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reaxc_basic_comm.cpp
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blob
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rLAMMPS lammps
reaxc_basic_comm.cpp
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/*----------------------------------------------------------------------
PuReMD - Purdue ReaxFF Molecular Dynamics Program
Copyright (2010) Purdue University
Hasan Metin Aktulga, hmaktulga@lbl.gov
Joseph Fogarty, jcfogart@mail.usf.edu
Sagar Pandit, pandit@usf.edu
Ananth Y Grama, ayg@cs.purdue.edu
Please cite the related publication:
H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama,
"Parallel Reactive Molecular Dynamics: Numerical Methods and
Algorithmic Techniques", Parallel Computing, in press.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
#include "pair_reax_c.h"
#if defined(PURE_REAX)
#include "basic_comm.h"
#include "vector.h"
#elif defined(LAMMPS_REAX)
#include "reaxc_basic_comm.h"
#include "reaxc_vector.h"
#endif
#if defined(PURE_REAX)
void
real_packer
(
void
*
dummy
,
mpi_out_data
*
out_buf
)
{
int
i
;
real
*
buf
=
(
real
*
)
dummy
;
real
*
out
=
(
real
*
)
out_buf
->
out_atoms
;
for
(
i
=
0
;
i
<
out_buf
->
cnt
;
++
i
)
out
[
i
]
=
buf
[
out_buf
->
index
[
i
]
];
}
void
rvec_packer
(
void
*
dummy
,
mpi_out_data
*
out_buf
)
{
int
i
;
rvec
*
buf
=
(
rvec
*
)
dummy
;
rvec
*
out
=
(
rvec
*
)
out_buf
->
out_atoms
;
for
(
i
=
0
;
i
<
out_buf
->
cnt
;
++
i
)
memcpy
(
out
[
i
],
buf
[
out_buf
->
index
[
i
]
],
sizeof
(
rvec
)
);
}
void
rvec2_packer
(
void
*
dummy
,
mpi_out_data
*
out_buf
)
{
int
i
;
rvec2
*
buf
=
(
rvec2
*
)
dummy
;
rvec2
*
out
=
(
rvec2
*
)
out_buf
->
out_atoms
;
for
(
i
=
0
;
i
<
out_buf
->
cnt
;
++
i
)
memcpy
(
out
[
i
],
buf
[
out_buf
->
index
[
i
]
],
sizeof
(
rvec2
)
);
}
void
Dist
(
reax_system
*
system
,
mpi_datatypes
*
mpi_data
,
void
*
buf
,
MPI_Datatype
type
,
int
scale
,
dist_packer
pack
)
{
int
d
;
mpi_out_data
*
out_bufs
;
MPI_Comm
comm
;
MPI_Request
req1
,
req2
;
MPI_Status
stat1
,
stat2
;
neighbor_proc
*
nbr1
,
*
nbr2
;
#if defined(DEBUG)
fprintf
(
stderr
,
"p%d dist: entered
\n
"
,
system
->
my_rank
);
#endif
comm
=
mpi_data
->
comm_mesh3D
;
out_bufs
=
mpi_data
->
out_buffers
;
for
(
d
=
0
;
d
<
3
;
++
d
)
{
/* initiate recvs */
nbr1
=
&
(
system
->
my_nbrs
[
2
*
d
]);
if
(
nbr1
->
atoms_cnt
)
MPI_Irecv
(
buf
+
nbr1
->
atoms_str
*
scale
,
nbr1
->
atoms_cnt
,
type
,
nbr1
->
rank
,
2
*
d
+
1
,
comm
,
&
req1
);
nbr2
=
&
(
system
->
my_nbrs
[
2
*
d
+
1
]);
if
(
nbr2
->
atoms_cnt
)
MPI_Irecv
(
buf
+
nbr2
->
atoms_str
*
scale
,
nbr2
->
atoms_cnt
,
type
,
nbr2
->
rank
,
2
*
d
,
comm
,
&
req2
);
/* send both messages in dimension d */
if
(
out_bufs
[
2
*
d
].
cnt
)
{
pack
(
buf
,
out_bufs
+
(
2
*
d
)
);
MPI_Send
(
out_bufs
[
2
*
d
].
out_atoms
,
out_bufs
[
2
*
d
].
cnt
,
type
,
nbr1
->
rank
,
2
*
d
,
comm
);
}
if
(
out_bufs
[
2
*
d
+
1
].
cnt
)
{
pack
(
buf
,
out_bufs
+
(
2
*
d
+
1
)
);
MPI_Send
(
out_bufs
[
2
*
d
+
1
].
out_atoms
,
out_bufs
[
2
*
d
+
1
].
cnt
,
type
,
nbr2
->
rank
,
2
*
d
+
1
,
comm
);
}
if
(
nbr1
->
atoms_cnt
)
MPI_Wait
(
&
req1
,
&
stat1
);
if
(
nbr2
->
atoms_cnt
)
MPI_Wait
(
&
req2
,
&
stat2
);
}
#if defined(DEBUG)
fprintf
(
stderr
,
"p%d dist: done
\n
"
,
system
->
my_rank
);
#endif
}
void
real_unpacker
(
void
*
dummy_in
,
void
*
dummy_buf
,
mpi_out_data
*
out_buf
)
{
int
i
;
real
*
in
=
(
real
*
)
dummy_in
;
real
*
buf
=
(
real
*
)
dummy_buf
;
for
(
i
=
0
;
i
<
out_buf
->
cnt
;
++
i
)
buf
[
out_buf
->
index
[
i
]
]
+=
in
[
i
];
}
void
rvec_unpacker
(
void
*
dummy_in
,
void
*
dummy_buf
,
mpi_out_data
*
out_buf
)
{
int
i
;
rvec
*
in
=
(
rvec
*
)
dummy_in
;
rvec
*
buf
=
(
rvec
*
)
dummy_buf
;
for
(
i
=
0
;
i
<
out_buf
->
cnt
;
++
i
)
{
rvec_Add
(
buf
[
out_buf
->
index
[
i
]
],
in
[
i
]
);
#if defined(DEBUG)
fprintf
(
stderr
,
"rvec_unpacker: cnt=%d i =%d index[i]=%d
\n
"
,
out_buf
->
cnt
,
i
,
out_buf
->
index
[
i
]
);
#endif
}
}
void
rvec2_unpacker
(
void
*
dummy_in
,
void
*
dummy_buf
,
mpi_out_data
*
out_buf
)
{
int
i
;
rvec2
*
in
=
(
rvec2
*
)
dummy_in
;
rvec2
*
buf
=
(
rvec2
*
)
dummy_buf
;
for
(
i
=
0
;
i
<
out_buf
->
cnt
;
++
i
)
{
buf
[
out_buf
->
index
[
i
]
][
0
]
+=
in
[
i
][
0
];
buf
[
out_buf
->
index
[
i
]
][
1
]
+=
in
[
i
][
1
];
}
}
void
Coll
(
reax_system
*
system
,
mpi_datatypes
*
mpi_data
,
void
*
buf
,
MPI_Datatype
type
,
int
scale
,
coll_unpacker
unpack
)
{
int
d
;
void
*
in1
,
*
in2
;
mpi_out_data
*
out_bufs
;
MPI_Comm
comm
;
MPI_Request
req1
,
req2
;
MPI_Status
stat1
,
stat2
;
neighbor_proc
*
nbr1
,
*
nbr2
;
#if defined(DEBUG)
fprintf
(
stderr
,
"p%d coll: entered
\n
"
,
system
->
my_rank
);
#endif
comm
=
mpi_data
->
comm_mesh3D
;
in1
=
mpi_data
->
in1_buffer
;
in2
=
mpi_data
->
in2_buffer
;
out_bufs
=
mpi_data
->
out_buffers
;
for
(
d
=
2
;
d
>=
0
;
--
d
)
{
/* initiate recvs */
nbr1
=
&
(
system
->
my_nbrs
[
2
*
d
]);
if
(
out_bufs
[
2
*
d
].
cnt
)
MPI_Irecv
(
in1
,
out_bufs
[
2
*
d
].
cnt
,
type
,
nbr1
->
rank
,
2
*
d
+
1
,
comm
,
&
req1
);
nbr2
=
&
(
system
->
my_nbrs
[
2
*
d
+
1
]);
if
(
out_bufs
[
2
*
d
+
1
].
cnt
)
MPI_Irecv
(
in2
,
out_bufs
[
2
*
d
+
1
].
cnt
,
type
,
nbr2
->
rank
,
2
*
d
,
comm
,
&
req2
);
/* send both messages in dimension d */
if
(
nbr1
->
atoms_cnt
)
MPI_Send
(
buf
+
nbr1
->
atoms_str
*
scale
,
nbr1
->
atoms_cnt
,
type
,
nbr1
->
rank
,
2
*
d
,
comm
);
if
(
nbr2
->
atoms_cnt
)
MPI_Send
(
buf
+
nbr2
->
atoms_str
*
scale
,
nbr2
->
atoms_cnt
,
type
,
nbr2
->
rank
,
2
*
d
+
1
,
comm
);
#if defined(DEBUG)
fprintf
(
stderr
,
"p%d coll[%d] nbr1: str=%d cnt=%d recv=%d
\n
"
,
system
->
my_rank
,
d
,
nbr1
->
atoms_str
,
nbr1
->
atoms_cnt
,
out_bufs
[
2
*
d
].
cnt
);
fprintf
(
stderr
,
"p%d coll[%d] nbr2: str=%d cnt=%d recv=%d
\n
"
,
system
->
my_rank
,
d
,
nbr2
->
atoms_str
,
nbr2
->
atoms_cnt
,
out_bufs
[
2
*
d
+
1
].
cnt
);
#endif
if
(
out_bufs
[
2
*
d
].
cnt
)
{
MPI_Wait
(
&
req1
,
&
stat1
);
unpack
(
in1
,
buf
,
out_bufs
+
(
2
*
d
)
);
}
if
(
out_bufs
[
2
*
d
+
1
].
cnt
)
{
MPI_Wait
(
&
req2
,
&
stat2
);
unpack
(
in2
,
buf
,
out_bufs
+
(
2
*
d
+
1
)
);
}
}
#if defined(DEBUG)
fprintf
(
stderr
,
"p%d coll: done
\n
"
,
system
->
my_rank
);
#endif
}
#endif
/*PURE_REAX*/
/*****************************************************************************/
real
Parallel_Norm
(
real
*
v
,
int
n
,
MPI_Comm
comm
)
{
int
i
;
real
my_sum
,
norm_sqr
;
my_sum
=
0
;
for
(
i
=
0
;
i
<
n
;
++
i
)
my_sum
+=
SQR
(
v
[
i
]
);
MPI_Allreduce
(
&
my_sum
,
&
norm_sqr
,
1
,
MPI_DOUBLE
,
MPI_SUM
,
comm
);
return
sqrt
(
norm_sqr
);
}
real
Parallel_Dot
(
real
*
v1
,
real
*
v2
,
int
n
,
MPI_Comm
comm
)
{
int
i
;
real
my_dot
,
res
;
my_dot
=
0
;
for
(
i
=
0
;
i
<
n
;
++
i
)
my_dot
+=
v1
[
i
]
*
v2
[
i
];
MPI_Allreduce
(
&
my_dot
,
&
res
,
1
,
MPI_DOUBLE
,
MPI_SUM
,
comm
);
return
res
;
}
real
Parallel_Vector_Acc
(
real
*
v
,
int
n
,
MPI_Comm
comm
)
{
int
i
;
real
my_acc
,
res
;
my_acc
=
0
;
for
(
i
=
0
;
i
<
n
;
++
i
)
my_acc
+=
v
[
i
];
MPI_Allreduce
(
&
my_acc
,
&
res
,
1
,
MPI_DOUBLE
,
MPI_SUM
,
comm
);
return
res
;
}
/*****************************************************************************/
#if defined(TEST_FORCES)
void
Coll_ids_at_Master
(
reax_system
*
system
,
storage
*
workspace
,
mpi_datatypes
*
mpi_data
)
{
int
i
;
int
*
id_list
;
MPI_Gather
(
&
system
->
n
,
1
,
MPI_INT
,
workspace
->
rcounts
,
1
,
MPI_INT
,
MASTER_NODE
,
mpi_data
->
world
);
if
(
system
->
my_rank
==
MASTER_NODE
){
workspace
->
displs
[
0
]
=
0
;
for
(
i
=
1
;
i
<
system
->
wsize
;
++
i
)
workspace
->
displs
[
i
]
=
workspace
->
displs
[
i
-
1
]
+
workspace
->
rcounts
[
i
-
1
];
}
id_list
=
(
int
*
)
malloc
(
system
->
n
*
sizeof
(
int
)
);
for
(
i
=
0
;
i
<
system
->
n
;
++
i
)
id_list
[
i
]
=
system
->
my_atoms
[
i
].
orig_id
;
MPI_Gatherv
(
id_list
,
system
->
n
,
MPI_INT
,
workspace
->
id_all
,
workspace
->
rcounts
,
workspace
->
displs
,
MPI_INT
,
MASTER_NODE
,
mpi_data
->
world
);
free
(
id_list
);
#if defined(DEBUG)
if
(
system
->
my_rank
==
MASTER_NODE
)
{
for
(
i
=
0
;
i
<
system
->
bigN
;
++
i
)
fprintf
(
stderr
,
"id_all[%d]: %d
\n
"
,
i
,
workspace
->
id_all
[
i
]
);
}
#endif
}
void
Coll_rvecs_at_Master
(
reax_system
*
system
,
storage
*
workspace
,
mpi_datatypes
*
mpi_data
,
rvec
*
v
)
{
MPI_Gatherv
(
v
,
system
->
n
,
mpi_data
->
mpi_rvec
,
workspace
->
f_all
,
workspace
->
rcounts
,
workspace
->
displs
,
mpi_data
->
mpi_rvec
,
MASTER_NODE
,
mpi_data
->
world
);
}
#endif
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