Merge branch 'master' into lammps-icms

python/examples/pizza/vmd.py

@@ -1,13 +1,20 @@
+# Pizza.py toolkit, www.cs.sandia.gov/~sjplimp/pizza.html
+# Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
 #
-# Minimalistic VMD embedding for Pizza.py
-#
-# This class will replace the VMD startup script,
-# open a pipe to the executable, and feed it Tcl
-# command lines one at a time.
-#
-# (c) 2010 Axel Kohlmeyer <akohlmey@gmail.com>
+# Copyright (2005) Sandia Corporation.  Under the terms of Contract
+# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+# certain rights in this software.  This software is distributed under 
+# the GNU General Public License.
 
-oneline = "Control VMD from python."
+# vmd tool
+
+# Minimalistic VMD embedding for Pizza.py
+# (c) 2010 Axel Kohlmeyer <akohlmey@gmail.com>
+# This class will replace the VMD startup script,
+#   open a pipe to the executable,
+#   and feed it Tcl command lines one at a time
+
+oneline = "Control VMD from python"
 
 docstr = """
 v = vmd()		       start up VMD
@@ -30,6 +37,9 @@ v.enter()		       enter interactive shell
 v.debug([True|False])	       display generated VMD script commands?
 """
 
+# History
+#   11/10, Axel Kohlmeyer (Temple U): original version
+
 # Imports and external programs
 
 import types, os
@@ -42,12 +52,14 @@ except: PIZZA_VMDDIR = "/usr/local/lib/vmd"
 try: from DEFAULTS import PIZZA_VMDDEV
 except: PIZZA_VMDDEV = "win"
 try: from DEFAULTS import PIZZA_VMDARCH
-except: PIZZA_VMDARCH = "LINUXAMD64"
+except: PIZZA_VMDARCH = "LINUX"
 
 try: import pexpect
 except: 
-  print "pexpect from http://pypi.python.org/pypi/pexpect/ is required for vmd module"
+  print "pexpect from http://pypi.python.org/pypi/pexpect", \
+      "is required for vmd tool"
   raise
+
 # Class definition
 
 class vmd:

python/examples/viz_atomeye.py

@@ -1,9 +1,9 @@
 #!/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
+# viz_atomeye.py
+# Purpose: viz running LAMMPS simulation via AtomEye
+# Syntax:  viz_atomeye.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
@@ -11,14 +11,15 @@
 import sys,os
 
 # set this to point to AtomEye version 3 executable
-
-ATOMEYE3 = "/home/sjplimp/tools/atomeye3/A3.i686-20060530"
+# 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"
 
 # parse command line
 
 argv = sys.argv
 if len(argv) != 4:
-  print "Syntax: viz.py in.lammps Nfreq Nsteps"
+  print "Syntax: viz_atomeye.py in.lammps Nfreq Nsteps"
   sys.exit()
 
 infile = sys.argv[1]

python/examples/viz_gl.py

@@ -1,9 +1,9 @@
 #!/usr/local/bin/python -i
 # preceeding line should have path for Python on your machine
 
-# viz.py
+# viz_gl.py
 # Purpose: viz running LAMMPS simulation via GL tool in Pizza.py
-# Syntax:  viz.py in.lammps Nfreq Nsteps
+# Syntax:  viz_gl.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
@@ -15,7 +15,7 @@ sys.path.append("./pizza")
 
 argv = sys.argv
 if len(argv) != 4:
-  print "Syntax: viz.py in.lammps Nfreq Nsteps"
+  print "Syntax: viz_gl.py in.lammps Nfreq Nsteps"
   sys.exit()
 
 infile = sys.argv[1]

python/examples/viz_vmd.py

@@ -81,9 +81,9 @@ lmp.command("run 0 pre no post yes")
 if me == 0:
   v.flush()
   # uncomment the following, if you want to work with the viz some more.
-  v('menu main on')
-  # print "type quit to terminate."
-  v.enter()
+  #v('menu main on')
+  #print "type quit to terminate."
+  #v.enter()
   #v.stop()
 
 # uncomment if running in parallel via Pypar

python/examples/vizplotgui_atomeye.py

@@ -1,9 +1,9 @@
 #!/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
+# vizplotgui_atomeye.py
+# Purpose: viz running LAMMPS simulation via AtomEye with plot and GUI
+# Syntax:  vizplotgui_atomeye.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
@@ -15,6 +15,7 @@
 import sys,os,time
 sys.path.append("./pizza")
 
+# set this to point to AtomEye version 3 executable
 # 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"
@@ -49,7 +50,7 @@ def update(ntimestep):
 
 argv = sys.argv
 if len(argv) != 4:
-  print "Syntax: vizplotgui.py in.lammps Nfreq compute-ID"
+  print "Syntax: vizplotgui_atomeye.py in.lammps Nfreq compute-ID"
   sys.exit()
 
 infile = sys.argv[1]
@@ -85,7 +86,7 @@ breakflag = 0
 runflag = 0
 temptarget = 1.0
 
-# wrapper on GL window via Pizza.py gl tool
+# wrapper on AtomEye
 # just proc 0 handles reading of dump file and viz
 
 if me == 0:

python/examples/vizplotgui_gl.py

@@ -1,9 +1,9 @@
 #!/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
+# vizplotgui_gl.py
+# Purpose: viz running LAMMPS simulation via GL tool with plot and GUI
+# Syntax:  vizplotgui_gl.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
@@ -46,7 +46,7 @@ def update(ntimestep):
 
 argv = sys.argv
 if len(argv) != 4:
-  print "Syntax: vizplotgui.py in.lammps Nfreq compute-ID"
+  print "Syntax: vizplotgui_gl.py in.lammps Nfreq compute-ID"
   sys.exit()
 
 infile = sys.argv[1]

python/examples/vizplotgui_pymol.py

@@ -2,7 +2,7 @@
 # preceeding line should have path for Python on your machine
 
 # vizplotgui_pymol.py
-# Purpose: viz running LAMMPS simulation with plot and GUI
+# Purpose: viz running LAMMPS simulation via PyMol 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
@@ -48,7 +48,7 @@ def update(ntimestep):
 
 argv = sys.argv
 if len(argv) != 4:
-  print "Syntax: vizplotgui.py in.lammps Nfreq compute-ID"
+  print "Syntax: vizplotgui_pymol.py in.lammps Nfreq compute-ID"
   sys.exit()
 
 infile = sys.argv[1]

python/examples/vizplotgui_vmd.py

@@ -0,0 +1,173 @@
+#!/usr/local/bin/python -i
+# preceeding 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
+
+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:
+  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()