git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5229 f3b2605a-c512-4ea7-a41b-209d697bcdaa

python/examples/viz_atomeye.py

@@ -0,0 +1,71 @@
+#!/usr/local/bin/python -i
+# preceeding line should have path for Python on your machine
+
+# viz.py
+# Purpose: viz running LAMMPS simulation via GL tool in Pizza.py
+# Syntax:  viz.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,os
+
+# set this to point to AtomEye version 3 executable
+
+ATOMEYE3 = "/home/sjplimp/tools/atomeye3/A3.i686-20060530"
+
+# parse command line
+
+argv = sys.argv
+if len(argv) != 4:
+  print "Syntax: viz.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 extended CFG format for AtomEye
+
+lmp.file(infile)
+lmp.command("thermo %d" % nfreq)
+lmp.command("dump python all cfg %d tmp.cfg.* id type xs ys zs" % nfreq)
+
+# initial 0-step run to generate dump file and image
+
+lmp.command("run 0 pre yes post no")
+ntimestep = 0
+
+# wrapper on GL window via Pizza.py gl tool
+# just proc 0 handles reading of dump file and viz
+
+if me == 0:
+  a = os.popen(ATOMEYE3,'w')
+  a.write("load_config tmp.cfg.0\n")
+  a.flush()
+
+# 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:
+    a.write("load_config tmp.cfg.%d\n" % ntimestep)
+    a.flush()
+
+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()

python/examples/viz_gl.py

@@ -33,6 +33,7 @@ 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)

python/examples/viz_pymol.py

@@ -0,0 +1,82 @@
+#!/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 GL window via Pizza.py gl tool
+# 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()

python/examples/vizplotgui_atomeye.py

@@ -0,0 +1,164 @@
+#!/usr/local/bin/python -i
+# preceeding line should have path for Python on your machine
+
+# vizplotgui.py
+# Purpose: viz running LAMMPS simulation with plot and GUI
+# Syntax:  vizplotgui.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
+
+import sys,os,time
+sys.path.append("./pizza")
+
+# first line if want AtomEye output to screen, 2nd line to file
+#ATOMEYE3 = "/home/sjplimp/tools/atomeye3/A3.i686-20060530"
+ATOMEYE3 = "/home/sjplimp/tools/atomeye3/A3.i686-20060530 > atomeye.out"
+
+# 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):
+  a.write("load_config tmp.cfg.%d\n" % ntimestep)
+  a.flush()
+  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.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 extended CFG format for AtomEye
+
+lmp.file(infile)
+lmp.command("thermo %d" % nfreq)
+lmp.command("dump python all cfg %d tmp.cfg.* id type xs ys zs" % 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 GL window via Pizza.py gl tool
+# just proc 0 handles reading of dump file and viz
+
+if me == 0:
+  a = os.popen(ATOMEYE3,'w')
+  a.write("load_config tmp.cfg.0\n")
+  a.flush()
+
+# display GUI with run/stop buttons and slider for temperature
+
+if me == 0:
+  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()

python/examples/vizplotgui_gl.py

@@ -64,6 +64,7 @@ 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)

python/examples/vizplotgui_pymol.py

@@ -0,0 +1,174 @@
+#!/usr/local/bin/python -i
+# preceeding line should have path for Python on your machine
+
+# vizplotgui_pymol.py
+# Purpose: viz running LAMMPS simulation with plot and GUI
+# Syntax:  vizplotgui_pymol.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
+
+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)
+  pm.load("tmp.pdb")
+  pm.forward()
+  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.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 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")
+
+# display GUI with run/stop buttons and slider for temperature
+
+if me == 0:
+  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()