UT theoretical chemistry code forum

Dear all,

I have two questions regarding the BADER charge analysis software and I would be really grateful if someone takes time to guide me:

1-As you may already know, the SIESTA program outputs charge density files as "grid" files and there is a program called "grid2cube" which converts these ...

Thank you very much for your support.

Dear all,

I would be really grateful if you help me about the above issues.

Bests,

I am really sorry. I have checked my files with VESTA. Indeed I have no negative values in my Mysys.RHO.cube file. However, I have negative values in my Mysys.BADER.cube file.

Also, for atoms #76,77,78, 80 in the .ACF file generated by using "-vac off", the numbers in columns MIN DIST & ATOMIC VOL ...

One issue is still remaining and that is about zero charges for Mo atoms when using "bader Mysys.RHO.cube -ref Mysys.BADER.cube". Does fragmented core charges also account for this? What is the origin of this fragmented charges? Do they come from the vdW density functional I have used?

Sorry, but I have no idea whether this is considered a problem or not. Please guide me on how to deal with it.

Thank you very much for your sincere support. I am really indebted.

Thank you very much for your instant reply. I still would be really thankful if you elaborate more on this. I should note here that I have used 300 Ry cut-off energy in my SIESTA calculations and my supercells are not cubic (I am still able to convert my SIESTA outputs to .cube files using "g2c_ng ...

Dear all,

I have used vdW pseudos to calculate Adenine adsorption on monolayer MoS2 in SIESTA. To calculate the charge transfer, I have used the useful bader code from "http://theory.cm.utexas.edu/henkelman/code/bader/". I actually used the recommendation in SIESTA manual as "bader Mysys.RHO.cube ...