when I computer the two-probe system,how to setup the initial density type?choose EquivalentBulk or NeutralAtom? Thank you!
This is my structure Script:
from ATK.TwoProbe import *
# Scattering elements
left_surface_elements = [Gold, Gold, Gold, Gold,
Gold, Gold, Gold, Gold,
Gold, Gold, Gold, Gold,
Gold, Gold, Gold, Gold,
Gold, Gold, Gold, Gold,
Gold, Gold, Gold, Gold,
Gold, Gold, Gold, Gold,
Gold, Gold, Gold, Gold]
central_atom_elements = [Carbon, Carbon, Carbon, Carbon,
Carbon, Carbon, Carbon, Carbon,
Hydrogen, Hydrogen, Hydrogen, Hydrogen,
Hydrogen, Hydrogen, Hydrogen, Hydrogen,
Iron, Carbon, Carbon, Carbon,
Carbon, Carbon, Carbon, Carbon,
Carbon, Hydrogen, Hydrogen, Hydrogen,
Hydrogen, Hydrogen, Hydrogen, Hydrogen,
Hydrogen]
right_surface_elements = [Gold, Gold, Gold, Gold,
Gold, Gold, Gold, Gold,
Gold, Gold, Gold, Gold,
Gold, Gold, Gold, Gold,
Gold, Gold, Gold, Gold,
Gold, Gold, Gold, Gold,
Gold, Gold, Gold, Gold,
Gold, Gold, Gold, Gold]
scattering_elements = left_surface_elements + central_atom_elements + right_surface_elements
# Scattering coordinates
left_surface_coordinates = [[ 0. , 0. , 8.15600014],
[ 0. , 2.8835814 , 8.15600014],
[ 0. , 5.7671628 , 8.15600014],
[ 0. , 8.65074444, 8.15600014],
[ 2.8835814 , 0. , 8.15600014],
[ 2.8835814 , 2.8835814 , 8.15600014],
[ 2.8835814 , 5.7671628 , 8.15600014],
[ 2.8835814 , 8.65074444, 8.15600014],
[ 5.7671628 , 0. , 8.15600014],
[ 5.7671628 , 2.8835814 , 8.15600014],
[ 5.7671628 , 5.7671628 , 8.15600014],
[ 5.7671628 , 8.65074444, 8.15600014],
[ 8.65074444, 0. , 8.15600014],
[ 8.65074444, 2.8835814 , 8.15600014],
[ 8.65074444, 5.7671628 , 8.15600014],
[ 8.65074444, 8.65074444, 8.15600014],
[ 1.4417907 , 1.4417907 , 10.19499969],
[ 1.4417907 , 4.32537222, 10.19499969],
[ 1.4417907 , 7.20895386, 10.19499969],
[ 1.4417907 , 10.09253502, 10.19499969],
[ 4.32537222, 1.4417907 , 10.19499969],
[ 4.32537222, 4.32537222, 10.19499969],
[ 4.32537222, 7.20895386, 10.19499969],
[ 4.32537222, 10.09253502, 10.19499969],
[ 7.20895386, 1.4417907 , 10.19499969],
[ 7.20895386, 4.32537222, 10.19499969],
[ 7.20895386, 7.20895386, 10.19499969],
[ 7.20895386, 10.09253502, 10.19499969],
[ 10.09253502, 1.4417907 , 10.19499969],
[ 10.09253502, 4.32537222, 10.19499969],
[ 10.09253502, 7.20895386, 10.19499969],
[ 10.09253502, 10.09253502, 10.19499969]]*Angstrom
central_atom_coordinates = [[ 3.00554715, 5.06825432, 13.20798956],
[ 3.60000394, 3.64764951, 13.20501758],
[ 5.02483884, 3.06347858, 13.19524344],
[ 6.44540297, 3.65794097, 13.18439271],
[ 7.02954911, 5.08280861, 13.17882158],
[ 6.43509244, 6.50341343, 13.18179356],
[ 5.01025753, 7.08758436, 13.1915677 ],
[ 3.58969341, 6.49312197, 13.20241844],
[ 1.8750888 , 5.06416577, 13.21637116],
[ 2.80354606, 2.84538208, 13.21172935],
[ 5.02893651, 1.9329897 , 13.19646353],
[ 7.24765669, 2.86145579, 13.17951621],
[ 8.16001021, 5.08689752, 13.1708149 ],
[ 7.23155295, 7.30568133, 13.17545671],
[ 5.00616257, 8.21807347, 13.19072253],
[ 2.78744231, 7.28960739, 13.20766985],
[ 5.02913646, 5.07703446, 14.79286948],
[ 3.02872382, 5.0712603 , 16.40691737],
[ 3.6231805 , 3.6506555 , 16.40394524],
[ 5.04801539, 3.06648456, 16.39417127],
[ 6.46857952, 3.66094695, 16.38332036],
[ 7.05272566, 5.0858146 , 16.37774924],
[ 6.45826899, 6.50641941, 16.38072136],
[ 5.03343408, 7.09059034, 16.39049533],
[ 3.61286997, 6.49612795, 16.40134624],
[ 1.89826261, 5.0671714 , 16.41492394],
[ 2.82671987, 2.84838759, 16.41028217],
[ 5.05211035, 1.93599545, 16.39501646],
[ 7.2708305 , 2.86446153, 16.37806896],
[ 8.18318401, 5.08990314, 16.36936763],
[ 7.25472699, 7.30868684, 16.37400964],
[ 5.0293364 , 8.22107922, 16.38927535],
[ 2.81061636, 7.29261314, 16.40622261]]*Angstrom
right_surface_coordinates = [[ 2.8835814 , 2.8835814 , 19.55499903],
[ 2.8835814 , 5.7671628 , 19.55499903],
[ 2.8835814 , 8.65074444, 19.55499903],
[ 2.8835814 , 0. , 19.55499903],
[ 5.7671628 , 2.8835814 , 19.55499903],
[ 5.7671628 , 5.7671628 , 19.55499903],
[ 5.7671628 , 8.65074444, 19.55499903],
[ 5.7671628 , 0. , 19.55499903],
[ 8.65074444, 2.8835814 , 19.55499903],
[ 8.65074444, 5.7671628 , 19.55499903],
[ 8.65074444, 8.65074444, 19.55499903],
[ 8.65074444, 0. , 19.55499903],
[ 0. , 2.8835814 , 19.55499903],
[ 0. , 5.7671628 , 19.55499903],
[ 0. , 8.65074444, 19.55499903],
[ 0. , 0. , 19.55499903],
[ 4.32537222, 4.32537222, 21.5939993 ],
[ 4.32537222, 7.20895386, 21.5939993 ],
[ 4.32537222, 10.09253502, 21.5939993 ],
[ 4.32537222, 1.4417907 , 21.5939993 ],
[ 7.20895386, 4.32537222, 21.5939993 ],
[ 7.20895386, 7.20895386, 21.5939993 ],
[ 7.20895386, 10.09253502, 21.5939993 ],
[ 7.20895386, 1.4417907 , 21.5939993 ],
[ 10.09253502, 4.32537222, 21.5939993 ],
[ 10.09253502, 7.20895386, 21.5939993 ],
[ 10.09253502, 10.09253502, 21.5939993 ],
[ 10.09253502, 1.4417907 , 21.5939993 ],
[ 1.4417907 , 4.32537222, 21.5939993 ],
[ 1.4417907 , 7.20895386, 21.5939993 ],
[ 1.4417907 , 10.09253502, 21.5939993 ],
[ 1.4417907 , 1.4417907 , 21.5939993 ]]*Angstrom
scattering_coordinates = left_surface_coordinates + central_atom_coordinates + right_surface_coordinates
electrode_elements = [Gold, Gold, Gold, Gold]
electrode_coordinates = [[ 0. , 0. , 0. ],
[ 1.44179073, 1.44179073, 2.039 ],
[ 0. , 0. , 4.078 ],
[ 1.44179073, 1.44179073, 6.117 ]]*Angstrom
electrode_cell = [[ 2.88358145, 0. , 0. ],
[ 0. , 2.88358145, 0. ],
[ 0. , 0. , 8.156 ]]*Angstrom
# Set up electrodes
electrode_configuration = PeriodicAtomConfiguration(
electrode_cell,
electrode_elements,
electrode_coordinates
)
# Set up two-probe configuration
twoprobe_configuration = TwoProbeConfiguration(
(electrode_configuration,electrode_configuration),
scattering_elements,
scattering_coordinates,
electrode_repetitions=[[4,4],[4,4]],
equivalent_atoms=([0,0],[-1,-1])
)
# Export the two-probe system to VNL file.
vnl_file = VNLFile("AuFeCOT2Au.vnl")
vnl_file.addToSample(twoprobe_configuration, "AuFeCOT2Au")
