Simplify box code

[brucefan1983]

Summary

• Remove the int triclinic variable in the Box class and simplify coding.

• The downside is that fast potentials such as Tersoff will lose about 25% speed when the box is orthogonal.

• But for triclinic box, there is even a little gain of speed for any potential due the absence of an if.

Modification

• The doc for thermo.out has been updated.

Others

These bugs have been solved: #757 #755

Future work

• Examples/tutorials will be updated in a separate PR.

[psn417]

I've tested MTTK and MSST. They work.