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

amepproject / amep

The Active Matter Evaluation Package (AMEP) - a Python library for the analysis of particle-based and continuum simulation data of soft and active matter systems

https://amepproject.de/

GNU General Public License v3.0

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gromacs+gsd/hoomd readers, general dist function, issues fixed #70

Closed kay-ro closed 1 week ago

kay-ro commented 1 month ago

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 commented 1 month ago

Todo:

[x] check kdtree calculation in evaluate.GrowthRate() (and others)

kay-ro commented 1 month ago

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.