def notestSaveReadWaveFunctionsTest(self):
band = 21
kn = 4
ws = 2
potential = Topographic(voltage=-2)
rho, r, dh_cell = readCubeDensity(label=test_label)
dh = np.array(map(vectorLength, dh_cell))
rho = rho.sum(axis=0)
c, variables, domain = surfaceIntegrator(rho=rho, variables=r, rho0=1e-3, DS=1)
thick_surface = vectorLength(c, axis=0) > 1e-9
take_z = thick_surface.sum(axis=0)
take_z = take_z.sum(axis=0) > 0
wf, r, dh_cell = readCubeWavefunction(label=test_label, band=band, kn=kn)
EF, eigs= readEigenvalues(label=test_label)
kpts = readKpoints(label=test_label)
energy = eigs[kn-1, band-1, 0]
we = STMWeighting(energies=[energy], potential=potential, EF=EF)
we = we[0]
kpt, wk = kpts[kn-1]
kappa = getVacuumDecayRate(energy)
eikr = phaseFactor(kpt, r)
u = wf/eikr
grad_u = np.array(np.gradient(u, *dh))
A = (c*grad_u).sum(axis=0)
B = u*c
A=A[:,:,take_z]
B=B[:,:,:,take_z]
r=r[:,:,:,take_z]
u, variables = propagateWaveFunction(
A=A,
B=B,
kpt=kpt,
r=r,
kappa=kappa,
height=10,
)
weight = we*ws*wk
Itest = weight*abs(u)**2
self.assertFalse(os.path.exists(testfile))
saveWavefunctionsToPlane(filename=testfile, label=test_label)
self.assertTrue(os.path.exists(testfile))
f = netcdf.netcdf_file(testfile, 'r')
self.assertTrue(len(f.variables.keys()) >0)
f.close()
I, r = STMFromFile(
label=join(test_folder, 'test'),
potentials=[potential],
cells=None,
)
self.assertArraysEqual(np.log(Itest[0,0]), np.log(I[0,0,0]), 5)
def readInfoForSTMSimulation(label='./siesta'):
kpts = readKpoints(label=label)
EF, eigs = readEigenvalues(label=label)
n_eigs = []
sh = eigs.shape
for kn, band, spin in itertools.product(range(sh[0]), range(sh[1]), range(sh[2])):
n_eigs.append((eigs[kn, band, spin], kn, band, spin))
n_eigs.sort()
eigs = n_eigs
return eigs, kpts, EF