Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F88669196
dihedral_multi_harmonic_omp.cpp
No One
Temporary
Actions
Download File
Edit File
Delete File
View Transforms
Subscribe
Mute Notifications
Award Token
Subscribers
None
File Metadata
Details
File Info
Storage
Attached
Created
Sun, Oct 20, 02:06
Size
11 KB
Mime Type
text/x-c++
Expires
Tue, Oct 22, 02:06 (2 d)
Engine
blob
Format
Raw Data
Handle
21805389
Attached To
rLAMMPS lammps
dihedral_multi_harmonic_omp.cpp
View Options
/* ----------------------------------------------------------------------
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: Mathias Puetz (SNL) and friends
------------------------------------------------------------------------- */
#include "math.h"
#include "stdlib.h"
#include "dihedral_multi_harmonic_omp.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"
#if defined(_OPENMP)
#include <omp.h>
#endif
using
namespace
LAMMPS_NS
;
#define MIN(A,B) ((A) < (B)) ? (A) : (B)
#define MAX(A,B) ((A) > (B)) ? (A) : (B)
#define TOLERANCE 0.05
#define SMALL 0.001
/* ---------------------------------------------------------------------- */
DihedralMultiHarmonicOMP
::
DihedralMultiHarmonicOMP
(
LAMMPS
*
lmp
)
:
DihedralOMP
(
lmp
)
{}
/* ---------------------------------------------------------------------- */
DihedralMultiHarmonicOMP
::~
DihedralMultiHarmonicOMP
()
{
if
(
allocated
)
{
memory
->
sfree
(
setflag
);
memory
->
sfree
(
a1
);
memory
->
sfree
(
a2
);
memory
->
sfree
(
a3
);
memory
->
sfree
(
a4
);
memory
->
sfree
(
a5
);
}
}
/* ---------------------------------------------------------------------- */
void
DihedralMultiHarmonicOMP
::
compute
(
int
eflag
,
int
vflag
)
{
if
(
eflag
||
vflag
)
{
ev_setup
(
eflag
,
vflag
);
ev_setup_thr
(
eflag
,
vflag
);
}
else
evflag
=
0
;
if
(
evflag
)
{
if
(
eflag
)
{
if
(
force
->
newton_pair
)
return
eval
<
1
,
1
,
1
>
();
else
return
eval
<
1
,
1
,
0
>
();
}
else
{
if
(
force
->
newton_pair
)
return
eval
<
1
,
0
,
1
>
();
else
return
eval
<
1
,
0
,
0
>
();
}
}
else
{
if
(
force
->
newton_pair
)
return
eval
<
0
,
0
,
1
>
();
else
return
eval
<
0
,
0
,
0
>
();
}
}
template
<
int
EVFLAG
,
int
EFLAG
,
int
NEWTON_BOND
>
void
DihedralMultiHarmonicOMP
::
eval
()
{
#if defined(_OPENMP)
#pragma omp parallel default(shared)
#endif
{
int
i1
,
i2
,
i3
,
i4
,
n
,
type
,
tid
;
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
,
r12c1
,
c1mag
,
r12c2
;
double
c2mag
,
sc1
,
sc2
,
s1
,
s12
,
c
,
p
,
pd
,
a
,
a11
,
a22
;
double
a33
,
a12
,
a13
,
a23
,
sx2
,
sy2
,
sz2
;
double
s2
,
sin2
;
edihedral
=
0.0
;
const
int
nlocal
=
atom
->
nlocal
;
const
int
nall
=
nlocal
+
atom
->
nghost
;
const
int
nthreads
=
comm
->
nthreads
;
double
**
x
=
atom
->
x
;
double
**
f
=
atom
->
f
;
int
**
dihedrallist
=
neighbor
->
dihedrallist
;
int
ndihedrallist
=
neighbor
->
ndihedrallist
;
// loop over neighbors of my atoms
int
nfrom
,
nto
;
f
=
loop_setup_thr
(
f
,
nfrom
,
nto
,
tid
,
ndihedrallist
,
nall
,
nthreads
);
for
(
n
=
nfrom
;
n
<
nto
;
++
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
];
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
);
// 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
))
{
if
(
screen
)
{
char
str
[
128
];
sprintf
(
str
,
"Dihedral problem: %d %d %d %d %d %d"
,
comm
->
me
,
update
->
ntimestep
,
atom
->
tag
[
i1
],
atom
->
tag
[
i2
],
atom
->
tag
[
i3
],
atom
->
tag
[
i4
]);
error
->
warning
(
str
);
fprintf
(
screen
,
" 1st atom: %d %g %g %g
\n
"
,
comm
->
me
,
x
[
i1
][
0
],
x
[
i1
][
1
],
x
[
i1
][
2
]);
fprintf
(
screen
,
" 2nd atom: %d %g %g %g
\n
"
,
comm
->
me
,
x
[
i2
][
0
],
x
[
i2
][
1
],
x
[
i2
][
2
]);
fprintf
(
screen
,
" 3rd atom: %d %g %g %g
\n
"
,
comm
->
me
,
x
[
i3
][
0
],
x
[
i3
][
1
],
x
[
i3
][
2
]);
fprintf
(
screen
,
" 4th atom: %d %g %g %g
\n
"
,
comm
->
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=1,5) a_i * c**(i-1)
// pd = dp/dc
p
=
a1
[
type
]
+
c
*
(
a2
[
type
]
+
c
*
(
a3
[
type
]
+
c
*
(
a4
[
type
]
+
c
*
a5
[
type
])));
pd
=
a2
[
type
]
+
c
*
(
2.0
*
a3
[
type
]
+
c
*
(
3.0
*
a4
[
type
]
+
c
*
4.0
*
a5
[
type
]));
if
(
EFLAG
)
edihedral
=
p
;
a
=
pd
;
c
=
c
*
a
;
s12
=
s12
*
a
;
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_thr
(
i1
,
i2
,
i3
,
i4
,
nlocal
,
NEWTON_BOND
,
edihedral
,
f1
,
f3
,
f4
,
vb1x
,
vb1y
,
vb1z
,
vb2x
,
vb2y
,
vb2z
,
vb3x
,
vb3y
,
vb3z
,
tid
);
}
// reduce per thread forces into global force array.
force_reduce_thr
(
atom
->
f
,
nall
,
nthreads
,
tid
);
}
ev_reduce_thr
();
}
/* ---------------------------------------------------------------------- */
void
DihedralMultiHarmonicOMP
::
allocate
()
{
allocated
=
1
;
int
n
=
atom
->
ndihedraltypes
;
a1
=
(
double
*
)
memory
->
smalloc
((
n
+
1
)
*
sizeof
(
double
),
"dihedral:a1"
);
a2
=
(
double
*
)
memory
->
smalloc
((
n
+
1
)
*
sizeof
(
double
),
"dihedral:a2"
);
a3
=
(
double
*
)
memory
->
smalloc
((
n
+
1
)
*
sizeof
(
double
),
"dihedral:a3"
);
a4
=
(
double
*
)
memory
->
smalloc
((
n
+
1
)
*
sizeof
(
double
),
"dihedral:a4"
);
a5
=
(
double
*
)
memory
->
smalloc
((
n
+
1
)
*
sizeof
(
double
),
"dihedral:a5"
);
setflag
=
(
int
*
)
memory
->
smalloc
((
n
+
1
)
*
sizeof
(
int
),
"dihedral:setflag"
);
for
(
int
i
=
1
;
i
<=
n
;
i
++
)
setflag
[
i
]
=
0
;
}
/* ----------------------------------------------------------------------
set coeffs for one type
------------------------------------------------------------------------- */
void
DihedralMultiHarmonicOMP
::
coeff
(
int
which
,
int
narg
,
char
**
arg
)
{
if
(
which
>
0
)
return
;
if
(
narg
!=
6
)
error
->
all
(
"Incorrect args for dihedral coefficients"
);
if
(
!
allocated
)
allocate
();
int
ilo
,
ihi
;
force
->
bounds
(
arg
[
0
],
atom
->
ndihedraltypes
,
ilo
,
ihi
);
double
a1_one
=
force
->
numeric
(
arg
[
1
]);
double
a2_one
=
force
->
numeric
(
arg
[
2
]);
double
a3_one
=
force
->
numeric
(
arg
[
3
]);
double
a4_one
=
force
->
numeric
(
arg
[
4
]);
double
a5_one
=
force
->
numeric
(
arg
[
5
]);
int
count
=
0
;
for
(
int
i
=
ilo
;
i
<=
ihi
;
i
++
)
{
a1
[
i
]
=
a1_one
;
a2
[
i
]
=
a2_one
;
a3
[
i
]
=
a3_one
;
a4
[
i
]
=
a4_one
;
a5
[
i
]
=
a5_one
;
setflag
[
i
]
=
1
;
count
++
;
}
if
(
count
==
0
)
error
->
all
(
"Incorrect args for dihedral coefficients"
);
}
/* ----------------------------------------------------------------------
proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void
DihedralMultiHarmonicOMP
::
write_restart
(
FILE
*
fp
)
{
fwrite
(
&
a1
[
1
],
sizeof
(
double
),
atom
->
ndihedraltypes
,
fp
);
fwrite
(
&
a2
[
1
],
sizeof
(
double
),
atom
->
ndihedraltypes
,
fp
);
fwrite
(
&
a3
[
1
],
sizeof
(
double
),
atom
->
ndihedraltypes
,
fp
);
fwrite
(
&
a4
[
1
],
sizeof
(
double
),
atom
->
ndihedraltypes
,
fp
);
fwrite
(
&
a5
[
1
],
sizeof
(
double
),
atom
->
ndihedraltypes
,
fp
);
}
/* ----------------------------------------------------------------------
proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void
DihedralMultiHarmonicOMP
::
read_restart
(
FILE
*
fp
)
{
allocate
();
if
(
comm
->
me
==
0
)
{
fread
(
&
a1
[
1
],
sizeof
(
double
),
atom
->
ndihedraltypes
,
fp
);
fread
(
&
a2
[
1
],
sizeof
(
double
),
atom
->
ndihedraltypes
,
fp
);
fread
(
&
a3
[
1
],
sizeof
(
double
),
atom
->
ndihedraltypes
,
fp
);
fread
(
&
a4
[
1
],
sizeof
(
double
),
atom
->
ndihedraltypes
,
fp
);
fread
(
&
a5
[
1
],
sizeof
(
double
),
atom
->
ndihedraltypes
,
fp
);
}
MPI_Bcast
(
&
a1
[
1
],
atom
->
ndihedraltypes
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
a2
[
1
],
atom
->
ndihedraltypes
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
a3
[
1
],
atom
->
ndihedraltypes
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
a4
[
1
],
atom
->
ndihedraltypes
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
a5
[
1
],
atom
->
ndihedraltypes
,
MPI_DOUBLE
,
0
,
world
);
for
(
int
i
=
1
;
i
<=
atom
->
ndihedraltypes
;
i
++
)
setflag
[
i
]
=
1
;
}
/* ---------------------------------------------------------------------- */
double
DihedralMultiHarmonicOMP
::
memory_usage
()
{
const
int
n
=
atom
->
ntypes
;
double
bytes
=
DihedralOMP
::
memory_usage
();
bytes
+=
9
*
((
n
+
1
)
*
(
n
+
1
)
*
sizeof
(
double
)
+
(
n
+
1
)
*
sizeof
(
double
*
));
bytes
+=
1
*
((
n
+
1
)
*
(
n
+
1
)
*
sizeof
(
int
)
+
(
n
+
1
)
*
sizeof
(
int
*
));
return
bytes
;
}
Event Timeline
Log In to Comment