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compute_stress_tally.cpp
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Thu, Oct 17, 01:13
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text/x-c
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Sat, Oct 19, 01:13 (1 d, 23 h)
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rLAMMPS lammps
compute_stress_tally.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_tally.h"
#include "atom.h"
#include "group.h"
#include "pair.h"
#include "update.h"
#include "memory.h"
#include "error.h"
#include "force.h"
using
namespace
LAMMPS_NS
;
/* ---------------------------------------------------------------------- */
ComputeStressTally
::
ComputeStressTally
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
Compute
(
lmp
,
narg
,
arg
)
{
if
(
narg
<
4
)
error
->
all
(
FLERR
,
"Illegal compute stress/tally command"
);
igroup2
=
group
->
find
(
arg
[
3
]);
if
(
igroup2
==
-
1
)
error
->
all
(
FLERR
,
"Could not find compute stress/tally second group ID"
);
groupbit2
=
group
->
bitmask
[
igroup2
];
scalar_flag
=
1
;
vector_flag
=
0
;
peratom_flag
=
1
;
timeflag
=
1
;
comm_reverse
=
size_peratom_cols
=
6
;
extscalar
=
0
;
peflag
=
1
;
// we need Pair::ev_tally() to be run
did_compute
=
0
;
invoked_peratom
=
invoked_scalar
=
-
1
;
nmax
=
-
1
;
stress
=
NULL
;
vector
=
new
double
[
size_peratom_cols
];
}
/* ---------------------------------------------------------------------- */
ComputeStressTally
::~
ComputeStressTally
()
{
if
(
force
&&
force
->
pair
)
force
->
pair
->
del_tally_callback
(
this
);
memory
->
destroy
(
stress
);
delete
[]
vector
;
}
/* ---------------------------------------------------------------------- */
void
ComputeStressTally
::
init
()
{
if
(
force
->
pair
==
NULL
)
error
->
all
(
FLERR
,
"Trying to use compute stress/tally with no pair style"
);
else
force
->
pair
->
add_tally_callback
(
this
);
if
(
force
->
pair
->
single_enable
==
0
||
force
->
pair
->
manybody_flag
)
error
->
all
(
FLERR
,
"Compute stress/tally used with incompatible pair style."
);
if
((
comm
->
me
==
0
)
&&
(
force
->
bond
||
force
->
angle
||
force
->
dihedral
||
force
->
improper
||
force
->
kspace
))
error
->
warning
(
FLERR
,
"Compute stress/tally only called from pair style"
);
did_compute
=
-
1
;
}
/* ---------------------------------------------------------------------- */
void
ComputeStressTally
::
pair_tally_callback
(
int
i
,
int
j
,
int
nlocal
,
int
newton
,
double
,
double
,
double
fpair
,
double
dx
,
double
dy
,
double
dz
)
{
const
int
ntotal
=
atom
->
nlocal
+
atom
->
nghost
;
const
int
*
const
mask
=
atom
->
mask
;
// do setup work that needs to be done only once per timestep
if
(
did_compute
!=
update
->
ntimestep
)
{
did_compute
=
update
->
ntimestep
;
// grow local stress array if necessary
// needs to be atom->nmax in length
if
(
atom
->
nmax
>
nmax
)
{
memory
->
destroy
(
stress
);
nmax
=
atom
->
nmax
;
memory
->
create
(
stress
,
nmax
,
size_peratom_cols
,
"stress/tally:stress"
);
array_atom
=
stress
;
}
// clear storage as needed
if
(
newton
)
{
for
(
int
i
=
0
;
i
<
ntotal
;
++
i
)
for
(
int
j
=
0
;
j
<
size_peratom_cols
;
++
j
)
stress
[
i
][
j
]
=
0.0
;
}
else
{
for
(
int
i
=
0
;
i
<
atom
->
nlocal
;
++
i
)
for
(
int
j
=
0
;
j
<
size_peratom_cols
;
++
j
)
stress
[
i
][
j
]
=
0.0
;
}
for
(
int
i
=
0
;
i
<
size_peratom_cols
;
++
i
)
vector
[
i
]
=
virial
[
i
]
=
0.0
;
}
if
(
((
mask
[
i
]
&
groupbit
)
&&
(
mask
[
j
]
&
groupbit2
))
||
((
mask
[
i
]
&
groupbit2
)
&&
(
mask
[
j
]
&
groupbit
))
)
{
fpair
*=
0.5
;
const
double
v0
=
dx
*
dx
*
fpair
;
const
double
v1
=
dy
*
dy
*
fpair
;
const
double
v2
=
dz
*
dz
*
fpair
;
const
double
v3
=
dx
*
dy
*
fpair
;
const
double
v4
=
dx
*
dz
*
fpair
;
const
double
v5
=
dy
*
dz
*
fpair
;
if
(
newton
||
i
<
nlocal
)
{
virial
[
0
]
+=
v0
;
stress
[
i
][
0
]
+=
v0
;
virial
[
1
]
+=
v1
;
stress
[
i
][
1
]
+=
v1
;
virial
[
2
]
+=
v2
;
stress
[
i
][
2
]
+=
v2
;
virial
[
3
]
+=
v3
;
stress
[
i
][
3
]
+=
v3
;
virial
[
4
]
+=
v4
;
stress
[
i
][
4
]
+=
v4
;
virial
[
5
]
+=
v5
;
stress
[
i
][
5
]
+=
v5
;
}
if
(
newton
||
j
<
nlocal
)
{
virial
[
0
]
+=
v0
;
stress
[
j
][
0
]
+=
v0
;
virial
[
1
]
+=
v1
;
stress
[
j
][
1
]
+=
v1
;
virial
[
2
]
+=
v2
;
stress
[
j
][
2
]
+=
v2
;
virial
[
3
]
+=
v3
;
stress
[
j
][
3
]
+=
v3
;
virial
[
4
]
+=
v4
;
stress
[
j
][
4
]
+=
v4
;
virial
[
5
]
+=
v5
;
stress
[
j
][
5
]
+=
v5
;
}
}
}
/* ---------------------------------------------------------------------- */
int
ComputeStressTally
::
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
m
;
}
/* ---------------------------------------------------------------------- */
void
ComputeStressTally
::
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
++
];
}
}
/* ---------------------------------------------------------------------- */
double
ComputeStressTally
::
compute_scalar
()
{
invoked_scalar
=
update
->
ntimestep
;
if
((
did_compute
!=
invoked_scalar
)
||
(
update
->
eflag_global
!=
invoked_scalar
))
error
->
all
(
FLERR
,
"Energy was not tallied on needed timestep"
);
// sum accumulated forces across procs
MPI_Allreduce
(
virial
,
vector
,
size_peratom_cols
,
MPI_DOUBLE
,
MPI_SUM
,
world
);
if
(
domain
->
dimension
==
3
)
scalar
=
(
vector
[
0
]
+
vector
[
1
]
+
vector
[
2
])
/
3.0
;
else
scalar
=
(
vector
[
0
]
+
vector
[
1
])
/
2.0
;
return
scalar
;
}
/* ---------------------------------------------------------------------- */
void
ComputeStressTally
::
compute_peratom
()
{
invoked_peratom
=
update
->
ntimestep
;
if
((
did_compute
!=
invoked_peratom
)
||
(
update
->
eflag_global
!=
invoked_peratom
))
error
->
all
(
FLERR
,
"Energy was not tallied on needed timestep"
);
// collect contributions from ghost atoms
if
(
force
->
newton_pair
)
{
comm
->
reverse_comm_compute
(
this
);
const
int
nall
=
atom
->
nlocal
+
atom
->
nghost
;
for
(
int
i
=
atom
->
nlocal
;
i
<
nall
;
++
i
)
for
(
int
j
=
0
;
j
<
size_peratom_cols
;
++
j
)
stress
[
i
][
j
]
=
0.0
;
}
// convert to stress*volume units = -pressure*volume
const
double
nktv2p
=
-
force
->
nktv2p
;
for
(
int
i
=
0
;
i
<
atom
->
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
;
}
}
/* ----------------------------------------------------------------------
memory usage of local atom-based array
------------------------------------------------------------------------- */
double
ComputeStressTally
::
memory_usage
()
{
double
bytes
=
nmax
*
size_peratom_cols
*
sizeof
(
double
);
return
bytes
;
}
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