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compute_stress_atom.cpp
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Wed, Sep 25, 09:05
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6 KB
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text/x-c
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Fri, Sep 27, 09:05 (2 d)
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blob
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21069312
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rLAMMPS lammps
compute_stress_atom.cpp
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/* ----------------------------------------------------------------------
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_stress_atom.h"
#include "atom.h"
#include "neighbor.h"
#include "modify.h"
#include "comm.h"
#include "update.h"
#include "force.h"
#include "pair.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
/* ---------------------------------------------------------------------- */
ComputeStressAtom
::
ComputeStressAtom
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
Compute
(
lmp
,
narg
,
arg
)
{
if
(
narg
!=
3
)
error
->
all
(
"Illegal compute stress/atom command"
);
peratom_flag
=
1
;
size_peratom
=
6
;
comm_reverse
=
6
;
neigh_half_once
=
1
;
nmax
=
0
;
stress
=
NULL
;
}
/* ---------------------------------------------------------------------- */
ComputeStressAtom
::~
ComputeStressAtom
()
{
memory
->
destroy_2d_double_array
(
stress
);
}
/* ---------------------------------------------------------------------- */
void
ComputeStressAtom
::
init
()
{
if
(
force
->
pair
==
NULL
||
force
->
pair
->
single_enable
==
0
)
error
->
all
(
"Pair style does not support computing per-atom stress"
);
int
count
=
0
;
for
(
int
i
=
0
;
i
<
modify
->
ncompute
;
i
++
)
if
(
strcmp
(
modify
->
compute
[
i
]
->
style
,
"stress/atom"
)
==
0
)
count
++
;
if
(
count
>
1
&&
comm
->
me
==
0
)
error
->
warning
(
"More than one compute stress/atom"
);
}
/* ---------------------------------------------------------------------- */
void
ComputeStressAtom
::
compute_peratom
()
{
int
i
,
j
,
k
,
n
,
itype
,
jtype
,
numneigh
;
double
xtmp
,
ytmp
,
ztmp
,
delx
,
dely
,
delz
,
rsq
;
double
factor_coul
,
factor_lj
,
fforce
,
rmass
;
int
*
neighs
;
Pair
::
One
one
;
// grow stress array if necessary
if
(
atom
->
nmax
>
nmax
)
{
memory
->
destroy_2d_double_array
(
stress
);
nmax
=
atom
->
nmax
;
stress
=
memory
->
create_2d_double_array
(
nmax
,
6
,
"compute/stress/atom:stress"
);
vector_atom
=
stress
;
}
// clear stress array
// n includes ghosts only if newton_pair flag is set
if
(
force
->
newton_pair
)
n
=
atom
->
nlocal
+
atom
->
nghost
;
else
n
=
atom
->
nlocal
;
for
(
i
=
0
;
i
<
n
;
i
++
)
{
stress
[
i
][
0
]
=
0.0
;
stress
[
i
][
1
]
=
0.0
;
stress
[
i
][
2
]
=
0.0
;
stress
[
i
][
3
]
=
0.0
;
stress
[
i
][
4
]
=
0.0
;
stress
[
i
][
5
]
=
0.0
;
}
// if needed, build a half neighbor list
if
(
!
neighbor
->
half_every
)
neighbor
->
build_half
();
// compute pairwise stress for all atoms via pair->single()
// use half neighbor list
double
*
special_coul
=
force
->
special_coul
;
double
*
special_lj
=
force
->
special_lj
;
double
**
cutsq
=
force
->
pair
->
cutsq
;
double
**
x
=
atom
->
x
;
int
*
type
=
atom
->
type
;
int
nlocal
=
atom
->
nlocal
;
int
nall
=
atom
->
nlocal
+
atom
->
nghost
;
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
{
xtmp
=
x
[
i
][
0
];
ytmp
=
x
[
i
][
1
];
ztmp
=
x
[
i
][
2
];
itype
=
type
[
i
];
neighs
=
neighbor
->
firstneigh
[
i
];
numneigh
=
neighbor
->
numneigh
[
i
];
for
(
k
=
0
;
k
<
numneigh
;
k
++
)
{
j
=
neighs
[
k
];
if
(
j
<
nall
)
factor_coul
=
factor_lj
=
1.0
;
else
{
factor_coul
=
special_coul
[
j
/
nall
];
factor_lj
=
special_lj
[
j
/
nall
];
j
%=
nall
;
}
delx
=
xtmp
-
x
[
j
][
0
];
dely
=
ytmp
-
x
[
j
][
1
];
delz
=
ztmp
-
x
[
j
][
2
];
rsq
=
delx
*
delx
+
dely
*
dely
+
delz
*
delz
;
jtype
=
type
[
j
];
if
(
rsq
<
cutsq
[
itype
][
jtype
])
{
force
->
pair
->
single
(
i
,
j
,
itype
,
jtype
,
rsq
,
factor_coul
,
factor_lj
,
0
,
one
);
fforce
=
one
.
fforce
;
stress
[
i
][
0
]
-=
delx
*
delx
*
fforce
;
stress
[
i
][
1
]
-=
dely
*
dely
*
fforce
;
stress
[
i
][
2
]
-=
delz
*
delz
*
fforce
;
stress
[
i
][
3
]
-=
delx
*
dely
*
fforce
;
stress
[
i
][
4
]
-=
delx
*
delz
*
fforce
;
stress
[
i
][
5
]
-=
dely
*
delz
*
fforce
;
if
(
force
->
newton_pair
||
j
<
nlocal
)
{
stress
[
j
][
0
]
-=
delx
*
delx
*
fforce
;
stress
[
j
][
1
]
-=
dely
*
dely
*
fforce
;
stress
[
j
][
2
]
-=
delz
*
delz
*
fforce
;
stress
[
j
][
3
]
-=
delx
*
dely
*
fforce
;
stress
[
j
][
4
]
-=
delx
*
delz
*
fforce
;
stress
[
j
][
5
]
-=
dely
*
delz
*
fforce
;
}
}
}
}
// communicate stress between neighbor procs
if
(
force
->
newton_pair
)
comm
->
reverse_comm_compute
(
this
);
// remove double counting of per-atom stress
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
{
stress
[
i
][
0
]
*=
0.5
;
stress
[
i
][
1
]
*=
0.5
;
stress
[
i
][
2
]
*=
0.5
;
stress
[
i
][
3
]
*=
0.5
;
stress
[
i
][
4
]
*=
0.5
;
stress
[
i
][
5
]
*=
0.5
;
}
// include kinetic energy term for each atom
// mvv2e converts mv^2 to energy
double
**
v
=
atom
->
v
;
double
*
mass
=
atom
->
mass
;
double
mvv2e
=
force
->
mvv2e
;
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
{
rmass
=
mvv2e
*
mass
[
type
[
i
]];
stress
[
i
][
0
]
-=
rmass
*
v
[
i
][
0
]
*
v
[
i
][
0
];
stress
[
i
][
1
]
-=
rmass
*
v
[
i
][
1
]
*
v
[
i
][
1
];
stress
[
i
][
2
]
-=
rmass
*
v
[
i
][
2
]
*
v
[
i
][
2
];
stress
[
i
][
3
]
-=
rmass
*
v
[
i
][
0
]
*
v
[
i
][
1
];
stress
[
i
][
4
]
-=
rmass
*
v
[
i
][
0
]
*
v
[
i
][
2
];
stress
[
i
][
5
]
-=
rmass
*
v
[
i
][
1
]
*
v
[
i
][
2
];
}
// convert to pressure units (actually stress/volume = pressure)
double
nktv2p
=
force
->
nktv2p
;
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
{
stress
[
i
][
0
]
*=
nktv2p
;
stress
[
i
][
1
]
*=
nktv2p
;
stress
[
i
][
2
]
*=
nktv2p
;
stress
[
i
][
3
]
*=
nktv2p
;
stress
[
i
][
4
]
*=
nktv2p
;
stress
[
i
][
5
]
*=
nktv2p
;
}
}
/* ---------------------------------------------------------------------- */
int
ComputeStressAtom
::
pack_reverse_comm
(
int
n
,
int
first
,
double
*
buf
)
{
int
i
,
m
,
last
;
m
=
0
;
last
=
first
+
n
;
for
(
i
=
first
;
i
<
last
;
i
++
)
{
buf
[
m
++
]
=
stress
[
i
][
0
];
buf
[
m
++
]
=
stress
[
i
][
1
];
buf
[
m
++
]
=
stress
[
i
][
2
];
buf
[
m
++
]
=
stress
[
i
][
3
];
buf
[
m
++
]
=
stress
[
i
][
4
];
buf
[
m
++
]
=
stress
[
i
][
5
];
}
return
6
;
}
/* ---------------------------------------------------------------------- */
void
ComputeStressAtom
::
unpack_reverse_comm
(
int
n
,
int
*
list
,
double
*
buf
)
{
int
i
,
j
,
m
;
m
=
0
;
for
(
i
=
0
;
i
<
n
;
i
++
)
{
j
=
list
[
i
];
stress
[
j
][
0
]
+=
buf
[
m
++
];
stress
[
j
][
1
]
+=
buf
[
m
++
];
stress
[
j
][
2
]
+=
buf
[
m
++
];
stress
[
j
][
3
]
+=
buf
[
m
++
];
stress
[
j
][
4
]
+=
buf
[
m
++
];
stress
[
j
][
5
]
+=
buf
[
m
++
];
}
}
/* ----------------------------------------------------------------------
memory usage of local atom-based array
------------------------------------------------------------------------- */
int
ComputeStressAtom
::
memory_usage
()
{
int
bytes
=
nmax
*
6
*
sizeof
(
double
);
return
bytes
;
}
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