Comments (7)
I would appreciate a link to an example cube file. I am working with a relativistic code where it is less trivial to get real valued orbitals.
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Ask, and ye shall receive: https://github.com/bskinn/h5cube/blob/70d8d8ccee43a2b0e9ed641bb3e86c95e50be6fe/h5cube/test/resource/grid25mo.cube
It's a rather low-resolution CUBE, but it should be sufficient for testing the +/- coloration.
from blob.
Thanks so much! +/- coloration coming up soon.
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The cube file has negative number of centers on line 3 and line 14 was unexpected for me and the parser as well. I have fixed that for my local testing so no problem for my debugging, I was just wondering whether there is anything in the format definition that I am missing.
from blob.
See here.
The negative value and extra line(s) must be accounted for in parsing...CUBEs can contain more than one dataset (e.g., three, or seven, or twelve different orbitals), and this mechanism is how it's bookkept.
from blob.
Thanks a lot Brian - I was indeed unaware of this convention and also did not know this great doc. I will link to it, adjust the parser for this and soon have a working +/- example. Thanks again!
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Parsing has been fixed in 6ccba72.
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Related Issues (20)
- Make clear that data does not leave the computer HOT 1
- Show molecular structures HOT 5
- Give hints on how to rotate/zoom
- Do not recompute mesh every time we change the color/opacity
- Add a reset button to go to original settings
- Indicate range of values HOT 2
- Light source rotates with the molecule
- Reading a new cube file does not remove old molecule
- Consider using 3Dmol.js and/or nglview as backend
- Interoperability with Jupyter a la nglview
- Make it possible to save/embed the visualization
- Simple animation from a series of cube files
- Inconsistency with paraview HOT 2
- Internal data object is overcomplete for regular grids
- Document keyboard shortcuts
- Would be nice to be able to plot files from a web address
- Annotate atom centers
- Enable hi-res export to pdf or similar
- Verify that it works on Firefox HOT 1
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