Several people have asked about a plot for relative energies, etc.
Here’s an example for an NEB trajectory.
My idea is that this “Plot Conformers…” dialog would allow you to switch between RMSD or relative energies. It would also offer a “Scale Energies” to convert from Hartree, eV, etc. to kcal/mol as needed. (In this case, the relative energies were in Hartree.)
And you can click on the plot to switch conformers.
Other ideas or suggestions?
And related - what are other properties to track (e.g., forces / gradients, velocities, etc.)
I think that it would be nice to track forces, although I think it would add quite a lot of complexity.
For example, do you plot the total force, the total force in the x, y, and z directions individually, the force on each atom, the force in each direction on each atom, or something else entirely?
I would really enjoy seeing all of those as options, but that adds a lot of complexity right off the bat.
Also, in general I feel like plotting introduces a lot of desire for customization (if you give a mouse a cookie…). For example in NEB plots like the one you have shown, I would really prefer a way to label key points, for example the reactant/product energies and the saddle point energy.
It has been a long time since I’ve used Spartan, but IIRC they had a pretty reasonable plotting interface. One thing I especially liked was that right next to the plot they had a table where you could see all of the energies listed out, and if you were plotting say, dihedral angle on the x-axis then you could see that listed in the table as well. I’m not sure how easy that sort of thing would be to pull off though since I am not sure if Avogadro can retain that sort of information across the individual geometries in an XYZ file.
For conformers it would be nice to be able to plot a Boltzmann distribution, since realistically a scatter plot or line plot doesn’t really contain all that much information.
Some of this is simply the need to add some tutorials.
The plot code already offers the ability to temporarily label:
It’s obviously not perfect - I’d like to add a “click to add manual label” mode for the spectra as well. At the moment these don’t export into a PDF or other image and the needs differ (e.g here you probably just want the y value to a few decimal places.)
In this particular plot, clicking will jump to that frame, so maybe a control-click or shift-click would add a manual label?
I think you want some sort of histogram of energies with Boltzmann weighting or something, which makes sense. Submit a feature request, but it’s definitely “after 2.0 is released.”
One of the changes with the AutoOpt tool is that measurements, etc. will persist across multiple frames. So yes, if you create a measurement of a dihedral angle, that could show up in a table. Certainly even now if you have this, you can display the distances across the frames:
I’ll set this down as a tutorial to add to the website.
As far as forces, it’ll take a bit of time to get some of the “plumbing” in place (e.g., reading it from files for each frame, etc.). But I can easily imagine wanting to plot maximum force or RMS magnitude or something over time. (As you said, I can imagine a lot of things you might want on the plot.)
Another program I use to visualise my calculation shows indeed both the energy and RMS force (which I personally like). They are overlapped in one plot with two different y-axis.
Seeing as it is an NEB you could also consider using a spline to connect the points. It is more of an visual choice but a cubic spline would porbably better present the PES than straight lines.
There’s an argument to be made both for and against spline interpolation for NEB plots.
The density of sampling on the potential energy surface is directly proportional to the probability of a continuous energy profile; for smaller calculations, say 5 points between reactant and product, there is not a guarantee of the PES being free of discontinuity and/or unresolved features.
I for example have been running many calculations of a sort of “PES” in my research, and if my sample number was lower than it is now I would absolutely not have a good picture of the trend. With how high my sampling step is though, I can nearly guarantee that a smooth, interpolated line is indeed the correct way to plot the data.
For right now, I’m going to stick to connecting lines. It’s something worth discussing for post-2.0 (e.g., identifying the type of multiple coordinate sets - NEB, IRC, conformers, trajectory, etc.)
I’ll put in some initial work to handle force and velocity magnitudes, but at the moment, it’s not a high priority. (i.e., just because the window can plot them, they have to be read in from various formats)
