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eljost / pysisyphus

Python suite for optimization of stationary points on ground- and excited states PES and determination of reaction paths.
GNU General Public License v3.0
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Visualization of Normal Modes #194

Open Kr0n0ss opened 2 years ago

Kr0n0ss commented 2 years ago

Hi, From what I read in the release notes, there is a way to visualize the normal modes (at least the imaginary one from a TS) with modes3d.py How do I use it? Also, I would guess that the hessian calculation would be stored on qm_calcs which could be used for visualization with the appropriate program for each calculator, is this correct? Thanks.

eljost commented 2 years ago

Hi Kr0n0ss, yes with modes3d.py you can (quite crudely) visualize geometries in 3D. For it to work you have to install ursina (python -m pip install ursina). Then you can execute modes3d.py with either a pysisyphus HDF5-Hessian file or a .trj/.xyz file. I'd really like to improve the script but I don't really have any experience with 3d programming and not much time to dive into this topic.

The whole thing is by no means in any way "production ready" but is handy, sometimes.

Regarding Hessian calculations: If logs are produced they are stored in qm_calcs. When you use Gaussian via pysisyphus you can find the .log/.chk/.fchk files in qm_calcs.

All the best, Johannes

Kr0n0ss commented 2 years ago

Thanks!