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rLAMMPS lammps
pair_colloid_gpu.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: Trung Dac Nguyen (ORNL)
------------------------------------------------------------------------- */
#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
,
instance_me
);
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
);
}
}
}
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