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split.py
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Created
Sat, Aug 31, 14:16
Size
1 KB
Mime Type
text/x-python
Expires
Mon, Sep 2, 14:16 (1 d, 23 h)
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blob
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20253700
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rLAMMPS lammps
split.py
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#!/usr/bin/env python -i
# preceeding line should have path for Python on your machine
# split.py
# Purpose: similar to simple.py, but first the world communicator
# is split in two halves and LAMMPS is run only on one partition
# Syntax: split.py in.lammps
# in.lammps = LAMMPS input script
from
__future__
import
print_function
import
sys
# parse command line
argv
=
sys
.
argv
if
len
(
argv
)
!=
2
:
print
(
"Syntax: simple.py in.lammps"
)
sys
.
exit
()
infile
=
sys
.
argv
[
1
]
me
=
0
# this example *only* works with mpi4py version 2.0.0 or later
from
mpi4py
import
MPI
comm
=
MPI
.
COMM_WORLD
me
=
comm
.
Get_rank
()
nprocs
=
comm
.
Get_size
()
# create two subcommunicators
if
me
<
nprocs
//
2
:
color
=
0
else
:
color
=
1
split
=
comm
.
Split
(
color
,
key
=
0
)
if
color
==
0
:
from
lammps
import
lammps
lmp
=
lammps
(
comm
=
split
)
# run infile one line at a time
lines
=
open
(
infile
,
'r'
)
.
readlines
()
for
line
in
lines
:
lmp
.
command
(
line
)
# run 10 more steps
# get coords from LAMMPS
# change coords of 1st atom
# put coords back into LAMMPS
# run a single step with changed coords
lmp
.
command
(
"run 10"
)
x
=
lmp
.
gather_atoms
(
"x"
,
1
,
3
)
epsilon
=
0.1
x
[
0
]
+=
epsilon
lmp
.
scatter_atoms
(
"x"
,
1
,
3
,
x
)
lmp
.
command
(
"run 1"
);
f
=
lmp
.
extract_atom
(
"f"
,
3
)
print
(
"Force on 1 atom via extract_atom: "
,
f
[
0
][
0
])
fx
=
lmp
.
extract_variable
(
"fx"
,
"all"
,
1
)
print
(
"Force on 1 atom via extract_variable:"
,
fx
[
0
])
print
(
"Proc
%d
out of
%d
procs has"
%
(
me
,
nprocs
),
lmp
)
print
(
"Calculation on partition 0 complete"
)
else
:
# could run a 2nd calculation on second partition
# with different LAMMPS instance or another code
# in this case, just sleep on second partition
import
time
time
.
sleep
(
2
)
print
(
"Calculation on partition 1 complete"
)
# shutdown mpi4py
comm
.
Barrier
()
MPI
.
Finalize
()
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