Change log¶

v0.0.21¶

Bug Fixes 🐛¶

switch to CONTCAR read for LOBSTERTaskDoc by @naik-aakash in https://github.com/materialsproject/atomate2/pull/1204
cover cases where optimizer does additional steps even though step is set to 0 or 1 for writing xyz files by @JaGeo in https://github.com/materialsproject/atomate2/pull/1207
Remove walrus operator to avoid unassigned vmax by @Jonas-Finkler in https://github.com/materialsproject/atomate2/pull/1203

Enhancements 🛠¶

add file output xyz file including final atoms object to ase and forcefield jobs by @JaGeo in https://github.com/materialsproject/atomate2/pull/1206

Documentation 📖¶

Add video tutorials to README by @JaGeo in https://github.com/materialsproject/atomate2/pull/1191
be more concrete for tutorial video names in readme by @JaGeo in https://github.com/materialsproject/atomate2/pull/1192
Adding download statistics to readme by @JaGeo in https://github.com/materialsproject/atomate2/pull/1209

New Contributors¶

@Jonas-Finkler made their first contribution in https://github.com/materialsproject/atomate2/pull/1203

Full Changelog: https://github.com/materialsproject/atomate2/compare/v0.0.20…v0.0.21

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.