first pass at new api
Moved material instantiation out of driver and to physics.
big update
big update
update
Big new commit, new API, input file format, reorg of code.

COMMENTS
This is a huge change, more than can be fit in to a single commit
message.  The code has been reorganized substantially.  I think it is
much better than before.  Gone are the xml input files.  Now, input
files are python files and models are set up and run more like scripts.
Some of the previous functionality has not been ported, but the new
way is infinitely easier to extend and customize.

TODO:
optimize, permutate, runtests

I'm sure there are others.  When runtests is done and all tests pass,
this will become v2.0
adding input showing visualization
vonmises model works
update to transisoelas, but i do not see tests for it?
permutation finished up
first pass at optimization
adding some forgotten optimize files
finished up optimization, bug fix for multiple runs
start of testing script, documentation to come
update to testing, almost complete
fix up to testing.  multiprocessing not yet supported
logger handling improved
test multiprocessing
html post processing
update to fix some input files