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rLAMMPS lammps
pair_table_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 authors: Trung Dac Nguyen (ORNL)
------------------------------------------------------------------------- */
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include "pair_table_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"
#define LOOKUP 0
#define LINEAR 1
#define SPLINE 2
#define BITMAP 3
using
namespace
LAMMPS_NS
;
// External functions from cuda library for atom decomposition
int
table_gpu_init
(
const
int
ntypes
,
double
**
cutsq
,
double
***
host_table_coeffs
,
double
**
host_table_data
,
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
,
int
tabstyle
,
int
ntables
,
int
tablength
);
void
table_gpu_clear
();
int
**
table_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
table_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
table_gpu_bytes
();
/* ---------------------------------------------------------------------- */
PairTableGPU
::
PairTableGPU
(
LAMMPS
*
lmp
)
:
PairTable
(
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
------------------------------------------------------------------------- */
PairTableGPU
::~
PairTableGPU
()
{
table_gpu_clear
();
}
/* ---------------------------------------------------------------------- */
void
PairTableGPU
::
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
=
table_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
;
table_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
PairTableGPU
::
init_style
()
{
if
(
force
->
newton_pair
)
error
->
all
(
FLERR
,
"Cannot use newton pair with table/gpu pair style"
);
int
ntypes
=
atom
->
ntypes
;
// 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
;
// pack tables and send them to device
double
***
table_coeffs
=
NULL
;
double
**
table_data
=
NULL
;
memory
->
create
(
table_coeffs
,
ntypes
+
1
,
ntypes
+
1
,
6
,
"table:coeffs"
);
Table
*
tb
;
for
(
int
i
=
1
;
i
<=
atom
->
ntypes
;
i
++
)
for
(
int
j
=
1
;
j
<=
atom
->
ntypes
;
j
++
)
{
int
n
=
tabindex
[
i
][
j
];
tb
=
&
tables
[
n
];
table_coeffs
[
i
][
j
][
0
]
=
n
;
table_coeffs
[
i
][
j
][
1
]
=
tb
->
nshiftbits
;
table_coeffs
[
i
][
j
][
2
]
=
tb
->
nmask
;
table_coeffs
[
i
][
j
][
3
]
=
tb
->
innersq
;
table_coeffs
[
i
][
j
][
4
]
=
tb
->
invdelta
;
table_coeffs
[
i
][
j
][
5
]
=
tb
->
deltasq6
;
}
if
(
tabstyle
!=
BITMAP
)
{
memory
->
create
(
table_data
,
ntables
,
6
*
tablength
,
"table:data"
);
for
(
int
n
=
0
;
n
<
ntables
;
n
++
)
{
tb
=
&
tables
[
n
];
if
(
tabstyle
==
LOOKUP
)
{
for
(
int
k
=
0
;
k
<
tablength
-
1
;
k
++
)
{
table_data
[
n
][
6
*
k
+
1
]
=
tb
->
e
[
k
];
table_data
[
n
][
6
*
k
+
2
]
=
tb
->
f
[
k
];
}
}
else
if
(
tabstyle
==
LINEAR
)
{
for
(
int
k
=
0
;
k
<
tablength
;
k
++
)
{
table_data
[
n
][
6
*
k
+
0
]
=
tb
->
rsq
[
k
];
table_data
[
n
][
6
*
k
+
1
]
=
tb
->
e
[
k
];
table_data
[
n
][
6
*
k
+
2
]
=
tb
->
f
[
k
];
if
(
k
<
tablength
-
1
)
{
table_data
[
n
][
6
*
k
+
3
]
=
tb
->
de
[
k
];
table_data
[
n
][
6
*
k
+
4
]
=
tb
->
df
[
k
];
}
}
}
else
if
(
tabstyle
==
SPLINE
)
{
for
(
int
k
=
0
;
k
<
tablength
;
k
++
)
{
table_data
[
n
][
6
*
k
+
0
]
=
tb
->
rsq
[
k
];
table_data
[
n
][
6
*
k
+
1
]
=
tb
->
e
[
k
];
table_data
[
n
][
6
*
k
+
2
]
=
tb
->
f
[
k
];
table_data
[
n
][
6
*
k
+
3
]
=
tb
->
e2
[
k
];
table_data
[
n
][
6
*
k
+
4
]
=
tb
->
f2
[
k
];
}
}
}
}
else
{
int
ntable
=
1
<<
tablength
;
memory
->
create
(
table_data
,
ntables
,
6
*
ntable
,
"table:data"
);
for
(
int
n
=
0
;
n
<
ntables
;
n
++
)
{
tb
=
&
tables
[
n
];
for
(
int
k
=
0
;
k
<
ntable
;
k
++
)
{
table_data
[
n
][
6
*
k
+
0
]
=
tb
->
rsq
[
k
];
table_data
[
n
][
6
*
k
+
1
]
=
tb
->
e
[
k
];
table_data
[
n
][
6
*
k
+
2
]
=
tb
->
f
[
k
];
table_data
[
n
][
6
*
k
+
3
]
=
tb
->
de
[
k
];
table_data
[
n
][
6
*
k
+
4
]
=
tb
->
df
[
k
];
table_data
[
n
][
6
*
k
+
5
]
=
tb
->
drsq
[
k
];
}
}
}
int
maxspecial
=
0
;
if
(
atom
->
molecular
)
maxspecial
=
atom
->
maxspecial
;
int
success
=
table_gpu_init
(
atom
->
ntypes
+
1
,
cutsq
,
table_coeffs
,
table_data
,
force
->
special_lj
,
atom
->
nlocal
,
atom
->
nlocal
+
atom
->
nghost
,
300
,
maxspecial
,
cell_size
,
gpu_mode
,
screen
,
tabstyle
,
ntables
,
tablength
);
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
;
}
memory
->
destroy
(
table_coeffs
);
memory
->
destroy
(
table_data
);
}
/* ---------------------------------------------------------------------- */
double
PairTableGPU
::
memory_usage
()
{
double
bytes
=
Pair
::
memory_usage
();
return
bytes
+
table_gpu_bytes
();
}
/* ---------------------------------------------------------------------- */
void
PairTableGPU
::
cpu_compute
(
int
start
,
int
inum
,
int
eflag
,
int
vflag
,
int
*
ilist
,
int
*
numneigh
,
int
**
firstneigh
)
{
int
i
,
j
,
ii
,
jj
,
jnum
,
itype
,
jtype
,
itable
;
double
xtmp
,
ytmp
,
ztmp
,
delx
,
dely
,
delz
,
evdwl
,
fpair
;
double
rsq
,
factor_lj
,
fraction
,
value
,
a
,
b
;
int
*
jlist
;
Table
*
tb
;
union_int_float_t
rsq_lookup
;
int
tlm1
=
tablength
-
1
;
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
])
{
tb
=
&
tables
[
tabindex
[
itype
][
jtype
]];
if
(
rsq
<
tb
->
innersq
)
error
->
one
(
FLERR
,
"Pair distance < table inner cutoff"
);
if
(
tabstyle
==
LOOKUP
)
{
itable
=
static_cast
<
int
>
((
rsq
-
tb
->
innersq
)
*
tb
->
invdelta
);
if
(
itable
>=
tlm1
)
error
->
one
(
FLERR
,
"Pair distance > table outer cutoff"
);
fpair
=
factor_lj
*
tb
->
f
[
itable
];
}
else
if
(
tabstyle
==
LINEAR
)
{
itable
=
static_cast
<
int
>
((
rsq
-
tb
->
innersq
)
*
tb
->
invdelta
);
if
(
itable
>=
tlm1
)
error
->
one
(
FLERR
,
"Pair distance > table outer cutoff"
);
fraction
=
(
rsq
-
tb
->
rsq
[
itable
])
*
tb
->
invdelta
;
value
=
tb
->
f
[
itable
]
+
fraction
*
tb
->
df
[
itable
];
fpair
=
factor_lj
*
value
;
}
else
if
(
tabstyle
==
SPLINE
)
{
itable
=
static_cast
<
int
>
((
rsq
-
tb
->
innersq
)
*
tb
->
invdelta
);
if
(
itable
>=
tlm1
)
error
->
one
(
FLERR
,
"Pair distance > table outer cutoff"
);
b
=
(
rsq
-
tb
->
rsq
[
itable
])
*
tb
->
invdelta
;
a
=
1.0
-
b
;
value
=
a
*
tb
->
f
[
itable
]
+
b
*
tb
->
f
[
itable
+
1
]
+
((
a
*
a
*
a
-
a
)
*
tb
->
f2
[
itable
]
+
(
b
*
b
*
b
-
b
)
*
tb
->
f2
[
itable
+
1
])
*
tb
->
deltasq6
;
fpair
=
factor_lj
*
value
;
}
else
{
rsq_lookup
.
f
=
rsq
;
itable
=
rsq_lookup
.
i
&
tb
->
nmask
;
itable
>>=
tb
->
nshiftbits
;
fraction
=
(
rsq_lookup
.
f
-
tb
->
rsq
[
itable
])
*
tb
->
drsq
[
itable
];
value
=
tb
->
f
[
itable
]
+
fraction
*
tb
->
df
[
itable
];
fpair
=
factor_lj
*
value
;
}
f
[
i
][
0
]
+=
delx
*
fpair
;
f
[
i
][
1
]
+=
dely
*
fpair
;
f
[
i
][
2
]
+=
delz
*
fpair
;
if
(
eflag
)
{
if
(
tabstyle
==
LOOKUP
)
evdwl
=
tb
->
e
[
itable
];
else
if
(
tabstyle
==
LINEAR
||
tabstyle
==
BITMAP
)
evdwl
=
tb
->
e
[
itable
]
+
fraction
*
tb
->
de
[
itable
];
else
evdwl
=
a
*
tb
->
e
[
itable
]
+
b
*
tb
->
e
[
itable
+
1
]
+
((
a
*
a
*
a
-
a
)
*
tb
->
e2
[
itable
]
+
(
b
*
b
*
b
-
b
)
*
tb
->
e2
[
itable
+
1
])
*
tb
->
deltasq6
;
evdwl
*=
factor_lj
;
}
if
(
evflag
)
ev_tally_full
(
i
,
evdwl
,
0.0
,
fpair
,
delx
,
dely
,
delz
);
}
}
}
}
Event Timeline
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