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rLIBMULTISCALE LibMultiScale
kobayashi.cc
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/**
* @file kobayashi.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
*
* @date Fri Jul 11 15:47:44 2014
*
* @brief Kobayashi's bridging method
*
* @section LICENSE
*
* Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* LibMultiScale is free software: you can redistribute it and/or modify it
* under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* LibMultiScale is distributed in the hope that it will be useful, but
* WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with LibMultiScale. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "kobayashi.hh"
#include "arlequin_template.hh"
#include "lib_bridging.hh"
#include "lm_common.hh"
/* -------------------------------------------------------------------------- */
__BEGIN_LIBMULTISCALE__
/* -------------------------------------------------------------------------- */
Kobayashi
::
Kobayashi
(
const
std
::
string
&
name
)
:
LMObject
(
name
),
ArlequinTemplate
(
name
)
{
// naming the bridging zones
std
::
stringstream
fname
;
fname
<<
name
<<
"-bridging"
;
}
/* -------------------------------------------------------------------------- */
Kobayashi
::~
Kobayashi
()
{}
/* -------------------------------------------------------------------------- */
template
<
typename
DomainA
,
typename
DomainC
>
void
Kobayashi
::
init
(
DomainA
&
domA
,
DomainC
&
domC
)
{
const
UInt
Dim
=
spatial_dimension
;
if
(
lm_world_size
>
1
)
LM_FATAL
(
"this coupler work only in sequential"
);
std
::
stringstream
fname
;
// initialize the bridging_zone object
bridging_zone
.
init
(
domA
,
domC
);
// allocate the vectors necessary to continue
UInt
size
=
bridging_zone
.
getNumberPoints
();
this
->
allocate
(
size
);
// build weights
this
->
computeContinuumWeights
(
domC
.
getContainer
());
this
->
computeAtomWeights
(
domA
.
getContainer
());
UInt
_size
=
bridging_zone
.
getNumberElems
();
DUMP
(
"Allocating vectors"
,
DBG_INFO
);
rhs
.
resize
(
size
,
Dim
);
CG_vel
.
resize
(
_size
,
Dim
);
CG_disp
.
resize
(
_size
,
Dim
);
DUMP
(
"Computing initial least square constraint"
,
DBG_INFO
);
buildCGMatrix
();
// treat now MD boundary zone
MDboundary_zone
.
init
(
domA
,
domC
);
DUMP
(
"Init ... done"
,
DBG_INFO_STARTUP
);
}
/* -------------------------------------------------------------------------- */
template
<
typename
DomainA
,
typename
DomainC
>
void
Kobayashi
::
coupling
(
CouplingStage
stage
,
DomainA
&
domA
,
DomainC
&
domC
)
{
if
(
stage
!=
COUPLING_STEP4
)
return
;
MDboundary_zone
.
projectAtomicFieldOnMesh
(
_velocity
);
MDboundary_zone
.
projectAtomicFieldOnMesh
(
_displacement
);
buildLeastSquareRHS
(
domA
.
getContainer
());
correctContinuum
(
domC
.
getContainer
());
correctAtoms
(
domA
.
getContainer
());
}
/* -------------------------------------------------------------------------- */
void
Kobayashi
::
buildCGMatrix
()
{
UInt
nb_nodes
=
bridging_zone
.
getNumberNodes
();
UInt
nb_atoms
[[
gnu
::
unused
]]
=
bridging_zone
.
getNumberPoints
();
Eigen
::
MatrixXf
ls_mat
(
nb_nodes
,
nb_nodes
);
bridging_zone
.
buildLeastSquareMatrix
(
ls_mat
);
LM_TOIMPLEMENT
;
// ls_mat.factoLU();
// ls_mat.inverse();
// math::Matrix shapes(nb_atoms, nb_nodes);
// bridging_zone.extractShapeMatrix(shapes);
// shapes.transpose();
// A = new math::Matrix(nb_nodes, nb_atoms);
// A->matProduct(ls_mat, shapes);
}
/* -------------------------------------------------------------------------- */
template
<
typename
ContA
>
void
Kobayashi
::
buildLeastSquareRHS
(
ContA
&
pointList
)
{
rhs
.
setZero
();
UInt
at_index
=
0
;
for
(
auto
&&
at
:
pointList
)
{
rhs
(
at_index
)
=
at
.
velocity
()[
0
];
++
at_index
;
}
CG_vel
=
A
*
rhs
.
matrix
();
at_index
=
0
;
for
(
auto
&&
at
:
pointList
)
{
rhs
(
at_index
)
=
at
.
displacement
()[
0
];
++
at_index
;
}
CG_disp
=
A
*
rhs
.
matrix
();
}
/* -------------------------------------------------------------------------- */
template
<
typename
ContB
>
void
Kobayashi
::
correctContinuum
(
ContB
&
meshList
)
{
auto
&
weightFE
=
this
->
weightFE
.
getArray
();
UInt
j
=
0
;
for
(
auto
&&
n
:
meshList
)
{
if
(
weightFE
[
j
]
<=
.5
)
{
Real
speed_projection
=
this
->
quality
;
if
(
weightFE
[
j
]
<=
1e-2
)
speed_projection
=
1
;
Real
&
vel
=
n
.
velocity
()[
0
];
Real
&
disp
=
n
.
displacement
()[
0
];
Real
corrected
=
vel
+
speed_projection
*
(
CG_vel
(
j
)
-
vel
);
n
.
velocity
()[
0
]
=
corrected
;
corrected
=
disp
+
speed_projection
*
(
CG_disp
(
j
)
-
disp
);
n
.
displacement
()[
0
]
=
corrected
;
}
++
j
;
}
}
/* -------------------------------------------------------------------------- */
template
<
typename
ContA
>
void
Kobayashi
::
correctAtoms
(
ContA
&
pointList
)
{
UInt
natom
=
bridging_zone
.
getNumberLocalMatchedPoints
();
constexpr
UInt
Dim
=
ContA
::
Dim
;
ContainerArray
<
Real
>
atomic_vel
;
ContainerArray
<
Real
>
atomic_disp
;
atomic_vel
.
assign
(
natom
*
Dim
,
0
);
atomic_disp
.
assign
(
natom
*
Dim
,
0
);
bridging_zone
.
projectAtomicFieldOnMesh
(
_displacement
,
atomic_disp
);
bridging_zone
.
projectAtomicFieldOnMesh
(
_velocity
,
atomic_vel
);
auto
&
weightMD
=
this
->
weightMD
.
getArray
();
UInt
at_index
=
0
;
for
(
auto
&&
at
:
pointList
)
{
if
(
weightMD
[
at_index
]
<=
.5
)
{
Real
speed_projection
=
this
->
quality
;
if
(
weightMD
[
at_index
]
<=
1e-2
)
speed_projection
=
1
;
Real
&
vel
=
at
.
velocity
()[
0
];
Real
disp
=
at
.
displacement
()[
0
];
vel
=
vel
+
speed_projection
*
(
atomic_vel
[
at_index
]
-
vel
);
Vector
<
Dim
>
corrected
;
corrected
[
0
]
=
disp
+
this
->
quality
*
(
atomic_disp
[
at_index
]
-
disp
);
at
.
displacement
()
=
corrected
;
}
++
at_index
;
}
}
/* -------------------------------------------------------------------------- */
/* LMDESC KOBAYASHI
This keyword is used to set a coupling method
which will implement the method of Kobayashi and co-workers \\ \\
\textit{A simple dynamical scale-coupling method for concurrent simulation of
hybridized atomistic/coarse-grained-particle system,} \\
\textbf{Ryo Kobayashi, Takahide Nakamura, Shuji Ogata,} \\
\textit{International Journal for Numerical Methods in Engineering Volume 83,
Issue 2, pages 249-268, 9 July 2010.} \\ \\
This coupling component works only in 1D and in sequential.
*/
/* LMHERITANCE arlequin_template */
/* LMEXAMPLE
COUPLING_CODE md fe KOBAYASHI GEOMETRY 3 BOUNDARY 4 GRID_DIVISIONX 10 QUALITY
1e-3 VERBOSE
*/
void
Kobayashi
::
declareParams
()
{
ArlequinTemplate
::
declareParams
();
}
/* -------------------------------------------------------------------------- */
DECLARE_COUPLER_MAKE_CALL
(
Kobayashi
,
domA
,
domC
)
__END_LIBMULTISCALE__
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