Added --profile and --profiler_log_file command line arguments to enable running the simulation in profiler
added some parsers and tests.
added more tests and made the parsing more consistent
added a small test for the utilities
Merge pull request #87 from orbitfold/master

Added --profile and --profiler_log_file command line arguments to enable...
added a few minor tweaks to atomic.py
fix for distutils version disaster
making atomic data reads read-only