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rLAMMPS lammps
fix_smd.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: Axel Kohlmeyer (UPenn)
based on fix spring by: Paul Crozier (SNL)
------------------------------------------------------------------------- */
#include "math.h"
#include "stdlib.h"
#include "string.h"
#include "fix_smd.h"
#include "atom.h"
#include "comm.h"
#include "update.h"
#include "respa.h"
#include "domain.h"
#include "error.h"
#include "group.h"
using
namespace
LAMMPS_NS
;
enum
{
SMD_NONE
=
0
,
SMD_TETHER
=
1
<<
0
,
SMD_COUPLE
=
1
<<
1
,
SMD_CVEL
=
1
<<
2
,
SMD_CFOR
=
1
<<
3
,
SMD_AUTOX
=
1
<<
4
,
SMD_AUTOY
=
1
<<
5
,
SMD_AUTOZ
=
1
<<
6
};
#define SMALL 0.001
/* ---------------------------------------------------------------------- */
FixSMD
::
FixSMD
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
Fix
(
lmp
,
narg
,
arg
)
{
styleflag
=
SMD_NONE
;
k_smd
=
f_smd
=
v_smd
=
-
1.0
;
xflag
=
yflag
=
zflag
=
1
;
xc
=
yc
=
zc
=
0.0
;
xn
=
yn
=
zn
=
1.0
;
pmf
=
r_old
=
r_now
=
r0
=
0.0
;
restart_global
=
1
;
vector_flag
=
1
;
size_vector
=
7
;
global_freq
=
1
;
extvector
=
1
;
int
argoffs
=
3
;
if
(
strcmp
(
arg
[
argoffs
],
"cvel"
)
==
0
)
{
if
(
narg
<
argoffs
+
3
)
error
->
all
(
"Illegal fix smd command"
);
styleflag
|=
SMD_CVEL
;
k_smd
=
atof
(
arg
[
argoffs
+
1
]);
v_smd
=
atof
(
arg
[
argoffs
+
2
]);
// to be multiplied by update->dt when used.
argoffs
+=
3
;
}
else
if
(
strcmp
(
arg
[
argoffs
],
"cfor"
)
==
0
)
{
if
(
narg
<
argoffs
+
2
)
error
->
all
(
"Illegal fix smd command"
);
styleflag
|=
SMD_CFOR
;
f_smd
=
atof
(
arg
[
argoffs
+
1
]);
argoffs
+=
2
;
}
else
error
->
all
(
"Illegal fix smd command"
);
if
(
strcmp
(
arg
[
argoffs
],
"tether"
)
==
0
)
{
if
(
narg
<
argoffs
+
5
)
error
->
all
(
"Illegal fix smd command"
);
styleflag
|=
SMD_TETHER
;
if
(
strcmp
(
arg
[
argoffs
+
1
],
"NULL"
)
==
0
)
xflag
=
0
;
else
xc
=
atof
(
arg
[
argoffs
+
1
]);
if
(
strcmp
(
arg
[
argoffs
+
2
],
"NULL"
)
==
0
)
yflag
=
0
;
else
yc
=
atof
(
arg
[
argoffs
+
2
]);
if
(
strcmp
(
arg
[
argoffs
+
3
],
"NULL"
)
==
0
)
zflag
=
0
;
else
zc
=
atof
(
arg
[
argoffs
+
3
]);
r0
=
atof
(
arg
[
argoffs
+
4
]);
if
(
r0
<
0
)
error
->
all
(
"R0 < 0 for fix smd command"
);
argoffs
+=
5
;
}
else
if
(
strcmp
(
arg
[
argoffs
],
"couple"
)
==
0
)
{
if
(
narg
<
argoffs
+
6
)
error
->
all
(
"Illegal fix smd command"
);
styleflag
|=
SMD_COUPLE
;
igroup2
=
group
->
find
(
arg
[
argoffs
+
1
]);
if
(
igroup2
==
-
1
)
error
->
all
(
"Could not find fix smd couple group ID"
);
if
(
igroup2
==
igroup
)
error
->
all
(
"Two groups cannot be the same in fix smd couple"
);
group2bit
=
group
->
bitmask
[
igroup2
];
if
(
strcmp
(
arg
[
argoffs
+
2
],
"NULL"
)
==
0
)
xflag
=
0
;
else
if
(
strcmp
(
arg
[
argoffs
+
2
],
"auto"
)
==
0
)
styleflag
|=
SMD_AUTOX
;
else
xc
=
atof
(
arg
[
argoffs
+
2
]);
if
(
strcmp
(
arg
[
argoffs
+
3
],
"NULL"
)
==
0
)
yflag
=
0
;
else
if
(
strcmp
(
arg
[
argoffs
+
3
],
"auto"
)
==
0
)
styleflag
|=
SMD_AUTOY
;
else
yc
=
atof
(
arg
[
argoffs
+
3
]);
if
(
strcmp
(
arg
[
argoffs
+
4
],
"NULL"
)
==
0
)
zflag
=
0
;
else
if
(
strcmp
(
arg
[
argoffs
+
4
],
"auto"
)
==
0
)
styleflag
|=
SMD_AUTOZ
;
else
zc
=
atof
(
arg
[
argoffs
+
4
]);
r0
=
atof
(
arg
[
argoffs
+
5
]);
if
(
r0
<
0
)
error
->
all
(
"R0 < 0 for fix smd command"
);
argoffs
+=
6
;
}
else
error
->
all
(
"Illegal fix smd command"
);
force_flag
=
0
;
ftotal
[
0
]
=
ftotal
[
1
]
=
ftotal
[
2
]
=
0.0
;
}
/* ---------------------------------------------------------------------- */
int
FixSMD
::
setmask
()
{
int
mask
=
0
;
mask
|=
POST_FORCE
;
mask
|=
POST_FORCE_RESPA
;
return
mask
;
}
/* ---------------------------------------------------------------------- */
void
FixSMD
::
init
()
{
double
xcm
[
3
],
xcm2
[
3
];
masstotal
=
group
->
mass
(
igroup
);
group
->
xcm
(
igroup
,
masstotal
,
xcm
);
double
dx
,
dy
,
dz
;
if
(
styleflag
&
SMD_TETHER
)
{
dx
=
xc
-
xcm
[
0
];
dy
=
yc
-
xcm
[
1
];
dz
=
zc
-
xcm
[
2
];
}
else
{
/* SMD_COUPLE */
masstotal2
=
group
->
mass
(
igroup2
);
group
->
xcm
(
igroup2
,
masstotal2
,
xcm2
);
if
(
styleflag
&
SMD_AUTOX
)
dx
=
xcm2
[
0
]
-
xcm
[
0
];
else
dx
=
xc
;
if
(
styleflag
&
SMD_AUTOY
)
dy
=
xcm2
[
1
]
-
xcm
[
1
];
else
dy
=
yc
;
if
(
styleflag
&
SMD_AUTOZ
)
dz
=
xcm2
[
2
]
-
xcm
[
2
];
else
dz
=
zc
;
}
if
(
!
xflag
)
dx
=
0.0
;
if
(
!
yflag
)
dy
=
0.0
;
if
(
!
zflag
)
dz
=
0.0
;
r_old
=
sqrt
(
dx
*
dx
+
dy
*
dy
+
dz
*
dz
);
if
(
r_old
>
SMALL
)
{
xn
=
dx
/
r_old
;
yn
=
dy
/
r_old
;
zn
=
dz
/
r_old
;
}
if
(
strcmp
(
update
->
integrate_style
,
"respa"
)
==
0
)
nlevels_respa
=
((
Respa
*
)
update
->
integrate
)
->
nlevels
;
}
/* ---------------------------------------------------------------------- */
void
FixSMD
::
setup
(
int
vflag
)
{
if
(
strcmp
(
update
->
integrate_style
,
"verlet"
)
==
0
)
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
FixSMD
::
post_force
(
int
vflag
)
{
if
(
styleflag
&
SMD_TETHER
)
smd_tether
();
else
smd_couple
();
if
(
styleflag
&
SMD_CVEL
)
r_old
+=
v_smd
*
update
->
dt
;
}
/* ---------------------------------------------------------------------- */
void
FixSMD
::
smd_tether
()
{
double
xcm
[
3
];
group
->
xcm
(
igroup
,
masstotal
,
xcm
);
// fx,fy,fz = components of k * (r-r0)
double
dx
,
dy
,
dz
,
fx
,
fy
,
fz
,
r
,
dr
;
dx
=
xcm
[
0
]
-
xc
;
dy
=
xcm
[
1
]
-
yc
;
dz
=
xcm
[
2
]
-
zc
;
r_now
=
sqrt
(
dx
*
dx
+
dy
*
dy
+
dz
*
dz
);
if
(
!
xflag
)
dx
=
0.0
;
if
(
!
yflag
)
dy
=
0.0
;
if
(
!
zflag
)
dz
=
0.0
;
r
=
sqrt
(
dx
*
dx
+
dy
*
dy
+
dz
*
dz
);
if
(
styleflag
&
SMD_CVEL
)
{
if
(
r
>
SMALL
)
{
double
fsign
;
fsign
=
(
v_smd
<
0.0
)
?
-
1.0
:
1.0
;
dr
=
r
-
r0
-
r_old
;
fx
=
k_smd
*
dx
*
dr
/
r
;
fy
=
k_smd
*
dy
*
dr
/
r
;
fz
=
k_smd
*
dz
*
dr
/
r
;
pmf
+=
(
fx
*
xn
+
fy
*
yn
+
fz
*
zn
)
*
v_smd
*
update
->
dt
;
}
}
else
{
r_old
=
r
;
fx
=
f_smd
*
dx
/
r
;
fy
=
f_smd
*
dy
/
r
;
fz
=
f_smd
*
dz
/
r
;
}
// apply restoring force to atoms in group
// f = -k*(r-r0)*mass/masstotal
double
**
f
=
atom
->
f
;
int
*
mask
=
atom
->
mask
;
int
*
type
=
atom
->
type
;
double
*
mass
=
atom
->
mass
;
int
nlocal
=
atom
->
nlocal
;
ftotal
[
0
]
=
ftotal
[
1
]
=
ftotal
[
2
]
=
0.0
;
force_flag
=
0
;
double
massfrac
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
massfrac
=
mass
[
type
[
i
]]
/
masstotal
;
f
[
i
][
0
]
-=
fx
*
massfrac
;
f
[
i
][
1
]
-=
fy
*
massfrac
;
f
[
i
][
2
]
-=
fz
*
massfrac
;
ftotal
[
0
]
-=
fx
*
massfrac
;
ftotal
[
1
]
-=
fy
*
massfrac
;
ftotal
[
2
]
-=
fz
*
massfrac
;
}
}
/* ---------------------------------------------------------------------- */
void
FixSMD
::
smd_couple
()
{
double
xcm
[
3
],
xcm2
[
3
];
group
->
xcm
(
igroup
,
masstotal
,
xcm
);
group
->
xcm
(
igroup2
,
masstotal2
,
xcm2
);
// renormalize direction of spring
double
dx
,
dy
,
dz
,
r
,
dr
;
if
(
styleflag
&
SMD_AUTOX
)
dx
=
xcm2
[
0
]
-
xcm
[
0
];
else
dx
=
xn
*
r_old
;
if
(
styleflag
&
SMD_AUTOY
)
dy
=
xcm2
[
1
]
-
xcm
[
1
];
else
dy
=
yn
*
r_old
;
if
(
styleflag
&
SMD_AUTOZ
)
dz
=
xcm2
[
2
]
-
xcm
[
2
];
else
dz
=
zn
*
r_old
;
if
(
!
xflag
)
dx
=
0.0
;
if
(
!
yflag
)
dy
=
0.0
;
if
(
!
zflag
)
dz
=
0.0
;
r
=
sqrt
(
dx
*
dx
+
dy
*
dy
+
dz
*
dz
);
if
(
r
>
SMALL
)
{
xn
=
dx
/
r
;
yn
=
dy
/
r
;
zn
=
dz
/
r
;
}
double
fx
,
fy
,
fz
;
if
(
styleflag
&
SMD_CVEL
)
{
dx
=
xcm2
[
0
]
-
xcm
[
0
];
dy
=
xcm2
[
1
]
-
xcm
[
1
];
dz
=
xcm2
[
2
]
-
xcm
[
2
];
r_now
=
sqrt
(
dx
*
dx
+
dy
*
dy
+
dz
*
dz
);
dx
-=
xn
*
r_old
;
dy
-=
yn
*
r_old
;
dz
-=
zn
*
r_old
;
if
(
!
xflag
)
dx
=
0.0
;
if
(
!
yflag
)
dy
=
0.0
;
if
(
!
zflag
)
dz
=
0.0
;
r
=
sqrt
(
dx
*
dx
+
dy
*
dy
+
dz
*
dz
);
dr
=
r
-
r0
;
if
(
r
>
SMALL
)
{
double
fsign
;
fsign
=
(
v_smd
<
0.0
)
?
-
1.0
:
1.0
;
fx
=
k_smd
*
dx
*
dr
/
r
;
fy
=
k_smd
*
dy
*
dr
/
r
;
fz
=
k_smd
*
dz
*
dr
/
r
;
pmf
+=
(
fx
*
xn
+
fy
*
yn
+
fz
*
zn
)
*
fsign
*
v_smd
*
update
->
dt
;
}
}
else
{
dx
=
xcm2
[
0
]
-
xcm
[
0
];
dy
=
xcm2
[
1
]
-
xcm
[
1
];
dz
=
xcm2
[
2
]
-
xcm
[
2
];
r_now
=
sqrt
(
dx
*
dx
+
dy
*
dy
+
dz
*
dz
);
r_old
=
r
;
fx
=
f_smd
*
xn
;
fy
=
f_smd
*
yn
;
fz
=
f_smd
*
zn
;
}
// apply restoring force to atoms in group
// f = -k*(r-r0)*mass/masstotal
double
**
f
=
atom
->
f
;
int
*
mask
=
atom
->
mask
;
int
*
type
=
atom
->
type
;
double
*
mass
=
atom
->
mass
;
int
nlocal
=
atom
->
nlocal
;
ftotal
[
0
]
=
ftotal
[
1
]
=
ftotal
[
2
]
=
0.0
;
force_flag
=
0
;
double
massfrac
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
{
massfrac
=
mass
[
type
[
i
]]
/
masstotal
;
f
[
i
][
0
]
+=
fx
*
massfrac
;
f
[
i
][
1
]
+=
fy
*
massfrac
;
f
[
i
][
2
]
+=
fz
*
massfrac
;
ftotal
[
0
]
+=
fx
*
massfrac
;
ftotal
[
1
]
+=
fy
*
massfrac
;
ftotal
[
2
]
+=
fz
*
massfrac
;
}
if
(
mask
[
i
]
&
group2bit
)
{
massfrac
=
mass
[
type
[
i
]]
/
masstotal2
;
f
[
i
][
0
]
-=
fx
*
massfrac
;
f
[
i
][
1
]
-=
fy
*
massfrac
;
f
[
i
][
2
]
-=
fz
*
massfrac
;
}
}
}
/* ---------------------------------------------------------------------- */
void
FixSMD
::
write_restart
(
FILE
*
fp
)
{
#define RESTART_ITEMS 5
double
buf
[
RESTART_ITEMS
],
fsign
;
if
(
comm
->
me
==
0
)
{
// make sure we project the force into the direction of the pulling.
fsign
=
(
v_smd
<
0.0
)
?
-
1.0
:
1.0
;
buf
[
0
]
=
r_old
;
buf
[
1
]
=
xn
*
fsign
;
buf
[
2
]
=
yn
*
fsign
;
buf
[
3
]
=
zn
*
fsign
;
buf
[
4
]
=
pmf
;
int
size
=
RESTART_ITEMS
*
sizeof
(
double
);
fwrite
(
&
size
,
sizeof
(
int
),
1
,
fp
);
fwrite
(
&
buf
[
0
],
sizeof
(
double
),
RESTART_ITEMS
,
fp
);
}
}
/* ---------------------------------------------------------------------- */
void
FixSMD
::
restart
(
char
*
buf
)
{
double
*
list
=
(
double
*
)
buf
;
r_old
=
list
[
0
];
xn
=
list
[
1
];
yn
=
list
[
2
];
zn
=
list
[
3
];
pmf
=
list
[
4
];
}
/* ---------------------------------------------------------------------- */
void
FixSMD
::
post_force_respa
(
int
vflag
,
int
ilevel
,
int
iloop
)
{
if
(
ilevel
==
nlevels_respa
-
1
)
post_force
(
vflag
);
}
/* ----------------------------------------------------------------------
return components of total smd force on fix group
------------------------------------------------------------------------- */
double
FixSMD
::
compute_vector
(
int
n
)
{
// only sum across procs one time
if
(
force_flag
==
0
)
{
MPI_Allreduce
(
ftotal
,
ftotal_all
,
3
,
MPI_DOUBLE
,
MPI_SUM
,
world
);
force_flag
=
1
;
if
(
styleflag
&
SMD_CVEL
)
{
ftotal_all
[
3
]
=
ftotal_all
[
0
]
*
xn
+
ftotal_all
[
1
]
*
yn
+
ftotal_all
[
2
]
*
zn
;
ftotal_all
[
4
]
=
r_old
;
}
else
{
ftotal_all
[
3
]
=
f_smd
;
ftotal_all
[
4
]
=
r_old
;
}
ftotal_all
[
5
]
=
r_now
;
ftotal_all
[
6
]
=
pmf
;
}
return
ftotal_all
[
n
];
}
Event Timeline
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