def notestPropagatePlaneRealistic(self):
label = join(test_folder, 'siesta')
eigs, kpts, EF = readInfoForSTMSimulation(label=label)
rho, variables, dh_cell = readCubeDensity(label=label)
dh = np.array(map(vectorLength, dh_cell))
band = 30
kn = 4
kappa = 1.0
rho = rho.sum(axis=0)
c, variables, domain = surfaceIntegrator(rho=rho, variables=variables)
wf, variables1, dh_cell = readCubeWavefunction(label=label, band=band, kn=kn)
kpt, wk = kpts[kn-1]
eikr = phaseFactor(kpt, variables1)
u1 = wf/eikr
u2, variables2 = propagateWaveFunction(
c=c,
kpt=kpt,
u=u1,
variables=variables,
kappa=kappa,
)
grad_u = np.array(np.gradient(u2, *dh))
index = 5
grad_uz = grad_u[2, :, :, index]
u2_plane = u2[:,:, index]
plane_z = variables2[2,0,0, index]
r_plane = variables2[:2, :,:, index]
u3, variables3 = propagateWaveFunctionPlane(
kpt=kpt,
u=u2_plane,
grad_uz=grad_uz,
variables=r_plane,
kappa=kappa,
plane_z=plane_z,
)
from matplotlib import pylab as plt
fig = plt.figure(figsize=(8, 8))
ax = plt.gca()
z = variables[2,0,0,:]
v = abs(u1).sum(axis=(0,1))
ax.semilogy(z, v)
z = variables2[2,0,0,:]
v = abs(u2).sum(axis=(0,1))
ax.semilogy(z, v)
z = variables3[2,0,0,:]
v = abs(u3).sum(axis=(0,1))
#ax.semilogy(z, v)
print abs(u2).sum(axis=(0,1))
print variables2[2,0,0,:]
plt.show()
eeeeee
def notestPropagatePlane(self):
r = np.mgrid[0:10:1.1,1:10:0.8]
u = np.ones(r.shape[1:], dtype=complex)
grad_uz = np.ones(r.shape[1:], dtype=complex)
u, r = propagateWaveFunctionPlane(
u=u,
grad_uz=grad_uz,
variables=r,
kappa=2,
)
from matplotlib import pylab as plt
plt.pcolormesh(u.real)