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fix_event.cpp
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Mon, Jun 10, 05:54
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Wed, Jun 12, 05:54 (1 d, 23 h)
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rLAMMPS lammps
fix_event.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: Mike Brown (SNL), Aidan Thompson (SNL)
------------------------------------------------------------------------- */
#include <stdlib.h>
#include <string.h>
#include "fix_event.h"
#include "atom.h"
#include "update.h"
#include "domain.h"
#include "neighbor.h"
#include "comm.h"
#include "universe.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
using
namespace
FixConst
;
/* ---------------------------------------------------------------------- */
FixEvent
::
FixEvent
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
Fix
(
lmp
,
narg
,
arg
)
{
if
(
narg
!=
3
)
error
->
all
(
FLERR
,
"Illegal fix event command"
);
restart_global
=
1
;
// perform initial allocation of atom-based array
// register with Atom class
xevent
=
NULL
;
xold
=
NULL
;
vold
=
NULL
;
imageold
=
NULL
;
xorig
=
NULL
;
vorig
=
NULL
;
imageorig
=
NULL
;
grow_arrays
(
atom
->
nmax
);
atom
->
add_callback
(
0
);
}
/* ---------------------------------------------------------------------- */
FixEvent
::~
FixEvent
()
{
// unregister callbacks to this fix from Atom class
atom
->
delete_callback
(
id
,
0
);
// delete locally stored array
memory
->
destroy
(
xevent
);
memory
->
destroy
(
xold
);
memory
->
destroy
(
vold
);
memory
->
destroy
(
imageold
);
memory
->
destroy
(
xorig
);
memory
->
destroy
(
vorig
);
memory
->
destroy
(
imageorig
);
}
/* ---------------------------------------------------------------------- */
int
FixEvent
::
setmask
()
{
return
0
;
}
/* ----------------------------------------------------------------------
save current atom coords as an event
called when an event occurs
------------------------------------------------------------------------- */
void
FixEvent
::
store_event
()
{
double
**
x
=
atom
->
x
;
imageint
*
image
=
atom
->
image
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
domain
->
unmap
(
x
[
i
],
image
[
i
],
xevent
[
i
]);
}
/* ----------------------------------------------------------------------
restore atom coords to quenched initial state
called prior to NEB calculation
------------------------------------------------------------------------- */
void
FixEvent
::
restore_event
()
{
double
**
x
=
atom
->
x
;
imageint
*
image
=
atom
->
image
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
x
[
i
][
0
]
=
xevent
[
i
][
0
];
x
[
i
][
1
]
=
xevent
[
i
][
1
];
x
[
i
][
2
]
=
xevent
[
i
][
2
];
// since xevent is unwrapped coordinate,
// need to adjust image flag from default when remapping
// same as in read_data -> Atom::data_atoms()
image
[
i
]
=
((
imageint
)
IMGMAX
<<
IMG2BITS
)
|
((
imageint
)
IMGMAX
<<
IMGBITS
)
|
IMGMAX
;
domain
->
remap
(
x
[
i
],
image
[
i
]);
}
}
/* ----------------------------------------------------------------------
store state of all atoms
called before quench and subsequent check for event
so can later restore pre-quench state if no event occurs
------------------------------------------------------------------------- */
void
FixEvent
::
store_state_quench
()
{
double
**
x
=
atom
->
x
;
double
**
v
=
atom
->
v
;
imageint
*
image
=
atom
->
image
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
xold
[
i
][
0
]
=
x
[
i
][
0
];
xold
[
i
][
1
]
=
x
[
i
][
1
];
xold
[
i
][
2
]
=
x
[
i
][
2
];
vold
[
i
][
0
]
=
v
[
i
][
0
];
vold
[
i
][
1
]
=
v
[
i
][
1
];
vold
[
i
][
2
]
=
v
[
i
][
2
];
imageold
[
i
]
=
image
[
i
];
}
}
/* ----------------------------------------------------------------------
restore state of all atoms to pre-quench state
called after no event detected so can continue
------------------------------------------------------------------------- */
void
FixEvent
::
restore_state_quench
()
{
double
**
x
=
atom
->
x
;
double
**
v
=
atom
->
v
;
imageint
*
image
=
atom
->
image
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
x
[
i
][
0
]
=
xold
[
i
][
0
];
x
[
i
][
1
]
=
xold
[
i
][
1
];
x
[
i
][
2
]
=
xold
[
i
][
2
];
v
[
i
][
0
]
=
vold
[
i
][
0
];
v
[
i
][
1
]
=
vold
[
i
][
1
];
v
[
i
][
2
]
=
vold
[
i
][
2
];
image
[
i
]
=
imageold
[
i
];
}
}
/* ----------------------------------------------------------------------
store original state of all atoms
------------------------------------------------------------------------- */
void
FixEvent
::
store_state_dephase
()
{
double
**
x
=
atom
->
x
;
double
**
v
=
atom
->
v
;
imageint
*
image
=
atom
->
image
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
xorig
[
i
][
0
]
=
x
[
i
][
0
];
xorig
[
i
][
1
]
=
x
[
i
][
1
];
xorig
[
i
][
2
]
=
x
[
i
][
2
];
vorig
[
i
][
0
]
=
v
[
i
][
0
];
vorig
[
i
][
1
]
=
v
[
i
][
1
];
vorig
[
i
][
2
]
=
v
[
i
][
2
];
imageorig
[
i
]
=
image
[
i
];
}
}
/* ----------------------------------------------------------------------
restore state of all atoms to original state
------------------------------------------------------------------------- */
void
FixEvent
::
restore_state_dephase
()
{
double
**
x
=
atom
->
x
;
double
**
v
=
atom
->
v
;
imageint
*
image
=
atom
->
image
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
x
[
i
][
0
]
=
xorig
[
i
][
0
];
x
[
i
][
1
]
=
xorig
[
i
][
1
];
x
[
i
][
2
]
=
xorig
[
i
][
2
];
v
[
i
][
0
]
=
vorig
[
i
][
0
];
v
[
i
][
1
]
=
vorig
[
i
][
1
];
v
[
i
][
2
]
=
vorig
[
i
][
2
];
image
[
i
]
=
imageorig
[
i
];
}
}
/* ----------------------------------------------------------------------
memory usage of local atom-based array
------------------------------------------------------------------------- */
double
FixEvent
::
memory_usage
()
{
double
bytes
=
12
*
atom
->
nmax
*
sizeof
(
double
);
bytes
+=
atom
->
nmax
*
sizeof
(
int
);
return
bytes
;
}
/* ----------------------------------------------------------------------
allocate atom-based array
------------------------------------------------------------------------- */
void
FixEvent
::
grow_arrays
(
int
nmax
)
{
memory
->
grow
(
xevent
,
nmax
,
3
,
"event:xevent"
);
memory
->
grow
(
xold
,
nmax
,
3
,
"event:xold"
);
memory
->
grow
(
vold
,
nmax
,
3
,
"event:vold"
);
memory
->
grow
(
imageold
,
nmax
,
"event:imageold"
);
memory
->
grow
(
xorig
,
nmax
,
3
,
"event:xorig"
);
memory
->
grow
(
vorig
,
nmax
,
3
,
"event:vorig"
);
memory
->
grow
(
imageorig
,
nmax
,
"event:imageorig"
);
// allow compute event to access stored event coords
array_atom
=
xevent
;
}
/* ----------------------------------------------------------------------
copy values within local atom-based array
------------------------------------------------------------------------- */
void
FixEvent
::
copy_arrays
(
int
i
,
int
j
,
int
delflag
)
{
xevent
[
j
][
0
]
=
xevent
[
i
][
0
];
xevent
[
j
][
1
]
=
xevent
[
i
][
1
];
xevent
[
j
][
2
]
=
xevent
[
i
][
2
];
xold
[
j
][
0
]
=
xold
[
i
][
0
];
xold
[
j
][
1
]
=
xold
[
i
][
1
];
xold
[
j
][
2
]
=
xold
[
i
][
2
];
vold
[
j
][
0
]
=
vold
[
i
][
0
];
vold
[
j
][
1
]
=
vold
[
i
][
1
];
vold
[
j
][
2
]
=
vold
[
i
][
2
];
imageold
[
j
]
=
imageold
[
i
];
xorig
[
j
][
0
]
=
xorig
[
i
][
0
];
xorig
[
j
][
1
]
=
xorig
[
i
][
1
];
xorig
[
j
][
2
]
=
xorig
[
i
][
2
];
vorig
[
j
][
0
]
=
vorig
[
i
][
0
];
vorig
[
j
][
1
]
=
vorig
[
i
][
1
];
vorig
[
j
][
2
]
=
vorig
[
i
][
2
];
imageorig
[
j
]
=
imageorig
[
i
];
}
/* ----------------------------------------------------------------------
pack values in local atom-based array for exchange with another proc
------------------------------------------------------------------------- */
int
FixEvent
::
pack_exchange
(
int
i
,
double
*
buf
)
{
buf
[
0
]
=
xevent
[
i
][
0
];
buf
[
1
]
=
xevent
[
i
][
1
];
buf
[
2
]
=
xevent
[
i
][
2
];
buf
[
3
]
=
xold
[
i
][
0
];
buf
[
4
]
=
xold
[
i
][
1
];
buf
[
5
]
=
xold
[
i
][
2
];
buf
[
6
]
=
vold
[
i
][
0
];
buf
[
7
]
=
vold
[
i
][
1
];
buf
[
8
]
=
vold
[
i
][
2
];
buf
[
9
]
=
imageold
[
i
];
buf
[
10
]
=
xorig
[
i
][
0
];
buf
[
11
]
=
xorig
[
i
][
1
];
buf
[
12
]
=
xorig
[
i
][
2
];
buf
[
13
]
=
vorig
[
i
][
0
];
buf
[
14
]
=
vorig
[
i
][
1
];
buf
[
15
]
=
vorig
[
i
][
2
];
buf
[
16
]
=
imageorig
[
i
];
return
17
;
}
/* ----------------------------------------------------------------------
unpack values in local atom-based array from exchange with another proc
------------------------------------------------------------------------- */
int
FixEvent
::
unpack_exchange
(
int
nlocal
,
double
*
buf
)
{
xevent
[
nlocal
][
0
]
=
buf
[
0
];
xevent
[
nlocal
][
1
]
=
buf
[
1
];
xevent
[
nlocal
][
2
]
=
buf
[
2
];
xold
[
nlocal
][
0
]
=
buf
[
3
];
xold
[
nlocal
][
1
]
=
buf
[
4
];
xold
[
nlocal
][
2
]
=
buf
[
5
];
vold
[
nlocal
][
0
]
=
buf
[
6
];
vold
[
nlocal
][
1
]
=
buf
[
7
];
vold
[
nlocal
][
2
]
=
buf
[
8
];
imageold
[
nlocal
]
=
static_cast
<
imageint
>
(
buf
[
9
]);
xorig
[
nlocal
][
0
]
=
buf
[
10
];
xorig
[
nlocal
][
1
]
=
buf
[
11
];
xorig
[
nlocal
][
2
]
=
buf
[
12
];
vorig
[
nlocal
][
0
]
=
buf
[
13
];
vorig
[
nlocal
][
1
]
=
buf
[
14
];
vorig
[
nlocal
][
2
]
=
buf
[
15
];
imageorig
[
nlocal
]
=
static_cast
<
imageint
>
(
buf
[
16
]);
return
17
;
}
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