Charge transfer calculation (between molecule and substrate) using the AIM utility (Bader charge analysis)

Hi all,

I started using abinit recently for my project and I need to calculate the charge transfer between a molecule and the substrate. I learned that I can use the abinit AIM utility for the calculation. Looking at the guide of AIM at Aim - abinit, and I am confused about which input variables (39 in total) to use and how to use?

Could anyone share a sample of input variables that I need for my calculation? or point to some resources and/or experts that I could reference to? I highly appreciate it.

Thank you!

Hi A,

As a nonexpert in this type of calculation I can suggest one simple thing.
Since all of the variables relate to topic/Bader in the ABINIT documentation webpage:

you can have a look at the test files that are related to the AIM variables.
You will note that tests are paired for this type of calculations, for example v4/t30 and t31.
This could serve as a good starting point from these input files.
Generally, if one needs a quick example input related to specific variables, one can search for the specific keywords in the tests subfolder in the ABINIT package.
If you encounter any difficulties, please feel free to provide feedback.

Good luck,

Hi Bogdan,

Thank you for your response and information. I was able to find an example v3/t56, t57 as a starting point. Using a list of similar variables, I was able to perform Bader analysis for O, C, Ag and Pt atoms of the complex, one at a time. But failed on running for Pd. The runtime error message of AIM is showing as below -

" initaim : will read the core densities

error: your core charge 36.003570851880539 does not correspond to the correct number
of valence electrons 18.000000000000000 and the nuclear charge 46.000000000000000
You have probably used a pseudopotential which has more valence electrons than the
original FHI ones. ACTION: make a .fc file with the correct core charge "

I was suspecting there might be some issue in Pd core density file (46-Pd.8.fc). Do you have any suggestions on how to resolve this issue?

Thanks again,

I was suspecting there might be some issue in Pd core density file (46-Pd.8.fc).

Right. Indeed the fc files should be consistent with the core-valence partitioning used
for generating the pseudopotentials employed in the calculation

Note that the fc files available on the Abinit website are compatible with core/valence partitioning used in the fhi pseudos
but this does not necessarily imply that one can use the same fc file with the pseudodojo psp8
pseudopotentials as there are several elements in which the pseudodojo version
includes semi-core states that are not treated in the fhi table

Can you try this fc file I’ve generated with a python script that extracts the core density from the psp8 file?

Pd-sp.fc (53.1 KB)