#Find the starting locations of atomic data in outcarfile
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")
for i,b in enumerate(bytenums):
outcar.seek(b)
outcar.readline()
outcar.readline()
atoms.append([map(float,outcar.readline().split()[:3]) for a in range(nAtoms)])
scale = 5E-15
if lammpsFlag:
nAtoms = lammpsIO.nAtoms(filename)
basisByteNums = lammpsIO.basisBytes(filename)
atomsByteNums = lammpsIO.atomsBytes(filename)
for i,(bByte,aByte) in enumerate(zip(basisByteNums,atomsByteNums)):
basis = lammpsIO.parseBasis(filename,bByte)
try:
a,dummy = lammpsIO.parseAtoms(filename,aByte,nAtoms,basis)
except IndexError:
break
atoms.append(a)
scale = 0.001E-12
scale /= 1E-12 #picosecond conversion
atoms = array(atoms)
steps,rmsd =rootMeanSquareDist.rootMeanSquareCorrelate(atoms,basis)
header = "#Generated by %s using file %s\n log(t) ISF \n"%(sys.argv[0].split("/")[-1],inputFile)
else:
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)
outcar.readline()
outcar.readline()
atoms = [
map(float,
outcar.readline().split()[:3]) for a in range(nAtoms)
]
tet, rcut = orderParam.tetrahedral(atoms, basis, rcut=rcut)
tAvg = sum(tet) / len(tet)
tets = " ".join(map(str, tet))
tetraOut.write(str(tAvg) + " " + tets + "\n")
if lammpsFlag:
nAtoms = lammpsIO.nAtoms(filename)
basisByteNums = lammpsIO.basisBytes(filename)
atomsByteNums = lammpsIO.atomsBytes(filename)
tetraOut = open(filename + ".tetra", "w")
tetraOut.write("AverageTetra PerAtomTetra\n")
for i, (bByte, aByte) in enumerate(zip(basisByteNums, atomsByteNums)):
basis = lammpsIO.parseBasis(filename, bByte)
atoms, dummy = lammpsIO.parseAtoms(filename, aByte, nAtoms, basis)
tet, rcut = orderParam.tetrahedral(atoms, basis, rcut=rcut)
tAvg = sum(tet) / len(tet)
tets = " ".join(map(str, tet))
tetraOut.write(str(tAvg) + " " + tets + "\n")
#mencoder "mf://*.png" -mf fps=25 -o output.avi -ovc lavc -lavcopts vcodec=mpeg4
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)
