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rLAMMPS lammps
displace_box.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 "mpi.h"
#include "math.h"
#include "stdlib.h"
#include "string.h"
#include "displace_box.h"
#include "atom.h"
#include "domain.h"
#include "lattice.h"
#include "comm.h"
#include "group.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
enum
{
NONE
,
FINAL
,
DELTA
,
SCALE
,
VOLUME
};
enum
{
ONE_FROM_ONE
,
ONE_FROM_TWO
,
TWO_FROM_ONE
};
enum
{
NO_REMAP
,
X_REMAP
};
/* ---------------------------------------------------------------------- */
DisplaceBox
::
DisplaceBox
(
LAMMPS
*
lmp
)
:
Pointers
(
lmp
)
{}
/* ---------------------------------------------------------------------- */
void
DisplaceBox
::
command
(
int
narg
,
char
**
arg
)
{
int
i
;
if
(
domain
->
box_exist
==
0
)
error
->
all
(
"Displace_box command before simulation box is defined"
);
if
(
narg
<
2
)
error
->
all
(
"Illegal displace_box command"
);
// init entire system since comm->irregular is done
// comm::init needs neighbor::init needs pair::init needs kspace::init, etc
if
(
comm
->
me
==
0
&&
screen
)
fprintf
(
screen
,
"System init for displace_box ...
\n
"
);
lmp
->
init
();
if
(
comm
->
me
==
0
&&
screen
)
fprintf
(
screen
,
"Displacing box ...
\n
"
);
// group
int
igroup
=
group
->
find
(
arg
[
0
]);
if
(
igroup
==
-
1
)
error
->
all
(
"Could not find displace_box group ID"
);
int
groupbit
=
group
->
bitmask
[
igroup
];
// set defaults
set
=
new
Set
[
6
];
set
[
0
].
style
=
set
[
1
].
style
=
set
[
2
].
style
=
set
[
3
].
style
=
set
[
4
].
style
=
set
[
5
].
style
=
NONE
;
// parse arguments
int
triclinic
=
domain
->
triclinic
;
int
index
;
int
iarg
=
1
;
while
(
iarg
<
narg
)
{
if
(
strcmp
(
arg
[
iarg
],
"x"
)
==
0
||
strcmp
(
arg
[
iarg
],
"y"
)
==
0
||
strcmp
(
arg
[
iarg
],
"z"
)
==
0
)
{
if
(
strcmp
(
arg
[
iarg
],
"x"
)
==
0
)
index
=
0
;
else
if
(
strcmp
(
arg
[
iarg
],
"y"
)
==
0
)
index
=
1
;
else
if
(
strcmp
(
arg
[
iarg
],
"z"
)
==
0
)
index
=
2
;
if
(
iarg
+
2
>
narg
)
error
->
all
(
"Illegal displace_box command"
);
if
(
strcmp
(
arg
[
iarg
+
1
],
"final"
)
==
0
)
{
if
(
iarg
+
4
>
narg
)
error
->
all
(
"Illegal displace_box command"
);
set
[
index
].
style
=
FINAL
;
set
[
index
].
flo
=
atof
(
arg
[
iarg
+
2
]);
set
[
index
].
fhi
=
atof
(
arg
[
iarg
+
3
]);
iarg
+=
4
;
}
else
if
(
strcmp
(
arg
[
iarg
+
1
],
"delta"
)
==
0
)
{
if
(
iarg
+
4
>
narg
)
error
->
all
(
"Illegal displace_box command"
);
set
[
index
].
style
=
DELTA
;
set
[
index
].
dlo
=
atof
(
arg
[
iarg
+
2
]);
set
[
index
].
dhi
=
atof
(
arg
[
iarg
+
3
]);
iarg
+=
4
;
}
else
if
(
strcmp
(
arg
[
iarg
+
1
],
"scale"
)
==
0
)
{
if
(
iarg
+
3
>
narg
)
error
->
all
(
"Illegal displace_box command"
);
set
[
index
].
style
=
SCALE
;
set
[
index
].
scale
=
atof
(
arg
[
iarg
+
2
]);
iarg
+=
3
;
}
else
if
(
strcmp
(
arg
[
iarg
+
1
],
"volume"
)
==
0
)
{
set
[
index
].
style
=
VOLUME
;
iarg
+=
2
;
}
else
error
->
all
(
"Illegal displace_box command"
);
}
else
if
(
strcmp
(
arg
[
iarg
],
"xy"
)
==
0
||
strcmp
(
arg
[
iarg
],
"xz"
)
==
0
||
strcmp
(
arg
[
iarg
],
"yz"
)
==
0
)
{
if
(
triclinic
==
0
)
error
->
all
(
"Displace_box tilt factors require triclinic box"
);
if
(
strcmp
(
arg
[
iarg
],
"xy"
)
==
0
)
index
=
5
;
else
if
(
strcmp
(
arg
[
iarg
],
"xz"
)
==
0
)
index
=
4
;
else
if
(
strcmp
(
arg
[
iarg
],
"yz"
)
==
0
)
index
=
3
;
if
(
iarg
+
2
>
narg
)
error
->
all
(
"Illegal displace_box command"
);
if
(
strcmp
(
arg
[
iarg
+
1
],
"final"
)
==
0
)
{
if
(
iarg
+
3
>
narg
)
error
->
all
(
"Illegal displace_box command"
);
set
[
index
].
style
=
FINAL
;
set
[
index
].
ftilt
=
atof
(
arg
[
iarg
+
2
]);
iarg
+=
3
;
}
else
if
(
strcmp
(
arg
[
iarg
+
1
],
"delta"
)
==
0
)
{
if
(
iarg
+
3
>
narg
)
error
->
all
(
"Illegal displace_box command"
);
set
[
index
].
style
=
DELTA
;
set
[
index
].
dtilt
=
atof
(
arg
[
iarg
+
2
]);
iarg
+=
3
;
}
else
error
->
all
(
"Illegal displace_box command"
);
}
else
break
;
}
// read options from end of input line
options
(
narg
-
iarg
,
&
arg
[
iarg
]);
// check periodicity
if
((
set
[
0
].
style
&&
domain
->
xperiodic
==
0
)
||
(
set
[
1
].
style
&&
domain
->
yperiodic
==
0
)
||
(
set
[
2
].
style
&&
domain
->
zperiodic
==
0
))
error
->
all
(
"Cannot displace_box on a non-periodic boundary"
);
if
(
set
[
3
].
style
&&
(
domain
->
yperiodic
==
0
||
domain
->
zperiodic
==
0
))
error
->
all
(
"Cannot displace_box on a non-periodic boundary"
);
if
(
set
[
4
].
style
&&
(
domain
->
xperiodic
==
0
||
domain
->
zperiodic
==
0
))
error
->
all
(
"Cannot displace_box on a non-periodic boundary"
);
if
(
set
[
5
].
style
&&
(
domain
->
xperiodic
==
0
||
domain
->
yperiodic
==
0
))
error
->
all
(
"Cannot displace_box on a non-periodic boundary"
);
// apply scaling to FINAL,DELTA since they have distance units
int
flag
=
0
;
for
(
int
i
=
0
;
i
<
6
;
i
++
)
if
(
set
[
i
].
style
==
FINAL
||
set
[
i
].
style
==
DELTA
)
flag
=
1
;
if
(
flag
&&
scaleflag
&&
domain
->
lattice
==
NULL
)
error
->
all
(
"Use of displace_box with undefined lattice"
);
double
xscale
,
yscale
,
zscale
;
if
(
flag
&&
scaleflag
)
{
xscale
=
domain
->
lattice
->
xlattice
;
yscale
=
domain
->
lattice
->
ylattice
;
zscale
=
domain
->
lattice
->
zlattice
;
}
else
xscale
=
yscale
=
zscale
=
1.0
;
// for 3,4,5 scaling is in 1st dimension, e.g. x for xz
double
map
[
6
];
map
[
0
]
=
xscale
;
map
[
1
]
=
yscale
;
map
[
2
]
=
zscale
;
map
[
3
]
=
yscale
;
map
[
4
]
=
xscale
;
map
[
5
]
=
xscale
;
for
(
int
i
=
0
;
i
<
3
;
i
++
)
{
if
(
set
[
i
].
style
==
FINAL
)
{
set
[
i
].
flo
*=
map
[
i
];
set
[
i
].
fhi
*=
map
[
i
];
}
else
if
(
set
[
i
].
style
==
DELTA
)
{
set
[
i
].
dlo
*=
map
[
i
];
set
[
i
].
dhi
*=
map
[
i
];
}
}
for
(
int
i
=
3
;
i
<
6
;
i
++
)
{
if
(
set
[
i
].
style
==
FINAL
)
set
[
i
].
ftilt
*=
map
[
i
];
else
if
(
set
[
i
].
style
==
DELTA
)
set
[
i
].
dtilt
*=
map
[
i
];
}
// set initial/final values for box size and shape
// final = initial if no setting
for
(
int
i
=
0
;
i
<
3
;
i
++
)
{
set
[
i
].
lo_stop
=
set
[
i
].
lo_start
=
domain
->
boxlo
[
i
];
set
[
i
].
hi_stop
=
set
[
i
].
hi_start
=
domain
->
boxhi
[
i
];
if
(
set
[
i
].
style
==
FINAL
)
{
set
[
i
].
lo_stop
=
set
[
i
].
flo
;
set
[
i
].
hi_stop
=
set
[
i
].
fhi
;
}
else
if
(
set
[
i
].
style
==
DELTA
)
{
set
[
i
].
lo_stop
=
set
[
i
].
lo_start
+
set
[
i
].
dlo
;
set
[
i
].
hi_stop
=
set
[
i
].
hi_start
+
set
[
i
].
dhi
;
}
else
if
(
set
[
i
].
style
==
SCALE
)
{
set
[
i
].
lo_stop
=
0.5
*
(
set
[
i
].
lo_start
+
set
[
i
].
hi_start
)
-
0.5
*
set
[
i
].
scale
*
(
set
[
i
].
hi_start
-
set
[
i
].
lo_start
);
set
[
i
].
hi_stop
=
0.5
*
(
set
[
i
].
lo_start
+
set
[
i
].
hi_start
)
+
0.5
*
set
[
i
].
scale
*
(
set
[
i
].
hi_start
-
set
[
i
].
lo_start
);
}
}
for
(
int
i
=
3
;
i
<
6
;
i
++
)
{
if
(
i
==
5
)
set
[
i
].
tilt_start
=
domain
->
xy
;
else
if
(
i
==
4
)
set
[
i
].
tilt_start
=
domain
->
xz
;
else
if
(
i
==
3
)
set
[
i
].
tilt_start
=
domain
->
yz
;
set
[
i
].
tilt_stop
=
set
[
i
].
tilt_start
;
if
(
set
[
i
].
style
==
FINAL
)
{
set
[
i
].
tilt_stop
=
set
[
i
].
ftilt
;
}
else
if
(
set
[
i
].
style
==
DELTA
)
{
set
[
i
].
tilt_stop
=
set
[
i
].
tilt_start
+
set
[
i
].
dtilt
;
}
}
// for VOLUME, setup links to other dims
// fixed, dynamic1,2, vol_start
for
(
int
i
=
0
;
i
<
3
;
i
++
)
{
set
[
i
].
vol_start
=
domain
->
xprd
*
domain
->
yprd
*
domain
->
zprd
;
if
(
set
[
i
].
style
!=
VOLUME
)
continue
;
int
other1
=
(
i
+
1
)
%
3
;
int
other2
=
(
i
+
2
)
%
3
;
if
(
set
[
other1
].
style
==
NONE
)
{
if
(
set
[
other2
].
style
==
NONE
||
set
[
other2
].
style
==
VOLUME
)
error
->
all
(
"Fix deform volume setting is invalid"
);
set
[
i
].
substyle
=
ONE_FROM_ONE
;
set
[
i
].
fixed
=
other1
;
set
[
i
].
dynamic1
=
other2
;
}
else
if
(
set
[
other2
].
style
==
NONE
)
{
if
(
set
[
other1
].
style
==
NONE
||
set
[
other1
].
style
==
VOLUME
)
error
->
all
(
"Fix deform volume setting is invalid"
);
set
[
i
].
substyle
=
ONE_FROM_ONE
;
set
[
i
].
fixed
=
other2
;
set
[
i
].
dynamic1
=
other1
;
}
else
if
(
set
[
other1
].
style
==
VOLUME
)
{
if
(
set
[
other2
].
style
==
NONE
||
set
[
other2
].
style
==
VOLUME
)
error
->
all
(
"Fix deform volume setting is invalid"
);
set
[
i
].
substyle
=
TWO_FROM_ONE
;
set
[
i
].
fixed
=
other1
;
set
[
i
].
dynamic1
=
other2
;
}
else
if
(
set
[
other2
].
style
==
VOLUME
)
{
if
(
set
[
other1
].
style
==
NONE
||
set
[
other1
].
style
==
VOLUME
)
error
->
all
(
"Fix deform volume setting is invalid"
);
set
[
i
].
substyle
=
TWO_FROM_ONE
;
set
[
i
].
fixed
=
other2
;
set
[
i
].
dynamic1
=
other1
;
}
else
{
set
[
i
].
substyle
=
ONE_FROM_TWO
;
set
[
i
].
dynamic2
=
other1
;
set
[
i
].
dynamic2
=
other2
;
}
}
// set new box size for VOLUME dims that are linked to other dims
for
(
int
i
=
0
;
i
<
3
;
i
++
)
{
if
(
set
[
i
].
style
!=
VOLUME
)
continue
;
if
(
set
[
i
].
substyle
==
ONE_FROM_ONE
)
{
set
[
i
].
lo_stop
=
0.5
*
(
set
[
i
].
lo_start
+
set
[
i
].
hi_start
)
-
0.5
*
(
set
[
i
].
vol_start
/
(
set
[
set
[
i
].
dynamic1
].
hi_stop
-
set
[
set
[
i
].
dynamic1
].
lo_stop
)
/
(
set
[
set
[
i
].
fixed
].
hi_start
-
set
[
set
[
i
].
fixed
].
lo_start
));
set
[
i
].
hi_stop
=
0.5
*
(
set
[
i
].
lo_start
+
set
[
i
].
hi_start
)
+
0.5
*
(
set
[
i
].
vol_start
/
(
set
[
set
[
i
].
dynamic1
].
hi_stop
-
set
[
set
[
i
].
dynamic1
].
lo_stop
)
/
(
set
[
set
[
i
].
fixed
].
hi_start
-
set
[
set
[
i
].
fixed
].
lo_start
));
}
else
if
(
set
[
i
].
substyle
==
ONE_FROM_TWO
)
{
set
[
i
].
lo_stop
=
0.5
*
(
set
[
i
].
lo_start
+
set
[
i
].
hi_start
)
-
0.5
*
(
set
[
i
].
vol_start
/
(
set
[
set
[
i
].
dynamic1
].
hi_stop
-
set
[
set
[
i
].
dynamic1
].
lo_stop
)
/
(
set
[
set
[
i
].
dynamic2
].
hi_stop
-
set
[
set
[
i
].
dynamic2
].
lo_stop
));
set
[
i
].
hi_stop
=
0.5
*
(
set
[
i
].
lo_start
+
set
[
i
].
hi_start
)
+
0.5
*
(
set
[
i
].
vol_start
/
(
set
[
set
[
i
].
dynamic1
].
hi_stop
-
set
[
set
[
i
].
dynamic1
].
lo_stop
)
/
(
set
[
set
[
i
].
dynamic2
].
hi_stop
-
set
[
set
[
i
].
dynamic2
].
lo_stop
));
}
else
if
(
set
[
i
].
substyle
==
TWO_FROM_ONE
)
{
set
[
i
].
lo_stop
=
0.5
*
(
set
[
i
].
lo_start
+
set
[
i
].
hi_start
)
-
0.5
*
sqrt
(
set
[
i
].
vol_start
/
(
set
[
set
[
i
].
dynamic1
].
hi_stop
-
set
[
set
[
i
].
dynamic1
].
lo_stop
)
/
(
set
[
set
[
i
].
fixed
].
hi_start
-
set
[
set
[
i
].
fixed
].
lo_start
)
*
(
set
[
i
].
hi_start
-
set
[
i
].
lo_start
));
set
[
i
].
hi_stop
=
0.5
*
(
set
[
i
].
lo_start
+
set
[
i
].
hi_start
)
+
0.5
*
sqrt
(
set
[
i
].
vol_start
/
(
set
[
set
[
i
].
dynamic1
].
hi_stop
-
set
[
set
[
i
].
dynamic1
].
lo_stop
)
/
(
set
[
set
[
i
].
fixed
].
hi_start
-
set
[
set
[
i
].
fixed
].
lo_start
)
*
(
set
[
i
].
hi_start
-
set
[
i
].
lo_start
));
}
}
// check that final tilt is not illegal value
double
xprd_stop
=
set
[
0
].
hi_stop
-
set
[
0
].
lo_stop
;
double
yprd_stop
=
set
[
0
].
hi_stop
-
set
[
0
].
lo_stop
;
if
(
set
[
3
].
tilt_stop
<
-
0.5
*
yprd_stop
||
set
[
3
].
tilt_stop
>
0.5
*
yprd_stop
||
set
[
4
].
tilt_stop
<
-
0.5
*
xprd_stop
||
set
[
4
].
tilt_stop
>
0.5
*
xprd_stop
||
set
[
5
].
tilt_stop
<
-
0.5
*
xprd_stop
||
set
[
5
].
tilt_stop
>
0.5
*
xprd_stop
)
error
->
all
(
"Induced tilt by displace_box is too large"
);
// convert atoms to lamda coords
if
(
remapflag
==
X_REMAP
)
{
double
**
x
=
atom
->
x
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
domain
->
x2lamda
(
x
[
i
],
x
[
i
]);
}
// reset global and local box to new size/shape
domain
->
boxlo
[
0
]
=
set
[
0
].
lo_stop
;
domain
->
boxlo
[
1
]
=
set
[
1
].
lo_stop
;
domain
->
boxlo
[
2
]
=
set
[
2
].
lo_stop
;
domain
->
boxhi
[
0
]
=
set
[
0
].
hi_stop
;
domain
->
boxhi
[
1
]
=
set
[
1
].
hi_stop
;
domain
->
boxhi
[
2
]
=
set
[
2
].
hi_stop
;
if
(
triclinic
)
{
domain
->
yz
=
set
[
3
].
tilt_stop
;
domain
->
xz
=
set
[
4
].
tilt_stop
;
domain
->
xy
=
set
[
5
].
tilt_stop
;
}
domain
->
set_global_box
();
domain
->
set_local_box
();
// convert atoms back to box coords
if
(
remapflag
==
X_REMAP
)
{
double
**
x
=
atom
->
x
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
domain
->
lamda2x
(
x
[
i
],
x
[
i
]);
}
// move atoms back inside simulation box and to new processors
// use remap() instead of pbc() in case box
// moved a long distance relative to atoms
// use irregular() instead of exchange() in case box
// moved a long distance relative to atoms
double
**
x
=
atom
->
x
;
int
*
image
=
atom
->
image
;
int
nlocal
=
atom
->
nlocal
;
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
domain
->
remap
(
x
[
i
],
image
[
i
]);
if
(
domain
->
triclinic
)
domain
->
x2lamda
(
atom
->
nlocal
);
domain
->
reset_box
();
comm
->
setup
();
comm
->
irregular
();
if
(
domain
->
triclinic
)
domain
->
lamda2x
(
atom
->
nlocal
);
// clean up
delete
[]
set
;
// check if any atoms were lost
double
natoms
;
double
rlocal
=
atom
->
nlocal
;
MPI_Allreduce
(
&
rlocal
,
&
natoms
,
1
,
MPI_DOUBLE
,
MPI_SUM
,
world
);
if
(
natoms
!=
atom
->
natoms
)
{
char
str
[
128
];
sprintf
(
str
,
"Lost atoms via displace_box: original %.15g current %.15g"
,
atom
->
natoms
,
natoms
);
error
->
all
(
str
);
}
}
/* ----------------------------------------------------------------------
parse optional parameters at end of displace_box input line
------------------------------------------------------------------------- */
void
DisplaceBox
::
options
(
int
narg
,
char
**
arg
)
{
if
(
narg
<
0
)
error
->
all
(
"Illegal displace_box command"
);
remapflag
=
X_REMAP
;
scaleflag
=
1
;
int
iarg
=
0
;
while
(
iarg
<
narg
)
{
if
(
strcmp
(
arg
[
iarg
],
"remap"
)
==
0
)
{
if
(
iarg
+
2
>
narg
)
error
->
all
(
"Illegal displace_box command"
);
if
(
strcmp
(
arg
[
iarg
+
1
],
"x"
)
==
0
)
remapflag
=
X_REMAP
;
else
if
(
strcmp
(
arg
[
iarg
+
1
],
"none"
)
==
0
)
remapflag
=
NO_REMAP
;
else
error
->
all
(
"Illegal displace_box command"
);
iarg
+=
2
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"units"
)
==
0
)
{
if
(
iarg
+
2
>
narg
)
error
->
all
(
"Illegal displace_box command"
);
if
(
strcmp
(
arg
[
iarg
+
1
],
"box"
)
==
0
)
scaleflag
=
0
;
else
if
(
strcmp
(
arg
[
iarg
+
1
],
"lattice"
)
==
0
)
scaleflag
=
1
;
else
error
->
all
(
"Illegal displace_box command"
);
iarg
+=
2
;
}
else
error
->
all
(
"Illegal displace_box command"
);
}
}
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