Release v4.0beta0

Reverted many of the changes from 3.5beta (was very slow in reading in the configurations). Now uses std::array to store data both in the coordinates class and triclinicbox class instead of inheriting the vector class. Various speed improvements in Utils, especially pbc and distance, mainly by not using "at()".

box.at(i).at(j) is no longer used to access the box dimensions. Instead use box(i, j).

coordinates.at(i) is no longer used to access the x, y, and z components. Instead use coordinates[i].