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specmicp/src/reactmicp/equilibrium_curve/chemistry.cpp
b174f1ddf352reactmicp/unsaturated

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chemistry.cpp
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/*-------------------------------------------------------------------------------
Copyright (c) 2014,2015 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 "chemistry.hpp"
#include "specmicp/adimensional/adimensional_system_solution_extractor.hpp"
#include "specmicp/adimensional/adimensional_system_solver.hpp"
#include "utils/log.hpp"
#include <iostream>
namespace specmicp {
namespace reactmicp {
namespace eqcurve {
// EquilibriumCurveSpeciation::
void EquilibriumCurveSpeciation::output()
{
index_t size = m_eqcurve.rows();
if (m_cnt == size) m_eqcurve.conservativeResize(size+500, 4);
m_eqcurve.block(size, 0, m_eqcurve.rows()-size, 4).setZero();
AdimensionalSystemSolutionExtractor sol(current_solution(), m_data, get_units());
m_eqcurve(m_cnt, 0) = sol.total_solid_concentration(m_idc);
m_eqcurve(m_cnt, 1) = sol.total_aqueous_concentration(m_idc);
m_eqcurve(m_cnt, 2) = sol.porosity();
m_eqcurve(m_cnt, 3) = m_eqcurve(m_cnt, 2)>0.92?2.219e-5:1e4*std::exp(9.95*m_eqcurve(m_cnt, 2)-29.08);
std::cout << m_eqcurve(m_cnt, 0) << " \t " << m_eqcurve(m_cnt, 1) << std::endl;
}
Matrix EquilibriumCurveSpeciation::get_equilibrium_curve(scalar_t end_total_concentration, scalar_t delta)
{
m_cnt = 0;
solve_first_problem();
output();
AdimensionalSystemSolutionExtractor sol(current_solution(), m_data, get_units());
index_t nb_steps = std::abs(end_total_concentration - constraints().total_concentrations(m_idc))/(
std::abs(delta)*sol.total_aqueous_concentration(m_idc));
std::cout << nb_steps << std::endl;
m_eqcurve = Matrix::Zero(nb_steps, 4);
m_delta = delta; ///(nb_steps-1);
while (constraints().total_concentrations(m_idc) > end_total_concentration)
{
//std::cout << m_cnt << " - " << conditions().total_concentrations(m_idc) << std::endl;
run_step();
++m_cnt;
}
m_eqcurve.conservativeResize(m_cnt, 4);
return m_eqcurve;
}
void EquilibriumCurveSpeciation::update_problem()
{
Vector diff_conc = get_perturbation();
scalar_t coeff = m_delta;
for (index_t component: m_data->range_component())
{
if (std::abs(constraints().total_concentrations(component)) < 1e-4) {
constraints().total_concentrations(component) = 0.0;
diff_conc(component) = 0.0;
}
if (constraints().total_concentrations(component) != 0 and
std::copysign(1.0, constraints().total_concentrations(component) + coeff*diff_conc(component))
!= std::copysign(1.0, constraints().total_concentrations(component))
)
{
//std::cout << "Component : " << component << std::endl;
coeff = std::copysign(0.9*constraints().total_concentrations(component), m_delta);
coeff /= diff_conc(component);
}
}
//std::cout << "Update : " << std::endl << coeff*diff_conc << std::endl;
constraints().total_concentrations += coeff*diff_conc;
// std::cout << "total concentrations : " << std::endl << conditions().total_concentrations << std::endl;
}
Vector EquilibriumCurveSpeciation::get_perturbation()
{
AdimensionalSystemSolutionExtractor sol(current_solution(), m_data, get_units());
Vector tot_aq_conc(m_data->nb_component());
tot_aq_conc.setZero();
for (index_t component: m_data->range_aqueous_component())
{
tot_aq_conc(component) = sol.total_aqueous_concentration(component);
}
//tot_aq_conc *= m_delta/tot_aq_conc.norm();
return tot_aq_conc;
}
void EquilibriumCurveSpeciation::error_handling(std::string msg) const
{
ERROR << msg;
ERROR << " Total concentration " << std::endl << constraints().total_concentrations << std::endl;
throw std::runtime_error(msg);
}
} // end namespace eqcurve
} // end namespace reactmicp
} // end namespace specmicp
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