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fix_smd_setvel.cpp
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rLAMMPS lammps
fix_smd_setvel.cpp
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/* ----------------------------------------------------------------------
*
* *** Smooth Mach Dynamics ***
*
* This file is part of the USER-SMD package for LAMMPS.
* Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de
* Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI,
* Eckerstrasse 4, D-79104 Freiburg i.Br, Germany.
*
* ----------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
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 <stdlib.h>
#include "fix_smd_setvel.h"
#include "atom.h"
#include "update.h"
#include "modify.h"
#include "domain.h"
#include "region.h"
#include "respa.h"
#include "input.h"
#include "variable.h"
#include "memory.h"
#include "error.h"
#include "force.h"
using
namespace
LAMMPS_NS
;
using
namespace
FixConst
;
enum
{
NONE
,
CONSTANT
,
EQUAL
,
ATOM
};
/* ---------------------------------------------------------------------- */
FixSMDSetVel
::
FixSMDSetVel
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
Fix
(
lmp
,
narg
,
arg
)
{
if
(
narg
<
6
)
error
->
all
(
FLERR
,
"Illegal fix setvelocity command"
);
dynamic_group_allow
=
1
;
vector_flag
=
1
;
size_vector
=
3
;
global_freq
=
1
;
extvector
=
1
;
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
if
(
strcmp
(
arg
[
3
],
"NULL"
)
==
0
)
{
xstyle
=
NONE
;
}
else
{
xvalue
=
force
->
numeric
(
FLERR
,
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
if
(
strcmp
(
arg
[
4
],
"NULL"
)
==
0
)
{
ystyle
=
NONE
;
}
else
{
yvalue
=
force
->
numeric
(
FLERR
,
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
if
(
strcmp
(
arg
[
5
],
"NULL"
)
==
0
)
{
zstyle
=
NONE
;
}
else
{
zvalue
=
force
->
numeric
(
FLERR
,
arg
[
5
]);
zstyle
=
CONSTANT
;
}
// optional args
iregion
=
-
1
;
idregion
=
NULL
;
int
iarg
=
6
;
while
(
iarg
<
narg
)
{
if
(
strcmp
(
arg
[
iarg
],
"region"
)
==
0
)
{
if
(
iarg
+
2
>
narg
)
error
->
all
(
FLERR
,
"Illegal fix setvelocity command"
);
iregion
=
domain
->
find_region
(
arg
[
iarg
+
1
]);
if
(
iregion
==
-
1
)
error
->
all
(
FLERR
,
"Region ID for fix setvelocity does not exist"
);
int
n
=
strlen
(
arg
[
iarg
+
1
])
+
1
;
idregion
=
new
char
[
n
];
strcpy
(
idregion
,
arg
[
iarg
+
1
]);
iarg
+=
2
;
}
else
error
->
all
(
FLERR
,
"Illegal fix setvelocity command"
);
}
force_flag
=
0
;
foriginal
[
0
]
=
foriginal
[
1
]
=
foriginal
[
2
]
=
0.0
;
maxatom
=
atom
->
nmax
;
memory
->
create
(
sforce
,
maxatom
,
3
,
"setvelocity:sforce"
);
}
/* ---------------------------------------------------------------------- */
FixSMDSetVel
::~
FixSMDSetVel
()
{
delete
[]
xstr
;
delete
[]
ystr
;
delete
[]
zstr
;
delete
[]
idregion
;
memory
->
destroy
(
sforce
);
}
/* ---------------------------------------------------------------------- */
int
FixSMDSetVel
::
setmask
()
{
int
mask
=
0
;
//mask |= INITIAL_INTEGRATE;
mask
|=
POST_FORCE
;
return
mask
;
}
/* ---------------------------------------------------------------------- */
void
FixSMDSetVel
::
init
()
{
// check variables
if
(
xstr
)
{
xvar
=
input
->
variable
->
find
(
xstr
);
if
(
xvar
<
0
)
error
->
all
(
FLERR
,
"Variable name for fix setvelocity 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 setvelocity is invalid style"
);
}
if
(
ystr
)
{
yvar
=
input
->
variable
->
find
(
ystr
);
if
(
yvar
<
0
)
error
->
all
(
FLERR
,
"Variable name for fix setvelocity 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 setvelocity is invalid style"
);
}
if
(
zstr
)
{
zvar
=
input
->
variable
->
find
(
zstr
);
if
(
zvar
<
0
)
error
->
all
(
FLERR
,
"Variable name for fix setvelocity 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 setvelocity is invalid style"
);
}
// set index and check validity of region
if
(
iregion
>=
0
)
{
iregion
=
domain
->
find_region
(
idregion
);
if
(
iregion
==
-
1
)
error
->
all
(
FLERR
,
"Region ID for fix setvelocity does not exist"
);
}
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
;
// cannot use non-zero forces for a minimization since no energy is integrated
// use fix addforce instead
int
flag
=
0
;
if
(
update
->
whichflag
==
2
)
{
if
(
xstyle
==
EQUAL
||
xstyle
==
ATOM
)
flag
=
1
;
if
(
ystyle
==
EQUAL
||
ystyle
==
ATOM
)
flag
=
1
;
if
(
zstyle
==
EQUAL
||
zstyle
==
ATOM
)
flag
=
1
;
if
(
xstyle
==
CONSTANT
&&
xvalue
!=
0.0
)
flag
=
1
;
if
(
ystyle
==
CONSTANT
&&
yvalue
!=
0.0
)
flag
=
1
;
if
(
zstyle
==
CONSTANT
&&
zvalue
!=
0.0
)
flag
=
1
;
}
if
(
flag
)
error
->
all
(
FLERR
,
"Cannot use non-zero forces in an energy minimization"
);
}
/* ---------------------------------------------------------------------- */
void
FixSMDSetVel
::
setup
(
int
vflag
)
{
if
(
strstr
(
update
->
integrate_style
,
"verlet"
))
post_force
(
vflag
);
else
for
(
int
ilevel
=
0
;
ilevel
<
nlevels_respa
;
ilevel
++
)
{
((
Respa
*
)
update
->
integrate
)
->
copy_flevel_f
(
ilevel
);
post_force_respa
(
vflag
,
ilevel
,
0
);
((
Respa
*
)
update
->
integrate
)
->
copy_f_flevel
(
ilevel
);
}
}
/* ---------------------------------------------------------------------- */
void
FixSMDSetVel
::
min_setup
(
int
vflag
)
{
post_force
(
vflag
);
}
/* ---------------------------------------------------------------------- */
//void FixSMDSetVel::initial_integrate(int vflag) {
void
FixSMDSetVel
::
post_force
(
int
vflag
)
{
double
**
x
=
atom
->
x
;
double
**
f
=
atom
->
f
;
double
**
v
=
atom
->
v
;
double
**
vest
=
atom
->
vest
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
// update region if necessary
Region
*
region
=
NULL
;
if
(
iregion
>=
0
)
{
region
=
domain
->
regions
[
iregion
];
region
->
prematch
();
}
// reallocate sforce array if necessary
if
(
varflag
==
ATOM
&&
nlocal
>
maxatom
)
{
maxatom
=
atom
->
nmax
;
memory
->
destroy
(
sforce
);
memory
->
create
(
sforce
,
maxatom
,
3
,
"setvelocity:sforce"
);
}
foriginal
[
0
]
=
foriginal
[
1
]
=
foriginal
[
2
]
=
0.0
;
force_flag
=
0
;
if
(
varflag
==
CONSTANT
)
{
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
if
(
region
&&
!
region
->
match
(
x
[
i
][
0
],
x
[
i
][
1
],
x
[
i
][
2
]))
continue
;
foriginal
[
0
]
+=
f
[
i
][
0
];
foriginal
[
1
]
+=
f
[
i
][
1
];
foriginal
[
2
]
+=
f
[
i
][
2
];
if
(
xstyle
)
{
v
[
i
][
0
]
=
xvalue
;
vest
[
i
][
0
]
=
xvalue
;
f
[
i
][
0
]
=
0.0
;
}
if
(
ystyle
)
{
v
[
i
][
1
]
=
yvalue
;
vest
[
i
][
1
]
=
yvalue
;
f
[
i
][
1
]
=
0.0
;
}
if
(
zstyle
)
{
v
[
i
][
2
]
=
zvalue
;
vest
[
i
][
2
]
=
zvalue
;
f
[
i
][
2
]
=
0.0
;
}
}
// variable force, wrap with clear/add
}
else
{
modify
->
clearstep_compute
();
if
(
xstyle
==
EQUAL
)
xvalue
=
input
->
variable
->
compute_equal
(
xvar
);
else
if
(
xstyle
==
ATOM
)
input
->
variable
->
compute_atom
(
xvar
,
igroup
,
&
sforce
[
0
][
0
],
3
,
0
);
if
(
ystyle
==
EQUAL
)
yvalue
=
input
->
variable
->
compute_equal
(
yvar
);
else
if
(
ystyle
==
ATOM
)
input
->
variable
->
compute_atom
(
yvar
,
igroup
,
&
sforce
[
0
][
1
],
3
,
0
);
if
(
zstyle
==
EQUAL
)
zvalue
=
input
->
variable
->
compute_equal
(
zvar
);
else
if
(
zstyle
==
ATOM
)
input
->
variable
->
compute_atom
(
zvar
,
igroup
,
&
sforce
[
0
][
2
],
3
,
0
);
modify
->
addstep_compute
(
update
->
ntimestep
+
1
);
//printf("setting velocity at timestep %d\n", update->ntimestep);
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
if
(
region
&&
!
region
->
match
(
x
[
i
][
0
],
x
[
i
][
1
],
x
[
i
][
2
]))
continue
;
foriginal
[
0
]
+=
f
[
i
][
0
];
foriginal
[
1
]
+=
f
[
i
][
1
];
foriginal
[
2
]
+=
f
[
i
][
2
];
if
(
xstyle
==
ATOM
)
{
vest
[
i
][
0
]
=
v
[
i
][
0
]
=
sforce
[
i
][
0
];
f
[
i
][
0
]
=
0.0
;
}
else
if
(
xstyle
)
{
vest
[
i
][
0
]
=
v
[
i
][
0
]
=
xvalue
;
f
[
i
][
0
]
=
0.0
;
}
if
(
ystyle
==
ATOM
)
{
vest
[
i
][
1
]
=
v
[
i
][
1
]
=
sforce
[
i
][
1
];
f
[
i
][
1
]
=
0.0
;
}
else
if
(
ystyle
)
{
vest
[
i
][
1
]
=
v
[
i
][
1
]
=
yvalue
;
f
[
i
][
1
]
=
0.0
;
}
if
(
zstyle
==
ATOM
)
{
vest
[
i
][
2
]
=
v
[
i
][
2
]
=
sforce
[
i
][
2
];
f
[
i
][
2
]
=
0.0
;
}
else
if
(
zstyle
)
{
vest
[
i
][
2
]
=
v
[
i
][
2
]
=
zvalue
;
f
[
i
][
2
]
=
0.0
;
}
}
}
}
/* ----------------------------------------------------------------------
return components of total force on fix group before force was changed
------------------------------------------------------------------------- */
double
FixSMDSetVel
::
compute_vector
(
int
n
)
{
// only sum across procs one time
if
(
force_flag
==
0
)
{
MPI_Allreduce
(
foriginal
,
foriginal_all
,
3
,
MPI_DOUBLE
,
MPI_SUM
,
world
);
force_flag
=
1
;
}
return
foriginal_all
[
n
];
}
/* ----------------------------------------------------------------------
memory usage of local atom-based array
------------------------------------------------------------------------- */
double
FixSMDSetVel
::
memory_usage
()
{
double
bytes
=
0.0
;
if
(
varflag
==
ATOM
)
bytes
=
atom
->
nmax
*
3
*
sizeof
(
double
);
return
bytes
;
}
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