FRQ: gsd/gromacs reader - basic features

[kay-ro]

Proposed new feature or change:

Basic features of gsd and gromacs readers to be implemented in AMEP as a minor release:

• gsd reader
• gromacs reader (FRQ: chemfiles reader. #13)
• molecule identifier

The new data such as molecule_id, molecule_type will be saved in the h5amep format as dataset in each frame.

(id) type mol_id mol_type charge coordinates ...
(1)    c1    1           coh            0.29      ....
2      c2    1           coh            0.0      ....
3      o1    1           coh            0.0      ....
4      h1    1           coh            -0.29      ....
5      c1    2           coh            0.29      ....
6      c2    2           coh            0.0      ....
7      o1    2           coh            0.0      ....
8      h1    2           coh            -0.29      ....
...

[kay-ro]

GSD reader TODOs:

• finalize list to get data from gsd file
• fix ptype name string/integer BUG: trajectory add/get_particle_info() not compatible with strings #46
• set up basic gsd reader framework
• implement individual data imports
• test reader
• write example
• reference base.BaseFrame in docstring

[kay-ro]

current issue very slow import times. Looking for solutions also with other readers.

[kay-ro]

MDAnalysis has outstandingly fast reader. Will stay with Chemfiles reader for now. Reasonable import times. For very large trajectories the initial reading by chemfiles (not storing it in h5amep format) may take several minutes.