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dihedral_nharmonic.cpp
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rLAMMPS lammps
dihedral_nharmonic.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: Loukas D. Peristeras (Scienomics SARL)
[ based on dihedral_multi_harmonic.cpp Mathias Puetz (SNL) and friends ]
------------------------------------------------------------------------- */
#include <math.h>
#include <stdlib.h>
#include "dihedral_nharmonic.h"
#include "atom.h"
#include "neighbor.h"
#include "domain.h"
#include "comm.h"
#include "force.h"
#include "update.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
#define TOLERANCE 0.05
#define SMALL 0.001
/* ---------------------------------------------------------------------- */
DihedralNHarmonic
::
DihedralNHarmonic
(
LAMMPS
*
lmp
)
:
Dihedral
(
lmp
)
{}
/* ---------------------------------------------------------------------- */
DihedralNHarmonic
::~
DihedralNHarmonic
()
{
if
(
allocated
)
{
memory
->
destroy
(
setflag
);
for
(
int
i
=
1
;
i
<=
atom
->
ndihedraltypes
;
i
++
)
delete
[]
a
[
i
];
delete
[]
a
;
delete
[]
nterms
;
}
}
/* ---------------------------------------------------------------------- */
void
DihedralNHarmonic
::
compute
(
int
eflag
,
int
vflag
)
{
int
i1
,
i2
,
i3
,
i4
,
n
,
type
;
double
vb1x
,
vb1y
,
vb1z
,
vb2x
,
vb2y
,
vb2z
,
vb3x
,
vb3y
,
vb3z
,
vb2xm
,
vb2ym
,
vb2zm
;
double
edihedral
,
f1
[
3
],
f2
[
3
],
f3
[
3
],
f4
[
3
];
double
sb1
,
sb2
,
sb3
,
rb1
,
rb3
,
c0
,
b1mag2
,
b1mag
,
b2mag2
;
double
b2mag
,
b3mag2
,
b3mag
,
ctmp
,
c_
,
r12c1
,
c1mag
,
r12c2
;
double
c2mag
,
sc1
,
sc2
,
s1
,
s12
,
c
,
p
,
pd
,
a11
,
a22
;
double
a33
,
a12
,
a13
,
a23
,
sx2
,
sy2
,
sz2
;
double
s2
,
sin2
;
edihedral
=
0.0
;
if
(
eflag
||
vflag
)
ev_setup
(
eflag
,
vflag
);
else
evflag
=
0
;
double
**
x
=
atom
->
x
;
double
**
f
=
atom
->
f
;
int
**
dihedrallist
=
neighbor
->
dihedrallist
;
int
ndihedrallist
=
neighbor
->
ndihedrallist
;
int
nlocal
=
atom
->
nlocal
;
int
newton_bond
=
force
->
newton_bond
;
for
(
n
=
0
;
n
<
ndihedrallist
;
n
++
)
{
i1
=
dihedrallist
[
n
][
0
];
i2
=
dihedrallist
[
n
][
1
];
i3
=
dihedrallist
[
n
][
2
];
i4
=
dihedrallist
[
n
][
3
];
type
=
dihedrallist
[
n
][
4
];
// 1st bond
vb1x
=
x
[
i1
][
0
]
-
x
[
i2
][
0
];
vb1y
=
x
[
i1
][
1
]
-
x
[
i2
][
1
];
vb1z
=
x
[
i1
][
2
]
-
x
[
i2
][
2
];
// 2nd bond
vb2x
=
x
[
i3
][
0
]
-
x
[
i2
][
0
];
vb2y
=
x
[
i3
][
1
]
-
x
[
i2
][
1
];
vb2z
=
x
[
i3
][
2
]
-
x
[
i2
][
2
];
vb2xm
=
-
vb2x
;
vb2ym
=
-
vb2y
;
vb2zm
=
-
vb2z
;
// 3rd bond
vb3x
=
x
[
i4
][
0
]
-
x
[
i3
][
0
];
vb3y
=
x
[
i4
][
1
]
-
x
[
i3
][
1
];
vb3z
=
x
[
i4
][
2
]
-
x
[
i3
][
2
];
// c0 calculation
sb1
=
1.0
/
(
vb1x
*
vb1x
+
vb1y
*
vb1y
+
vb1z
*
vb1z
);
sb2
=
1.0
/
(
vb2x
*
vb2x
+
vb2y
*
vb2y
+
vb2z
*
vb2z
);
sb3
=
1.0
/
(
vb3x
*
vb3x
+
vb3y
*
vb3y
+
vb3z
*
vb3z
);
rb1
=
sqrt
(
sb1
);
rb3
=
sqrt
(
sb3
);
c0
=
(
vb1x
*
vb3x
+
vb1y
*
vb3y
+
vb1z
*
vb3z
)
*
rb1
*
rb3
;
// 1st and 2nd angle
b1mag2
=
vb1x
*
vb1x
+
vb1y
*
vb1y
+
vb1z
*
vb1z
;
b1mag
=
sqrt
(
b1mag2
);
b2mag2
=
vb2x
*
vb2x
+
vb2y
*
vb2y
+
vb2z
*
vb2z
;
b2mag
=
sqrt
(
b2mag2
);
b3mag2
=
vb3x
*
vb3x
+
vb3y
*
vb3y
+
vb3z
*
vb3z
;
b3mag
=
sqrt
(
b3mag2
);
ctmp
=
vb1x
*
vb2x
+
vb1y
*
vb2y
+
vb1z
*
vb2z
;
r12c1
=
1.0
/
(
b1mag
*
b2mag
);
c1mag
=
ctmp
*
r12c1
;
ctmp
=
vb2xm
*
vb3x
+
vb2ym
*
vb3y
+
vb2zm
*
vb3z
;
r12c2
=
1.0
/
(
b2mag
*
b3mag
);
c2mag
=
ctmp
*
r12c2
;
// cos and sin of 2 angles and final c
sin2
=
MAX
(
1.0
-
c1mag
*
c1mag
,
0.0
);
sc1
=
sqrt
(
sin2
);
if
(
sc1
<
SMALL
)
sc1
=
SMALL
;
sc1
=
1.0
/
sc1
;
sin2
=
MAX
(
1.0
-
c2mag
*
c2mag
,
0.0
);
sc2
=
sqrt
(
sin2
);
if
(
sc2
<
SMALL
)
sc2
=
SMALL
;
sc2
=
1.0
/
sc2
;
s1
=
sc1
*
sc1
;
s2
=
sc2
*
sc2
;
s12
=
sc1
*
sc2
;
c
=
(
c0
+
c1mag
*
c2mag
)
*
s12
;
// 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
,
"Dihedral 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
,
0
);
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
;
// force & energy
// p = sum (i=1,n) a_i * c**(i-1)
// pd = dp/dc
c_
=
c
;
p
=
this
->
a
[
type
][
0
];
pd
=
this
->
a
[
type
][
1
];
for
(
int
i
=
1
;
i
<
nterms
[
type
]
-
1
;
i
++
)
{
p
+=
c_
*
this
->
a
[
type
][
i
];
pd
+=
c_
*
static_cast
<
double
>
(
i
+
1
)
*
this
->
a
[
type
][
i
+
1
];
c_
*=
c
;
}
p
+=
c_
*
this
->
a
[
type
][
nterms
[
type
]
-
1
];
if
(
eflag
)
edihedral
=
p
;
c
=
c
*
pd
;
s12
=
s12
*
pd
;
a11
=
c
*
sb1
*
s1
;
a22
=
-
sb2
*
(
2.0
*
c0
*
s12
-
c
*
(
s1
+
s2
));
a33
=
c
*
sb3
*
s2
;
a12
=
-
r12c1
*
(
c1mag
*
c
*
s1
+
c2mag
*
s12
);
a13
=
-
rb1
*
rb3
*
s12
;
a23
=
r12c2
*
(
c2mag
*
c
*
s2
+
c1mag
*
s12
);
sx2
=
a12
*
vb1x
+
a22
*
vb2x
+
a23
*
vb3x
;
sy2
=
a12
*
vb1y
+
a22
*
vb2y
+
a23
*
vb3y
;
sz2
=
a12
*
vb1z
+
a22
*
vb2z
+
a23
*
vb3z
;
f1
[
0
]
=
a11
*
vb1x
+
a12
*
vb2x
+
a13
*
vb3x
;
f1
[
1
]
=
a11
*
vb1y
+
a12
*
vb2y
+
a13
*
vb3y
;
f1
[
2
]
=
a11
*
vb1z
+
a12
*
vb2z
+
a13
*
vb3z
;
f2
[
0
]
=
-
sx2
-
f1
[
0
];
f2
[
1
]
=
-
sy2
-
f1
[
1
];
f2
[
2
]
=
-
sz2
-
f1
[
2
];
f4
[
0
]
=
a13
*
vb1x
+
a23
*
vb2x
+
a33
*
vb3x
;
f4
[
1
]
=
a13
*
vb1y
+
a23
*
vb2y
+
a33
*
vb3y
;
f4
[
2
]
=
a13
*
vb1z
+
a23
*
vb2z
+
a33
*
vb3z
;
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
];
}
if
(
evflag
)
ev_tally
(
i1
,
i2
,
i3
,
i4
,
nlocal
,
newton_bond
,
edihedral
,
f1
,
f3
,
f4
,
vb1x
,
vb1y
,
vb1z
,
vb2x
,
vb2y
,
vb2z
,
vb3x
,
vb3y
,
vb3z
);
}
}
/* ---------------------------------------------------------------------- */
void
DihedralNHarmonic
::
allocate
()
{
allocated
=
1
;
int
n
=
atom
->
ndihedraltypes
;
memory
->
create
(
nterms
,
n
+
1
,
"dihedral:nt"
);
a
=
new
double
*
[
n
+
1
];
memory
->
create
(
setflag
,
n
+
1
,
"dihedral:setflag"
);
for
(
int
i
=
1
;
i
<=
n
;
i
++
)
setflag
[
i
]
=
0
;
}
/* ----------------------------------------------------------------------
set coeffs for one type
------------------------------------------------------------------------- */
void
DihedralNHarmonic
::
coeff
(
int
narg
,
char
**
arg
)
{
if
(
narg
<
4
)
error
->
all
(
FLERR
,
"Incorrect args for dihedral coefficients"
);
int
n
=
force
->
inumeric
(
FLERR
,
arg
[
1
]);
if
(
narg
!=
n
+
2
)
error
->
all
(
FLERR
,
"Incorrect args for dihedral coefficients"
);
if
(
!
allocated
)
allocate
();
int
ilo
,
ihi
;
force
->
bounds
(
arg
[
0
],
atom
->
ndihedraltypes
,
ilo
,
ihi
);
int
count
=
0
;
for
(
int
i
=
ilo
;
i
<=
ihi
;
i
++
)
{
a
[
i
]
=
new
double
[
n
];
nterms
[
i
]
=
n
;
for
(
int
j
=
0
;
j
<
n
;
j
++
)
{
a
[
i
][
j
]
=
force
->
numeric
(
FLERR
,
arg
[
2
+
j
]);
setflag
[
i
]
=
1
;
}
count
++
;
}
if
(
count
==
0
)
error
->
all
(
FLERR
,
"Incorrect args for dihedral coefficients"
);
}
/* ----------------------------------------------------------------------
proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void
DihedralNHarmonic
::
write_restart
(
FILE
*
fp
)
{
fwrite
(
&
nterms
[
1
],
sizeof
(
int
),
atom
->
ndihedraltypes
,
fp
);
for
(
int
i
=
1
;
i
<=
atom
->
ndihedraltypes
;
i
++
)
fwrite
(
a
[
i
],
sizeof
(
double
),
nterms
[
i
],
fp
);
}
/* ----------------------------------------------------------------------
proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void
DihedralNHarmonic
::
read_restart
(
FILE
*
fp
)
{
allocate
();
if
(
comm
->
me
==
0
)
fread
(
&
nterms
[
1
],
sizeof
(
int
),
atom
->
ndihedraltypes
,
fp
);
MPI_Bcast
(
&
nterms
[
1
],
atom
->
ndihedraltypes
,
MPI_INT
,
0
,
world
);
// allocate
for
(
int
i
=
1
;
i
<=
atom
->
ndihedraltypes
;
i
++
)
a
[
i
]
=
new
double
[
nterms
[
i
]];
if
(
comm
->
me
==
0
)
{
for
(
int
i
=
1
;
i
<=
atom
->
ndihedraltypes
;
i
++
)
fread
(
a
[
i
],
sizeof
(
double
),
nterms
[
i
],
fp
);
}
for
(
int
i
=
1
;
i
<=
atom
->
ndihedraltypes
;
i
++
)
MPI_Bcast
(
a
[
i
],
nterms
[
i
],
MPI_DOUBLE
,
0
,
world
);
for
(
int
i
=
1
;
i
<=
atom
->
ndihedraltypes
;
i
++
)
setflag
[
i
]
=
1
;
}
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