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rLAMMPS lammps
displace_atoms.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 "lmptype.h"
#include "mpi.h"
#include "stdlib.h"
#include "string.h"
#include "displace_atoms.h"
#include "atom.h"
#include "modify.h"
#include "domain.h"
#include "lattice.h"
#include "comm.h"
#include "irregular.h"
#include "group.h"
#include "math_const.h"
#include "random_park.h"
#include "error.h"
#include "force.h"
using
namespace
LAMMPS_NS
;
using
namespace
MathConst
;
enum
{
MOVE
,
RAMP
,
RANDOM
,
ROTATE
};
/* ---------------------------------------------------------------------- */
DisplaceAtoms
::
DisplaceAtoms
(
LAMMPS
*
lmp
)
:
Pointers
(
lmp
)
{}
/* ---------------------------------------------------------------------- */
void
DisplaceAtoms
::
command
(
int
narg
,
char
**
arg
)
{
int
i
;
if
(
domain
->
box_exist
==
0
)
error
->
all
(
FLERR
,
"Displace_atoms command before simulation box is defined"
);
if
(
narg
<
2
)
error
->
all
(
FLERR
,
"Illegal displace_atoms command"
);
if
(
modify
->
nfix_restart_peratom
)
error
->
all
(
FLERR
,
"Cannot displace_atoms after "
"reading restart file with per-atom info"
);
if
(
comm
->
me
==
0
&&
screen
)
fprintf
(
screen
,
"Displacing atoms ...
\n
"
);
// group and style
int
igroup
=
group
->
find
(
arg
[
0
]);
if
(
igroup
==
-
1
)
error
->
all
(
FLERR
,
"Could not find displace_atoms group ID"
);
int
groupbit
=
group
->
bitmask
[
igroup
];
int
style
;
if
(
strcmp
(
arg
[
1
],
"move"
)
==
0
)
style
=
MOVE
;
else
if
(
strcmp
(
arg
[
1
],
"ramp"
)
==
0
)
style
=
RAMP
;
else
if
(
strcmp
(
arg
[
1
],
"random"
)
==
0
)
style
=
RANDOM
;
else
if
(
strcmp
(
arg
[
1
],
"rotate"
)
==
0
)
style
=
ROTATE
;
else
error
->
all
(
FLERR
,
"Illegal displace_atoms command"
);
// set option defaults
scaleflag
=
1
;
// read options from end of input line
if
(
style
==
MOVE
)
options
(
narg
-
5
,
&
arg
[
5
]);
else
if
(
style
==
RAMP
)
options
(
narg
-
8
,
&
arg
[
8
]);
else
if
(
style
==
RANDOM
)
options
(
narg
-
6
,
&
arg
[
6
]);
else
if
(
style
==
ROTATE
)
options
(
narg
-
9
,
&
arg
[
9
]);
// setup scaling
double
xscale
,
yscale
,
zscale
;
if
(
scaleflag
)
{
xscale
=
domain
->
lattice
->
xlattice
;
yscale
=
domain
->
lattice
->
ylattice
;
zscale
=
domain
->
lattice
->
zlattice
;
}
else
xscale
=
yscale
=
zscale
=
1.0
;
// move atoms by 3-vector
if
(
style
==
MOVE
)
{
double
delx
=
xscale
*
force
->
numeric
(
FLERR
,
arg
[
2
]);
double
dely
=
yscale
*
force
->
numeric
(
FLERR
,
arg
[
3
]);
double
delz
=
zscale
*
force
->
numeric
(
FLERR
,
arg
[
4
]);
double
**
x
=
atom
->
x
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
{
x
[
i
][
0
]
+=
delx
;
x
[
i
][
1
]
+=
dely
;
x
[
i
][
2
]
+=
delz
;
}
}
}
// move atoms in ramped fashion
if
(
style
==
RAMP
)
{
int
d_dim
;
if
(
strcmp
(
arg
[
2
],
"x"
)
==
0
)
d_dim
=
0
;
else
if
(
strcmp
(
arg
[
2
],
"y"
)
==
0
)
d_dim
=
1
;
else
if
(
strcmp
(
arg
[
2
],
"z"
)
==
0
)
d_dim
=
2
;
else
error
->
all
(
FLERR
,
"Illegal displace_atoms ramp command"
);
double
d_lo
,
d_hi
;
if
(
d_dim
==
0
)
{
d_lo
=
xscale
*
force
->
numeric
(
FLERR
,
arg
[
3
]);
d_hi
=
xscale
*
force
->
numeric
(
FLERR
,
arg
[
4
]);
}
else
if
(
d_dim
==
1
)
{
d_lo
=
yscale
*
force
->
numeric
(
FLERR
,
arg
[
3
]);
d_hi
=
yscale
*
force
->
numeric
(
FLERR
,
arg
[
4
]);
}
else
if
(
d_dim
==
2
)
{
d_lo
=
zscale
*
force
->
numeric
(
FLERR
,
arg
[
3
]);
d_hi
=
zscale
*
force
->
numeric
(
FLERR
,
arg
[
4
]);
}
int
coord_dim
;
if
(
strcmp
(
arg
[
5
],
"x"
)
==
0
)
coord_dim
=
0
;
else
if
(
strcmp
(
arg
[
5
],
"y"
)
==
0
)
coord_dim
=
1
;
else
if
(
strcmp
(
arg
[
5
],
"z"
)
==
0
)
coord_dim
=
2
;
else
error
->
all
(
FLERR
,
"Illegal displace_atoms ramp command"
);
double
coord_lo
,
coord_hi
;
if
(
coord_dim
==
0
)
{
coord_lo
=
xscale
*
force
->
numeric
(
FLERR
,
arg
[
6
]);
coord_hi
=
xscale
*
force
->
numeric
(
FLERR
,
arg
[
7
]);
}
else
if
(
coord_dim
==
1
)
{
coord_lo
=
yscale
*
force
->
numeric
(
FLERR
,
arg
[
6
]);
coord_hi
=
yscale
*
force
->
numeric
(
FLERR
,
arg
[
7
]);
}
else
if
(
coord_dim
==
2
)
{
coord_lo
=
zscale
*
force
->
numeric
(
FLERR
,
arg
[
6
]);
coord_hi
=
zscale
*
force
->
numeric
(
FLERR
,
arg
[
7
]);
}
double
**
x
=
atom
->
x
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
double
fraction
,
dramp
;
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
{
fraction
=
(
x
[
i
][
coord_dim
]
-
coord_lo
)
/
(
coord_hi
-
coord_lo
);
fraction
=
MAX
(
fraction
,
0.0
);
fraction
=
MIN
(
fraction
,
1.0
);
dramp
=
d_lo
+
fraction
*
(
d_hi
-
d_lo
);
x
[
i
][
d_dim
]
+=
dramp
;
}
}
}
// move atoms randomly
// makes atom result independent of what proc owns it via random->reset()
if
(
style
==
RANDOM
)
{
RanPark
*
random
=
new
RanPark
(
lmp
,
1
);
double
dx
=
xscale
*
force
->
numeric
(
FLERR
,
arg
[
2
]);
double
dy
=
yscale
*
force
->
numeric
(
FLERR
,
arg
[
3
]);
double
dz
=
zscale
*
force
->
numeric
(
FLERR
,
arg
[
4
]);
int
seed
=
force
->
inumeric
(
FLERR
,
arg
[
5
]);
if
(
seed
<=
0
)
error
->
all
(
FLERR
,
"Illegal displace_atoms random command"
);
double
**
x
=
atom
->
x
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
{
random
->
reset
(
seed
,
x
[
i
]);
x
[
i
][
0
]
+=
dx
*
2.0
*
(
random
->
uniform
()
-
0.5
);
x
[
i
][
1
]
+=
dy
*
2.0
*
(
random
->
uniform
()
-
0.5
);
x
[
i
][
2
]
+=
dz
*
2.0
*
(
random
->
uniform
()
-
0.5
);
}
}
delete
random
;
}
// rotate atoms by right-hand rule by theta around R
// P = point = vector = point of rotation
// R = vector = axis of rotation
// R0 = runit = unit vector for R
// D = X - P = vector from P to X
// C = (D dot R0) R0 = projection of atom coord onto R line
// A = D - C = vector from R line to X
// B = R0 cross A = vector perp to A in plane of rotation
// A,B define plane of circular rotation around R line
// X = P + C + A cos(theta) + B sin(theta)
if
(
style
==
ROTATE
)
{
double
axis
[
3
],
point
[
3
];
double
a
[
3
],
b
[
3
],
c
[
3
],
d
[
3
],
disp
[
3
],
runit
[
3
];
int
dim
=
domain
->
dimension
;
point
[
0
]
=
xscale
*
force
->
numeric
(
FLERR
,
arg
[
2
]);
point
[
1
]
=
yscale
*
force
->
numeric
(
FLERR
,
arg
[
3
]);
point
[
2
]
=
zscale
*
force
->
numeric
(
FLERR
,
arg
[
4
]);
axis
[
0
]
=
force
->
numeric
(
FLERR
,
arg
[
5
]);
axis
[
1
]
=
force
->
numeric
(
FLERR
,
arg
[
6
]);
axis
[
2
]
=
force
->
numeric
(
FLERR
,
arg
[
7
]);
double
theta
=
force
->
numeric
(
FLERR
,
arg
[
8
]);
if
(
dim
==
2
&&
(
axis
[
0
]
!=
0.0
||
axis
[
1
]
!=
0.0
))
error
->
all
(
FLERR
,
"Invalid displace_atoms rotate axis for 2d"
);
double
len
=
sqrt
(
axis
[
0
]
*
axis
[
0
]
+
axis
[
1
]
*
axis
[
1
]
+
axis
[
2
]
*
axis
[
2
]);
if
(
len
==
0.0
)
error
->
all
(
FLERR
,
"Zero length rotation vector with displace_atoms"
);
runit
[
0
]
=
axis
[
0
]
/
len
;
runit
[
1
]
=
axis
[
1
]
/
len
;
runit
[
2
]
=
axis
[
2
]
/
len
;
double
sine
=
sin
(
MY_PI
*
theta
/
180.0
);
double
cosine
=
cos
(
MY_PI
*
theta
/
180.0
);
double
ddotr
;
double
**
x
=
atom
->
x
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
{
d
[
0
]
=
x
[
i
][
0
]
-
point
[
0
];
d
[
1
]
=
x
[
i
][
1
]
-
point
[
1
];
d
[
2
]
=
x
[
i
][
2
]
-
point
[
2
];
ddotr
=
d
[
0
]
*
runit
[
0
]
+
d
[
1
]
*
runit
[
1
]
+
d
[
2
]
*
runit
[
2
];
c
[
0
]
=
ddotr
*
runit
[
0
];
c
[
1
]
=
ddotr
*
runit
[
1
];
c
[
2
]
=
ddotr
*
runit
[
2
];
a
[
0
]
=
d
[
0
]
-
c
[
0
];
a
[
1
]
=
d
[
1
]
-
c
[
1
];
a
[
2
]
=
d
[
2
]
-
c
[
2
];
b
[
0
]
=
runit
[
1
]
*
a
[
2
]
-
runit
[
2
]
*
a
[
1
];
b
[
1
]
=
runit
[
2
]
*
a
[
0
]
-
runit
[
0
]
*
a
[
2
];
b
[
2
]
=
runit
[
0
]
*
a
[
1
]
-
runit
[
1
]
*
a
[
0
];
disp
[
0
]
=
a
[
0
]
*
cosine
+
b
[
0
]
*
sine
;
disp
[
1
]
=
a
[
1
]
*
cosine
+
b
[
1
]
*
sine
;
disp
[
2
]
=
a
[
2
]
*
cosine
+
b
[
2
]
*
sine
;
x
[
i
][
0
]
=
point
[
0
]
+
c
[
0
]
+
disp
[
0
];
x
[
i
][
1
]
=
point
[
1
]
+
c
[
1
]
+
disp
[
1
];
if
(
dim
==
3
)
x
[
i
][
2
]
=
point
[
2
]
+
c
[
2
]
+
disp
[
2
];
}
}
}
// move atoms back inside simulation box and to new processors
// use remap() instead of pbc() in case atoms moved a long distance
// use irregular() in case atoms moved a long distance
double
**
x
=
atom
->
x
;
imageint
*
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
();
Irregular
*
irregular
=
new
Irregular
(
lmp
);
irregular
->
migrate_atoms
();
delete
irregular
;
if
(
domain
->
triclinic
)
domain
->
lamda2x
(
atom
->
nlocal
);
// check if any atoms were lost
bigint
natoms
;
bigint
nblocal
=
atom
->
nlocal
;
MPI_Allreduce
(
&
nblocal
,
&
natoms
,
1
,
MPI_LMP_BIGINT
,
MPI_SUM
,
world
);
if
(
natoms
!=
atom
->
natoms
&&
comm
->
me
==
0
)
{
char
str
[
128
];
sprintf
(
str
,
"Lost atoms via displace_atoms: original "
BIGINT_FORMAT
" current "
BIGINT_FORMAT
,
atom
->
natoms
,
natoms
);
error
->
warning
(
FLERR
,
str
);
}
}
/* ----------------------------------------------------------------------
parse optional parameters at end of displace_atoms input line
------------------------------------------------------------------------- */
void
DisplaceAtoms
::
options
(
int
narg
,
char
**
arg
)
{
if
(
narg
<
0
)
error
->
all
(
FLERR
,
"Illegal displace_atoms command"
);
int
iarg
=
0
;
while
(
iarg
<
narg
)
{
if
(
strcmp
(
arg
[
iarg
],
"units"
)
==
0
)
{
if
(
iarg
+
2
>
narg
)
error
->
all
(
FLERR
,
"Illegal displace_atoms command"
);
if
(
strcmp
(
arg
[
iarg
+
1
],
"box"
)
==
0
)
scaleflag
=
0
;
else
if
(
strcmp
(
arg
[
iarg
+
1
],
"lattice"
)
==
0
)
scaleflag
=
1
;
else
error
->
all
(
FLERR
,
"Illegal displace_atoms command"
);
iarg
+=
2
;
}
else
error
->
all
(
FLERR
,
"Illegal displace_atoms command"
);
}
}
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