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fix_efield.cpp
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Tue, Jul 16, 16:56
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Thu, Jul 18, 16:56 (1 d, 21 h)
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rLAMMPS lammps
fix_efield.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: Christina Payne (Vanderbilt U)
------------------------------------------------------------------------- */
#include "math.h"
#include "string.h"
#include "stdlib.h"
#include "fix_efield.h"
#include "atom.h"
#include "update.h"
#include "modify.h"
#include "force.h"
#include "respa.h"
#include "input.h"
#include "variable.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
using
namespace
FixConst
;
enum
{
CONSTANT
,
EQUAL
,
ATOM
};
/* ---------------------------------------------------------------------- */
FixEfield
::
FixEfield
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
Fix
(
lmp
,
narg
,
arg
)
{
if
(
narg
!=
6
)
error
->
all
(
FLERR
,
"Illegal fix efield command"
);
vector_flag
=
1
;
scalar_flag
=
1
;
size_vector
=
3
;
global_freq
=
1
;
extvector
=
1
;
extscalar
=
1
;
qe2f
=
force
->
qe2f
;
xstr
=
ystr
=
zstr
=
NULL
;
if
(
strstr
(
arg
[
3
],
"v_"
)
==
arg
[
3
])
{
int
n
=
strlen
(
&
arg
[
3
][
2
])
+
1
;
xstr
=
new
char
[
n
];
strcpy
(
xstr
,
&
arg
[
3
][
2
]);
}
else
{
ex
=
qe2f
*
atof
(
arg
[
3
]);
xstyle
=
CONSTANT
;
}
if
(
strstr
(
arg
[
4
],
"v_"
)
==
arg
[
4
])
{
int
n
=
strlen
(
&
arg
[
4
][
2
])
+
1
;
ystr
=
new
char
[
n
];
strcpy
(
ystr
,
&
arg
[
4
][
2
]);
}
else
{
ey
=
qe2f
*
atof
(
arg
[
4
]);
ystyle
=
CONSTANT
;
}
if
(
strstr
(
arg
[
5
],
"v_"
)
==
arg
[
5
])
{
int
n
=
strlen
(
&
arg
[
5
][
2
])
+
1
;
zstr
=
new
char
[
n
];
strcpy
(
zstr
,
&
arg
[
5
][
2
]);
}
else
{
ez
=
qe2f
*
atof
(
arg
[
5
]);
zstyle
=
CONSTANT
;
}
force_flag
=
0
;
fsum
[
0
]
=
fsum
[
1
]
=
fsum
[
2
]
=
fsum
[
3
]
=
0.0
;
maxatom
=
0
;
efield
=
NULL
;
}
/* ---------------------------------------------------------------------- */
FixEfield
::~
FixEfield
()
{
delete
[]
xstr
;
delete
[]
ystr
;
delete
[]
zstr
;
memory
->
destroy
(
efield
);
}
/* ---------------------------------------------------------------------- */
int
FixEfield
::
setmask
()
{
int
mask
=
0
;
mask
|=
THERMO_ENERGY
;
mask
|=
POST_FORCE
;
mask
|=
POST_FORCE_RESPA
;
mask
|=
MIN_POST_FORCE
;
return
mask
;
}
/* ---------------------------------------------------------------------- */
void
FixEfield
::
init
()
{
if
(
!
atom
->
q_flag
)
error
->
all
(
FLERR
,
"Fix efield requires atom attribute q"
);
// check variables
if
(
xstr
)
{
xvar
=
input
->
variable
->
find
(
xstr
);
if
(
xvar
<
0
)
error
->
all
(
FLERR
,
"Variable name for fix efield does not exist"
);
if
(
input
->
variable
->
equalstyle
(
xvar
))
xstyle
=
EQUAL
;
else
if
(
input
->
variable
->
atomstyle
(
xvar
))
xstyle
=
ATOM
;
else
error
->
all
(
FLERR
,
"Variable for fix efield is invalid style"
);
}
if
(
ystr
)
{
yvar
=
input
->
variable
->
find
(
ystr
);
if
(
yvar
<
0
)
error
->
all
(
FLERR
,
"Variable name for fix efield does not exist"
);
if
(
input
->
variable
->
equalstyle
(
yvar
))
ystyle
=
EQUAL
;
else
if
(
input
->
variable
->
atomstyle
(
yvar
))
ystyle
=
ATOM
;
else
error
->
all
(
FLERR
,
"Variable for fix efield is invalid style"
);
}
if
(
zstr
)
{
zvar
=
input
->
variable
->
find
(
zstr
);
if
(
zvar
<
0
)
error
->
all
(
FLERR
,
"Variable name for fix efield does not exist"
);
if
(
input
->
variable
->
equalstyle
(
zvar
))
zstyle
=
EQUAL
;
else
if
(
input
->
variable
->
atomstyle
(
zvar
))
zstyle
=
ATOM
;
else
error
->
all
(
FLERR
,
"Variable for fix efield is invalid style"
);
}
if
(
xstyle
==
ATOM
||
ystyle
==
ATOM
||
zstyle
==
ATOM
)
varflag
=
ATOM
;
else
if
(
xstyle
==
EQUAL
||
ystyle
==
EQUAL
||
zstyle
==
EQUAL
)
varflag
=
EQUAL
;
else
varflag
=
CONSTANT
;
if
(
strstr
(
update
->
integrate_style
,
"respa"
))
nlevels_respa
=
((
Respa
*
)
update
->
integrate
)
->
nlevels
;
}
/* ---------------------------------------------------------------------- */
void
FixEfield
::
setup
(
int
vflag
)
{
if
(
strstr
(
update
->
integrate_style
,
"verlet"
))
post_force
(
vflag
);
else
{
((
Respa
*
)
update
->
integrate
)
->
copy_flevel_f
(
nlevels_respa
-
1
);
post_force_respa
(
vflag
,
nlevels_respa
-
1
,
0
);
((
Respa
*
)
update
->
integrate
)
->
copy_f_flevel
(
nlevels_respa
-
1
);
}
}
/* ---------------------------------------------------------------------- */
void
FixEfield
::
min_setup
(
int
vflag
)
{
post_force
(
vflag
);
}
/* ----------------------------------------------------------------------
apply F = qE
------------------------------------------------------------------------- */
void
FixEfield
::
post_force
(
int
vflag
)
{
double
**
f
=
atom
->
f
;
double
*
q
=
atom
->
q
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
// reallocate efield array if necessary
if
(
varflag
==
ATOM
&&
nlocal
>
maxatom
)
{
maxatom
=
atom
->
nmax
;
memory
->
destroy
(
efield
);
memory
->
create
(
efield
,
maxatom
,
3
,
"efield:efield"
);
}
// fsum[0] = "potential energy" for added force
// fsum[123] = extra force added to atoms
fsum
[
0
]
=
fsum
[
1
]
=
fsum
[
2
]
=
fsum
[
3
]
=
0.0
;
force_flag
=
0
;
double
**
x
=
atom
->
x
;
double
fx
,
fy
,
fz
;
if
(
varflag
==
CONSTANT
)
{
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
fx
=
q
[
i
]
*
ex
;
fy
=
q
[
i
]
*
ey
;
fz
=
q
[
i
]
*
ez
;
f
[
i
][
0
]
+=
fx
;
f
[
i
][
1
]
+=
fy
;
f
[
i
][
2
]
+=
fz
;
fsum
[
0
]
-=
fx
*
x
[
i
][
0
]
+
fy
*
x
[
i
][
1
]
+
fz
*
x
[
i
][
2
];
fsum
[
1
]
+=
fx
;
fsum
[
2
]
+=
fy
;
fsum
[
3
]
+=
fz
;
}
// variable efield, wrap with clear/add
}
else
{
modify
->
clearstep_compute
();
if
(
xstyle
==
EQUAL
)
ex
=
qe2f
*
input
->
variable
->
compute_equal
(
xvar
);
else
if
(
xstyle
==
ATOM
&&
efield
)
input
->
variable
->
compute_atom
(
xvar
,
igroup
,
&
efield
[
0
][
0
],
3
,
0
);
if
(
ystyle
==
EQUAL
)
ey
=
qe2f
*
input
->
variable
->
compute_equal
(
yvar
);
else
if
(
ystyle
==
ATOM
&&
efield
)
input
->
variable
->
compute_atom
(
yvar
,
igroup
,
&
efield
[
0
][
1
],
3
,
0
);
if
(
zstyle
==
EQUAL
)
ez
=
qe2f
*
input
->
variable
->
compute_equal
(
zvar
);
else
if
(
zstyle
==
ATOM
&&
efield
)
input
->
variable
->
compute_atom
(
zvar
,
igroup
,
&
efield
[
0
][
2
],
3
,
0
);
modify
->
addstep_compute
(
update
->
ntimestep
+
1
);
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
if
(
xstyle
==
ATOM
)
fx
=
qe2f
*
q
[
i
]
*
efield
[
i
][
0
];
else
fx
=
q
[
i
]
*
ex
;
f
[
i
][
0
]
+=
fx
;
fsum
[
1
]
+=
fx
;
if
(
ystyle
==
ATOM
)
fy
=
qe2f
*
q
[
i
]
*
efield
[
i
][
1
];
else
fy
=
q
[
i
]
*
ey
;
f
[
i
][
1
]
+=
fy
;
fsum
[
2
]
+=
fy
;
if
(
zstyle
==
ATOM
)
fz
=
qe2f
*
q
[
i
]
*
efield
[
i
][
2
];
else
fz
=
q
[
i
]
*
ez
;
f
[
i
][
2
]
+=
fz
;
fsum
[
3
]
+=
fz
;
fsum
[
0
]
-=
fx
*
x
[
i
][
0
]
+
fy
*
x
[
i
][
1
]
+
fz
*
x
[
i
][
2
];
}
}
}
/* ---------------------------------------------------------------------- */
void
FixEfield
::
post_force_respa
(
int
vflag
,
int
ilevel
,
int
iloop
)
{
if
(
ilevel
==
nlevels_respa
-
1
)
post_force
(
vflag
);
}
/* ---------------------------------------------------------------------- */
void
FixEfield
::
min_post_force
(
int
vflag
)
{
post_force
(
vflag
);
}
/* ----------------------------------------------------------------------
memory usage of local atom-based array
------------------------------------------------------------------------- */
double
FixEfield
::
memory_usage
()
{
double
bytes
=
0.0
;
if
(
varflag
==
ATOM
)
bytes
=
atom
->
nmax
*
3
*
sizeof
(
double
);
return
bytes
;
}
/* ----------------------------------------------------------------------
return energy added by fix
------------------------------------------------------------------------- */
double
FixEfield
::
compute_scalar
(
void
)
{
if
(
force_flag
==
0
)
{
MPI_Allreduce
(
fsum
,
fsum_all
,
4
,
MPI_DOUBLE
,
MPI_SUM
,
world
);
force_flag
=
1
;
}
return
fsum_all
[
0
];
}
/* ----------------------------------------------------------------------
return total extra force due to fix
------------------------------------------------------------------------- */
double
FixEfield
::
compute_vector
(
int
n
)
{
if
(
force_flag
==
0
)
{
MPI_Allreduce
(
fsum
,
fsum_all
,
4
,
MPI_DOUBLE
,
MPI_SUM
,
world
);
force_flag
=
1
;
}
return
fsum_all
[
n
+
1
];
}
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