Added a draft for euler maruyama intergator for double well example. Not completely working yet
Cleaned EM code for double well
Metric is now based off of free-energy barrier, estimated from the traj
Added example picture and initial documentation
README cleanup
Moved SDE integ. into its own class
Moved overdamped L and double well potential into their own classes
Moved the equilibrium simulation into its own class
Refactored code into sep. files
Another large refactoring of double well code. Almost to the point where everything is compartmentalized.
Added proper command line access to load json and changed print statements to logging
Small typo fix
Added draft of double well replica exchange
Replica exchange swaps T instead of x for uniformity
Added a results plotter and made parallel simulation run possible for equilibrium dist
Working on replica exchange model and plotter
Fixed bug in replica exchange, add inital plots for convergence, updated README to show basic examples.
Updated README
Added JSON highlighting to README
Testing equation render in README