FRQ: gsd/gromacs reader - basic features

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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FRQ: gsd/gromacs reader - basic features #47

Closed kay-ro closed 6 days ago

kay-ro commented 4 months ago

Proposed new feature or change:

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

[x] gsd reader
[x] gromacs reader (#13)
[x] 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 commented 3 months ago

GSD reader TODOs:

[x] finalize list to get data from gsd file
[x] fix ptype name string/integer #46
[x] set up basic gsd reader framework
[x] implement individual data imports
[x] test reader
[x] write example
[ ] reference base.BaseFrame in docstring

kay-ro commented 1 month ago

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

kay-ro commented 1 month ago

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.