Topology Development Superissue

[astatide]

The topology-related classes are currently very barebone implementations that do almost nothing; right now. Currently, they consist of a few functions.

We want to take a given system and create a set of topology parameters for it; namely, SInFF should provide a set of methods/functions to generate a topology given a System. The output of this should be functions paired to a particle or particle pair (atoms are currently the only particle available) which a dynamics integrator can act upon (Lamia).

Two ideas present themselves as to how to store the resulting information

1. Graph-based method: in this instance, an Atom (or the System) contains information about its bonded neighbors in space (more formally, pairwise interactions between particles); an integrator merely has to iterate through the atoms's neighbor list to figure out where to go next. This may introduce a lot of complexity that results in very little benefit for a dynamics integrator like Lamia, but could be very useful for splitting up space for Behemoth.
2. Store everything on the system, iterate through all functions in the topology space and apply to the relevant atoms.

Method 2 is the easiest and sufficient for something like Lamia; method 1 will certainly be more fun to code althouugh it will require more planning, which will come later in this thread.