Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F87976614
fix_smd.cpp
No One
Temporary
Actions
Download File
Edit File
Delete File
View Transforms
Subscribe
Mute Notifications
Award Token
Subscribers
None
File Metadata
Details
File Info
Storage
Attached
Created
Wed, Oct 16, 02:50
Size
12 KB
Mime Type
text/x-c
Expires
Fri, Oct 18, 02:50 (2 d)
Engine
blob
Format
Raw Data
Handle
21540613
Attached To
rLAMMPS lammps
fix_smd.cpp
View Options
/* ----------------------------------------------------------------------
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 "force.h"
#include "group.h"
using
namespace
LAMMPS_NS
;
using
namespace
FixConst
;
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
;
respa_level_support
=
1
;
ilevel_respa
=
0
;
int
argoffs
=
3
;
if
(
strcmp
(
arg
[
argoffs
],
"cvel"
)
==
0
)
{
if
(
narg
<
argoffs
+
3
)
error
->
all
(
FLERR
,
"Illegal fix smd command"
);
styleflag
|=
SMD_CVEL
;
k_smd
=
force
->
numeric
(
FLERR
,
arg
[
argoffs
+
1
]);
v_smd
=
force
->
numeric
(
FLERR
,
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
(
FLERR
,
"Illegal fix smd command"
);
styleflag
|=
SMD_CFOR
;
f_smd
=
force
->
numeric
(
FLERR
,
arg
[
argoffs
+
1
]);
argoffs
+=
2
;
}
else
error
->
all
(
FLERR
,
"Illegal fix smd command"
);
if
(
strcmp
(
arg
[
argoffs
],
"tether"
)
==
0
)
{
if
(
narg
<
argoffs
+
5
)
error
->
all
(
FLERR
,
"Illegal fix smd command"
);
styleflag
|=
SMD_TETHER
;
if
(
strcmp
(
arg
[
argoffs
+
1
],
"NULL"
)
==
0
)
xflag
=
0
;
else
xc
=
force
->
numeric
(
FLERR
,
arg
[
argoffs
+
1
]);
if
(
strcmp
(
arg
[
argoffs
+
2
],
"NULL"
)
==
0
)
yflag
=
0
;
else
yc
=
force
->
numeric
(
FLERR
,
arg
[
argoffs
+
2
]);
if
(
strcmp
(
arg
[
argoffs
+
3
],
"NULL"
)
==
0
)
zflag
=
0
;
else
zc
=
force
->
numeric
(
FLERR
,
arg
[
argoffs
+
3
]);
r0
=
force
->
numeric
(
FLERR
,
arg
[
argoffs
+
4
]);
if
(
r0
<
0
)
error
->
all
(
FLERR
,
"R0 < 0 for fix smd command"
);
argoffs
+=
5
;
}
else
if
(
strcmp
(
arg
[
argoffs
],
"couple"
)
==
0
)
{
if
(
narg
<
argoffs
+
6
)
error
->
all
(
FLERR
,
"Illegal fix smd command"
);
styleflag
|=
SMD_COUPLE
;
igroup2
=
group
->
find
(
arg
[
argoffs
+
1
]);
if
(
igroup2
==
-
1
)
error
->
all
(
FLERR
,
"Could not find fix smd couple group ID"
);
if
(
igroup2
==
igroup
)
error
->
all
(
FLERR
,
"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
=
force
->
numeric
(
FLERR
,
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
=
force
->
numeric
(
FLERR
,
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
=
force
->
numeric
(
FLERR
,
arg
[
argoffs
+
4
]);
r0
=
force
->
numeric
(
FLERR
,
arg
[
argoffs
+
5
]);
if
(
r0
<
0
)
error
->
all
(
FLERR
,
"R0 < 0 for fix smd command"
);
argoffs
+=
6
;
}
else
error
->
all
(
FLERR
,
"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
(
strstr
(
update
->
integrate_style
,
"respa"
))
{
ilevel_respa
=
((
Respa
*
)
update
->
integrate
)
->
nlevels
-
1
;
if
(
respa_level
>=
0
)
ilevel_respa
=
MIN
(
respa_level
,
ilevel_respa
);
}
}
/* ---------------------------------------------------------------------- */
void
FixSMD
::
setup
(
int
vflag
)
{
if
(
strstr
(
update
->
integrate_style
,
"verlet"
))
post_force
(
vflag
);
else
{
((
Respa
*
)
update
->
integrate
)
->
copy_flevel_f
(
ilevel_respa
);
post_force_respa
(
vflag
,
ilevel_respa
,
0
);
((
Respa
*
)
update
->
integrate
)
->
copy_f_flevel
(
ilevel_respa
);
}
}
/* ---------------------------------------------------------------------- */
void
FixSMD
::
post_force
(
int
vflag
)
{
if
(
styleflag
&
SMD_TETHER
)
smd_tether
();
else
smd_couple
();
if
(
styleflag
&
SMD_CVEL
)
{
if
(
strstr
(
update
->
integrate_style
,
"verlet"
))
r_old
+=
v_smd
*
update
->
dt
;
else
r_old
+=
v_smd
*
((
Respa
*
)
update
->
integrate
)
->
step
[
ilevel_respa
];
}
}
/* ---------------------------------------------------------------------- */
void
FixSMD
::
smd_tether
()
{
double
xcm
[
3
];
group
->
xcm
(
igroup
,
masstotal
,
xcm
);
double
dt
=
update
->
dt
;
if
(
strstr
(
update
->
integrate_style
,
"respa"
))
dt
=
((
Respa
*
)
update
->
integrate
)
->
step
[
ilevel_respa
];
// 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
)
{
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
*
dt
;
}
else
{
fx
=
0.0
;
fy
=
0.0
;
fz
=
0.0
;
}
}
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
;
double
*
rmass
=
atom
->
rmass
;
double
massfrac
;
int
nlocal
=
atom
->
nlocal
;
ftotal
[
0
]
=
ftotal
[
1
]
=
ftotal
[
2
]
=
0.0
;
force_flag
=
0
;
if
(
rmass
)
{
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
massfrac
=
rmass
[
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
;
}
}
else
{
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
);
double
dt
=
update
->
dt
;
if
(
strstr
(
update
->
integrate_style
,
"respa"
))
dt
=
((
Respa
*
)
update
->
integrate
)
->
step
[
ilevel_respa
];
// 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
*
dt
;
}
else
{
fx
=
0.0
;
fy
=
0.0
;
fz
=
0.0
;
}
}
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
;
double
*
rmass
=
atom
->
rmass
;
int
nlocal
=
atom
->
nlocal
;
ftotal
[
0
]
=
ftotal
[
1
]
=
ftotal
[
2
]
=
0.0
;
force_flag
=
0
;
double
massfrac
;
if
(
rmass
)
{
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
{
massfrac
=
rmass
[
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
=
rmass
[
i
]
/
masstotal2
;
f
[
i
][
0
]
-=
fx
*
massfrac
;
f
[
i
][
1
]
-=
fy
*
massfrac
;
f
[
i
][
2
]
-=
fz
*
massfrac
;
}
}
}
else
{
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
==
ilevel_respa
)
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
Log In to Comment