def usage():
print "%s OUTCAR CONFIG" % sys.argv[0].split("/")[-1]
if len(sys.argv) != 3:
usage()
exit(0)
outcarFile = sys.argv[1]
configRequest = int(sys.argv[2])
nSteps = outcarIO.nSteps(outcarFile)
#unit is femto, but in 10E-10*10E-15 seconds to account for angstroms in distance
timestep = outcarIO.timestep(outcarFile) * 10E-1
#Error check requested configuration
if configRequest == -1:
configRequest = nSteps - 1
if configRequest > nSteps:
print "%d configurations available" % nSteps
exit(0)
if configRequest < 5:
print "Need more than 5 steps for backwards - finite difference method."
exit(0)
#Gather poscar information for last set of atoms
basis, atypes, atoms, head, poscar = outcarIO.outcar2poscar(
outcarFile, configRequest)
if "-linear" in sys.argv:
linEnable = True
i = sys.argv.index("-linear")
sys.argv.pop(i)
inputFile = sys.argv[1]
#steps = map(int,sys.argv[2].split(","))
isfType = "total"
if sys.argv[2][0] in ['s','S']:
isfType = "self"
else:
isfType = "total"
if scale == None:
if "OUTCAR" in inputFile:
scale = outcarIO.timestep(inputFile)*1E-15# 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("/"),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)
#parses an outcar, takes 3 nearest poscar information and uses finitie difference method to calculate velocities. Stick velocities at the end. Can take the place of a poscar to initialize velocities.
def usage():
print "%s OUTCAR CONFIG"%sys.argv[0].split("/")[-1]
if len(sys.argv)!=3:
usage()
exit(0)
outcarFile = sys.argv[1]
configRequest = int(sys.argv[2])
nSteps = outcarIO.nSteps(outcarFile)
#unit is femto, but in 10E-10*10E-15 seconds to account for angstroms in distance
timestep = outcarIO.timestep(outcarFile) * 10E-1
#Error check requested configuration
if configRequest == -1:
configRequest = nSteps-1
if configRequest > nSteps:
print "%d configurations available"%nSteps
exit(0)
if configRequest < 5:
print "Need more than 5 steps for backwards - finite difference method."
exit(0)
#Gather poscar information for last set of atoms
basis,atypes,atoms,head,poscar = outcarIO.outcar2poscar(outcarFile,configRequest)
#Convert from fractional units to cartesian
