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lammps/tools/eff/bohr2ang.py
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bohr2ang.py
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Info="""
Module name: bohr2ang.py
Author: (c) Andres Jaramillo-Botero
California Institute of Technology
ajaramil@caltech.edu
Project: pEFF
Version: August 2009
Usage: python bohr2ang.py
>>Name of data file (bohr): [datafile]
Results:
creates a datafile with extension .ang in real units
"""
import os
currdir=os.getcwd()
datafile=raw_input("Name of data file (bohr): ")
bohr2ang=0.529177249
bperatu2angperfs=0.512396271120794
f=open(currdir+'/'+datafile,'r')
w=open(currdir+'/'+datafile+'.ang','w')
lines=f.readlines()
atom_flag=False
vel_flag=False
for line in lines:
if line.find("xlo") > 0:
parse=line.split()
w.write("%f %f xlo xhi\n"%(float(parse[0])*bohr2ang,float(parse[1])*bohr2ang))
elif line.find("ylo") > 0:
parse=line.split()
w.write("%f %f ylo yhi\n"%(float(parse[0])*bohr2ang,float(parse[1])*bohr2ang))
elif line.find("zlo") > 0:
parse=line.split()
w.write("%f %f zlo zhi\n"%(float(parse[0])*bohr2ang,float(parse[1])*bohr2ang))
elif line.find("xy") >= 0:
parse=line.split()
w.write("%f %f %f xy xz yz\n"%(float(parse[0])*bohr2ang,float(parse[1])*bohr2ang,float(parse[2])*bohr2ang))
elif atom_flag and line.strip():
parse=line.split()
id=parse[0]
type=parse[1]
q=parse[2]
spin=parse[3]
eradius=float(parse[4])*bohr2ang
x=float(parse[5])*bohr2ang
y=float(parse[6])*bohr2ang
z=float(parse[7])*bohr2ang
rest=" ".join(parse[8:])
w.write("%s %s %s %s %f %f %f %f %s\n"%(id,type,q,spin,eradius,x,y,z,rest))
elif line.find("Atoms") >= 0:
w.write(line)
atom_flag=True
continue
elif vel_flag and line != "\n":
parse=line.split()
id=parse[0]
vx=float(parse[1])*bperatu2angperfs
vy=float(parse[2])*bperatu2angperfs
vz=float(parse[3])*bperatu2angperfs
erv=float(parse[4])*bperatu2angperfs
w.write("%s %f %f %f\n"%(id,vx,vy,vz,erv))
elif line.find("Velocities") >= 0:
w.write(line)
atom_flag=False
vel_flag=True
continue
else:
w.write(line)
f.close()
w.close()
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