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angle_charmm_kokkos.cpp
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rLAMMPS lammps
angle_charmm_kokkos.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: Stan Moore (SNL)
------------------------------------------------------------------------- */
#include <math.h>
#include <stdlib.h>
#include "angle_charmm_kokkos.h"
#include "atom_kokkos.h"
#include "neighbor_kokkos.h"
#include "domain.h"
#include "comm.h"
#include "force.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
#include "atom_masks.h"
using
namespace
LAMMPS_NS
;
using
namespace
MathConst
;
#define SMALL 0.001
/* ---------------------------------------------------------------------- */
template
<
class
DeviceType
>
AngleCharmmKokkos
<
DeviceType
>::
AngleCharmmKokkos
(
LAMMPS
*
lmp
)
:
AngleCharmm
(
lmp
)
{
atomKK
=
(
AtomKokkos
*
)
atom
;
neighborKK
=
(
NeighborKokkos
*
)
neighbor
;
execution_space
=
ExecutionSpaceFromDevice
<
DeviceType
>::
space
;
datamask_read
=
X_MASK
|
F_MASK
|
ENERGY_MASK
|
VIRIAL_MASK
;
datamask_modify
=
F_MASK
|
ENERGY_MASK
|
VIRIAL_MASK
;
}
/* ---------------------------------------------------------------------- */
template
<
class
DeviceType
>
AngleCharmmKokkos
<
DeviceType
>::~
AngleCharmmKokkos
()
{
if
(
!
copymode
)
{
memory
->
destroy_kokkos
(
k_eatom
,
eatom
);
memory
->
destroy_kokkos
(
k_vatom
,
vatom
);
}
}
/* ---------------------------------------------------------------------- */
template
<
class
DeviceType
>
void
AngleCharmmKokkos
<
DeviceType
>::
compute
(
int
eflag_in
,
int
vflag_in
)
{
eflag
=
eflag_in
;
vflag
=
vflag_in
;
if
(
eflag
||
vflag
)
ev_setup
(
eflag
,
vflag
);
else
evflag
=
0
;
// reallocate per-atom arrays if necessary
if
(
eflag_atom
)
{
if
(
k_eatom
.
dimension_0
()
<
maxeatom
)
{
memory
->
destroy_kokkos
(
k_eatom
,
eatom
);
memory
->
create_kokkos
(
k_eatom
,
eatom
,
maxeatom
,
"improper:eatom"
);
d_eatom
=
k_eatom
.
d_view
;
}
}
if
(
vflag_atom
)
{
if
(
k_vatom
.
dimension_0
()
<
maxvatom
)
{
memory
->
destroy_kokkos
(
k_vatom
,
vatom
);
memory
->
create_kokkos
(
k_vatom
,
vatom
,
maxvatom
,
6
,
"improper:vatom"
);
d_vatom
=
k_vatom
.
d_view
;
}
}
if
(
eflag
||
vflag
)
atomKK
->
modified
(
execution_space
,
datamask_modify
);
else
atomKK
->
modified
(
execution_space
,
F_MASK
);
x
=
atomKK
->
k_x
.
view
<
DeviceType
>
();
f
=
atomKK
->
k_f
.
view
<
DeviceType
>
();
neighborKK
->
k_anglelist
.
template
sync
<
DeviceType
>
();
anglelist
=
neighborKK
->
k_anglelist
.
view
<
DeviceType
>
();
int
nanglelist
=
neighborKK
->
nanglelist
;
nlocal
=
atom
->
nlocal
;
newton_bond
=
force
->
newton_bond
;
copymode
=
1
;
// loop over neighbors of my atoms
EV_FLOAT
ev
;
if
(
evflag
)
{
if
(
newton_bond
)
{
Kokkos
::
parallel_reduce
(
Kokkos
::
RangePolicy
<
DeviceType
,
TagAngleCharmmCompute
<
1
,
1
>
>
(
0
,
nanglelist
),
*
this
,
ev
);
}
else
{
Kokkos
::
parallel_reduce
(
Kokkos
::
RangePolicy
<
DeviceType
,
TagAngleCharmmCompute
<
0
,
1
>
>
(
0
,
nanglelist
),
*
this
,
ev
);
}
}
else
{
if
(
newton_bond
)
{
Kokkos
::
parallel_for
(
Kokkos
::
RangePolicy
<
DeviceType
,
TagAngleCharmmCompute
<
1
,
0
>
>
(
0
,
nanglelist
),
*
this
);
}
else
{
Kokkos
::
parallel_for
(
Kokkos
::
RangePolicy
<
DeviceType
,
TagAngleCharmmCompute
<
0
,
0
>
>
(
0
,
nanglelist
),
*
this
);
}
}
DeviceType
::
fence
();
if
(
eflag_global
)
energy
+=
ev
.
evdwl
;
if
(
vflag_global
)
{
virial
[
0
]
+=
ev
.
v
[
0
];
virial
[
1
]
+=
ev
.
v
[
1
];
virial
[
2
]
+=
ev
.
v
[
2
];
virial
[
3
]
+=
ev
.
v
[
3
];
virial
[
4
]
+=
ev
.
v
[
4
];
virial
[
5
]
+=
ev
.
v
[
5
];
}
if
(
eflag_atom
)
{
k_eatom
.
template
modify
<
DeviceType
>
();
k_eatom
.
template
sync
<
LMPHostType
>
();
}
if
(
vflag_atom
)
{
k_vatom
.
template
modify
<
DeviceType
>
();
k_vatom
.
template
sync
<
LMPHostType
>
();
}
copymode
=
0
;
}
template
<
class
DeviceType
>
template
<
int
NEWTON_BOND
,
int
EVFLAG
>
KOKKOS_INLINE_FUNCTION
void
AngleCharmmKokkos
<
DeviceType
>::
operator
()(
TagAngleCharmmCompute
<
NEWTON_BOND
,
EVFLAG
>
,
const
int
&
n
,
EV_FLOAT
&
ev
)
const
{
const
int
i1
=
anglelist
(
n
,
0
);
const
int
i2
=
anglelist
(
n
,
1
);
const
int
i3
=
anglelist
(
n
,
2
);
const
int
type
=
anglelist
(
n
,
3
);
// 1st bond
const
F_FLOAT
delx1
=
x
(
i1
,
0
)
-
x
(
i2
,
0
);
const
F_FLOAT
dely1
=
x
(
i1
,
1
)
-
x
(
i2
,
1
);
const
F_FLOAT
delz1
=
x
(
i1
,
2
)
-
x
(
i2
,
2
);
const
F_FLOAT
rsq1
=
delx1
*
delx1
+
dely1
*
dely1
+
delz1
*
delz1
;
const
F_FLOAT
r1
=
sqrt
(
rsq1
);
// 2nd bond
const
F_FLOAT
delx2
=
x
(
i3
,
0
)
-
x
(
i2
,
0
);
const
F_FLOAT
dely2
=
x
(
i3
,
1
)
-
x
(
i2
,
1
);
const
F_FLOAT
delz2
=
x
(
i3
,
2
)
-
x
(
i2
,
2
);
const
F_FLOAT
rsq2
=
delx2
*
delx2
+
dely2
*
dely2
+
delz2
*
delz2
;
const
F_FLOAT
r2
=
sqrt
(
rsq2
);
// Urey-Bradley bond
const
F_FLOAT
delxUB
=
x
(
i3
,
0
)
-
x
(
i1
,
0
);
const
F_FLOAT
delyUB
=
x
(
i3
,
1
)
-
x
(
i1
,
1
);
const
F_FLOAT
delzUB
=
x
(
i3
,
2
)
-
x
(
i1
,
2
);
const
F_FLOAT
rsqUB
=
delxUB
*
delxUB
+
delyUB
*
delyUB
+
delzUB
*
delzUB
;
const
F_FLOAT
rUB
=
sqrt
(
rsqUB
);
// Urey-Bradley force & energy
const
F_FLOAT
dr
=
rUB
-
d_r_ub
[
type
];
const
F_FLOAT
rk
=
d_k_ub
[
type
]
*
dr
;
F_FLOAT
forceUB
=
0.0
;
if
(
rUB
>
0.0
)
forceUB
=
-
2.0
*
rk
/
rUB
;
E_FLOAT
eangle
=
0.0
;
if
(
eflag
)
eangle
=
rk
*
dr
;
// angle (cos and sin)
F_FLOAT
c
=
delx1
*
delx2
+
dely1
*
dely2
+
delz1
*
delz2
;
c
/=
r1
*
r2
;
if
(
c
>
1.0
)
c
=
1.0
;
if
(
c
<
-
1.0
)
c
=
-
1.0
;
F_FLOAT
s
=
sqrt
(
1.0
-
c
*
c
);
if
(
s
<
SMALL
)
s
=
SMALL
;
s
=
1.0
/
s
;
// harmonic force & energy
const
F_FLOAT
dtheta
=
acos
(
c
)
-
d_theta0
[
type
];
const
F_FLOAT
tk
=
d_k
[
type
]
*
dtheta
;
if
(
eflag
)
eangle
+=
tk
*
dtheta
;
const
F_FLOAT
a
=
-
2.0
*
tk
*
s
;
const
F_FLOAT
a11
=
a
*
c
/
rsq1
;
const
F_FLOAT
a12
=
-
a
/
(
r1
*
r2
);
const
F_FLOAT
a22
=
a
*
c
/
rsq2
;
F_FLOAT
f1
[
3
],
f3
[
3
];
f1
[
0
]
=
a11
*
delx1
+
a12
*
delx2
-
delxUB
*
forceUB
;
f1
[
1
]
=
a11
*
dely1
+
a12
*
dely2
-
delyUB
*
forceUB
;
f1
[
2
]
=
a11
*
delz1
+
a12
*
delz2
-
delzUB
*
forceUB
;
f3
[
0
]
=
a22
*
delx2
+
a12
*
delx1
+
delxUB
*
forceUB
;
f3
[
1
]
=
a22
*
dely2
+
a12
*
dely1
+
delyUB
*
forceUB
;
f3
[
2
]
=
a22
*
delz2
+
a12
*
delz1
+
delzUB
*
forceUB
;
// apply force to each of 3 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
)
-=
f1
[
0
]
+
f3
[
0
];
f
(
i2
,
1
)
-=
f1
[
1
]
+
f3
[
1
];
f
(
i2
,
2
)
-=
f1
[
2
]
+
f3
[
2
];
}
if
(
NEWTON_BOND
||
i3
<
nlocal
)
{
f
(
i3
,
0
)
+=
f3
[
0
];
f
(
i3
,
1
)
+=
f3
[
1
];
f
(
i3
,
2
)
+=
f3
[
2
];
}
if
(
EVFLAG
)
ev_tally
(
ev
,
i1
,
i2
,
i3
,
eangle
,
f1
,
f3
,
delx1
,
dely1
,
delz1
,
delx2
,
dely2
,
delz2
);
}
template
<
class
DeviceType
>
template
<
int
NEWTON_BOND
,
int
EVFLAG
>
KOKKOS_INLINE_FUNCTION
void
AngleCharmmKokkos
<
DeviceType
>::
operator
()(
TagAngleCharmmCompute
<
NEWTON_BOND
,
EVFLAG
>
,
const
int
&
n
)
const
{
EV_FLOAT
ev
;
this
->
template
operator
()
<
NEWTON_BOND
,
EVFLAG
>
(
TagAngleCharmmCompute
<
NEWTON_BOND
,
EVFLAG
>
(),
n
,
ev
);
}
/* ---------------------------------------------------------------------- */
template
<
class
DeviceType
>
void
AngleCharmmKokkos
<
DeviceType
>::
allocate
()
{
AngleCharmm
::
allocate
();
}
/* ----------------------------------------------------------------------
set coeffs for one or more types
------------------------------------------------------------------------- */
template
<
class
DeviceType
>
void
AngleCharmmKokkos
<
DeviceType
>::
coeff
(
int
narg
,
char
**
arg
)
{
AngleCharmm
::
coeff
(
narg
,
arg
);
int
n
=
atom
->
nangletypes
;
Kokkos
::
DualView
<
F_FLOAT
*
,
DeviceType
>
k_k
(
"AngleCharmm::k"
,
n
+
1
);
Kokkos
::
DualView
<
F_FLOAT
*
,
DeviceType
>
k_theta0
(
"AngleCharmm::theta0"
,
n
+
1
);
Kokkos
::
DualView
<
F_FLOAT
*
,
DeviceType
>
k_k_ub
(
"AngleCharmm::k_ub"
,
n
+
1
);
Kokkos
::
DualView
<
F_FLOAT
*
,
DeviceType
>
k_r_ub
(
"AngleCharmm::r_ub"
,
n
+
1
);
d_k
=
k_k
.
d_view
;
d_theta0
=
k_theta0
.
d_view
;
d_k_ub
=
k_k_ub
.
d_view
;
d_r_ub
=
k_r_ub
.
d_view
;
for
(
int
i
=
1
;
i
<=
n
;
i
++
)
{
k_k
.
h_view
[
i
]
=
k
[
i
];
k_theta0
.
h_view
[
i
]
=
theta0
[
i
];
k_k_ub
.
h_view
[
i
]
=
k_ub
[
i
];
k_r_ub
.
h_view
[
i
]
=
r_ub
[
i
];
}
k_k
.
template
modify
<
LMPHostType
>
();
k_theta0
.
template
modify
<
LMPHostType
>
();
k_k_ub
.
template
modify
<
LMPHostType
>
();
k_r_ub
.
template
modify
<
LMPHostType
>
();
k_k
.
template
sync
<
DeviceType
>
();
k_theta0
.
template
sync
<
DeviceType
>
();
k_k_ub
.
template
sync
<
DeviceType
>
();
k_r_ub
.
template
sync
<
DeviceType
>
();
}
/* ----------------------------------------------------------------------
tally energy and virial into global and per-atom accumulators
virial = r1F1 + r2F2 + r3F3 = (r1-r2) F1 + (r3-r2) F3 = del1*f1 + del2*f3
------------------------------------------------------------------------- */
template
<
class
DeviceType
>
//template<int NEWTON_BOND>
KOKKOS_INLINE_FUNCTION
void
AngleCharmmKokkos
<
DeviceType
>::
ev_tally
(
EV_FLOAT
&
ev
,
const
int
i
,
const
int
j
,
const
int
k
,
F_FLOAT
&
eangle
,
F_FLOAT
*
f1
,
F_FLOAT
*
f3
,
const
F_FLOAT
&
delx1
,
const
F_FLOAT
&
dely1
,
const
F_FLOAT
&
delz1
,
const
F_FLOAT
&
delx2
,
const
F_FLOAT
&
dely2
,
const
F_FLOAT
&
delz2
)
const
{
E_FLOAT
eanglethird
;
F_FLOAT
v
[
6
];
if
(
eflag_either
)
{
if
(
eflag_global
)
{
if
(
newton_bond
)
ev
.
evdwl
+=
eangle
;
else
{
eanglethird
=
THIRD
*
eangle
;
if
(
i
<
nlocal
)
ev
.
evdwl
+=
eanglethird
;
if
(
j
<
nlocal
)
ev
.
evdwl
+=
eanglethird
;
if
(
k
<
nlocal
)
ev
.
evdwl
+=
eanglethird
;
}
}
if
(
eflag_atom
)
{
eanglethird
=
THIRD
*
eangle
;
if
(
newton_bond
||
i
<
nlocal
)
d_eatom
[
i
]
+=
eanglethird
;
if
(
newton_bond
||
j
<
nlocal
)
d_eatom
[
j
]
+=
eanglethird
;
if
(
newton_bond
||
k
<
nlocal
)
d_eatom
[
k
]
+=
eanglethird
;
}
}
if
(
vflag_either
)
{
v
[
0
]
=
delx1
*
f1
[
0
]
+
delx2
*
f3
[
0
];
v
[
1
]
=
dely1
*
f1
[
1
]
+
dely2
*
f3
[
1
];
v
[
2
]
=
delz1
*
f1
[
2
]
+
delz2
*
f3
[
2
];
v
[
3
]
=
delx1
*
f1
[
1
]
+
delx2
*
f3
[
1
];
v
[
4
]
=
delx1
*
f1
[
2
]
+
delx2
*
f3
[
2
];
v
[
5
]
=
dely1
*
f1
[
2
]
+
dely2
*
f3
[
2
];
if
(
vflag_global
)
{
if
(
newton_bond
)
{
ev
.
v
[
0
]
+=
v
[
0
];
ev
.
v
[
1
]
+=
v
[
1
];
ev
.
v
[
2
]
+=
v
[
2
];
ev
.
v
[
3
]
+=
v
[
3
];
ev
.
v
[
4
]
+=
v
[
4
];
ev
.
v
[
5
]
+=
v
[
5
];
}
else
{
if
(
i
<
nlocal
)
{
ev
.
v
[
0
]
+=
THIRD
*
v
[
0
];
ev
.
v
[
1
]
+=
THIRD
*
v
[
1
];
ev
.
v
[
2
]
+=
THIRD
*
v
[
2
];
ev
.
v
[
3
]
+=
THIRD
*
v
[
3
];
ev
.
v
[
4
]
+=
THIRD
*
v
[
4
];
ev
.
v
[
5
]
+=
THIRD
*
v
[
5
];
}
if
(
j
<
nlocal
)
{
ev
.
v
[
0
]
+=
THIRD
*
v
[
0
];
ev
.
v
[
1
]
+=
THIRD
*
v
[
1
];
ev
.
v
[
2
]
+=
THIRD
*
v
[
2
];
ev
.
v
[
3
]
+=
THIRD
*
v
[
3
];
ev
.
v
[
4
]
+=
THIRD
*
v
[
4
];
ev
.
v
[
5
]
+=
THIRD
*
v
[
5
];
}
if
(
k
<
nlocal
)
{
ev
.
v
[
0
]
+=
THIRD
*
v
[
0
];
ev
.
v
[
1
]
+=
THIRD
*
v
[
1
];
ev
.
v
[
2
]
+=
THIRD
*
v
[
2
];
ev
.
v
[
3
]
+=
THIRD
*
v
[
3
];
ev
.
v
[
4
]
+=
THIRD
*
v
[
4
];
ev
.
v
[
5
]
+=
THIRD
*
v
[
5
];
}
}
}
if
(
vflag_atom
)
{
if
(
newton_bond
||
i
<
nlocal
)
{
d_vatom
(
i
,
0
)
+=
THIRD
*
v
[
0
];
d_vatom
(
i
,
1
)
+=
THIRD
*
v
[
1
];
d_vatom
(
i
,
2
)
+=
THIRD
*
v
[
2
];
d_vatom
(
i
,
3
)
+=
THIRD
*
v
[
3
];
d_vatom
(
i
,
4
)
+=
THIRD
*
v
[
4
];
d_vatom
(
i
,
5
)
+=
THIRD
*
v
[
5
];
}
if
(
newton_bond
||
j
<
nlocal
)
{
d_vatom
(
j
,
0
)
+=
THIRD
*
v
[
0
];
d_vatom
(
j
,
1
)
+=
THIRD
*
v
[
1
];
d_vatom
(
j
,
2
)
+=
THIRD
*
v
[
2
];
d_vatom
(
j
,
3
)
+=
THIRD
*
v
[
3
];
d_vatom
(
j
,
4
)
+=
THIRD
*
v
[
4
];
d_vatom
(
j
,
5
)
+=
THIRD
*
v
[
5
];
}
if
(
newton_bond
||
k
<
nlocal
)
{
d_vatom
(
k
,
0
)
+=
THIRD
*
v
[
0
];
d_vatom
(
k
,
1
)
+=
THIRD
*
v
[
1
];
d_vatom
(
k
,
2
)
+=
THIRD
*
v
[
2
];
d_vatom
(
k
,
3
)
+=
THIRD
*
v
[
3
];
d_vatom
(
k
,
4
)
+=
THIRD
*
v
[
4
];
d_vatom
(
k
,
5
)
+=
THIRD
*
v
[
5
];
}
}
}
}
/* ---------------------------------------------------------------------- */
namespace
LAMMPS_NS
{
template
class
AngleCharmmKokkos
<
LMPDeviceType
>
;
#ifdef KOKKOS_HAVE_CUDA
template
class
AngleCharmmKokkos
<
LMPHostType
>
;
#endif
}
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