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specmicp/src/reactmicp/equilibrium_curve/eqcurve_solid_transport.cpp
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eqcurve_solid_transport.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 "eqcurve_solid_transport.hpp"
#include "dfpm/meshes/mesh1d.hpp"
#include <iostream>
namespace specmicp {
namespace reactmicp {
namespace eqcurve {
// SolidDiffusion::
SolidDiffusion::SolidDiffusion(
mesh::Mesh1DPtr the_mesh,
const Matrix& eq_curve,
std::vector<index_t> list_bcs
):
m_tot_ndf(the_mesh->nb_nodes()),
m_mesh(the_mesh),
m_eqcurve(eq_curve),
m_internal_flow(Vector::Zero(m_tot_ndf)),
m_external_flow(Vector::Zero(m_tot_ndf)),
m_in_jac(false)
{
number_equations(list_bcs);
}
void SolidDiffusion::number_equations(std::vector<index_t> list_bcs)
{
m_id_equations = Eigen::VectorXi::Zero(m_tot_ndf);
for (auto it=list_bcs.begin(); it!=list_bcs.end(); ++it)
{
m_id_equations(*it) = no_equation;
}
index_t neq = 0;
for (index_t node: m_mesh->range_nodes())
{
if (m_id_equations(node) == no_equation) continue;
m_id_equations(node) = neq;
++ neq;
}
m_neq = neq;
}
void SolidDiffusion::compute_residuals(
const Vector& displacement,
const Vector& velocity,
Vector& residual
)
{
m_internal_flow.setZero();
residual.resize(get_neq());
residual.setZero();
for (index_t element: m_mesh->range_elements())
{
Vector elem_residuals(2);
elem_residuals.setZero();
element_residuals(element, displacement, velocity, elem_residuals);
for (index_t enode: m_mesh->range_nen())
{
const index_t id_eq = id_equation(m_mesh->get_node(element, enode));
if (id_eq == no_equation) continue;
residual(id_eq) += elem_residuals(enode);
}
}
//std::cout << "residual : " << std::endl << residual << std::endl;
//std::cout << "flow : " << std::endl << m_internal_flow << std::endl;
}
void SolidDiffusion::element_residuals(
index_t element,
const Vector& displacement,
const Vector& velocity,
Vector& elem_residuals
)
{
Eigen::Matrix<scalar_t, 2, 2> jacob;
Eigen::Matrix<scalar_t, 2, 1> evelocity, econc;
//scalar_t mass_coeff = -(m_mesh->get_volume_element(element)/2.0);
const index_t node_0 = m_mesh->get_node(element, 0);
const index_t node_1 = m_mesh->get_node(element, 1);
const scalar_t mass_coeff_0 = m_mesh->get_volume_cell_element(element, 0);
const scalar_t mass_coeff_1 = m_mesh->get_volume_cell_element(element, 1);
const scalar_t sc_0 = displacement(node_0);
const scalar_t sc_1 = displacement(node_1);
const index_t index_0 = m_eqcurve.find_point(sc_0);
const index_t index_1 = m_eqcurve.find_point(sc_1);
//std::cout << element << " # " << index_0 << " - " << index_1 << std::endl;
const scalar_t cc_0 = m_eqcurve.interpolate(index_0, sc_0, 1);
//std::max(m_eqcurve.totaq_concentration(m_eqcurve.last()), m_eqcurve.interpolate(index_0, sc_0, 1));
const scalar_t cc_1 = m_eqcurve.interpolate(index_1, sc_1, 1);
//std::max(m_eqcurve.totaq_concentration(m_eqcurve.last()), m_eqcurve.interpolate(index_1, sc_1, 1));
const scalar_t porosity_0 = m_eqcurve.interpolate(index_0, sc_0, 2);
const scalar_t porosity_1 = m_eqcurve.interpolate(index_1, sc_1, 2);
//const scalar_t diffcoeff_0 = m_eqcurve.interpolate(index_0, sc_0, 3);
//const scalar_t diffcoeff_1 = m_eqcurve.interpolate(index_1, sc_1, 3);
const scalar_t porosity = ( porosity_0
+ porosity_1
)/2.0;
const scalar_t diff_coeff = porosity>0.92?2.219e-5:1e4*std::exp(9.95*porosity-29.08);
// const scalar_t diff_coeff = 1.0/(0.5/diffcoeff_0 +
// 0.5/diffcoeff_1);
scalar_t flux_coeff = ( m_mesh->get_face_area(element) / m_mesh->get_dx(element)
//* porosity
* diff_coeff
);
// if (m_eqcurve.slope(index_1, 1) != 0)
// {
// std::cout << element << " # " << m_eqcurve.slope(index_0, 1) << " - " << m_eqcurve.slope(index_0, 2)
// << " # " << m_eqcurve.slope(index_1, 1) << " - " << m_eqcurve.slope(index_1, 2) << std::endl;
// }
evelocity << (+ m_eqcurve.slope(index_0, 1)*porosity_0
+ m_eqcurve.slope(index_0, 2)*cc_0
+ 1.0)*mass_coeff_0*velocity(node_0),
(+ m_eqcurve.slope(index_1, 1)*porosity_1
+ m_eqcurve.slope(index_1, 2)*cc_1
+ 1.0)*mass_coeff_1*velocity(node_1);
jacob << 1.0, -1.0, -1.0, 1.0;
jacob *= flux_coeff;
econc << cc_0,
cc_1;
// if (element == 0)
// std::cout << econc << std::endl;
elem_residuals += jacob*econc;
m_internal_flow(node_0) += elem_residuals(0);
m_internal_flow(node_1) += elem_residuals(1);
elem_residuals += evelocity;
// for (index_t en: m_mesh->range_nen())
// {
// elem_residuals(en) += evelocity(en);
// elem_residuals(en) += (m_mesh->get_volume_element(element)/2.0
// *external_flow(m_mesh->get_node(element, en)));
// }
}
void SolidDiffusion::compute_jacobian(
Vector& displacement,
Vector& velocity,
Eigen::SparseMatrix<scalar_t>& jacobian,
scalar_t alphadt
)
{
m_in_jac = true;
dfpm::list_triplet_t jacob;
const index_t estimation = m_mesh->nb_nodes()*(m_mesh->nen);
jacob.reserve(estimation);
for (index_t element: m_mesh->range_elements())
{
element_jacobian(element, displacement, velocity, jacob, alphadt);
}
jacobian = Eigen::SparseMatrix<scalar_t>(get_neq(), get_neq());
jacobian.setFromTriplets(jacob.begin(), jacob.end());
m_in_jac = false;
}
void SolidDiffusion::element_jacobian(
index_t element,
Vector& displacement,
Vector& velocity,
dfpm::list_triplet_t& jacobian,
scalar_t alphadt)
{
Eigen::VectorXd element_residual_orig(Eigen::VectorXd::Zero(2));
element_residuals(element, displacement, velocity, element_residual_orig);
for (index_t en: m_mesh->range_nen())
{
Eigen::VectorXd element_residual(Eigen::VectorXd::Zero(2));
const index_t node = m_mesh->get_node(element, en);
const index_t dof = node;
const index_t idc = id_equation(dof);
if (idc == no_equation) continue;
const scalar_t tmp_v = velocity(dof);
const scalar_t tmp_d = displacement(dof);
scalar_t h = eps_jacobian*std::abs(tmp_v);
if (h < 1e-6) h = eps_jacobian;
velocity(dof) = tmp_v + h;
h = velocity(dof) - tmp_v;
displacement(dof) = tmp_d + alphadt*h;
element_residuals(element, displacement, velocity, element_residual);
velocity(dof) = tmp_v;
displacement(dof) = tmp_d;
for (index_t enr: m_mesh->range_nen())
{
const index_t noder = m_mesh->get_node(element, enr);
const index_t idr = id_equation(noder);
if (idr == no_equation) continue;
jacobian.push_back(dfpm::triplet_t(idr, idc, (element_residual(enr) - element_residual_orig(enr))/h));
}
}
}
void SolidDiffusion::update_solution(const Vector &update,
scalar_t lambda,
scalar_t alpha_dt,
Vector &predictor,
Vector &displacement,
Vector &velocity
)
{
for (index_t node: m_mesh->range_nodes())
{
const index_t id = id_equation(node);
if (id == no_equation) continue;
velocity(node) += lambda*update(id);
}
displacement = predictor + alpha_dt*velocity;
}
} // end namespace eqcurve
} // end namespace reactmicp
} // end namespace specmicp
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