[DFTB-Plus-User] Question regarding FirstLayerAtoms in transport calculations

[Reinaldo Pis Diez]

Dear folks,

We, in our group, are beginning some studies on organic conductors and 
are evaluating the performance of the NEGF as implemented in version 
21.1 of dftb+.

I reproduced without problem the example within 
'transport/molecular-junction' of recipes, but the meaning of the 
FirstLayerAtoms is not clear to me. Moreover, in the example developed 
in 'dftbplus-recipes.readthedocs.io' there are different values for the 
same system:

1) After using 'setupgeom' in 
'https://dftbplus-recipes.readthedocs.io/en/latest/transport/setup-geometry.html', 
one gets 'FirstLayerAtoms = { 1 25 40 50 60 76 }' from the program.

2) When doing the calculation without bias, following 
'https://dftbplus-recipes.readthedocs.io/en/latest/transport/molecule-junction.html', 
one gets 'FirstLayerAtoms = 1, 21, 43, 54' from the example.

3) Finally, looking at the file 'dftb_in.hds_transport' shipped with 
recipes,one gets 'FirstLayerAtoms = { 1 43}'.

I cannot follow the rationale of those numbers, why can I choose 
different options for that keyword? And, most important, how can I 
choose them by looking at the system using a visualizer instead of 
setupgeom?

Sorry for the rather long mail. Regards,

Reinaldo
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