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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5712 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2011-02-22 22:32:28 +00:00
parent 46104f1588
commit 49b72ac36e
8 changed files with 162 additions and 49 deletions
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33
tools/eff/VMD-input.py
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@ -12,8 +12,8 @@ ajaramil@wag.caltech.edu
Project: pEFF
Version: August 2009
Usage: python VMD-input.py lammps_dump_filename radii_column_number
Example: python VMD-input.py dump.lammpstrj 6
Usage: python VMD-input.py lammps_dump_filename radii_column xpos_column
Example: python VMD-input.py dump.lammpstrj 5 6
1. Extracts the electron radii from a lammps trajectory dump into %s.out
2. Creates %s.xyz file
@ -28,20 +28,31 @@ def printHelp(input):
Info%(input,input,input)
if __name__ == '__main__':
# if no input, print help and exit
if len(sys.argv) < 2:
print "Usage: python VMD-input.py lammps_dump_filename radii_column_number\n"
print "Usage: python VMD-input.py lammps_dump_filename radii_column xpos_column\n"
sys.exit(1)
else:
infile=sys.argv[1]
workdir=os.getcwd()
tools=sys.argv[0].split('VMD-input.py')[0]
# set defaults
outfile = infile.split('.')[0]
if len(sys.argv) == 2:
print sys.argv
if len(sys.argv) == 4:
column = int(sys.argv[2])
else:
column=6 # default = radius for dump -> id type x y z spin radius
xpos = int(sys.argv[3])
print "Assuming xpos=eradius+1"
elif len(sys.argv) == 3:
column = int(sys.argv[2])
xpos = column+1
print "Assuming xpos=eradius+1"
elif len(sys.argv) == 2:
column=5 # default = radius for dump -> id type q spin eradius x y z
xpos=6
else: print "Incorrect number of arguments"
# check for input:
opts, argv = getopt(sys.argv[1:], 'c:o:ha')
@ -54,12 +65,12 @@ if __name__ == '__main__':
outfile=arg
if opt == '-c': # select column from lammpstrj file to tabulate
column=int(arg)
print column,xpos
makeradii(infile,outfile+".out",column,True)
lmp2xyz(infile,outfile+".xyz")
lmp2xyz(infile,outfile+".xyz",xpos)
print "Creating %s file ..."%(outfile+".vmd")
os.system("cat %s | sed 's/xyzfile/%s/' > %s"%("radii.vmd",outfile+".xyz","temp"))
os.system("cat %s | sed 's/radiifile/%s/' > %s; rm temp"%("temp",outfile+".out",outfile+".vmd"))
os.system("cat %s | sed 's/xyzfile/%s/' > %s"%(tools+"radii.vmd",outfile+".xyz","temp"))
os.system("cat %s | sed 's/radiifile/%s/' > %s; rm temp"%("temp",outfile+".out",workdir+'/'+outfile+".vmd"))
print "Done !! (you can now source %s using VMD's console) \n"%(outfile+".vmd")
print "NOTE: In VMD, set graphics representation for electrons to transparency,"