Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F71460595
eqcurve_solid_transport.cpp
No One
Temporary
Actions
Download File
Edit File
Delete File
View Transforms
Subscribe
Mute Notifications
Award Token
Subscribers
None
File Metadata
Details
File Info
Storage
Attached
Created
Thu, Jul 11, 23:23
Size
7 KB
Mime Type
text/x-c
Expires
Sat, Jul 13, 23:23 (2 d)
Engine
blob
Format
Raw Data
Handle
18954102
Attached To
rSPECMICP SpecMiCP / ReactMiCP
eqcurve_solid_transport.cpp
View Options
#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
Event Timeline
Log In to Comment