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kinetic_stagger.cpp
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rSPECMICP SpecMiCP / ReactMiCP
kinetic_stagger.cpp
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/*-------------------------------------------------------------------------------
Copyright (c) 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 "kinetic_stagger.hpp"
#include "variables.hpp"
#include "../../../specmicp/adimensional/adimensional_system_solver.hpp"
#include "../../../specmicp/adimensional/adimensional_system_solution_extractor.hpp"
#include "../../../utils/log.hpp"
#include "../../../reactmicp/solver/staggers_base/stagger_structs.hpp"
#include <iostream>
namespace
specmicp
{
namespace
reactmicp
{
namespace
systems
{
namespace
satdiff
{
using
TrueConstPtr
=
SaturatedVariables
*
const
;
inline
TrueConstPtr
cast_to_var
(
VariablesBase
*
const
var
)
{
return
static_cast
<
TrueConstPtr
>
(
var
);
}
//! \brief Initialize the stagger at the beginning of an iteration
void
KineticStagger
::
initialize_timestep
(
scalar_t
dt
,
VariablesBase
*
const
var
)
{
TrueConstPtr
true_var
=
cast_to_var
(
var
);
m_dt
=
dt
;
// Initialize velocity using values from previous timestep
for
(
index_t
node
=
0
;
node
<
true_var
->
nb_nodes
();
++
node
)
{
if
(
true_var
->
is_fixed_composition
(
node
))
continue
;
scalar_t
alpha
=
1.0
;
for
(
index_t
component:
true_var
->
get_database
()
->
range_aqueous_component
())
{
alpha
=
std
::
max
(
alpha
,
0.9
*
dt
*
true_var
->
solid_concentration
(
node
,
component
,
true_var
->
chemistry_rate
())
/
(
true_var
->
solid_concentration
(
node
,
component
,
true_var
->
displacement
()))
);
}
auto
solid_velocity
=
true_var
->
velocity
().
segment
(
true_var
->
offset_node
(
node
)
+
true_var
->
offset_solid_concentration
(),
true_var
->
nb_component
());
auto
solid_chemistry_rate
=
true_var
->
chemistry_rate
().
segment
(
true_var
->
offset_node
(
node
)
+
true_var
->
offset_solid_concentration
(),
true_var
->
nb_component
());
solid_velocity
=
1
/
alpha
*
solid_chemistry_rate
;
}
m_model
->
initialize_timestep
(
dt
,
true_var
->
kinetic_variables
());
for
(
index_t
node
=
0
;
node
<
true_var
->
nb_nodes
();
++
node
)
{
if
(
true_var
->
is_fixed_composition
(
node
))
continue
;
m_model
->
restart_timestep
(
node
,
true_var
->
equilibrium_solution
(
node
),
true_var
->
kinetic_variables
());
for
(
index_t
component
=
0
;
component
<
true_var
->
nb_component
();
++
component
)
{
true_var
->
aqueous_concentration
(
node
,
component
,
true_var
->
chemistry_rate
())
=
-
m_model
->
get_velocity_kinetic
(
node
,
component
,
true_var
->
kinetic_variables
());
true_var
->
aqueous_concentration
(
node
,
component
,
true_var
->
velocity
())
+=
(
//true_var->aqueous_concentration(node, component, true_var->transport_rate())
+
true_var
->
aqueous_concentration
(
node
,
component
,
true_var
->
chemistry_rate
())
//- true_var->solid_concentration(node, component, true_var->chemistry_rate())
);
true_var
->
aqueous_concentration
(
node
,
component
,
true_var
->
displacement
())
=
true_var
->
aqueous_concentration
(
node
,
component
,
true_var
->
predictor
())
+
m_dt
*
true_var
->
aqueous_concentration
(
node
,
component
,
true_var
->
velocity
());
}
}
}
//! \brief Solve the equation for the timestep
solver
::
StaggerReturnCode
KineticStagger
::
restart_timestep
(
VariablesBase
*
const
var
)
{
TrueConstPtr
true_var
=
cast_to_var
(
var
);
int
failed_chemistry
=
0
;
#ifdef SPECMICP_USE_OPENMP
#pragma omp parallel default(none) shared(failed_chemistry)
// node true_var being const is shared by default, can't be mentionned again
{
#pragma omp for schedule(dynamic, 5)
for
(
index_t
node
=
0
;
node
<
true_var
->
nb_nodes
();
++
node
)
{
// only solve if necessary
if
(
true_var
->
is_fixed_composition
(
node
)
or
failed_chemistry
>
0
)
continue
;
const
auto
retcode
=
solve_one_node
(
node
,
true_var
);
if
(
retcode
>
0
)
{
++
failed_chemistry
;
}
}
}
#else
{
for
(
index_t
node
=
0
;
node
<
true_var
->
nb_nodes
();
++
node
)
{
if
(
true_var
->
is_fixed_composition
(
node
))
continue
;
const
auto
retcode
=
solve_one_node
(
node
,
true_var
);
if
(
retcode
>
0
)
{
++
failed_chemistry
;
break
;
}
}
}
#endif
// SPECMICP_USE_OPENMP
if
(
failed_chemistry
>
0
)
return
solver
::
StaggerReturnCode
::
UnknownError
;
return
solver
::
StaggerReturnCode
::
ResidualMinimized
;
}
//!
int
KineticStagger
::
solve_one_node
(
index_t
node
,
SaturatedVariables
*
const
true_var
)
{
AdimensionalSystemConstraints
constraints
(
get_constraints
(
node
));
constraints
.
total_concentrations
=
true_var
->
total_concentrations
(
node
);
constraints
.
set_inert_volume_fraction
(
m_model
->
get_volume_fraction_kinetic
(
node
,
true_var
->
kinetic_variables
()));
AdimensionalSystemSolver
adim_solver
(
true_var
->
get_database
(),
constraints
,
true_var
->
equilibrium_solution
(
node
),
m_options
);
Vector
variables
(
true_var
->
equilibrium_solution
(
node
).
main_variables
);
micpsolver
::
MiCPPerformance
perf
=
adim_solver
.
solve
(
variables
);
micpsolver
::
MiCPSolverReturnCode
retcode
=
perf
.
return_code
;
if
(
retcode
<=
micpsolver
::
MiCPSolverReturnCode
::
NotConvergedYet
)
{
ERROR
<<
"Failed to solve chemistry problem at node "
<<
node
<<
", return code = "
<<
static_cast
<
int
>
(
retcode
)
<<
", residual = "
<<
perf
.
current_residual
;
ERROR
<<
"Total concentration :
\n
"
<<
constraints
.
total_concentrations
;
return
1
;
}
true_var
->
equilibrium_solution
(
node
)
=
adim_solver
.
get_raw_solution
(
variables
);
AdimensionalSystemSolutionExtractor
extractor
(
true_var
->
equilibrium_solution
(
node
),
true_var
->
get_database
(),
m_options
.
units_set
);
for
(
index_t
component
=
0
;
component
<
true_var
->
nb_component
();
++
component
)
{
const
scalar_t
c_aq
=
extractor
.
density_water
()
*
extractor
.
total_aqueous_concentration
(
component
);
true_var
->
aqueous_concentration
(
node
,
component
,
true_var
->
displacement
())
=
c_aq
;
const
scalar_t
c_aq_0
=
true_var
->
aqueous_concentration
(
node
,
component
,
true_var
->
predictor
());
const
scalar_t
vel_aq
=
(
c_aq
-
c_aq_0
)
/
m_dt
;
true_var
->
aqueous_concentration
(
node
,
component
,
true_var
->
velocity
())
=
vel_aq
;
const
scalar_t
c_sol
=
extractor
.
total_immobile_concentration
(
component
);
true_var
->
solid_concentration
(
node
,
component
,
true_var
->
displacement
())
=
c_sol
;
const
scalar_t
c_sol_0
=
true_var
->
solid_concentration
(
node
,
component
,
true_var
->
predictor
());
const
scalar_t
vel_sol
=
(
c_sol
-
c_sol_0
)
/
m_dt
;
true_var
->
solid_concentration
(
node
,
component
,
true_var
->
velocity
())
=
vel_sol
;
true_var
->
solid_concentration
(
node
,
component
,
true_var
->
chemistry_rate
())
=
vel_sol
;
}
return
0
;
}
}
// end namespace satdiff
}
// end namespace systems
}
// end namespace reactmicp
}
// end namespace specmicp
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