Fix Lammps h5md parser

[jan-janssen]

No description provided.

[jan-janssen]

The HDF5 file no longer contains the indices:

h5md
    version: [1 0]
h5md/author
    name: b'N/A'
h5md/creator
    name: b'lammps'
    version: b'29 Sep 2021'
observables
parameters
particles
particles/all
particles/all/box
    boundary: [b'periodic' b'periodic' b'periodic']
    dimension: 3
particles/all/box/edges
particles/all/box/edges/step
particles/all/box/edges/time
particles/all/box/edges/value
particles/all/force
particles/all/force/step
particles/all/force/time
particles/all/force/value
particles/all/position
particles/all/position/value

[coveralls]

Pull Request Test Coverage Report for Build 1511022241

• 0 of 1 (0.0%) changed or added relevant line in 1 file are covered.
• No unchanged relevant lines lost coverage.
• Overall coverage increased (+0.009%) to 69.797%

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Changes Missing Coverage	Covered Lines	Changed/Added Lines	%
pyiron_atomistics/lammps/base.py	0	1	0.0%

Totals
Change from base Build 1509233391:	0.009%
Covered Lines:	11439
Relevant Lines:	16389

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💛 - Coveralls

[jan-janssen]

An example expository is available at https://github.com/jan-janssen/pyiron-lammps-h5md

[pmrv]

Not having the indices in the HDF5 will break get_structure or not?

[jan-janssen]

Not having the indices in the HDF5 will break get_structure or not?

get_structure works just fine - it is using the indices from the input structure. I tested it with the example notebook above.