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rLAMMPS lammps
dihedral_nharmonic_omp.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 (Temple U)
------------------------------------------------------------------------- */
#include "math.h"
#include "dihedral_nharmonic_omp.h"
#include "atom.h"
#include "comm.h"
#include "neighbor.h"
#include "domain.h"
#include "force.h"
#include "update.h"
#include "error.h"
#include "suffix.h"
using
namespace
LAMMPS_NS
;
#define TOLERANCE 0.05
#define SMALL 0.001
/* ---------------------------------------------------------------------- */
DihedralNHarmonicOMP
::
DihedralNHarmonicOMP
(
class
LAMMPS
*
lmp
)
:
DihedralNHarmonic
(
lmp
),
ThrOMP
(
lmp
,
THR_DIHEDRAL
)
{
suffix_flag
|=
Suffix
::
OMP
;
}
/* ---------------------------------------------------------------------- */
void
DihedralNHarmonicOMP
::
compute
(
int
eflag
,
int
vflag
)
{
if
(
eflag
||
vflag
)
{
ev_setup
(
eflag
,
vflag
);
}
else
evflag
=
0
;
const
int
nall
=
atom
->
nlocal
+
atom
->
nghost
;
const
int
nthreads
=
comm
->
nthreads
;
const
int
inum
=
neighbor
->
ndihedrallist
;
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(eflag,vflag)
#endif
{
int
ifrom
,
ito
,
tid
;
loop_setup_thr
(
ifrom
,
ito
,
tid
,
inum
,
nthreads
);
ThrData
*
thr
=
fix
->
get_thr
(
tid
);
ev_setup_thr
(
eflag
,
vflag
,
nall
,
eatom
,
vatom
,
thr
);
if
(
inum
>
0
)
{
if
(
evflag
)
{
if
(
eflag
)
{
if
(
force
->
newton_bond
)
eval
<
1
,
1
,
1
>
(
ifrom
,
ito
,
thr
);
else
eval
<
1
,
1
,
0
>
(
ifrom
,
ito
,
thr
);
}
else
{
if
(
force
->
newton_bond
)
eval
<
1
,
0
,
1
>
(
ifrom
,
ito
,
thr
);
else
eval
<
1
,
0
,
0
>
(
ifrom
,
ito
,
thr
);
}
}
else
{
if
(
force
->
newton_bond
)
eval
<
0
,
0
,
1
>
(
ifrom
,
ito
,
thr
);
else
eval
<
0
,
0
,
0
>
(
ifrom
,
ito
,
thr
);
}
}
reduce_thr
(
this
,
eflag
,
vflag
,
thr
);
}
// end of omp parallel region
}
template
<
int
EVFLAG
,
int
EFLAG
,
int
NEWTON_BOND
>
void
DihedralNHarmonicOMP
::
eval
(
int
nfrom
,
int
nto
,
ThrData
*
const
thr
)
{
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
;
const
dbl3_t
*
_noalias
const
x
=
(
dbl3_t
*
)
atom
->
x
[
0
];
dbl3_t
*
_noalias
const
f
=
(
dbl3_t
*
)
thr
->
get_f
()[
0
];
const
int5_t
*
_noalias
const
dihedrallist
=
(
int5_t
*
)
neighbor
->
dihedrallist
[
0
];
const
int
nlocal
=
atom
->
nlocal
;
for
(
n
=
nfrom
;
n
<
nto
;
n
++
)
{
i1
=
dihedrallist
[
n
].
a
;
i2
=
dihedrallist
[
n
].
b
;
i3
=
dihedrallist
[
n
].
c
;
i4
=
dihedrallist
[
n
].
d
;
type
=
dihedrallist
[
n
].
t
;
// 1st bond
vb1x
=
x
[
i1
].
x
-
x
[
i2
].
x
;
vb1y
=
x
[
i1
].
y
-
x
[
i2
].
y
;
vb1z
=
x
[
i1
].
z
-
x
[
i2
].
z
;
// 2nd bond
vb2x
=
x
[
i3
].
x
-
x
[
i2
].
x
;
vb2y
=
x
[
i3
].
y
-
x
[
i2
].
y
;
vb2z
=
x
[
i3
].
z
-
x
[
i2
].
z
;
vb2xm
=
-
vb2x
;
vb2ym
=
-
vb2y
;
vb2zm
=
-
vb2z
;
// 3rd bond
vb3x
=
x
[
i4
].
x
-
x
[
i3
].
x
;
vb3y
=
x
[
i4
].
y
-
x
[
i3
].
y
;
vb3z
=
x
[
i4
].
z
-
x
[
i3
].
z
;
// 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
=
comm
->
me
;
if
(
screen
)
{
char
str
[
128
];
sprintf
(
str
,
"Dihedral problem: %d/%d "
BIGINT_FORMAT
" %d %d %d %d"
,
me
,
thr
->
get_tid
(),
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
].
x
,
x
[
i1
].
y
,
x
[
i1
].
z
);
fprintf
(
screen
,
" 2nd atom: %d %g %g %g
\n
"
,
me
,
x
[
i2
].
x
,
x
[
i2
].
y
,
x
[
i2
].
z
);
fprintf
(
screen
,
" 3rd atom: %d %g %g %g
\n
"
,
me
,
x
[
i3
].
x
,
x
[
i3
].
y
,
x
[
i3
].
z
);
fprintf
(
screen
,
" 4th atom: %d %g %g %g
\n
"
,
me
,
x
[
i4
].
x
,
x
[
i4
].
y
,
x
[
i4
].
z
);
}
}
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
=
a
[
type
][
0
];
pd
=
a
[
type
][
1
];
for
(
int
i
=
1
;
i
<
nterms
[
type
]
-
1
;
i
++
)
{
p
+=
c_
*
a
[
type
][
i
];
pd
+=
c_
*
static_cast
<
double
>
(
i
+
1
)
*
a
[
type
][
i
+
1
];
c_
*=
c
;
}
p
+=
c_
*
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
].
x
+=
f1
[
0
];
f
[
i1
].
y
+=
f1
[
1
];
f
[
i1
].
z
+=
f1
[
2
];
}
if
(
NEWTON_BOND
||
i2
<
nlocal
)
{
f
[
i2
].
x
+=
f2
[
0
];
f
[
i2
].
y
+=
f2
[
1
];
f
[
i2
].
z
+=
f2
[
2
];
}
if
(
NEWTON_BOND
||
i3
<
nlocal
)
{
f
[
i3
].
x
+=
f3
[
0
];
f
[
i3
].
y
+=
f3
[
1
];
f
[
i3
].
z
+=
f3
[
2
];
}
if
(
NEWTON_BOND
||
i4
<
nlocal
)
{
f
[
i4
].
x
+=
f4
[
0
];
f
[
i4
].
y
+=
f4
[
1
];
f
[
i4
].
z
+=
f4
[
2
];
}
if
(
EVFLAG
)
ev_tally_thr
(
this
,
i1
,
i2
,
i3
,
i4
,
nlocal
,
NEWTON_BOND
,
edihedral
,
f1
,
f3
,
f4
,
vb1x
,
vb1y
,
vb1z
,
vb2x
,
vb2y
,
vb2z
,
vb3x
,
vb3y
,
vb3z
,
thr
);
}
}
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