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compute_temp_region_eff.cpp
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Mon, Jul 1, 20:47
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rLAMMPS lammps
compute_temp_region_eff.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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Andres Jaramillo-Botero (Caltech)
------------------------------------------------------------------------- */
#include "mpi.h"
#include "math.h"
#include "string.h"
#include "compute_temp_region_eff.h"
#include "atom.h"
#include "update.h"
#include "force.h"
#include "modify.h"
#include "domain.h"
#include "region.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
/* ---------------------------------------------------------------------- */
ComputeTempRegionEff
::
ComputeTempRegionEff
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
Compute
(
lmp
,
narg
,
arg
)
{
if
(
!
atom
->
electron_flag
)
error
->
all
(
"Compute temp/region/eff requires atom style electron"
);
if
(
narg
!=
4
)
error
->
all
(
"Illegal compute temp/region/eff command"
);
iregion
=
domain
->
find_region
(
arg
[
3
]);
if
(
iregion
==
-
1
)
error
->
all
(
"Region ID for compute temp/region/eff does not exist"
);
int
n
=
strlen
(
arg
[
3
])
+
1
;
idregion
=
new
char
[
n
];
strcpy
(
idregion
,
arg
[
3
]);
scalar_flag
=
vector_flag
=
1
;
size_vector
=
6
;
extscalar
=
0
;
extvector
=
1
;
tempflag
=
1
;
tempbias
=
1
;
maxbias
=
0
;
vbiasall
=
NULL
;
vector
=
new
double
[
6
];
}
/* ---------------------------------------------------------------------- */
ComputeTempRegionEff
::~
ComputeTempRegionEff
()
{
delete
[]
idregion
;
memory
->
destroy
(
vbiasall
);
delete
[]
vector
;
}
/* ---------------------------------------------------------------------- */
void
ComputeTempRegionEff
::
init
()
{
// set index and check validity of region
iregion
=
domain
->
find_region
(
idregion
);
if
(
iregion
==
-
1
)
error
->
all
(
"Region ID for compute temp/region/eff does not exist"
);
dof
=
0.0
;
}
/* ---------------------------------------------------------------------- */
int
ComputeTempRegionEff
::
dof_remove
(
int
i
)
{
double
*
x
=
atom
->
x
[
i
];
if
(
domain
->
regions
[
iregion
]
->
match
(
x
[
0
],
x
[
1
],
x
[
2
]))
return
0
;
return
1
;
}
/* ---------------------------------------------------------------------- */
double
ComputeTempRegionEff
::
compute_scalar
()
{
invoked_scalar
=
update
->
ntimestep
;
double
**
x
=
atom
->
x
;
double
**
v
=
atom
->
v
;
double
*
ervel
=
atom
->
ervel
;
double
*
mass
=
atom
->
mass
;
int
*
spin
=
atom
->
spin
;
int
*
type
=
atom
->
type
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
Region
*
region
=
domain
->
regions
[
iregion
];
int
count
=
0
;
double
t
=
0.0
;
if
(
mass
)
{
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
&&
region
->
match
(
x
[
i
][
0
],
x
[
i
][
1
],
x
[
i
][
2
]))
{
count
++
;
t
+=
(
v
[
i
][
0
]
*
v
[
i
][
0
]
+
v
[
i
][
1
]
*
v
[
i
][
1
]
+
v
[
i
][
2
]
*
v
[
i
][
2
])
*
mass
[
type
[
i
]];
if
(
fabs
(
spin
[
i
])
==
1
)
t
+=
0.75
*
mass
[
type
[
i
]]
*
ervel
[
i
]
*
ervel
[
i
];
}
}
double
tarray
[
2
],
tarray_all
[
2
];
tarray
[
0
]
=
count
;
tarray
[
1
]
=
t
;
MPI_Allreduce
(
tarray
,
tarray_all
,
2
,
MPI_DOUBLE
,
MPI_SUM
,
world
);
dof
=
domain
->
dimension
*
tarray_all
[
0
]
-
extra_dof
;
int
one
=
0
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
&&
region
->
match
(
x
[
i
][
0
],
x
[
i
][
1
],
x
[
i
][
2
]))
{
if
(
fabs
(
spin
[
i
])
==
1
)
one
++
;
}
int
nelectrons_region
;
MPI_Allreduce
(
&
one
,
&
nelectrons_region
,
1
,
MPI_INT
,
MPI_SUM
,
world
);
// average over nuclear dof only
dof
-=
domain
->
dimension
*
nelectrons_region
;
if
(
dof
>
0
)
scalar
=
force
->
mvv2e
*
tarray_all
[
1
]
/
(
dof
*
force
->
boltz
);
else
scalar
=
0.0
;
return
scalar
;
}
/* ---------------------------------------------------------------------- */
void
ComputeTempRegionEff
::
compute_vector
()
{
int
i
;
invoked_vector
=
update
->
ntimestep
;
double
**
x
=
atom
->
x
;
double
**
v
=
atom
->
v
;
double
*
ervel
=
atom
->
ervel
;
double
*
mass
=
atom
->
mass
;
int
*
spin
=
atom
->
spin
;
int
*
type
=
atom
->
type
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
Region
*
region
=
domain
->
regions
[
iregion
];
double
massone
,
t
[
6
];
for
(
i
=
0
;
i
<
6
;
i
++
)
t
[
i
]
=
0.0
;
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
&&
region
->
match
(
x
[
i
][
0
],
x
[
i
][
1
],
x
[
i
][
2
]))
{
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
];
if
(
fabs
(
spin
[
i
])
==
1
)
{
t
[
0
]
+=
0.75
*
massone
*
ervel
[
i
]
*
ervel
[
i
];
t
[
1
]
+=
0.75
*
massone
*
ervel
[
i
]
*
ervel
[
i
];
t
[
2
]
+=
0.75
*
massone
*
ervel
[
i
]
*
ervel
[
i
];
}
}
MPI_Allreduce
(
t
,
vector
,
6
,
MPI_DOUBLE
,
MPI_SUM
,
world
);
for
(
i
=
0
;
i
<
6
;
i
++
)
vector
[
i
]
*=
force
->
mvv2e
;
}
/* ----------------------------------------------------------------------
remove velocity bias from atom I to leave thermal velocity
NOTE: the following commands do not bias the radial electron velocities
------------------------------------------------------------------------- */
void
ComputeTempRegionEff
::
remove_bias
(
int
i
,
double
*
v
)
{
double
*
x
=
atom
->
x
[
i
];
if
(
domain
->
regions
[
iregion
]
->
match
(
x
[
0
],
x
[
1
],
x
[
2
]))
vbias
[
0
]
=
vbias
[
1
]
=
vbias
[
2
]
=
0.0
;
else
{
vbias
[
0
]
=
v
[
0
];
vbias
[
1
]
=
v
[
1
];
vbias
[
2
]
=
v
[
2
];
v
[
0
]
=
v
[
1
]
=
v
[
2
]
=
0.0
;
}
}
/* ----------------------------------------------------------------------
remove velocity bias from all atoms to leave thermal velocity
------------------------------------------------------------------------- */
void
ComputeTempRegionEff
::
remove_bias_all
()
{
double
**
x
=
atom
->
x
;
double
**
v
=
atom
->
v
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
if
(
nlocal
>
maxbias
)
{
memory
->
destroy
(
vbiasall
);
maxbias
=
atom
->
nmax
;
memory
->
create
(
vbiasall
,
maxbias
,
3
,
"temp/region:vbiasall"
);
}
Region
*
region
=
domain
->
regions
[
iregion
];
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
if
(
region
->
match
(
x
[
i
][
0
],
x
[
i
][
1
],
x
[
i
][
2
]))
vbiasall
[
i
][
0
]
=
vbiasall
[
i
][
1
]
=
vbiasall
[
i
][
2
]
=
0.0
;
else
{
vbiasall
[
i
][
0
]
=
v
[
i
][
0
];
vbiasall
[
i
][
1
]
=
v
[
i
][
1
];
vbiasall
[
i
][
2
]
=
v
[
i
][
2
];
v
[
i
][
0
]
=
v
[
i
][
1
]
=
v
[
i
][
2
]
=
0.0
;
}
}
}
/* ----------------------------------------------------------------------
add back in velocity bias to atom I removed by remove_bias()
assume remove_bias() was previously called
------------------------------------------------------------------------- */
void
ComputeTempRegionEff
::
restore_bias
(
int
i
,
double
*
v
)
{
v
[
0
]
+=
vbias
[
0
];
v
[
1
]
+=
vbias
[
1
];
v
[
2
]
+=
vbias
[
2
];
}
/* ----------------------------------------------------------------------
add back in velocity bias to all atoms removed by remove_bias_all()
assume remove_bias_all() was previously called
------------------------------------------------------------------------- */
void
ComputeTempRegionEff
::
restore_bias_all
()
{
double
**
v
=
atom
->
v
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
v
[
i
][
0
]
+=
vbiasall
[
i
][
0
];
v
[
i
][
1
]
+=
vbiasall
[
i
][
1
];
v
[
i
][
2
]
+=
vbiasall
[
i
][
2
];
}
}
/* ---------------------------------------------------------------------- */
double
ComputeTempRegionEff
::
memory_usage
()
{
double
bytes
=
maxbias
*
sizeof
(
double
);
return
bytes
;
}
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