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pair_lj_gromacs_kokkos.cpp
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rLAMMPS lammps
pair_lj_gromacs_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: Ray Shan (SNL)
------------------------------------------------------------------------- */
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "pair_lj_gromacs_kokkos.h"
#include "kokkos.h"
#include "atom_kokkos.h"
#include "comm.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "update.h"
#include "integrate.h"
#include "respa.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
#include "atom_masks.h"
using
namespace
LAMMPS_NS
;
using
namespace
MathConst
;
#define KOKKOS_CUDA_MAX_THREADS 256
#define KOKKOS_CUDA_MIN_BLOCKS 8
/* ---------------------------------------------------------------------- */
template
<
class
DeviceType
>
PairLJGromacsKokkos
<
DeviceType
>::
PairLJGromacsKokkos
(
LAMMPS
*
lmp
)
:
PairLJGromacs
(
lmp
)
{
respa_enable
=
0
;
atomKK
=
(
AtomKokkos
*
)
atom
;
execution_space
=
ExecutionSpaceFromDevice
<
DeviceType
>::
space
;
datamask_read
=
X_MASK
|
F_MASK
|
TYPE_MASK
|
Q_MASK
|
ENERGY_MASK
|
VIRIAL_MASK
;
datamask_modify
=
F_MASK
|
ENERGY_MASK
|
VIRIAL_MASK
;
cutsq
=
NULL
;
cut_inner
=
NULL
;
cut_inner_sq
=
NULL
;
}
/* ---------------------------------------------------------------------- */
template
<
class
DeviceType
>
PairLJGromacsKokkos
<
DeviceType
>::~
PairLJGromacsKokkos
()
{
if
(
!
copymode
)
{
memory
->
destroy_kokkos
(
k_eatom
,
eatom
);
memory
->
destroy_kokkos
(
k_vatom
,
vatom
);
k_cutsq
=
DAT
::
tdual_ffloat_2d
();
k_cut_inner_sq
=
DAT
::
tdual_ffloat_2d
();
memory
->
sfree
(
cutsq
);
eatom
=
NULL
;
vatom
=
NULL
;
cutsq
=
NULL
;
cut_inner
=
NULL
;
cut_inner_sq
=
NULL
;
}
}
/* ---------------------------------------------------------------------- */
template
<
class
DeviceType
>
void
PairLJGromacsKokkos
<
DeviceType
>::
cleanup_copy
()
{
// WHY needed: this prevents parent copy from deallocating any arrays
allocated
=
0
;
cutsq
=
NULL
;
cut_inner
=
NULL
;
cut_inner_sq
=
NULL
;
eatom
=
NULL
;
vatom
=
NULL
;
}
/* ---------------------------------------------------------------------- */
template
<
class
DeviceType
>
void
PairLJGromacsKokkos
<
DeviceType
>::
compute
(
int
eflag_in
,
int
vflag_in
)
{
eflag
=
eflag_in
;
vflag
=
vflag_in
;
if
(
neighflag
==
FULL
||
neighflag
==
FULLCLUSTER
)
no_virial_fdotr_compute
=
1
;
if
(
eflag
||
vflag
)
ev_setup
(
eflag
,
vflag
);
else
evflag
=
vflag_fdotr
=
0
;
atomKK
->
sync
(
execution_space
,
datamask_read
);
k_cutsq
.
template
sync
<
DeviceType
>
();
k_cut_inner
.
template
sync
<
DeviceType
>
();
k_cut_inner_sq
.
template
sync
<
DeviceType
>
();
k_params
.
template
sync
<
DeviceType
>
();
if
(
eflag
||
vflag
)
atomKK
->
modified
(
execution_space
,
datamask_modify
);
else
atomKK
->
modified
(
execution_space
,
F_MASK
);
x
=
atomKK
->
k_x
.
view
<
DeviceType
>
();
c_x
=
atomKK
->
k_x
.
view
<
DeviceType
>
();
f
=
atomKK
->
k_f
.
view
<
DeviceType
>
();
q
=
atomKK
->
k_q
.
view
<
DeviceType
>
();
type
=
atomKK
->
k_type
.
view
<
DeviceType
>
();
nlocal
=
atom
->
nlocal
;
nall
=
atom
->
nlocal
+
atom
->
nghost
;
special_lj
[
0
]
=
force
->
special_lj
[
0
];
special_lj
[
1
]
=
force
->
special_lj
[
1
];
special_lj
[
2
]
=
force
->
special_lj
[
2
];
special_lj
[
3
]
=
force
->
special_lj
[
3
];
qqrd2e
=
force
->
qqrd2e
;
newton_pair
=
force
->
newton_pair
;
// loop over neighbors of my atoms
copymode
=
1
;
EV_FLOAT
ev
=
pair_compute
<
PairLJGromacsKokkos
<
DeviceType
>
,
CoulLongTable
<
0
>
>
(
this
,(
NeighListKokkos
<
DeviceType
>*
)
list
);
DeviceType
::
fence
();
if
(
eflag
)
{
eng_vdwl
+=
ev
.
evdwl
;
eng_coul
+=
0.0
;
}
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
(
vflag_fdotr
)
pair_virial_fdotr_compute
(
this
);
copymode
=
0
;
}
/* ----------------------------------------------------------------------
compute LJ GROMACS pair force between atoms i and j
---------------------------------------------------------------------- */
template
<
class
DeviceType
>
template
<
bool
STACKPARAMS
,
class
Specialisation
>
KOKKOS_INLINE_FUNCTION
F_FLOAT
PairLJGromacsKokkos
<
DeviceType
>::
compute_fpair
(
const
F_FLOAT
&
rsq
,
const
int
&
i
,
const
int
&
j
,
const
int
&
itype
,
const
int
&
jtype
)
const
{
const
F_FLOAT
r2inv
=
1.0
/
rsq
;
const
F_FLOAT
r6inv
=
r2inv
*
r2inv
*
r2inv
;
F_FLOAT
forcelj
=
r6inv
*
((
STACKPARAMS
?
m_params
[
itype
][
jtype
].
lj1:
params
(
itype
,
jtype
).
lj1
)
*
r6inv
-
(
STACKPARAMS
?
m_params
[
itype
][
jtype
].
lj2:
params
(
itype
,
jtype
).
lj2
));
if
(
rsq
>
(
STACKPARAMS
?
m_params
[
itype
][
jtype
].
cut_inner_sq:
params
(
itype
,
jtype
).
cut_inner_sq
))
{
const
F_FLOAT
r
=
sqrt
(
rsq
);
const
F_FLOAT
tlj
=
r
-
(
STACKPARAMS
?
m_params
[
itype
][
jtype
].
cut_inner:
params
(
itype
,
jtype
).
cut_inner
);
const
F_FLOAT
fswitch
=
r
*
tlj
*
tlj
*
((
STACKPARAMS
?
m_params
[
itype
][
jtype
].
ljsw1:
params
(
itype
,
jtype
).
ljsw1
)
+
(
STACKPARAMS
?
m_params
[
itype
][
jtype
].
ljsw2:
params
(
itype
,
jtype
).
ljsw2
)
*
tlj
);
forcelj
+=
fswitch
;
}
return
forcelj
*
r2inv
;
}
/* ----------------------------------------------------------------------
compute LJ GROMACS pair potential energy between atoms i and j
---------------------------------------------------------------------- */
template
<
class
DeviceType
>
template
<
bool
STACKPARAMS
,
class
Specialisation
>
KOKKOS_INLINE_FUNCTION
F_FLOAT
PairLJGromacsKokkos
<
DeviceType
>::
compute_evdwl
(
const
F_FLOAT
&
rsq
,
const
int
&
i
,
const
int
&
j
,
const
int
&
itype
,
const
int
&
jtype
)
const
{
const
F_FLOAT
r2inv
=
1.0
/
rsq
;
const
F_FLOAT
r6inv
=
r2inv
*
r2inv
*
r2inv
;
F_FLOAT
englj
=
r6inv
*
((
STACKPARAMS
?
m_params
[
itype
][
jtype
].
lj3:
params
(
itype
,
jtype
).
lj3
)
*
r6inv
-
(
STACKPARAMS
?
m_params
[
itype
][
jtype
].
lj4:
params
(
itype
,
jtype
).
lj4
));
englj
+=
(
STACKPARAMS
?
m_params
[
itype
][
jtype
].
ljsw5:
params
(
itype
,
jtype
).
ljsw5
);
if
(
rsq
>
(
STACKPARAMS
?
m_params
[
itype
][
jtype
].
cut_inner_sq:
params
(
itype
,
jtype
).
cut_inner_sq
))
{
const
F_FLOAT
r
=
sqrt
(
rsq
);
const
F_FLOAT
tlj
=
r
-
(
STACKPARAMS
?
m_params
[
itype
][
jtype
].
cut_inner:
params
(
itype
,
jtype
).
cut_inner
);
const
F_FLOAT
eswitch
=
tlj
*
tlj
*
tlj
*
((
STACKPARAMS
?
m_params
[
itype
][
jtype
].
ljsw3:
params
(
itype
,
jtype
).
ljsw3
)
+
(
STACKPARAMS
?
m_params
[
itype
][
jtype
].
ljsw4:
params
(
itype
,
jtype
).
ljsw4
)
*
tlj
);
englj
+=
eswitch
;
}
return
englj
;
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
template
<
class
DeviceType
>
void
PairLJGromacsKokkos
<
DeviceType
>::
allocate
()
{
PairLJGromacs
::
allocate
();
int
n
=
atom
->
ntypes
;
memory
->
destroy
(
cutsq
);
memory
->
create_kokkos
(
k_cutsq
,
cutsq
,
n
+
1
,
n
+
1
,
"pair:cutsq"
);
d_cutsq
=
k_cutsq
.
template
view
<
DeviceType
>
();
memory
->
destroy
(
cut_inner
);
memory
->
create_kokkos
(
k_cut_inner
,
cut_inner
,
n
+
1
,
n
+
1
,
"pair:cut_inner"
);
d_cut_inner
=
k_cut_inner
.
template
view
<
DeviceType
>
();
memory
->
destroy
(
cut_inner_sq
);
memory
->
create_kokkos
(
k_cut_inner_sq
,
cut_inner_sq
,
n
+
1
,
n
+
1
,
"pair:cut_inner_sq"
);
d_cut_inner_sq
=
k_cut_inner_sq
.
template
view
<
DeviceType
>
();
k_params
=
Kokkos
::
DualView
<
params_lj
**
,
Kokkos
::
LayoutRight
,
DeviceType
>
(
"PairLJGromacs::params"
,
n
+
1
,
n
+
1
);
params
=
k_params
.
d_view
;
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
template
<
class
DeviceType
>
void
PairLJGromacsKokkos
<
DeviceType
>::
settings
(
int
narg
,
char
**
arg
)
{
if
(
narg
!=
2
)
error
->
all
(
FLERR
,
"Illegal pair_style command"
);
PairLJGromacs
::
settings
(
narg
,
arg
);
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
template
<
class
DeviceType
>
void
PairLJGromacsKokkos
<
DeviceType
>::
init_style
()
{
PairLJGromacs
::
init_style
();
// error if rRESPA with inner levels
if
(
update
->
whichflag
==
1
&&
strstr
(
update
->
integrate_style
,
"respa"
))
{
int
respa
=
0
;
if
(((
Respa
*
)
update
->
integrate
)
->
level_inner
>=
0
)
respa
=
1
;
if
(((
Respa
*
)
update
->
integrate
)
->
level_middle
>=
0
)
respa
=
2
;
if
(
respa
)
error
->
all
(
FLERR
,
"Cannot use Kokkos pair style with rRESPA inner/middle"
);
}
// irequest = neigh request made by parent class
neighflag
=
lmp
->
kokkos
->
neighflag
;
int
irequest
=
neighbor
->
nrequest
-
1
;
neighbor
->
requests
[
irequest
]
->
kokkos_host
=
Kokkos
::
Impl
::
is_same
<
DeviceType
,
LMPHostType
>::
value
&&
!
Kokkos
::
Impl
::
is_same
<
DeviceType
,
LMPDeviceType
>::
value
;
neighbor
->
requests
[
irequest
]
->
kokkos_device
=
Kokkos
::
Impl
::
is_same
<
DeviceType
,
LMPDeviceType
>::
value
;
if
(
neighflag
==
FULL
)
{
neighbor
->
requests
[
irequest
]
->
full
=
1
;
neighbor
->
requests
[
irequest
]
->
half
=
0
;
neighbor
->
requests
[
irequest
]
->
full_cluster
=
0
;
}
else
if
(
neighflag
==
HALF
||
neighflag
==
HALFTHREAD
)
{
neighbor
->
requests
[
irequest
]
->
full
=
0
;
neighbor
->
requests
[
irequest
]
->
half
=
1
;
neighbor
->
requests
[
irequest
]
->
full_cluster
=
0
;
}
else
{
error
->
all
(
FLERR
,
"Cannot use chosen neighbor list style with lj/gromacs/kk"
);
}
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
template
<
class
DeviceType
>
double
PairLJGromacsKokkos
<
DeviceType
>::
init_one
(
int
i
,
int
j
)
{
double
cutone
=
PairLJGromacs
::
init_one
(
i
,
j
);
double
cut_inner_sqm
=
cut_inner_sq
[
i
][
j
];
k_params
.
h_view
(
i
,
j
).
lj1
=
lj1
[
i
][
j
];
k_params
.
h_view
(
i
,
j
).
lj2
=
lj2
[
i
][
j
];
k_params
.
h_view
(
i
,
j
).
lj3
=
lj3
[
i
][
j
];
k_params
.
h_view
(
i
,
j
).
lj4
=
lj4
[
i
][
j
];
k_params
.
h_view
(
i
,
j
).
ljsw1
=
ljsw1
[
i
][
j
];
k_params
.
h_view
(
i
,
j
).
ljsw2
=
ljsw2
[
i
][
j
];
k_params
.
h_view
(
i
,
j
).
ljsw3
=
ljsw3
[
i
][
j
];
k_params
.
h_view
(
i
,
j
).
ljsw4
=
ljsw4
[
i
][
j
];
k_params
.
h_view
(
i
,
j
).
ljsw5
=
ljsw5
[
i
][
j
];
k_params
.
h_view
(
i
,
j
).
cut_inner_sq
=
cut_inner_sqm
;
k_params
.
h_view
(
i
,
j
).
cut_inner
=
cut_inner
[
i
][
j
];
k_params
.
h_view
(
j
,
i
)
=
k_params
.
h_view
(
i
,
j
);
if
(
i
<
MAX_TYPES_STACKPARAMS
+
1
&&
j
<
MAX_TYPES_STACKPARAMS
+
1
)
{
m_params
[
i
][
j
]
=
m_params
[
j
][
i
]
=
k_params
.
h_view
(
i
,
j
);
m_cutsq
[
j
][
i
]
=
m_cutsq
[
i
][
j
]
=
cutone
*
cutone
;
m_cut_inner_sq
[
j
][
i
]
=
m_cut_inner_sq
[
i
][
j
]
=
cut_inner_sqm
;
}
k_cutsq
.
h_view
(
i
,
j
)
=
cutone
*
cutone
;
k_cutsq
.
template
modify
<
LMPHostType
>
();
k_cut_inner_sq
.
h_view
(
i
,
j
)
=
cut_inner_sqm
;
k_cut_inner_sq
.
template
modify
<
LMPHostType
>
();
k_params
.
template
modify
<
LMPHostType
>
();
return
cutone
;
}
template
class
PairLJGromacsKokkos
<
LMPDeviceType
>
;
#ifdef KOKKOS_HAVE_CUDA
template
class
PairLJGromacsKokkos
<
LMPHostType
>
;
#endif
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