# Which axes should be integrated out?
assert len(axes_str) == 2
ax2index = {"x": 0, "y": 1, "z": 2}
axes_integrate = [ax2index[s] for s in axes_str]
# Which axis remains?
axis_remains = None
for i in range(0,3):
if not (i in axes_integrate):
axis_remains = i
break
print "axes %s are integrated out" % str(axes_integrate)
print "remaining axis: %s" % axis_remains
# load the cube file
atomlist, origin, axes, data = Cube.readCube(cube_file)
axes = [np.array(ax) for ax in axes]
x0 = np.array(origin)
nx,ny,nz = data.shape
ns = [nx,ny,nz]
# remaining coordinate is called u
du = la.norm(axes[axis_remains])
print "du = %s" % du
nu = ns[axis_remains]
u = np.linspace(origin[axis_remains], nu*du, nu)
# shift axis so that the center is located at u=0
u = u-u[len(u)/2]
# rho(u), 1D curve after integrating
rho_u = np.zeros(ns[axis_remains])
(opts, args) = parser.parse_args()
if len(args) < 6:
print usage
exit(-1)
# input cube files
Mx_cube_file = args[0]
My_cube_file = args[1]
Mz_cube_file = args[2]
# output cube files
Ax_cube_file = args[3]
Ay_cube_file = args[4]
Az_cube_file = args[5]
# load cube files with magnetic dipole density
print "load magnetic dipole density from cube files..."
atomlist, origin, axes, Mx = Cube.readCube(Mx_cube_file)
atomlist, origin, axes, My = Cube.readCube(My_cube_file)
atomlist, origin, axes, Mz = Cube.readCube(Mz_cube_file)
print "compute vector potential..."
Ax,Ay,Az = vector_potential_Poisson(atomlist, origin, axes, Mx, My, Mz,
poisson_solver=opts.solver,
conv_eps=opts.conv_eps, maxiter=opts.maxiter)
# save vector potential
Cube.writeCube(Ax_cube_file, atomlist, origin, axes, Ax)
Cube.writeCube(Ay_cube_file, atomlist, origin, axes, Ay)
Cube.writeCube(Az_cube_file, atomlist, origin, axes, Az)
print "x-,y- and z-components of vector potential saved to '%s', '%s' and '%s'" % (Ax_cube_file, Ay_cube_file, Az_cube_file)
# input cube files
# ... for magnetic dipole density
Mx_cube_file = args[0]
My_cube_file = args[1]
Mz_cube_file = args[2]
# ... vector potential
Ax_cube_file = args[3]
Ay_cube_file = args[4]
Az_cube_file = args[5]
# output file
dat_file = args[6]
# load cube files components of magnetic dipole density
print "load magnetic dipole densities from cube files..."
atomlist, origin, axes, Mx = Cube.readCube(Mx_cube_file)
atomlist, origin, axes, My = Cube.readCube(My_cube_file)
atomlist, origin, axes, Mz = Cube.readCube(Mz_cube_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)
dest="nuclear_potential",
type=int,
help=
"Should the nuclear potential be added to the electrostatic potential (0: no, 1: yes) [default: %default]",
default=1)
(opts, args) = parser.parse_args()
if len(args) < 2:
print usage
exit(-1)
rho_cube_file = args[0]
pot_cube_file = args[1]
# load cube file with electronic density
print "load density from cube file..."
atomlist, origin, axes, rho = Cube.readCube(rho_cube_file)
print "compute electrostatic potential..."
pot = electrostatic_potential_Poisson(
atomlist,
origin,
axes,
rho,
poisson_solver=opts.solver,
conv_eps=opts.conv_eps,
maxiter=opts.maxiter,
nuclear_potential=opts.nuclear_potential)
# save potential
Cube.writeCube(pot_cube_file, atomlist, origin, axes, pot)
print "electrostatic potential saved to '%s'" % pot_cube_file