The Atomic Manipulator contains a very handy functionality to cleave any crystal along an arbitrary direction, specified via the Miller indices. This makes it powerful to use VNL to set up structures for e.g. slab calculations, in addition to making it easy to construct two-probe systems from surfaces.
The Atomic Manipulator always creates "minimal electrodes", and then uses the "repetitions" keywords for the TwoProbeConfiguration()
construction to expand the electrodes to their full configuration. This saves calculation time for the electrode part by converting a lot of atoms into a lot of k-points, but sometimes it is desirable to obtain the full, explicitly repeated configuration of the electrode cell instead.
For slab calculations
, the best way to do this is to save the "Equivalent BulK" system (there is a ready button for this in the Atomic Manipulator), but if you want to keep the system as a two-probe system, then you can use the attached script instead. It converts a two-probe system with
repetitions to one without
. Up-front this may seem a bit useless, since it generates an identical configuration which just takes more time to calculation. It can however be used as a first step towards a more complex two-probe geometry, e.g. one where the electrodes are shifted in X or Y with respect to each other (after the electrode cell has been expanded accordingly).
Anyway, the script is attached, and hopefully someone will find it useful! To use it as-is, just type
atk expand_numrep.py file.vnl
to expand the first
two-probe configuration in file.vnl
. The expanded two-probe configuration will be put back in the VNL file with "_expanded_reps" appended to the sample name. (The name "numrep" comes from the original name for this keyword in ATK 2.0 and TranSIESTA-C.)