Defining centers of mass wrt given atoms

[Juanes]

I’m beginning a project that requires me to scan PESs in Jacobi coordinate systems. It would be nice to have some tools to visualize these in Avogadro.

I envision something like being able to visualize the center of mass with respect to some given atoms, and then being able to define distances and angles with respect to it. In this simple example, I would like to see the center of mass of the NO diatom and then measure the distance to the Cl from it, as well as the angle set by the CM-N and the CM-Cl vectors.

Would this be a possibility?

~ Juan

[ghutchis]

Yep. You can already do that. If you select a set of atoms (e.g., N=O) then you will get a dummy atom (element 0) at the center of mass:

Note there was a bug in 1.99 and earlier versions that’s fixed in 1.100 and nightly builds.

Once you have the CM, it’s just another “atom” as far as distance or angle measurements.

[Juanes]

Wonderful, it works! Thank you

[Juanes]

When I build N and O on the cartesian editor along the y axis, equi-distant from the origin, and generate the center of mass, it places it outside the y axis. Naturally, distance from the CM to any of the atoms is not what I would calculate by hand.

Why is the CM being placed outside the internuclear axis here?

[ghutchis]

I have no idea. I can reproduce it in the 1.100 release, but not in my development version. I’m wondering if it’s some sort of weird optimizer bug?

I’ll definitely add some unit tests to make sure it’s calculating these correctly.