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compute_pe_atom.cpp
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Created
Wed, Nov 6, 23:23
Size
4 KB
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text/x-c
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Fri, Nov 8, 23:23 (1 d, 23 h)
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rLAMMPS lammps
compute_pe_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_pe_atom.h"
#include "atom.h"
#include "update.h"
#include "comm.h"
#include "force.h"
#include "pair.h"
#include "bond.h"
#include "angle.h"
#include "dihedral.h"
#include "improper.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
/* ---------------------------------------------------------------------- */
ComputePEAtom
::
ComputePEAtom
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
Compute
(
lmp
,
narg
,
arg
)
{
if
(
narg
<
3
)
error
->
all
(
FLERR
,
"Illegal compute pe/atom command"
);
peratom_flag
=
1
;
size_peratom_cols
=
0
;
peatomflag
=
1
;
timeflag
=
1
;
comm_reverse
=
1
;
if
(
narg
==
3
)
{
pairflag
=
1
;
bondflag
=
angleflag
=
dihedralflag
=
improperflag
=
1
;
}
else
{
pairflag
=
0
;
bondflag
=
angleflag
=
dihedralflag
=
improperflag
=
0
;
int
iarg
=
3
;
while
(
iarg
<
narg
)
{
if
(
strcmp
(
arg
[
iarg
],
"pair"
)
==
0
)
pairflag
=
1
;
else
if
(
strcmp
(
arg
[
iarg
],
"bond"
)
==
0
)
bondflag
=
1
;
else
if
(
strcmp
(
arg
[
iarg
],
"angle"
)
==
0
)
angleflag
=
1
;
else
if
(
strcmp
(
arg
[
iarg
],
"dihedral"
)
==
0
)
dihedralflag
=
1
;
else
if
(
strcmp
(
arg
[
iarg
],
"improper"
)
==
0
)
improperflag
=
1
;
else
error
->
all
(
FLERR
,
"Illegal compute pe/atom command"
);
iarg
++
;
}
}
nmax
=
0
;
energy
=
NULL
;
}
/* ---------------------------------------------------------------------- */
ComputePEAtom
::~
ComputePEAtom
()
{
memory
->
destroy
(
energy
);
}
/* ---------------------------------------------------------------------- */
void
ComputePEAtom
::
compute_peratom
()
{
int
i
;
invoked_peratom
=
update
->
ntimestep
;
if
(
update
->
eflag_atom
!=
invoked_peratom
)
error
->
all
(
FLERR
,
"Per-atom energy was not tallied on needed timestep"
);
// grow local energy array if necessary
// needs to be atom->nmax in length
if
(
atom
->
nmax
>
nmax
)
{
memory
->
destroy
(
energy
);
nmax
=
atom
->
nmax
;
memory
->
create
(
energy
,
nmax
,
"pe/atom:energy"
);
vector_atom
=
energy
;
}
// npair includes ghosts if either newton flag is set
// b/c some bonds/dihedrals call pair::ev_tally with pairwise info
// nbond includes ghosts if newton_bond is set
// ntotal includes ghosts if either newton flag is set
int
nlocal
=
atom
->
nlocal
;
int
npair
=
nlocal
;
int
nbond
=
nlocal
;
int
ntotal
=
nlocal
;
if
(
force
->
newton
)
npair
+=
atom
->
nghost
;
if
(
force
->
newton_bond
)
nbond
+=
atom
->
nghost
;
if
(
force
->
newton
)
ntotal
+=
atom
->
nghost
;
// clear local energy array
for
(
i
=
0
;
i
<
ntotal
;
i
++
)
energy
[
i
]
=
0.0
;
// add in per-atom contributions from each force
if
(
pairflag
&&
force
->
pair
)
{
double
*
eatom
=
force
->
pair
->
eatom
;
for
(
i
=
0
;
i
<
npair
;
i
++
)
energy
[
i
]
+=
eatom
[
i
];
}
if
(
bondflag
&&
force
->
bond
)
{
double
*
eatom
=
force
->
bond
->
eatom
;
for
(
i
=
0
;
i
<
nbond
;
i
++
)
energy
[
i
]
+=
eatom
[
i
];
}
if
(
angleflag
&&
force
->
angle
)
{
double
*
eatom
=
force
->
angle
->
eatom
;
for
(
i
=
0
;
i
<
nbond
;
i
++
)
energy
[
i
]
+=
eatom
[
i
];
}
if
(
dihedralflag
&&
force
->
dihedral
)
{
double
*
eatom
=
force
->
dihedral
->
eatom
;
for
(
i
=
0
;
i
<
nbond
;
i
++
)
energy
[
i
]
+=
eatom
[
i
];
}
if
(
improperflag
&&
force
->
improper
)
{
double
*
eatom
=
force
->
improper
->
eatom
;
for
(
i
=
0
;
i
<
nbond
;
i
++
)
energy
[
i
]
+=
eatom
[
i
];
}
// communicate ghost energy between neighbor procs
if
(
force
->
newton
)
comm
->
reverse_comm_compute
(
this
);
// zero energy of atoms not in group
// only do this after comm since ghost contributions must be included
int
*
mask
=
atom
->
mask
;
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
!
(
mask
[
i
]
&
groupbit
))
energy
[
i
]
=
0.0
;
}
/* ---------------------------------------------------------------------- */
int
ComputePEAtom
::
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
++
]
=
energy
[
i
];
return
1
;
}
/* ---------------------------------------------------------------------- */
void
ComputePEAtom
::
unpack_reverse_comm
(
int
n
,
int
*
list
,
double
*
buf
)
{
int
i
,
j
,
m
;
m
=
0
;
for
(
i
=
0
;
i
<
n
;
i
++
)
{
j
=
list
[
i
];
energy
[
j
]
+=
buf
[
m
++
];
}
}
/* ----------------------------------------------------------------------
memory usage of local atom-based array
------------------------------------------------------------------------- */
double
ComputePEAtom
::
memory_usage
()
{
double
bytes
=
nmax
*
sizeof
(
double
);
return
bytes
;
}
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