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Change log

v0.0.17

Bug Fixes 🐛

  • Fix prev_dir behavior in input set generator of MPGGAStaticMaker by @Andrew-S-Rosen in #996

Documentation 📖

  • Bump min supported Python to 3.10 by @janosh in #992

House-Keeping 🧹

  • Excise openff dependency from OpenMM testing by @orionarcher in #993
  • Use pytest-split to parallelize across 3 runners and speedup CI by @esoteric-ephemera in #985

Full Changelog: https://github.com/materialsproject/atomate2/compare/v0.0.16...v0.0.17

v0.0.16

This release brings lots of new workflows and support for all ASE calculators.

New Features 🎉

  • Anharmonicity Quantification workflow by @4kevinbeck5 in #901
  • Workflow for Quasi-harmonic approximation (forcefields and VASP) by @JaGeo in #903
  • Atomate2 OpenMM integration & broader classical MD framework by @orionarcher in #782
  • Frequency Flattening Optimizer by @rohithsrinivaas in #863
  • Including VASP surface adsorption flow by @itsduowang in #691
  • Generalize forcefields for generic ASE calculator support by @esoteric-ephemera in #940

Documentation 📖

  • Input set tutorial by @JonathanSchmidt1 in #780

House-Keeping 🧹

  • Remove emmet == pin in pyproject.toml and update version in strict by @Andrew-S-Rosen in #988

New Contributors

  • @4kevinbeck5 made their first contribution in #901
  • @orionarcher made their first contribution in #782
  • @rohithsrinivaas made their first contribution in #863
  • @itsduowang made their first contribution in #691

Full Changelog: https://github.com/materialsproject/atomate2/compare/v0.0.15...v0.0.16

v0.0.15

NOTE: This version updates the VASP workflows to use input sets defined in pymatgen. Please make sure your pymatgen version is updated accordingly.

New Features 🎉

  • Add nequip force field relax- and staticmaker and corresponding tests by @JonathanSchmidt1 in #764
  • Porting qchem into atomate2 by @rdguha1995 in #689
  • Forcefield molecular dynamics and forcefield refactor by @esoteric-ephemera in #722
  • Abinit workflows: static, non-scf and relaxation. by @davidwaroquiers in #183
  • Add magnetic orderings workflow by @mattmcdermott in #432
  • Add elastic workflow for FHI-aims by @tpurcell90 in #871
  • Transition to pymatgen VASP input sets by @esoteric-ephemera in #854
  • Add workflow to compute Gruneisen parameters by @naik-aakash in #752

Bug Fixes 🐛

  • Fix tests and installation bug by @jmmshn in #765
  • Add revert_default_dtype context manager to fix clashing global torch.dtype between MACE and CHGNet by @janosh in #766
  • Fix TrajectoryObserver.to_ase_trajectory return type by @janosh in #852
  • Fix JobStoreDocument attribute access by @mjwen in #710
  • fix CP2K TaskDocument by @lory-w in #900
  • Add back symprec kwarg to MP and MatPES set generators by @janosh in #947
  • Fix MPID assignment in electrode workflow by @esoteric-ephemera in #956

Enhancements 🛠

  • Add dir_name to ForceFieldMaker and **task_document_kwargs to from_ase_compatible_result by @QuantumChemist in #791
  • Add flexible filename and extension to phonon new_plotter by @QuantumChemist in #792
  • Simplify phonon get_supercell_size() and test clean up by @janosh in #783
  • Add fix_symmetry: bool = False option to forcefield relax makers by @JonathanSchmidt1 in #789
  • Update LobsterTaskDoc by @naik-aakash in #723
  • from_... class methods now return typing_extensions.Self by @janosh in #840
  • Make Fermi Energy Optional for FHI-aims by @tpurcell90 in #793
  • Handling failures in elastic flow by @gpetretto in #861
  • Bug in supercell matrix determination in phonon workflow by @JaGeo in #872
  • Add possibility to use your own M3GNet potential by @QuantumChemist in #911
  • Equation of State workflow for FHI-aims by @ansobolev in #889
  • Add NEP MLIP relax, static, and MD makers by @naik-aakash in #893
  • add additional fields as kwargs to PhononBSDOSDoc by @naik-aakash in #910
  • Defect: Allow bulk SC calculation to be skipped. by @jmmshn in #742
  • Add SevenNetRelaxMaker + SevenNetStaticMaker to force field jobs by @janosh in #918
  • Lobster schema updates by @naik-aakash in #924

Documentation 📖

  • Corrected typo in doc by @rul048 in #775
  • Add more details to the installation guide by @JaGeo in #810
  • Add missing calculator_kwargs and remove outdated model/model_kwargs in ForceFieldRelaxMaker doc strings by @janosh in #830
  • Document the option to run LOBSTER with one jobscript only by @JaGeo in #811
  • Fix title hierarchies in VASP documentation by @JaGeo in #853
  • Docs: add Document Models / emmet tutorial by @rkingsbury in #917
  • Writing tutorial for high level overview of atomate2 concepts. by @QuantumChemist in #757
  • Tutorial for blob storage with test by @jmmshn in #776
  • [WIP] Documentation update by @AntObi in #850
  • Added documentation about JSONStore usage within Installation by @abhardwaj73 in #945
  • Remove README note about atomate2 mostly being for VASP by @Andrew-S-Rosen in #957
  • Increase k-point density for MP GGA static calculations to close issue #844 by @esoteric-ephemera in #854
  • Adds missing MAGMOMs for MatPES jobs by @esoteric-ephemera in #854

House-Keeping 🧹

  • Make functions prefixed with _ but cross-imported public by @janosh in #767
  • Warn on non-default ATOMATE2_CONFIG_FILE that's not found by @janosh in #794
  • Remove abinit __all__ module star exports by @janosh in #804
  • Turn ForceFieldRelaxMaker._calculator method into calculator property by @janosh in #839
  • Update LobsterPy version in standard installation by @JaGeo in #841
  • CI add repository_dispatch event for pymatgen_ci_trigger by @janosh in #835
  • Add test for supercell matrix creation in phonon workflow by @JaGeo in #873
  • ruff fixes by @janosh in #894
  • ruff fixes by @janosh in #946

New Contributors

  • @rul048 made their first contribution in #775
  • @davidwaroquiers made their first contribution in #183
  • @ansobolev made their first contribution in #889
  • @lory-w made their first contribution in #900
  • @AntObi made their first contribution in #850
  • @abhardwaj73 made their first contribution in #945

Full Changelog: https://github.com/materialsproject/atomate2/compare/v0.0.14...v0.0.15

v0.0.14

New Features 🎉

  • Add lobster mp workflow by @JaGeo in #634
  • Add FHI-aims DFT calculator by @tpurcell90 in #562
  • Electrode Workflow by @jmmshn in #655
  • Equation of state (EOS) workflows by @esoteric-ephemera in #623

Bug Fixes 🐛

  • Skip final LDAU/J/L/MAGMOM updates and fix setting MAGMOM via user_incar_settings by @JonathanSchmidt1 in #648
  • Prep for next pymatgen release by @janosh in #690
  • fix SC Matrix Checking Logic by @jmmshn in #704
  • Fix elastic conventional structure by @mjwen in #706
  • Add KspacingMetalHandler to VASP _DEFAULT_HANDLERS by @janosh in #600
  • Fix import error [ijson] by @naik-aakash in #708
  • Print invalid value and list valid ones in PhononMaker error messages by @janosh in #728
  • Update minimum monty version, allow newer pydantic by @mkhorton in #720
  • Fix phonon + Lobster flow by removing magmoms before passing to phonopy by @naik-aakash in #751
  • Fix MP query by @utf in #755

Enhancements 🛠

  • add directory of task doc generation to phonon schema by @JaGeo in #674
  • Ensure MP VASP sets don't use auto_ismear, few other fixes by @esoteric-ephemera in #673
  • Schema update > Update plot example LOBSTER workflow by @naik-aakash in #682
  • Modify BadInputSetWarning logic for relaxations of a likely metal by @Andrew-S-Rosen in #727
  • Define MLFF Enum to ensure consistent force field names by @janosh in #729

Documentation 📖

  • Update doc: adding metadata to flow by @naik-aakash in #638
  • Fix hyperlink in Docs by @naik-aakash in #686
  • Correct typo in doc by @JiQi535 in #716
  • Fix docstring on MatPesMetaGGAStaticSetGenerator by @Andrew-S-Rosen in #725
  • Add citation.cff file, Zenodo record and readme "How to cite" section by @janosh in #731

House-Keeping 🧹

  • Address TODO re missing asserts in test_elastic_wf_with_mace() by @janosh in #679
  • Update lobsterpy version by @naik-aakash in #683
  • Fix all ruff PT011 (not checking error message when testing exceptions) by @janosh in #698

New Contributors

  • @JonathanSchmidt1 made their first contribution in #648
  • @rdguha1995 made their first contribution in #161
  • @JiQi535 made their first contribution in #716

Full Changelog: https://github.com/materialsproject/atomate2/compare/v0.0.13...v0.0.14

v0.0.13

BREAKING CHANGE

The API of Maker.maker for all workflows (VASP, CP2K, force fields) have been modified. Previously, this function had custom arguments for previous calculation directories (e.g., prev_vasp_dir, prev_cp2k_dir). These arguments have been standardised to prev_dir. Accordingly, the approach used to chain workflows has now changed.

New Features 🎉

  • Add setting VASP_RUN_DDEC6: bool = False by @janosh in #587

Bug Fixes 🐛

  • Resolve bandstructure datastore bug by @JaGeo in #605
  • Fix TypeError: PhononBSPlotter.save_plot() got an unexpected keyword argument img_format by @janosh in #625
  • ForceFieldRelaxMaker default relax_cell to True by @janosh in #635
  • Replace ase ExpCellFilter with FrechetCellFilter in Relaxer by @janosh in #636
  • update lobsterpy version and schemas to match new version changes by @naik-aakash in #637
  • Default create_thermal_displacements to False in VASP and forcefield PhononMaker by @janosh in #647
  • Fix import of ASE filters when user has installed from PyPI and not gitlab by @esoteric-ephemera in #650
  • Mark schema fields with None default as Optional to pass pydantic v2 validation by @danielzuegner in #651

Enhancements 🛠

  • Breaking: Unify previous directory Maker API by @janosh in #593
  • Add keyword incar_exclude: Sequence[str] = None to fake_run_vasp() by @janosh in #599
  • Allow prv_dir to be used more in defect wf by @jmmshn in #585
  • Add MACE RelaxMaker and StaticMaker by @CompRhys in #611
  • Update lobster task schema by @naik-aakash in #529
  • Allow optimizer to be configured for MACE/GAP by @CompRhys in #615
  • MACE Static/RelaxMakers default to loading mace_mp instead of test model by @janosh in #614
  • Add optional 3rd static for PBE+U to MatPesStaticFlowMaker by @janosh in #606
  • Use PyPI version of MACE by @utf in #668
  • Multi step MD flow by @gpetretto in #489

Documentation 📖

  • Add @CompRhys to contributors.md by @CompRhys in #612

House-Keeping 🧹

  • Update GitHub Action versions by @janosh in #640
  • Drop flake8 by @janosh in #658
  • Enable all ruff rules by default by @janosh in #663

New Contributors

  • @CompRhys made their first contribution in #612
  • @danielzuegner made their first contribution in #651

Full Changelog: https://github.com/materialsproject/atomate2/compare/v0.0.12...v0.0.13

v0.0.12

  • Breaking: default Atomate2Settings.VASP_INHERIT_INCAR to False by @janosh in #594

Bug Fixes 🐛

  • Enforce magmom precedence in INCAR creation by @mattmcdermott in #506
  • Warn on empty config by @janosh in #522
  • CP2K use calcs_reversed[0] instead of calcs_reversed[-1] to not reverse again by @janosh in #534
  • Fix wrong INCAR values in MP workflows by @janosh in #550
  • Fix failing tests from Pydantic v2 migration by @hrushikesh-s in #558
  • fixing pydantic v2 test errors by @hrushikesh-s in #565
  • parse_additional_json() ignore FW.json.gz in output directories by @janosh in #574
  • Fix bandgap_tol and delete bandgap_override on MPMetaGGARelaxSetGenerator by @janosh in #553
  • Fix VaspInputGenerator's _set_kspacing not respecting auto_ismear = False nor auto_kspacing = False by @janosh in #576
  • Clean up VASP powerups, correct params in MP flows, test for _set_u_params, test for _set_kspacing, fix _get_incar method of VaspInputSet by @esoteric-ephemera in #561
  • Fix Lobster workflow by @JaGeo in #583
  • Change MatPesGGAPlusMetaGGAStaticMaker.output to dict containing both statics by @janosh in #586
  • Test MP + MatPES set generators by @janosh in #596

Enhancements 🛠

  • Add StructureMetadata as baseclass for output documents by @gpetretto in #514
  • Materials Project GGA and meta-GGA workflows by @janosh in #504
  • MP-compatible r2SCAN workflow (and a few general INCAR improvements) by @Andrew-S-Rosen in #362
  • Update to Pydantic v2 by @hrushikesh-s in #567
  • Add MatPES GGA and r2SCAN static makers by @janosh in #532
  • Move elastic workflow to common and build force-field elastic workflow by @JaGeo in #581

Documentation 📖

  • Update @arosen93 to @Andrew-S-Rosen by @Andrew-S-Rosen in #516
  • Add Aaron Kaplan and Matthew McDermott to contributors.md by @janosh in #560
  • Document architectural difference between atomate 1 and 2 by @janosh in #381
  • Add Thomas Purcell to contributors.md by @tpurcell90 in #568
  • Add Alex Bonkowski to contributors list by @JaGeo in #573
  • Add @matthewkuner to contributors by @matthewkuner in #575
  • Update contributors.md by @utf in #579

House-Keeping 🧹

  • Remove __all__ from all modules by @janosh in #540
  • removed py38 support, and add py 3.11 support by @naik-aakash in #537
  • Check full INCAR by default in mock_vasp fixture by @janosh in #551
  • skip validate charge test by @jmmshn in #563
  • Add some type annotations by @ab5424 in #578
  • Future type annotations by @janosh in #580
  • Use numpy.testing.assert_allclose over assert np.(all|is)close by @janosh in #582

New Contributors

  • @mattmcdermott made their first contribution in #506
  • @tpurcell90 made their first contribution in #568
  • @esoteric-ephemera made their first contribution in #561
  • @ab5424 made their first contribution in #578

Full Changelog: https://github.com/materialsproject/atomate2/compare/v0.0.11...v0.0.12

v0.0.11

Task Document Changes

Merge atomate2 VASP task document with the one in emmet. The changes to the atomate2 schemas are:

  • PsuedoPotentialSummary -> Potcar
    • labels -> symbols
  • AnalysisSymmary -> AnalysisDoc
    • delta_volume_as_percent -> delta_volume_percent
  • InputSummary -> InputDoc
  • OutputSummary -> OutputDoc
    • density added
  • Status -> TaskState
  • TaskDocument -> TaskDoc
    • task_type added
  • Status -> TaskState

VASP input set updates

The VASP input sets have been reconfigured based on user feedback. The auto_kspacing option has been removed and KSPACING is no longer used in the atomate2 input sets by default. We have returned to using reciprocal_density as in atomate1. These changes mean the k-point mesh is no longer dependent on the precise band gap of the system. Instead, there are now two k-points settings, one for insulators and one for metals. This should remove issues when changing the functional from PBEsol -> HSE, in which the band gap increases but the k-point mesh would be expected to stay the same.

Two new options have been added to the BaseVaspInputSetGenerator:

  • auto_metal_kpoints: If true and the system is metallic, try and use reciprocal_density_metal instead of reciprocal_density for metallic systems.
  • auto_ismear: If true, the values for ISMEAR and SIGMA will be set automatically depending on the bandgap of the system. If the bandgap is not known (e.g., there is no previous VASP directory) then ISMEAR=0 and SIGMA=0.2; if the bandgap is zero (a metallic system) then ISMEAR=2 and SIGMA=0.2; if the system is an insulator, then ISMEAR=-5 (tetrahedron smearing).

New Features 🎉

  • CP2K Support by @nwinner in #157
  • Add forcefield schemas/makers to atomate2 by @matthewkuner in #322
  • Add m3gnet support to Atomate2 by @matthewkuner in #380
  • Phonons for forcefields by @JaGeo in #398

Bug Fixes 🐛

  • Fix Lobster Schema by @JaGeo in #266
  • fix lso dos of lobster being not saved in schema by @naik-aakash in #279
  • fix _get_strong_bonds function by @naik-aakash in #289
  • [Bug Fix] For stringing defect calculations together by @jmmshn in #292
  • BUGFIX auto_lreal by @jmmshn in #297
  • Fix Yb PSP: change Yb_2 to Yb_3 by @janosh in #319
  • Fix typo by @janosh in #321
  • Fix overriding magmoms in update_user_incar_settings( by @janosh in #375
  • Fix encoding of input Molecule coordinates in cclib TaskDocument by @Andrew-S-Rosen in #411
  • [FIX] fix elastic tensor flow by @mjwen in #415
  • [BUG FIX] Edge case for Magmoms by @jmmshn in #460
  • [FIX] Fix major bug that caused user_incar_settings to be overwritten in some cases by @matthewkuner in #412
  • Test for zip_outputs by @gpetretto in #503

Enhancements 🛠

  • Extension of Lobster schema and additional tests by @JaGeo in #272
  • Use emmet VASP task document by @utf in #269
  • VASP inputset updates by @utf in #270
  • Linting by @utf in #274
  • Improve Lobster workflow preconverge step, kpoints, docs by @JaGeo in #277
  • add has_doscar_lso field to Lobsterout schema model and update lobsterpy version by @naik-aakash in #286
  • added simple chg check by @jmmshn in #320
  • Switch to emmet's MoleculeMetadata by @Andrew-S-Rosen in #301
  • Update update-precommit.yml by @utf in #330
  • Update dependencies by @utf in #329
  • Add missing molecule field to cclib TaskDocument by @Andrew-S-Rosen in #353
  • allow elastically unstable structures by @matthewkuner in #355
  • update lobstertask schema: add bandoverlaps,grosspop and sitepotentials fields by @naik-aakash in #404
  • Update CondensedBondingAnalysis schema by @naik-aakash in #469
  • Phonon tweaks by @utf in #276
  • Update to Defects WF by @jmmshn in #430
  • Small change to gunzip to allow better restarting by @jmmshn in #476
  • Remove VASP calc types schema by @mjwen in #407
  • Optionally zip files at the end of jobs by @gpetretto in #414

Documentation 📖

  • Add more documentation for Lobster by @JaGeo in #267
  • Use furo for docs theme by @utf in #331
  • Update Lobster documentation by @JaGeo in #376
  • Fix docs typos by @janosh in #373
  • Update FireWorks section of docs by @Andrew-S-Rosen in #378
  • Add a copy button to code blocks by @Andrew-S-Rosen in #382
  • clean up doc, remove left-overs from amset example by @JaGeo in #394
  • More details for lobster documentation by @JaGeo in #431
  • Deploy docs on every commit to main by @janosh in #422
  • Add clearer documentation on lobster worker by @JaGeo in #440
  • Docs: add basic workflow tutorial by @rkingsbury in #408
  • Use GitHub's deploy-pages action to deploy docs by @janosh in #475

House-Keeping 🧹

  • More ruff by @janosh in #344
  • Move all type-hint only imports behind if TYPE_CHECKING by @janosh in #354
  • ruff select perflint flake8-slots by @janosh in #395
  • Bump ruff and fix PERF401: Use a list comprehension to create transformed list by @janosh in #421
  • Simplify: dict.get(key, None) -> dict.get(key) by @janosh in #429
  • dict.setdefault instead of if key not in dict: dict[key] = ... by @janosh in #452

New Contributors

  • @naik-aakash made their first contribution in #279
  • @matthewkuner made their first contribution in #322
  • @gpetretto made their first contribution in #414

Full Changelog: https://github.com/materialsproject/atomate2/compare/v0.0.10...v0.0.11)

v0.0.10

Lobster workflow with VASP implementation (@JaGeo, @naik-aakash #200)

v0.0.9

New features:

  • Defect formation energy workflow with VASP implementation (@jmmshn, #215)
  • Job to retrieve a structure from the MP API at run-time (@mkhorton, #176)

Enhancements:

Bug fixes:

v0.0.8

New features:

Enhancements:

  • Update IO classes to use pymatgen base classes (@rkingsbury, #141)
  • Read and write VASP structures with higher precision (@JaGeo, #167)

Bug fixes:

v0.0.7

New features:

  • Include band-related features (e.g. band center, bandwidth, skewness, kurtosis) in VASP schema (@Andrew-S-Rosen, #92)
  • Add use_auto_ispin and update_user_potcar_functional powerups

Enhancements:

  • Add is_hubbard and hubbards to VASP task doc.
  • Migrate build system to pyproject.toml.
  • Migrate docs to jupyter-book.
  • Docs improvements (@janosh, @mjwen)

Bug fixes:

  • Fix HSE tags.
  • Fix running bader.
  • Make potcar_spec argument usable (@jmmshn, #83)
  • Replace monty which with shutil which (@Andrew-S-Rosen, #92)
  • Fix calculate_deformation_potentials() (@janosh, #94)
  • Fix gzipping of files with numerical suffixes (@jmmshn, #116)

v0.0.6

New features:

  • cclib task document supporting virtually all popular molecular DFT codes out-of-the-box (@Andrew-S-Rosen, #64)

Enhancements:

Bug fixes:

  • Store band structure efermi in CalculationOutput (@Andrew-S-Rosen, #66)
  • Support for VASP6 and latest pymatgen (@Andrew-S-Rosen, #75)
  • Fixed atomate2 version string.
  • Disabled orbital projections in the electron-phonon workflow.

v0.0.5

This version removed Python 3.7 support following numpy and pymatgen.

New features:

Bug fixes:

  • Fix VASP relaxation using custodian "FULL_OPT" (@Andrew-S-Rosen, #42)
  • Fix supercell generation and input sets in electron-phonon workflow.
  • Fix HSEBSSetGenerator INCAR settings.
  • Fix issue with magnetism in SOC structures.
  • Fix bug with Fermi level and IBRION=1
  • Better handling of URI generation.
  • Tweak k-spacing formula to stop large band gaps giving negative values

v0.0.4

Lots of improvements and bug fixes this release.

New features:

  • AMSET workflow.
  • Electron phonon band gap renormalisation workflow.
  • Specific uniform and line mode band structure makers.
  • Optics maker.
  • Transmuter maker.

Enhancements:

  • Support for automatic handling of ISPIN.
  • Add MP base sets (@Andrew-S-Rosen, #27)
  • Docs updates (@Andrew-S-Rosen, #13 #17)
  • Options to strip band structure and DOS projects to reduce object sizes.
  • Input sets now use generators to avoid serialization issues.
  • Use smart efermi finding to remove errors with tetrahedron integration in VASP 6.
  • Powerups can now work on Maker objects directly.

Bug fixes:

  • Use PBEsol by default.
  • Increase number of significant figures when writing POSCAR files.
  • Remove unused INCAR settings (@Andrew-S-Rosen)
  • Add missing LASPH flags on vdW functionals (@Andrew-S-Rosen, #31)
  • Use NSW=0 in static calculations (@Andrew-S-Rosen, #10)
  • LREAL = False in static jobs by default (@Andrew-S-Rosen, #23)
  • Add missing functionals in output schema (@Andrew-S-Rosen, #12)
  • Many output schema fixes.
  • Better support for FireWorks.
  • Support writing additional files in VASP jobs.

v0.0.3

Many updates to use the latest jobflow store features.

v0.0.2

Automated releases.

v0.0.1

Initial release.