integrate vmd wrapper module for pizza.py
this wrapper allows to spawn an instance of VMD as an ancillary process under python and supports a few simple manipulations through converting them to tcl commands. also arbitrary tcl commands can be forwarded by the object to the vmd instance.
This commit is contained in:
Axel Kohlmeyer
205
python/examples/pizza/vmd.py
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205
python/examples/pizza/vmd.py
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#
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# Minimalistic VMD embedding for Pizza.py
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#
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# This class will replace the VMD startup script,
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# open a pipe to the executable, and feed it Tcl
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# command lines one at a time.
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#
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# (c) 2010 Axel Kohlmeyer <akohlmey@gmail.com>
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oneline = "Control VMD from python."
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docstr = """
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v = vmd() start up VMD
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v.stop() shut down VMD instance
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v.clear() delete all visualizations
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v.rep(style) set default representation style. One of
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(Lines|VDW|Licorice|DynamicBonds|Points|CPK)
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v.new(file[,type]) load new file (default file type 'lammpstrj')
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v.data(file[,atomstyle]) load new data file (default atom style 'full')
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v.replace(file[,type]) replace current frames with new file
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v.append(file[,type]) append file to current frame(s)
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v.set(snap,x,y,z,(True|False)) set coordinates from a pizza.py snapshot to new or current frame
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v.frame(frame) set current frame
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v.flush() flush pending input to VMD and update GUI
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v.read(file) read Tcl script file (e.g. saved state)
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v.enter() enter interactive shell
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v.debug([True|False]) display generated VMD script commands?
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"""
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# Imports and external programs
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import types, os
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import numpy
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try: from DEFAULTS import PIZZA_VMDNAME
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except: PIZZA_VMDNAME = "vmd"
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try: from DEFAULTS import PIZZA_VMDDIR
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except: PIZZA_VMDDIR = "/usr/local/lib/vmd"
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try: from DEFAULTS import PIZZA_VMDDEV
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except: PIZZA_VMDDEV = "win"
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try: from DEFAULTS import PIZZA_VMDARCH
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except: PIZZA_VMDARCH = "LINUXAMD64"
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try: import pexpect
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except:
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print "pexpect from http://pypi.python.org/pypi/pexpect/ is required for vmd module"
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raise
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# Class definition
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class vmd:
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# --------------------------------------------------------------------
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def __init__(self):
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self.vmddir = PIZZA_VMDDIR
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self.vmdexe = PIZZA_VMDDIR + '/' + PIZZA_VMDNAME + '_' + PIZZA_VMDARCH
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# these are all defaults copied from the vmd launch script
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os.environ['VMDDIR'] = PIZZA_VMDDIR
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os.environ['VMDDISPLAYDEVICE'] = PIZZA_VMDDEV
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os.environ['VMDSCRPOS'] = "596 190"
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os.environ['VMDSCRSIZE'] = "669 834"
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os.environ['VMDSCRHEIGHT'] = "6.0"
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os.environ['VMDSCRDIST'] = "-2.0"
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os.environ['VMDTITLE'] = "on"
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os.environ['TCL_LIBRARY'] = PIZZA_VMDDIR + "/scripts/tcl"
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os.environ['STRIDE_BIN'] = PIZZA_VMDDIR + "/stride_" + PIZZA_VMDARCH
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os.environ['SURF_BIN'] = PIZZA_VMDDIR + "/surf_" + PIZZA_VMDARCH
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os.environ['TACHYON_BIN'] = PIZZA_VMDDIR + "/tachyon_" + PIZZA_VMDARCH
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ldpath = os.environ.get('LD_LIBRARY_PATH','')
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if ldpath == '':
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os.environ['LD_LIBRARY_PATH'] = PIZZA_VMDDIR
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else:
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os.environ['LD_LIBRARY_PATH'] = ldpath + ':' + PIZZA_VMDDIR
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ldpath = os.environ.get('LD_LIBRARY_PATH','')
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if ldpath == '':
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os.environ['PYTHONPATH'] = PIZZA_VMDDIR
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else:
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os.environ['PYTHONPATH'] = PIZZA_VMDDIR + "/scripts/python"
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self.debugme = False
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# open pipe to vmd and wait until we have a prompt
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self.VMD = pexpect.spawn(self.vmdexe)
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self.VMD.expect('vmd >')
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# --------------------------------------------------------------------
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# post command to vmd and wait until the prompt returns.
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def __call__(self,command):
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if self.VMD.isalive():
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self.VMD.sendline(command)
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self.VMD.expect('vmd >')
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if self.debugme:
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print "call+result:"+self.VMD.before
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return
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# --------------------------------------------------------------------
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# exit VMD
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def stop(self):
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self.__call__("quit")
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del self.VMD
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# --------------------------------------------------------------------
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# force VMD display and GUI update.
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def flush(self):
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self.__call__('display update ui')
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# --------------------------------------------------------------------
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# turn on debugging info
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def debug(self,status=True):
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if status and not self.debugme:
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print 'Turning vmd.py debugging ON.'
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if not status and self.debugme:
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print 'Turning vmd.py debugging OFF.'
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self.debugme = status
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# --------------------------------------------------------------------
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# emulate a regular tcl command prompt
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def enter(self,mode='tcl'):
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self.__call__('menu main off')
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self.__call__('menu main on')
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while 1:
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try:
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command = raw_input("vmd > ")
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except EOFError:
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print "(EOF)"
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self.__call__('menu main off')
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return
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if command == "quit" or command == "exit":
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self.__call__('menu main off')
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return
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if command == "gopython":
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print "gopython not supported here"
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continue
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self.__call__(command)
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# --------------------------------------------------------------------
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# read and execute tcl script file (e.g. a saved state)
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def read(self,filename):
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self.__call__('play ' + filename)
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self.flush()
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# --------------------------------------------------------------------
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# remove all molecules, data and visualizations
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def clear(self):
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self.__call__("mol delete all")
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# --------------------------------------------------------------------
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# navigate to a given frame
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def rep(self,style='Lines'):
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if style == 'Lines' or style == 'VDW' or style == 'Licorice' \
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or style == 'DynamicBonds' or style == 'Points' or style == 'CPK':
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self.__call__('mol default style ' + style)
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# --------------------------------------------------------------------
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# navigate to a given frame
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def frame(self,framespec):
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self.__call__('animate goto ' + str(framespec))
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# --------------------------------------------------------------------
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# load a new molecule from a file supported by a molfile plugin
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def new(self,filename,filetype='lammpstrj'):
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self.__call__('mol new ' + filename + ' type ' + filetype + ' waitfor all')
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self.flush()
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# --------------------------------------------------------------------
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# load a new molecule from a data file via the topotools plugin
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def data(self,filename,atomstyle='full'):
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self.__call__('package require topotools 1.0')
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self.__call__('topo readlammpsdata ' + filename + ' ' + atomstyle)
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self.flush()
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# --------------------------------------------------------------------
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# append all frames from a given file to the current molecule
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def append(self,filename,filetype='lammpstrj'):
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self.__call__('set tmol [molinfo top]')
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self.__call__('array set viewpoints {}')
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self.__call__('foreach mol [molinfo list] { set viewpoints($mol) [molinfo $mol get { center_matrix rotate_matrix scale_matrix global_matrix}]}')
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self.__call__('mol addfile ' + filename + ' mol $tmol type ' + filetype + ' waitfor all')
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self.__call__('foreach mol [molinfo list] { molinfo $mol set {center_matrix rotate_matrix scale_matrix global_matrix} $viewpoints($mol)}')
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self.flush()
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# --------------------------------------------------------------------
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# replace all frames of a molecule with those from a given file
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def update(self,filename,filetype='lammpstrj'):
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self.__call__('set tmol [molinfo top]')
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self.__call__('array set viewpoints {}')
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self.__call__('foreach mol [molinfo list] {set viewpoints($mol) [molinfo $mol get { center_matrix rotate_matrix scale_matrix global_matrix}]}')
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self.__call__('animate delete all $tmol')
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self.__call__('mol addfile ' + filename + ' mol $tmol type ' + filetype + ' waitfor all')
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self.__call__('foreach mol [molinfo list] {molinfo $mol set {center_matrix rotate_matrix scale_matrix global_matrix} $viewpoints($mol)}')
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self.flush()
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# --------------------------------------------------------------------
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# add or overwrite coordinates with coordinates in a snapshot
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def set(self,snap,x,y,z,append=True):
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self.__call__('set vmdsel [atomselect top all]')
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if append:
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self.__call__('animate dup [molinfo top]')
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cmd = '$vmdsel set {x y z} {'
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for idx in range(0,snap.natoms):
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cmd += ' {'+str(snap[idx,x])+' '+str(snap[idx,y])+' '+str(snap[idx,z])+'}'
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cmd += '}'
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self.__call__(cmd)
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self.__call__('$vmdsel delete ; unset vmdsel')
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self.flush()
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91
python/examples/viz_vmd.py
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91
python/examples/viz_vmd.py
Executable file
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#!/usr/local/bin/python -i
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# preceeding line should have path for Python on your machine
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# viz_vmd.py
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# Purpose: viz running LAMMPS simulation via VMD
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# Syntax: viz_vmd.py in.lammps Nfreq Nsteps
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# in.lammps = LAMMPS input script
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# Nfreq = dump and viz shapshot every this many steps
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# Nsteps = run for this many steps
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import sys
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sys.path.append("./pizza")
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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: viz_vmd.py in.lammps Nfreq Nsteps"
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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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nsteps = int(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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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 dump file and image
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lmp.command("run 0 pre yes post no")
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ntimestep = 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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# run nfreq steps at a time w/out pre/post, read dump snapshot, display it
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while ntimestep < nsteps:
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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:
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d.next()
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d.unscale()
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p.single(ntimestep)
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# add frame to current data set
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v.append('tmp.pdb','pdb')
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# delete all frame and add new.
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#v.update('tmp.dump')
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lmp.command("run 0 pre no post yes")
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if me == 0:
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v.flush()
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# uncomment the following, if you want to work with the viz some more.
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v('menu main on')
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# print "type quit to terminate."
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v.enter()
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#v.stop()
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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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