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rLAMMPS lammps
pair_gayberne_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: Mike Brown (SNL)
------------------------------------------------------------------------- */
#include "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "pair_gayberne_gpu.h"
#include "math_extra.h"
#include "atom.h"
#include "atom_vec.h"
#include "atom_vec_ellipsoid.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 "domain.h"
#include "update.h"
#include "string.h"
#include "gpu_extra.h"
using
namespace
LAMMPS_NS
;
// External functions from cuda library for atom decomposition
int
gb_gpu_init
(
const
int
ntypes
,
const
double
gamma
,
const
double
upsilon
,
const
double
mu
,
double
**
shape
,
double
**
well
,
double
**
cutsq
,
double
**
sigma
,
double
**
epsilon
,
double
*
host_lshape
,
int
**
form
,
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
gb_gpu_clear
();
int
**
gb_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
,
double
**
host_quat
);
int
*
gb_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
**
host_quat
);
double
gb_gpu_bytes
();
enum
{
SPHERE_SPHERE
,
SPHERE_ELLIPSE
,
ELLIPSE_SPHERE
,
ELLIPSE_ELLIPSE
};
/* ---------------------------------------------------------------------- */
PairGayBerneGPU
::
PairGayBerneGPU
(
LAMMPS
*
lmp
)
:
PairGayBerne
(
lmp
),
gpu_mode
(
GPU_FORCE
)
{
quat_nmax
=
0
;
quat
=
NULL
;
GPU_EXTRA
::
gpu_ready
(
lmp
->
modify
,
lmp
->
error
);
}
/* ----------------------------------------------------------------------
free all arrays
------------------------------------------------------------------------- */
PairGayBerneGPU
::~
PairGayBerneGPU
()
{
gb_gpu_clear
();
cpu_time
=
0.0
;
memory
->
destroy
(
quat
);
}
/* ---------------------------------------------------------------------- */
void
PairGayBerneGPU
::
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
(
nall
>
quat_nmax
)
{
quat_nmax
=
static_cast
<
int
>
(
1.1
*
nall
);
memory
->
grow
(
quat
,
quat_nmax
,
4
,
"pair:quat"
);
}
AtomVecEllipsoid
::
Bonus
*
bonus
=
avec
->
bonus
;
int
*
ellipsoid
=
atom
->
ellipsoid
;
for
(
int
i
=
0
;
i
<
nall
;
i
++
)
{
int
qi
=
ellipsoid
[
i
];
if
(
qi
>
-
1
)
{
quat
[
i
][
0
]
=
bonus
[
qi
].
quat
[
0
];
quat
[
i
][
1
]
=
bonus
[
qi
].
quat
[
1
];
quat
[
i
][
2
]
=
bonus
[
qi
].
quat
[
2
];
quat
[
i
][
3
]
=
bonus
[
qi
].
quat
[
3
];
}
}
if
(
gpu_mode
!=
GPU_FORCE
)
{
inum
=
atom
->
nlocal
;
firstneigh
=
gb_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
,
quat
);
}
else
{
inum
=
list
->
inum
;
numneigh
=
list
->
numneigh
;
firstneigh
=
list
->
firstneigh
;
ilist
=
gb_gpu_compute
(
neighbor
->
ago
,
inum
,
nall
,
atom
->
x
,
atom
->
type
,
list
->
ilist
,
numneigh
,
firstneigh
,
eflag
,
vflag
,
eflag_atom
,
vflag_atom
,
host_start
,
cpu_time
,
success
,
quat
);
}
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
PairGayBerneGPU
::
init_style
()
{
avec
=
(
AtomVecEllipsoid
*
)
atom
->
style_match
(
"ellipsoid"
);
if
(
!
avec
)
error
->
all
(
FLERR
,
"Pair gayberne/gpu requires atom style ellipsoid"
);
if
(
force
->
newton_pair
)
error
->
all
(
FLERR
,
"Cannot use newton pair with gayberne/gpu pair style"
);
if
(
!
atom
->
ellipsoid_flag
)
error
->
all
(
FLERR
,
"Pair gayberne/gpu requires atom style ellipsoid"
);
// per-type shape precalculations
// require that atom shapes are identical within each type
// if shape = 0 for point particle, set shape = 1 as required by Gay-Berne
for
(
int
i
=
1
;
i
<=
atom
->
ntypes
;
i
++
)
{
if
(
!
atom
->
shape_consistency
(
i
,
shape1
[
i
][
0
],
shape1
[
i
][
1
],
shape1
[
i
][
2
]))
error
->
all
(
FLERR
,
"Pair gayberne/gpu requires atoms with same type have same shape"
);
if
(
shape1
[
i
][
0
]
==
0.0
)
shape1
[
i
][
0
]
=
shape1
[
i
][
1
]
=
shape1
[
i
][
2
]
=
1.0
;
shape2
[
i
][
0
]
=
shape1
[
i
][
0
]
*
shape1
[
i
][
0
];
shape2
[
i
][
1
]
=
shape1
[
i
][
1
]
*
shape1
[
i
][
1
];
shape2
[
i
][
2
]
=
shape1
[
i
][
2
]
*
shape1
[
i
][
2
];
lshape
[
i
]
=
(
shape1
[
i
][
0
]
*
shape1
[
i
][
1
]
+
shape1
[
i
][
2
]
*
shape1
[
i
][
2
])
*
sqrt
(
shape1
[
i
][
0
]
*
shape1
[
i
][
1
]);
}
// 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
=
gb_gpu_init
(
atom
->
ntypes
+
1
,
gamma
,
upsilon
,
mu
,
shape2
,
well
,
cutsq
,
sigma
,
epsilon
,
lshape
,
form
,
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
);
neighbor
->
requests
[
irequest
]
->
half
=
0
;
neighbor
->
requests
[
irequest
]
->
full
=
1
;
}
quat_nmax
=
static_cast
<
int
>
(
1.1
*
(
atom
->
nlocal
+
atom
->
nghost
));
memory
->
grow
(
quat
,
quat_nmax
,
4
,
"pair:quat"
);
}
/* ---------------------------------------------------------------------- */
double
PairGayBerneGPU
::
memory_usage
()
{
double
bytes
=
Pair
::
memory_usage
();
return
bytes
+
memory
->
usage
(
quat
,
quat_nmax
)
+
gb_gpu_bytes
();
}
/* ---------------------------------------------------------------------- */
void
PairGayBerneGPU
::
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
evdwl
,
one_eng
,
rsq
,
r2inv
,
r6inv
,
forcelj
,
factor_lj
;
double
fforce
[
3
],
ttor
[
3
],
rtor
[
3
],
r12
[
3
];
double
a1
[
3
][
3
],
b1
[
3
][
3
],
g1
[
3
][
3
],
a2
[
3
][
3
],
b2
[
3
][
3
],
g2
[
3
][
3
],
temp
[
3
][
3
];
int
*
jlist
;
double
*
iquat
,
*
jquat
;
AtomVecEllipsoid
::
Bonus
*
bonus
=
avec
->
bonus
;
int
*
ellipsoid
=
atom
->
ellipsoid
;
double
**
x
=
atom
->
x
;
double
**
f
=
atom
->
f
;
double
**
tor
=
atom
->
torque
;
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
];
itype
=
type
[
i
];
if
(
form
[
itype
][
itype
]
==
ELLIPSE_ELLIPSE
)
{
iquat
=
bonus
[
ellipsoid
[
i
]].
quat
;
MathExtra
::
quat_to_mat_trans
(
iquat
,
a1
);
MathExtra
::
diag_times3
(
well
[
itype
],
a1
,
temp
);
MathExtra
::
transpose_times3
(
a1
,
temp
,
b1
);
MathExtra
::
diag_times3
(
shape2
[
itype
],
a1
,
temp
);
MathExtra
::
transpose_times3
(
a1
,
temp
,
g1
);
}
jlist
=
firstneigh
[
i
];
jnum
=
numneigh
[
i
];
for
(
jj
=
0
;
jj
<
jnum
;
jj
++
)
{
j
=
jlist
[
jj
];
factor_lj
=
special_lj
[
sbmask
(
j
)];
j
&=
NEIGHMASK
;
// r12 = center to center vector
r12
[
0
]
=
x
[
j
][
0
]
-
x
[
i
][
0
];
r12
[
1
]
=
x
[
j
][
1
]
-
x
[
i
][
1
];
r12
[
2
]
=
x
[
j
][
2
]
-
x
[
i
][
2
];
rsq
=
MathExtra
::
dot3
(
r12
,
r12
);
jtype
=
type
[
j
];
// compute if less than cutoff
if
(
rsq
<
cutsq
[
itype
][
jtype
])
{
switch
(
form
[
itype
][
jtype
])
{
case
SPHERE_SPHERE:
r2inv
=
1.0
/
rsq
;
r6inv
=
r2inv
*
r2inv
*
r2inv
;
forcelj
=
r6inv
*
(
lj1
[
itype
][
jtype
]
*
r6inv
-
lj2
[
itype
][
jtype
]);
forcelj
*=
-
r2inv
;
if
(
eflag
)
one_eng
=
r6inv
*
(
r6inv
*
lj3
[
itype
][
jtype
]
-
lj4
[
itype
][
jtype
])
-
offset
[
itype
][
jtype
];
fforce
[
0
]
=
r12
[
0
]
*
forcelj
;
fforce
[
1
]
=
r12
[
1
]
*
forcelj
;
fforce
[
2
]
=
r12
[
2
]
*
forcelj
;
ttor
[
0
]
=
ttor
[
1
]
=
ttor
[
2
]
=
0.0
;
rtor
[
0
]
=
rtor
[
1
]
=
rtor
[
2
]
=
0.0
;
break
;
case
SPHERE_ELLIPSE:
jquat
=
bonus
[
ellipsoid
[
j
]].
quat
;
MathExtra
::
quat_to_mat_trans
(
jquat
,
a2
);
MathExtra
::
diag_times3
(
well
[
jtype
],
a2
,
temp
);
MathExtra
::
transpose_times3
(
a2
,
temp
,
b2
);
MathExtra
::
diag_times3
(
shape2
[
jtype
],
a2
,
temp
);
MathExtra
::
transpose_times3
(
a2
,
temp
,
g2
);
one_eng
=
gayberne_lj
(
j
,
i
,
a2
,
b2
,
g2
,
r12
,
rsq
,
fforce
,
rtor
);
ttor
[
0
]
=
ttor
[
1
]
=
ttor
[
2
]
=
0.0
;
break
;
case
ELLIPSE_SPHERE:
one_eng
=
gayberne_lj
(
i
,
j
,
a1
,
b1
,
g1
,
r12
,
rsq
,
fforce
,
ttor
);
rtor
[
0
]
=
rtor
[
1
]
=
rtor
[
2
]
=
0.0
;
break
;
default
:
jquat
=
bonus
[
ellipsoid
[
j
]].
quat
;
MathExtra
::
quat_to_mat_trans
(
jquat
,
a2
);
MathExtra
::
diag_times3
(
well
[
jtype
],
a2
,
temp
);
MathExtra
::
transpose_times3
(
a2
,
temp
,
b2
);
MathExtra
::
diag_times3
(
shape2
[
jtype
],
a2
,
temp
);
MathExtra
::
transpose_times3
(
a2
,
temp
,
g2
);
one_eng
=
gayberne_analytic
(
i
,
j
,
a1
,
a2
,
b1
,
b2
,
g1
,
g2
,
r12
,
rsq
,
fforce
,
ttor
,
rtor
);
break
;
}
fforce
[
0
]
*=
factor_lj
;
fforce
[
1
]
*=
factor_lj
;
fforce
[
2
]
*=
factor_lj
;
ttor
[
0
]
*=
factor_lj
;
ttor
[
1
]
*=
factor_lj
;
ttor
[
2
]
*=
factor_lj
;
f
[
i
][
0
]
+=
fforce
[
0
];
f
[
i
][
1
]
+=
fforce
[
1
];
f
[
i
][
2
]
+=
fforce
[
2
];
tor
[
i
][
0
]
+=
ttor
[
0
];
tor
[
i
][
1
]
+=
ttor
[
1
];
tor
[
i
][
2
]
+=
ttor
[
2
];
if
(
eflag
)
evdwl
=
factor_lj
*
one_eng
;
if
(
evflag
)
ev_tally_xyz_full
(
i
,
evdwl
,
0.0
,
fforce
[
0
],
fforce
[
1
],
fforce
[
2
],
-
r12
[
0
],
-
r12
[
1
],
-
r12
[
2
]);
}
}
}
}
Event Timeline
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