Correct eigenvecs
Correct indexing for runcopy
With calculated eq
Typo fix
Submit faster
Refactor simulation into a new function
added one long trajectory test
Changed to one long traj run
Added actual boltzmann constant
Small fixes
No more report interval in tmatsim
olt
Refactor
refactor
Modify to use mle
Small change to use new results (mle)
Argparse (and added check to make sure we get equilib distribution)
Legit eigenvec finding
Fixed disconnected graphs
pep8