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viz_pymol.py
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Created
Sun, Aug 25, 03:51
Size
1 KB
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text/x-python
Expires
Tue, Aug 27, 03:51 (2 d)
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blob
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rLAMMPS lammps
viz_pymol.py
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#!/usr/local/bin/python -i
# preceeding line should have path for Python on your machine
# viz_pymol.py
# Purpose: viz running LAMMPS simulation via PyMol
# Syntax: viz_pymol.py in.lammps Nfreq Nsteps
# in.lammps = LAMMPS input script
# Nfreq = dump and viz shapshot every this many steps
# Nsteps = run for this many steps
import
sys
sys
.
path
.
append
(
"./pizza"
)
# parse command line
argv
=
sys
.
argv
if
len
(
argv
)
!=
4
:
print
"Syntax: viz_pymol.py in.lammps Nfreq Nsteps"
sys
.
exit
()
infile
=
sys
.
argv
[
1
]
nfreq
=
int
(
sys
.
argv
[
2
])
nsteps
=
int
(
sys
.
argv
[
3
])
me
=
0
# uncomment if running in parallel via Pypar
#import pypar
#me = pypar.rank()
#nprocs = pypar.size()
from
lammps
import
lammps
lmp
=
lammps
()
# run infile all at once
# assumed to have no run command in it
# dump a file in native LAMMPS dump format for Pizza.py dump tool
lmp
.
file
(
infile
)
lmp
.
command
(
"thermo
%d
"
%
nfreq
)
lmp
.
command
(
"dump python all atom
%d
tmp.dump"
%
nfreq
)
# initial 0-step run to generate dump file and image
lmp
.
command
(
"run 0 pre yes post no"
)
ntimestep
=
0
# wrapper on PyMol
# just proc 0 handles reading of dump file and viz
if
me
==
0
:
import
pymol
pymol
.
finish_launching
()
from
dump
import
dump
from
pdbfile
import
pdbfile
from
pymol
import
cmd
as
pm
d
=
dump
(
"tmp.dump"
,
0
)
p
=
pdbfile
(
d
)
d
.
next
()
d
.
unscale
()
p
.
single
(
ntimestep
)
pm
.
load
(
"tmp.pdb"
)
pm
.
show
(
"spheres"
,
"tmp"
)
# run nfreq steps at a time w/out pre/post, read dump snapshot, display it
while
ntimestep
<
nsteps
:
lmp
.
command
(
"run
%d
pre no post no"
%
nfreq
)
ntimestep
+=
nfreq
if
me
==
0
:
d
.
next
()
d
.
unscale
()
p
.
single
(
ntimestep
)
pm
.
load
(
"tmp.pdb"
)
pm
.
forward
()
lmp
.
command
(
"run 0 pre no post yes"
)
# uncomment if running in parallel via Pypar
#print "Proc %d out of %d procs has" % (me,nprocs), lmp
#pypar.finalize()
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