header = "#Generated by %s using file %s\n t(ps) ISF \n"%(sys.argv[0].split("/")[-1],inputFile)
if "OUTCAR" in inputFile:
ocarFile = inputFile
atomByteNums = outcarIO.atomBytes(ocarFile)
nAtom = outcarIO.nAtoms(ocarFile)
basis = outcarIO.basis(ocarFile)
configIterator = parserGens.parseOutcarAtoms(atomByteNums,ocarFile,nAtom)
atomsTime = [array(atoms) for atoms in configIterator]
atomsTime = unwrap(atomsTime,basis)
else:
lmpFile = inputFile
atomByteNums = lammpsIO.atomsBytes(lmpFile)
nAtom = lammpsIO.nAtoms(lmpFile)
basis = lammpsIO.basis(lmpFile)
bounds=[[0,basis[0][0]],[0,basis[1][1]],[0,basis[2][2]]]
configIterator = parserGens.parseLammpsAtoms(atomByteNums,lmpFile,nAtom)
atomsTime = [array(atoms) for atoms in configIterator]
bounds=[[0,basis[0][0]],[0,basis[1][1]],[0,basis[2][2]]]
if len(crTime)+1 == nAtom:
crTime=crTime[1:] #chop off the average if necessary
if sh2Enable:
rcut = 3.1
neighbs = secondShell( neighbors(array(atomsTime[-1]),bounds,rcut) )
ns = map(len,neighbs)
crTime = [sum([crTime[j] for j in neighbs[i]])/ns[i] if ns[i]>0 else crTime[i] for i in range(len(neighbs))]
dumpFilename = fname+"lmp.dump"
possibleSuffix = [i for i in possibleSuffix if os.path.isfile(fname+i)]
print possibleSuffix
ensembleHead = " ".join([i.strip(".") for i in possibleSuffix])
ensembles = None
if len(possibleSuffix)>0:
ensembles = [parserGens.parseEnsemble(fname+i) for i in possibleSuffix]
if "OUTCAR" in fname:
nAtoms = outcarIO.nAtoms(fname)
basis = array(map(array,outcarIO.basis(fname)))
bounds = [[0,basis[0][0]],[0,basis[1][1]],[0,basis[2][2]]]
types = outcarIO.types(fname)
#Find the starting locations of atomic data in outcarfile
grepResults = subprocess.check_output("grep -b POSITION %s"%fname,shell=True).split("\n")
bytenums=[int(i.split(":")[0]) for i in grepResults if len(i)>2]
outcarParsed = parserGens.parseOutcarAtoms(bytenums,fname,nAtoms)
lammpsIO.writeDump(dumpFilename,basis,types,outcarParsed,ensembles,ensembleHead)
else:
nAtoms = lammpsIO.nAtoms(fname)
basis = lammpsIO.basis(fname)
bounds = [[0,basis[0][0]],[0,basis[1][1]],[0,basis[2][2]]]
b = lammpsIO.atomsBytes(fname)
dummy,types = lammpsIO.parseAtoms(fname,b[0],nAtoms,basis)
dumpParsed = parserGens.parseLammpsAtoms(b,fname,nAtoms)
lammpsIO.writeDump(dumpFilename,basis,types,dumpParsed,ensembles,ensembleHead)