Optimization of molecular crystals (and other periodic systems) about geometric HOT 1 OPEN

Supporting periodic boundary conditions is something I've wanted to do for a long time. I agree the TRIC coordinate system could yield performance improvements for molecular crystals, but we should be able to support general periodic systems.

The Molecule object, which is used to determine the bond lists, currently supports cubic cells. It would need to be extended to support triclinic cells. We would also need to add primitive internal coordinates for changes in the lattice vectors. I currently don't know whether it's better to directly modify the lattice vector components, or the three lengths + three angles. For molecular crystals, I think that the lattice vectors should be coupled to the centers of the molecules in the lattice, so that as the lattice deforms, the molecules move rigidly such that the fractional coordinates of the centers in the cell are the same.

Lastly we need an Engine object to communicate with a periodic code. If you have an example geometry optimization with CP2K, that would be very helpful to get started.

from geometric.