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pair_coul_dsf_gpu.cpp
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Tue, Aug 20, 07:44
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Thu, Aug 22, 07:44 (2 d)
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rLAMMPS lammps
pair_coul_dsf_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_coul_dsf_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 MY_PIS 1.77245385090551602729
#define EWALD_F 1.12837917
#define EWALD_P 0.3275911
#define A1 0.254829592
#define A2 -0.284496736
#define A3 1.421413741
#define A4 -1.453152027
#define A5 1.061405429
using
namespace
LAMMPS_NS
;
// External functions from cuda library for atom decomposition
int
cdsf_gpu_init
(
const
int
ntypes
,
const
int
nlocal
,
const
int
nall
,
const
int
max_nbors
,
const
int
maxspecial
,
const
double
cell_size
,
int
&
gpu_mode
,
FILE
*
screen
,
const
double
host_cut_coulsq
,
double
*
host_special_coul
,
const
double
qqrd2e
,
const
double
e_shift
,
const
double
f_shift
,
const
double
alpha
);
void
cdsf_gpu_clear
();
int
**
cdsf_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_q
,
double
*
boxlo
,
double
*
prd
);
void
cdsf_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_q
,
const
int
nlocal
,
double
*
boxlo
,
double
*
prd
);
double
cdsf_gpu_bytes
();
/* ---------------------------------------------------------------------- */
PairCoulDSFGPU
::
PairCoulDSFGPU
(
LAMMPS
*
lmp
)
:
PairCoulDSF
(
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
------------------------------------------------------------------------- */
PairCoulDSFGPU
::~
PairCoulDSFGPU
()
{
cdsf_gpu_clear
();
}
/* ---------------------------------------------------------------------- */
void
PairCoulDSFGPU
::
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
=
cdsf_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
,
atom
->
q
,
domain
->
boxlo
,
domain
->
prd
);
}
else
{
inum
=
list
->
inum
;
ilist
=
list
->
ilist
;
numneigh
=
list
->
numneigh
;
firstneigh
=
list
->
firstneigh
;
cdsf_gpu_compute
(
neighbor
->
ago
,
inum
,
nall
,
atom
->
x
,
atom
->
type
,
ilist
,
numneigh
,
firstneigh
,
eflag
,
vflag
,
eflag_atom
,
vflag_atom
,
host_start
,
cpu_time
,
success
,
atom
->
q
,
atom
->
nlocal
,
domain
->
boxlo
,
domain
->
prd
);
}
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
PairCoulDSFGPU
::
init_style
()
{
if
(
!
atom
->
q_flag
)
error
->
all
(
FLERR
,
"Pair style coul/dsf/gpu requires atom attribute q"
);
if
(
force
->
newton_pair
)
error
->
all
(
FLERR
,
"Cannot use newton pair with coul/dsf/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
;
cut_coulsq
=
cut_coul
*
cut_coul
;
double
erfcc
=
erfc
(
alpha
*
cut_coul
);
double
erfcd
=
exp
(
-
alpha
*
alpha
*
cut_coul
*
cut_coul
);
f_shift
=
-
(
erfcc
/
cut_coulsq
+
2.0
/
MY_PIS
*
alpha
*
erfcd
/
cut_coul
);
e_shift
=
erfcc
/
cut_coul
-
f_shift
*
cut_coul
;
int
maxspecial
=
0
;
if
(
atom
->
molecular
)
maxspecial
=
atom
->
maxspecial
;
int
success
=
cdsf_gpu_init
(
atom
->
ntypes
+
1
,
atom
->
nlocal
,
atom
->
nlocal
+
atom
->
nghost
,
300
,
maxspecial
,
cell_size
,
gpu_mode
,
screen
,
cut_coulsq
,
force
->
special_coul
,
force
->
qqrd2e
,
e_shift
,
f_shift
,
alpha
);
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
PairCoulDSFGPU
::
memory_usage
()
{
double
bytes
=
Pair
::
memory_usage
();
return
bytes
+
cdsf_gpu_bytes
();
}
/* ---------------------------------------------------------------------- */
void
PairCoulDSFGPU
::
cpu_compute
(
int
start
,
int
inum
,
int
eflag
,
int
vflag
,
int
*
ilist
,
int
*
numneigh
,
int
**
firstneigh
)
{
int
i
,
j
,
ii
,
jj
,
jnum
;
double
qtmp
,
xtmp
,
ytmp
,
ztmp
,
delx
,
dely
,
delz
,
ecoul
,
fpair
;
double
r
,
rsq
,
r2inv
,
forcecoul
,
factor_coul
;
double
prefactor
,
erfcc
,
erfcd
,
t
;
int
*
jlist
;
ecoul
=
0.0
;
double
**
x
=
atom
->
x
;
double
**
f
=
atom
->
f
;
double
*
q
=
atom
->
q
;
int
nlocal
=
atom
->
nlocal
;
double
*
special_coul
=
force
->
special_coul
;
double
qqrd2e
=
force
->
qqrd2e
;
// loop over neighbors of my atoms
for
(
ii
=
start
;
ii
<
inum
;
ii
++
)
{
i
=
ilist
[
ii
];
qtmp
=
q
[
i
];
xtmp
=
x
[
i
][
0
];
ytmp
=
x
[
i
][
1
];
ztmp
=
x
[
i
][
2
];
jlist
=
firstneigh
[
i
];
jnum
=
numneigh
[
i
];
if
(
evflag
)
{
double
e_self
=
-
(
e_shift
/
2.0
+
alpha
/
MY_PIS
)
*
qtmp
*
qtmp
*
qqrd2e
;
ev_tally
(
i
,
i
,
nlocal
,
0
,
0.0
,
e_self
,
0.0
,
0.0
,
0.0
,
0.0
);
}
for
(
jj
=
0
;
jj
<
jnum
;
jj
++
)
{
j
=
jlist
[
jj
];
factor_coul
=
special_coul
[
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
;
if
(
rsq
<
cut_coulsq
)
{
r2inv
=
1.0
/
rsq
;
r
=
sqrt
(
rsq
);
prefactor
=
qqrd2e
*
qtmp
*
q
[
j
]
/
r
;
erfcd
=
exp
(
-
alpha
*
alpha
*
r
*
r
);
t
=
1.0
/
(
1.0
+
EWALD_P
*
alpha
*
r
);
erfcc
=
t
*
(
A1
+
t
*
(
A2
+
t
*
(
A3
+
t
*
(
A4
+
t
*
A5
))))
*
erfcd
;
forcecoul
=
prefactor
*
(
erfcc
/
r
+
2.0
*
alpha
/
MY_PIS
*
erfcd
+
r
*
f_shift
)
*
r
;
if
(
factor_coul
<
1.0
)
forcecoul
-=
(
1.0
-
factor_coul
)
*
prefactor
;
fpair
=
forcecoul
*
r2inv
;
f
[
i
][
0
]
+=
delx
*
fpair
;
f
[
i
][
1
]
+=
dely
*
fpair
;
f
[
i
][
2
]
+=
delz
*
fpair
;
if
(
eflag
)
{
if
(
rsq
<
cut_coulsq
)
{
ecoul
=
prefactor
*
(
erfcc
-
r
*
e_shift
-
rsq
*
f_shift
);
if
(
factor_coul
<
1.0
)
ecoul
-=
(
1.0
-
factor_coul
)
*
prefactor
;
}
else
ecoul
=
0.0
;
}
if
(
evflag
)
ev_tally_full
(
i
,
0.0
,
ecoul
,
fpair
,
delx
,
dely
,
delz
);
}
}
}
}
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