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compute_msd.cpp
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Tue, Oct 8, 06:10
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Thu, Oct 10, 06:10 (2 d)
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rLAMMPS lammps
compute_msd.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_msd.h"
#include "atom.h"
#include "update.h"
#include "group.h"
#include "domain.h"
#include "modify.h"
#include "fix_store.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
/* ---------------------------------------------------------------------- */
ComputeMSD
::
ComputeMSD
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
Compute
(
lmp
,
narg
,
arg
),
id_fix
(
NULL
)
{
if
(
narg
<
3
)
error
->
all
(
FLERR
,
"Illegal compute msd command"
);
vector_flag
=
1
;
size_vector
=
4
;
extvector
=
0
;
create_attribute
=
1
;
dynamic_group_allow
=
0
;
// optional args
comflag
=
0
;
avflag
=
0
;
int
iarg
=
3
;
while
(
iarg
<
narg
)
{
if
(
strcmp
(
arg
[
iarg
],
"com"
)
==
0
)
{
if
(
iarg
+
2
>
narg
)
error
->
all
(
FLERR
,
"Illegal compute msd command"
);
if
(
strcmp
(
arg
[
iarg
+
1
],
"no"
)
==
0
)
comflag
=
0
;
else
if
(
strcmp
(
arg
[
iarg
+
1
],
"yes"
)
==
0
)
comflag
=
1
;
else
error
->
all
(
FLERR
,
"Illegal compute msd command"
);
iarg
+=
2
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"average"
)
==
0
)
{
if
(
iarg
+
2
>
narg
)
error
->
all
(
FLERR
,
"Illegal compute msd command"
);
if
(
strcmp
(
arg
[
iarg
+
1
],
"no"
)
==
0
)
avflag
=
0
;
else
if
(
strcmp
(
arg
[
iarg
+
1
],
"yes"
)
==
0
)
avflag
=
1
;
else
error
->
all
(
FLERR
,
"Illegal compute msd command"
);
iarg
+=
2
;
}
else
error
->
all
(
FLERR
,
"Illegal compute msd command"
);
}
// create a new fix STORE style for reference positions
// id = compute-ID + COMPUTE_STORE, fix group = compute group
int
n
=
strlen
(
id
)
+
strlen
(
"_COMPUTE_STORE"
)
+
1
;
id_fix
=
new
char
[
n
];
strcpy
(
id_fix
,
id
);
strcat
(
id_fix
,
"_COMPUTE_STORE"
);
char
**
newarg
=
new
char
*
[
6
];
newarg
[
0
]
=
id_fix
;
newarg
[
1
]
=
group
->
names
[
igroup
];
newarg
[
2
]
=
(
char
*
)
"STORE"
;
newarg
[
3
]
=
(
char
*
)
"peratom"
;
newarg
[
4
]
=
(
char
*
)
"1"
;
newarg
[
5
]
=
(
char
*
)
"3"
;
modify
->
add_fix
(
6
,
newarg
);
fix
=
(
FixStore
*
)
modify
->
fix
[
modify
->
nfix
-
1
];
delete
[]
newarg
;
// calculate xu,yu,zu for fix store array
// skip if reset from restart file
if
(
fix
->
restart_reset
)
fix
->
restart_reset
=
0
;
else
{
double
**
xoriginal
=
fix
->
astore
;
double
**
x
=
atom
->
x
;
int
*
mask
=
atom
->
mask
;
imageint
*
image
=
atom
->
image
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
domain
->
unmap
(
x
[
i
],
image
[
i
],
xoriginal
[
i
]);
else
xoriginal
[
i
][
0
]
=
xoriginal
[
i
][
1
]
=
xoriginal
[
i
][
2
]
=
0.0
;
// adjust for COM if requested
if
(
comflag
)
{
double
cm
[
3
];
masstotal
=
group
->
mass
(
igroup
);
group
->
xcm
(
igroup
,
masstotal
,
cm
);
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
xoriginal
[
i
][
0
]
-=
cm
[
0
];
xoriginal
[
i
][
1
]
-=
cm
[
1
];
xoriginal
[
i
][
2
]
-=
cm
[
2
];
}
}
// initialize counter for average positions if requested
naverage
=
0
;
}
// displacement vector
vector
=
new
double
[
4
];
}
/* ---------------------------------------------------------------------- */
ComputeMSD
::~
ComputeMSD
()
{
// check nfix in case all fixes have already been deleted
if
(
modify
->
nfix
)
modify
->
delete_fix
(
id_fix
);
delete
[]
id_fix
;
delete
[]
vector
;
}
/* ---------------------------------------------------------------------- */
void
ComputeMSD
::
init
()
{
// set fix which stores reference atom coords
int
ifix
=
modify
->
find_fix
(
id_fix
);
if
(
ifix
<
0
)
error
->
all
(
FLERR
,
"Could not find compute msd fix ID"
);
fix
=
(
FixStore
*
)
modify
->
fix
[
ifix
];
// nmsd = # of atoms in group
nmsd
=
group
->
count
(
igroup
);
masstotal
=
group
->
mass
(
igroup
);
}
/* ---------------------------------------------------------------------- */
void
ComputeMSD
::
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 reference position
// reference 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
;
imageint
*
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
[
4
];
msd
[
0
]
=
msd
[
1
]
=
msd
[
2
]
=
msd
[
3
]
=
0.0
;
double
xtmp
,
ytmp
,
ztmp
;
// update number of averages if requested
double
navfac
;
if
(
avflag
)
{
naverage
++
;
navfac
=
1.0
/
(
naverage
+
1
);
}
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
;
xtmp
=
x
[
i
][
0
]
+
xbox
*
xprd
-
cm
[
0
];
ytmp
=
x
[
i
][
1
]
+
ybox
*
yprd
-
cm
[
1
];
ztmp
=
x
[
i
][
2
]
+
zbox
*
zprd
-
cm
[
2
];
// use running average position for reference if requested
if
(
avflag
)
{
xoriginal
[
i
][
0
]
=
(
xoriginal
[
i
][
0
]
*
naverage
+
xtmp
)
*
navfac
;
xoriginal
[
i
][
1
]
=
(
xoriginal
[
i
][
1
]
*
naverage
+
ytmp
)
*
navfac
;
xoriginal
[
i
][
2
]
=
(
xoriginal
[
i
][
2
]
*
naverage
+
ztmp
)
*
navfac
;
}
dx
=
xtmp
-
xoriginal
[
i
][
0
];
dy
=
ytmp
-
xoriginal
[
i
][
1
];
dz
=
ztmp
-
xoriginal
[
i
][
2
];
msd
[
0
]
+=
dx
*
dx
;
msd
[
1
]
+=
dy
*
dy
;
msd
[
2
]
+=
dz
*
dz
;
msd
[
3
]
+=
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
;
xtmp
=
x
[
i
][
0
]
+
h
[
0
]
*
xbox
+
h
[
5
]
*
ybox
+
h
[
4
]
*
zbox
-
cm
[
0
];
ytmp
=
x
[
i
][
1
]
+
h
[
1
]
*
ybox
+
h
[
3
]
*
zbox
-
cm
[
1
];
ztmp
=
x
[
i
][
2
]
+
h
[
2
]
*
zbox
-
cm
[
2
];
// use running average position for reference if requested
if
(
avflag
)
{
xoriginal
[
i
][
0
]
=
(
xoriginal
[
i
][
0
]
*
naverage
+
xtmp
)
*
navfac
;
xoriginal
[
i
][
1
]
=
(
xoriginal
[
i
][
0
]
*
naverage
+
xtmp
)
*
navfac
;
xoriginal
[
i
][
2
]
=
(
xoriginal
[
i
][
0
]
*
naverage
+
xtmp
)
*
navfac
;
}
dx
=
xtmp
-
xoriginal
[
i
][
0
];
dy
=
ytmp
-
xoriginal
[
i
][
1
];
dz
=
ztmp
-
xoriginal
[
i
][
2
];
msd
[
0
]
+=
dx
*
dx
;
msd
[
1
]
+=
dy
*
dy
;
msd
[
2
]
+=
dz
*
dz
;
msd
[
3
]
+=
dx
*
dx
+
dy
*
dy
+
dz
*
dz
;
}
}
MPI_Allreduce
(
msd
,
vector
,
4
,
MPI_DOUBLE
,
MPI_SUM
,
world
);
if
(
nmsd
)
{
vector
[
0
]
/=
nmsd
;
vector
[
1
]
/=
nmsd
;
vector
[
2
]
/=
nmsd
;
vector
[
3
]
/=
nmsd
;
}
}
/* ----------------------------------------------------------------------
initialize one atom's storage values, called when atom is created
------------------------------------------------------------------------- */
void
ComputeMSD
::
set_arrays
(
int
i
)
{
double
**
xoriginal
=
fix
->
astore
;
double
**
x
=
atom
->
x
;
xoriginal
[
i
][
0
]
=
x
[
i
][
0
];
xoriginal
[
i
][
1
]
=
x
[
i
][
1
];
xoriginal
[
i
][
2
]
=
x
[
i
][
2
];
}
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