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Unreleased

pyiron_atomistics-0.2.41

  • Symmetrize vectors (#576)
  • Rename unit test workflow (#572)
  • Add cache to StructureStorage.get_elements (#568)
  • Modify where number of bond types is chosen from (#561)
  • dont write kpoints file (#558)
  • replace triu by triu_indices (#539)
  • Dependency updates: #573, #560, #559, #562

pyiron_atomistics-0.2.40

  • Vasp Outcar: elegant split of electronic and ionic steps #556

pyiron_atomistics-0.2.39

  • Add save in ElasticTensor (#551)
  • Raising errors when restart files don't exist (#422)
  • Save more input variables in calc_md (#547)
  • Support cube files without atoms (#526)

pyiron_atomistics-0.2.38

  • Store VASP volumes as numpy arrays (#546)
  • Adjust n_print to be at most max_iter in calc_minimize (#541)
  • Check SPHInX output class format_black integration (#534)
  • Improve Murngahan (#531)
  • Revert "include DataConatiner check" (#533)
  • include DataConatiner check (#514)
  • Dependency updates: #538, #537, #536, #543, #548

pyiron_atomistics-0.2.37

  • Remove _QhullUser import (#527)
  • Add pint as dependency (#529)
  • Some docstrings for phono (#447)
  • Dependency updates: #522, #523, #524

pyiron_atomistics-0.2.36

pyiron_atomistics-0.2.35

  • High index surfaces (#400)
  • Consistent indices for StructureStorage.get_structures (#482)
  • Dependency updates: #504

pyiron_atomistics-0.2.34

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 provides a fix by storing the stress as an unambiguous matrix.

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

pyiron_atomistics-0.2.33

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

pyiron_atomistics-0.2.32

  • More structures (#259)
  • Add proper smearing for VASP (#454)
  • Try Python 3.10 (#450)
  • Remove unused properties in NeighborsTrajectory (#457)
  • Do not polute resource_path (#453)
  • dependencies: #459

pyiron_atomistics-0.2.31

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

pyiron_atomistics-0.2.30

  • Parse irreductible kpoints properly (#423)
  • Cluster (atom) positions (#419)
  • Make Methfessel Paxton default in SPHInX (#416)
  • Pyscal solid liquid (#414)
  • dependency updates: #410, #411, #431
  • Infrastructure: #429

The update to the new pyiron_base version > 0.4 (#431) fixes some bugs in the writing of numerical data to our storage backend (hdf), see pyiron_base release notes.

pyiron_atomistics-0.2.29

  • VASP doesn't save stresses to HDF when run on ISIF=2 (default) (#354)
  • Allow hcp 4-axes indices as well (#390)
  • [minor] clean up find_mic (#403)
  • Fix scaled test (#389)
  • dependency updates: #398, #406, #404, #408

pyiron_atomistics-0.2.28

  • Fix structure check in restart() (#392)

pyiron_atomistics-0.2.27

  • Adapt to removal of load_object (#386)
  • Don't conflict with HasHDF in StructureStorage (#376)

pyiron_atomistics-0.2.26

  • pep8 for sphinx (#373)
  • Bind creator at import (#347)
  • Lammps style full - fix numpy warnings (#367)
  • Water interactive fix (#366)
  • Update base.py (#346)
  • Support full style without bonds (#365)
  • Strain (#364)
  • Use StructureStorage in StructureContainer (#344)
  • Explicitly specify water potential (#353)
  • Add automatic labeling for integration tests (#361)
  • Consistent atoms order (#338)
  • Add Wrapper for Atomsk Structure Creation (#260)
  • replace strain by master job name (#355)
  • change pointer to copy (#350)
  • Fixes for pyiron table (#329)
  • Don't specify force tolerance if only optimizing cell (#339)

pyiron_atomistics-0.2.25

  • Strain (#328)
  • Properly implement HasStructure for StructureContainer (#331)
  • Move StructureStorage from pyiron_contrib (#327)
  • Use correct role name for sphinx (#330)

pyiron_atomistics-0.2.24

Update to pyiron_base-0.3.0

pyiron_atomistics-0.2.23

  • Hotfix: Handle empty indices (#284)
  • Interactive units (#295)

pyiron_atomistics-0.2.22

  • Outcar bands (#299)
  • Add error message if Murnaghan.plot is called on unfinished jobs (#291)
  • Make Atoms() faster via caches (#224)
  • Create new Atoms in get_structure if size changes (#241)
  • add mode in get_neighborhood (#285)
  • Equivalent points (#280)

pyiron_atomistics-0.2.21

  • Neighbor analysis for the entire trajectory (#251)
  • Get neighbors (#239)
  • Save all VCSGC parameters in generic input (#262)
  • Only force skew when tensions are applied(#263)

pyiron_atomistics-0.2.20

Bugfix:

  • Estimate width (#272)

pyiron_atomistics-0.2.19

  • Extending the units class (#271)
  • interactive_prepare (#235)
  • Centrosymmetry (#261)
  • Add HasStructure to Trajectory (#270)
  • scf_residue unit corrected (#266)

pyiron_atomistics-0.2.18

  • Analysis of Atomic structure updated
  • Update to vasp job: raise error for non-zero pressure

pyiron_atomistics-0.2.17

  • Enable use_pressure = False (#237)

pyiron_atomistics-0.2.16

  • Get interstitials: New feature to find interstitial sites (#219)
  • Phonopy options: Expose additional argument number_of_snapshots (#213)
  • VASP - change NSW if interactive (#220)
  • Use new copy hook (#201)

pyiron_atomistics-0.2.15

  • Proper conversion of LAMMPS output into pyiron units on parsing
  • Fix to stop convergence checks for interactive jobs!
  • Support newest LAMMPS version

pyiron_atomistics-0.2.14

  • Add optional method to allow non-integer frames
  • Bump to pyiron_base-0.2.15 to avoid breaking copy bug, see here

pyiron_atomistics-0.2.13

  • Steinhardt interface
  • remove tree-internal periodic boundary detection
  • Make ´delete_existing_job´ available to the ´AtomisticGenericJob´ class

pyiron_atomistics-0.2.12

  • getting structure faster
  • updating atoms symbols via atoms.symbols
  • Steinhardt parameter implementation
  • Badr analysis

pyiron_atomistics-0.2.11

pyiron_atomistics-0.2.10

pyiron_atomistics-0.2.7

Last release didn't have consistent requirements (aimsgb missing).

pyiron_atomistics-0.2.2

pyiron_atomistics-0.2.1