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transport_program.hpp
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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.
-----------------------------------------------------------------------------*/
#ifndef SPECMICP_REACTMICP_SYSTEMS_SATURATED_TRANSPORTPROGRAM_HPP
#define SPECMICP_REACTMICP_SYSTEMS_SATURATED_TRANSPORTPROGRAM_HPP
#include "dfpmsolver/parabolic_program.hpp"
#include "variablesfwd.hpp"
#include "dfpm/meshes/mesh1dfwd.hpp"
#include "dfpm/types.hpp"
namespace specmicp {
namespace reactmicp {
namespace systems {
namespace satdiff {
class SaturatedDiffusion: public dfpmsolver::ParabolicProgram<SaturatedDiffusion>
{
public:
SaturatedDiffusion(SaturatedVariablesPtr variables,
std::vector<index_t> list_fixed_nodes,
std::map<index_t, index_t> list_slave_nodes,
std::vector<index_t> list_immobile_components);
SaturatedDiffusion(SaturatedVariablesPtr variables,
std::vector<index_t> list_fixed_nodes);
//! \brief Return the number of equations
index_t get_neq() const {return m_neq;}
//! \brief Return the number of degrees of freedom per node
index_t get_ndf() const {return m_ndf;}
//! \brief Return the total number of degrees of freedom
index_t get_tot_ndf() const {return m_tot_ndf;}
//! \brief Method to update the variables
void set_variables(SaturatedVariablesPtr variables) {m_variables = variables;}
//! \brief Return the id of the equation corresponding to the degree of freedom 'id_dof'
//!
//! Return 'no_equation' if no equation exist
index_t id_equation(index_t id_dof) const {return m_ideq(id_dof);}
//! \brief Compute the residuals
void compute_residuals(const Vector& displacement,
const Vector& velocity,
Vector& residual
);
//! Compute the residuals inside 'element' for 'component'
void residuals_element_component(
index_t element,
index_t component,
const Vector& displacement,
const Vector& velocity,
Eigen::Vector2d& element_residual
);
//! \brief Compute the jacobian
void compute_jacobian(Vector& displacement,
Vector& velocity,
Eigen::SparseMatrix<scalar_t>& jacobian,
scalar_t alphadt
);
//! \brief Compute the contribution of 'element' in the jacobian
void jacobian_element(
index_t element,
Vector& displacement,
Vector& velocity,
dfpm::list_triplet_t& jacobian,
scalar_t alphadt);
//! \brief Update the solutions
void update_solution(const Vector& update,
scalar_t lambda,
scalar_t alpha_dt,
Vector& predictor,
Vector& displacement,
Vector& velocity);
//! \brief Apply boundary conditions to the velocity vector
//!
//! by default do nothing.
void apply_bc(scalar_t dt,
const Vector& displacement,
Vector& velocity)
{}
private:
// number the equations
void number_equations(std::vector<index_t> list_fixed_nodes,
std::map<index_t, index_t> list_slave_nodes, std::vector<index_t> list_immobile_components);
index_t m_neq;
index_t m_ndf;
index_t m_tot_ndf;
Eigen::Matrix<index_t, Eigen::Dynamic, 1> m_ideq;
mesh::Mesh1DPtr m_mesh;
SaturatedVariablesPtr m_variables;
bool m_is_in_residual_computation;
};
} // end namespace satdiff
} // end namespace systems
} // end namespace reactmicp
} // end namespace specmicp
#endif // SPECMICP_REACTMICP_SYSTEMS_SATURATED_TRANSPORTPROGRAM_HPP

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