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compute_smd_triangle_mesh_vertices.cpp
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Wed, Sep 4, 23:29
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Fri, Sep 6, 23:29 (2 d)
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rLAMMPS lammps
compute_smd_triangle_mesh_vertices.cpp
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/* ----------------------------------------------------------------------
*
* *** Smooth Mach Dynamics ***
*
* This file is part of the USER-SMD package for LAMMPS.
* Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de
* Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI,
* Eckerstrasse 4, D-79104 Freiburg i.Br, Germany.
*
* ----------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include <string.h>
#include "compute_smd_triangle_mesh_vertices.h"
#include "atom.h"
#include "update.h"
#include "modify.h"
#include "comm.h"
#include "force.h"
#include "memory.h"
#include "error.h"
#include "pair.h"
#include <iostream>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <Eigen/Eigen>
using
namespace
Eigen
;
using
namespace
std
;
using
namespace
LAMMPS_NS
;
/* ---------------------------------------------------------------------- */
ComputeSMDTriangleVertices
::
ComputeSMDTriangleVertices
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
Compute
(
lmp
,
narg
,
arg
)
{
if
(
narg
!=
3
)
error
->
all
(
FLERR
,
"Illegal compute smd/triangle_vertices command"
);
peratom_flag
=
1
;
size_peratom_cols
=
9
;
nmax
=
0
;
outputVector
=
NULL
;
}
/* ---------------------------------------------------------------------- */
ComputeSMDTriangleVertices
::~
ComputeSMDTriangleVertices
()
{
memory
->
sfree
(
outputVector
);
}
/* ---------------------------------------------------------------------- */
void
ComputeSMDTriangleVertices
::
init
()
{
int
count
=
0
;
for
(
int
i
=
0
;
i
<
modify
->
ncompute
;
i
++
)
if
(
strcmp
(
modify
->
compute
[
i
]
->
style
,
"smd/triangle_vertices"
)
==
0
)
count
++
;
if
(
count
>
1
&&
comm
->
me
==
0
)
error
->
warning
(
FLERR
,
"More than one compute smd/triangle_vertices"
);
}
/* ---------------------------------------------------------------------- */
void
ComputeSMDTriangleVertices
::
compute_peratom
()
{
double
**
smd_data_9
=
atom
->
smd_data_9
;
tagint
*
mol
=
atom
->
molecule
;
invoked_peratom
=
update
->
ntimestep
;
// grow vector array if necessary
if
(
atom
->
nmax
>
nmax
)
{
memory
->
destroy
(
outputVector
);
nmax
=
atom
->
nmax
;
memory
->
create
(
outputVector
,
nmax
,
size_peratom_cols
,
"defgradVector"
);
array_atom
=
outputVector
;
}
/*
* triangle vertices are stored using the smd_data_9 array ...
* this is a hack but ok for now as I do not have to create additional storage space
* all triangle particles have molecule id >= 65535
*/
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
((
mask
[
i
]
&
groupbit
)
&&
(
mol
[
i
]
>=
65535
)
){
outputVector
[
i
][
0
]
=
smd_data_9
[
i
][
0
];
outputVector
[
i
][
1
]
=
smd_data_9
[
i
][
1
];
outputVector
[
i
][
2
]
=
smd_data_9
[
i
][
2
];
outputVector
[
i
][
3
]
=
smd_data_9
[
i
][
3
];
outputVector
[
i
][
4
]
=
smd_data_9
[
i
][
4
];
outputVector
[
i
][
5
]
=
smd_data_9
[
i
][
5
];
outputVector
[
i
][
6
]
=
smd_data_9
[
i
][
6
];
outputVector
[
i
][
7
]
=
smd_data_9
[
i
][
7
];
outputVector
[
i
][
8
]
=
smd_data_9
[
i
][
8
];
}
else
{
for
(
int
j
=
0
;
j
<
size_peratom_cols
;
j
++
)
{
outputVector
[
i
][
j
]
=
0.0
;
}
}
}
}
/* ----------------------------------------------------------------------
memory usage of local atom-based array
------------------------------------------------------------------------- */
double
ComputeSMDTriangleVertices
::
memory_usage
()
{
double
bytes
=
size_peratom_cols
*
nmax
*
sizeof
(
double
);
return
bytes
;
}
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