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specmicp/src/reactmicp/systems/chloride/transport_program.hpp
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transport_program.hpp
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/* =============================================================================
Copyright (c) 2014-2017 F. Georget <fabieng@princeton.edu> Princeton University
Copyright (c) 2017 F. Georget <fabien.georget@epfl.ch> EPFL
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 REACTMICP_CHLORIDE_TRANSPORTPROGRAM_HPP
#define REACTMICP_CHLORIDE_TRANSPORTPROGRAM_HPP
#include "dfpm/solver/parabolic_program.hpp"
#include "variables.hpp"
#include "dfpm/meshes/mesh1dfwd.hpp"
#include "dfpm/types.hpp"
#include <functional>
#include "specmicp_common/return_code.hpp"
#include "specmicp_database/database_holder.hpp"
#include "reactmicp/systems/chloride/transport_program_struct.hpp"
#include <iostream>
namespace specmicp {
struct AdimensionalSystemSolution;
struct AdimensionalSystemConstraints;
namespace reactmicp {
namespace solver {
class ChemistryStaggerBase;
} // namespace solver
namespace systems {
namespace chloride {
//! \brief Concept class for a program
class ChlorideProgram:
public dfpmsolver::ParabolicProgram<ChlorideProgram>,
public database::DatabaseHolder
{
public:
constexpr static bool USE_CHEMISTRY_RATE = true;
constexpr static bool NO_CHEMISTRY_RATE = false;
ChlorideProgram(ChlorideVariablesPtr vars,
std::vector<index_t> list_fixed_dof);
//! \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_vars->ndof();}
//! \brief Return the total number of degrees of freedom
index_t get_tot_ndf() const {return m_vars->ndof()*m_mesh->nb_nodes();}
//! \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);}
void initialize_timestep(scalar_t dt) {
m_dt = dt;
}
//! \brief Compute the residuals
void compute_residuals(
const Vector& displacement,
const Vector& velocity,
Vector& residual,
bool use_chemistry_rate,
bool use_grad_psi
);
//! \brief Compute the residuals
void compute_residuals(const Vector& displacement,
const Vector& velocity,
Vector& residual
) {
compute_residuals(displacement, velocity, residual, USE_CHEMISTRY_RATE, true);
//std::cout << "Res : " << residual.norm() << std::endl;
}
//! \brief Compute the initial residuals
//!
//! By default, it calls the same residuals as compute_residuals
void compute_residuals_0(const Vector& displacement,
const Vector& velocity,
Vector& residual
) {
compute_residuals(displacement, velocity, residual, NO_CHEMISTRY_RATE, false);
//std::cout << "Res 0 : " << residual.norm() << std::endl;
}
//! \brief Compute the jacobian
void compute_jacobian(Vector& displacement,
Vector& velocity,
Eigen::SparseMatrix<scalar_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) {}
//! \brief Register Chemistry stagger
void register_chem_stagger(std::shared_ptr<solver::ChemistryStaggerBase> chem_stagger);
//! \brief Compute residuals element
void compute_element_residuals(
index_t element,
const Vector& displacement,
const Vector& velocity,
const AdimensionalSystemSolution& adim_sol_0,
const AdimensionalSystemSolution& adim_sol_1,
Vector& eresidual,
bool use_chemistry_rate,
bool use_grad_psi
);
//! \brief Set the approximation method
void set_approx_method(AdimSolutionPerturbationMethod method) {
m_approx_method = method;
}
//! \brief Compute the transport rates
void compute_transport_rate(scalar_t dt, const Vector& displacement);
void set_scaling(Vector scaling_vector) {
m_scaling = scaling_vector;
}
Vector get_current() {
return m_current;
}
private:
//! Return {velocity, displacement} for an element
std::pair<Vector, Vector> get_element_displacements(index_t element, const Vector& velocity, const Vector& displacement);
void number_equations(std::vector<index_t>& list_fixed_dof);
void compute_element_jacobian(
index_t element,
Vector& displacement,
Vector& velocity,
dfpm::list_triplet_t& jacobian,
scalar_t alphadt
);
ChlorideVariablesPtr m_vars;
mesh::Mesh1DPtr m_mesh;
index_t m_neq;
Vector m_ideq; // ndof*node
scalar_t m_dt; //!< Current timestep
std::shared_ptr<solver::ChemistryStaggerBase> m_chem_stagger;
AdimSolutionPerturbationMethod m_approx_method {AdimSolutionPerturbationMethod::full};
void perturb_adim_solution(index_t node, Vector& displacement);
// Scaling vector (size : ndof)
Vector m_scaling;
Vector m_current;
};
} // namespace chloride
} // namespace systems
} // namespace reactmicp
} // namespace specmicp
#endif // REACTMICP_CHLORIDE_TRANSPORTPROGRAM_HPP
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