from ATK.TwoProbe import *

# Restoring the SCF from the previous calculation
scf = restoreSelfConsistentCalculation('imperfect_chain.nc')

# Specify the range of energies
energy_scan = [ i/200.0*Units.eV for i in range(-1601,601)]

# Calculate the Transmission Spectrum
bz_int_parm = brillouinZoneIntegrationParameters( (1,1) )
spectrum = calculateTransmissionSpectrum(
    self_consistent_calculation=scf,
    energies = energy_scan,
    brillouin_zone_integration_parameters=bz_int_parm)

# Save the Transmission Spectrum to VNL file
vnlfile = VNLFile("imperfect_alwire_trans.vnl")
vnlfile.addToSample(spectrum,'imperfect_alwire_trans')

# Print at screen the Transmission Spectrum
print 'Transmission Spectrum'
print '-----------------------------------------------------------------------'
print 'Energies(eV)  Coefficients' 
for i in range(len(spectrum.energies())):
    print '%17.3f %17.6f' %(
            spectrum.energies()[i].inUnitsOf(Units.eV),
            spectrum.coefficients()[i])