset_rate();
solver.solve(solver.current_dt(), 100000.0);
// solver.solve(1.0, 2000.0);
// solver.solve(1.0, 2000.0);
std::cout << "Solution : " << solver.variables().moles_mineral(0) << std::endl;
std::cout << "flux : " << std::endl << solver.variables().rate_components() << std::endl;
}
int main()
{
specmicp::logger::ErrFile::stream() = &std::cerr;
specmicp::stdlog::ReportLevel() = specmicp::logger::Warning;
using_kinetic_solver();
//by_hand();
return EXIT_SUCCESS;
}

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