QTAIM; legend for symbols?

General Discussion Support
1

Thank you for your extremely useful Avogadro tool.

I have been following the QTAIM tutorial at https://avogadro.cc/docs/tutorials/using-qtaim-and-wfn/ and I have been able to have this working with a NWChem generated output, using the aimfile property keyword.

Quick question, is there a key/legend/mapping to the BCPs, NACP etc and the actual balls on the display?

Thanks,

Mark

1 Like
2

Excellent point. It should be here: https://avogadro.cc/docs/display-types/#qtaim-quantum-theory-of-atoms-in-molecules

But that doesn’t outline the various components of the display. I’ll mark that on the list.

  • Bond paths: little white spheres if the Laplacian at the bond critical point > 0.0
  • Bond paths: white cylinders if \nabla^2 \lt 0
  • Nuclear critical points: purple spheres
  • Bond critical points: yellow spheres
  • Electron density sources (e.g. lone pairs): blue spheres

I think that’s it - I’ll check later today and update the docs.

Thanks!

3

This is perfect; many thanks for the quick, clear and complete response.

As a reference for any visitors from the future, this was my NWChem input for the QTAIM analysis:

start CSCPPACGZOOCGX-UHFFFAOYSA-N

title "Title"
charge 0

geometry units angstroms print xyz autosym
   C       -2.74560        0.83024       -0.00000
   O       -1.51554        0.83024        0.00000
   C       -3.53489       -0.27822        0.64238
   C       -3.53489        1.93870       -0.64238
   H       -2.85190        2.67758       -1.07059
   H       -4.15834        2.42799        0.10997
   H       -4.15834        1.52918       -1.44097
   H       -2.85190       -1.01710        1.07059
   H       -4.15834       -0.76751       -0.10997
   H       -4.15834        0.13130        1.44097
end

basis
  * library 6-31G*
end

dft
  xc b3lyp
  mult 1
end

task dft optimize

property
  aimfile
end

task dft property

Then executed with:

nwchem CSCPPACGZOOCGX-UHFFFAOYSA-N.nwin &> CSCPPACGZOOCGX-UHFFFAOYSA-N.nwlog

Using Ubuntu 18.04.3 with NWChem 6.8.1 with debs from https://github.com/nwchemgit/nwchem/releases/tag/6.8.1-release .