Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F64426998
pair_lj_sdk_gpu.cpp
No One
Temporary
Actions
Download File
Edit File
Delete File
View Transforms
Subscribe
Mute Notifications
Award Token
Subscribers
None
File Metadata
Details
File Info
Storage
Attached
Created
Sun, May 26, 19:41
Size
8 KB
Mime Type
text/x-c++
Expires
Tue, May 28, 19:41 (1 d, 23 h)
Engine
blob
Format
Raw Data
Handle
17766588
Attached To
rLAMMPS lammps
pair_lj_sdk_gpu.cpp
View Options
/* ----------------------------------------------------------------------
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: Mike Brown (SNL)
------------------------------------------------------------------------- */
#include "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "pair_lj_sdk_gpu.h"
#include "atom.h"
#include "atom_vec.h"
#include "comm.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "integrate.h"
#include "memory.h"
#include "error.h"
#include "neigh_request.h"
#include "universe.h"
#include "update.h"
#include "domain.h"
#include "string.h"
#include "gpu_extra.h"
using
namespace
LAMMPS_NS
;
// External functions from cuda library for atom decomposition
int
cmm_gpu_init
(
const
int
ntypes
,
double
**
cutsq
,
int
**
cg_types
,
double
**
host_lj1
,
double
**
host_lj2
,
double
**
host_lj3
,
double
**
host_lj4
,
double
**
offset
,
double
*
special_lj
,
const
int
nlocal
,
const
int
nall
,
const
int
max_nbors
,
const
int
maxspecial
,
const
double
cell_size
,
int
&
gpu_mode
,
FILE
*
screen
);
void
cmm_gpu_clear
();
int
**
cmm_gpu_compute_n
(
const
int
ago
,
const
int
inum
,
const
int
nall
,
double
**
host_x
,
int
*
host_type
,
double
*
sublo
,
double
*
subhi
,
tagint
*
tag
,
int
**
nspecial
,
tagint
**
special
,
const
bool
eflag
,
const
bool
vflag
,
const
bool
eatom
,
const
bool
vatom
,
int
&
host_start
,
int
**
ilist
,
int
**
jnum
,
const
double
cpu_time
,
bool
&
success
);
void
cmm_gpu_compute
(
const
int
ago
,
const
int
inum
,
const
int
nall
,
double
**
host_x
,
int
*
host_type
,
int
*
ilist
,
int
*
numj
,
int
**
firstneigh
,
const
bool
eflag
,
const
bool
vflag
,
const
bool
eatom
,
const
bool
vatom
,
int
&
host_start
,
const
double
cpu_time
,
bool
&
success
);
double
cmm_gpu_bytes
();
#include "lj_sdk_common.h"
using
namespace
LJSDKParms
;
/* ---------------------------------------------------------------------- */
PairLJSDKGPU
::
PairLJSDKGPU
(
LAMMPS
*
lmp
)
:
PairLJSDK
(
lmp
),
gpu_mode
(
GPU_FORCE
)
{
respa_enable
=
0
;
reinitflag
=
0
;
cpu_time
=
0.0
;
GPU_EXTRA
::
gpu_ready
(
lmp
->
modify
,
lmp
->
error
);
}
/* ----------------------------------------------------------------------
free all arrays
------------------------------------------------------------------------- */
PairLJSDKGPU
::~
PairLJSDKGPU
()
{
cmm_gpu_clear
();
}
/* ---------------------------------------------------------------------- */
void
PairLJSDKGPU
::
compute
(
int
eflag
,
int
vflag
)
{
if
(
eflag
||
vflag
)
ev_setup
(
eflag
,
vflag
);
else
evflag
=
vflag_fdotr
=
0
;
int
nall
=
atom
->
nlocal
+
atom
->
nghost
;
int
inum
,
host_start
;
bool
success
=
true
;
int
*
ilist
,
*
numneigh
,
**
firstneigh
;
if
(
gpu_mode
!=
GPU_FORCE
)
{
inum
=
atom
->
nlocal
;
firstneigh
=
cmm_gpu_compute_n
(
neighbor
->
ago
,
inum
,
nall
,
atom
->
x
,
atom
->
type
,
domain
->
sublo
,
domain
->
subhi
,
atom
->
tag
,
atom
->
nspecial
,
atom
->
special
,
eflag
,
vflag
,
eflag_atom
,
vflag_atom
,
host_start
,
&
ilist
,
&
numneigh
,
cpu_time
,
success
);
}
else
{
inum
=
list
->
inum
;
ilist
=
list
->
ilist
;
numneigh
=
list
->
numneigh
;
firstneigh
=
list
->
firstneigh
;
cmm_gpu_compute
(
neighbor
->
ago
,
inum
,
nall
,
atom
->
x
,
atom
->
type
,
ilist
,
numneigh
,
firstneigh
,
eflag
,
vflag
,
eflag_atom
,
vflag_atom
,
host_start
,
cpu_time
,
success
);
}
if
(
!
success
)
error
->
one
(
FLERR
,
"Insufficient memory on accelerator"
);
if
(
host_start
<
inum
)
{
cpu_time
=
MPI_Wtime
();
if
(
evflag
)
{
if
(
eflag
)
cpu_compute
<
1
,
1
>
(
host_start
,
inum
,
ilist
,
numneigh
,
firstneigh
);
else
cpu_compute
<
1
,
0
>
(
host_start
,
inum
,
ilist
,
numneigh
,
firstneigh
);
}
else
cpu_compute
<
0
,
0
>
(
host_start
,
inum
,
ilist
,
numneigh
,
firstneigh
);
cpu_time
=
MPI_Wtime
()
-
cpu_time
;
}
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void
PairLJSDKGPU
::
init_style
()
{
if
(
force
->
newton_pair
)
error
->
all
(
FLERR
,
"Cannot use newton pair with lj/sdk/gpu pair style"
);
// Repeat cutsq calculation because done after call to init_style
double
maxcut
=
-
1.0
;
double
cut
;
for
(
int
i
=
1
;
i
<=
atom
->
ntypes
;
i
++
)
{
for
(
int
j
=
i
;
j
<=
atom
->
ntypes
;
j
++
)
{
if
(
setflag
[
i
][
j
]
!=
0
||
(
setflag
[
i
][
i
]
!=
0
&&
setflag
[
j
][
j
]
!=
0
))
{
cut
=
init_one
(
i
,
j
);
cut
*=
cut
;
if
(
cut
>
maxcut
)
maxcut
=
cut
;
cutsq
[
i
][
j
]
=
cutsq
[
j
][
i
]
=
cut
;
}
else
cutsq
[
i
][
j
]
=
cutsq
[
j
][
i
]
=
0.0
;
}
}
double
cell_size
=
sqrt
(
maxcut
)
+
neighbor
->
skin
;
int
maxspecial
=
0
;
if
(
atom
->
molecular
)
maxspecial
=
atom
->
maxspecial
;
int
success
=
cmm_gpu_init
(
atom
->
ntypes
+
1
,
cutsq
,
lj_type
,
lj1
,
lj2
,
lj3
,
lj4
,
offset
,
force
->
special_lj
,
atom
->
nlocal
,
atom
->
nlocal
+
atom
->
nghost
,
300
,
maxspecial
,
cell_size
,
gpu_mode
,
screen
);
GPU_EXTRA
::
check_flag
(
success
,
error
,
world
);
if
(
gpu_mode
==
GPU_FORCE
)
{
int
irequest
=
neighbor
->
request
(
this
,
instance_me
);
neighbor
->
requests
[
irequest
]
->
half
=
0
;
neighbor
->
requests
[
irequest
]
->
full
=
1
;
}
}
/* ---------------------------------------------------------------------- */
double
PairLJSDKGPU
::
memory_usage
()
{
double
bytes
=
Pair
::
memory_usage
();
return
bytes
+
cmm_gpu_bytes
();
}
/* ---------------------------------------------------------------------- */
template
<
int
EVFLAG
,
int
EFLAG
>
void
PairLJSDKGPU
::
cpu_compute
(
int
start
,
int
inum
,
int
*
ilist
,
int
*
numneigh
,
int
**
firstneigh
)
{
int
i
,
j
,
ii
,
jj
,
jtype
;
double
xtmp
,
ytmp
,
ztmp
,
delx
,
dely
,
delz
,
evdwl
,
fpair
;
double
rsq
,
r2inv
,
forcelj
,
factor_lj
;
const
double
*
const
*
const
x
=
atom
->
x
;
double
*
const
*
const
f
=
atom
->
f
;
const
int
*
const
type
=
atom
->
type
;
const
double
*
const
special_lj
=
force
->
special_lj
;
double
fxtmp
,
fytmp
,
fztmp
;
evdwl
=
0.0
;
// loop over neighbors of my atoms
for
(
ii
=
start
;
ii
<
inum
;
ii
++
)
{
i
=
ilist
[
ii
];
xtmp
=
x
[
i
][
0
];
ytmp
=
x
[
i
][
1
];
ztmp
=
x
[
i
][
2
];
fxtmp
=
fytmp
=
fztmp
=
0.0
;
const
int
itype
=
type
[
i
];
const
int
*
const
jlist
=
firstneigh
[
i
];
const
int
jnum
=
numneigh
[
i
];
for
(
jj
=
0
;
jj
<
jnum
;
jj
++
)
{
j
=
jlist
[
jj
];
factor_lj
=
special_lj
[
sbmask
(
j
)];
j
&=
NEIGHMASK
;
delx
=
xtmp
-
x
[
j
][
0
];
dely
=
ytmp
-
x
[
j
][
1
];
delz
=
ztmp
-
x
[
j
][
2
];
rsq
=
delx
*
delx
+
dely
*
dely
+
delz
*
delz
;
jtype
=
type
[
j
];
if
(
rsq
<
cutsq
[
itype
][
jtype
])
{
r2inv
=
1.0
/
rsq
;
const
int
ljt
=
lj_type
[
itype
][
jtype
];
if
(
ljt
==
LJ12_4
)
{
const
double
r4inv
=
r2inv
*
r2inv
;
forcelj
=
r4inv
*
(
lj1
[
itype
][
jtype
]
*
r4inv
*
r4inv
-
lj2
[
itype
][
jtype
]);
if
(
EFLAG
)
evdwl
=
r4inv
*
(
lj3
[
itype
][
jtype
]
*
r4inv
*
r4inv
-
lj4
[
itype
][
jtype
])
-
offset
[
itype
][
jtype
];
}
else
if
(
ljt
==
LJ9_6
)
{
const
double
r3inv
=
r2inv
*
sqrt
(
r2inv
);
const
double
r6inv
=
r3inv
*
r3inv
;
forcelj
=
r6inv
*
(
lj1
[
itype
][
jtype
]
*
r3inv
-
lj2
[
itype
][
jtype
]);
if
(
EFLAG
)
evdwl
=
r6inv
*
(
lj3
[
itype
][
jtype
]
*
r3inv
-
lj4
[
itype
][
jtype
])
-
offset
[
itype
][
jtype
];
}
else
if
(
ljt
==
LJ12_6
)
{
const
double
r6inv
=
r2inv
*
r2inv
*
r2inv
;
forcelj
=
r6inv
*
(
lj1
[
itype
][
jtype
]
*
r6inv
-
lj2
[
itype
][
jtype
]);
if
(
EFLAG
)
evdwl
=
r6inv
*
(
lj3
[
itype
][
jtype
]
*
r6inv
-
lj4
[
itype
][
jtype
])
-
offset
[
itype
][
jtype
];
}
else
continue
;
fpair
=
factor_lj
*
forcelj
*
r2inv
;
fxtmp
+=
delx
*
fpair
;
fytmp
+=
dely
*
fpair
;
fztmp
+=
delz
*
fpair
;
if
(
EVFLAG
)
ev_tally_full
(
i
,
evdwl
,
0.0
,
fpair
,
delx
,
dely
,
delz
);
}
}
f
[
i
][
0
]
+=
fxtmp
;
f
[
i
][
1
]
+=
fytmp
;
f
[
i
][
2
]
+=
fztmp
;
}
}
Event Timeline
Log In to Comment