if scale == None:
if "OUTCAR" in inputFile:
scale = 5E-15 #5fs (potim=5)
else:
scale = 0.001E-12 #0.001ps (default for units = metal)
if logtEnable:
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]]]
filename = sys.argv[1]
header=["TimeStep AverageRMSD\n"]
rmsddata = header
outcarFlag=False
lammpsFlag=False
if "OUTCAR" in filename:
outcarFlag=True
lammpsFlag=False
else:
outcarFlag=False
lammpsFlag=True
atoms=list()
if outcarFlag:
nAtoms = outcarIO.nAtoms(filename)
basis = array(map(array,outcarIO.basis(filename)))
#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:
possibleSuffix = [".rmsd",".cn",".tetra",".rmsd50",".rmsd100",".rmsd1000",".rmsd5000",".rmsd10000",".2shelltetra",".2shellcn",".2shellrmsd100",".tetra.avg1000",".tetra.avg5000",".tetra.avg100",".tetra.avg500"]
utils.usage(["<outcar,lamps dump>"],1,1,"Note: Automatically looks for <OUTCAR/dump.suffix> for per atom ensembles. to include in the dump")
fname = sys.argv[1]
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]]]
