Add some functions to estimate the density of states

To make the minimization a bit faster.

Also, clean everything up a bit

Something is broken.  There is a bug, but I don't know what it is.
remove logSum.  use scipy.misc.logsumexp
add analytic histograms and dos to the tests
add a test for calc_Cv
clean up the calc_Cv function
fix a bug in Calc_Cv that I introduced today

I was dealing incorrectly with empty bins
start to update Wham2d
change the interface for estimate_dos

so that 2d histograms can use it also.

Just realized there is a bug.  probably from the last commit where I
changed the Cv
Wham2d now uses estimate_dos

Also, I forgot to add the unit tests for Wham2d
update test for Wham2d
clean up wham_potential a bit more
Merge pull request #1 from js850/clean_up

Clean up