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.
###############################################################################
OH_length = 1 #Angstroms
out_dict = Clath_xyz.correlateWaters(Oxy, Hyd, OH_length)
#Use 2D lists to store the vectors
OH_all = out_dict["OH_all_vec"]
#These lists store the H1 (or H2) indices that correlate with each O
OH1_all_cor = out_dict["OH1_all_cor"]
OH2_all_cor = out_dict["OH2_all_cor"]
print "Atoms correlated."
###############################################################################
#Calculate internal water molecule vectors OH1, OH2, and HH
###############################################################################
OH1 = []
OH2 = []
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. ############################################################################### OH_length = 1 #Angstroms out_dict = Clath_xyz.correlateWaters(Oxy, Hyd, OH_length) #Use 2D lists to store the vectors OH_all = out_dict["OH_all_vec"] #These lists store the H1 (or H2) indices that correlate with each O OH1_all_cor = out_dict["OH1_all_cor"] OH2_all_cor = out_dict["OH2_all_cor"] print "Atoms correlated." ############################################################################### #Calculate internal water molecule vectors OH1, OH2, and HH ############################################################################### OH1 = [] OH2 = []
# print "###################################################################################"
# print (i,j,k)
for l in range(0, len(Hyd)):
Hyd_cell.append(Hyd[l] + (Geo.Vector(i, j, k) * cellSize))
# print Hyd[l] + (Geo.Vector(i,j,k) * cellSize)
for m in range(0, len(Oxy)):
Oxy_cell.append(Oxy[m] + (Geo.Vector(i, j, k) * cellSize))
# print Oxy[m] + (Geo.Vector(i,j,k) * cellSize)
print "Made unit cell duplicates."
###############################################################################
# Determine which H's go with which O's
###############################################################################
out_dict = Clath_xyz.correlateWaters(Oxy_cell, Hyd_cell, lenOH)
OH1_all_cor = out_dict["OH1_all_cor"]
OH2_all_cor = out_dict["OH2_all_cor"]
print "Correlated O's and H's." # This piece takes the longest amount of time so far.
###############################################################################
# Calculate internal water molecule vectors OH1, OH2, and HH
###############################################################################
OH1 = []
OH2 = []
HH = []
for waterNo in range(0, len(Oxy_cell)):
OH1.append(Hyd_cell[OH1_all_cor[waterNo]] - Oxy_cell[waterNo])
#print "###################################################################################"
#print (i,j,k)
for l in range(0, len(Hyd)):
Hyd_cell.append(Hyd[l] + (Geo.Vector(i,j,k) * cellSize))
#print Hyd[l] + (Geo.Vector(i,j,k) * cellSize)
for m in range(0, len(Oxy)):
Oxy_cell.append(Oxy[m] + (Geo.Vector(i,j,k) * cellSize))
#print Oxy[m] + (Geo.Vector(i,j,k) * cellSize)
print "Made unit cell duplicates."
###############################################################################
#Determine which H's go with which O's
###############################################################################
out_dict = Clath_xyz.correlateWaters(Oxy_cell, Hyd_cell, lenOH)
OH1_all_cor = out_dict["OH1_all_cor"]
OH2_all_cor = out_dict["OH2_all_cor"]
print "Correlated O's and H's." #This piece takes the longest amount of time so far.
###############################################################################
#Calculate internal water molecule vectors OH1, OH2, and HH
###############################################################################
OH1 = []
OH2 = []
HH = []
for waterNo in range(0,len(Oxy_cell)):
OH1.append(Hyd_cell[OH1_all_cor[waterNo]] - Oxy_cell[waterNo])
