search

pyiron / pyiron_atomistics

pyiron_atomistics - an integrated development environment (IDE) for atomistic simulation in computational materials science.
https://pyiron-atomistics.readthedocs.io
BSD 3-Clause "New" or "Revised" License
44 stars 15 forks source link

Changes to lammps output hdf5 #1340

Closed Leimeroth closed 8 months ago

Leimeroth commented 8 months ago

The format of lammps h5 output seems to have changed recently. This broke the pyrionFileReader of ovito https://github.com/ovito-org/pyironFileReader. I implemented a fix in https://github.com/ovito-org/pyironFileReader/pull/1, which reads pbc and species from input/structure instead of the removed output/structure. This works for both, old and new lammps hdf5 files. However, I am not sure whether it could cause problems due to internal mappings changing species or similar. So the question is has output/structure been removed because it doubled data or are there actual differences?

jan-janssen commented 8 months ago

Let me have a look - I feel this is a bug in the current pyiron version.