from ATK.TwoProbe import *

# The spacing between the wires - the distance should be large
# enough for the wire not to interact.
xy = 10.0

# The lattice distance in the wire.
zs = 2.39

# The lattice vectors of the electode.
unit_cell = [[  xy, 0.0, 0.0],
             [ 0.0, xy , 0.0],
             [ 0.0, 0.0, 6*zs]]*Angstrom 

# Setting up the position of the atoms in the electrode.
positions = [(xy/2,  xy/2,  zs*0),
             (xy/2,  xy/2,  zs*1), 
             (xy/2,  xy/2,  zs*2), 
             (xy/2,  xy/2,  zs*3), 
             (xy/2,  xy/2,  zs*4), 
             (xy/2,  xy/2,  zs*5)]*Angstrom 

# Combining the lattice vectors, and positions together with elements.
electrode = PeriodicAtomConfiguration(unit_cell,[Aluminium]*6,positions)


# Setting up the scattering positions for the doped system.
# Doping is placed a small distance from the chain in the middle
# of the scattering region.
scattering_positions = [(xy/2,  xy/2,  zs*0),
                       (xy/2,  xy/2,  zs*1), 
                       (xy/2,  xy/2,  zs*2), 
                       (xy/2,  xy/2,  zs*3), 
                       (xy/2,  xy/2,  zs*4), 
                       (xy/2,  xy/2,  zs*5), 
                       (xy/2,  xy/2,  zs*6), 
                       (xy/2,  xy/2,  zs*7), 
                       (xy/2,  xy/2+1.2,zs*7.5), 
                       (xy/2,  xy/2,  zs*8), 
                       (xy/2,  xy/2,  zs*9), 
                       (xy/2,  xy/2,  zs*10), 
                       (xy/2,  xy/2,  zs*11), 
                       (xy/2,  xy/2,  zs*12), 
                       (xy/2,  xy/2,  zs*13), 
                       (xy/2,  xy/2,  zs*14)]*Angstrom 

# Creating the perfect Aluminium wire.
aluminum_wire = TwoProbeConfiguration((electrode,electrode),
                                       [Aluminium]*8+[Oxygen]+[Aluminium]*7,
                                        scattering_positions)

vnl_file = VNLFile("imperfect_alwire.vnl")
vnl_file.addToSample(aluminum_wire,"imperfect_alwire")