Molcas Forum

winter

Member

Registered: 2025-03-10

Posts: 1

visualizing branching plane vectors / CI topologies

Hi there,

Is there a good way (software) to visualize the branching plane vectors of a CI from the Molcas output file (x̂ and ŷ vectors)?  I have the numerical vectors from the output file but I don't know how to plot them overlaid on an image of the molecule.

Similarly, is there any good way to visualize the topology (branching plane) around the CI?  I assume it would require a script to get the energies in a circle surrounding the CI.

I see both of these kinds of plots in papers (e.g. Figure 5 in https://pubs.acs.org/doi/10.1021/acs.jctc.6b00384) but there is no info on how the plots were made.

Ignacio

Administrator

From: Uppsala

Registered: 2015-11-03

Posts: 1,127

Re: visualizing branching plane vectors / CI topologies

There's no ready-made tool that I know of. Those figures were generated manually: the vectors with VMD, the surfaces with LaTeX and pgfplots. If you have a software that displays vectors for vibrational normal modes, you could abuse it for the branching plane vectors. For the surfaces, you have the equations that can be used in any plotting software.

Kalpa

Member

Registered: 2022-04-09

Posts: 13

Re: visualizing branching plane vectors / CI topologies

Hi winter and Ignacio,

Replying to this older thread because I faced the exact same problem and wanted to share a solution for the community. After struggling to find a tool to visualize conical intersections, I ended up building my own package, ConeZen, which I've now made public.

The package can automatically visualize the branching plane vectors ( x and  y) directly from SHARC-MOLCAS output files, which should solve the original problem discussed here.

My hope is that this tool will be helpful to other researchers. It's open-source and available on GitHub, and I would be very grateful for any community feedback, bug reports, or suggestions to make it better.

You can find the package here: https://github.com/Kalpa08/ConeZen

Hope this helps!

P.S. Ignacio, I really appreciated your original reply on this topic. If you happen to have a moment to look at the package, I would be thrilled to hear any thoughts you might have.