Geometry at the displacement

General Discussion Support
1

Hello,

I was wondering if it’s possible to extract the XYZ coordinates corresponding to a displacement along the imaginary mode. Currently, when I play the animation, it shows the motion, but the coordinates change dynamically and aren’t accessible. Stopping the animation just reverts everything back to the original geometry.

Environment Information

Avogadro version: 1.100.0
Operating system and version: MacOS Sequioa

1 Like
2

This is actually something I’ve also wanted in the past, would be quite useful I think.

1 Like
3

It’s not exactly intuitive, but you can do this already.

Pick a vibrational mode in the dialog and adjust the amplitude. (For this example, I drove up the amplitude to make it clear.)

Go to the animation tool. You’ll see there are a set of animation frames – corresponding to each of the steps of the vibration out, back - one way then another:

Animated Vibration for Formaldehyde
Animated Vibration for Formaldehyde1030×560 37 KB

You should be able to pick one of the frames and then export the modified coordinates.

Suggestions? (I just noticed that the vibrations list has redundant stop and start animation buttons.)

4

I’d actually suggest that instead of having the frames available in the Animation tool it should probably go in the Vibrations list. It’s a much more intuitive spot and would make it so there’s less switching between dialogs.

The current issue is that the Stop button in the vibrations list just resets the coordinates. Instead I’d like to see a similar slider in the vibrations list that lets you pick the frame, and a Pause button that stops at a certain point in the animated frequency.

5

Ok that’s great that it’s possible! Just clearly the discoverability is low.

I guess actually unlike @brockdyer03 I don’t have anything massively against the way the animation of vibrations is delegated to the animation tool, but I see a couple of major issues:

  1. I didn’t even realise that it did that – maybe the Animation Tool should open automatically when the vibrational frequencies window is opened? Or maybe instead of Start/Stop Animation there should just be a single button called “Animate”, and when that is clicked the Animation Tool is opened and the animation starts playing?
  2. The default speed of the Animation Tool is way slower than that of the buttons in the vibrational frequencies dialog, which makes those buttons kind of useful
  3. What happens when a file contains an animation/set of frames/multiple geometries already and then a vibration animation is started? Does the original animation just disappear?

I think this also ties into the problem I have with the Animation Tool being the only way to view structures from a multi-structure set. Wouldn’t the best place to navigate within a set of geometries would be from a third tab next to Files and Layers, called Structures or Geometries or something? Then what I’m thinking is that, if that was the case, the Animation Tool could have a drop-down selection box called “Source”, and there the user could select from a list e.g.

  • Structures [i.e. if this was selected it would work similarly to how it works now]
  • Vibrational Mode 1
  • Vibrational Mode 2
  • etc.

And the list would only be populated with those options that are actually available/relevant.