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:
nAtoms = lammpsIO.nAtoms(filename)
rcut = 3.2
filename = sys.argv[1]
outcarFlag = False
lammpsFlag = False
if "OUTCAR" in filename:
outcarFlag = True
lammpsFlag = False
else:
outcarFlag = False
lammpsFlag = True
if outcarFlag:
nAtoms = outcarIO.nIons(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")
tetraOut = open(filename + ".tetra", "w")
tetraOut.write("AverageTetra PerAtomTetra\n")
for i, b in enumerate(bytenums):
outcar.seek(b)
outcar.readline()
outcar.readline()
#make a directory for the movie
#for configs in outcar
# read in a config from outcar
# calculate tetrahedral order param or CN
# generate the image and save as a file
def usage():
print "Usage: %s <Outcar> <Reference Config #>"%sys.argv[0].split("/")[-1]
if len(sys.argv)<2:
usage()
exit(0)
outcarFile = sys.argv[1]
nAtoms = outcarIO.nIons(outcarFile)
basis = array(map(array,outcarIO.basis(outcarFile)))
movieDir = "./outcarMovie/"
prefix = "outcarTet"
suffix = ".png"
if not os.path.exists(movieDir): os.makedirs(movieDir)
#Find the starting locations of atomic data in outcarfile
grepResults = subprocess.check_output("grep -b POSITION %s"%outcarFile,shell=True).split("\n")
bytenums=[int(i.split(":")[0]) for i in grepResults if len(i)>2]
outcar= open(outcarFile,"r")
mlab.figure(bgcolor=(0.8,0.8,0.8))
for i,b in enumerate(bytenums):
if i%2==0:
continue
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]]]
# calculate tetrahedral order param or CN
# generate the image and save as a file
def usage():
print "Usage: %s <Outcar> <Reference Config #>" % sys.argv[0].split(
"/")[-1]
if len(sys.argv) < 2:
usage()
exit(0)
outcarFile = sys.argv[1]
nAtoms = outcarIO.nIons(outcarFile)
basis = array(map(array, outcarIO.basis(outcarFile)))
movieDir = "./outcarMovie/"
prefix = "outcarTet"
suffix = ".png"
if not os.path.exists(movieDir): os.makedirs(movieDir)
#Find the starting locations of atomic data in outcarfile
grepResults = subprocess.check_output("grep -b POSITION %s" % outcarFile,
shell=True).split("\n")
bytenums = [int(i.split(":")[0]) for i in grepResults if len(i) > 2]
outcar = open(outcarFile, "r")
mlab.figure(bgcolor=(0.8, 0.8, 0.8))
for i, b in enumerate(bytenums):
if i % 2 == 0:
