fix a bug in pathsample rates

was multiplying instead of dividing by T in computing equilibrium
occupation probabilities
remove pele dependence from pathsample_rates.py
a bit of clean up
add symmetric version of solving the matrix
add optional conjugate gradient method

also add script that I forgot to add a while ago
add a method to estimate the rates

it seems to work, but it's pretty slow
speed up the rate estimate calculation