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improper_cossq_omp.cpp
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Fri, May 24, 19:41
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text/x-c++
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Sun, May 26, 19:41 (2 d)
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rLAMMPS lammps
improper_cossq_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 "improper_cossq_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
/* ---------------------------------------------------------------------- */
ImproperCossqOMP
::
ImproperCossqOMP
(
class
LAMMPS
*
lmp
)
:
ImproperCossq
(
lmp
),
ThrOMP
(
lmp
,
THR_IMPROPER
)
{
suffix_flag
|=
Suffix
::
OMP
;
}
/* ---------------------------------------------------------------------- */
void
ImproperCossqOMP
::
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
->
nimproperlist
;
#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
(
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
ImproperCossqOMP
::
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
;
double
eimproper
,
f1
[
3
],
f2
[
3
],
f3
[
3
],
f4
[
3
];
double
rjisq
,
rji
,
rlksq
,
rlk
,
cosphi
,
angfac
;
double
cjiji
,
clkji
,
clklk
,
cfact1
,
cfact2
,
cfact3
;
eimproper
=
0.0
;
const
double
*
const
*
const
x
=
atom
->
x
;
double
*
const
*
const
f
=
thr
->
get_f
();
const
int
*
const
*
const
improperlist
=
neighbor
->
improperlist
;
const
int
nlocal
=
atom
->
nlocal
;
for
(
n
=
nfrom
;
n
<
nto
;
n
++
)
{
i1
=
improperlist
[
n
][
0
];
i2
=
improperlist
[
n
][
1
];
i3
=
improperlist
[
n
][
2
];
i4
=
improperlist
[
n
][
3
];
type
=
improperlist
[
n
][
4
];
/* separation vector between i1 and i2, (i2-i1) */
vb1x
=
x
[
i2
][
0
]
-
x
[
i1
][
0
];
vb1y
=
x
[
i2
][
1
]
-
x
[
i1
][
1
];
vb1z
=
x
[
i2
][
2
]
-
x
[
i1
][
2
];
rjisq
=
vb1x
*
vb1x
+
vb1y
*
vb1y
+
vb1z
*
vb1z
;
rji
=
sqrt
(
rjisq
);
/* separation vector between i2 and i3 (i3-i2) */
vb2x
=
x
[
i3
][
0
]
-
x
[
i2
][
0
];
vb2y
=
x
[
i3
][
1
]
-
x
[
i2
][
1
];
vb2z
=
x
[
i3
][
2
]
-
x
[
i2
][
2
];
/* separation vector between i3 and i4, (i4-i3) */
vb3x
=
x
[
i4
][
0
]
-
x
[
i3
][
0
];
vb3y
=
x
[
i4
][
1
]
-
x
[
i3
][
1
];
vb3z
=
x
[
i4
][
2
]
-
x
[
i3
][
2
];
rlksq
=
vb3x
*
vb3x
+
vb3y
*
vb3y
+
vb3z
*
vb3z
;
rlk
=
sqrt
(
rlksq
);
cosphi
=
(
vb3x
*
vb1x
+
vb3y
*
vb1y
+
vb3z
*
vb1z
)
/
(
rji
*
rlk
);
/* Check that cos(phi) is in the correct limits. */
if
(
cosphi
>
1.0
+
TOLERANCE
||
cosphi
<
(
-
1.0
-
TOLERANCE
))
{
int
me
=
comm
->
me
;
if
(
screen
)
{
char
str
[
128
];
sprintf
(
str
,
"Improper 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
][
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
]);
}
/* Apply corrections to round-off errors. */
if
(
cosphi
>
1.0
)
cosphi
-=
SMALL
;
if
(
cosphi
<
-
1.0
)
cosphi
+=
SMALL
;
/* Calculate the angle: */
double
torangle
=
acos
(
cosphi
);
cosphi
=
cos
(
torangle
-
chi
[
type
]);
if
(
EFLAG
)
eimproper
=
0.5
*
k
[
type
]
*
cosphi
*
cosphi
;
/*
printf("The tags: %d-%d-%d-%d, of type %d .\n",atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4],type);
printf("The ji vector: %f, %f, %f.\nThe lk vector: %f, %f, %f.\n", vb1x,vb1y,vb1z,vb3x,vb3y,vb3z);
printf("The cosine of the angle: %-1.16e.\n", cosphi);
printf("The energy of the improper: %-1.16e with prefactor %-1.16e.\n", eimproper, 0.5*k[type]);
*/
/* Work out forces. */
angfac
=
-
k
[
type
]
*
cosphi
;
cjiji
=
rjisq
;
clklk
=
rlksq
;
/*CLKJI = RXLK * RXJI + RYLK * RYJI + RZLK * RZJI */
clkji
=
vb3x
*
vb1x
+
vb3y
*
vb1y
+
vb3z
*
vb1z
;
/*CFACT1 = CLKLK * CJIJI
CFACT1 = SQRT(CFACT1)
CFACT1 = ANGFAC / CFACT1*/
cfact1
=
angfac
/
sqrt
(
clklk
*
cjiji
);
/*CFACT2 = CLKJI / CLKLK*/
cfact2
=
clkji
/
clklk
;
/*CFACT3 = CLKJI / CJIJI*/
cfact3
=
clkji
/
cjiji
;
/*FIX = -RXLK + CFACT3 * RXJI
FIY = -RYLK + CFACT3 * RYJI
FIZ = -RZLK + CFACT3 * RZJI*/
f1
[
0
]
=
-
vb3x
+
cfact3
*
vb1x
;
f1
[
1
]
=
-
vb3y
+
cfact3
*
vb1y
;
f1
[
2
]
=
-
vb3z
+
cfact3
*
vb1z
;
/*FJX = -FIX
FJY = -FIY
FJZ = -FIZ*/
f2
[
0
]
=
-
f1
[
0
];
f2
[
1
]
=
-
f1
[
1
];
f2
[
2
]
=
-
f1
[
2
];
/*FKX = CFACT2 * RXLK - RXJI
FKY = CFACT2 * RYLK - RYJI
FKZ = CFACT2 * RZLK - RZJI*/
f3
[
0
]
=
cfact2
*
vb3x
-
vb1x
;
f3
[
1
]
=
cfact2
*
vb3y
-
vb1y
;
f3
[
2
]
=
cfact2
*
vb3z
-
vb1z
;
/*FLX = -FKX
FLY = -FKY
FLZ = -FKZ*/
f4
[
0
]
=
-
f3
[
0
];
f4
[
1
]
=
-
f3
[
1
];
f4
[
2
]
=
-
f3
[
2
];
/*FIX = FIX * CFACT1
FIY = FIY * CFACT1
FIZ = FIZ * CFACT1*/
f1
[
0
]
*=
cfact1
;
f1
[
1
]
*=
cfact1
;
f1
[
2
]
*=
cfact1
;
/*FJX = FJX * CFACT1
FJY = FJY * CFACT1
FJZ = FJZ * CFACT1*/
f2
[
0
]
*=
cfact1
;
f2
[
1
]
*=
cfact1
;
f2
[
2
]
*=
cfact1
;
/*FKX = FKX * CFACT1
FKY = FKY * CFACT1
FKZ = FKZ * CFACT1*/
f3
[
0
]
*=
cfact1
;
f3
[
1
]
*=
cfact1
;
f3
[
2
]
*=
cfact1
;
/*FLX = FLX * CFACT1
FLY = FLY * CFACT1
FLZ = FLZ * CFACT1*/
f4
[
0
]
*=
cfact1
;
f4
[
1
]
*=
cfact1
;
f4
[
2
]
*=
cfact1
;
/* 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_thr
(
this
,
i1
,
i2
,
i3
,
i4
,
nlocal
,
NEWTON_BOND
,
eimproper
,
f1
,
f3
,
f4
,
-
vb1x
,
-
vb1y
,
-
vb1z
,
vb2x
,
vb2y
,
vb2z
,
vb3x
,
vb3y
,
vb3z
,
thr
);
}
}
}
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