Major changes: 1. Used abbreviate words for options for POR, CycleClosingAmple. 2. Added options for printing log file and setting/getting log file names.
Major changes:
1. Used abbreviate words for options for POR, CycleClosingAmple.
2. Added options for printing log file and setting/getting log file names.

MyersResearchGroup/iBioSim,MyersResearchGroup/iBioSim,MyersResearchGroup/iBioSim