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rLAMMPS lammps
dihedral_opls_intel.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: W. Michael Brown (Intel)
------------------------------------------------------------------------- */
#include "mpi.h"
#include "math.h"
#include "dihedral_opls_intel.h"
#include "atom.h"
#include "comm.h"
#include "memory.h"
#include "neighbor.h"
#include "domain.h"
#include "force.h"
#include "pair.h"
#include "update.h"
#include "error.h"
#include "suffix.h"
using
namespace
LAMMPS_NS
;
#define PTOLERANCE (flt_t)1.05
#define MTOLERANCE (flt_t)-1.05
#define SMALL2 (flt_t)0.000001
#define INVSMALL (flt_t)1000.0
#define SMALLER2 (flt_t)0.0000000001
#define INVSMALLER (flt_t)100000.0
typedef
struct
{
int
a
,
b
,
c
,
d
,
t
;
}
int5_t
;
/* ---------------------------------------------------------------------- */
DihedralOPLSIntel
::
DihedralOPLSIntel
(
class
LAMMPS
*
lmp
)
:
DihedralOPLS
(
lmp
)
{
suffix_flag
|=
Suffix
::
INTEL
;
}
/* ---------------------------------------------------------------------- */
void
DihedralOPLSIntel
::
compute
(
int
eflag
,
int
vflag
)
{
#ifdef _LMP_INTEL_OFFLOAD
if
(
_use_base
)
{
DihedralOPLS
::
compute
(
eflag
,
vflag
);
return
;
}
#endif
if
(
fix
->
precision
()
==
FixIntel
::
PREC_MODE_MIXED
)
compute
<
float
,
double
>
(
eflag
,
vflag
,
fix
->
get_mixed_buffers
(),
force_const_single
);
else
if
(
fix
->
precision
()
==
FixIntel
::
PREC_MODE_DOUBLE
)
compute
<
double
,
double
>
(
eflag
,
vflag
,
fix
->
get_double_buffers
(),
force_const_double
);
else
compute
<
float
,
float
>
(
eflag
,
vflag
,
fix
->
get_single_buffers
(),
force_const_single
);
}
/* ---------------------------------------------------------------------- */
template
<
class
flt_t
,
class
acc_t
>
void
DihedralOPLSIntel
::
compute
(
int
eflag
,
int
vflag
,
IntelBuffers
<
flt_t
,
acc_t
>
*
buffers
,
const
ForceConst
<
flt_t
>
&
fc
)
{
if
(
eflag
||
vflag
)
{
ev_setup
(
eflag
,
vflag
);
}
else
evflag
=
0
;
if
(
evflag
)
{
if
(
eflag
)
{
if
(
force
->
newton_bond
)
eval
<
1
,
1
,
1
>
(
vflag
,
buffers
,
fc
);
else
eval
<
1
,
1
,
0
>
(
vflag
,
buffers
,
fc
);
}
else
{
if
(
force
->
newton_bond
)
eval
<
1
,
0
,
1
>
(
vflag
,
buffers
,
fc
);
else
eval
<
1
,
0
,
0
>
(
vflag
,
buffers
,
fc
);
}
}
else
{
if
(
force
->
newton_bond
)
eval
<
0
,
0
,
1
>
(
vflag
,
buffers
,
fc
);
else
eval
<
0
,
0
,
0
>
(
vflag
,
buffers
,
fc
);
}
}
template
<
int
EVFLAG
,
int
EFLAG
,
int
NEWTON_BOND
,
class
flt_t
,
class
acc_t
>
void
DihedralOPLSIntel
::
eval
(
const
int
vflag
,
IntelBuffers
<
flt_t
,
acc_t
>
*
buffers
,
const
ForceConst
<
flt_t
>
&
fc
)
{
const
int
inum
=
neighbor
->
ndihedrallist
;
if
(
inum
==
0
)
return
;
ATOM_T
*
_noalias
const
x
=
buffers
->
get_x
(
0
);
const
int
nlocal
=
atom
->
nlocal
;
const
int
nall
=
nlocal
+
atom
->
nghost
;
int
f_stride
;
if
(
NEWTON_BOND
)
f_stride
=
buffers
->
get_stride
(
nall
);
else
f_stride
=
buffers
->
get_stride
(
nlocal
);
int
tc
;
FORCE_T
*
_noalias
f_start
;
acc_t
*
_noalias
ev_global
;
IP_PRE_get_buffers
(
0
,
buffers
,
fix
,
tc
,
f_start
,
ev_global
);
const
int
nthreads
=
tc
;
acc_t
oedihedral
,
ov0
,
ov1
,
ov2
,
ov3
,
ov4
,
ov5
;
if
(
EVFLAG
)
{
if
(
EFLAG
)
oedihedral
=
(
acc_t
)
0.0
;
if
(
vflag
)
{
ov0
=
ov1
=
ov2
=
ov3
=
ov4
=
ov5
=
(
acc_t
)
0.0
;
}
}
#if defined(_OPENMP)
#pragma omp parallel default(none) \
shared(f_start,f_stride,fc) \
reduction(+:oedihedral,ov0,ov1,ov2,ov3,ov4,ov5)
#endif
{
int
nfrom
,
nto
,
tid
;
IP_PRE_omp_range_id
(
nfrom
,
nto
,
tid
,
inum
,
nthreads
);
FORCE_T
*
_noalias
const
f
=
f_start
+
(
tid
*
f_stride
);
if
(
fix
->
need_zero
(
tid
))
memset
(
f
,
0
,
f_stride
*
sizeof
(
FORCE_T
));
const
int5_t
*
_noalias
const
dihedrallist
=
(
int5_t
*
)
neighbor
->
dihedrallist
[
0
];
acc_t
sedihedral
,
sv0
,
sv1
,
sv2
,
sv3
,
sv4
,
sv5
;
if
(
EVFLAG
)
{
if
(
EFLAG
)
sedihedral
=
(
acc_t
)
0.0
;
if
(
vflag
)
{
sv0
=
sv1
=
sv2
=
sv3
=
sv4
=
sv5
=
(
acc_t
)
0.0
;
}
}
for
(
int
n
=
nfrom
;
n
<
nto
;
n
++
)
{
const
int
i1
=
dihedrallist
[
n
].
a
;
const
int
i2
=
dihedrallist
[
n
].
b
;
const
int
i3
=
dihedrallist
[
n
].
c
;
const
int
i4
=
dihedrallist
[
n
].
d
;
const
int
type
=
dihedrallist
[
n
].
t
;
// 1st bond
const
flt_t
vb1x
=
x
[
i1
].
x
-
x
[
i2
].
x
;
const
flt_t
vb1y
=
x
[
i1
].
y
-
x
[
i2
].
y
;
const
flt_t
vb1z
=
x
[
i1
].
z
-
x
[
i2
].
z
;
// 2nd bond
const
flt_t
vb2xm
=
x
[
i2
].
x
-
x
[
i3
].
x
;
const
flt_t
vb2ym
=
x
[
i2
].
y
-
x
[
i3
].
y
;
const
flt_t
vb2zm
=
x
[
i2
].
z
-
x
[
i3
].
z
;
// 3rd bond
const
flt_t
vb3x
=
x
[
i4
].
x
-
x
[
i3
].
x
;
const
flt_t
vb3y
=
x
[
i4
].
y
-
x
[
i3
].
y
;
const
flt_t
vb3z
=
x
[
i4
].
z
-
x
[
i3
].
z
;
// 1-4
const
flt_t
delx
=
x
[
i1
].
x
-
x
[
i4
].
x
;
const
flt_t
dely
=
x
[
i1
].
y
-
x
[
i4
].
y
;
const
flt_t
delz
=
x
[
i1
].
z
-
x
[
i4
].
z
;
// c0 calculation
// 1st and 2nd angle
const
flt_t
b1mag2
=
vb1x
*
vb1x
+
vb1y
*
vb1y
+
vb1z
*
vb1z
;
const
flt_t
rb1
=
(
flt_t
)
1.0
/
sqrt
(
b1mag2
);
const
flt_t
sb1
=
(
flt_t
)
1.0
/
b1mag2
;
const
flt_t
b2mag2
=
vb2xm
*
vb2xm
+
vb2ym
*
vb2ym
+
vb2zm
*
vb2zm
;
const
flt_t
rb2
=
(
flt_t
)
1.0
/
sqrt
(
b2mag2
);
const
flt_t
sb2
=
(
flt_t
)
1.0
/
b2mag2
;
const
flt_t
b3mag2
=
vb3x
*
vb3x
+
vb3y
*
vb3y
+
vb3z
*
vb3z
;
const
flt_t
rb3
=
(
flt_t
)
1.0
/
sqrt
(
b3mag2
);
const
flt_t
sb3
=
(
flt_t
)
1.0
/
b3mag2
;
const
flt_t
c0
=
(
vb1x
*
vb3x
+
vb1y
*
vb3y
+
vb1z
*
vb3z
)
*
rb1
*
rb3
;
flt_t
ctmp
=
-
vb1x
*
vb2xm
-
vb1y
*
vb2ym
-
vb1z
*
vb2zm
;
const
flt_t
r12c1
=
rb1
*
rb2
;
const
flt_t
c1mag
=
ctmp
*
r12c1
;
ctmp
=
vb2xm
*
vb3x
+
vb2ym
*
vb3y
+
vb2zm
*
vb3z
;
const
flt_t
r12c2
=
rb2
*
rb3
;
const
flt_t
c2mag
=
ctmp
*
r12c2
;
// cos and sin of 2 angles and final c
flt_t
sin2
=
MAX
((
flt_t
)
1.0
-
c1mag
*
c1mag
,(
flt_t
)
0.0
);
flt_t
sc1
=
(
flt_t
)
1.0
/
sqrt
(
sin2
);
if
(
sin2
<
SMALL2
)
sc1
=
INVSMALL
;
sin2
=
MAX
((
flt_t
)
1.0
-
c2mag
*
c2mag
,(
flt_t
)
0.0
);
flt_t
sc2
=
(
flt_t
)
1.0
/
sqrt
(
sin2
);
if
(
sin2
<
SMALL2
)
sc2
=
INVSMALL
;
const
flt_t
s1
=
sc1
*
sc1
;
const
flt_t
s2
=
sc2
*
sc2
;
flt_t
s12
=
sc1
*
sc2
;
flt_t
c
=
(
c0
+
c1mag
*
c2mag
)
*
s12
;
const
flt_t
cx
=
vb1z
*
vb2ym
-
vb1y
*
vb2zm
;
const
flt_t
cy
=
vb1x
*
vb2zm
-
vb1z
*
vb2xm
;
const
flt_t
cz
=
vb1y
*
vb2xm
-
vb1x
*
vb2ym
;
const
flt_t
cmag
=
(
flt_t
)
1.0
/
sqrt
(
cx
*
cx
+
cy
*
cy
+
cz
*
cz
);
const
flt_t
dx
=
(
cx
*
vb3x
+
cy
*
vb3y
+
cz
*
vb3z
)
*
cmag
*
rb3
;
// error check
if
(
c
>
PTOLERANCE
||
c
<
MTOLERANCE
)
{
int
me
=
comm
->
me
;
if
(
screen
)
{
char
str
[
128
];
sprintf
(
str
,
"Dihedral problem: %d/%d "
BIGINT_FORMAT
" "
TAGINT_FORMAT
" "
TAGINT_FORMAT
" "
TAGINT_FORMAT
" "
TAGINT_FORMAT
,
me
,
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
>
(
flt_t
)
1.0
)
c
=
(
flt_t
)
1.0
;
if
(
c
<
(
flt_t
)
-
1.0
)
c
=
(
flt_t
)
-
1.0
;
// force & energy
// p = sum (i=1,4) k_i * (1 + (-1)**(i+1)*cos(i*phi) )
// pd = dp/dc
const
flt_t
cossq
=
c
*
c
;
const
flt_t
sinsq
=
(
flt_t
)
1.0
-
cossq
;
flt_t
siinv
=
(
flt_t
)
1.0
/
sqrt
(
sinsq
);
if
(
sinsq
<
SMALLER2
)
siinv
=
INVSMALLER
;
if
(
dx
<
(
flt_t
)
0.0
)
siinv
=
-
siinv
;
const
flt_t
cos_2phi
=
cossq
-
sinsq
;
const
flt_t
sin_2phim
=
(
flt_t
)
2.0
*
c
;
const
flt_t
cos_3phi
=
(
flt_t
)
2.0
*
c
*
cos_2phi
-
c
;
const
flt_t
sin_3phim
=
(
flt_t
)
2.0
*
cos_2phi
+
(
flt_t
)
1.0
;
const
flt_t
cos_4phi
=
(
flt_t
)
2.0
*
cos_2phi
*
cos_2phi
-
(
flt_t
)
1.0
;
const
flt_t
sin_4phim
=
(
flt_t
)
2.0
*
cos_2phi
*
sin_2phim
;
flt_t
p
,
pd
;
p
=
fc
.
bp
[
type
].
k1
*
((
flt_t
)
1.0
+
c
)
+
fc
.
bp
[
type
].
k2
*
((
flt_t
)
1.0
-
cos_2phi
)
+
fc
.
bp
[
type
].
k3
*
((
flt_t
)
1.0
+
cos_3phi
)
+
fc
.
bp
[
type
].
k4
*
((
flt_t
)
1.0
-
cos_4phi
)
;
pd
=
fc
.
bp
[
type
].
k1
-
(
flt_t
)
2.0
*
fc
.
bp
[
type
].
k2
*
sin_2phim
+
(
flt_t
)
3.0
*
fc
.
bp
[
type
].
k3
*
sin_3phim
-
(
flt_t
)
4.0
*
fc
.
bp
[
type
].
k4
*
sin_4phim
;
flt_t
edihed
;
if
(
EFLAG
)
edihed
=
p
;
const
flt_t
a
=
pd
;
c
=
c
*
a
;
s12
=
s12
*
a
;
const
flt_t
a11
=
c
*
sb1
*
s1
;
const
flt_t
a22
=
-
sb2
*
((
flt_t
)
2.0
*
c0
*
s12
-
c
*
(
s1
+
s2
));
const
flt_t
a33
=
c
*
sb3
*
s2
;
const
flt_t
a12
=
-
r12c1
*
(
c1mag
*
c
*
s1
+
c2mag
*
s12
);
const
flt_t
a13
=
-
rb1
*
rb3
*
s12
;
const
flt_t
a23
=
r12c2
*
(
c2mag
*
c
*
s2
+
c1mag
*
s12
);
const
flt_t
sx2
=
a12
*
vb1x
-
a22
*
vb2xm
+
a23
*
vb3x
;
const
flt_t
sy2
=
a12
*
vb1y
-
a22
*
vb2ym
+
a23
*
vb3y
;
const
flt_t
sz2
=
a12
*
vb1z
-
a22
*
vb2zm
+
a23
*
vb3z
;
const
flt_t
f1x
=
a11
*
vb1x
-
a12
*
vb2xm
+
a13
*
vb3x
;
const
flt_t
f1y
=
a11
*
vb1y
-
a12
*
vb2ym
+
a13
*
vb3y
;
const
flt_t
f1z
=
a11
*
vb1z
-
a12
*
vb2zm
+
a13
*
vb3z
;
const
flt_t
f2x
=
-
sx2
-
f1x
;
const
flt_t
f2y
=
-
sy2
-
f1y
;
const
flt_t
f2z
=
-
sz2
-
f1z
;
const
flt_t
f4x
=
a13
*
vb1x
-
a23
*
vb2xm
+
a33
*
vb3x
;
const
flt_t
f4y
=
a13
*
vb1y
-
a23
*
vb2ym
+
a33
*
vb3y
;
const
flt_t
f4z
=
a13
*
vb1z
-
a23
*
vb2zm
+
a33
*
vb3z
;
const
flt_t
f3x
=
sx2
-
f4x
;
const
flt_t
f3y
=
sy2
-
f4y
;
const
flt_t
f3z
=
sz2
-
f4z
;
if
(
EVFLAG
)
{
IP_PRE_ev_tally_dihed
(
EFLAG
,
eatom
,
vflag
,
edihed
,
i1
,
i2
,
i3
,
i4
,
f1x
,
f1y
,
f1z
,
f3x
,
f3y
,
f3z
,
f4x
,
f4y
,
f4z
,
vb1x
,
vb1y
,
vb1z
,
-
vb2xm
,
-
vb2ym
,
-
vb2zm
,
vb3x
,
vb3y
,
vb3z
,
sedihedral
,
f
,
NEWTON_BOND
,
nlocal
,
sv0
,
sv1
,
sv2
,
sv3
,
sv4
,
sv5
);
}
{
if
(
NEWTON_BOND
||
i1
<
nlocal
)
{
f
[
i1
].
x
+=
f1x
;
f
[
i1
].
y
+=
f1y
;
f
[
i1
].
z
+=
f1z
;
}
if
(
NEWTON_BOND
||
i2
<
nlocal
)
{
f
[
i2
].
x
+=
f2x
;
f
[
i2
].
y
+=
f2y
;
f
[
i2
].
z
+=
f2z
;
}
if
(
NEWTON_BOND
||
i3
<
nlocal
)
{
f
[
i3
].
x
+=
f3x
;
f
[
i3
].
y
+=
f3y
;
f
[
i3
].
z
+=
f3z
;
}
if
(
NEWTON_BOND
||
i4
<
nlocal
)
{
f
[
i4
].
x
+=
f4x
;
f
[
i4
].
y
+=
f4y
;
f
[
i4
].
z
+=
f4z
;
}
}
}
// for n
if
(
EVFLAG
)
{
if
(
EFLAG
)
oedihedral
+=
sedihedral
;
if
(
vflag
)
{
ov0
+=
sv0
;
ov1
+=
sv1
;
ov2
+=
sv2
;
ov3
+=
sv3
;
ov4
+=
sv4
;
ov5
+=
sv5
;
}
}
}
// omp parallel
if
(
EVFLAG
)
{
if
(
EFLAG
)
energy
+=
oedihedral
;
if
(
vflag
)
{
virial
[
0
]
+=
ov0
;
virial
[
1
]
+=
ov1
;
virial
[
2
]
+=
ov2
;
virial
[
3
]
+=
ov3
;
virial
[
4
]
+=
ov4
;
virial
[
5
]
+=
ov5
;
}
}
fix
->
set_reduce_flag
();
}
/* ---------------------------------------------------------------------- */
void
DihedralOPLSIntel
::
init_style
()
{
DihedralOPLS
::
init_style
();
int
ifix
=
modify
->
find_fix
(
"package_intel"
);
if
(
ifix
<
0
)
error
->
all
(
FLERR
,
"The 'package intel' command is required for /intel styles"
);
fix
=
static_cast
<
FixIntel
*>
(
modify
->
fix
[
ifix
]);
#ifdef _LMP_INTEL_OFFLOAD
_use_base
=
0
;
if
(
fix
->
offload_balance
()
!=
0.0
)
{
_use_base
=
1
;
return
;
}
#endif
fix
->
bond_init_check
();
if
(
fix
->
precision
()
==
FixIntel
::
PREC_MODE_MIXED
)
pack_force_const
(
force_const_single
,
fix
->
get_mixed_buffers
());
else
if
(
fix
->
precision
()
==
FixIntel
::
PREC_MODE_DOUBLE
)
pack_force_const
(
force_const_double
,
fix
->
get_double_buffers
());
else
pack_force_const
(
force_const_single
,
fix
->
get_single_buffers
());
}
/* ---------------------------------------------------------------------- */
template
<
class
flt_t
,
class
acc_t
>
void
DihedralOPLSIntel
::
pack_force_const
(
ForceConst
<
flt_t
>
&
fc
,
IntelBuffers
<
flt_t
,
acc_t
>
*
buffers
)
{
const
int
bp1
=
atom
->
ndihedraltypes
+
1
;
fc
.
set_ntypes
(
bp1
,
memory
);
for
(
int
i
=
0
;
i
<
bp1
;
i
++
)
{
fc
.
bp
[
i
].
k1
=
k1
[
i
];
fc
.
bp
[
i
].
k2
=
k2
[
i
];
fc
.
bp
[
i
].
k3
=
k3
[
i
];
fc
.
bp
[
i
].
k4
=
k4
[
i
];
}
}
/* ---------------------------------------------------------------------- */
template
<
class
flt_t
>
void
DihedralOPLSIntel
::
ForceConst
<
flt_t
>::
set_ntypes
(
const
int
nbondtypes
,
Memory
*
memory
)
{
if
(
nbondtypes
!=
_nbondtypes
)
{
if
(
_nbondtypes
>
0
)
_memory
->
destroy
(
bp
);
if
(
nbondtypes
>
0
)
_memory
->
create
(
bp
,
nbondtypes
,
"dihedralcharmmintel.bp"
);
}
_nbondtypes
=
nbondtypes
;
_memory
=
memory
;
}
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