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compute_msd_nongauss.cpp
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Tue, Aug 27, 00:14
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Thu, Aug 29, 00:14 (2 d)
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rLAMMPS lammps
compute_msd_nongauss.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 authors: Rob Hoy
------------------------------------------------------------------------- */
#include "string.h"
#include "compute_msd_nongauss.h"
#include "atom.h"
#include "update.h"
#include "group.h"
#include "domain.h"
#include "fix_store.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
/* ---------------------------------------------------------------------- */
ComputeMSDNonGauss
::
ComputeMSDNonGauss
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
ComputeMSD
(
lmp
,
narg
,
arg
)
{
size_vector
=
3
;
}
/* ---------------------------------------------------------------------- */
void
ComputeMSDNonGauss
::
compute_vector
()
{
invoked_vector
=
update
->
ntimestep
;
// cm = current center of mass
double
cm
[
3
];
if
(
comflag
)
group
->
xcm
(
igroup
,
masstotal
,
cm
);
else
cm
[
0
]
=
cm
[
1
]
=
cm
[
2
]
=
0.0
;
// dx,dy,dz = displacement of atom from original position
// original unwrapped position is stored by fix
// relative to center of mass if comflag is set
// for triclinic, need to unwrap current atom coord via h matrix
double
**
xoriginal
=
fix
->
astore
;
double
**
x
=
atom
->
x
;
int
*
mask
=
atom
->
mask
;
tagint
*
image
=
atom
->
image
;
int
nlocal
=
atom
->
nlocal
;
double
*
h
=
domain
->
h
;
double
xprd
=
domain
->
xprd
;
double
yprd
=
domain
->
yprd
;
double
zprd
=
domain
->
zprd
;
double
dx
,
dy
,
dz
;
int
xbox
,
ybox
,
zbox
;
double
msd
[
2
];
msd
[
0
]
=
msd
[
1
]
=
0.0
;
if
(
domain
->
triclinic
==
0
)
{
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
xbox
=
(
image
[
i
]
&
IMGMASK
)
-
IMGMAX
;
ybox
=
(
image
[
i
]
>>
IMGBITS
&
IMGMASK
)
-
IMGMAX
;
zbox
=
(
image
[
i
]
>>
IMG2BITS
)
-
IMGMAX
;
dx
=
x
[
i
][
0
]
+
xbox
*
xprd
-
cm
[
0
]
-
xoriginal
[
i
][
0
];
dy
=
x
[
i
][
1
]
+
ybox
*
yprd
-
cm
[
1
]
-
xoriginal
[
i
][
1
];
dz
=
x
[
i
][
2
]
+
zbox
*
zprd
-
cm
[
2
]
-
xoriginal
[
i
][
2
];
msd
[
0
]
+=
dx
*
dx
+
dy
*
dy
+
dz
*
dz
;
msd
[
1
]
+=
(
dx
*
dx
+
dy
*
dy
+
dz
*
dz
)
*
(
dx
*
dx
+
dy
*
dy
+
dz
*
dz
);
}
}
else
{
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
xbox
=
(
image
[
i
]
&
IMGMASK
)
-
IMGMAX
;
ybox
=
(
image
[
i
]
>>
IMGBITS
&
IMGMASK
)
-
IMGMAX
;
zbox
=
(
image
[
i
]
>>
IMG2BITS
)
-
IMGMAX
;
dx
=
x
[
i
][
0
]
+
h
[
0
]
*
xbox
+
h
[
5
]
*
ybox
+
h
[
4
]
*
zbox
-
cm
[
0
]
-
xoriginal
[
i
][
0
];
dy
=
x
[
i
][
1
]
+
h
[
1
]
*
ybox
+
h
[
3
]
*
zbox
-
cm
[
1
]
-
xoriginal
[
i
][
1
];
dz
=
x
[
i
][
2
]
+
h
[
2
]
*
zbox
-
cm
[
2
]
-
xoriginal
[
i
][
2
];
msd
[
0
]
+=
dx
*
dx
+
dy
*
dy
+
dz
*
dz
;
msd
[
1
]
+=
(
dx
*
dx
+
dy
*
dy
+
dz
*
dz
)
*
(
dx
*
dx
+
dy
*
dy
+
dz
*
dz
);
}
}
MPI_Allreduce
(
msd
,
vector
,
2
,
MPI_DOUBLE
,
MPI_SUM
,
world
);
if
(
nmsd
)
{
vector
[
0
]
/=
nmsd
;
vector
[
1
]
/=
nmsd
;
vector
[
2
]
=
(
3
*
vector
[
1
])
/
(
5
*
vector
[
0
]
*
vector
[
0
])
-
1
;
}
}
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