# creating unrelaxed structure.
input.vff.lattice.set_as_crystal_lattice()
cell = matrix([[0.5,-0.5,0],[0.5,0.5,0.5],[0,0,2.5]])
structure = sort_layers(input.lattice.to_structure(cell), array([0,0,2.5]))
for i, atom in enumerate(structure.atoms):
atom.type = "Si" if i % 10 < 6 else "Ge"
# structure = fill_structure(input.escan.vff.lattice.cell)
# structure.atoms[0].type = "Si"
structure.scale = 5.65
structure.freeze = FreezeCell.a0 | FreezeCell.a1
input.escan.fft_mesh = 14, 14, 50
out = bandgap( input.escan, structure,\
outdir=join("results", "osc"),\
references=(0.1, -0.4),\
nbstates = 4,\
comm=world )
# gvectors = out.extract_cbm.gvectors
# vol = det(out.extract_vbm.structure.cell * out.extract_vbm.structure.scale / a0("A"))
# for i, awfn in enumerate(out.extract_vbm.gwfns):
# for j, bwfn in enumerate(out.extract_cbm.gwfns):
# a = awfn.braket(transpose(gvectors), bwfn, attenuate=True)
# if world.rank == 0:, FreezeCell
# print multiply(a, a.conjugate()) * vol * vol, dot(a, a.conjugate()).real * (vol * vol)
# break
# print
osc = out.oscillator_strength()
if world.rank == 0: print osc
###############################
# davezac@hopper08:~/SiGe/old/jwluo/SiGe_SL_001/Si6Ge4_on_Ge/vff
from numpy import array
from quantities import angstrom
from pylada.escan import read_input, bandgap
from pylada.crystal import sort_layers
from pylada.crystal.binary import zinc_blende
from pylada.physics import a0
input = read_input("input.py")
cell = [[2.5,0,0],[0.5,0.5,0.5],[0,-0.5,0.5]]
subs = {'A':'Si', 'B':'Ge'}
structure = zinc_blende().to_structure(cell, subs)
structure.scale = float(5.33847592 / 0.5 * a0.rescale(angstrom))
structure = sort_layers(structure, array([2.5,0,0]))
for i, atom in enumerate(structure.atoms):
atom.type = 'Si' if i % 10 < 6 else 'Ge'
result = bandgap( input.escan, structure, eref=None,
outdir="results/dipoles", references = (-0.2, 0.2),
nbstates=4, direction = array([1., 0,0]),
fft_mesh = (50,14,14) )
tot = array([0e0] * 3) / a0 / a0
for e0, e1, u in result.dipole(degeneracy = 5e1 * input.escan.tolerance, attenuate=False):
tot += (u * u.conjugate()).real
check = array([1.13753549e-03, 5.87932303e-05, 5.87932303e-05]) * 1/a0**2
for a, b in zip(abs(check - tot), abs(check)*1e-2): assert a < max(b, 1e-6), (a, b)
