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Wed, Aug 21, 23:19
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rLAMMPS lammps
compute_temp_rotate.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: Laurent Joly (U Lyon, France), ljoly.ulyon@gmail.com
------------------------------------------------------------------------- */
#include <mpi.h>
#include <stdlib.h>
#include <string.h>
#include "compute_temp_rotate.h"
#include "atom.h"
#include "update.h"
#include "force.h"
#include "group.h"
#include "domain.h"
#include "lattice.h"
#include "error.h"
#include "memory.h"
using
namespace
LAMMPS_NS
;
/* ---------------------------------------------------------------------- */
ComputeTempRotate
::
ComputeTempRotate
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
Compute
(
lmp
,
narg
,
arg
)
{
if
(
narg
!=
3
)
error
->
all
(
FLERR
,
"Illegal compute temp/rotate command"
);
scalar_flag
=
vector_flag
=
1
;
size_vector
=
6
;
extscalar
=
0
;
extvector
=
1
;
tempflag
=
1
;
tempbias
=
1
;
maxbias
=
0
;
vbiasall
=
NULL
;
vector
=
new
double
[
6
];
}
/* ---------------------------------------------------------------------- */
ComputeTempRotate
::~
ComputeTempRotate
()
{
memory
->
destroy
(
vbiasall
);
delete
[]
vector
;
}
/* ---------------------------------------------------------------------- */
void
ComputeTempRotate
::
init
()
{
masstotal
=
group
->
mass
(
igroup
);
}
/* ---------------------------------------------------------------------- */
void
ComputeTempRotate
::
setup
()
{
dynamic
=
0
;
if
(
dynamic_user
||
group
->
dynamic
[
igroup
])
dynamic
=
1
;
dof_compute
();
}
/* ---------------------------------------------------------------------- */
void
ComputeTempRotate
::
dof_compute
()
{
adjust_dof_fix
();
natoms_temp
=
group
->
count
(
igroup
);
dof
=
domain
->
dimension
*
natoms_temp
;
dof
-=
extra_dof
+
fix_dof
;
if
(
dof
>
0
)
tfactor
=
force
->
mvv2e
/
(
dof
*
force
->
boltz
);
else
tfactor
=
0.0
;
}
/* ---------------------------------------------------------------------- */
double
ComputeTempRotate
::
compute_scalar
()
{
double
vthermal
[
3
];
double
vcm
[
3
],
xcm
[
3
],
inertia
[
3
][
3
],
angmom
[
3
],
omega
[
3
];
double
dx
,
dy
,
dz
;
double
unwrap
[
3
];
invoked_scalar
=
update
->
ntimestep
;
if
(
dynamic
)
masstotal
=
group
->
mass
(
igroup
);
group
->
vcm
(
igroup
,
masstotal
,
vcm
);
group
->
xcm
(
igroup
,
masstotal
,
xcm
);
group
->
inertia
(
igroup
,
xcm
,
inertia
);
group
->
angmom
(
igroup
,
xcm
,
angmom
);
group
->
omega
(
angmom
,
inertia
,
omega
);
double
**
x
=
atom
->
x
;
double
**
v
=
atom
->
v
;
double
*
mass
=
atom
->
mass
;
double
*
rmass
=
atom
->
rmass
;
int
*
type
=
atom
->
type
;
imageint
*
image
=
atom
->
image
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
if
(
atom
->
nmax
>
maxbias
)
{
memory
->
destroy
(
vbiasall
);
maxbias
=
atom
->
nmax
;
memory
->
create
(
vbiasall
,
maxbias
,
3
,
"temp/rotate:vbiasall"
);
}
double
t
=
0.0
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
domain
->
unmap
(
x
[
i
],
image
[
i
],
unwrap
);
dx
=
unwrap
[
0
]
-
xcm
[
0
];
dy
=
unwrap
[
1
]
-
xcm
[
1
];
dz
=
unwrap
[
2
]
-
xcm
[
2
];
vbiasall
[
i
][
0
]
=
vcm
[
0
]
+
dz
*
omega
[
1
]
-
dy
*
omega
[
2
];
vbiasall
[
i
][
1
]
=
vcm
[
1
]
+
dx
*
omega
[
2
]
-
dz
*
omega
[
0
];
vbiasall
[
i
][
2
]
=
vcm
[
2
]
+
dy
*
omega
[
0
]
-
dx
*
omega
[
1
];
vthermal
[
0
]
=
v
[
i
][
0
]
-
vbiasall
[
i
][
0
];
vthermal
[
1
]
=
v
[
i
][
1
]
-
vbiasall
[
i
][
1
];
vthermal
[
2
]
=
v
[
i
][
2
]
-
vbiasall
[
i
][
2
];
if
(
rmass
)
t
+=
(
vthermal
[
0
]
*
vthermal
[
0
]
+
vthermal
[
1
]
*
vthermal
[
1
]
+
vthermal
[
2
]
*
vthermal
[
2
])
*
rmass
[
i
];
else
t
+=
(
vthermal
[
0
]
*
vthermal
[
0
]
+
vthermal
[
1
]
*
vthermal
[
1
]
+
vthermal
[
2
]
*
vthermal
[
2
])
*
mass
[
type
[
i
]];
}
MPI_Allreduce
(
&
t
,
&
scalar
,
1
,
MPI_DOUBLE
,
MPI_SUM
,
world
);
if
(
dynamic
)
dof_compute
();
if
(
dof
<
0.0
&&
natoms_temp
>
0.0
)
error
->
all
(
FLERR
,
"Temperature compute degrees of freedom < 0"
);
scalar
*=
tfactor
;
return
scalar
;
}
/* ---------------------------------------------------------------------- */
void
ComputeTempRotate
::
compute_vector
()
{
double
vthermal
[
3
];
double
vcm
[
3
],
xcm
[
3
],
inertia
[
3
][
3
],
angmom
[
3
],
omega
[
3
];
double
dx
,
dy
,
dz
;
double
unwrap
[
3
];
invoked_vector
=
update
->
ntimestep
;
if
(
dynamic
)
masstotal
=
group
->
mass
(
igroup
);
group
->
vcm
(
igroup
,
masstotal
,
vcm
);
group
->
xcm
(
igroup
,
masstotal
,
xcm
);
group
->
inertia
(
igroup
,
xcm
,
inertia
);
group
->
angmom
(
igroup
,
xcm
,
angmom
);
group
->
omega
(
angmom
,
inertia
,
omega
);
double
**
x
=
atom
->
x
;
double
**
v
=
atom
->
v
;
double
*
mass
=
atom
->
mass
;
double
*
rmass
=
atom
->
rmass
;
int
*
type
=
atom
->
type
;
imageint
*
image
=
atom
->
image
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
if
(
atom
->
nmax
>
maxbias
)
{
memory
->
destroy
(
vbiasall
);
maxbias
=
atom
->
nmax
;
memory
->
create
(
vbiasall
,
maxbias
,
3
,
"temp/rotate:vbiasall"
);
}
double
massone
,
t
[
6
];
for
(
int
i
=
0
;
i
<
6
;
i
++
)
t
[
i
]
=
0.0
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
domain
->
unmap
(
x
[
i
],
image
[
i
],
unwrap
);
dx
=
unwrap
[
0
]
-
xcm
[
0
];
dy
=
unwrap
[
1
]
-
xcm
[
1
];
dz
=
unwrap
[
2
]
-
xcm
[
2
];
vbiasall
[
i
][
0
]
=
vcm
[
0
]
+
dz
*
omega
[
1
]
-
dy
*
omega
[
2
];
vbiasall
[
i
][
1
]
=
vcm
[
1
]
+
dx
*
omega
[
2
]
-
dz
*
omega
[
0
];
vbiasall
[
i
][
2
]
=
vcm
[
2
]
+
dy
*
omega
[
0
]
-
dx
*
omega
[
1
];
vthermal
[
0
]
=
v
[
i
][
0
]
-
vbiasall
[
i
][
0
];
vthermal
[
1
]
=
v
[
i
][
1
]
-
vbiasall
[
i
][
1
];
vthermal
[
2
]
=
v
[
i
][
2
]
-
vbiasall
[
i
][
2
];
if
(
rmass
)
massone
=
rmass
[
i
];
else
massone
=
mass
[
type
[
i
]];
t
[
0
]
+=
massone
*
vthermal
[
0
]
*
vthermal
[
0
];
t
[
1
]
+=
massone
*
vthermal
[
1
]
*
vthermal
[
1
];
t
[
2
]
+=
massone
*
vthermal
[
2
]
*
vthermal
[
2
];
t
[
3
]
+=
massone
*
vthermal
[
0
]
*
vthermal
[
1
];
t
[
4
]
+=
massone
*
vthermal
[
0
]
*
vthermal
[
2
];
t
[
5
]
+=
massone
*
vthermal
[
1
]
*
vthermal
[
2
];
}
MPI_Allreduce
(
t
,
vector
,
6
,
MPI_DOUBLE
,
MPI_SUM
,
world
);
for
(
int
i
=
0
;
i
<
6
;
i
++
)
vector
[
i
]
*=
force
->
mvv2e
;
}
/* ----------------------------------------------------------------------
remove velocity bias from atom I to leave thermal velocity
------------------------------------------------------------------------- */
void
ComputeTempRotate
::
remove_bias
(
int
i
,
double
*
v
)
{
v
[
0
]
-=
vbiasall
[
i
][
0
];
v
[
1
]
-=
vbiasall
[
i
][
1
];
v
[
2
]
-=
vbiasall
[
i
][
2
];
}
/* ----------------------------------------------------------------------
remove velocity bias from all atoms to leave thermal velocity
------------------------------------------------------------------------- */
void
ComputeTempRotate
::
remove_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
];
}
}
/* ----------------------------------------------------------------------
add back in velocity bias to atom I removed by remove_bias()
assume remove_bias() was previously called
------------------------------------------------------------------------- */
void
ComputeTempRotate
::
restore_bias
(
int
i
,
double
*
v
)
{
v
[
0
]
+=
vbiasall
[
i
][
0
];
v
[
1
]
+=
vbiasall
[
i
][
1
];
v
[
2
]
+=
vbiasall
[
i
][
2
];
}
/* ----------------------------------------------------------------------
add back in velocity bias to all atoms removed by remove_bias_all()
assume remove_bias_all() was previously called
------------------------------------------------------------------------- */
void
ComputeTempRotate
::
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
ComputeTempRotate
::
memory_usage
()
{
double
bytes
=
maxbias
*
sizeof
(
double
);
return
bytes
;
}
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