from ATK.TwoProbe import *

# Read the Atomic configuration from a VNL file
vnl_file = VNLFile("imperfect_alwire.vnl")
configurations = vnl_file.readAtomicConfigurations()
perfect_wire = configurations["imperfect_alwire"]


# Setting the Electrode parameters
bz_int_param = brillouinZoneIntegrationParameters( (1,1,20) )
electrode_parameters = ElectrodeParameters(
    brillouin_zone_integration_parameters= bz_int_param 
    )

# Creating the TwoProbeMethod
ele_den_para = electronDensityParameters(mesh_cutoff=150*Units.Ry)
twoprobe_method = TwoProbeMethod(
    (electrode_parameters,electrode_parameters),
     electron_density_parameters=ele_den_para,
     basis_set_parameters=basisSetParameters(
     type=DoubleZetaDoublePolarized)
    )

# Execute the Self Consistent Field
scf = executeSelfConsistentCalculation(perfect_wire,
    twoprobe_method,
    runtime_parameters=runtimeParameters(verbosity_level=1,
    checkpoint_filename='imperfect_chain.nc'))