Multi-Domain use cases

[JakeWags]

Multi-Domain use cases simply seem to be broken.

Optimization:
wrong particle count, possibly not even running the optimization

Analysis:
only reconstructing one domain
good-bad particle display only working for one domain

[JakeWags]

Edit to above:
Analysis:
only reconstructing one domain
good-bad particle display only working for one domain
only displaying one mean_shape mean_particle file