forked from lijiext/lammps
178 lines
4.4 KiB
Python
Executable File
178 lines
4.4 KiB
Python
Executable File
#!/usr/bin/env python -i
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# preceding line should have path for Python on your machine
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# vizplotgui_vmd.py
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# Purpose: viz running LAMMPS simulation via VMD with plot and GUI
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# Syntax: vizplotgui_vmd.py in.lammps Nfreq compute-ID
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# in.lammps = LAMMPS input script
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# Nfreq = plot data point and viz shapshot every this many steps
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# compute-ID = ID of compute that calculates temperature
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# (or any other scalar quantity)
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# IMPORTANT: this script cannot yet be run in parallel via Pypar,
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# because I can't seem to do a MPI-style broadcast in Pypar
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from __future__ import print_function
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import sys,time
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sys.path.append("./pizza")
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# methods called by GUI
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def run():
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global runflag
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runflag = 1
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def stop():
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global runflag
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runflag = 0
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def settemp(value):
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global temptarget
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temptarget = slider.get()
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def quit():
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global breakflag
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breakflag = 1
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# method called by timestep loop every Nfreq steps
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# read dump snapshot and viz it, update plot with compute value
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def update(ntimestep):
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d.next()
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d.unscale()
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p.single(ntimestep)
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v.append('tmp.pdb','pdb')
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value = lmp.extract_compute(compute,0,0)
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xaxis.append(ntimestep)
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yaxis.append(value)
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gn.plot(xaxis,yaxis)
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# parse command line
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argv = sys.argv
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if len(argv) != 4:
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print("Syntax: vizplotgui_vmd.py in.lammps Nfreq compute-ID")
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sys.exit()
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infile = sys.argv[1]
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nfreq = int(sys.argv[2])
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compute = sys.argv[3]
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me = 0
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# uncomment if running in parallel via Pypar
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#import pypar
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#me = pypar.rank()
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#nprocs = pypar.size()
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from lammps import lammps
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lmp = lammps()
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# run infile all at once
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# assumed to have no run command in it
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# dump a file in native LAMMPS dump format for Pizza.py dump tool
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lmp.file(infile)
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lmp.command("thermo %d" % nfreq)
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lmp.command("dump python all atom %d tmp.dump" % nfreq)
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# initial 0-step run to generate initial 1-point plot, dump file, and image
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lmp.command("run 0 pre yes post no")
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value = lmp.extract_compute(compute,0,0)
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ntimestep = 0
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xaxis = [ntimestep]
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yaxis = [value]
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breakflag = 0
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runflag = 0
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temptarget = 1.0
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# wrapper on VMD window via Pizza.py vmd tool
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# just proc 0 handles reading of dump file and viz
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if me == 0:
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from vmd import vmd
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v = vmd()
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v('menu main off')
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v.rep('VDW')
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from dump import dump
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from pdbfile import pdbfile
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d = dump('tmp.dump',0)
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p = pdbfile(d)
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d.next()
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d.unscale()
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p.single(ntimestep)
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v.new('tmp.pdb','pdb')
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# display GUI with run/stop buttons and slider for temperature
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if me == 0:
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try:
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from Tkinter import *
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except:
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from tkinter import *
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tkroot = Tk()
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tkroot.withdraw()
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root = Toplevel(tkroot)
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root.title("LAMMPS GUI")
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frame = Frame(root)
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Button(frame,text="Run",command=run).pack(side=LEFT)
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Button(frame,text="Stop",command=stop).pack(side=LEFT)
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slider = Scale(frame,from_=0.0,to=5.0,resolution=0.1,
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orient=HORIZONTAL,label="Temperature")
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slider.bind('<ButtonRelease-1>',settemp)
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slider.set(temptarget)
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slider.pack(side=LEFT)
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Button(frame,text="Quit",command=quit).pack(side=RIGHT)
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frame.pack()
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tkroot.update()
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# wrapper on GnuPlot via Pizza.py gnu tool
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if me == 0:
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from gnu import gnu
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gn = gnu()
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gn.plot(xaxis,yaxis)
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gn.title(compute,"Timestep","Temperature")
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# endless loop, checking status of GUI settings every Nfreq steps
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# run with pre yes/no and post yes/no depending on go/stop status
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# re-invoke fix langevin with new seed when temperature slider changes
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# after re-invoke of fix langevin, run with pre yes
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running = 0
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temp = temptarget
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seed = 12345
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lmp.command("fix 2 all langevin %g %g 0.1 %d" % (temp,temp,seed))
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while 1:
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if me == 0: tkroot.update()
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if temp != temptarget:
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temp = temptarget
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seed += me+1
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lmp.command("fix 2 all langevin %g %g 0.1 12345" % (temp,temp))
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running = 0
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if runflag and running:
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lmp.command("run %d pre no post no" % nfreq)
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ntimestep += nfreq
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if me == 0: update(ntimestep)
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elif runflag and not running:
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lmp.command("run %d pre yes post no" % nfreq)
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ntimestep += nfreq
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if me == 0: update(ntimestep)
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elif not runflag and running:
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lmp.command("run %d pre no post yes" % nfreq)
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ntimestep += nfreq
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if me == 0: update(ntimestep)
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if breakflag: break
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if runflag: running = 1
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else: running = 0
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time.sleep(0.01)
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lmp.command("run 0 pre no post yes")
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# uncomment if running in parallel via Pypar
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#print("Proc %d out of %d procs has" % (me,nprocs), lmp)
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#pypar.finalize()
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