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specmicp/src/reactmicp/systems/saturated_diffusion/transport_program.hpp
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transport_program.hpp
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#ifndef SPECMICP_REACTMICP_SATURATED_DIFFUSION_TRANSPORTPROGRAM_HPP
#define SPECMICP_REACTMICP_SATURATED_DIFFUSION_TRANSPORTPROGRAM_HPP
#include <memory>
#include "database/data_container.hpp"
#include "dfpmsolver/parabolic_program.hpp"
#include "transport_parameters.hpp"
#include "reactmicp/meshes/mesh1d.hpp"
namespace specmicp {
namespace reactmicp {
namespace systems {
namespace siasaturated {
//! \brief Transport program for saturated diffusion
class SaturatedDiffusionProgram: dfpmsolver::ParabolicProgram<SaturatedDiffusionProgram>
{
public:
using triplet_t = Eigen::Triplet<scalar_t>; //!< Triplet type for building the transport matrix
using list_triplet_t = std::vector<triplet_t>; //!< List of triplet for building the sparse matrix
SaturatedDiffusionProgram(
std::shared_ptr<mesh::Mesh1D> the_mesh,
std::shared_ptr<database::DataContainer> the_data,
std::shared_ptr<SaturatedDiffusionTransportParameters> the_param
):
m_mesh(the_mesh),
m_data(the_data),
m_param(the_param),
m_external_flux(Eigen::VectorXd::Zero(the_mesh->nnodes()*(the_data->nb_component-1)))
{}
//! \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_data->nb_component-1;}
// number the equations
void number_equations(std::vector<index_t> list_fixed_nodes);
//! \brief Compute the residuals
void compute_residuals(const Vector &displacement,
const Vector &velocity,
Vector &residual
);
//! \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)
{}
//! Return the degree of freedom number of 'component' at 'node'
index_t get_dof_component(index_t node, index_t component) const {
specmicp_assert(component >=1 and component < m_data->nb_component);
specmicp_assert(node >= 0 and node < m_mesh->nnodes());
return (component - 1)+get_ndf()*node;
}
//! Return the degree of freedom number of 'component' at 'node'
index_t get_dof_mineral(index_t node, index_t mineral) const {
specmicp_assert(mineral >= 0 and mineral < m_data->nb_mineral);
specmicp_assert(node >= 0 and node < m_mesh->nnodes());
return mineral+m_data->nb_mineral*node;
}
//! Return the total mobile concentration
scalar_t& get_total_mobile_concentration(index_t node, index_t component, Vector& concentrations) const
{
return concentrations.coeffRef(get_dof_component(node, component));
}
//! Return the total mobile concentration
scalar_t get_total_mobile_concentration(index_t node, index_t component, const Vector& concentrations) const
{
return concentrations.coeff(get_dof_component(node, component));
}
//! Return the external flux
Vector& external_flux() {return m_external_flux;}
//! Return the external flux for 'component' at 'node'
scalar_t& external_flux(index_t node, index_t component) {return m_external_flux(get_dof_component(node, component));}
private:
void element_residual_transport(
index_t element,
const Eigen::VectorXd& displacement,
const Eigen::VectorXd& velocity,
Eigen::VectorXd& residual);
void element_residual_transport_component(
index_t element,
index_t component,
const Vector& displacement,
const Vector& velocity,
Vector& element_residual);
void element_jacobian_transport(
index_t element,
Vector& displacement,
Vector& velocity,
list_triplet_t& jacobian,
scalar_t alphadt);
index_t m_neq;
Vector m_ideq;
std::shared_ptr<mesh::Mesh1D> m_mesh;
std::shared_ptr<database::DataContainer> m_data;
std::shared_ptr<SaturatedDiffusionTransportParameters> m_param;
Vector m_external_flux;
};
} // end namespace siasaturated
} // end namespace systems
} // end namespace reactmicp
} // end namespace specmicp
#endif // SPECMICP_REACTMICP_SATURATED_DIFFUSION_TRANSPORTPROGRAM_HPP
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