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transport_program.hpp
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rSPECMICP SpecMiCP / ReactMiCP
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
{
class
SaturatedDiffusionProgram
:
dfpmsolver
::
ParabolicProgram
<
SaturatedDiffusionProgram
>
{
public
:
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
)))
{}
const
int
no_equation
=
-
1
;
//! \brief Return the number of equations
int
get_neq
()
const
{
return
m_neq
;}
//! \brief Return the number of degrees of freedom per node
int
get_ndf
()
const
{
return
m_data
->
nb_component
-
1
;}
// number the equations
void
number_equations
(
std
::
vector
<
int
>
list_fixed_nodes
);
//! \brief Compute the residuals
void
compute_residuals
(
const
Eigen
::
VectorXd
&
displacement
,
const
Eigen
::
VectorXd
&
velocity
,
Eigen
::
VectorXd
&
residual
);
//! \brief Compute the jacobian
void
compute_jacobian
(
Eigen
::
VectorXd
&
displacement
,
Eigen
::
VectorXd
&
velocity
,
Eigen
::
SparseMatrix
<
double
>
&
jacobian
,
double
alphadt
);
//! \brief Update the solutions
void
update_solution
(
const
Eigen
::
VectorXd
&
update
,
double
lambda
,
double
alpha_dt
,
Eigen
::
VectorXd
&
predictor
,
Eigen
::
VectorXd
&
displacement
,
Eigen
::
VectorXd
&
velocity
);
//! \brief Apply boundary conditions to the velocity vector
//!
//! by default do nothing.
void
apply_bc
(
double
dt
,
const
Eigen
::
VectorXd
&
displacement
,
Eigen
::
VectorXd
velocity
)
{}
//! Return the degree of freedom number of 'component' at 'node'
int
get_dof_component
(
int
node
,
int
component
)
const
{
assert
(
component
>=
1
and
component
<
m_data
->
nb_component
);
assert
(
node
>=
0
and
node
<
m_mesh
->
nnodes
());
return
(
component
-
1
)
+
get_ndf
()
*
node
;
}
//! Return the degree of freedom number of 'component' at 'node'
int
get_dof_mineral
(
int
node
,
int
mineral
)
const
{
assert
(
mineral
>=
0
and
mineral
<
m_data
->
nb_mineral
);
assert
(
node
>=
0
and
node
<
m_mesh
->
nnodes
());
return
mineral
+
m_data
->
nb_mineral
*
node
;
}
//! Return the total mobile concentration
double
&
get_total_mobile_concentration
(
int
node
,
int
component
,
Eigen
::
VectorXd
&
concentrations
)
const
{
return
concentrations
.
coeffRef
(
get_dof_component
(
node
,
component
));
}
//! Return the total mobile concentration
double
get_total_mobile_concentration
(
int
node
,
int
component
,
const
Eigen
::
VectorXd
&
concentrations
)
const
{
return
concentrations
.
coeff
(
get_dof_component
(
node
,
component
));
}
//! Return the external flux
Eigen
::
VectorXd
&
external_flux
()
{
return
m_external_flux
;}
//! Return the external flux for 'component' at 'node'
double
&
external_flux
(
int
node
,
int
component
)
{
return
m_external_flux
(
get_dof_component
(
node
,
component
));}
private
:
void
element_residual_transport
(
ind_t
element
,
const
Eigen
::
VectorXd
&
displacement
,
const
Eigen
::
VectorXd
&
velocity
,
Eigen
::
VectorXd
&
residual
);
void
element_residual_transport_component
(
ind_t
element
,
int
component
,
const
Eigen
::
VectorXd
&
displacement
,
const
Eigen
::
VectorXd
&
velocity
,
Vector
&
element_residual
);
double
nodal_mineral_transient_term_transport
(
ind_t
node
,
ind_t
component
);
void
element_jacobian_transport
(
ind_t
element
,
Eigen
::
VectorXd
&
displacement
,
Eigen
::
VectorXd
&
velocity
,
list_triplet_t
&
jacobian
,
double
alphadt
);
int
m_neq
;
Eigen
::
VectorXd
m_ideq
;
std
::
shared_ptr
<
mesh
::
Mesh1D
>
m_mesh
;
std
::
shared_ptr
<
database
::
DataContainer
>
m_data
;
std
::
shared_ptr
<
SaturatedDiffusionTransportParameters
>
m_param
;
Eigen
::
VectorXd
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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