MSM and outputwrapper

MSM
MSM model has been added. It can build permeation-mechanisms Markov model. It can lump multiple states into one node.

output wrapper
An outputwrapper is also added. You can use it to read the permeation output and std output.

bugfix
The simulation time that was used in current calculation is now (frame - 1) * time_step

Known bug

The __init__.py file under the util folder is missing, this package cannot be properly pip installed.

match xtck ready

match_xtck.py can match the counting result with xtck. It uses dynamic programming to solve the longest common subsequence problem.

first release of the ion counting tool

The command line tool count_cylinder.py is ready. The matching tool is still under development.