Pyiron-atomistics

- High index surfaces ([400](https://github.com/pyiron/pyiron_atomistics/pull/400))
- Consistent indices for StructureStorage.get_structures ([482](https://github.com/pyiron/pyiron_atomistics/pull/482))
- Dependency updates: [504](https://github.com/pyiron/pyiron_atomistics/pull/504)

Since pyiron_atomistics-0.2.29 stresses are by default calculated and stored for VASP calculations. However, the stored values were stored in an undocumented order and had the wrong sign. [497](https://github.com/pyiron/pyiron_atomistics/pull/497) provides a fix by storing the stress as an unambiguous matrix.

- Update to pyiron_base-0.5.0 and add changelog ([501](https://github.com/pyiron/pyiron_atomistics/pull/501))
- Save VASP stresses as matrix ([497](https://github.com/pyiron/pyiron_atomistics/pull/497))
- Drop python3.7 support ([500](https://github.com/pyiron/pyiron_atomistics/pull/500))
- Add cell_only to Vasp.calc_minimize ([498](https://github.com/pyiron/pyiron_atomistics/pull/498))
- Use current structure instead of output to update previous structure ([483](https://github.com/pyiron/pyiron_atomistics/pull/483))
- give possibility of setting log_file in LAMMPS ([488](https://github.com/pyiron/pyiron_atomistics/pull/488))
- Replace Random Atomistics by Lennard Jones in testing ([478](https://github.com/pyiron/pyiron_atomistics/pull/478))
- Dependency updates: [485](https://github.com/pyiron/pyiron_atomistics/pull/485), [#496](https://github.com/pyiron/pyiron_atomistics/pull/496), [#493](https://github.com/pyiron/pyiron_atomistics/pull/493), [#489](https://github.com/pyiron/pyiron_atomistics/pull/489)

- Some test modernization ([425](https://github.com/pyiron/pyiron_atomistics/pull/425))
- Decrease convergence goal ([479](https://github.com/pyiron/pyiron_atomistics/pull/479))
- revert error ([474](https://github.com/pyiron/pyiron_atomistics/pull/474))
- Write POSCAR in direct coordinate when selective dynamics is on ([448](https://github.com/pyiron/pyiron_atomistics/pull/448))
- Strain ([465](https://github.com/pyiron/pyiron_atomistics/pull/465))
- Tessellation neighbors ([413](https://github.com/pyiron/pyiron_atomistics/pull/413))
- add error message in qha ([466](https://github.com/pyiron/pyiron_atomistics/pull/466))
- add assertion test to symmetry permutation ([463](https://github.com/pyiron/pyiron_atomistics/pull/463))
- Refactor symmetrize_vectors ([462](https://github.com/pyiron/pyiron_atomistics/pull/462))
- Add callback function for LAMMPS ([458](https://github.com/pyiron/pyiron_atomistics/pull/458))
- Use numpy.all in NeighborsTrajectory ([461](https://github.com/pyiron/pyiron_atomistics/pull/461))
- dependency updates: [472](https://github.com/pyiron/pyiron_atomistics/pull/472), [#471](https://github.com/pyiron/pyiron_atomistics/pull/471), [#469](https://github.com/pyiron/pyiron_atomistics/pull/469), [#470](https://github.com/pyiron/pyiron_atomistics/pull/470), [#480](https://github.com/pyiron/pyiron_atomistics/pull/480)

- More structures ([259](https://github.com/pyiron/pyiron_atomistics/pull/259))
- Add proper smearing for VASP ([454](https://github.com/pyiron/pyiron_atomistics/pull/454))
- Try Python 3.10 ([450](https://github.com/pyiron/pyiron_atomistics/pull/450))
- Remove unused properties in NeighborsTrajectory ([457](https://github.com/pyiron/pyiron_atomistics/pull/457))
- Do not polute resource_path ([453](https://github.com/pyiron/pyiron_atomistics/pull/453))
- dependencies: [459](https://github.com/pyiron/pyiron_atomistics/pull/459)

- Make NeighborTrajectory simpler ([445](https://github.com/pyiron/pyiron_atomistics/pull/445))
- Use state instead of Settings ([424](https://github.com/pyiron/pyiron_atomistics/pull/424))
- use unwrapped_positions in displacements ([451](https://github.com/pyiron/pyiron_atomistics/pull/451))
- Store shells in Neighbors Trajectory ([444](https://github.com/pyiron/pyiron_atomistics/pull/444))
- replace full output info in __str__ by chemical formula ([439](https://github.com/pyiron/pyiron_atomistics/pull/439))
- Fix Lammps h5md parser ([446](https://github.com/pyiron/pyiron_atomistics/pull/446))
- Use FlattenedStorage in NeighborsTrajectory ([387](https://github.com/pyiron/pyiron_atomistics/pull/387))
- Clear up TypeError in StructureContainer.append ([441](https://github.com/pyiron/pyiron_atomistics/pull/441))
- Add clear error when calling animate_structure on empty job ([442](https://github.com/pyiron/pyiron_atomistics/pull/442))
- add get_primitive_cell from spglib ([433](https://github.com/pyiron/pyiron_atomistics/pull/433))
- dependencies: [449](https://github.com/pyiron/pyiron_atomistics/pull/449), [#432](https://github.com/pyiron/pyiron_atomistics/pull/432), [#437](https://github.com/pyiron/pyiron_atomistics/pull/437), [#430](https://github.com/pyiron/pyiron_atomistics/pull/430), [#456](https://github.com/pyiron/pyiron_atomistics/pull/456)
- GitHub infrastructure: [438](https://github.com/pyiron/pyiron_atomistics/pull/438)

- Parse irreductible kpoints properly ([423](https://github.com/pyiron/pyiron_atomistics/pull/423))
- Cluster (atom) positions ([419](https://github.com/pyiron/pyiron_atomistics/pull/419))
- Make Methfessel Paxton default in SPHInX ([416](https://github.com/pyiron/pyiron_atomistics/pull/416))
- Pyscal solid liquid ([414](https://github.com/pyiron/pyiron_atomistics/pull/414))
- dependency updates: [410](https://github.com/pyiron/pyiron_atomistics/pull/410), [#411](https://github.com/pyiron/pyiron_atomistics/pull/411), [#431](https://github.com/pyiron/pyiron_atomistics/pull/431)
- Infrastructure: [429](https://github.com/pyiron/pyiron_atomistics/pull/429)

The update to the new `pyiron_base` version > 0.4 ([431](https://github.com/pyiron/pyiron_atomistics/pull/431)) fixes some bugs in the writing of numerical data to our storage backend (hdf), see [pyiron_base release notes](https://github.com/pyiron/pyiron_base/releases/tag/pyiron_base-0.4.0).