(opts, args) = parser.parse_args()
if len(args) < 2:
print(usage)
exit(-1)
esp_cube_file = args[0]
chg_file = args[1]
# load cube file with electrostatic potential (esp)
print("load ESP from cube file...")
atomlist, origin, axes, data = Cube.readCube(esp_cube_file)
if opts.fit_centers != "":
print("loading fit centers from '%s'" % opts.fit_centers)
atomlist = XYZ.read_xyz(opts.fit_centers)[0]
# extract positions of points and values of ESP
points, epot = Cube.get_points_and_values(origin, axes, data)
# fit point charges
chelpg = CHELPG()
chelpg.setFitPoints(points, epot)
chelpg.setAtomicCenters(atomlist, charge=0)
partial_charges = chelpg.fitESP()
# save point charges
if opts.format == 'charges':
np.savetxt(chg_file, partial_charges)
else:
XYZ.write_charges(chg_file, atomlist, partial_charges)
print("partial charges saved to '%s'" % chg_file)
dx = la.norm(axes[0])
dy = la.norm(axes[1])
dz = la.norm(axes[2])
# volume element, assuming the axes are orthogonal
dV = dx * dy * dz
# find total magnetic dipole moment
mtot = np.array([np.sum(Mx * dV), np.sum(My * dV), np.sum(Mz * dV)])
# load cube files for components of vector potential
print "load magnetic vector potential from cube files..."
atomlist, origin, axes, Ax_data = Cube.readCube(Ax_cube_file)
atomlist, origin, axes, Ay_data = Cube.readCube(Ay_cube_file)
atomlist, origin, axes, Az_data = Cube.readCube(Az_cube_file)
# extract positions of points and values of A
points, Ax = Cube.get_points_and_values(origin, axes, Ax_data)
points, Ay = Cube.get_points_and_values(origin, axes, Ay_data)
points, Az = Cube.get_points_and_values(origin, axes, Az_data)
# fit magnetic dipoles
fitter = MagneticDipoleFitter()
fitter.setFitPoints(points, Ax, Ay, Az)
# fitting centers
if opts.fit_centers != "":
print "loading fit centers from '%s'" % opts.fit_centers
atomlist = XYZ.read_xyz(opts.fit_centers)[0]
fitter.setAtomicCenters(atomlist)
magnetic_dipoles = fitter.fitVectorPotential(mtot)
# save magnetic dipoles