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rLAMMPS lammps
dihedral_fourier.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_charmm.cpp Paul Crozier (SNL) ]
------------------------------------------------------------------------- */
#include <mpi.h>
#include <math.h>
#include <stdlib.h>
#include "dihedral_fourier.h"
#include "atom.h"
#include "comm.h"
#include "neighbor.h"
#include "domain.h"
#include "force.h"
#include "pair.h"
#include "update.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
using
namespace
MathConst
;
#define TOLERANCE 0.05
/* ---------------------------------------------------------------------- */
DihedralFourier
::
DihedralFourier
(
LAMMPS
*
lmp
)
:
Dihedral
(
lmp
)
{}
/* ---------------------------------------------------------------------- */
DihedralFourier
::~
DihedralFourier
()
{
if
(
allocated
)
{
memory
->
destroy
(
setflag
);
memory
->
destroy
(
nterms
);
for
(
int
i
=
1
;
i
<=
atom
->
ndihedraltypes
;
i
++
)
{
if
(
k
[
i
]
)
delete
[]
k
[
i
];
if
(
multiplicity
[
i
]
)
delete
[]
multiplicity
[
i
];
if
(
shift
[
i
]
)
delete
[]
shift
[
i
];
if
(
cos_shift
[
i
]
)
delete
[]
cos_shift
[
i
];
if
(
sin_shift
[
i
]
)
delete
[]
sin_shift
[
i
];
}
delete
[]
k
;
delete
[]
multiplicity
;
delete
[]
shift
;
delete
[]
cos_shift
;
delete
[]
sin_shift
;
}
}
/* ---------------------------------------------------------------------- */
void
DihedralFourier
::
compute
(
int
eflag
,
int
vflag
)
{
int
i1
,
i2
,
i3
,
i4
,
i
,
j
,
m
,
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
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
;
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
];
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
,
"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 and energy
// p = sum(i=1,nterms) k_i*(1+cos(n_i*phi-d_i)
// dp = dp / dphi
edihedral
=
0.0
;
df
=
0.0
;
for
(
j
=
0
;
j
<
nterms
[
type
];
j
++
)
{
m
=
multiplicity
[
type
][
j
];
p_
=
1.0
;
ddf1_
=
df1_
=
0.0
;
for
(
i
=
0
;
i
<
m
;
i
++
)
{
ddf1_
=
p_
*
c
-
df1_
*
s
;
df1_
=
p_
*
s
+
df1_
*
c
;
p_
=
ddf1_
;
}
p_
=
p_
*
cos_shift
[
type
][
j
]
+
df1_
*
sin_shift
[
type
][
j
];
df1_
=
df1_
*
cos_shift
[
type
][
j
]
-
ddf1_
*
sin_shift
[
type
][
j
];
df1_
*=
-
m
;
p_
+=
1.0
;
if
(
m
==
0
)
{
p_
=
1.0
+
cos_shift
[
type
][
j
];
df1_
=
0.0
;
}
if
(
eflag
)
edihedral
+=
k
[
type
][
j
]
*
p_
;
df
+=
(
-
k
[
type
][
j
]
*
df1_
);
}
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
;
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
];
}
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
DihedralFourier
::
allocate
()
{
allocated
=
1
;
int
n
=
atom
->
ndihedraltypes
;
memory
->
create
(
nterms
,
n
+
1
,
"dihedral:nterms"
);
k
=
new
double
*
[
n
+
1
];
multiplicity
=
new
int
*
[
n
+
1
];
shift
=
new
double
*
[
n
+
1
];
cos_shift
=
new
double
*
[
n
+
1
];
sin_shift
=
new
double
*
[
n
+
1
];
for
(
int
i
=
1
;
i
<=
n
;
i
++
)
{
k
[
i
]
=
shift
[
i
]
=
cos_shift
[
i
]
=
sin_shift
[
i
]
=
0
;
multiplicity
[
i
]
=
0
;
}
memory
->
create
(
setflag
,
n
+
1
,
"dihedral:setflag"
);
for
(
int
i
=
1
;
i
<=
n
;
i
++
)
setflag
[
i
]
=
0
;
}
/* ----------------------------------------------------------------------
set coeffs for one type
------------------------------------------------------------------------- */
void
DihedralFourier
::
coeff
(
int
narg
,
char
**
arg
)
{
if
(
narg
<
4
)
error
->
all
(
FLERR
,
"Incorrect args for dihedral coefficients"
);
if
(
!
allocated
)
allocate
();
int
ilo
,
ihi
;
force
->
bounds
(
arg
[
0
],
atom
->
ndihedraltypes
,
ilo
,
ihi
);
// require integer values of shift for backwards compatibility
// arbitrary phase angle shift could be allowed, but would break
// backwards compatibility and is probably not needed
double
k_one
;
int
multiplicity_one
;
double
shift_one
;
int
nterms_one
=
force
->
inumeric
(
FLERR
,
arg
[
1
]);
if
(
nterms_one
<
1
)
error
->
all
(
FLERR
,
"Incorrect number of terms arg for dihedral coefficients"
);
if
(
2
+
3
*
nterms_one
<
narg
)
error
->
all
(
FLERR
,
"Incorrect number of arguments for dihedral coefficients"
);
int
count
=
0
;
for
(
int
i
=
ilo
;
i
<=
ihi
;
i
++
)
{
nterms
[
i
]
=
nterms_one
;
k
[
i
]
=
new
double
[
nterms_one
];
multiplicity
[
i
]
=
new
int
[
nterms_one
];
shift
[
i
]
=
new
double
[
nterms_one
];
cos_shift
[
i
]
=
new
double
[
nterms_one
];
sin_shift
[
i
]
=
new
double
[
nterms_one
];
for
(
int
j
=
0
;
j
<
nterms_one
;
j
++
)
{
int
offset
=
1
+
3
*
j
;
k_one
=
force
->
numeric
(
FLERR
,
arg
[
offset
+
1
]);
multiplicity_one
=
force
->
inumeric
(
FLERR
,
arg
[
offset
+
2
]);
shift_one
=
force
->
numeric
(
FLERR
,
arg
[
offset
+
3
]);
k
[
i
][
j
]
=
k_one
;
multiplicity
[
i
][
j
]
=
multiplicity_one
;
shift
[
i
][
j
]
=
shift_one
;
cos_shift
[
i
][
j
]
=
cos
(
MY_PI
*
shift_one
/
180.0
);
sin_shift
[
i
][
j
]
=
sin
(
MY_PI
*
shift_one
/
180.0
);
}
setflag
[
i
]
=
1
;
count
++
;
}
if
(
count
==
0
)
error
->
all
(
FLERR
,
"Incorrect args for dihedral coefficients"
);
}
/* ----------------------------------------------------------------------
proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void
DihedralFourier
::
write_restart
(
FILE
*
fp
)
{
fwrite
(
&
nterms
[
1
],
sizeof
(
int
),
atom
->
ndihedraltypes
,
fp
);
for
(
int
i
=
1
;
i
<=
atom
->
ndihedraltypes
;
i
++
)
{
fwrite
(
k
[
i
],
sizeof
(
double
),
nterms
[
i
],
fp
);
fwrite
(
multiplicity
[
i
],
sizeof
(
int
),
nterms
[
i
],
fp
);
fwrite
(
shift
[
i
],
sizeof
(
double
),
nterms
[
i
],
fp
);
}
}
/* ----------------------------------------------------------------------
proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void
DihedralFourier
::
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
++
)
{
k
[
i
]
=
new
double
[
nterms
[
i
]];
multiplicity
[
i
]
=
new
int
[
nterms
[
i
]];
shift
[
i
]
=
new
double
[
nterms
[
i
]];
cos_shift
[
i
]
=
new
double
[
nterms
[
i
]];
sin_shift
[
i
]
=
new
double
[
nterms
[
i
]];
}
if
(
comm
->
me
==
0
)
{
for
(
int
i
=
1
;
i
<=
atom
->
ndihedraltypes
;
i
++
)
{
fread
(
k
[
i
],
sizeof
(
double
),
nterms
[
i
],
fp
);
fread
(
multiplicity
[
i
],
sizeof
(
int
),
nterms
[
i
],
fp
);
fread
(
shift
[
i
],
sizeof
(
double
),
nterms
[
i
],
fp
);
}
}
for
(
int
i
=
1
;
i
<=
atom
->
ndihedraltypes
;
i
++
)
{
MPI_Bcast
(
k
[
i
],
nterms
[
i
],
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
multiplicity
[
i
],
nterms
[
i
],
MPI_INT
,
0
,
world
);
MPI_Bcast
(
shift
[
i
],
nterms
[
i
],
MPI_DOUBLE
,
0
,
world
);
}
for
(
int
i
=
1
;
i
<=
atom
->
ndihedraltypes
;
i
++
)
{
setflag
[
i
]
=
1
;
for
(
int
j
=
0
;
j
<
nterms
[
i
];
j
++
)
{
cos_shift
[
i
][
j
]
=
cos
(
MY_PI
*
shift
[
i
][
j
]
/
180.0
);
sin_shift
[
i
][
j
]
=
sin
(
MY_PI
*
shift
[
i
][
j
]
/
180.0
);
}
}
}
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