negative charge density

[Masoudrahbar]

I am calculating the bonding properties of NiMn alloy in bulk and slab structures. in the bulk structure all the charge densities are positive at critical points but in the slab structure some of them (actually most of them) get negative. can somebody please explain this?

[aoterodelaroza]

Hi @masoudrahbar,

The densities from a cube file in interstitial or vacuum regions can become slightly negative because of numerical noise either from the electronic structure program or from critic2's interpolation. For more specifics, can you please provide your density, structure, and input files?

• Masoudrahbar notifications@github.com [2018-01-19 17:24:46 +0000]:

  I am calculating the bonding properties of NiMn alloy in bulk and slab structures. in the bulk structure all the charge densities are positive at critical points but in the slab structure some of them (actually most of them) get negative. can somebody please explain this?

  -- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/aoterodelaroza/critic2/issues/10

[Masoudrahbar]

thank you for the response yes just the regions near the vacuum shows negative values. I have another question and that is about the laplacian. in the bulk all of them are positive but in the slab most of them are negative is this normal?I attached the input files attachments.zip

[aoterodelaroza]

Yep, it's clearly noise. If you try:

crystal zero-case.cube load cube zero-case.cube auto cpreport bleh.cml

and then view the resulting cml with avogadro (you need to set up openbabel's element.txt, as described in the manual), you will see that the vacuum is packed with spurious CPs. The easiest way to get rid of them is to use the DISCARD keyword to prune those that have density less than a very small value:

crystal zero-case.cube load cube zero-case.cube auto discard "$1 < 1e-3" cpreport bleh.cml

With this you get:

• Critical point list, final report (non-equivalent cps) Topological class (n|b|r|c): 6(10) 33(62) 37(74) 11(21) Morse sum: 1

and the vacuum CPs are gone. As for the Laplacian, the same comment applies. The Laplacian is even more noisy than the density in regions of low density.

• Masoudrahbar notifications@github.com [2018-01-19 17:48:21 +0000]:

  thank you for the response yes just the regions near the vacuum shows negative values. I have another question and that is about the laplacian. in the bulk all of them are positive but in the slab most of them are negative is this normal?I attached the input files attachments.zip

  -- You are receiving this because you commented. Reply to this email directly or view it on GitHub: https://github.com/aoterodelaroza/critic2/issues/10#issuecomment-359039891

[Masoudrahbar]

I really appreciate. solved

[Masoudrahbar]

I really appreciate. solved