Fixed graphing, add out file suffix, fixed pstc

* Fixed graphing so that a new figure is created and saved for each
graph instead of one  big one.

* Added a suffix to be added to the data file names which gives info
on the run configuration (eg unitary, id, etc). Also removed the ms
part on the output file name.

* Fixed the pstc so that it could easily be specified. Also, fixed it
so that setting the number of steps to use for the neural run from
the command line would actually have an effect.