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#! /usr/bin/python
####################################################################
# MaterialsStudio Cell File To Abinit Config file Converter
# zhoubo
# 2006.9.26
####################################################################
import sys
import re
if __name__=="__main__":
if len(sys.argv) >2:
useage()
sys.exit()
try:
fp=open(sys.argv[1])
except:
print "Cannot open Cell file !"
sys.exit()
data=fp.readlines()
#lattice paramenters
a=b=c=0.0
#primitive vectors
a_=b_=c_=[]
# atoms
atoms=[]
atompos=[]
ntypat=""
natom=0
typat=""
n=0
while n<len(data):
if data[n].find("%BLOCK LATTICE_CART")>-1:
t1=re.split("\s+",data[n+1].strip())
a_=map(float,t1)
for x in a_:
if x > a: a=x
for x in xrange(len(a_)):
a_[x]=a_[x]/a
t1=re.split("\s+",data[n+2].strip())
b_=map(float,t1)
for x in b_:
if x > b: b=x
for x in xrange(len(b_)):
b_[x]=b_[x]/b
t1=re.split("\s+",data[n+3].strip())
c_=map(float,t1)
for x in c_:
if x > c: c=x
for x in xrange(len(c_)):
c_[x]=c_[x]/c
n+=4
if data[n].find("%ENDBLOCK LATTICE_CART") > -1:
n+=1
continue
if data[n].find("%BLOCK POSITIONS_FRAC") > -1:
n+=1
while data[n].find( "%ENDBLOCK POSITIONS_FRAC")==-1:
t1=re.split("\s+",data[n].strip())
if t1[0] not in atoms:
atoms.append(t1[0])
ntypat+=str(len(atoms))+" "
natom+=1
typat+=str(len(atoms))+" "
atompos.append(map(float,t1[1:]))
else:
natom+=1
typat+=str(atoms.index(t1[0])+1)+" "
atompos.append(map(float,t1[1:]))
n+=1
if data[n].find("%ENDBLOCK POSITIONS_FRAC") > -1:
break
n+=1
# Prepare the output
print "####################################################"
print "# Atoms Stucture created by CellToAbinit Converter !"
print "####################################################"
print ""
print "# Definition of the unit cell"
print "#The length of the primitive vectors "
print "# 1 Bohr=0.5291772108 Angstroms "
print "# acell %f %f %f" % (round(a,6),round(b,6),round(c,6)),"Angstroms"
print "acell %f %f %f" % (round(a/0.5291772108,6),round(b/0.5291772108,6),round(c/0.5291772108,6))
print "rprim "
print " %8f %8f %8f"%(a_[0],a_[1],a_[2])
print " %8f %8f %8f"%(b_[0],b_[1],b_[2])
print " %8f %8f %8f"%(c_[0],c_[1],c_[2])
print ""
print "#Definition of the atom types"
print "# %d kind of atoms" %( natom)
print "# ",atoms
print "ntypat "+ntypat
print "znucl "+"Needed"
print ""
print "#Definition of tha atoms"
print "natom ",natom
print "typat ",typat
print "xred"
for x in atompos:
print " %8s %8s %8s"%(round(x[0],6),round(x[1],6),round(x[2],6))
print ""
print "##### End of CellToAbinit Conveter ! #####"
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