Atomic groups much faster than molecular group

[mlund]

Salt particles can be treated either as atomic or molecular groups. For a speciation system with equal number of particles with and without nonbonded interactions:

group	ideal	nonbonded
atomic=true	0.4s	4.0s
atomic=false	12s	20s

Run using proposed code in #259 with this input: input.zip

Things to check:

• [ ] Benchmark for bottlenecks
• [ ] It is likely that the difference is in Space::findMolecules() for locating active/inactive particle. For atomic the call is more or less independent of N since the atomic group is ordered with active then inactive particles. For molecules, the operation scales with N. A Space particle tracker would solve this and was implemented in earlier Faunus versions.

ping @rc83

Update: Removing the sanity analysis reduces the molecular time by a factor of six (ideal) or two (nonbonded). Atomic is still significantly faster.

[mlund]

ping @Smutekj