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pair_hbond_dreiding_lj_omp.cpp
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Created
Thu, Sep 5, 07:48
Size
9 KB
Mime Type
text/x-c++
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Sat, Sep 7, 07:48 (1 d, 23 h)
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blob
Format
Raw Data
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20548704
Attached To
rLAMMPS lammps
pair_hbond_dreiding_lj_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
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 "pair_hbond_dreiding_lj_omp.h"
#include "atom.h"
#include "atom_vec.h"
#include "molecule.h"
#include "comm.h"
#include "domain.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "math_const.h"
#include "math_special.h"
#include "suffix.h"
using
namespace
LAMMPS_NS
;
using
namespace
MathConst
;
using
namespace
MathSpecial
;
#define SMALL 0.001
/* ---------------------------------------------------------------------- */
PairHbondDreidingLJOMP
::
PairHbondDreidingLJOMP
(
LAMMPS
*
lmp
)
:
PairHbondDreidingLJ
(
lmp
),
ThrOMP
(
lmp
,
THR_PAIR
)
{
suffix_flag
|=
Suffix
::
OMP
;
respa_enable
=
0
;
hbcount_thr
=
hbeng_thr
=
NULL
;
}
/* ---------------------------------------------------------------------- */
PairHbondDreidingLJOMP
::~
PairHbondDreidingLJOMP
()
{
if
(
hbcount_thr
)
{
delete
[]
hbcount_thr
;
delete
[]
hbeng_thr
;
}
}
/* ---------------------------------------------------------------------- */
void
PairHbondDreidingLJOMP
::
compute
(
int
eflag
,
int
vflag
)
{
if
(
eflag
||
vflag
)
{
ev_setup
(
eflag
,
vflag
);
}
else
evflag
=
vflag_fdotr
=
0
;
const
int
nall
=
atom
->
nlocal
+
atom
->
nghost
;
const
int
nthreads
=
comm
->
nthreads
;
const
int
inum
=
list
->
inum
;
if
(
!
hbcount_thr
)
{
hbcount_thr
=
new
double
[
nthreads
];
hbeng_thr
=
new
double
[
nthreads
];
}
for
(
int
i
=
0
;
i
<
nthreads
;
++
i
)
{
hbcount_thr
[
i
]
=
0.0
;
hbeng_thr
[
i
]
=
0.0
;
}
#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
);
thr
->
timer
(
Timer
::
START
);
ev_setup_thr
(
eflag
,
vflag
,
nall
,
eatom
,
vatom
,
thr
);
if
(
evflag
)
{
if
(
eflag
)
{
if
(
force
->
newton_pair
)
eval
<
1
,
1
,
1
>
(
ifrom
,
ito
,
thr
);
else
eval
<
1
,
1
,
0
>
(
ifrom
,
ito
,
thr
);
}
else
{
if
(
force
->
newton_pair
)
eval
<
1
,
0
,
1
>
(
ifrom
,
ito
,
thr
);
else
eval
<
1
,
0
,
0
>
(
ifrom
,
ito
,
thr
);
}
}
else
{
if
(
force
->
newton_pair
)
eval
<
0
,
0
,
1
>
(
ifrom
,
ito
,
thr
);
else
eval
<
0
,
0
,
0
>
(
ifrom
,
ito
,
thr
);
}
thr
->
timer
(
Timer
::
PAIR
);
reduce_thr
(
this
,
eflag
,
vflag
,
thr
);
}
// end of omp parallel region
// reduce per thread hbond data
if
(
eflag_global
)
{
pvector
[
0
]
=
0.0
;
pvector
[
1
]
=
0.0
;
for
(
int
i
=
0
;
i
<
nthreads
;
++
i
)
{
pvector
[
0
]
+=
hbcount_thr
[
i
];
pvector
[
1
]
+=
hbeng_thr
[
i
];
}
}
}
template
<
int
EVFLAG
,
int
EFLAG
,
int
NEWTON_PAIR
>
void
PairHbondDreidingLJOMP
::
eval
(
int
iifrom
,
int
iito
,
ThrData
*
const
thr
)
{
int
i
,
j
,
k
,
m
,
ii
,
jj
,
kk
,
jnum
,
knum
,
itype
,
jtype
,
ktype
,
iatom
,
imol
;
tagint
tagprev
;
double
xtmp
,
ytmp
,
ztmp
,
delx
,
dely
,
delz
,
rsq
,
rsq1
,
rsq2
,
r1
,
r2
;
double
factor_hb
,
force_angle
,
force_kernel
,
evdwl
,
eng_lj
;
double
c
,
s
,
a
,
b
,
ac
,
a11
,
a12
,
a22
,
vx1
,
vx2
,
vy1
,
vy2
,
vz1
,
vz2
;
double
fi
[
3
],
fj
[
3
],
delr1
[
3
],
delr2
[
3
];
double
r2inv
,
r10inv
;
double
switch1
,
switch2
;
int
*
ilist
,
*
jlist
,
*
numneigh
,
**
firstneigh
;
const
tagint
*
klist
;
evdwl
=
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
tagint
*
_noalias
const
tag
=
atom
->
tag
;
const
int
*
_noalias
const
molindex
=
atom
->
molindex
;
const
int
*
_noalias
const
molatom
=
atom
->
molatom
;
const
int
*
_noalias
const
type
=
atom
->
type
;
const
double
*
_noalias
const
special_lj
=
force
->
special_lj
;
const
int
*
const
*
const
nspecial
=
atom
->
nspecial
;
const
tagint
*
const
*
const
special
=
atom
->
special
;
const
int
molecular
=
atom
->
molecular
;
Molecule
*
const
*
const
onemols
=
atom
->
avec
->
onemols
;
double
fxtmp
,
fytmp
,
fztmp
;
ilist
=
list
->
ilist
;
numneigh
=
list
->
numneigh
;
firstneigh
=
list
->
firstneigh
;
// ii = loop over donors
// jj = loop over acceptors
// kk = loop over hydrogens bonded to donor
int
hbcount
=
0
;
double
hbeng
=
0.0
;
for
(
ii
=
iifrom
;
ii
<
iito
;
++
ii
)
{
i
=
ilist
[
ii
];
itype
=
type
[
i
];
if
(
!
donor
[
itype
])
continue
;
if
(
molecular
==
1
)
{
klist
=
special
[
i
];
knum
=
nspecial
[
i
][
0
];
}
else
{
if
(
molindex
[
i
]
<
0
)
continue
;
imol
=
molindex
[
i
];
iatom
=
molatom
[
i
];
klist
=
onemols
[
imol
]
->
special
[
iatom
];
knum
=
onemols
[
imol
]
->
nspecial
[
iatom
][
0
];
tagprev
=
tag
[
i
]
-
iatom
-
1
;
}
jlist
=
firstneigh
[
i
];
jnum
=
numneigh
[
i
];
fxtmp
=
fytmp
=
fztmp
=
0.0
;
xtmp
=
x
[
i
].
x
;
ytmp
=
x
[
i
].
y
;
ztmp
=
x
[
i
].
z
;
for
(
jj
=
0
;
jj
<
jnum
;
jj
++
)
{
j
=
jlist
[
jj
];
factor_hb
=
special_lj
[
sbmask
(
j
)];
j
&=
NEIGHMASK
;
jtype
=
type
[
j
];
if
(
!
acceptor
[
jtype
])
continue
;
delx
=
xtmp
-
x
[
j
].
x
;
dely
=
ytmp
-
x
[
j
].
y
;
delz
=
ztmp
-
x
[
j
].
z
;
rsq
=
delx
*
delx
+
dely
*
dely
+
delz
*
delz
;
for
(
kk
=
0
;
kk
<
knum
;
kk
++
)
{
if
(
molecular
==
1
)
k
=
atom
->
map
(
klist
[
kk
]);
else
k
=
atom
->
map
(
klist
[
kk
]
+
tagprev
);
if
(
k
<
0
)
continue
;
ktype
=
type
[
k
];
m
=
type2param
[
itype
][
jtype
][
ktype
];
if
(
m
<
0
)
continue
;
const
Param
&
pm
=
params
[
m
];
if
(
rsq
<
pm
.
cut_outersq
)
{
delr1
[
0
]
=
xtmp
-
x
[
k
].
x
;
delr1
[
1
]
=
ytmp
-
x
[
k
].
y
;
delr1
[
2
]
=
ztmp
-
x
[
k
].
z
;
domain
->
minimum_image
(
delr1
);
rsq1
=
delr1
[
0
]
*
delr1
[
0
]
+
delr1
[
1
]
*
delr1
[
1
]
+
delr1
[
2
]
*
delr1
[
2
];
r1
=
sqrt
(
rsq1
);
delr2
[
0
]
=
x
[
j
].
x
-
x
[
k
].
x
;
delr2
[
1
]
=
x
[
j
].
y
-
x
[
k
].
y
;
delr2
[
2
]
=
x
[
j
].
z
-
x
[
k
].
z
;
domain
->
minimum_image
(
delr2
);
rsq2
=
delr2
[
0
]
*
delr2
[
0
]
+
delr2
[
1
]
*
delr2
[
1
]
+
delr2
[
2
]
*
delr2
[
2
];
r2
=
sqrt
(
rsq2
);
// angle (cos and sin)
c
=
delr1
[
0
]
*
delr2
[
0
]
+
delr1
[
1
]
*
delr2
[
1
]
+
delr1
[
2
]
*
delr2
[
2
];
c
/=
r1
*
r2
;
if
(
c
>
1.0
)
c
=
1.0
;
if
(
c
<
-
1.0
)
c
=
-
1.0
;
ac
=
acos
(
c
);
if
(
ac
>
pm
.
cut_angle
&&
ac
<
(
2.0
*
MY_PI
-
pm
.
cut_angle
))
{
s
=
sqrt
(
1.0
-
c
*
c
);
if
(
s
<
SMALL
)
s
=
SMALL
;
// LJ-specific kernel
r2inv
=
1.0
/
rsq
;
r10inv
=
r2inv
*
r2inv
*
r2inv
*
r2inv
*
r2inv
;
force_kernel
=
r10inv
*
(
pm
.
lj1
*
r2inv
-
pm
.
lj2
)
*
r2inv
*
powint
(
c
,
pm
.
ap
);
force_angle
=
pm
.
ap
*
r10inv
*
(
pm
.
lj3
*
r2inv
-
pm
.
lj4
)
*
powint
(
c
,
pm
.
ap
-
1
)
*
s
;
eng_lj
=
r10inv
*
(
pm
.
lj3
*
r2inv
-
pm
.
lj4
);
if
(
rsq
>
pm
.
cut_innersq
)
{
switch1
=
(
pm
.
cut_outersq
-
rsq
)
*
(
pm
.
cut_outersq
-
rsq
)
*
(
pm
.
cut_outersq
+
2.0
*
rsq
-
3.0
*
pm
.
cut_innersq
)
/
pm
.
denom_vdw
;
switch2
=
12.0
*
rsq
*
(
pm
.
cut_outersq
-
rsq
)
*
(
rsq
-
pm
.
cut_innersq
)
/
pm
.
denom_vdw
;
force_kernel
=
force_kernel
*
switch1
+
eng_lj
*
switch2
/
rsq
;
force_angle
*=
switch1
;
eng_lj
*=
switch1
;
}
if
(
EFLAG
)
{
evdwl
=
eng_lj
*
powint
(
c
,
pm
.
ap
);
evdwl
*=
factor_hb
;
}
a
=
factor_hb
*
force_angle
/
s
;
b
=
factor_hb
*
force_kernel
;
a11
=
a
*
c
/
rsq1
;
a12
=
-
a
/
(
r1
*
r2
);
a22
=
a
*
c
/
rsq2
;
vx1
=
a11
*
delr1
[
0
]
+
a12
*
delr2
[
0
];
vx2
=
a22
*
delr2
[
0
]
+
a12
*
delr1
[
0
];
vy1
=
a11
*
delr1
[
1
]
+
a12
*
delr2
[
1
];
vy2
=
a22
*
delr2
[
1
]
+
a12
*
delr1
[
1
];
vz1
=
a11
*
delr1
[
2
]
+
a12
*
delr2
[
2
];
vz2
=
a22
*
delr2
[
2
]
+
a12
*
delr1
[
2
];
fi
[
0
]
=
vx1
+
b
*
delx
;
fi
[
1
]
=
vy1
+
b
*
dely
;
fi
[
2
]
=
vz1
+
b
*
delz
;
fj
[
0
]
=
vx2
-
b
*
delx
;
fj
[
1
]
=
vy2
-
b
*
dely
;
fj
[
2
]
=
vz2
-
b
*
delz
;
fxtmp
+=
fi
[
0
];
fytmp
+=
fi
[
1
];
fztmp
+=
fi
[
2
];
f
[
j
].
x
+=
fj
[
0
];
f
[
j
].
y
+=
fj
[
1
];
f
[
j
].
z
+=
fj
[
2
];
f
[
k
].
x
-=
vx1
+
vx2
;
f
[
k
].
y
-=
vy1
+
vy2
;
f
[
k
].
z
-=
vz1
+
vz2
;
// KIJ instead of IJK b/c delr1/delr2 are both with respect to k
if
(
EVFLAG
)
ev_tally3_thr
(
this
,
k
,
i
,
j
,
evdwl
,
0.0
,
fi
,
fj
,
delr1
,
delr2
,
thr
);
if
(
EFLAG
)
{
hbcount
++
;
hbeng
+=
evdwl
;
}
}
}
}
}
f
[
i
].
x
+=
fxtmp
;
f
[
i
].
y
+=
fytmp
;
f
[
i
].
z
+=
fztmp
;
}
const
int
tid
=
thr
->
get_tid
();
hbcount_thr
[
tid
]
=
static_cast
<
double
>
(
hbcount
);
hbeng_thr
[
tid
]
=
hbeng
;
}
/* ---------------------------------------------------------------------- */
double
PairHbondDreidingLJOMP
::
memory_usage
()
{
double
bytes
=
memory_usage_thr
();
bytes
+=
comm
->
nthreads
*
2
*
sizeof
(
double
);
bytes
+=
PairHbondDreidingLJ
::
memory_usage
();
return
bytes
;
}
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