else:
atomsOP = []#[[] for i in range(nAtom)]
count = 0
for i,line in enumerate(open(opFile,"r")):
line = line.split()
if len(line)<20:continue
count+=1
atomsOP.append(map(float,line[1:]))
atomsOP = zip(*atomsOP)
atoms = array(atomsTraj).swapaxes(0,1)
basis = eye(3)
atoms = rootMeanSquareDist.unwrap(atoms,basis)
atomsTraj = atoms.swapaxes(0,1).swapaxes(1,2)
def coarseGrain(x, cg=10):
return array([sum(x[i*cg:i*cg+cg])/cg for i in range(int(len(x)/cg))])
#brg
#winter
#RdBu
#jet
def colorLine(x, y, z, c=None, cmap=plt.get_cmap('cool'),alpha=0.4):
if c==None:
c = linspace(0.0, 1.0, len(x))
c = array(c)
points = array([x, y, z]).T.reshape(-1, 1, 3)
segments = concatenate([points[:-1], points[1:]], axis=1)
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]]]
if len(crTime)+1 == nAtom:
crTime=crTime[1:] #chop off the average if necessary
if sh2Enable:
