One user on ask.bc-pf.org wondered whether there's software that can visualize molecular orbitals, reflecting their continious character. Software that I was aware of (Avogadro, JMol, GView) only plots a uniform isosurface, so I thought it'd be good to try to write the script that creates "fog plots".
- wrappers -- endpoints for scripts. Start from here.
- geometries -- if you want to plot MO of a molecule, you need to place its optimized geometry as a regular
.xyzfile in that folder. - tools -- helper functions. Contain analytical forms of hydrogen AOs (required by wrappers/hfwavefunctions.py)
- output -- for svg, jpg, and html graphs.
- modules -- modules used by functions in wrappers
wrappers/hydrogenaos.py allows you to plot single AO functions of H or overlap of any two AOs as a function of internuclear distance.
wrappers/hfwavefunctions.py allows you to plot MO based on RHF calculations.
You can plot MO in 3 different representations: as a heat map, as a surface, and a classical 3D representation.
This project uses plotly, numpy, and pyscf.
- Create a command based endpoint for
hfwavefunctions.pyso that you can specify molecule name, orbital to be visualized, and representation and get results. - Improve documentation (add README.md to modules)
- Add docstrings
- Add tests?
- Figure out whether there's a bug in my code or the "max" colorscale for volume plots works worse with negative values.