Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F88358358
pair_colloid_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
Fri, Oct 18, 09:21
Size
10 KB
Mime Type
text/x-c
Expires
Sun, Oct 20, 09:21 (1 d, 22 h)
Engine
blob
Format
Raw Data
Handle
21759325
Attached To
rLAMMPS lammps
pair_colloid_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: Trung Dac Nguyen (ORNL)
------------------------------------------------------------------------- */
#include "lmptype.h"
#include "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "pair_colloid_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
colloid_gpu_init
(
const
int
ntypes
,
double
**
cutsq
,
double
**
host_lj1
,
double
**
host_lj2
,
double
**
host_lj3
,
double
**
host_lj4
,
double
**
offset
,
double
*
special_lj
,
double
**
host_a12
,
double
**
host_a1
,
double
**
host_a2
,
double
**
host_d1
,
double
**
host_d2
,
double
**
host_sigma3
,
double
**
host_sigma6
,
int
**
host_form
,
const
int
nlocal
,
const
int
nall
,
const
int
max_nbors
,
const
int
maxspecial
,
const
double
cell_size
,
int
&
gpu_mode
,
FILE
*
screen
);
void
colloid_gpu_clear
();
int
**
colloid_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
colloid_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
colloid_gpu_bytes
();
/* ---------------------------------------------------------------------- */
PairColloidGPU
::
PairColloidGPU
(
LAMMPS
*
lmp
)
:
PairColloid
(
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
------------------------------------------------------------------------- */
PairColloidGPU
::~
PairColloidGPU
()
{
colloid_gpu_clear
();
}
/* ---------------------------------------------------------------------- */
void
PairColloidGPU
::
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
=
colloid_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
;
colloid_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
();
cpu_compute
(
host_start
,
inum
,
eflag
,
vflag
,
ilist
,
numneigh
,
firstneigh
);
cpu_time
=
MPI_Wtime
()
-
cpu_time
;
}
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void
PairColloidGPU
::
init_style
()
{
if
(
force
->
newton_pair
)
error
->
all
(
FLERR
,
"Cannot use newton pair with colloid/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
**
_form
=
NULL
;
int
n
=
atom
->
ntypes
;
memory
->
create
(
_form
,
n
+
1
,
n
+
1
,
"colloid/gpu:_form"
);
for
(
int
i
=
1
;
i
<=
n
;
i
++
)
{
for
(
int
j
=
1
;
j
<=
n
;
j
++
)
{
if
(
form
[
i
][
j
]
==
SMALL_SMALL
)
_form
[
i
][
j
]
=
0
;
else
if
(
form
[
i
][
j
]
==
SMALL_LARGE
)
_form
[
i
][
j
]
=
1
;
else
if
(
form
[
i
][
j
]
==
LARGE_LARGE
)
_form
[
i
][
j
]
=
2
;
}
}
int
maxspecial
=
0
;
if
(
atom
->
molecular
)
maxspecial
=
atom
->
maxspecial
;
int
success
=
colloid_gpu_init
(
atom
->
ntypes
+
1
,
cutsq
,
lj1
,
lj2
,
lj3
,
lj4
,
offset
,
force
->
special_lj
,
a12
,
a1
,
a2
,
d1
,
d2
,
sigma3
,
sigma6
,
_form
,
atom
->
nlocal
,
atom
->
nlocal
+
atom
->
nghost
,
300
,
maxspecial
,
cell_size
,
gpu_mode
,
screen
);
memory
->
destroy
(
_form
);
GPU_EXTRA
::
check_flag
(
success
,
error
,
world
);
if
(
gpu_mode
==
GPU_FORCE
)
{
int
irequest
=
neighbor
->
request
(
this
);
neighbor
->
requests
[
irequest
]
->
half
=
0
;
neighbor
->
requests
[
irequest
]
->
full
=
1
;
}
}
/* ---------------------------------------------------------------------- */
double
PairColloidGPU
::
memory_usage
()
{
double
bytes
=
Pair
::
memory_usage
();
return
bytes
+
colloid_gpu_bytes
();
}
/* ---------------------------------------------------------------------- */
void
PairColloidGPU
::
cpu_compute
(
int
start
,
int
inum
,
int
eflag
,
int
vflag
,
int
*
ilist
,
int
*
numneigh
,
int
**
firstneigh
)
{
int
i
,
j
,
ii
,
jj
,
jnum
,
itype
,
jtype
;
double
xtmp
,
ytmp
,
ztmp
,
delx
,
dely
,
delz
,
evdwl
,
fpair
;
double
r
,
rsq
,
r2inv
,
r6inv
,
forcelj
,
factor_lj
;
double
c1
,
c2
,
fR
,
dUR
,
dUA
;
double
K
[
9
],
h
[
4
],
g
[
4
];
int
*
jlist
;
double
**
x
=
atom
->
x
;
double
**
f
=
atom
->
f
;
int
*
type
=
atom
->
type
;
double
*
special_lj
=
force
->
special_lj
;
// 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
];
itype
=
type
[
i
];
jlist
=
firstneigh
[
i
];
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
])
continue
;
switch
(
form
[
itype
][
jtype
])
{
case
SMALL_SMALL:
r2inv
=
1.0
/
rsq
;
r6inv
=
r2inv
*
r2inv
*
r2inv
;
forcelj
=
r6inv
*
(
lj1
[
itype
][
jtype
]
*
r6inv
-
lj2
[
itype
][
jtype
]);
fpair
=
factor_lj
*
forcelj
*
r2inv
;
if
(
eflag
)
evdwl
=
r6inv
*
(
r6inv
*
lj3
[
itype
][
jtype
]
-
lj4
[
itype
][
jtype
])
-
offset
[
itype
][
jtype
];
break
;
case
SMALL_LARGE:
c2
=
a2
[
itype
][
jtype
];
K
[
1
]
=
c2
*
c2
;
K
[
2
]
=
rsq
;
K
[
0
]
=
K
[
1
]
-
rsq
;
K
[
4
]
=
rsq
*
rsq
;
K
[
3
]
=
K
[
1
]
-
K
[
2
];
K
[
3
]
*=
K
[
3
]
*
K
[
3
];
K
[
6
]
=
K
[
3
]
*
K
[
3
];
fR
=
sigma3
[
itype
][
jtype
]
*
a12
[
itype
][
jtype
]
*
c2
*
K
[
1
]
/
K
[
3
];
fpair
=
4.0
/
15.0
*
fR
*
factor_lj
*
(
2.0
*
(
K
[
1
]
+
K
[
2
])
*
(
K
[
1
]
*
(
5.0
*
K
[
1
]
+
22.0
*
K
[
2
])
+
5.0
*
K
[
4
])
*
sigma6
[
itype
][
jtype
]
/
K
[
6
]
-
5.0
)
/
K
[
0
];
if
(
eflag
)
evdwl
=
2.0
/
9.0
*
fR
*
(
1.0
-
(
K
[
1
]
*
(
K
[
1
]
*
(
K
[
1
]
/
3.0
+
3.0
*
K
[
2
])
+
4.2
*
K
[
4
])
+
K
[
2
]
*
K
[
4
])
*
sigma6
[
itype
][
jtype
]
/
K
[
6
])
-
offset
[
itype
][
jtype
];
if
(
rsq
<=
K
[
1
])
error
->
one
(
FLERR
,
"Overlapping small/large in pair colloid"
);
break
;
case
LARGE_LARGE:
r
=
sqrt
(
rsq
);
c1
=
a1
[
itype
][
jtype
];
c2
=
a2
[
itype
][
jtype
];
K
[
0
]
=
c1
*
c2
;
K
[
1
]
=
c1
+
c2
;
K
[
2
]
=
c1
-
c2
;
K
[
3
]
=
K
[
1
]
+
r
;
K
[
4
]
=
K
[
1
]
-
r
;
K
[
5
]
=
K
[
2
]
+
r
;
K
[
6
]
=
K
[
2
]
-
r
;
K
[
7
]
=
1.0
/
(
K
[
3
]
*
K
[
4
]);
K
[
8
]
=
1.0
/
(
K
[
5
]
*
K
[
6
]);
g
[
0
]
=
pow
(
K
[
3
],
-
7.0
);
g
[
1
]
=
pow
(
K
[
4
],
-
7.0
);
g
[
2
]
=
pow
(
K
[
5
],
-
7.0
);
g
[
3
]
=
pow
(
K
[
6
],
-
7.0
);
h
[
0
]
=
((
K
[
3
]
+
5.0
*
K
[
1
])
*
K
[
3
]
+
30.0
*
K
[
0
])
*
g
[
0
];
h
[
1
]
=
((
K
[
4
]
+
5.0
*
K
[
1
])
*
K
[
4
]
+
30.0
*
K
[
0
])
*
g
[
1
];
h
[
2
]
=
((
K
[
5
]
+
5.0
*
K
[
2
])
*
K
[
5
]
-
30.0
*
K
[
0
])
*
g
[
2
];
h
[
3
]
=
((
K
[
6
]
+
5.0
*
K
[
2
])
*
K
[
6
]
-
30.0
*
K
[
0
])
*
g
[
3
];
g
[
0
]
*=
42.0
*
K
[
0
]
/
K
[
3
]
+
6.0
*
K
[
1
]
+
K
[
3
];
g
[
1
]
*=
42.0
*
K
[
0
]
/
K
[
4
]
+
6.0
*
K
[
1
]
+
K
[
4
];
g
[
2
]
*=
-
42.0
*
K
[
0
]
/
K
[
5
]
+
6.0
*
K
[
2
]
+
K
[
5
];
g
[
3
]
*=
-
42.0
*
K
[
0
]
/
K
[
6
]
+
6.0
*
K
[
2
]
+
K
[
6
];
fR
=
a12
[
itype
][
jtype
]
*
sigma6
[
itype
][
jtype
]
/
r
/
37800.0
;
evdwl
=
fR
*
(
h
[
0
]
-
h
[
1
]
-
h
[
2
]
+
h
[
3
]);
dUR
=
evdwl
/
r
+
5.0
*
fR
*
(
g
[
0
]
+
g
[
1
]
-
g
[
2
]
-
g
[
3
]);
dUA
=
-
a12
[
itype
][
jtype
]
/
3.0
*
r
*
((
2.0
*
K
[
0
]
*
K
[
7
]
+
1.0
)
*
K
[
7
]
+
(
2.0
*
K
[
0
]
*
K
[
8
]
-
1.0
)
*
K
[
8
]);
fpair
=
factor_lj
*
(
dUR
+
dUA
)
/
r
;
if
(
eflag
)
evdwl
+=
a12
[
itype
][
jtype
]
/
6.0
*
(
2.0
*
K
[
0
]
*
(
K
[
7
]
+
K
[
8
])
-
log
(
K
[
8
]
/
K
[
7
]))
-
offset
[
itype
][
jtype
];
if
(
r
<=
K
[
1
])
error
->
one
(
FLERR
,
"Overlapping large/large in pair colloid"
);
break
;
}
if
(
eflag
)
evdwl
*=
factor_lj
;
f
[
i
][
0
]
+=
delx
*
fpair
;
f
[
i
][
1
]
+=
dely
*
fpair
;
f
[
i
][
2
]
+=
delz
*
fpair
;
if
(
evflag
)
ev_tally_full
(
i
,
evdwl
,
0.0
,
fpair
,
delx
,
dely
,
delz
);
}
}
}
Event Timeline
Log In to Comment