)
(opts, args) = parser.parse_args()
if len(args) < 3:
parser.print_help()
exit(-1)
# input files
chg_file = args[0]
# output file
nac_file = args[1]
# S0-S1 excitation energy (in eV)
en_diff = float(args[2]) / AtomicData.hartree_to_eV
# load molecular geometry and transition charges
atomlist, transition_charges = XYZ.read_charges(chg_file)
# compute NAC vector
nac = coupling_vector(atomlist,
transition_charges,
en_diff,
nuclear_charge=opts.nuclear_charge)
# and save it to a file
fh_nac = open(nac_file, "w")
# write header for NAC vector
print("# non-adiabatic coupling vector ( in bohr^-1 ) ", file=fh_nac)
print("# X Y Z ", file=fh_nac)
# print non-adiabatic coupling vector as (Nat,3) matrix
Nat = len(atomlist)
files = sys.argv[1:]
cubes = []
molecules = []
charge_lists = []
for f in files:
if ".cub" in f:
cube = CubeData()
cube.loadFromFile(f)
cubes.append(cube)
molecules.append(cube.atomlist)
elif ".xyz" in f:
atomlist = XYZ.read_xyz(f)[-1]
molecules.append(atomlist)
elif ".chg" in f:
atomlist, charges = XYZ.read_charges(f)
molecules.append(atomlist)
charge_lists.append(charges)
else:
print "Unknown file type: %s" % f
window.setWindowTitle(window.windowTitle() + " %s " % f)
viewer.setCubes(cubes)
viewer.setGeometries(molecules)
if len(charge_lists) > 0:
viewer.setGeometriesAndCharges(molecules, charge_lists)
viewer.selectShowOptions(options=["surfaces", "charges", "transition charges"])
"""
# plot E-field
mlab = viewer.visualization.scene.mlab