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rLAMMPS lammps
compute_temp_chunk.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_temp_chunk.h"
#include "atom.h"
#include "update.h"
#include "force.h"
#include "modify.h"
#include "compute_chunk_atom.h"
#include "domain.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
enum
{
TEMP
,
KECOM
,
INTERNAL
};
/* ---------------------------------------------------------------------- */
ComputeTempChunk
::
ComputeTempChunk
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
Compute
(
lmp
,
narg
,
arg
)
{
if
(
narg
<
4
)
error
->
all
(
FLERR
,
"Illegal compute temp/chunk command"
);
scalar_flag
=
vector_flag
=
1
;
size_vector
=
6
;
extscalar
=
0
;
extvector
=
1
;
tempflag
=
1
;
// ID of compute chunk/atom
int
n
=
strlen
(
arg
[
3
])
+
1
;
idchunk
=
new
char
[
n
];
strcpy
(
idchunk
,
arg
[
3
]);
biasflag
=
0
;
init
();
// optional per-chunk values
nvalues
=
narg
-
4
;
which
=
new
int
[
nvalues
];
nvalues
=
0
;
int
iarg
=
4
;
while
(
iarg
<
narg
)
{
if
(
strcmp
(
arg
[
iarg
],
"temp"
)
==
0
)
which
[
nvalues
]
=
TEMP
;
else
if
(
strcmp
(
arg
[
iarg
],
"kecom"
)
==
0
)
which
[
nvalues
]
=
KECOM
;
else
if
(
strcmp
(
arg
[
iarg
],
"internal"
)
==
0
)
which
[
nvalues
]
=
INTERNAL
;
else
break
;
iarg
++
;
nvalues
++
;
}
// optional args
comflag
=
0
;
biasflag
=
0
;
id_bias
=
NULL
;
adof
=
domain
->
dimension
;
cdof
=
0.0
;
while
(
iarg
<
narg
)
{
if
(
strcmp
(
arg
[
iarg
],
"com"
)
==
0
)
{
if
(
iarg
+
2
>
narg
)
error
->
all
(
FLERR
,
"Illegal compute temp/chunk command"
);
if
(
strcmp
(
arg
[
iarg
+
1
],
"yes"
)
==
0
)
comflag
=
1
;
else
if
(
strcmp
(
arg
[
iarg
+
1
],
"no"
)
==
0
)
comflag
=
0
;
else
error
->
all
(
FLERR
,
"Illegal compute temp/chunk command"
);
iarg
+=
2
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"bias"
)
==
0
)
{
if
(
iarg
+
2
>
narg
)
error
->
all
(
FLERR
,
"Illegal compute temp/chunk command"
);
biasflag
=
1
;
int
n
=
strlen
(
arg
[
iarg
+
1
])
+
1
;
id_bias
=
new
char
[
n
];
strcpy
(
id_bias
,
arg
[
iarg
+
1
]);
iarg
+=
2
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"adof"
)
==
0
)
{
if
(
iarg
+
2
>
narg
)
error
->
all
(
FLERR
,
"Illegal compute temp/chunk command"
);
adof
=
force
->
numeric
(
FLERR
,
arg
[
iarg
+
1
]);
iarg
+=
2
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"cdof"
)
==
0
)
{
if
(
iarg
+
2
>
narg
)
error
->
all
(
FLERR
,
"Illegal compute temp/chunk command"
);
cdof
=
force
->
numeric
(
FLERR
,
arg
[
iarg
+
1
]);
iarg
+=
2
;
}
else
error
->
all
(
FLERR
,
"Illegal compute temp/chunk command"
);
}
// error check on bias compute
if
(
biasflag
)
{
int
i
=
modify
->
find_compute
(
id_bias
);
if
(
i
<
0
)
error
->
all
(
FLERR
,
"Could not find compute ID for temperature bias"
);
tbias
=
modify
->
compute
[
i
];
if
(
tbias
->
tempflag
==
0
)
error
->
all
(
FLERR
,
"Bias compute does not calculate temperature"
);
if
(
tbias
->
tempbias
==
0
)
error
->
all
(
FLERR
,
"Bias compute does not calculate a velocity bias"
);
}
// this compute only calculates a bias, if comflag is set
// won't be two biases since comflag and biasflag cannot both be set
if
(
comflag
&&
biasflag
)
error
->
all
(
FLERR
,
"Cannot use both com and bias with compute temp/chunk"
);
if
(
comflag
)
tempbias
=
1
;
// vector data
vector
=
new
double
[
6
];
// chunk-based data
nchunk
=
1
;
maxchunk
=
0
;
sum
=
sumall
=
NULL
;
count
=
countall
=
NULL
;
massproc
=
masstotal
=
NULL
;
vcm
=
vcmall
=
NULL
;
array
=
NULL
;
if
(
nvalues
)
{
array_flag
=
1
;
size_array_cols
=
nvalues
;
size_array_rows
=
0
;
size_array_rows_variable
=
1
;
extarray
=
0
;
}
allocate
();
comstep
=
-
1
;
}
/* ---------------------------------------------------------------------- */
ComputeTempChunk
::~
ComputeTempChunk
()
{
delete
[]
idchunk
;
delete
[]
which
;
delete
[]
id_bias
;
delete
[]
vector
;
memory
->
destroy
(
sum
);
memory
->
destroy
(
sumall
);
memory
->
destroy
(
count
);
memory
->
destroy
(
countall
);
memory
->
destroy
(
array
);
memory
->
destroy
(
massproc
);
memory
->
destroy
(
masstotal
);
memory
->
destroy
(
vcm
);
memory
->
destroy
(
vcmall
);
}
/* ---------------------------------------------------------------------- */
void
ComputeTempChunk
::
init
()
{
int
icompute
=
modify
->
find_compute
(
idchunk
);
if
(
icompute
<
0
)
error
->
all
(
FLERR
,
"Chunk/atom compute does not exist for "
"compute temp/chunk"
);
cchunk
=
(
ComputeChunkAtom
*
)
modify
->
compute
[
icompute
];
if
(
strcmp
(
cchunk
->
style
,
"chunk/atom"
)
!=
0
)
error
->
all
(
FLERR
,
"Compute temp/chunk does not use chunk/atom compute"
);
if
(
biasflag
)
{
int
i
=
modify
->
find_compute
(
id_bias
);
if
(
i
<
0
)
error
->
all
(
FLERR
,
"Could not find compute ID for temperature bias"
);
tbias
=
modify
->
compute
[
i
];
}
}
/* ---------------------------------------------------------------------- */
double
ComputeTempChunk
::
compute_scalar
()
{
int
i
,
index
;
invoked_scalar
=
update
->
ntimestep
;
// calculate chunk assignments,
// since only atoms in chunks contribute to global temperature
// compute chunk/atom assigns atoms to chunk IDs
// extract ichunk index vector from compute
// ichunk = 1 to Nchunk for included atoms, 0 for excluded atoms
nchunk
=
cchunk
->
setup_chunks
();
cchunk
->
compute_ichunk
();
int
*
ichunk
=
cchunk
->
ichunk
;
// remove velocity bias
if
(
biasflag
)
{
if
(
tbias
->
invoked_scalar
!=
update
->
ntimestep
)
tbias
->
compute_scalar
();
tbias
->
remove_bias_all
();
}
// calculate COM velocity for each chunk
// won't be invoked with bias also removed = 2 biases
if
(
comflag
&&
comstep
!=
update
->
ntimestep
)
vcm_compute
();
// calculate global temperature, optionally removing COM velocity
double
**
v
=
atom
->
v
;
double
*
mass
=
atom
->
mass
;
double
*
rmass
=
atom
->
rmass
;
int
*
type
=
atom
->
type
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
double
t
=
0.0
;
int
mycount
=
0
;
if
(
!
comflag
)
{
if
(
rmass
)
{
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
index
=
ichunk
[
i
]
-
1
;
if
(
index
<
0
)
continue
;
t
+=
(
v
[
i
][
0
]
*
v
[
i
][
0
]
+
v
[
i
][
1
]
*
v
[
i
][
1
]
+
v
[
i
][
2
]
*
v
[
i
][
2
])
*
rmass
[
i
];
mycount
++
;
}
}
else
{
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
index
=
ichunk
[
i
]
-
1
;
if
(
index
<
0
)
continue
;
t
+=
(
v
[
i
][
0
]
*
v
[
i
][
0
]
+
v
[
i
][
1
]
*
v
[
i
][
1
]
+
v
[
i
][
2
]
*
v
[
i
][
2
])
*
mass
[
type
[
i
]];
mycount
++
;
}
}
}
else
{
double
vx
,
vy
,
vz
;
if
(
rmass
)
{
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
index
=
ichunk
[
i
]
-
1
;
if
(
index
<
0
)
continue
;
vx
=
v
[
i
][
0
]
-
vcmall
[
index
][
0
];
vy
=
v
[
i
][
1
]
-
vcmall
[
index
][
1
];
vz
=
v
[
i
][
2
]
-
vcmall
[
index
][
2
];
t
+=
(
vx
*
vx
+
vy
*
vy
+
vz
*
vz
)
*
rmass
[
i
];
mycount
++
;
}
}
else
{
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
index
=
ichunk
[
i
]
-
1
;
if
(
index
<
0
)
continue
;
vx
=
v
[
i
][
0
]
-
vcmall
[
index
][
0
];
vy
=
v
[
i
][
1
]
-
vcmall
[
index
][
1
];
vz
=
v
[
i
][
2
]
-
vcmall
[
index
][
2
];
t
+=
(
vx
*
vx
+
vy
*
vy
+
vz
*
vz
)
*
mass
[
type
[
i
]];
mycount
++
;
}
}
}
// restore velocity bias
if
(
biasflag
)
tbias
->
restore_bias_all
();
// final temperature
MPI_Allreduce
(
&
t
,
&
scalar
,
1
,
MPI_DOUBLE
,
MPI_SUM
,
world
);
double
rcount
=
mycount
;
double
allcount
;
MPI_Allreduce
(
&
rcount
,
&
allcount
,
1
,
MPI_DOUBLE
,
MPI_SUM
,
world
);
double
dof
=
nchunk
*
cdof
+
adof
*
allcount
;
if
(
dof
<
0.0
&&
allcount
>
0.0
)
error
->
all
(
FLERR
,
"Temperature compute degrees of freedom < 0"
);
double
tfactor
=
0.0
;
if
(
dof
>
0.0
)
tfactor
=
force
->
mvv2e
/
(
dof
*
force
->
boltz
);
scalar
*=
tfactor
;
return
scalar
;
}
/* ---------------------------------------------------------------------- */
void
ComputeTempChunk
::
compute_vector
()
{
int
i
,
index
;
invoked_vector
=
update
->
ntimestep
;
// calculate chunk assignments,
// since only atoms in chunks contribute to global temperature
// compute chunk/atom assigns atoms to chunk IDs
// extract ichunk index vector from compute
// ichunk = 1 to Nchunk for included atoms, 0 for excluded atoms
nchunk
=
cchunk
->
setup_chunks
();
cchunk
->
compute_ichunk
();
int
*
ichunk
=
cchunk
->
ichunk
;
// remove velocity bias
if
(
biasflag
)
{
if
(
tbias
->
invoked_scalar
!=
update
->
ntimestep
)
tbias
->
compute_scalar
();
tbias
->
remove_bias_all
();
}
// calculate COM velocity for each chunk
// won't be invoked with bias also removed = 2 biases
if
(
comflag
&&
comstep
!=
update
->
ntimestep
)
vcm_compute
();
// calculate KE tensor, optionally removing COM velocity
double
**
v
=
atom
->
v
;
double
*
mass
=
atom
->
mass
;
double
*
rmass
=
atom
->
rmass
;
int
*
type
=
atom
->
type
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
double
massone
,
t
[
6
];
for
(
i
=
0
;
i
<
6
;
i
++
)
t
[
i
]
=
0.0
;
if
(
!
comflag
)
{
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
index
=
ichunk
[
i
]
-
1
;
if
(
index
<
0
)
continue
;
if
(
rmass
)
massone
=
rmass
[
i
];
else
massone
=
mass
[
type
[
i
]];
t
[
0
]
+=
massone
*
v
[
i
][
0
]
*
v
[
i
][
0
];
t
[
1
]
+=
massone
*
v
[
i
][
1
]
*
v
[
i
][
1
];
t
[
2
]
+=
massone
*
v
[
i
][
2
]
*
v
[
i
][
2
];
t
[
3
]
+=
massone
*
v
[
i
][
0
]
*
v
[
i
][
1
];
t
[
4
]
+=
massone
*
v
[
i
][
0
]
*
v
[
i
][
2
];
t
[
5
]
+=
massone
*
v
[
i
][
1
]
*
v
[
i
][
2
];
}
}
else
{
double
vx
,
vy
,
vz
;
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
index
=
ichunk
[
i
]
-
1
;
if
(
index
<
0
)
continue
;
if
(
rmass
)
massone
=
rmass
[
i
];
else
massone
=
mass
[
type
[
i
]];
vx
=
v
[
i
][
0
]
-
vcmall
[
index
][
0
];
vy
=
v
[
i
][
1
]
-
vcmall
[
index
][
1
];
vz
=
v
[
i
][
2
]
-
vcmall
[
index
][
2
];
t
[
0
]
+=
massone
*
vx
*
vx
;
t
[
1
]
+=
massone
*
vy
*
vy
;
t
[
2
]
+=
massone
*
vz
*
vz
;
t
[
3
]
+=
massone
*
vx
*
vy
;
t
[
4
]
+=
massone
*
vx
*
vz
;
t
[
5
]
+=
massone
*
vy
*
vz
;
}
}
// restore velocity bias
if
(
biasflag
)
tbias
->
restore_bias_all
();
// final KE
MPI_Allreduce
(
t
,
vector
,
6
,
MPI_DOUBLE
,
MPI_SUM
,
world
);
for
(
i
=
0
;
i
<
6
;
i
++
)
vector
[
i
]
*=
force
->
mvv2e
;
}
/* ---------------------------------------------------------------------- */
void
ComputeTempChunk
::
compute_array
()
{
invoked_array
=
update
->
ntimestep
;
// compute chunk/atom assigns atoms to chunk IDs
// extract ichunk index vector from compute
// ichunk = 1 to Nchunk for included atoms, 0 for excluded atoms
nchunk
=
cchunk
->
setup_chunks
();
cchunk
->
compute_ichunk
();
if
(
nchunk
>
maxchunk
)
allocate
();
size_array_rows
=
nchunk
;
// remove velocity bias
if
(
biasflag
)
{
if
(
tbias
->
invoked_scalar
!=
update
->
ntimestep
)
tbias
->
compute_scalar
();
tbias
->
remove_bias_all
();
}
// calculate COM velocity for each chunk whether comflag set or not
// needed by some values even if comflag not set
// important to do this after velocity bias is removed
// otherwise per-chunk values that use both v and vcm will be inconsistent
if
(
comstep
!=
update
->
ntimestep
)
vcm_compute
();
// compute each value
for
(
int
i
=
0
;
i
<
nvalues
;
i
++
)
{
if
(
which
[
i
]
==
TEMP
)
temperature
(
i
);
else
if
(
which
[
i
]
==
KECOM
)
kecom
(
i
);
else
if
(
which
[
i
]
==
INTERNAL
)
internal
(
i
);
}
// restore velocity bias
if
(
biasflag
)
tbias
->
restore_bias_all
();
}
/* ----------------------------------------------------------------------
calculate velocity of COM for each chunk
------------------------------------------------------------------------- */
void
ComputeTempChunk
::
vcm_compute
()
{
int
i
,
index
;
double
massone
;
// avoid re-computing VCM more than once per step
comstep
=
update
->
ntimestep
;
int
*
ichunk
=
cchunk
->
ichunk
;
for
(
int
i
=
0
;
i
<
nchunk
;
i
++
)
{
vcm
[
i
][
0
]
=
vcm
[
i
][
1
]
=
vcm
[
i
][
2
]
=
0.0
;
massproc
[
i
]
=
0.0
;
}
double
**
v
=
atom
->
v
;
int
*
mask
=
atom
->
mask
;
int
*
type
=
atom
->
type
;
double
*
mass
=
atom
->
mass
;
double
*
rmass
=
atom
->
rmass
;
int
nlocal
=
atom
->
nlocal
;
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
index
=
ichunk
[
i
]
-
1
;
if
(
index
<
0
)
continue
;
if
(
rmass
)
massone
=
rmass
[
i
];
else
massone
=
mass
[
type
[
i
]];
vcm
[
index
][
0
]
+=
v
[
i
][
0
]
*
massone
;
vcm
[
index
][
1
]
+=
v
[
i
][
1
]
*
massone
;
vcm
[
index
][
2
]
+=
v
[
i
][
2
]
*
massone
;
massproc
[
index
]
+=
massone
;
}
MPI_Allreduce
(
&
vcm
[
0
][
0
],
&
vcmall
[
0
][
0
],
3
*
nchunk
,
MPI_DOUBLE
,
MPI_SUM
,
world
);
MPI_Allreduce
(
massproc
,
masstotal
,
nchunk
,
MPI_DOUBLE
,
MPI_SUM
,
world
);
for
(
i
=
0
;
i
<
nchunk
;
i
++
)
{
vcmall
[
i
][
0
]
/=
masstotal
[
i
];
vcmall
[
i
][
1
]
/=
masstotal
[
i
];
vcmall
[
i
][
2
]
/=
masstotal
[
i
];
}
}
/* ----------------------------------------------------------------------
temperature of each chunk
------------------------------------------------------------------------- */
void
ComputeTempChunk
::
temperature
(
int
icol
)
{
int
i
,
index
;
int
*
ichunk
=
cchunk
->
ichunk
;
// zero local per-chunk values
for
(
int
i
=
0
;
i
<
nchunk
;
i
++
)
{
count
[
i
]
=
0
;
sum
[
i
]
=
0.0
;
}
// per-chunk temperature, option for removing COM velocity
double
**
v
=
atom
->
v
;
double
*
mass
=
atom
->
mass
;
double
*
rmass
=
atom
->
rmass
;
int
*
mask
=
atom
->
mask
;
int
*
type
=
atom
->
type
;
int
nlocal
=
atom
->
nlocal
;
if
(
!
comflag
)
{
if
(
rmass
)
{
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
index
=
ichunk
[
i
]
-
1
;
if
(
index
<
0
)
continue
;
sum
[
index
]
+=
(
v
[
i
][
0
]
*
v
[
i
][
0
]
+
v
[
i
][
1
]
*
v
[
i
][
1
]
+
v
[
i
][
2
]
*
v
[
i
][
2
])
*
rmass
[
i
];
count
[
index
]
++
;
}
}
else
{
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
index
=
ichunk
[
i
]
-
1
;
if
(
index
<
0
)
continue
;
sum
[
index
]
+=
(
v
[
i
][
0
]
*
v
[
i
][
0
]
+
v
[
i
][
1
]
*
v
[
i
][
1
]
+
v
[
i
][
2
]
*
v
[
i
][
2
])
*
mass
[
type
[
i
]];
count
[
index
]
++
;
}
}
}
else
{
double
vx
,
vy
,
vz
;
if
(
rmass
)
{
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
index
=
ichunk
[
i
]
-
1
;
if
(
index
<
0
)
continue
;
vx
=
v
[
i
][
0
]
-
vcmall
[
index
][
0
];
vy
=
v
[
i
][
1
]
-
vcmall
[
index
][
1
];
vz
=
v
[
i
][
2
]
-
vcmall
[
index
][
2
];
sum
[
index
]
+=
(
vx
*
vx
+
vy
*
vy
+
vz
*
vz
)
*
rmass
[
i
];
count
[
index
]
++
;
}
}
else
{
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
index
=
ichunk
[
i
]
-
1
;
if
(
index
<
0
)
continue
;
vx
=
v
[
i
][
0
]
-
vcmall
[
index
][
0
];
vy
=
v
[
i
][
1
]
-
vcmall
[
index
][
1
];
vz
=
v
[
i
][
2
]
-
vcmall
[
index
][
2
];
sum
[
index
]
+=
(
vx
*
vx
+
vy
*
vy
+
vz
*
vz
)
*
mass
[
type
[
i
]];
count
[
index
]
++
;
}
}
}
// sum across procs
MPI_Allreduce
(
sum
,
sumall
,
nchunk
,
MPI_DOUBLE
,
MPI_SUM
,
world
);
MPI_Allreduce
(
count
,
countall
,
nchunk
,
MPI_INT
,
MPI_SUM
,
world
);
// normalize temperatures by per-chunk DOF
double
dof
,
tfactor
;
double
mvv2e
=
force
->
mvv2e
;
double
boltz
=
force
->
boltz
;
for
(
int
i
=
0
;
i
<
nchunk
;
i
++
)
{
dof
=
cdof
+
adof
*
countall
[
i
];
if
(
dof
>
0.0
)
tfactor
=
mvv2e
/
(
dof
*
boltz
);
else
tfactor
=
0.0
;
array
[
i
][
icol
]
=
tfactor
*
sumall
[
i
];
}
}
/* ----------------------------------------------------------------------
KE of entire chunk moving at VCM
------------------------------------------------------------------------- */
void
ComputeTempChunk
::
kecom
(
int
icol
)
{
int
index
;
int
*
ichunk
=
cchunk
->
ichunk
;
// zero local per-chunk values
for
(
int
i
=
0
;
i
<
nchunk
;
i
++
)
sum
[
i
]
=
0.0
;
// per-chunk COM KE
double
*
mass
=
atom
->
mass
;
double
*
rmass
=
atom
->
rmass
;
int
*
mask
=
atom
->
mask
;
int
*
type
=
atom
->
type
;
int
nlocal
=
atom
->
nlocal
;
double
vx
,
vy
,
vz
;
if
(
rmass
)
{
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
index
=
ichunk
[
i
]
-
1
;
if
(
index
<
0
)
continue
;
vx
=
vcmall
[
index
][
0
];
vy
=
vcmall
[
index
][
1
];
vz
=
vcmall
[
index
][
2
];
sum
[
index
]
+=
(
vx
*
vx
+
vy
*
vy
+
vz
*
vz
)
*
rmass
[
i
];
}
}
else
{
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
index
=
ichunk
[
i
]
-
1
;
if
(
index
<
0
)
continue
;
vx
=
vcmall
[
index
][
0
];
vy
=
vcmall
[
index
][
1
];
vz
=
vcmall
[
index
][
2
];
sum
[
index
]
+=
(
vx
*
vx
+
vy
*
vy
+
vz
*
vz
)
*
mass
[
type
[
i
]];
}
}
// sum across procs
MPI_Allreduce
(
sum
,
sumall
,
nchunk
,
MPI_DOUBLE
,
MPI_SUM
,
world
);
double
mvv2e
=
force
->
mvv2e
;
for
(
int
i
=
0
;
i
<
nchunk
;
i
++
)
array
[
i
][
icol
]
=
0.5
*
mvv2e
*
sumall
[
i
];
}
/* ----------------------------------------------------------------------
internal KE of each chunk around its VCM
computed using per-atom velocities with chunk VCM subtracted off
------------------------------------------------------------------------- */
void
ComputeTempChunk
::
internal
(
int
icol
)
{
int
index
;
int
*
ichunk
=
cchunk
->
ichunk
;
// zero local per-chunk values
for
(
int
i
=
0
;
i
<
nchunk
;
i
++
)
sum
[
i
]
=
0.0
;
// per-chunk internal KE
double
**
v
=
atom
->
v
;
double
*
mass
=
atom
->
mass
;
double
*
rmass
=
atom
->
rmass
;
int
*
mask
=
atom
->
mask
;
int
*
type
=
atom
->
type
;
int
nlocal
=
atom
->
nlocal
;
double
vx
,
vy
,
vz
;
if
(
rmass
)
{
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
index
=
ichunk
[
i
]
-
1
;
if
(
index
<
0
)
continue
;
vx
=
v
[
i
][
0
]
-
vcmall
[
index
][
0
];
vy
=
v
[
i
][
1
]
-
vcmall
[
index
][
1
];
vz
=
v
[
i
][
2
]
-
vcmall
[
index
][
2
];
sum
[
index
]
+=
(
vx
*
vx
+
vy
*
vy
+
vz
*
vz
)
*
rmass
[
i
];
}
}
else
{
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
index
=
ichunk
[
i
]
-
1
;
if
(
index
<
0
)
continue
;
vx
=
v
[
i
][
0
]
-
vcmall
[
index
][
0
];
vy
=
v
[
i
][
1
]
-
vcmall
[
index
][
1
];
vz
=
v
[
i
][
2
]
-
vcmall
[
index
][
2
];
sum
[
index
]
+=
(
vx
*
vx
+
vy
*
vy
+
vz
*
vz
)
*
mass
[
type
[
i
]];
}
}
// sum across procs
MPI_Allreduce
(
sum
,
sumall
,
nchunk
,
MPI_DOUBLE
,
MPI_SUM
,
world
);
double
mvv2e
=
force
->
mvv2e
;
for
(
int
i
=
0
;
i
<
nchunk
;
i
++
)
array
[
i
][
icol
]
=
0.5
*
mvv2e
*
sumall
[
i
];
}
/* ----------------------------------------------------------------------
bias methods: called by thermostats
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
remove velocity bias from atom I to leave thermal velocity
------------------------------------------------------------------------- */
void
ComputeTempChunk
::
remove_bias
(
int
i
,
double
*
v
)
{
int
index
=
cchunk
->
ichunk
[
i
];
if
(
index
<
0
)
return
;
v
[
0
]
-=
vcmall
[
index
][
0
];
v
[
1
]
-=
vcmall
[
index
][
1
];
v
[
2
]
-=
vcmall
[
index
][
2
];
}
/* ----------------------------------------------------------------------
remove velocity bias from all atoms to leave thermal velocity
------------------------------------------------------------------------- */
void
ComputeTempChunk
::
remove_bias_all
()
{
int
index
;
int
*
ichunk
=
cchunk
->
ichunk
;
double
**
v
=
atom
->
v
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
index
=
ichunk
[
i
];
if
(
index
<
0
)
continue
;
v
[
i
][
0
]
-=
vbias
[
0
];
v
[
i
][
1
]
-=
vbias
[
1
];
v
[
i
][
2
]
-=
vbias
[
2
];
}
}
/* ----------------------------------------------------------------------
add back in velocity bias to atom I removed by remove_bias()
assume remove_bias() was previously called
------------------------------------------------------------------------- */
void
ComputeTempChunk
::
restore_bias
(
int
i
,
double
*
v
)
{
int
index
=
cchunk
->
ichunk
[
i
];
if
(
index
<
0
)
return
;
v
[
0
]
+=
vcmall
[
index
][
0
];
v
[
1
]
+=
vcmall
[
index
][
1
];
v
[
2
]
+=
vcmall
[
index
][
2
];
}
/* ----------------------------------------------------------------------
add back in velocity bias to all atoms removed by remove_bias_all()
assume remove_bias_all() was previously called
------------------------------------------------------------------------- */
void
ComputeTempChunk
::
restore_bias_all
()
{
int
index
;
int
*
ichunk
=
cchunk
->
ichunk
;
double
**
v
=
atom
->
v
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
index
=
ichunk
[
i
];
if
(
index
<
0
)
continue
;
v
[
i
][
0
]
+=
vbias
[
0
];
v
[
i
][
1
]
+=
vbias
[
1
];
v
[
i
][
2
]
+=
vbias
[
2
];
}
}
/* ----------------------------------------------------------------------
lock methods: called by fix ave/time
these methods insure vector/array size is locked for Nfreq epoch
by passing lock info along to compute chunk/atom
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
increment lock counter
------------------------------------------------------------------------- */
void
ComputeTempChunk
::
lock_enable
()
{
cchunk
->
lockcount
++
;
}
/* ----------------------------------------------------------------------
decrement lock counter in compute chunk/atom, it if still exists
------------------------------------------------------------------------- */
void
ComputeTempChunk
::
lock_disable
()
{
int
icompute
=
modify
->
find_compute
(
idchunk
);
if
(
icompute
>=
0
)
{
cchunk
=
(
ComputeChunkAtom
*
)
modify
->
compute
[
icompute
];
cchunk
->
lockcount
--
;
}
}
/* ----------------------------------------------------------------------
calculate and return # of chunks = length of vector/array
------------------------------------------------------------------------- */
int
ComputeTempChunk
::
lock_length
()
{
nchunk
=
cchunk
->
setup_chunks
();
return
nchunk
;
}
/* ----------------------------------------------------------------------
set the lock from startstep to stopstep
------------------------------------------------------------------------- */
void
ComputeTempChunk
::
lock
(
Fix
*
fixptr
,
bigint
startstep
,
bigint
stopstep
)
{
cchunk
->
lock
(
fixptr
,
startstep
,
stopstep
);
}
/* ----------------------------------------------------------------------
unset the lock
------------------------------------------------------------------------- */
void
ComputeTempChunk
::
unlock
(
Fix
*
fixptr
)
{
cchunk
->
unlock
(
fixptr
);
}
/* ----------------------------------------------------------------------
free and reallocate per-chunk arrays
------------------------------------------------------------------------- */
void
ComputeTempChunk
::
allocate
()
{
memory
->
destroy
(
sum
);
memory
->
destroy
(
sumall
);
memory
->
destroy
(
count
);
memory
->
destroy
(
countall
);
memory
->
destroy
(
array
);
maxchunk
=
nchunk
;
memory
->
create
(
sum
,
maxchunk
,
"temp/chunk:sum"
);
memory
->
create
(
sumall
,
maxchunk
,
"temp/chunk:sumall"
);
memory
->
create
(
count
,
maxchunk
,
"temp/chunk:count"
);
memory
->
create
(
countall
,
maxchunk
,
"temp/chunk:countall"
);
memory
->
create
(
array
,
maxchunk
,
nvalues
,
"temp/chunk:array"
);
if
(
comflag
||
nvalues
)
{
memory
->
destroy
(
massproc
);
memory
->
destroy
(
masstotal
);
memory
->
destroy
(
vcm
);
memory
->
destroy
(
vcmall
);
memory
->
create
(
massproc
,
maxchunk
,
"vcm/chunk:massproc"
);
memory
->
create
(
masstotal
,
maxchunk
,
"vcm/chunk:masstotal"
);
memory
->
create
(
vcm
,
maxchunk
,
3
,
"vcm/chunk:vcm"
);
memory
->
create
(
vcmall
,
maxchunk
,
3
,
"vcm/chunk:vcmall"
);
}
}
/* ----------------------------------------------------------------------
memory usage of local data
------------------------------------------------------------------------- */
double
ComputeTempChunk
::
memory_usage
()
{
double
bytes
=
(
bigint
)
maxchunk
*
2
*
sizeof
(
double
);
bytes
=
(
bigint
)
maxchunk
*
2
*
sizeof
(
int
);
bytes
=
(
bigint
)
maxchunk
*
nvalues
*
sizeof
(
double
);
if
(
comflag
||
nvalues
)
{
bytes
+=
(
bigint
)
maxchunk
*
2
*
sizeof
(
double
);
bytes
+=
(
bigint
)
maxchunk
*
2
*
3
*
sizeof
(
double
);
}
return
bytes
;
}
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