A series updates coming from developing mpvmpr sample

[YifanC]

1. Update simulation properties for 2x2 mpvmpr and module0
2. Save the updated segments to output files
3. For non beam simulation, add event times to segment t0 to match with beam simulation
4. logger name in module-to-module variation cases
5. Sync trajectory length updates from 2x2_sim convert2h5 (Zach)
6. Fill correct vertex information for mpvmpr

Sorry for having all these in the same PR. If you prefer to move 6. in a separate PR, please let me know. All of these are tested, 1.-5. should be purely improvements.

6. will change the use of dumptree. It is tailored for non-beam simulation (no event builder to tell event id and vertex id as external information) which can have multiple interactions in one edep event (note that the definition may differ from a larnd event). Currently beam larnd event merges multiple edep event (one interaction per edep event), while mpvmpr (particle bomb) larnd event can natively hold multiple interactions in one edep event (=larnd event). I think it makes sense to me to merge 6. in develop, as currently the vertex information is just not filled properly. We need to be careful what to do with cosmic simulation, but as it is currently in development, it can be adjusted accordingly in my opinion.