ajjackson
commented
8 years ago On closer inspection, that code uses shape keys to animate the mesh of each atom type, and replaces the vertex list for each frame. The approach is feasible but is not a simple change.
Moving this to Low Priority for now, as the move to icospheres has resulted in a satisfactory speed boost.
One of the projects which inspired this is Clemens Barth's Atomic Blender packages, which renders animated .XYZ files in Blender. Instead of assigning unique meshes to each atom, they are grouped by type and specified as duplicates of a hidden reference atom.
This approach was originally avoided because it makes further modelling more complicated; however, if there is a significant performance advantage to be gained then this is worth doing.