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vizplotgui_vmd.py
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Created
Sat, Aug 31, 05:03
Size
4 KB
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text/x-python
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Mon, Sep 2, 05:03 (2 d)
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blob
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rLAMMPS lammps
vizplotgui_vmd.py
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#!/usr/bin/env python -i
# preceding line should have path for Python on your machine
# vizplotgui_vmd.py
# Purpose: viz running LAMMPS simulation via VMD with plot and GUI
# Syntax: vizplotgui_vmd.py in.lammps Nfreq compute-ID
# in.lammps = LAMMPS input script
# Nfreq = plot data point and viz shapshot every this many steps
# compute-ID = ID of compute that calculates temperature
# (or any other scalar quantity)
# IMPORTANT: this script cannot yet be run in parallel via Pypar,
# because I can't seem to do a MPI-style broadcast in Pypar
from
__future__
import
print_function
import
sys
,
time
sys
.
path
.
append
(
"./pizza"
)
# methods called by GUI
def
run
():
global
runflag
runflag
=
1
def
stop
():
global
runflag
runflag
=
0
def
settemp
(
value
):
global
temptarget
temptarget
=
slider
.
get
()
def
quit
():
global
breakflag
breakflag
=
1
# method called by timestep loop every Nfreq steps
# read dump snapshot and viz it, update plot with compute value
def
update
(
ntimestep
):
d
.
next
()
d
.
unscale
()
p
.
single
(
ntimestep
)
v
.
append
(
'tmp.pdb'
,
'pdb'
)
value
=
lmp
.
extract_compute
(
compute
,
0
,
0
)
xaxis
.
append
(
ntimestep
)
yaxis
.
append
(
value
)
gn
.
plot
(
xaxis
,
yaxis
)
# parse command line
argv
=
sys
.
argv
if
len
(
argv
)
!=
4
:
print
(
"Syntax: vizplotgui_vmd.py in.lammps Nfreq compute-ID"
)
sys
.
exit
()
infile
=
sys
.
argv
[
1
]
nfreq
=
int
(
sys
.
argv
[
2
])
compute
=
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 initial 1-point plot, dump file, and image
lmp
.
command
(
"run 0 pre yes post no"
)
value
=
lmp
.
extract_compute
(
compute
,
0
,
0
)
ntimestep
=
0
xaxis
=
[
ntimestep
]
yaxis
=
[
value
]
breakflag
=
0
runflag
=
0
temptarget
=
1.0
# wrapper on VMD window via Pizza.py vmd tool
# just proc 0 handles reading of dump file and viz
if
me
==
0
:
from
vmd
import
vmd
v
=
vmd
()
v
(
'menu main off'
)
v
.
rep
(
'VDW'
)
from
dump
import
dump
from
pdbfile
import
pdbfile
d
=
dump
(
'tmp.dump'
,
0
)
p
=
pdbfile
(
d
)
d
.
next
()
d
.
unscale
()
p
.
single
(
ntimestep
)
v
.
new
(
'tmp.pdb'
,
'pdb'
)
# display GUI with run/stop buttons and slider for temperature
if
me
==
0
:
try
:
from
Tkinter
import
*
except
:
from
tkinter
import
*
tkroot
=
Tk
()
tkroot
.
withdraw
()
root
=
Toplevel
(
tkroot
)
root
.
title
(
"LAMMPS GUI"
)
frame
=
Frame
(
root
)
Button
(
frame
,
text
=
"Run"
,
command
=
run
)
.
pack
(
side
=
LEFT
)
Button
(
frame
,
text
=
"Stop"
,
command
=
stop
)
.
pack
(
side
=
LEFT
)
slider
=
Scale
(
frame
,
from_
=
0.0
,
to
=
5.0
,
resolution
=
0.1
,
orient
=
HORIZONTAL
,
label
=
"Temperature"
)
slider
.
bind
(
'<ButtonRelease-1>'
,
settemp
)
slider
.
set
(
temptarget
)
slider
.
pack
(
side
=
LEFT
)
Button
(
frame
,
text
=
"Quit"
,
command
=
quit
)
.
pack
(
side
=
RIGHT
)
frame
.
pack
()
tkroot
.
update
()
# wrapper on GnuPlot via Pizza.py gnu tool
if
me
==
0
:
from
gnu
import
gnu
gn
=
gnu
()
gn
.
plot
(
xaxis
,
yaxis
)
gn
.
title
(
compute
,
"Timestep"
,
"Temperature"
)
# endless loop, checking status of GUI settings every Nfreq steps
# run with pre yes/no and post yes/no depending on go/stop status
# re-invoke fix langevin with new seed when temperature slider changes
# after re-invoke of fix langevin, run with pre yes
running
=
0
temp
=
temptarget
seed
=
12345
lmp
.
command
(
"fix 2 all langevin
%g
%g
0.1
%d
"
%
(
temp
,
temp
,
seed
))
while
1
:
if
me
==
0
:
tkroot
.
update
()
if
temp
!=
temptarget
:
temp
=
temptarget
seed
+=
me
+
1
lmp
.
command
(
"fix 2 all langevin
%g
%g
0.1 12345"
%
(
temp
,
temp
))
running
=
0
if
runflag
and
running
:
lmp
.
command
(
"run
%d
pre no post no"
%
nfreq
)
ntimestep
+=
nfreq
if
me
==
0
:
update
(
ntimestep
)
elif
runflag
and
not
running
:
lmp
.
command
(
"run
%d
pre yes post no"
%
nfreq
)
ntimestep
+=
nfreq
if
me
==
0
:
update
(
ntimestep
)
elif
not
runflag
and
running
:
lmp
.
command
(
"run
%d
pre no post yes"
%
nfreq
)
ntimestep
+=
nfreq
if
me
==
0
:
update
(
ntimestep
)
if
breakflag
:
break
if
runflag
:
running
=
1
else
:
running
=
0
time
.
sleep
(
0.01
)
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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