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eqcurve_solid_transport.cpp
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rSPECMICP SpecMiCP / ReactMiCP
eqcurve_solid_transport.cpp
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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.
-----------------------------------------------------------------------------*/
#include "eqcurve_solid_transport.hpp"
#include "dfpm/meshes/mesh1d.hpp"
#include <iostream>
namespace
specmicp
{
namespace
reactmicp
{
namespace
eqcurve
{
// SolidDiffusion::
SolidDiffusion
::
SolidDiffusion
(
mesh
::
Mesh1DPtr
the_mesh
,
const
Matrix
&
eq_curve
,
std
::
vector
<
index_t
>
list_bcs
)
:
m_tot_ndf
(
the_mesh
->
nb_nodes
()),
m_mesh
(
the_mesh
),
m_eqcurve
(
eq_curve
),
m_internal_flow
(
Vector
::
Zero
(
m_tot_ndf
)),
m_external_flow
(
Vector
::
Zero
(
m_tot_ndf
)),
m_in_jac
(
false
)
{
number_equations
(
list_bcs
);
}
void
SolidDiffusion
::
number_equations
(
std
::
vector
<
index_t
>
list_bcs
)
{
m_id_equations
=
Eigen
::
VectorXi
::
Zero
(
m_tot_ndf
);
for
(
auto
it
=
list_bcs
.
begin
();
it
!=
list_bcs
.
end
();
++
it
)
{
m_id_equations
(
*
it
)
=
no_equation
;
}
index_t
neq
=
0
;
for
(
index_t
node:
m_mesh
->
range_nodes
())
{
if
(
m_id_equations
(
node
)
==
no_equation
)
continue
;
m_id_equations
(
node
)
=
neq
;
++
neq
;
}
m_neq
=
neq
;
}
void
SolidDiffusion
::
compute_residuals
(
const
Vector
&
displacement
,
const
Vector
&
velocity
,
Vector
&
residual
)
{
m_internal_flow
.
setZero
();
residual
.
resize
(
get_neq
());
residual
.
setZero
();
for
(
index_t
element:
m_mesh
->
range_elements
())
{
Vector
elem_residuals
(
2
);
elem_residuals
.
setZero
();
element_residuals
(
element
,
displacement
,
velocity
,
elem_residuals
);
for
(
index_t
enode:
m_mesh
->
range_nen
())
{
const
index_t
id_eq
=
id_equation
(
m_mesh
->
get_node
(
element
,
enode
));
if
(
id_eq
==
no_equation
)
continue
;
residual
(
id_eq
)
+=
elem_residuals
(
enode
);
}
}
//std::cout << "residual : " << std::endl << residual << std::endl;
//std::cout << "flow : " << std::endl << m_internal_flow << std::endl;
}
void
SolidDiffusion
::
element_residuals
(
index_t
element
,
const
Vector
&
displacement
,
const
Vector
&
velocity
,
Vector
&
elem_residuals
)
{
Eigen
::
Matrix
<
scalar_t
,
2
,
2
>
jacob
;
Eigen
::
Matrix
<
scalar_t
,
2
,
1
>
evelocity
,
econc
;
//scalar_t mass_coeff = -(m_mesh->get_volume_element(element)/2.0);
const
index_t
node_0
=
m_mesh
->
get_node
(
element
,
0
);
const
index_t
node_1
=
m_mesh
->
get_node
(
element
,
1
);
const
scalar_t
mass_coeff_0
=
m_mesh
->
get_volume_cell_element
(
element
,
0
);
const
scalar_t
mass_coeff_1
=
m_mesh
->
get_volume_cell_element
(
element
,
1
);
const
scalar_t
sc_0
=
displacement
(
node_0
);
const
scalar_t
sc_1
=
displacement
(
node_1
);
const
index_t
index_0
=
m_eqcurve
.
find_point
(
sc_0
);
const
index_t
index_1
=
m_eqcurve
.
find_point
(
sc_1
);
//std::cout << element << " # " << index_0 << " - " << index_1 << std::endl;
const
scalar_t
cc_0
=
m_eqcurve
.
interpolate
(
index_0
,
sc_0
,
1
);
//std::max(m_eqcurve.totaq_concentration(m_eqcurve.last()), m_eqcurve.interpolate(index_0, sc_0, 1));
const
scalar_t
cc_1
=
m_eqcurve
.
interpolate
(
index_1
,
sc_1
,
1
);
//std::max(m_eqcurve.totaq_concentration(m_eqcurve.last()), m_eqcurve.interpolate(index_1, sc_1, 1));
const
scalar_t
porosity_0
=
m_eqcurve
.
interpolate
(
index_0
,
sc_0
,
2
);
const
scalar_t
porosity_1
=
m_eqcurve
.
interpolate
(
index_1
,
sc_1
,
2
);
//const scalar_t diffcoeff_0 = m_eqcurve.interpolate(index_0, sc_0, 3);
//const scalar_t diffcoeff_1 = m_eqcurve.interpolate(index_1, sc_1, 3);
const
scalar_t
porosity
=
(
porosity_0
+
porosity_1
)
/
2.0
;
const
scalar_t
diff_coeff
=
porosity
>
0.92
?
2.219e-5
:
1e4
*
std
::
exp
(
9.95
*
porosity
-
29.08
);
// const scalar_t diff_coeff = 1.0/(0.5/diffcoeff_0 +
// 0.5/diffcoeff_1);
scalar_t
flux_coeff
=
(
m_mesh
->
get_face_area
(
element
)
/
m_mesh
->
get_dx
(
element
)
//* porosity
*
diff_coeff
);
// if (m_eqcurve.slope(index_1, 1) != 0)
// {
// std::cout << element << " # " << m_eqcurve.slope(index_0, 1) << " - " << m_eqcurve.slope(index_0, 2)
// << " # " << m_eqcurve.slope(index_1, 1) << " - " << m_eqcurve.slope(index_1, 2) << std::endl;
// }
evelocity
<<
(
+
m_eqcurve
.
slope
(
index_0
,
1
)
*
porosity_0
+
m_eqcurve
.
slope
(
index_0
,
2
)
*
cc_0
+
1.0
)
*
mass_coeff_0
*
velocity
(
node_0
),
(
+
m_eqcurve
.
slope
(
index_1
,
1
)
*
porosity_1
+
m_eqcurve
.
slope
(
index_1
,
2
)
*
cc_1
+
1.0
)
*
mass_coeff_1
*
velocity
(
node_1
);
jacob
<<
1.0
,
-
1.0
,
-
1.0
,
1.0
;
jacob
*=
flux_coeff
;
econc
<<
cc_0
,
cc_1
;
// if (element == 0)
// std::cout << econc << std::endl;
elem_residuals
+=
jacob
*
econc
;
m_internal_flow
(
node_0
)
+=
elem_residuals
(
0
);
m_internal_flow
(
node_1
)
+=
elem_residuals
(
1
);
elem_residuals
+=
evelocity
;
// for (index_t en: m_mesh->range_nen())
// {
// elem_residuals(en) += evelocity(en);
// elem_residuals(en) += (m_mesh->get_volume_element(element)/2.0
// *external_flow(m_mesh->get_node(element, en)));
// }
}
void
SolidDiffusion
::
compute_jacobian
(
Vector
&
displacement
,
Vector
&
velocity
,
Eigen
::
SparseMatrix
<
scalar_t
>&
jacobian
,
scalar_t
alphadt
)
{
m_in_jac
=
true
;
dfpm
::
list_triplet_t
jacob
;
const
index_t
estimation
=
m_mesh
->
nb_nodes
()
*
(
m_mesh
->
nen
);
jacob
.
reserve
(
estimation
);
for
(
index_t
element:
m_mesh
->
range_elements
())
{
element_jacobian
(
element
,
displacement
,
velocity
,
jacob
,
alphadt
);
}
jacobian
=
Eigen
::
SparseMatrix
<
scalar_t
>
(
get_neq
(),
get_neq
());
jacobian
.
setFromTriplets
(
jacob
.
begin
(),
jacob
.
end
());
m_in_jac
=
false
;
}
void
SolidDiffusion
::
element_jacobian
(
index_t
element
,
Vector
&
displacement
,
Vector
&
velocity
,
dfpm
::
list_triplet_t
&
jacobian
,
scalar_t
alphadt
)
{
Eigen
::
VectorXd
element_residual_orig
(
Eigen
::
VectorXd
::
Zero
(
2
));
element_residuals
(
element
,
displacement
,
velocity
,
element_residual_orig
);
for
(
index_t
en:
m_mesh
->
range_nen
())
{
Eigen
::
VectorXd
element_residual
(
Eigen
::
VectorXd
::
Zero
(
2
));
const
index_t
node
=
m_mesh
->
get_node
(
element
,
en
);
const
index_t
dof
=
node
;
const
index_t
idc
=
id_equation
(
dof
);
if
(
idc
==
no_equation
)
continue
;
const
scalar_t
tmp_v
=
velocity
(
dof
);
const
scalar_t
tmp_d
=
displacement
(
dof
);
scalar_t
h
=
eps_jacobian
*
std
::
abs
(
tmp_v
);
if
(
h
<
1e-6
)
h
=
eps_jacobian
;
velocity
(
dof
)
=
tmp_v
+
h
;
h
=
velocity
(
dof
)
-
tmp_v
;
displacement
(
dof
)
=
tmp_d
+
alphadt
*
h
;
element_residuals
(
element
,
displacement
,
velocity
,
element_residual
);
velocity
(
dof
)
=
tmp_v
;
displacement
(
dof
)
=
tmp_d
;
for
(
index_t
enr:
m_mesh
->
range_nen
())
{
const
index_t
noder
=
m_mesh
->
get_node
(
element
,
enr
);
const
index_t
idr
=
id_equation
(
noder
);
if
(
idr
==
no_equation
)
continue
;
jacobian
.
push_back
(
dfpm
::
triplet_t
(
idr
,
idc
,
(
element_residual
(
enr
)
-
element_residual_orig
(
enr
))
/
h
));
}
}
}
void
SolidDiffusion
::
update_solution
(
const
Vector
&
update
,
scalar_t
lambda
,
scalar_t
alpha_dt
,
Vector
&
predictor
,
Vector
&
displacement
,
Vector
&
velocity
)
{
for
(
index_t
node:
m_mesh
->
range_nodes
())
{
const
index_t
id
=
id_equation
(
node
);
if
(
id
==
no_equation
)
continue
;
velocity
(
node
)
+=
lambda
*
update
(
id
);
}
displacement
=
predictor
+
alpha_dt
*
velocity
;
}
}
// end namespace eqcurve
}
// end namespace reactmicp
}
// end namespace specmicp
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