pyiron_atomistics 0.3.8

What's Changed

• Bump scipy from 1.11.3 to 1.11.4 by @dependabot in #1216
• Bump numpy from 1.26.0 to 1.26.2 by @dependabot in #1204
• Bump structuretoolkit from 0.0.12 to 0.0.14 by @dependabot in #1221
• Bump mp-api from 0.37.5 to 0.39.0 by @dependabot in #1219
• Spx log parser by @samwaseda in #1222
• SPHInX: Separate other output parsers by @samwaseda in #1223
• Correctly scale output from phonopy jobs in QuasiHarmonic by @pmrv in #1196
• [minor] Set cwd to None by default by @samwaseda in #1225
• Return dictionary for SPHInX log parser to be a full parser by @samwaseda in #1229
• [minor] Use more solid condition for a more stable parsing by @samwaseda in #1231
• Update structuretoolkit, atomistics and pylammpsmpi by @jan-janssen in #1235

Full Changelog: pyiron_atomistics-0.3.7...pyiron_atomistics-0.3.8

pyiron_atomistics 0.3.7

What's Changed

• Move standalone parser to separate submodule by @jan-janssen in #1160
• Bump matplotlib from 3.8.1 to 3.8.2 by @dependabot in #1215
• Update atomistics to 0.1.3 by @jan-janssen in #1217
• lammps interactive: move functionality to separate class by @jan-janssen in #973

Full Changelog: pyiron_atomistics-0.3.6...pyiron_atomistics-0.3.7

pyiron_atomistics 0.3.6

What's Changed

• Calphy: Set npt input flag by @pmrv in #1195
• Bump pandas from 2.1.1 to 2.1.2 by @dependabot in #1198
• Bump scikit-learn from 1.3.1 to 1.3.2 by @dependabot in #1197
• Bump matplotlib from 3.8.0 to 3.8.1 by @dependabot in #1199
• Spare a poor phd student from the horrible numpy ragged array problem by @samwaseda in #1200
• Bump pandas from 2.1.2 to 2.1.3 by @dependabot in #1203
• Update interactive.py by @samwaseda in #1212
• Update atomistics and structuretoolkit by @jan-janssen in #1213
• Update pyiron_base to 0.6.9 by @jan-janssen in #1214
• use trusted publisher action by @jan-janssen in #1211

Full Changelog: pyiron_atomistics-0.3.5...pyiron_atomistics-0.3.6

pyiron_atomistics 0.3.4

What's Changed

• Bump pandas from 2.1.0 to 2.1.1 by @dependabot in #1172
• Bump scikit-learn from 1.3.0 to 1.3.1 by @dependabot in #1171
• Bump spglib from 2.0.2 to 2.1.0 by @dependabot in #1162
• Bump matplotlib from 3.7.2 to 3.8.0 by @dependabot in #1166
• Bump scipy from 1.11.2 to 1.11.3 by @dependabot in #1178
• versioneer update to 0.29 by @jan-janssen in #1179
• Bump mp-api from 0.36.1 to 0.37.1 by @dependabot in #1177
• Bump numpy from 1.24.3 to 1.26.0 by @dependabot in #1167
• Update atomistics to 0.0.6 by @jan-janssen in #1180
• Update pyiron_base to 0.6.7 by @jan-janssen in #1181

Full Changelog: pyiron_atomistics-0.3.3...pyiron_atomistics-0.3.4

pyiron_atomistics-0.3.0.dev.0

Testing a pre-release

What's Changed

• Use remove_jobs() rather than remove_jobs_silently() by @jan-janssen in #1079
• flux calculator support for VASP by @jan-janssen in #1080
• Update pyiron_base to 0.6.1 by @jan-janssen in #1081
• Bump mendeleev from 0.13.1 to 0.14.0 by @dependabot in #1082
• Bump structuretoolkit from 0.0.3 to 0.0.5 by @dependabot in #1083
• Move structure.calc setting into the initializer by @liamhuber in #1068
• Fix SPHInX integration tests by @samwaseda in #1086
• Allow to plot not converged Murnaghans by @pmrv in #1088
• StructureStorage: Add a few more plots and add options by @pmrv in #1062
• Bump h5py from 3.8.0 to 3.9.0 by @dependabot in #1091
• Bump pymatgen from 2023.5.31 to 2023.6.23 by @dependabot in #1092
• Bump scipy from 1.10.1 to 1.11.0 by @dependabot in #1090
• Bump pymatgen from 2023.6.23 to 2023.6.28 by @dependabot in #1095
• Bump scikit-learn from 1.2.2 to 1.3.0 by @dependabot in #1099
• Bump pandas from 2.0.2 to 2.0.3 by @dependabot in #1097

Full Changelog: pyiron_atomistics-0.3.0...pyiron_atomistics-0.3.0.dev.0

pyiron_atomistics 0.3.0

With the release of pyiron_atomistics 0.3.0 Python 3.8 support is dropped in favor of typing in Python >= 3.9.

What's Changed

• Bump mp-api from 0.33.2 to 0.33.3 by @dependabot in #1049
• Bump seekpath from 2.0.1 to 2.1.0 by @dependabot in #1050
• Bump phonopy from 2.19.0 to 2.19.1 by @dependabot in #1051
• Not store useless extra species info in Atoms by @samwaseda in #982
• Update pyiron_base to 0.5.39 by @jan-janssen in #1052
• VASP: Parse the number of steps correctly from OUTCAR by @pmrv in #1018
• [minor] Remove superfluous cell multiplication by @samwaseda in #1061
• Bump pandas from 2.0.1 to 2.0.2 by @dependabot in #1065
• Make potential algebraic by @samwaseda in #1008
• Correct spelling issues by @jan-janssen in #1063
• Remove Atoms().visualize by @jan-janssen in #1053
• Fix for spins by @jan-janssen in #1055
• Fix test for spins by @niklassiemer in #1074
• Bump pymatgen from 2023.5.10 to 2023.5.31 by @dependabot in #1075
• Pickle atoms by @liamhuber in #1036
• Use intermediate PR_TITLE variable to secure workflow by @niklassiemer in #1076
• Update pyiron_base to 0.5.42 by @jan-janssen in #1077
• Disable Python 3.8 - update pyiron_base 0.6.0 by @jan-janssen in #1078

Full Changelog: pyiron_atomistics-0.2.67...pyiron_atomistics-0.3.0

pyiron_atomistics-0.2.63

What's Changed

• 📝 Add new exception for calc_minimize. by @KuhnMn in #933
• Bump matplotlib from 3.6.2 to 3.6.3 by @dependabot in #931
• Bump pandas from 1.5.2 to 1.5.3 by @dependabot in #936
• Fix ase selective dynamics read bug by @ligerzero-ai in #934
• Sx run addon by @freyso in #829
• Fix SPHInX bandstructure restarts by @freyso in #908
• Fix integration tests by @jan-janssen in #940
• Removes implicit assumption of sorting from potcar gen by @ligerzero-ai in #943
• Don't reconstitute job object in pyiron table func by @ligerzero-ai in #945
• Revert "Don't reconstitute job object in pyiron table func" by @ligerzero-ai in #946
• Bump scikit-learn from 1.2.0 to 1.2.1 by @dependabot in #947
• Bump numpy from 1.24.1 to 1.24.2 by @dependabot in #952
• Bump h5py from 3.7.0 to 3.8.0 by @dependabot in #948
• Bump mp-api from 0.30.5 to 0.30.8 by @dependabot in #935
• Bump mp-api from 0.30.8 to 0.30.9 by @dependabot in #955
• LAMMPS: Enable setting external MPI communicators by @jan-janssen in #957
• Bump mp-api from 0.30.9 to 0.30.10 by @dependabot in #963
• Bump matplotlib from 3.6.3 to 3.7.0 by @dependabot in #965
• [minor] Remove check_consistency which is not used by @samwaseda in #961
• Clean up Murnaghan HDF5 storeage by @jan-janssen in #960
• Bump pyiron-base from 0.5.31 to 0.5.32 by @dependabot in #954

Full Changelog: pyiron_atomistics-0.2.62...pyiron_atomistics-0.2.63

pyiron_atomistics-0.2.62

What's Changed

• Set initial magnetic moments by @samwaseda in #895
• Bump scikit-learn from 1.1.3 to 1.2.0 by @dependabot in #899
• Bump mp-api from 0.29.8 to 0.30.3 by @dependabot in #900
• [minor] update url of materials project by @samwaseda in #901
• [minor] correct error message in SPHInX by @samwaseda in #902
• Bump phonopy from 2.15.1 to 2.17.0 by @dependabot in #898
• Add python 3.11 support by @jan-janssen in #886
• Communicate Python 3.11 compatibility to pypi by @jan-janssen in #903
• Bump pyiron-base from 0.5.29 to 0.5.30 by @dependabot in #893
• Bump mp-api from 0.30.3 to 0.30.5 by @dependabot in #905
• fix issues cause by deprecated numpy float by @Leimeroth in #914
• Bump phonopy from 2.17.0 to 2.17.1 by @dependabot in #916
• Bump numpy from 1.23.5 to 1.24.1 by @dependabot in #917
• Add functional style methods to HasStructure by @pmrv in #854
• Remove redundant property consuming huge amounts of memory in vasprun object by @ligerzero-ai in #920
• Iteratively parse vasprun instead of having entire object in memory by @ligerzero-ai in #922
• Bump scipy from 1.9.3 to 1.10.0 by @dependabot in #923
• Fix Docs Test by @jan-janssen in #927
• Update pyiron_base to 0.5.31 by @jan-janssen in #926

Full Changelog: pyiron_atomistics-0.2.61...pyiron_atomistics-0.2.62

pyiron_atomistics-0.2.61

What's Changed

• Bugfixes in StructurePlot and error handling for Atoms.get_symmetry by @pmrv in #812
• Bump pymatgen from 2022.10.22 to 2022.11.1 by @dependabot in #857
• Bump matplotlib from 3.6.1 to 3.6.2 by @dependabot in #858
• Bump spglib from 2.0.1 to 2.0.2 by @dependabot in #855
• Bump pyiron-base from 0.5.27 to 0.5.28 by @dependabot in #856
• Fixes outcar parsing for VASP >6.1.0 by @ligerzero-ai in #864
• Bump mp-api from 0.29.3 to 0.29.4 by @dependabot in #872
• Bump pymatgen from 2022.11.1 to 2022.11.7 by @dependabot in #870
• [minor] replace first name blabla by child name in serial master by @samwaseda in #874
• Bump mp-api from 0.29.4 to 0.29.7 by @dependabot in #876
• Bump numpy from 1.23.4 to 1.23.5 by @dependabot in #875
• setup: Add more folders to exclude list by @jan-janssen in #877
• Simplify get_elements by @pmrv in #860
• Allow to configure strains used in Murnaghan by @pmrv in #816
• Bump pyiron-base from 0.5.28 to 0.5.29 by @dependabot in #882
• Bump pandas from 1.5.1 to 1.5.2 by @dependabot in #884
• Bump mp-api from 0.29.7 to 0.29.8 by @dependabot in #883
• Bump mendeleev from 0.11.0 to 0.12.1 by @dependabot in #891
• make lazy input standard by @samwaseda in #588
• Rename master to main by @liamhuber in #894

Full Changelog: pyiron_atomistics-0.2.60...pyiron_atomistics-0.2.61

pyiron_atomistics-0.2.60

What's Changed

• [minor] add warning when job already compressed by @samwaseda in #849
• Add methods to convert MP results to StructureStorage/list by @pmrv in #846
• Check for negative occupation by @pmrv in #847
• Bump pint from 0.19.2 to 0.20.1 by @dependabot in #850
• Codacy only for PRs, continue on error by @niklassiemer in #852
• Bump scikit-learn from 1.1.2 to 1.1.3 by @dependabot in #851
• StructureStorage: do not add extra elements by @pmrv in #848
• Adding animate method to Trajectory by @prince-mathews in #853
• Alternative lammps parse by @Leimeroth in #658
• Properly parse energy states and occupations by @pmrv in #832

New Contributors

• @prince-mathews made their first contribution in #853

Full Changelog: pyiron_atomistics-0.2.59...pyiron_atomistics-0.2.60