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Computing atom-in-molecule electron densities #295

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Easyoakland opened this issue Jul 12, 2022 · 0 comments
Open

Computing atom-in-molecule electron densities #295

Easyoakland opened this issue Jul 12, 2022 · 0 comments

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@Easyoakland
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  • Using horton 2.3.0 from conda create -n horton -c conda-forge horton
  • I have followed the AIM instructions in 5.1 in http://theochem.github.io/horton/2.1.1.
  • I am attempting to get the electron densities, corresponding to each atom-in-molecule density, in a diatomic molecule. I am using Hirshfeld and Iterative Hirshfeld.
  • I have run horton-wpart.py with the nessessary information and then converted the output to a .csv file.
  • The .csv file contains the charges corresponding to each atom (and they look like the correct charge for the partitioning scheme) amongst other information. This makes me think that I have followed the procedure to do this correctly.
  • The website states that for horton-wpart.py "This script computes atomic weight functions, and derives all AIM observables that are implemented for that scheme. These results are stored in the specified HDF5 output file."
  • I can not find atomic weight functions in the .csv output. It does, however, contain many sections that have a header that looks like: Dataset,atom_00000/density_decomposition/spline_00000/d, Dataset,atom_00001/hartree_decomposition/spline_00001/y, orDataset,atom_00001/spline_prodensity/d, etc...
  • I assume that this is where the information for the atomic weight functions / atom-in-molecule densities is stored? How do I convert all of these splines to a .cube file or .xyz or some other method where I have the actual electron density for a grid of points in a human readable format?
  • What do these splines represent/mean? How is one supposed to do a Hirshfeld decomposition and output the results of the decomposition?
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