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rLAMMPS lammps
angle_charmm_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 <math.h>
#include <stdlib.h>
#include "angle_charmm_intel.h"
#include "atom.h"
#include "neighbor.h"
#include "domain.h"
#include "comm.h"
#include "force.h"
#include "math_const.h"
#include "memory.h"
#include "suffix.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
using
namespace
MathConst
;
#define SMALL2 (flt_t)0.000001
#define INVSMALL (flt_t)1000.0
typedef
struct
{
int
a
,
b
,
c
,
t
;
}
int4_t
;
/* ---------------------------------------------------------------------- */
AngleCharmmIntel
::
AngleCharmmIntel
(
LAMMPS
*
lmp
)
:
AngleCharmm
(
lmp
)
{
suffix_flag
|=
Suffix
::
INTEL
;
}
/* ---------------------------------------------------------------------- */
AngleCharmmIntel
::~
AngleCharmmIntel
()
{
}
/* ---------------------------------------------------------------------- */
void
AngleCharmmIntel
::
compute
(
int
eflag
,
int
vflag
)
{
#ifdef _LMP_INTEL_OFFLOAD
if
(
_use_base
)
{
AngleCharmm
::
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
AngleCharmmIntel
::
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
AngleCharmmIntel
::
eval
(
const
int
vflag
,
IntelBuffers
<
flt_t
,
acc_t
>
*
buffers
,
const
ForceConst
<
flt_t
>
&
fc
)
{
const
int
inum
=
neighbor
->
nanglelist
;
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
oeangle
,
ov0
,
ov1
,
ov2
,
ov3
,
ov4
,
ov5
;
if
(
EVFLAG
)
{
if
(
EFLAG
)
oeangle
=
(
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(+:oeangle,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
int4_t
*
_noalias
const
anglelist
=
(
int4_t
*
)
neighbor
->
anglelist
[
0
];
for
(
int
n
=
nfrom
;
n
<
nto
;
n
++
)
{
const
int
i1
=
anglelist
[
n
].
a
;
const
int
i2
=
anglelist
[
n
].
b
;
const
int
i3
=
anglelist
[
n
].
c
;
const
int
type
=
anglelist
[
n
].
t
;
// 1st bond
const
flt_t
delx1
=
x
[
i1
].
x
-
x
[
i2
].
x
;
const
flt_t
dely1
=
x
[
i1
].
y
-
x
[
i2
].
y
;
const
flt_t
delz1
=
x
[
i1
].
z
-
x
[
i2
].
z
;
const
flt_t
rsq1
=
delx1
*
delx1
+
dely1
*
dely1
+
delz1
*
delz1
;
flt_t
ir12
=
(
flt_t
)
1.0
/
sqrt
(
rsq1
);
// 2nd bond
const
flt_t
delx2
=
x
[
i3
].
x
-
x
[
i2
].
x
;
const
flt_t
dely2
=
x
[
i3
].
y
-
x
[
i2
].
y
;
const
flt_t
delz2
=
x
[
i3
].
z
-
x
[
i2
].
z
;
const
flt_t
rsq2
=
delx2
*
delx2
+
dely2
*
dely2
+
delz2
*
delz2
;
ir12
*=
(
flt_t
)
1.0
/
sqrt
(
rsq2
);
// Urey-Bradley bond
const
flt_t
delxUB
=
x
[
i3
].
x
-
x
[
i1
].
x
;
const
flt_t
delyUB
=
x
[
i3
].
y
-
x
[
i1
].
y
;
const
flt_t
delzUB
=
x
[
i3
].
z
-
x
[
i1
].
z
;
const
flt_t
rsqUB
=
delxUB
*
delxUB
+
delyUB
*
delyUB
+
delzUB
*
delzUB
;
const
flt_t
irUB
=
(
flt_t
)
1.0
/
sqrt
(
rsqUB
);
// Urey-Bradley force & energy
const
flt_t
dr
=
(
flt_t
)
1.0
/
irUB
-
fc
.
fc
[
type
].
r_ub
;
const
flt_t
rk
=
fc
.
fc
[
type
].
k_ub
*
dr
;
flt_t
forceUB
;
if
(
rsqUB
>
(
flt_t
)
0.0
)
forceUB
=
(
flt_t
)
-
2.0
*
rk
*
irUB
;
else
forceUB
=
0.0
;
flt_t
eangle
;
if
(
EFLAG
)
eangle
=
rk
*
dr
;
// angle (cos and sin)
flt_t
c
=
delx1
*
delx2
+
dely1
*
dely2
+
delz1
*
delz2
;
c
*=
ir12
;
if
(
c
>
(
flt_t
)
1.0
)
c
=
(
flt_t
)
1.0
;
if
(
c
<
(
flt_t
)
-
1.0
)
c
=
(
flt_t
)
-
1.0
;
const
flt_t
sd
=
(
flt_t
)
1.0
-
c
*
c
;
flt_t
s
=
(
flt_t
)
1.0
/
sqrt
(
sd
);
if
(
sd
<
SMALL2
)
s
=
INVSMALL
;
// harmonic force & energy
const
flt_t
dtheta
=
acos
(
c
)
-
fc
.
fc
[
type
].
theta0
;
const
flt_t
tk
=
fc
.
fc
[
type
].
k
*
dtheta
;
if
(
EFLAG
)
eangle
+=
tk
*
dtheta
;
const
flt_t
a
=
(
flt_t
)
-
2.0
*
tk
*
s
;
const
flt_t
a11
=
a
*
c
/
rsq1
;
const
flt_t
a12
=
-
a
*
ir12
;
const
flt_t
a22
=
a
*
c
/
rsq2
;
const
flt_t
f1x
=
a11
*
delx1
+
a12
*
delx2
-
delxUB
*
forceUB
;
const
flt_t
f1y
=
a11
*
dely1
+
a12
*
dely2
-
delyUB
*
forceUB
;
const
flt_t
f1z
=
a11
*
delz1
+
a12
*
delz2
-
delzUB
*
forceUB
;
const
flt_t
f3x
=
a22
*
delx2
+
a12
*
delx1
+
delxUB
*
forceUB
;
const
flt_t
f3y
=
a22
*
dely2
+
a12
*
dely1
+
delyUB
*
forceUB
;
const
flt_t
f3z
=
a22
*
delz2
+
a12
*
delz1
+
delzUB
*
forceUB
;
// apply force to each of 3 atoms
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
-=
f1x
+
f3x
;
f
[
i2
].
y
-=
f1y
+
f3y
;
f
[
i2
].
z
-=
f1z
+
f3z
;
}
if
(
NEWTON_BOND
||
i3
<
nlocal
)
{
f
[
i3
].
x
+=
f3x
;
f
[
i3
].
y
+=
f3y
;
f
[
i3
].
z
+=
f3z
;
}
if
(
EVFLAG
)
{
IP_PRE_ev_tally_angle
(
EFLAG
,
eatom
,
vflag
,
eangle
,
i1
,
i2
,
i3
,
f1x
,
f1y
,
f1z
,
f3x
,
f3y
,
f3z
,
delx1
,
dely1
,
delz1
,
delx2
,
dely2
,
delz2
,
oeangle
,
f
,
NEWTON_BOND
,
nlocal
,
ov0
,
ov1
,
ov2
,
ov3
,
ov4
,
ov5
);
}
}
// for n
}
// omp parallel
if
(
EVFLAG
)
{
if
(
EFLAG
)
energy
+=
oeangle
;
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
AngleCharmmIntel
::
init_style
()
{
AngleCharmm
::
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
AngleCharmmIntel
::
pack_force_const
(
ForceConst
<
flt_t
>
&
fc
,
IntelBuffers
<
flt_t
,
acc_t
>
*
buffers
)
{
const
int
bp1
=
atom
->
nangletypes
+
1
;
fc
.
set_ntypes
(
bp1
,
memory
);
for
(
int
i
=
0
;
i
<
bp1
;
i
++
)
{
fc
.
fc
[
i
].
k
=
k
[
i
];
fc
.
fc
[
i
].
theta0
=
theta0
[
i
];
fc
.
fc
[
i
].
k_ub
=
k_ub
[
i
];
fc
.
fc
[
i
].
r_ub
=
r_ub
[
i
];
}
}
/* ---------------------------------------------------------------------- */
template
<
class
flt_t
>
void
AngleCharmmIntel
::
ForceConst
<
flt_t
>::
set_ntypes
(
const
int
nangletypes
,
Memory
*
memory
)
{
if
(
nangletypes
!=
_nangletypes
)
{
if
(
_nangletypes
>
0
)
_memory
->
destroy
(
fc
);
if
(
nangletypes
>
0
)
_memory
->
create
(
fc
,
nangletypes
,
"anglecharmmintel.fc"
);
}
_nangletypes
=
nangletypes
;
_memory
=
memory
;
}
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