Path enhancements

[SCiarella]

• [x] Pathway objects should return their total length in Angstrom
• [x] Pathway should also compute and report the energy difference between connected sites, and report this information which is more relevant than the total free energy of the sites
• [ ] The current implementation for optimal_n_paths is inefficient if the user wants paths with large differences. The reason is that the algorithm is based on netwokx.all_shortest_paths which starts the search from the optimal one with small variations. We should address that:
• • [ ] the documentation of gemdat.optimal_n_paths should report that it is suited only for small path variations,
• • [ ] an approach with graph pruning may be optimal to identify strongly distinct paths, but this may deserve a separate issue
• • [ ] the shaded background in the path_energy plots representing the sites explored, should be made optional in case of multiple paths that explore different sites

[stefsmeets]

I would also like to suggest these changes to Pathway:

• [x] Pathway should have a lattice
• [x] Pathway should have a dims (volume.dims())

I think this will help decouple Pathway from Volume so that it can stand better on its own. At the moment we have several places where we are dragging volume along just to axes the dims or lattice.

The lattice is also needed to calculate the total length in Angstrom.

When we have that in place, I think we can move more methods to Pathway.

[stefsmeets]

• Pathway should also compute and report the energy difference between connected sites, and report this information which is more relevant than the total free energy of the sites

@SCiarella Is this essentially np.diff(path.energy)? Does this need its own method?

[SCiarella]

• Pathway should also compute and report the energy difference between connected sites, and report this information which is more relevant than the total free energy of the sites

@SCiarella Is this essentially np.diff(path.energy)? Does this need its own method?

Probably a dedicated method is not too useful, but it could be nice to have a plot for the energy difference along the path instead of the total energy.

[stefsmeets]

For 3. the shaded background can be turned off by not providing a structure since #313

[SCiarella]

Once #323 is merged, this issue can be closed. Task 2. has not been addressed and will be left for a future issue if the need arises.