Update of Model

[enzocxt]

This issue will only be used for notifications about updates of the model.
When there is an update of the model, you will be notified here.

As I might not be able to test correctness for all existing functions of the model after every update, the updates would raise errors about some functions. If this happens, please notify me in this issue where and what is the error.

[enzocxt]

Recent days, the TypeTokenMatrix class is updated and also its submatrix(), load() and initialization method. Give comment here if you find errors. Thanks!