gromacs+gsd/hoomd readers, general dist function, issues fixed

[kay-ro]

Fixed a lot of issues. These include

• added gromacs reader
• added gsd/hoomd reader
• wrong times from average_func
• a few small documentation issues
• Cluster growth issues
• added general distribution function
• and others...

[kay-ro]

Todo:

• check kdtree calculation in evaluate.GrowthRate() (and others)

[kay-ro]

I have checked the calculation of the kdtree. compared to the previous implementation, the coordinates used for the kdtree are at most different by values that are smaller than the precision of the used float32.
Only particle positions that are slightly outside the box have the periodic in-box coordinates compared to before.