Timestep documentation and implementation consistency

[apcraig]

PR #83 was closed and still needs to be addressed. See initial discussion there. Basically, I this is a documentation issue, but maybe also an implementation issue. The last comment in the PR was

"Then it makes sense to make the code and the documentation consistent. We can certainly use dt_dyn in the documentation instead of dt, in reference to the dynamics. It's true that dt is used both as the thermodynamic time step and as a generic one. I'm open to creating an explicit dt_therm time step but also happy to stick with dt, since the way the code is written, the thermo step is the main one and others cycle around it."

[eclare108213]

I recommend just documenting this more clearly, and later taking a look at the implementation as part of the time manager planning work for #162.