if len(sys.argv)==3:
refStructure=int(sys.argv[2])
#First and last configurations
dummy,dummy,basisFirst,atomsFirst,dummy,typesFirst = outcarIO.outcarReadConfig(outcarFile,wantconfig=0)
dummy,dummy,basisLast,atomsLast,dummy,typesLast = outcarIO.outcarReadConfig(outcarFile,wantconfig=-1)
#MSD
delT,msdAtom=outcarMeanSquareDisplaceAtom(outcarFile,refStructure)
#TET
tetsFirst,rcutFirst=tetrahedral(atomsFirst,basisFirst,rcut=rcut)
print "First Tetra/rcut",sum(tetsFirst)/len(tetsFirst),rcutFirst
tetsLast,rcutLast=tetrahedral(atomsLast,basisLast,rcut=rcut)
print "Last Tetra/rcut",sum(tetsLast)/len(tetsLast),rcutLast
#CN
cnFirst,rcutFirst=coordinationNumber(atomsFirst,basisFirst,rcut=rcut)
print "First CN/rcut",float(sum(cnFirst))/len(cnFirst),rcutFirst
cnLast,rcutLast=coordinationNumber(atomsLast,basisLast,rcut=rcut)
print "Last CN/rcut",float(sum(cnLast))/len(cnLast),rcutLast
wFile = open(outcarFile+".MSDatom","w")
wFile.write("#File generated by %s\n"%sys.argv[0].split("/")[-1])
wFile.write("#%d atoms, %5.5f timestep size, %d number of steps\n"%(len(msdAtom),delT[0],len(delT)))
wFile.write("msd$(\AA^2)$ tetraFirst tetraLast cnFirst cnLast\n")
wFile.writelines([str(n[-1])+" "+str(t1)+" "+str(t2)+" "+str(cn1)+" "+str(cn2)+"\n" for n,t1,t2,cn1,cn2 in zip(msdAtom,tetsFirst,tetsLast,cnFirst,cnLast)])
wFile.close()
bytenums = [int(i.split(":")[0]) for i in grepResults if len(i) > 2]
outcar = open(filename, "r")
cnOut = open(filename + ".cn", "w")
cnOut.write("AverageCN PerAtomCN\n")
for i, b in enumerate(bytenums):
outcar.seek(b)
outcar.readline()
outcar.readline()
atoms = [
map(float,
outcar.readline().split()[:3]) for a in range(nAtoms)
]
cn, dummy = orderParam.coordinationNumber(atoms, basis, rcut=rcut)
cnAvg = float(sum(cn)) / len(cn)
cns = " ".join(map(str, cn))
cnOut.write(str(cnAvg) + " " + cns + "\n")
if lammpsFlag:
nAtoms = lammpsIO.nAtoms(filename)
basisByteNums = lammpsIO.basisBytes(filename)
atomsByteNums = lammpsIO.atomsBytes(filename)
cnOut = open(filename + ".cn", "w")
cnOut.write("AverageCN PerAtomCN\n")
for i, (bByte, aByte) in enumerate(zip(basisByteNums, atomsByteNums)):
basis = lammpsIO.parseBasis(filename, bByte)
atoms, dummy = lammpsIO.parseAtoms(filename, aByte, nAtoms, basis)
#Find the starting locations of atomic data in filename
grepResults = subprocess.check_output("grep -b POSITION %s"%filename,shell=True).split("\n")
bytenums=[int(i.split(":")[0]) for i in grepResults if len(i)>2]
outcar= open(filename,"r")
cnOut =open(filename+".cn","w")
cnOut.write("AverageCN PerAtomCN\n")
for i,b in enumerate(bytenums):
outcar.seek(b)
outcar.readline()
outcar.readline()
atoms = [map(float,outcar.readline().split()[:3]) for a in range(nAtoms)]
cn,dummy = orderParam.coordinationNumber(atoms,basis,rcut=rcut)
cnAvg=float(sum(cn))/len(cn)
cns=" ".join(map(str,cn))
cnOut.write(str(cnAvg)+" "+cns+"\n")
if lammpsFlag:
nAtoms = lammpsIO.nAtoms(filename)
basisByteNums = lammpsIO.basisBytes(filename)
atomsByteNums = lammpsIO.atomsBytes(filename)
cnOut = open(filename+".cn","w")
cnOut.write("AverageCN PerAtomCN\n")
for i,(bByte,aByte) in enumerate(zip(basisByteNums,atomsByteNums)):
basis = lammpsIO.parseBasis(filename,bByte)
atoms,dummy = lammpsIO.parseAtoms(filename,aByte,nAtoms,basis)
dummy, dummy, basisFirst, atomsFirst, dummy, typesFirst = outcarIO.outcarReadConfig(
outcarFile, wantconfig=0)
dummy, dummy, basisLast, atomsLast, dummy, typesLast = outcarIO.outcarReadConfig(
outcarFile, wantconfig=-1)
#MSD
delT, msdAtom = outcarMeanSquareDisplaceAtom(outcarFile, refStructure)
#TET
tetsFirst, rcutFirst = tetrahedral(atomsFirst, basisFirst, rcut=rcut)
print "First Tetra/rcut", sum(tetsFirst) / len(tetsFirst), rcutFirst
tetsLast, rcutLast = tetrahedral(atomsLast, basisLast, rcut=rcut)
print "Last Tetra/rcut", sum(tetsLast) / len(tetsLast), rcutLast
#CN
cnFirst, rcutFirst = coordinationNumber(atomsFirst, basisFirst, rcut=rcut)
print "First CN/rcut", float(sum(cnFirst)) / len(cnFirst), rcutFirst
cnLast, rcutLast = coordinationNumber(atomsLast, basisLast, rcut=rcut)
print "Last CN/rcut", float(sum(cnLast)) / len(cnLast), rcutLast
wFile = open(outcarFile + ".MSDatom", "w")
wFile.write("#File generated by %s\n" % sys.argv[0].split("/")[-1])
wFile.write("#%d atoms, %5.5f timestep size, %d number of steps\n" %
(len(msdAtom), delT[0], len(delT)))
wFile.write("msd$(\AA^2)$ tetraFirst tetraLast cnFirst cnLast\n")
wFile.writelines([
str(n[-1]) + " " + str(t1) + " " + str(t2) + " " + str(cn1) +
" " + str(cn2) + "\n" for n, t1, t2, cn1, cn2 in zip(
msdAtom, tetsFirst, tetsLast, cnFirst, cnLast)