Create Topology module

[khs26]

As discussed in Create MolecularSystem class, it would be nice if we could create some sort of topology module for PyGMIN.

So far, we want to be able to include:

• Molecular systems with bonding, angles and dihedrals;
• Crystal systems (including information on boundary conditions);
• Angle-axis topologies (e.g. water networks).

I am wondering whether we also need to separate all this information from information about symmetry and our various forms of coarse-graining.

I think we also need to think carefully about how this module will be related to the System classes, e.g. when individual particles are bonded by harmonic potentials, such as in AMBER, they cannot dissociate and you can't meaningfully rearrange the system to some other type of connectivity.

[ruehle]

How I used the topology class so far:

• the system class has an attribute topology
• when initializing the step taking or other objects which need the topology, I pass the topology object
• that means, angle axis minpermdist need a topology, which contains all information about symmetry

If I understood your separation question correctly: Coarse-graining would be a wrapper (cg topology) around an atomistic topology (e.g. generalized rigid bodies)

I'm currently pulling all the crystal stuff out of pygmin to a separate repository, this can be added later when it has reached a stable state.

I'm not sure if we should make a generic topology module, or rather implement the topology concept in the according use cases, but just trying to follow some sort of standard protocol.