Change log

v0.0.20

Enhancements 🛠

• Add MatPES forcefields by @esoteric-ephemera in https://github.com/materialsproject/atomate2/pull/1158

• Add DynamicOpenMMFlowMaker for dynamic OpenMM Simulations by @shehan807 in https://github.com/materialsproject/atomate2/pull/1115

• atomate2 / OpenMM OPLS-AA Enhancements by @shehan807 in https://github.com/materialsproject/atomate2/pull/1111

• Add updated MP workflows + cleanup by @esoteric-ephemera in https://github.com/materialsproject/atomate2/pull/1139

Documentation 📖

• Improve documentation LOBSTER and PHONON workflow by @JaGeo in https://github.com/materialsproject/atomate2/pull/1117

• Add key concept tutorial to tutorial list in README by @QuantumChemist in https://github.com/materialsproject/atomate2/pull/1120

• Fixing headline levels in key_concepts_overview.md by @QuantumChemist in https://github.com/materialsproject/atomate2/pull/1121

• try to fix the doc by @JaGeo in https://github.com/materialsproject/atomate2/pull/1125

• Added code snippets for Grüneisen, QHA and EOS wfs documentation by @QuantumChemist in https://github.com/materialsproject/atomate2/pull/1130

• a few improvements for the tutorials by @QuantumChemist in https://github.com/materialsproject/atomate2/pull/1132

• Update tutorials.md by @JaGeo in https://github.com/materialsproject/atomate2/pull/1138

• Electrode workflow and documentation improvements by @esoteric-ephemera in https://github.com/materialsproject/atomate2/pull/1055

• Update index.md by @JaGeo in https://github.com/materialsproject/atomate2/pull/1155

House-Keeping 🧹

• More CI fixes by @esoteric-ephemera in https://github.com/materialsproject/atomate2/pull/1141

Other Changes

• Pin MACE calculator version, add missing metadata to AseStructureTaskDoc by @esoteric-ephemera in https://github.com/materialsproject/atomate2/pull/1119

• Tutorials for QHA and Grüneisen workflows by @JaGeo in https://github.com/materialsproject/atomate2/pull/1122

• add more headlines to tutorials and fix a typo by @JaGeo in https://github.com/materialsproject/atomate2/pull/1126

• Minor update to tutorials by @naik-aakash in https://github.com/materialsproject/atomate2/pull/1128

• adjust example flow names by @QuantumChemist in https://github.com/materialsproject/atomate2/pull/1131

• Aims phonon tutorials by @tpurcell90 in https://github.com/materialsproject/atomate2/pull/1136

• fix gruneisen tutorial by @JaGeo in https://github.com/materialsproject/atomate2/pull/1142

• fix link again for aims tutorial by @JaGeo in https://github.com/materialsproject/atomate2/pull/1143

• Append name relax by @JaGeo in https://github.com/materialsproject/atomate2/pull/1150

• add more info on jobflow-remote by @JaGeo in https://github.com/materialsproject/atomate2/pull/1154

• Add example MP-compatible phase diagram tutorial by @esoteric-ephemera in https://github.com/materialsproject/atomate2/pull/1159

v0.0.19

Bug Fixes 🐛

• CP2K fixes by @janosh in https://github.com/materialsproject/atomate2/pull/1056

• bug fix for linear strain passing in qha by @JaGeo in https://github.com/materialsproject/atomate2/pull/1061

• Fix generate_phonon_displacements magmom removal side effect by @janosh in https://github.com/materialsproject/atomate2/pull/1064

• Fixed Failing Abinit tests bis by @VicTrqt in https://github.com/materialsproject/atomate2/pull/1108

Enhancements 🛠

• Add trajectory reporter to openmm workflow by @orionarcher in https://github.com/materialsproject/atomate2/pull/1053

• PhononMaker add options to calculate_pdos and save force constants to file by @chouyoudou in https://github.com/materialsproject/atomate2/pull/1008

• Allow MatPesStaticFlowMaker(static2=None) by @janosh in https://github.com/materialsproject/atomate2/pull/997

Documentation 📖

• Minor docs cleanup by @esoteric-ephemera in https://github.com/materialsproject/atomate2/pull/1047

• add openmm description to docs by @JaGeo in https://github.com/materialsproject/atomate2/pull/1069

• Docs update, forcefield elastic convenience maker, forcefield enum hydration by @esoteric-ephemera in https://github.com/materialsproject/atomate2/pull/1072

• Added the ChemRxiv citation by @hrushikesh-s in https://github.com/materialsproject/atomate2/pull/1107

• Fix docs by @janosh in https://github.com/materialsproject/atomate2/pull/1109

House-Keeping 🧹

• Fix minor phonon code formatting issues + typos by @janosh in https://github.com/materialsproject/atomate2/pull/1070

• Fix bump phonopy by @naik-aakash in https://github.com/materialsproject/atomate2/pull/1006

• update calorine version by @naik-aakash in https://github.com/materialsproject/atomate2/pull/1083

• Deprecated Structure.ntypesp in pymatgen by @jmmshn in https://github.com/materialsproject/atomate2/pull/1105

New Contributors

• @chouyoudou made their first contribution in https://github.com/materialsproject/atomate2/pull/1008

• @VicTrqt made their first contribution in https://github.com/materialsproject/atomate2/pull/1108

Full Changelog: https://github.com/materialsproject/atomate2/compare/v0.0.18…v0.0.19

v0.0.18

New Features 🎉

• Aims magnetic ordering by @tpurcell90 in https://github.com/materialsproject/atomate2/pull/922

• Ferroelectric Workflow 2 by @fraricci in https://github.com/materialsproject/atomate2/pull/1012

• Feat: GW workflow with VASP by @yanghan234 in https://github.com/materialsproject/atomate2/pull/808

Enhancements 🛠

• Allow energy minimization maker to report energies by @orionarcher in https://github.com/materialsproject/atomate2/pull/1004

• Implementation to adjust get_supercell_size to also generate orthorhombic supercells by @QuantumChemist in https://github.com/materialsproject/atomate2/pull/923

• MPMorph Flows by @BryantLi-BLI in https://github.com/materialsproject/atomate2/pull/938

House-Keeping 🧹

• Fix ruff PLC0206 by @janosh in https://github.com/materialsproject/atomate2/pull/1009

• Update MACE to 0.3.6 by @orionarcher in https://github.com/materialsproject/atomate2/pull/1032

• Allow custom mace model by specifying “model” in calculator kwargs” by @orionarcher in https://github.com/materialsproject/atomate2/pull/1017

• feat: add dedicated fireworks optional dependency (Fix #1033). by @hongyi-zhao in https://github.com/materialsproject/atomate2/pull/1035

• Make testing utils importable by @jmmshn in https://github.com/materialsproject/atomate2/pull/1037

New Contributors

• @fraricci made their first contribution in https://github.com/materialsproject/atomate2/pull/1012

• @hongyi-zhao made their first contribution in https://github.com/materialsproject/atomate2/pull/1035

• @BryantLi-BLI made their first contribution in https://github.com/materialsproject/atomate2/pull/938

• @yanghan234 made their first contribution in https://github.com/materialsproject/atomate2/pull/808

Full Changelog: https://github.com/materialsproject/atomate2/compare/v0.0.17…v0.0.18

v0.0.17

Bug Fixes 🐛

• Fix prev_dir behavior in input set generator of MPGGAStaticMaker by @Andrew-S-Rosen in https://github.com/materialsproject/atomate2/pull/996

Documentation 📖

• Bump min supported Python to 3.10 by @janosh in https://github.com/materialsproject/atomate2/pull/992

House-Keeping 🧹

• Excise openff dependency from OpenMM testing by @orionarcher in https://github.com/materialsproject/atomate2/pull/993

• Use pytest-split to parallelize across 3 runners and speedup CI by @esoteric-ephemera in https://github.com/materialsproject/atomate2/pull/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 https://github.com/materialsproject/atomate2/pull/901

• Workflow for Quasi-harmonic approximation (forcefields and VASP) by @JaGeo in https://github.com/materialsproject/atomate2/pull/903

• Atomate2 OpenMM integration & broader classical MD framework by @orionarcher in https://github.com/materialsproject/atomate2/pull/782

• Frequency Flattening Optimizer by @rohithsrinivaas in https://github.com/materialsproject/atomate2/pull/863

• Including VASP surface adsorption flow by @itsduowang in https://github.com/materialsproject/atomate2/pull/691

• Generalize forcefields for generic ASE calculator support by @esoteric-ephemera in https://github.com/materialsproject/atomate2/pull/940

Documentation 📖

• Input set tutorial by @JonathanSchmidt1 in https://github.com/materialsproject/atomate2/pull/780

House-Keeping 🧹

• Remove emmet == pin in pyproject.toml and update version in strict by @Andrew-S-Rosen in https://github.com/materialsproject/atomate2/pull/988

New Contributors

• @4kevinbeck5 made their first contribution in https://github.com/materialsproject/atomate2/pull/901

• @orionarcher made their first contribution in https://github.com/materialsproject/atomate2/pull/782

• @rohithsrinivaas made their first contribution in https://github.com/materialsproject/atomate2/pull/863

• @itsduowang made their first contribution in https://github.com/materialsproject/atomate2/pull/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 https://github.com/materialsproject/atomate2/pull/764

• Porting qchem into atomate2 by @rdguha1995 in https://github.com/materialsproject/atomate2/pull/689

• Forcefield molecular dynamics and forcefield refactor by @esoteric-ephemera in https://github.com/materialsproject/atomate2/pull/722

• Abinit workflows: static, non-scf and relaxation. by @davidwaroquiers in https://github.com/materialsproject/atomate2/pull/183

• Add magnetic orderings workflow by @mattmcdermott in https://github.com/materialsproject/atomate2/pull/432

• Add elastic workflow for FHI-aims by @tpurcell90 in https://github.com/materialsproject/atomate2/pull/871

• Transition to pymatgen VASP input sets by @esoteric-ephemera in https://github.com/materialsproject/atomate2/pull/854

• Add workflow to compute Gruneisen parameters by @naik-aakash in https://github.com/materialsproject/atomate2/pull/752

Bug Fixes 🐛

• Fix tests and installation bug by @jmmshn in https://github.com/materialsproject/atomate2/pull/765

• Add revert_default_dtype context manager to fix clashing global torch.dtype between MACE and CHGNet by @janosh in https://github.com/materialsproject/atomate2/pull/766

• Fix TrajectoryObserver.to_ase_trajectory return type by @janosh in https://github.com/materialsproject/atomate2/pull/852

• Fix JobStoreDocument attribute access by @mjwen in https://github.com/materialsproject/atomate2/pull/710

• fix CP2K TaskDocument by @lory-w in https://github.com/materialsproject/atomate2/pull/900

• Add back symprec kwarg to MP and MatPES set generators by @janosh in https://github.com/materialsproject/atomate2/pull/947

• Fix MPID assignment in electrode workflow by @esoteric-ephemera in https://github.com/materialsproject/atomate2/pull/956

Enhancements 🛠

• Add dir_name to ForceFieldMaker and **task_document_kwargs to from_ase_compatible_result by @QuantumChemist in https://github.com/materialsproject/atomate2/pull/791

• Add flexible filename and extension to phonon new_plotter by @QuantumChemist in https://github.com/materialsproject/atomate2/pull/792

• Simplify phonon get_supercell_size() and test clean up by @janosh in https://github.com/materialsproject/atomate2/pull/783

• Add fix_symmetry: bool = False option to forcefield relax makers by @JonathanSchmidt1 in https://github.com/materialsproject/atomate2/pull/789

• Update LobsterTaskDoc by @naik-aakash in https://github.com/materialsproject/atomate2/pull/723

• from_... class methods now return typing_extensions.Self by @janosh in https://github.com/materialsproject/atomate2/pull/840

• Make Fermi Energy Optional for FHI-aims by @tpurcell90 in https://github.com/materialsproject/atomate2/pull/793

• Handling failures in elastic flow by @gpetretto in https://github.com/materialsproject/atomate2/pull/861

• Bug in supercell matrix determination in phonon workflow by @JaGeo in https://github.com/materialsproject/atomate2/pull/872

• Add possibility to use your own M3GNet potential by @QuantumChemist in https://github.com/materialsproject/atomate2/pull/911

• Equation of State workflow for FHI-aims by @ansobolev in https://github.com/materialsproject/atomate2/pull/889

• Add NEP MLIP relax, static, and MD makers by @naik-aakash in https://github.com/materialsproject/atomate2/pull/893

• add additional fields as kwargs to PhononBSDOSDoc by @naik-aakash in https://github.com/materialsproject/atomate2/pull/910

• Defect: Allow bulk SC calculation to be skipped. by @jmmshn in https://github.com/materialsproject/atomate2/pull/742

• Add SevenNetRelaxMaker + SevenNetStaticMaker to force field jobs by @janosh in https://github.com/materialsproject/atomate2/pull/918

• Lobster schema updates by @naik-aakash in https://github.com/materialsproject/atomate2/pull/924

Documentation 📖

• Corrected typo in doc by @rul048 in https://github.com/materialsproject/atomate2/pull/775

• Add more details to the installation guide by @JaGeo in https://github.com/materialsproject/atomate2/pull/810

• Add missing calculator_kwargs and remove outdated model/model_kwargs in ForceFieldRelaxMaker doc strings by @janosh in https://github.com/materialsproject/atomate2/pull/830

• Document the option to run LOBSTER with one jobscript only by @JaGeo in https://github.com/materialsproject/atomate2/pull/811

• Fix title hierarchies in VASP documentation by @JaGeo in https://github.com/materialsproject/atomate2/pull/853

• Docs: add Document Models / emmet tutorial by @rkingsbury in https://github.com/materialsproject/atomate2/pull/917

• Writing tutorial for high level overview of atomate2 concepts. by @QuantumChemist in https://github.com/materialsproject/atomate2/pull/757

• Tutorial for blob storage with test by @jmmshn in https://github.com/materialsproject/atomate2/pull/776

• [WIP] Documentation update by @AntObi in https://github.com/materialsproject/atomate2/pull/850

• Added documentation about JSONStore usage within Installation by @abhardwaj73 in https://github.com/materialsproject/atomate2/pull/945

• Remove README note about atomate2 mostly being for VASP by @Andrew-S-Rosen in https://github.com/materialsproject/atomate2/pull/957

• Increase k-point density for MP GGA static calculations to close issue https://github.com/materialsproject/atomate2/issues/844 by @esoteric-ephemera in https://github.com/materialsproject/atomate2/pull/854

• Adds missing MAGMOMs for MatPES jobs by @esoteric-ephemera in https://github.com/materialsproject/atomate2/pull/854

House-Keeping 🧹

• Make functions prefixed with _ but cross-imported public by @janosh in https://github.com/materialsproject/atomate2/pull/767

• Warn on non-default ATOMATE2_CONFIG_FILE that’s not found by @janosh in https://github.com/materialsproject/atomate2/pull/794

• Remove abinit __all__ module star exports by @janosh in https://github.com/materialsproject/atomate2/pull/804

• Turn ForceFieldRelaxMaker._calculator method into calculator property by @janosh in https://github.com/materialsproject/atomate2/pull/839

• Update LobsterPy version in standard installation by @JaGeo in https://github.com/materialsproject/atomate2/pull/841

• CI add repository_dispatch event for pymatgen_ci_trigger by @janosh in https://github.com/materialsproject/atomate2/pull/835

• Add test for supercell matrix creation in phonon workflow by @JaGeo in https://github.com/materialsproject/atomate2/pull/873

• ruff fixes by @janosh in https://github.com/materialsproject/atomate2/pull/894

• ruff fixes by @janosh in https://github.com/materialsproject/atomate2/pull/946

New Contributors

• @rul048 made their first contribution in https://github.com/materialsproject/atomate2/pull/775

• @davidwaroquiers made their first contribution in https://github.com/materialsproject/atomate2/pull/183

• @ansobolev made their first contribution in https://github.com/materialsproject/atomate2/pull/889

• @lory-w made their first contribution in https://github.com/materialsproject/atomate2/pull/900

• @AntObi made their first contribution in https://github.com/materialsproject/atomate2/pull/850

• @abhardwaj73 made their first contribution in https://github.com/materialsproject/atomate2/pull/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 https://github.com/materialsproject/atomate2/pull/634

• Add FHI-aims DFT calculator by @tpurcell90 in https://github.com/materialsproject/atomate2/pull/562

• Electrode Workflow by @jmmshn in https://github.com/materialsproject/atomate2/pull/655

• Equation of state (EOS) workflows by @esoteric-ephemera in https://github.com/materialsproject/atomate2/pull/623

Bug Fixes 🐛

• Skip final LDAU/J/L/MAGMOM updates and fix setting MAGMOM via user_incar_settings by @JonathanSchmidt1 in https://github.com/materialsproject/atomate2/pull/648

• Prep for next pymatgen release by @janosh in https://github.com/materialsproject/atomate2/pull/690

• fix SC Matrix Checking Logic by @jmmshn in https://github.com/materialsproject/atomate2/pull/704

• Fix elastic conventional structure by @mjwen in https://github.com/materialsproject/atomate2/pull/706

• Add KspacingMetalHandler to VASP _DEFAULT_HANDLERS by @janosh in https://github.com/materialsproject/atomate2/pull/600

• Fix import error [ijson] by @naik-aakash in https://github.com/materialsproject/atomate2/pull/708

• Print invalid value and list valid ones in PhononMaker error messages by @janosh in https://github.com/materialsproject/atomate2/pull/728

• Update minimum monty version, allow newer pydantic by @mkhorton in https://github.com/materialsproject/atomate2/pull/720

• Fix phonon + Lobster flow by removing magmoms before passing to phonopy by @naik-aakash in https://github.com/materialsproject/atomate2/pull/751

• Fix MP query by @utf in https://github.com/materialsproject/atomate2/pull/755

Enhancements 🛠

• add directory of task doc generation to phonon schema by @JaGeo in https://github.com/materialsproject/atomate2/pull/674

• Ensure MP VASP sets don’t use auto_ismear, few other fixes by @esoteric-ephemera in https://github.com/materialsproject/atomate2/pull/673

• Schema update > Update plot example LOBSTER workflow by @naik-aakash in https://github.com/materialsproject/atomate2/pull/682

• Modify BadInputSetWarning logic for relaxations of a likely metal by @Andrew-S-Rosen in https://github.com/materialsproject/atomate2/pull/727

• Define MLFF Enum to ensure consistent force field names by @janosh in https://github.com/materialsproject/atomate2/pull/729

Documentation 📖

• Update doc: adding metadata to flow by @naik-aakash in https://github.com/materialsproject/atomate2/pull/638

• Fix hyperlink in Docs by @naik-aakash in https://github.com/materialsproject/atomate2/pull/686

• Correct typo in doc by @JiQi535 in https://github.com/materialsproject/atomate2/pull/716

• Fix docstring on MatPesMetaGGAStaticSetGenerator by @Andrew-S-Rosen in https://github.com/materialsproject/atomate2/pull/725

• Add citation.cff file, Zenodo record and readme “How to cite” section by @janosh in https://github.com/materialsproject/atomate2/pull/731

House-Keeping 🧹

• Address TODO re missing asserts in test_elastic_wf_with_mace() by @janosh in https://github.com/materialsproject/atomate2/pull/679

• Update lobsterpy version by @naik-aakash in https://github.com/materialsproject/atomate2/pull/683

• Fix all ruff PT011 (not checking error message when testing exceptions) by @janosh in https://github.com/materialsproject/atomate2/pull/698

New Contributors

• @JonathanSchmidt1 made their first contribution in https://github.com/materialsproject/atomate2/pull/648

• @rdguha1995 made their first contribution in https://github.com/materialsproject/atomate2/pull/161

• @JiQi535 made their first contribution in https://github.com/materialsproject/atomate2/pull/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 https://github.com/materialsproject/atomate2/pull/587

Bug Fixes 🐛

• Resolve bandstructure datastore bug by @JaGeo in https://github.com/materialsproject/atomate2/pull/605

• Fix TypeError: PhononBSPlotter.save_plot() got an unexpected keyword argument img_format by @janosh in https://github.com/materialsproject/atomate2/pull/625

• ForceFieldRelaxMaker default relax_cell to True by @janosh in https://github.com/materialsproject/atomate2/pull/635

• Replace ase ExpCellFilter with FrechetCellFilter in Relaxer by @janosh in https://github.com/materialsproject/atomate2/pull/636

• update lobsterpy version and schemas to match new version changes by @naik-aakash in https://github.com/materialsproject/atomate2/pull/637

• Default create_thermal_displacements to False in VASP and forcefield PhononMaker by @janosh in https://github.com/materialsproject/atomate2/pull/647

• Fix import of ASE filters when user has installed from PyPI and not gitlab by @esoteric-ephemera in https://github.com/materialsproject/atomate2/pull/650

• Mark schema fields with None default as Optional to pass pydantic v2 validation by @danielzuegner in https://github.com/materialsproject/atomate2/pull/651

Enhancements 🛠

• Breaking: Unify previous directory Maker API by @janosh in https://github.com/materialsproject/atomate2/pull/593

• Add keyword incar_exclude: Sequence[str] = None to fake_run_vasp() by @janosh in https://github.com/materialsproject/atomate2/pull/599

• Allow prv_dir to be used more in defect wf by @jmmshn in https://github.com/materialsproject/atomate2/pull/585

• Add MACE RelaxMaker and StaticMaker by @CompRhys in https://github.com/materialsproject/atomate2/pull/611

• Update lobster task schema by @naik-aakash in https://github.com/materialsproject/atomate2/pull/529

• Allow optimizer to be configured for MACE/GAP by @CompRhys in https://github.com/materialsproject/atomate2/pull/615

• MACE Static/RelaxMakers default to loading mace_mp instead of test model by @janosh in https://github.com/materialsproject/atomate2/pull/614

• Add optional 3rd static for PBE+U to MatPesStaticFlowMaker by @janosh in https://github.com/materialsproject/atomate2/pull/606

• Use PyPI version of MACE by @utf in https://github.com/materialsproject/atomate2/pull/668

• Multi step MD flow by @gpetretto in https://github.com/materialsproject/atomate2/pull/489

Documentation 📖

• Add @CompRhys to contributors.md by @CompRhys in https://github.com/materialsproject/atomate2/pull/612

House-Keeping 🧹

• Update GitHub Action versions by @janosh in https://github.com/materialsproject/atomate2/pull/640

• Drop flake8 by @janosh in https://github.com/materialsproject/atomate2/pull/658

• Enable all ruff rules by default by @janosh in https://github.com/materialsproject/atomate2/pull/663

New Contributors

• @CompRhys made their first contribution in https://github.com/materialsproject/atomate2/pull/612

• @danielzuegner made their first contribution in https://github.com/materialsproject/atomate2/pull/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 https://github.com/materialsproject/atomate2/pull/594

Bug Fixes 🐛

• Enforce magmom precedence in INCAR creation by @mattmcdermott in https://github.com/materialsproject/atomate2/pull/506

• Warn on empty config by @janosh in https://github.com/materialsproject/atomate2/pull/522

• CP2K use calcs_reversed[0] instead of calcs_reversed[-1] to not reverse again by @janosh in https://github.com/materialsproject/atomate2/pull/534

• Fix wrong INCAR values in MP workflows by @janosh in https://github.com/materialsproject/atomate2/pull/550

• Fix failing tests from Pydantic v2 migration by @hrushikesh-s in https://github.com/materialsproject/atomate2/pull/558

• fixing pydantic v2 test errors by @hrushikesh-s in https://github.com/materialsproject/atomate2/pull/565

• parse_additional_json() ignore FW.json.gz in output directories by @janosh in https://github.com/materialsproject/atomate2/pull/574

• Fix bandgap_tol and delete bandgap_override on MPMetaGGARelaxSetGenerator by @janosh in https://github.com/materialsproject/atomate2/pull/553

• Fix VaspInputGenerator’s _set_kspacing not respecting auto_ismear = False nor auto_kspacing = False by @janosh in https://github.com/materialsproject/atomate2/pull/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 https://github.com/materialsproject/atomate2/pull/561

• Fix Lobster workflow by @JaGeo in https://github.com/materialsproject/atomate2/pull/583

• Change MatPesGGAPlusMetaGGAStaticMaker.output to dict containing both statics by @janosh in https://github.com/materialsproject/atomate2/pull/586

• Test MP + MatPES set generators by @janosh in https://github.com/materialsproject/atomate2/pull/596

Enhancements 🛠

• Add StructureMetadata as baseclass for output documents by @gpetretto in https://github.com/materialsproject/atomate2/pull/514

• Materials Project GGA and meta-GGA workflows by @janosh in https://github.com/materialsproject/atomate2/pull/504

• MP-compatible r2SCAN workflow (and a few general INCAR improvements) by @Andrew-S-Rosen in https://github.com/materialsproject/atomate2/pull/362

• Update to Pydantic v2 by @hrushikesh-s in https://github.com/materialsproject/atomate2/pull/567

• Add MatPES GGA and r2SCAN static makers by @janosh in https://github.com/materialsproject/atomate2/pull/532

• Move elastic workflow to common and build force-field elastic workflow by @JaGeo in https://github.com/materialsproject/atomate2/pull/581

Documentation 📖

• Update @arosen93 to @Andrew-S-Rosen by @Andrew-S-Rosen in https://github.com/materialsproject/atomate2/pull/516

• Add Aaron Kaplan and Matthew McDermott to contributors.md by @janosh in https://github.com/materialsproject/atomate2/pull/560

• Document architectural difference between atomate 1 and 2 by @janosh in https://github.com/materialsproject/atomate2/pull/381

• Add Thomas Purcell to contributors.md by @tpurcell90 in https://github.com/materialsproject/atomate2/pull/568

• Add Alex Bonkowski to contributors list by @JaGeo in https://github.com/materialsproject/atomate2/pull/573

• Add @matthewkuner to contributors by @matthewkuner in https://github.com/materialsproject/atomate2/pull/575

• Update contributors.md by @utf in https://github.com/materialsproject/atomate2/pull/579

House-Keeping 🧹

• Remove __all__ from all modules by @janosh in https://github.com/materialsproject/atomate2/pull/540

• removed py38 support, and add py 3.11 support by @naik-aakash in https://github.com/materialsproject/atomate2/pull/537

• Check full INCAR by default in mock_vasp fixture by @janosh in https://github.com/materialsproject/atomate2/pull/551

• skip validate charge test by @jmmshn in https://github.com/materialsproject/atomate2/pull/563

• Add some type annotations by @ab5424 in https://github.com/materialsproject/atomate2/pull/578

• Future type annotations by @janosh in https://github.com/materialsproject/atomate2/pull/580

• Use numpy.testing.assert_allclose over assert np.(all|is)close by @janosh in https://github.com/materialsproject/atomate2/pull/582

New Contributors

• @mattmcdermott made their first contribution in https://github.com/materialsproject/atomate2/pull/506

• @tpurcell90 made their first contribution in https://github.com/materialsproject/atomate2/pull/568

• @esoteric-ephemera made their first contribution in https://github.com/materialsproject/atomate2/pull/561

• @ab5424 made their first contribution in https://github.com/materialsproject/atomate2/pull/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 https://github.com/materialsproject/atomate2/pull/157

• Add forcefield schemas/makers to atomate2 by @matthewkuner in https://github.com/materialsproject/atomate2/pull/322

• Add m3gnet support to Atomate2 by @matthewkuner in https://github.com/materialsproject/atomate2/pull/380

• Phonons for forcefields by @JaGeo in https://github.com/materialsproject/atomate2/pull/398

Bug Fixes 🐛

• Fix Lobster Schema by @JaGeo in https://github.com/materialsproject/atomate2/pull/266

• fix lso dos of lobster being not saved in schema by @naik-aakash in https://github.com/materialsproject/atomate2/pull/279

• fix _get_strong_bonds function by @naik-aakash in https://github.com/materialsproject/atomate2/pull/289

• [Bug Fix] For stringing defect calculations together by @jmmshn in https://github.com/materialsproject/atomate2/pull/292

• BUGFIX auto_lreal by @jmmshn in https://github.com/materialsproject/atomate2/pull/297

• Fix Yb PSP: change Yb_2 to Yb_3 by @janosh in https://github.com/materialsproject/atomate2/pull/319

• Fix typo by @janosh in https://github.com/materialsproject/atomate2/pull/321

• Fix overriding magmoms in update_user_incar_settings( by @janosh in https://github.com/materialsproject/atomate2/pull/375

• Fix encoding of input Molecule coordinates in cclib TaskDocument by @Andrew-S-Rosen in https://github.com/materialsproject/atomate2/pull/411

• [FIX] fix elastic tensor flow by @mjwen in https://github.com/materialsproject/atomate2/pull/415

• [BUG FIX] Edge case for Magmoms by @jmmshn in https://github.com/materialsproject/atomate2/pull/460

• [FIX] Fix major bug that caused user_incar_settings to be overwritten in some cases by @matthewkuner in https://github.com/materialsproject/atomate2/pull/412

• Test for zip_outputs by @gpetretto in https://github.com/materialsproject/atomate2/pull/503

Enhancements 🛠

• Extension of Lobster schema and additional tests by @JaGeo in https://github.com/materialsproject/atomate2/pull/272

• Use emmet VASP task document by @utf in https://github.com/materialsproject/atomate2/pull/269

• VASP inputset updates by @utf in https://github.com/materialsproject/atomate2/pull/270

• Linting by @utf in https://github.com/materialsproject/atomate2/pull/274

• Improve Lobster workflow preconverge step, kpoints, docs by @JaGeo in https://github.com/materialsproject/atomate2/pull/277

• add has_doscar_lso field to Lobsterout schema model and update lobsterpy version by @naik-aakash in https://github.com/materialsproject/atomate2/pull/286

• added simple chg check by @jmmshn in https://github.com/materialsproject/atomate2/pull/320

• Switch to emmet’s MoleculeMetadata by @Andrew-S-Rosen in https://github.com/materialsproject/atomate2/pull/301

• Update update-precommit.yml by @utf in https://github.com/materialsproject/atomate2/pull/330

• Update dependencies by @utf in https://github.com/materialsproject/atomate2/pull/329

• Add missing molecule field to cclib TaskDocument by @Andrew-S-Rosen in https://github.com/materialsproject/atomate2/pull/353

• allow elastically unstable structures by @matthewkuner in https://github.com/materialsproject/atomate2/pull/355

• update lobstertask schema: add bandoverlaps,grosspop and sitepotentials fields by @naik-aakash in https://github.com/materialsproject/atomate2/pull/404

• Update CondensedBondingAnalysis schema by @naik-aakash in https://github.com/materialsproject/atomate2/pull/469

• Phonon tweaks by @utf in https://github.com/materialsproject/atomate2/pull/276

• Update to Defects WF by @jmmshn in https://github.com/materialsproject/atomate2/pull/430

• Small change to gunzip to allow better restarting by @jmmshn in https://github.com/materialsproject/atomate2/pull/476

• Remove VASP calc types schema by @mjwen in https://github.com/materialsproject/atomate2/pull/407

• Optionally zip files at the end of jobs by @gpetretto in https://github.com/materialsproject/atomate2/pull/414

Documentation 📖

• Add more documentation for Lobster by @JaGeo in https://github.com/materialsproject/atomate2/pull/267

• Use furo for docs theme by @utf in https://github.com/materialsproject/atomate2/pull/331

• Update Lobster documentation by @JaGeo in https://github.com/materialsproject/atomate2/pull/376

• Fix docs typos by @janosh in https://github.com/materialsproject/atomate2/pull/373

• Update FireWorks section of docs by @Andrew-S-Rosen in https://github.com/materialsproject/atomate2/pull/378

• Add a copy button to code blocks by @Andrew-S-Rosen in https://github.com/materialsproject/atomate2/pull/382

• clean up doc, remove left-overs from amset example by @JaGeo in https://github.com/materialsproject/atomate2/pull/394

• More details for lobster documentation by @JaGeo in https://github.com/materialsproject/atomate2/pull/431

• Deploy docs on every commit to main by @janosh in https://github.com/materialsproject/atomate2/pull/422

• Add clearer documentation on lobster worker by @JaGeo in https://github.com/materialsproject/atomate2/pull/440

• Docs: add basic workflow tutorial by @rkingsbury in https://github.com/materialsproject/atomate2/pull/408

• Use GitHub’s deploy-pages action to deploy docs by @janosh in https://github.com/materialsproject/atomate2/pull/475

House-Keeping 🧹

• More ruff by @janosh in https://github.com/materialsproject/atomate2/pull/344

• Move all type-hint only imports behind if TYPE_CHECKING by @janosh in https://github.com/materialsproject/atomate2/pull/354

• ruff select perflint flake8-slots by @janosh in https://github.com/materialsproject/atomate2/pull/395

• Bump ruff and fix PERF401: Use a list comprehension to create transformed list by @janosh in https://github.com/materialsproject/atomate2/pull/421

• Simplify: dict.get(key, None) -> dict.get(key) by @janosh in https://github.com/materialsproject/atomate2/pull/429

• dict.setdefault instead of if key not in dict: dict[key] = ... by @janosh in https://github.com/materialsproject/atomate2/pull/452

New Contributors

• @naik-aakash made their first contribution in https://github.com/materialsproject/atomate2/pull/279

• @matthewkuner made their first contribution in https://github.com/materialsproject/atomate2/pull/322

• @gpetretto made their first contribution in https://github.com/materialsproject/atomate2/pull/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:

• Documentation of phonon workflow (@QuantumChemist, #232)

• Refactor defect code (@jmmshn, #214)

• Use ruff for linting (@janosh, #250)

Bug fixes:

• Use correct k-point density in phonon workflow (@JaGeo, #177)

• Fix use of expanduser path (@nwinner, #180)

• Correct calcs_reversed to be in the proper order (@Zhuoying, #182)

• Bugfix for store_volumetric_data (@jmmshn, #212)

v0.0.8

New features:

• VASP Phonopy workflow (@JaGeo, #137)

• Molecular dynamics VASP job (@mjwen, #134)

Enhancements:

• Update IO classes to use pymatgen base classes (@rkingsbury, #141)

• Read and write VASP structures with higher precision (@JaGeo, #167)

Bug fixes:

• Fix code examples in docs (@JaGeo, #169)

• Fix f-orbital DOS properties (@Andrew-S-Rosen, #138)

• Fix mock_run_vasp testing to accept args (@mjwen, #151)

• Regenerate calc_types enum (@mjwen, #153)

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:

• Add mag_density to VASP output doc (@Andrew-S-Rosen, #65)

• Double relax maker now supports two different Makers (@Andrew-S-Rosen, #32)

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:

• Base schema for molecule task documents (@Andrew-S-Rosen, #54)

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.