if (N_trans/N_rot % 1 != 0):
raise CorrelationError("The number of translational beads must be a multiple of the number of rotaitonal beads")
#Strip output file extension and then replace it with _CM.xyz
CM_output_file = output_file[:(string.rfind(output_file, "."))] + "_CM.xyz"
CM_EA_zxz_output_file = output_file[:(string.rfind(output_file, "."))] + "_CM_EA_zxz.csv"
CM_EA_ZYZ_output_file = output_file[:(string.rfind(output_file, "."))] + "_CM_EA_ZYZ.csv"
CM_EA_ZYZ_xyz_output_file = output_file[:(string.rfind(output_file, "."))] + "_BEADS_CM_EA_ZYZ.xyz"
CM_EA_ZYZ_xyz_normal_output_file = output_file[:(string.rfind(output_file, "."))] + "_CM_EA_ZYZ.xyz"
###############################################################################
#Read in Cartesian coordinates
###############################################################################
out_dict = Clath_xyz.readWaterAtoms(input_file)
Oxy = out_dict["O"]
Hyd = out_dict["H"]
print "Atom positions read from file."
###############################################################################
#Determine the atom correlations for the water molecules
#For clathrates, all the H's are within 1A of the oxygen atom within
# the same water molecule, but further away from any other
# oxygen atom. Thus, this can be used to separate and sort out
# which atoms belong in which molecule. The index number of the
# oxygen atom is taken as the index number of the molecule.
###############################################################################
#Strip output file extension and then replace it with _CM.xyz
CM_output_file = output_file[:(string.rfind(output_file, "."))] + "_CM.xyz"
CM_EA_zxz_output_file = output_file[:(
string.rfind(output_file, "."))] + "_CM_EA_zxz.csv"
CM_EA_ZYZ_output_file = output_file[:(
string.rfind(output_file, "."))] + "_CM_EA_ZYZ.csv"
CM_EA_ZYZ_xyz_output_file = output_file[:(
string.rfind(output_file, "."))] + "_BEADS_CM_EA_ZYZ.xyz"
CM_EA_ZYZ_xyz_normal_output_file = output_file[:(
string.rfind(output_file, "."))] + "_CM_EA_ZYZ.xyz"
###############################################################################
#Read in Cartesian coordinates
###############################################################################
out_dict = Clath_xyz.readWaterAtoms(input_file)
Oxy = out_dict["O"]
Hyd = out_dict["H"]
print "Atom positions read from file."
###############################################################################
#Determine the atom correlations for the water molecules
#For clathrates, all the H's are within 1A of the oxygen atom within
# the same water molecule, but further away from any other
# oxygen atom. Thus, this can be used to separate and sort out
# which atoms belong in which molecule. The index number of the
# oxygen atom is taken as the index number of the molecule.
###############################################################################
# According to Takeuchi, et al.:
# Structure Lattice Constant (A)
# sII 17.31 (Takeuchi, et al.)
# sI 12.03 (Takeuchi, et al. say that Ratcliffe and Ripmeester have this, but I didn't find it after a quick look)
latticeConst = {"sI": 12.03, "sII": 17.31}
xyz_atomFilename = sys.argv[1]
xyz_cageFilename = sys.argv[2]
cellStructure = sys.argv[3]
cellSize = latticeConst[cellStructure]
# cellSize = float(sys.argv[4])
###############################################################################
# Read in the O and H atom locations
###############################################################################
out_dict = Clath_xyz.readWaterAtoms(xyz_atomFilename)
Hyd = out_dict["H"]
Oxy = out_dict["O"]
print "Read in atom positions. There are %d H atoms and %s O atoms." % (len(Hyd), len(Oxy))
###############################################################################
# Read in the Cage Centre locations
###############################################################################
large_cages = []
small_cages = []
# Open input file
xyz_file = TextFile(xyz_cageFilename)
# According to Takeuchi, et al.:
# Structure Lattice Constant (A)
# sII 17.31 (Takeuchi, et al.)
# sI 12.03 (Takeuchi, et al. say that Ratcliffe and Ripmeester have this, but I didn't find it after a quick look)
latticeConst = {"sI": 12.03, "sII": 17.31}
xyz_atomFilename = sys.argv[1]
xyz_cageFilename = sys.argv[2]
cellStructure = sys.argv[3]
cellSize = latticeConst[cellStructure]
#cellSize = float(sys.argv[4])
###############################################################################
#Read in the O and H atom locations
###############################################################################
out_dict = Clath_xyz.readWaterAtoms(xyz_atomFilename)
Hyd = out_dict["H"]
Oxy = out_dict["O"]
print "Read in atom positions. There are %d H atoms and %s O atoms." % (len(Hyd), len(Oxy))
###############################################################################
#Read in the Cage Centre locations
###############################################################################
large_cages = []
small_cages = []
#Open input file
xyz_file = TextFile(xyz_cageFilename)
