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rLAMMPS lammps
fix_restrain.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: Craig Tenney (University of Notre Dame)
support for bond and angle restraints by Andres Jaramillo-Botero (Caltech)
------------------------------------------------------------------------- */
#include <math.h>
#include <string.h>
#include <stdlib.h>
#include "fix_restrain.h"
#include "atom.h"
#include "force.h"
#include "update.h"
#include "domain.h"
#include "comm.h"
#include "respa.h"
#include "input.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
using
namespace
FixConst
;
using
namespace
MathConst
;
enum
{
BOND
,
ANGLE
,
DIHEDRAL
};
#define TOLERANCE 0.05
#define SMALL 0.001
#define DELTA 1
/* ---------------------------------------------------------------------- */
FixRestrain
::
FixRestrain
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
Fix
(
lmp
,
narg
,
arg
)
{
if
(
narg
<
4
)
error
->
all
(
FLERR
,
"Illegal fix restrain command"
);
scalar_flag
=
1
;
global_freq
=
1
;
extscalar
=
1
;
respa_level_support
=
1
;
ilevel_respa
=
0
;
// parse args
nrestrain
=
maxrestrain
=
0
;
rstyle
=
NULL
;
ids
=
NULL
;
kstart
=
kstop
=
NULL
;
target
=
cos_target
=
sin_target
=
NULL
;
int
iarg
=
3
;
while
(
iarg
<
narg
)
{
if
(
nrestrain
==
maxrestrain
)
{
maxrestrain
+=
DELTA
;
memory
->
grow
(
rstyle
,
maxrestrain
,
"restrain:rstyle"
);
memory
->
grow
(
ids
,
maxrestrain
,
4
,
"restrain:ids"
);
memory
->
grow
(
kstart
,
maxrestrain
,
"restrain:kstart"
);
memory
->
grow
(
kstop
,
maxrestrain
,
"restrain:kstop"
);
memory
->
grow
(
target
,
maxrestrain
,
"restrain:target"
);
memory
->
grow
(
cos_target
,
maxrestrain
,
"restrain:cos_target"
);
memory
->
grow
(
sin_target
,
maxrestrain
,
"restrain:sin_target"
);
}
if
(
strcmp
(
arg
[
iarg
],
"bond"
)
==
0
)
{
if
(
iarg
+
6
>
narg
)
error
->
all
(
FLERR
,
"Illegal fix restrain command"
);
rstyle
[
nrestrain
]
=
BOND
;
ids
[
nrestrain
][
0
]
=
force
->
inumeric
(
FLERR
,
arg
[
iarg
+
1
]);
ids
[
nrestrain
][
1
]
=
force
->
inumeric
(
FLERR
,
arg
[
iarg
+
2
]);
kstart
[
nrestrain
]
=
force
->
numeric
(
FLERR
,
arg
[
iarg
+
3
]);
kstop
[
nrestrain
]
=
force
->
numeric
(
FLERR
,
arg
[
iarg
+
4
]);
target
[
nrestrain
]
=
force
->
numeric
(
FLERR
,
arg
[
iarg
+
5
]);
iarg
+=
6
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"angle"
)
==
0
)
{
if
(
iarg
+
7
>
narg
)
error
->
all
(
FLERR
,
"Illegal fix restrain command"
);
rstyle
[
nrestrain
]
=
ANGLE
;
ids
[
nrestrain
][
0
]
=
force
->
inumeric
(
FLERR
,
arg
[
iarg
+
1
]);
ids
[
nrestrain
][
1
]
=
force
->
inumeric
(
FLERR
,
arg
[
iarg
+
2
]);
ids
[
nrestrain
][
2
]
=
force
->
inumeric
(
FLERR
,
arg
[
iarg
+
3
]);
kstart
[
nrestrain
]
=
force
->
numeric
(
FLERR
,
arg
[
iarg
+
4
]);
kstop
[
nrestrain
]
=
force
->
numeric
(
FLERR
,
arg
[
iarg
+
5
]);
target
[
nrestrain
]
=
force
->
numeric
(
FLERR
,
arg
[
iarg
+
6
]);
target
[
nrestrain
]
*=
MY_PI
/
180.0
;
iarg
+=
7
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"dihedral"
)
==
0
)
{
if
(
iarg
+
8
>
narg
)
error
->
all
(
FLERR
,
"Illegal fix restrain command"
);
rstyle
[
nrestrain
]
=
DIHEDRAL
;
ids
[
nrestrain
][
0
]
=
force
->
inumeric
(
FLERR
,
arg
[
iarg
+
1
]);
ids
[
nrestrain
][
1
]
=
force
->
inumeric
(
FLERR
,
arg
[
iarg
+
2
]);
ids
[
nrestrain
][
2
]
=
force
->
inumeric
(
FLERR
,
arg
[
iarg
+
3
]);
ids
[
nrestrain
][
3
]
=
force
->
inumeric
(
FLERR
,
arg
[
iarg
+
4
]);
kstart
[
nrestrain
]
=
force
->
numeric
(
FLERR
,
arg
[
iarg
+
5
]);
kstop
[
nrestrain
]
=
force
->
numeric
(
FLERR
,
arg
[
iarg
+
6
]);
target
[
nrestrain
]
=
force
->
numeric
(
FLERR
,
arg
[
iarg
+
7
]);
target
[
nrestrain
]
*=
MY_PI
/
180.0
;
cos_target
[
nrestrain
]
=
cos
(
target
[
nrestrain
]);
sin_target
[
nrestrain
]
=
sin
(
target
[
nrestrain
]);
iarg
+=
8
;
}
else
error
->
all
(
FLERR
,
"Illegal fix restrain command"
);
nrestrain
++
;
}
// require atom map to lookup atom IDs
if
(
atom
->
map_style
==
0
)
error
->
all
(
FLERR
,
"Fix restrain requires an atom map, see atom_modify"
);
}
/* ---------------------------------------------------------------------- */
FixRestrain
::~
FixRestrain
()
{
memory
->
destroy
(
rstyle
);
memory
->
destroy
(
ids
);
memory
->
destroy
(
kstart
);
memory
->
destroy
(
kstop
);
memory
->
destroy
(
target
);
memory
->
destroy
(
cos_target
);
memory
->
destroy
(
sin_target
);
}
/* ---------------------------------------------------------------------- */
int
FixRestrain
::
setmask
()
{
int
mask
=
0
;
mask
|=
POST_FORCE
;
mask
|=
THERMO_ENERGY
;
mask
|=
POST_FORCE_RESPA
;
mask
|=
MIN_POST_FORCE
;
return
mask
;
}
/* ---------------------------------------------------------------------- */
void
FixRestrain
::
init
()
{
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
FixRestrain
::
setup
(
int
vflag
)
{
if
(
strcmp
(
update
->
integrate_style
,
"verlet"
)
==
0
)
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
FixRestrain
::
min_setup
(
int
vflag
)
{
post_force
(
vflag
);
}
/* ---------------------------------------------------------------------- */
void
FixRestrain
::
post_force
(
int
vflag
)
{
energy
=
0.0
;
for
(
int
m
=
0
;
m
<
nrestrain
;
m
++
)
if
(
rstyle
[
m
]
==
BOND
)
restrain_bond
(
m
);
else
if
(
rstyle
[
m
]
==
ANGLE
)
restrain_angle
(
m
);
else
if
(
rstyle
[
m
]
==
DIHEDRAL
)
restrain_dihedral
(
m
);
}
/* ---------------------------------------------------------------------- */
void
FixRestrain
::
post_force_respa
(
int
vflag
,
int
ilevel
,
int
iloop
)
{
if
(
ilevel
==
ilevel_respa
)
post_force
(
vflag
);
}
/* ---------------------------------------------------------------------- */
void
FixRestrain
::
min_post_force
(
int
vflag
)
{
post_force
(
vflag
);
}
/* ----------------------------------------------------------------------
apply harmonic bond restraints
---------------------------------------------------------------------- */
void
FixRestrain
::
restrain_bond
(
int
m
)
{
int
i1
,
i2
;
double
delx
,
dely
,
delz
,
fbond
;
double
rsq
,
r
,
dr
,
rk
;
double
**
x
=
atom
->
x
;
double
**
f
=
atom
->
f
;
int
nlocal
=
atom
->
nlocal
;
int
newton_bond
=
force
->
newton_bond
;
double
delta
=
update
->
ntimestep
-
update
->
beginstep
;
if
(
delta
!=
0.0
)
delta
/=
update
->
endstep
-
update
->
beginstep
;
double
k
=
kstart
[
m
]
+
delta
*
(
kstop
[
m
]
-
kstart
[
m
]);
i1
=
atom
->
map
(
ids
[
m
][
0
]);
i2
=
atom
->
map
(
ids
[
m
][
1
]);
// newton_bond on: only processor owning i2 computes restraint
// newton_bond off: only processors owning either of i1,i2 computes restraint
if
(
newton_bond
)
{
if
(
i2
==
-
1
||
i2
>=
nlocal
)
return
;
if
(
i1
==
-
1
)
{
char
str
[
128
];
sprintf
(
str
,
"Restrain atoms %d %d missing on proc %d at step "
BIGINT_FORMAT
,
ids
[
m
][
0
],
ids
[
m
][
1
],
comm
->
me
,
update
->
ntimestep
);
error
->
one
(
FLERR
,
str
);
}
}
else
{
if
((
i1
==
-
1
||
i1
>=
nlocal
)
&&
(
i2
==
-
1
||
i2
>=
nlocal
))
return
;
if
(
i1
==
-
1
||
i2
==
-
1
)
{
char
str
[
128
];
sprintf
(
str
,
"Restrain atoms %d %d missing on proc %d at step "
BIGINT_FORMAT
,
ids
[
m
][
0
],
ids
[
m
][
1
],
comm
->
me
,
update
->
ntimestep
);
error
->
one
(
FLERR
,
str
);
}
}
delx
=
x
[
i1
][
0
]
-
x
[
i2
][
0
];
dely
=
x
[
i1
][
1
]
-
x
[
i2
][
1
];
delz
=
x
[
i1
][
2
]
-
x
[
i2
][
2
];
domain
->
minimum_image
(
delx
,
dely
,
delz
);
rsq
=
delx
*
delx
+
dely
*
dely
+
delz
*
delz
;
r
=
sqrt
(
rsq
);
dr
=
r
-
target
[
m
];
rk
=
k
*
dr
;
// force & energy
if
(
r
>
0.0
)
fbond
=
-
2.0
*
rk
/
r
;
else
fbond
=
0.0
;
energy
=
rk
*
dr
;
// apply force to each of 2 atoms
if
(
newton_bond
||
i1
<
nlocal
)
{
f
[
i1
][
0
]
+=
delx
*
fbond
;
f
[
i1
][
1
]
+=
dely
*
fbond
;
f
[
i1
][
2
]
+=
delz
*
fbond
;
}
if
(
newton_bond
||
i2
<
nlocal
)
{
f
[
i2
][
0
]
-=
delx
*
fbond
;
f
[
i2
][
1
]
-=
dely
*
fbond
;
f
[
i2
][
2
]
-=
delz
*
fbond
;
}
}
/* ----------------------------------------------------------------------
apply harmonic angle restraints
---------------------------------------------------------------------- */
void
FixRestrain
::
restrain_angle
(
int
m
)
{
int
i1
,
i2
,
i3
;
double
delx1
,
dely1
,
delz1
,
delx2
,
dely2
,
delz2
;
double
f1
[
3
],
f3
[
3
];
double
dtheta
,
tk
;
double
rsq1
,
rsq2
,
r1
,
r2
,
c
,
s
,
a
,
a11
,
a12
,
a22
;
double
**
x
=
atom
->
x
;
double
**
f
=
atom
->
f
;
int
nlocal
=
atom
->
nlocal
;
int
newton_bond
=
force
->
newton_bond
;
double
delta
=
update
->
ntimestep
-
update
->
beginstep
;
if
(
delta
!=
0.0
)
delta
/=
update
->
endstep
-
update
->
beginstep
;
double
k
=
kstart
[
m
]
+
delta
*
(
kstop
[
m
]
-
kstart
[
m
]);
i1
=
atom
->
map
(
ids
[
m
][
0
]);
i2
=
atom
->
map
(
ids
[
m
][
1
]);
i3
=
atom
->
map
(
ids
[
m
][
2
]);
// newton_bond on: only processor owning i2 computes restraint
// newton_bond off: only processors owning any of i1-i3 computes restraint
if
(
newton_bond
)
{
if
(
i2
==
-
1
||
i2
>=
nlocal
)
return
;
if
(
i1
==
-
1
||
i3
==
-
1
)
{
char
str
[
128
];
sprintf
(
str
,
"Restrain atoms %d %d %d missing on proc %d at step "
BIGINT_FORMAT
,
ids
[
m
][
0
],
ids
[
m
][
1
],
ids
[
m
][
2
],
comm
->
me
,
update
->
ntimestep
);
error
->
one
(
FLERR
,
str
);
}
}
else
{
if
((
i1
==
-
1
||
i1
>=
nlocal
)
&&
(
i2
==
-
1
||
i2
>=
nlocal
)
&&
(
i3
==
-
1
||
i3
>=
nlocal
))
return
;
if
(
i1
==
-
1
||
i2
==
-
1
||
i3
==
-
1
)
{
char
str
[
128
];
sprintf
(
str
,
"Restrain atoms %d %d %d missing on proc %d at step "
BIGINT_FORMAT
,
ids
[
m
][
0
],
ids
[
m
][
1
],
ids
[
m
][
2
],
comm
->
me
,
update
->
ntimestep
);
error
->
one
(
FLERR
,
str
);
}
}
// 1st bond
delx1
=
x
[
i1
][
0
]
-
x
[
i2
][
0
];
dely1
=
x
[
i1
][
1
]
-
x
[
i2
][
1
];
delz1
=
x
[
i1
][
2
]
-
x
[
i2
][
2
];
domain
->
minimum_image
(
delx1
,
dely1
,
delz1
);
rsq1
=
delx1
*
delx1
+
dely1
*
dely1
+
delz1
*
delz1
;
r1
=
sqrt
(
rsq1
);
// 2nd bond
delx2
=
x
[
i3
][
0
]
-
x
[
i2
][
0
];
dely2
=
x
[
i3
][
1
]
-
x
[
i2
][
1
];
delz2
=
x
[
i3
][
2
]
-
x
[
i2
][
2
];
domain
->
minimum_image
(
delx2
,
dely2
,
delz2
);
rsq2
=
delx2
*
delx2
+
dely2
*
dely2
+
delz2
*
delz2
;
r2
=
sqrt
(
rsq2
);
// angle (cos and sin)
c
=
delx1
*
delx2
+
dely1
*
dely2
+
delz1
*
delz2
;
c
/=
r1
*
r2
;
if
(
c
>
1.0
)
c
=
1.0
;
if
(
c
<
-
1.0
)
c
=
-
1.0
;
s
=
sqrt
(
1.0
-
c
*
c
);
if
(
s
<
SMALL
)
s
=
SMALL
;
s
=
1.0
/
s
;
// force & energy
dtheta
=
acos
(
c
)
-
target
[
m
];
tk
=
k
*
dtheta
;
energy
=
tk
*
dtheta
;
a
=
-
2.0
*
tk
*
s
;
a11
=
a
*
c
/
rsq1
;
a12
=
-
a
/
(
r1
*
r2
);
a22
=
a
*
c
/
rsq2
;
f1
[
0
]
=
a11
*
delx1
+
a12
*
delx2
;
f1
[
1
]
=
a11
*
dely1
+
a12
*
dely2
;
f1
[
2
]
=
a11
*
delz1
+
a12
*
delz2
;
f3
[
0
]
=
a22
*
delx2
+
a12
*
delx1
;
f3
[
1
]
=
a22
*
dely2
+
a12
*
dely1
;
f3
[
2
]
=
a22
*
delz2
+
a12
*
delz1
;
// apply force to each of 3 atoms
if
(
newton_bond
||
i1
<
nlocal
)
{
f
[
i1
][
0
]
+=
f1
[
0
];
f
[
i1
][
1
]
+=
f1
[
1
];
f
[
i1
][
2
]
+=
f1
[
2
];
}
if
(
newton_bond
||
i2
<
nlocal
)
{
f
[
i2
][
0
]
-=
f1
[
0
]
+
f3
[
0
];
f
[
i2
][
1
]
-=
f1
[
1
]
+
f3
[
1
];
f
[
i2
][
2
]
-=
f1
[
2
]
+
f3
[
2
];
}
if
(
newton_bond
||
i3
<
nlocal
)
{
f
[
i3
][
0
]
+=
f3
[
0
];
f
[
i3
][
1
]
+=
f3
[
1
];
f
[
i3
][
2
]
+=
f3
[
2
];
}
}
/* ----------------------------------------------------------------------
apply dihedral restraints
adopted from dihedral_charmm
---------------------------------------------------------------------- */
void
FixRestrain
::
restrain_dihedral
(
int
m
)
{
int
i1
,
i2
,
i3
,
i4
,
i
,
mult
;
double
vb1x
,
vb1y
,
vb1z
,
vb2x
,
vb2y
,
vb2z
,
vb3x
,
vb3y
,
vb3z
,
vb2xm
,
vb2ym
,
vb2zm
;
double
f1
[
3
],
f2
[
3
],
f3
[
3
],
f4
[
3
];
double
ax
,
ay
,
az
,
bx
,
by
,
bz
,
rasq
,
rbsq
,
rgsq
,
rg
,
rginv
,
ra2inv
,
rb2inv
,
rabinv
;
double
df
,
df1
,
ddf1
,
fg
,
hg
,
fga
,
hgb
,
gaa
,
gbb
;
double
dtfx
,
dtfy
,
dtfz
,
dtgx
,
dtgy
,
dtgz
,
dthx
,
dthy
,
dthz
;
double
c
,
s
,
p
,
sx2
,
sy2
,
sz2
;
double
**
x
=
atom
->
x
;
double
**
f
=
atom
->
f
;
int
nlocal
=
atom
->
nlocal
;
int
newton_bond
=
force
->
newton_bond
;
double
delta
=
update
->
ntimestep
-
update
->
beginstep
;
if
(
delta
!=
0.0
)
delta
/=
update
->
endstep
-
update
->
beginstep
;
double
k
=
kstart
[
m
]
+
delta
*
(
kstop
[
m
]
-
kstart
[
m
]);
i1
=
atom
->
map
(
ids
[
m
][
0
]);
i2
=
atom
->
map
(
ids
[
m
][
1
]);
i3
=
atom
->
map
(
ids
[
m
][
2
]);
i4
=
atom
->
map
(
ids
[
m
][
3
]);
// newton_bond on: only processor owning i2 computes restraint
// newton_bond off: only processors owning any of i1-i4 computes restraint
if
(
newton_bond
)
{
if
(
i2
==
-
1
||
i2
>=
nlocal
)
return
;
if
(
i1
==
-
1
||
i3
==
-
1
||
i4
==
-
1
)
{
char
str
[
128
];
sprintf
(
str
,
"Restrain atoms %d %d %d %d missing on proc %d at step "
BIGINT_FORMAT
,
ids
[
m
][
0
],
ids
[
m
][
1
],
ids
[
m
][
2
],
ids
[
m
][
3
],
comm
->
me
,
update
->
ntimestep
);
error
->
one
(
FLERR
,
str
);
}
}
else
{
if
((
i1
==
-
1
||
i1
>=
nlocal
)
&&
(
i2
==
-
1
||
i2
>=
nlocal
)
&&
(
i3
==
-
1
||
i3
>=
nlocal
)
&&
(
i4
==
-
1
||
i3
>=
nlocal
))
return
;
if
(
i1
==
-
1
||
i2
==
-
1
||
i3
==
-
1
||
i4
==
-
1
)
{
char
str
[
128
];
sprintf
(
str
,
"Restrain atoms %d %d %d %d missing on proc %d at step "
BIGINT_FORMAT
,
ids
[
m
][
0
],
ids
[
m
][
1
],
ids
[
m
][
2
],
ids
[
m
][
3
],
comm
->
me
,
update
->
ntimestep
);
error
->
one
(
FLERR
,
str
);
}
}
// 1st bond
vb1x
=
x
[
i1
][
0
]
-
x
[
i2
][
0
];
vb1y
=
x
[
i1
][
1
]
-
x
[
i2
][
1
];
vb1z
=
x
[
i1
][
2
]
-
x
[
i2
][
2
];
domain
->
minimum_image
(
vb1x
,
vb1y
,
vb1z
);
// 2nd bond
vb2x
=
x
[
i3
][
0
]
-
x
[
i2
][
0
];
vb2y
=
x
[
i3
][
1
]
-
x
[
i2
][
1
];
vb2z
=
x
[
i3
][
2
]
-
x
[
i2
][
2
];
domain
->
minimum_image
(
vb2x
,
vb2y
,
vb2z
);
vb2xm
=
-
vb2x
;
vb2ym
=
-
vb2y
;
vb2zm
=
-
vb2z
;
domain
->
minimum_image
(
vb2xm
,
vb2ym
,
vb2zm
);
// 3rd bond
vb3x
=
x
[
i4
][
0
]
-
x
[
i3
][
0
];
vb3y
=
x
[
i4
][
1
]
-
x
[
i3
][
1
];
vb3z
=
x
[
i4
][
2
]
-
x
[
i3
][
2
];
domain
->
minimum_image
(
vb3x
,
vb3y
,
vb3z
);
ax
=
vb1y
*
vb2zm
-
vb1z
*
vb2ym
;
ay
=
vb1z
*
vb2xm
-
vb1x
*
vb2zm
;
az
=
vb1x
*
vb2ym
-
vb1y
*
vb2xm
;
bx
=
vb3y
*
vb2zm
-
vb3z
*
vb2ym
;
by
=
vb3z
*
vb2xm
-
vb3x
*
vb2zm
;
bz
=
vb3x
*
vb2ym
-
vb3y
*
vb2xm
;
rasq
=
ax
*
ax
+
ay
*
ay
+
az
*
az
;
rbsq
=
bx
*
bx
+
by
*
by
+
bz
*
bz
;
rgsq
=
vb2xm
*
vb2xm
+
vb2ym
*
vb2ym
+
vb2zm
*
vb2zm
;
rg
=
sqrt
(
rgsq
);
rginv
=
ra2inv
=
rb2inv
=
0.0
;
if
(
rg
>
0
)
rginv
=
1.0
/
rg
;
if
(
rasq
>
0
)
ra2inv
=
1.0
/
rasq
;
if
(
rbsq
>
0
)
rb2inv
=
1.0
/
rbsq
;
rabinv
=
sqrt
(
ra2inv
*
rb2inv
);
c
=
(
ax
*
bx
+
ay
*
by
+
az
*
bz
)
*
rabinv
;
s
=
rg
*
rabinv
*
(
ax
*
vb3x
+
ay
*
vb3y
+
az
*
vb3z
);
// error check
if
(
c
>
1.0
+
TOLERANCE
||
c
<
(
-
1.0
-
TOLERANCE
))
{
int
me
;
MPI_Comm_rank
(
world
,
&
me
);
if
(
screen
)
{
char
str
[
128
];
sprintf
(
str
,
"Restrain problem: %d "
BIGINT_FORMAT
" "
TAGINT_FORMAT
" "
TAGINT_FORMAT
" "
TAGINT_FORMAT
" "
TAGINT_FORMAT
,
me
,
update
->
ntimestep
,
atom
->
tag
[
i1
],
atom
->
tag
[
i2
],
atom
->
tag
[
i3
],
atom
->
tag
[
i4
]);
error
->
warning
(
FLERR
,
str
);
fprintf
(
screen
,
" 1st atom: %d %g %g %g
\n
"
,
me
,
x
[
i1
][
0
],
x
[
i1
][
1
],
x
[
i1
][
2
]);
fprintf
(
screen
,
" 2nd atom: %d %g %g %g
\n
"
,
me
,
x
[
i2
][
0
],
x
[
i2
][
1
],
x
[
i2
][
2
]);
fprintf
(
screen
,
" 3rd atom: %d %g %g %g
\n
"
,
me
,
x
[
i3
][
0
],
x
[
i3
][
1
],
x
[
i3
][
2
]);
fprintf
(
screen
,
" 4th atom: %d %g %g %g
\n
"
,
me
,
x
[
i4
][
0
],
x
[
i4
][
1
],
x
[
i4
][
2
]);
}
}
if
(
c
>
1.0
)
c
=
1.0
;
if
(
c
<
-
1.0
)
c
=
-
1.0
;
mult
=
1
;
// multiplicity
p
=
1.0
;
df1
=
0.0
;
for
(
i
=
0
;
i
<
mult
;
i
++
)
{
ddf1
=
p
*
c
-
df1
*
s
;
df1
=
p
*
s
+
df1
*
c
;
p
=
ddf1
;
}
p
=
p
*
cos_target
[
m
]
+
df1
*
sin_target
[
m
];
df1
=
df1
*
cos_target
[
m
]
-
ddf1
*
sin_target
[
m
];
df1
*=
-
mult
;
p
+=
1.0
;
energy
=
k
*
p
;
fg
=
vb1x
*
vb2xm
+
vb1y
*
vb2ym
+
vb1z
*
vb2zm
;
hg
=
vb3x
*
vb2xm
+
vb3y
*
vb2ym
+
vb3z
*
vb2zm
;
fga
=
fg
*
ra2inv
*
rginv
;
hgb
=
hg
*
rb2inv
*
rginv
;
gaa
=
-
ra2inv
*
rg
;
gbb
=
rb2inv
*
rg
;
dtfx
=
gaa
*
ax
;
dtfy
=
gaa
*
ay
;
dtfz
=
gaa
*
az
;
dtgx
=
fga
*
ax
-
hgb
*
bx
;
dtgy
=
fga
*
ay
-
hgb
*
by
;
dtgz
=
fga
*
az
-
hgb
*
bz
;
dthx
=
gbb
*
bx
;
dthy
=
gbb
*
by
;
dthz
=
gbb
*
bz
;
df
=
-
k
*
df1
;
sx2
=
df
*
dtgx
;
sy2
=
df
*
dtgy
;
sz2
=
df
*
dtgz
;
f1
[
0
]
=
df
*
dtfx
;
f1
[
1
]
=
df
*
dtfy
;
f1
[
2
]
=
df
*
dtfz
;
f2
[
0
]
=
sx2
-
f1
[
0
];
f2
[
1
]
=
sy2
-
f1
[
1
];
f2
[
2
]
=
sz2
-
f1
[
2
];
f4
[
0
]
=
df
*
dthx
;
f4
[
1
]
=
df
*
dthy
;
f4
[
2
]
=
df
*
dthz
;
f3
[
0
]
=
-
sx2
-
f4
[
0
];
f3
[
1
]
=
-
sy2
-
f4
[
1
];
f3
[
2
]
=
-
sz2
-
f4
[
2
];
// apply force to each of 4 atoms
if
(
newton_bond
||
i1
<
nlocal
)
{
f
[
i1
][
0
]
+=
f1
[
0
];
f
[
i1
][
1
]
+=
f1
[
1
];
f
[
i1
][
2
]
+=
f1
[
2
];
}
if
(
newton_bond
||
i2
<
nlocal
)
{
f
[
i2
][
0
]
+=
f2
[
0
];
f
[
i2
][
1
]
+=
f2
[
1
];
f
[
i2
][
2
]
+=
f2
[
2
];
}
if
(
newton_bond
||
i3
<
nlocal
)
{
f
[
i3
][
0
]
+=
f3
[
0
];
f
[
i3
][
1
]
+=
f3
[
1
];
f
[
i3
][
2
]
+=
f3
[
2
];
}
if
(
newton_bond
||
i4
<
nlocal
)
{
f
[
i4
][
0
]
+=
f4
[
0
];
f
[
i4
][
1
]
+=
f4
[
1
];
f
[
i4
][
2
]
+=
f4
[
2
];
}
}
/* ----------------------------------------------------------------------
potential energy of added force
------------------------------------------------------------------------- */
double
FixRestrain
::
compute_scalar
()
{
MPI_Allreduce
(
&
energy
,
&
energy_all
,
1
,
MPI_DOUBLE
,
MPI_SUM
,
world
);
return
energy_all
;
}
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