from ATK.TwoProbe import *

# Restore calculation
scf = restoreSelfConsistentCalculation('lih2li-scf.nc')

# Reopen old two-probe configuration
vnl_file=VNLFile("lih2li.vnl")
atomic_configuration = vnl_file.readAtomicConfigurations()["lih2li"]

# Calculate HOMO and LUMO eigenstates for the H atoms in the two-probe system
eigenstates = calculateProjectedHamiltonianEigenstates(
    scf, projection_atoms = [3,4],
    quantum_numbers = [0,1]
    )

# Store results in VNL files
vnl_file = VNLFile("lih2li-mpsh.vnl")
vnl_file.addToSample(atomic_configuration,'lih2li_mpsh')
for eigenstate in eigenstates:
    vnl_file.addToSample(eigenstate, 'lih2li_mpsh')