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PROPERTIES

Discuss features, updates, and general use of the PROPERTIES module

9 Topics 29 Posts

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  • Input Format

    1 Topics
    4 Posts
    Aleksundefined

    Dear Jonas,

    first of all, 450 atoms is impressive indeed!
    Now moving on to a few comments/thoughts that might be of use to you.

    i) From your input file, it appears you still have a few symmetry operators in your simulation cell. Worth checking whether/if that applies to the atoms in the Fe-centred octahedra as that might force a particular solution to the electronic configurations.

    ii) Given that your octahedra are not aligned with any particular crystallographic axis in your system, it is not always straightforward to extract the (d-)orbital occupations. You can have a look at the ROTREF keyword in the manual by which you can rotate the eigenvectors in the properties calculation to orient the frame along a principal axis.

    iii) In Scenario 1 you are right - you removed 1 H atom, from which indeed the symmetry of the octahedron has been reduced/broken. You could test the case without "neutralization", to see whether the extra electron would stay on the site or delocalize...formation energies might be a good guide...?

    iv) Scenario 2 is a bit more complicated. Given that you removed a whole NH4+ tetrahedron, I would expect significant structural distortions occurring in the surrounding of the defect. From there, a conducting state might be not so unrealistic - did you optimize the atomic positions and/or cell parameters following the inclusion of that defect? If so, could be worth seeing where the metallic states originate from (e.g., in the DOS or a charge density difference plot would be sufficient...don't forget SMEAR). The question is where is the extra electron from the anticipated Fe3+ ending if you remove the whole tetrahedron?

    v) Finally, I guess it really depends on what you see experimentally and what would be the most representative simulation cell matching the measurements to be able to extract meaningful data for the oxidation state. What could be potentially useful is to take simple bulk structures for which you know the oxidation state of Fe (e.g., Fe2O3, Fe3O4, ...), analyse the corresponding charge densities (e.g., Mulliken) and have a reference state for comparing the charge on the Fe-ion in your Struvite structure.

    Hope any of this is useful.

    Cheers,
    Aleks

  • Total and AO-Projected

    5 Topics
    15 Posts
    Luzundefined

    Thanks a lot! I will take your advice.

  • 2D Maps, 3D Plots, X-Ray Structure Factors (Static and Dynamic), Mulliken and Hirshfeld Populations

    0 Topics
    0 Posts
    No new posts.

  • 2D Maps, Compton Profiles, Autocorrelation Function

    0 Topics
    0 Posts
    No new posts.

  • Topological Analysis of the Electron Density (QTAIMAC), Bader Populations

    0 Topics
    0 Posts
    No new posts.

  • Questions that do not fit in other categories

    3 Topics
    10 Posts
    mriveraaundefined

    Hi!

    In a COOP calculation you aim to have a description on the interaction between pairs of orbitals or atoms. In order to do that, you need to indicate each pair you are interested to analyze. In your input, in the first line after the COOP keyword, the initial number 1 indicates that you are interested in one pair of orbitals/atoms. You still need to indicate a pair of orbitals or atoms to be considered, writing them in separated lines. Consider this example, taken from the Tutorials webpage:

    NEWK 6 6 1 0 COOP 1 200 7 14 1 12 0 -1 1 -1 2 END

    Here, the two lines before the final END keyword indicate which atoms will be considered (atoms, given that the lines start with a negative value, as stated in the manual page 322). COOP will be evaluated considering the first and second atoms of the systems (with indices 1 and 2). From your previous calculations you can recover the indices of the atoms/orbitals you are interested.

    Let me know if this information has been useful 🙂