mirror of https://github.com/lammps/lammps.git
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5317 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
38ab9087ed
commit
3ed80aea4d
|
|
@ -0,0 +1,205 @@
|
||||||
|
#
|
||||||
|
# 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>
|
||||||
|
|
||||||
|
oneline = "Control VMD from python."
|
||||||
|
|
||||||
|
docstr = """
|
||||||
|
v = vmd() start up VMD
|
||||||
|
v.stop() shut down VMD instance
|
||||||
|
v.clear() delete all visualizations
|
||||||
|
|
||||||
|
v.rep(style) set default representation style. One of
|
||||||
|
(Lines|VDW|Licorice|DynamicBonds|Points|CPK)
|
||||||
|
v.new(file[,type]) load new file (default file type 'lammpstrj')
|
||||||
|
v.data(file[,atomstyle]) load new data file (default atom style 'full')
|
||||||
|
v.replace(file[,type]) replace current frames with new file
|
||||||
|
v.append(file[,type]) append file to current frame(s)
|
||||||
|
v.set(snap,x,y,z,(True|False)) set coordinates from a pizza.py snapshot to new or current frame
|
||||||
|
|
||||||
|
v.frame(frame) set current frame
|
||||||
|
v.flush() flush pending input to VMD and update GUI
|
||||||
|
v.read(file) read Tcl script file (e.g. saved state)
|
||||||
|
|
||||||
|
v.enter() enter interactive shell
|
||||||
|
v.debug([True|False]) display generated VMD script commands?
|
||||||
|
"""
|
||||||
|
|
||||||
|
# Imports and external programs
|
||||||
|
|
||||||
|
import types, os
|
||||||
|
import numpy
|
||||||
|
|
||||||
|
try: from DEFAULTS import PIZZA_VMDNAME
|
||||||
|
except: PIZZA_VMDNAME = "vmd"
|
||||||
|
try: from DEFAULTS import PIZZA_VMDDIR
|
||||||
|
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 = "LINUX"
|
||||||
|
|
||||||
|
try: import pexpect
|
||||||
|
except:
|
||||||
|
print "pexpect from http://pypi.python.org/pypi/pexpect/ is required for vmd module"
|
||||||
|
raise
|
||||||
|
# Class definition
|
||||||
|
|
||||||
|
class vmd:
|
||||||
|
|
||||||
|
# --------------------------------------------------------------------
|
||||||
|
|
||||||
|
def __init__(self):
|
||||||
|
self.vmddir = PIZZA_VMDDIR
|
||||||
|
self.vmdexe = PIZZA_VMDDIR + '/' + PIZZA_VMDNAME + '_' + PIZZA_VMDARCH
|
||||||
|
# these are all defaults copied from the vmd launch script
|
||||||
|
os.environ['VMDDIR'] = PIZZA_VMDDIR
|
||||||
|
os.environ['VMDDISPLAYDEVICE'] = PIZZA_VMDDEV
|
||||||
|
os.environ['VMDSCRPOS'] = "596 190"
|
||||||
|
os.environ['VMDSCRSIZE'] = "669 834"
|
||||||
|
os.environ['VMDSCRHEIGHT'] = "6.0"
|
||||||
|
os.environ['VMDSCRDIST'] = "-2.0"
|
||||||
|
os.environ['VMDTITLE'] = "on"
|
||||||
|
os.environ['TCL_LIBRARY'] = PIZZA_VMDDIR + "/scripts/tcl"
|
||||||
|
os.environ['STRIDE_BIN'] = PIZZA_VMDDIR + "/stride_" + PIZZA_VMDARCH
|
||||||
|
os.environ['SURF_BIN'] = PIZZA_VMDDIR + "/surf_" + PIZZA_VMDARCH
|
||||||
|
os.environ['TACHYON_BIN'] = PIZZA_VMDDIR + "/tachyon_" + PIZZA_VMDARCH
|
||||||
|
ldpath = os.environ.get('LD_LIBRARY_PATH','')
|
||||||
|
if ldpath == '':
|
||||||
|
os.environ['LD_LIBRARY_PATH'] = PIZZA_VMDDIR
|
||||||
|
else:
|
||||||
|
os.environ['LD_LIBRARY_PATH'] = ldpath + ':' + PIZZA_VMDDIR
|
||||||
|
ldpath = os.environ.get('LD_LIBRARY_PATH','')
|
||||||
|
if ldpath == '':
|
||||||
|
os.environ['PYTHONPATH'] = PIZZA_VMDDIR
|
||||||
|
else:
|
||||||
|
os.environ['PYTHONPATH'] = PIZZA_VMDDIR + "/scripts/python"
|
||||||
|
self.debugme = False
|
||||||
|
# open pipe to vmd and wait until we have a prompt
|
||||||
|
self.VMD = pexpect.spawn(self.vmdexe)
|
||||||
|
self.VMD.expect('vmd >')
|
||||||
|
|
||||||
|
# --------------------------------------------------------------------
|
||||||
|
# post command to vmd and wait until the prompt returns.
|
||||||
|
def __call__(self,command):
|
||||||
|
if self.VMD.isalive():
|
||||||
|
self.VMD.sendline(command)
|
||||||
|
self.VMD.expect('vmd >')
|
||||||
|
if self.debugme:
|
||||||
|
print "call+result:"+self.VMD.before
|
||||||
|
return
|
||||||
|
|
||||||
|
# --------------------------------------------------------------------
|
||||||
|
# exit VMD
|
||||||
|
def stop(self):
|
||||||
|
self.__call__("quit")
|
||||||
|
del self.VMD
|
||||||
|
|
||||||
|
# --------------------------------------------------------------------
|
||||||
|
# force VMD display and GUI update.
|
||||||
|
def flush(self):
|
||||||
|
self.__call__('display update ui')
|
||||||
|
|
||||||
|
# --------------------------------------------------------------------
|
||||||
|
# turn on debugging info
|
||||||
|
def debug(self,status=True):
|
||||||
|
if status and not self.debugme:
|
||||||
|
print 'Turning vmd.py debugging ON.'
|
||||||
|
if not status and self.debugme:
|
||||||
|
print 'Turning vmd.py debugging OFF.'
|
||||||
|
self.debugme = status
|
||||||
|
|
||||||
|
# --------------------------------------------------------------------
|
||||||
|
# emulate a regular tcl command prompt
|
||||||
|
def enter(self,mode='tcl'):
|
||||||
|
self.__call__('menu main off')
|
||||||
|
self.__call__('menu main on')
|
||||||
|
while 1:
|
||||||
|
try:
|
||||||
|
command = raw_input("vmd > ")
|
||||||
|
except EOFError:
|
||||||
|
print "(EOF)"
|
||||||
|
self.__call__('menu main off')
|
||||||
|
return
|
||||||
|
if command == "quit" or command == "exit":
|
||||||
|
self.__call__('menu main off')
|
||||||
|
return
|
||||||
|
if command == "gopython":
|
||||||
|
print "gopython not supported here"
|
||||||
|
continue
|
||||||
|
self.__call__(command)
|
||||||
|
|
||||||
|
# --------------------------------------------------------------------
|
||||||
|
# read and execute tcl script file (e.g. a saved state)
|
||||||
|
def read(self,filename):
|
||||||
|
self.__call__('play ' + filename)
|
||||||
|
self.flush()
|
||||||
|
|
||||||
|
# --------------------------------------------------------------------
|
||||||
|
# remove all molecules, data and visualizations
|
||||||
|
def clear(self):
|
||||||
|
self.__call__("mol delete all")
|
||||||
|
|
||||||
|
# --------------------------------------------------------------------
|
||||||
|
# navigate to a given frame
|
||||||
|
def rep(self,style='Lines'):
|
||||||
|
if style == 'Lines' or style == 'VDW' or style == 'Licorice' \
|
||||||
|
or style == 'DynamicBonds' or style == 'Points' or style == 'CPK':
|
||||||
|
self.__call__('mol default style ' + style)
|
||||||
|
# --------------------------------------------------------------------
|
||||||
|
# navigate to a given frame
|
||||||
|
def frame(self,framespec):
|
||||||
|
self.__call__('animate goto ' + str(framespec))
|
||||||
|
|
||||||
|
# --------------------------------------------------------------------
|
||||||
|
# load a new molecule from a file supported by a molfile plugin
|
||||||
|
def new(self,filename,filetype='lammpstrj'):
|
||||||
|
self.__call__('mol new ' + filename + ' type ' + filetype + ' waitfor all')
|
||||||
|
self.flush()
|
||||||
|
|
||||||
|
# --------------------------------------------------------------------
|
||||||
|
# load a new molecule from a data file via the topotools plugin
|
||||||
|
def data(self,filename,atomstyle='full'):
|
||||||
|
self.__call__('package require topotools 1.0')
|
||||||
|
self.__call__('topo readlammpsdata ' + filename + ' ' + atomstyle)
|
||||||
|
self.flush()
|
||||||
|
|
||||||
|
# --------------------------------------------------------------------
|
||||||
|
# append all frames from a given file to the current molecule
|
||||||
|
def append(self,filename,filetype='lammpstrj'):
|
||||||
|
self.__call__('set tmol [molinfo top]')
|
||||||
|
self.__call__('array set viewpoints {}')
|
||||||
|
self.__call__('foreach mol [molinfo list] { set viewpoints($mol) [molinfo $mol get { center_matrix rotate_matrix scale_matrix global_matrix}]}')
|
||||||
|
self.__call__('mol addfile ' + filename + ' mol $tmol type ' + filetype + ' waitfor all')
|
||||||
|
self.__call__('foreach mol [molinfo list] { molinfo $mol set {center_matrix rotate_matrix scale_matrix global_matrix} $viewpoints($mol)}')
|
||||||
|
self.flush()
|
||||||
|
|
||||||
|
# --------------------------------------------------------------------
|
||||||
|
# replace all frames of a molecule with those from a given file
|
||||||
|
def update(self,filename,filetype='lammpstrj'):
|
||||||
|
self.__call__('set tmol [molinfo top]')
|
||||||
|
self.__call__('array set viewpoints {}')
|
||||||
|
self.__call__('foreach mol [molinfo list] {set viewpoints($mol) [molinfo $mol get { center_matrix rotate_matrix scale_matrix global_matrix}]}')
|
||||||
|
self.__call__('animate delete all $tmol')
|
||||||
|
self.__call__('mol addfile ' + filename + ' mol $tmol type ' + filetype + ' waitfor all')
|
||||||
|
self.__call__('foreach mol [molinfo list] {molinfo $mol set {center_matrix rotate_matrix scale_matrix global_matrix} $viewpoints($mol)}')
|
||||||
|
self.flush()
|
||||||
|
|
||||||
|
# --------------------------------------------------------------------
|
||||||
|
# add or overwrite coordinates with coordinates in a snapshot
|
||||||
|
def set(self,snap,x,y,z,append=True):
|
||||||
|
self.__call__('set vmdsel [atomselect top all]')
|
||||||
|
if append:
|
||||||
|
self.__call__('animate dup [molinfo top]')
|
||||||
|
cmd = '$vmdsel set {x y z} {'
|
||||||
|
for idx in range(0,snap.natoms):
|
||||||
|
cmd += ' {'+str(snap[idx,x])+' '+str(snap[idx,y])+' '+str(snap[idx,z])+'}'
|
||||||
|
cmd += '}'
|
||||||
|
self.__call__(cmd)
|
||||||
|
self.__call__('$vmdsel delete ; unset vmdsel')
|
||||||
|
self.flush()
|
||||||
Loading…
Reference in New Issue