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diffusion_numbering.hpp
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rSPECMICP SpecMiCP / ReactMiCP
diffusion_numbering.hpp
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/*-------------------------------------------------------
- Module : reactmicp/systems/diffusion
- File : diffusion_numbering.hpp
- Author : Fabien Georget
Copyright (c) 2014, Fabien 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:
* Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
* 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.
* Neither the name of the Princeton University 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 OWNER 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_DIFFUSION_NUMBERING_HPP
#define SPECMICP_REACTMICP_SYSTEMS_DIFFUSION_NUMBERING_HPP
#include <memory>
#include "reactmicp/common.hpp"
#include "specmicp/equilibrium_data.hpp"
namespace
specmicp
{
namespace
reactmicp
{
namespace
mesh
{
// forward declaration
class
Mesh1D
;
}
// end namespace mesh
namespace
systems
{
namespace
diffusion
{
struct
BoundaryCondition
{
int
node
;
EquilibriumState
composition
;
std
::
vector
<
int
>
tot_mobile_concentration
;
std
::
vector
<
int
>
component
;
std
::
vector
<
int
>
mineral
;
void
fix_all
();
};
using
ListBoundaryCondition
=
std
::
vector
<
BoundaryCondition
>
;
//! \brief Equation numbering scheme
class
DiffusionNumbering
{
public
:
const
int
no_equation
=
-
1
;
using
Variables
=
ParabolicVariables
;
DiffusionNumbering
(
ind_t
number_nodes
,
std
::
shared_ptr
<
database
::
DataContainer
>
data
,
const
ListBoundaryCondition
&
list_bc
,
Variables
&
variable
)
:
DiffusionNumbering
(
number_nodes
,
data
->
nb_component
-
1
,
data
->
nb_mineral
,
list_bc
,
variable
)
{}
DiffusionNumbering
(
ind_t
number_nodes
,
ind_t
number_aqueous_component
,
ind_t
number_mineral
,
const
ListBoundaryCondition
&
list_bc
,
Variables
&
variable
);
//! \brief Return the number of equations
ind_t
get_neq
()
const
{
return
nb_neq
;}
//! \brief Return the number of degree of freedom (per node)
ind_t
get_ndf
()
const
{
return
nb_ndf
;}
// Degree of freedom numbering
// ===========================
//! \brief Return the number of the dof
ind_t
get_dof
(
ind_t
node
,
ind_t
elemental_dof
)
const
{
return
elemental_dof
+
nb_ndf
*
node
;}
//! \brief Return the ndof of a diffusion equation
ind_t
get_ndof_diffusion
(
ind_t
ind_component
)
const
{
return
ind_component
-
1
;}
//! \brief Return the ndof of a mass balance equation
ind_t
get_ndof_massbalance
(
ind_t
ind_component
)
const
{
return
nb_aq_component
+
ind_component
-
1
;}
//! \brief Return the ndof of a mineral equation
ind_t
get_ndof_mineral
(
ind_t
ind_mineral
)
const
{
return
2
*
nb_aq_component
+
ind_mineral
;}
//! \brief Return the dof of a diffusion equation
ind_t
get_dof_diffusion
(
ind_t
node
,
ind_t
ind_component
)
const
{
return
get_dof
(
node
,
get_ndof_diffusion
(
ind_component
));}
//! \brief Return the dof of a mass balance equation
ind_t
get_dof_massbalance
(
ind_t
node
,
ind_t
ind_component
)
const
{
return
get_dof
(
node
,
get_ndof_massbalance
(
ind_component
));}
//! \brief Return the dof of a mineral equation
ind_t
get_dof_mineral
(
ind_t
node
,
ind_t
ind_mineral
)
const
{
return
get_dof
(
node
,
get_ndof_mineral
(
ind_mineral
));}
//! \brief Return the index of the equation
//!
//! Return no_equation if there is no equation for this degree of freedom
ind_t
id_equation
(
ind_t
node
,
ind_t
elemental_dof
)
const
{
return
m_ideq
(
elemental_dof
,
node
);}
//! \brief Return the equation's index of a diffusion equation
ind_t
id_equation_diffusion
(
ind_t
node
,
ind_t
ind_component
)
const
{
return
id_equation
(
node
,
get_ndof_diffusion
(
ind_component
));}
//! \brief Return the equation's index of a mass balance equation
ind_t
id_equation_massbalance
(
ind_t
node
,
ind_t
ind_component
)
const
{
return
id_equation
(
node
,
get_ndof_massbalance
(
ind_component
));}
//! \brief Return the equation's index of a mineral equation
ind_t
id_equation_mineral
(
ind_t
node
,
ind_t
ind_mineral
)
const
{
return
id_equation
(
node
,
get_ndof_mineral
(
ind_mineral
));}
// Access primary variable
// =======================
//! \brief Return the total mobile concentration for 'component' at 'node'
double
mobile_total_concentration
(
ind_t
node
,
ind_t
component
,
const
Variables
&
var
)
const
{
return
var
.
displacement
(
get_dof_diffusion
(
node
,
component
));
}
//! \brief Return a reference to the total mobile concentration for 'component' at 'node'
double
&
mobile_total_concentration
(
ind_t
node
,
ind_t
component
,
Variables
&
var
)
{
return
var
.
displacement
.
coeffRef
(
get_dof_diffusion
(
node
,
component
));
}
//! \brief Return the component concentration for 'component' at 'node'
double
component_concentration
(
ind_t
node
,
ind_t
component
,
const
Variables
&
var
)
const
{
return
var
.
displacement
(
get_dof_massbalance
(
node
,
component
));
}
//! \brief Return a reference to the component concentration for 'component' at 'node'
double
&
component_concentration
(
ind_t
node
,
ind_t
component
,
Variables
&
var
)
{
return
var
.
displacement
.
coeffRef
(
get_dof_massbalance
(
node
,
component
));
}
//! \brief Return the mineral mole number for 'mineral' at 'node'
double
mole_mineral
(
ind_t
node
,
ind_t
mineral
,
const
Variables
&
var
)
const
{
return
var
.
displacement
(
get_dof_mineral
(
node
,
mineral
));
}
//! \brief Return a reference to the mineral mole number for 'mineral' at 'node'
double
&
mole_mineral
(
ind_t
node
,
ind_t
mineral
,
Variables
&
var
)
{
return
var
.
displacement
.
coeffRef
(
get_dof_mineral
(
node
,
mineral
));
}
//! \brief Return true if the node has a boundary condition
double
node_has_bc
(
ind_t
node
);
private
:
//! \brief Initialize the variable
void
initialize_variable
(
Variables
&
variable
);
//! \brief Parse the BCs and number the equations
void
number_equations
(
const
ListBoundaryCondition
&
list_bc
,
Variables
&
variable
);
//! \brief Parse the BCS, set the corresponding values in variable
void
parse_bcs
(
const
ListBoundaryCondition
&
list_bc
,
Variables
&
variable
);
//! \brief number the equations
void
do_numbering
();
ind_t
nb_aq_component
;
ind_t
nb_mineral
;
ind_t
nb_ndf
;
ind_t
nb_neq
;
Eigen
::
MatrixXi
m_ideq
;
std
::
vector
<
ind_t
>
m_nodes_with_bc
;
};
}
// end namespace diffusion
}
// end namespace systems
}
// end namespace reactmicp
}
// end namespace specmicp
#endif
// SPECMICP_REACTMICP_SYSTEMS_DIFFUSION_NUMBERING_HPP
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