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)