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2 changes: 1 addition & 1 deletion .pre-commit-config.yaml
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python: python3
repos:
- repo: https://github.com/charliermarsh/ruff-pre-commit
rev: v0.1.13
rev: v0.2.2
hooks:
- id: ruff
args: [--fix]
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53 changes: 52 additions & 1 deletion CHANGELOG.md
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# Change log

## 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
* [bug 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
Expand All @@ -18,7 +62,9 @@ The API of `Maker.maker` for all workflows (VASP, CP2K, force fields) have been
* 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
Expand All @@ -29,14 +75,19 @@ The API of `Maker.maker` for all workflows (VASP, CP2K, force fields) have been
* 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

Expand Down Expand Up @@ -66,7 +117,7 @@ The API of `Maker.maker` for all workflows (VASP, CP2K, force fields) have been

* 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
* [WIP] MP-compatible r2SCAN workflow (and a few general INCAR improvements) by @Andrew-S-Rosen in https://github.com/materialsproject/atomate2/pull/362
* 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
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18 changes: 18 additions & 0 deletions README.md
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[![code coverage](https://img.shields.io/codecov/c/gh/materialsproject/atomate2)](https://codecov.io/gh/materialsproject/atomate2)
[![pypi version](https://img.shields.io/pypi/v/atomate2?color=blue)](https://pypi.org/project/atomate2)
![supported python versions](https://img.shields.io/pypi/pyversions/atomate2)
[![Zenodo](https://img.shields.io/badge/DOI-10.5281/zenodo.10677081-blue?logo=Zenodo&logoColor=white)](https://zenodo.org/records/10677081)

[Documentation][docs] | [PyPI][pypi] | [GitHub][github]

Expand Down Expand Up @@ -123,6 +124,23 @@ Atomate2 is released under a modified BSD license; the full text can be found [h
The development of atomate2 has benefited from many people across several research groups.
A full list of contributors can be found [here][contributors].

## Citing atomate2

A journal submission for `atomate2` is planned. In the meantime, please use [`citation.cff`](citation.cff) and the [Zenodo record](https://zenodo.org/badge/latestdoi/306414371) to cite `atomate2`.

```bib
@software{ganose_atomate2_2024,
author = {Ganose, Alex and Riebesell, Janosh and George, J. and Shen, Jimmy and S. Rosen, Andrew and Ashok Naik, Aakash and nwinner and Wen, Mingjian and rdguha1995 and Kuner, Matthew and Petretto, Guido and Zhu, Zhuoying and Horton, Matthew and Sahasrabuddhe, Hrushikesh and Kaplan, Aaron and Schmidt, Jonathan and Ertural, Christina and Kingsbury, Ryan and McDermott, Matt and Goodall, Rhys and Bonkowski, Alexander and Purcell, Thomas and Zügner, Daniel and Qi, Ji},
doi = {10.5281/zenodo.10677081},
license = {cc-by-4.0},
month = jan,
title = {atomate2},
url = {https://github.com/materialsproject/atomate2},
version = {0.0.13},
year = {2024}
}
```

[pymatgen]: https://pymatgen.org
[fireworks]: https://materialsproject.github.io/fireworks/
[jobflow]: https://materialsproject.github.io/jobflow/
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116 changes: 116 additions & 0 deletions citation.cff
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cff-version: 1.2.0
message: If you use this software, please cite it using these metadata.
title: atomate2
doi: 10.5281/zenodo.10677081
authors:
- given-names: Alex
family-names: Ganose
github: https://github.com/utf
affiliation: Imperial College London
orcid: 0000-0002-4486-3321
- given-names: Janosh
family-names: Riebesell
github: https://github.com/janosh
affiliation: Cambridge University, Lawrence Berkeley National Laboratory
orcid: 0000-0001-5233-3462
- given-names: Janine
family-names: George
github: https://github.com/JaGeo
affiliation: Federal Institute for Materials Research and Testing (BAM)
orcid: 0000-0001-8907-0336
- given-names: Jimmy-Xuan
family-names: Shen
github: https://github.com/jmmshn
affiliation: Lawrence Livermore National Laboratory
orcid: 0000-0002-2743-7531
- given-names: Andrew
family-names: Rosen
github: https://github.com/Andrew-S-Rosen
name-particle: S.
affiliation: Princeton University
orcid: 0000-0002-0141-7006
- given-names: Aakash
family-names: Naik
github: https://github.com/naik-aakash
name-particle: Ashok
affiliation: Federal Institute for Materials Research and Testing (BAM)
- given-names: Nick
family-names: Winner
email: [email protected]
github: https://github.com/nwinner
affiliation: University of California, Berkeley
- given-names: Mingjian
family-names: Wen
github: https://github.com/mjwen
affiliation: University of Houston
- given-names: Rishabh
family-names: Guha
github: https://github.com/rdguha1995
affiliation: Lawrence Berkeley National Laboratory
- given-names: Matthew
family-names: Kuner
github: https://github.com/matthewkuner
affiliation: University of California, Berkeley
- given-names: Guido
family-names: Petretto
github: https://github.com/gpetretto
affiliation: Université catholique de Louvain
- given-names: Zhuoying
family-names: Zhu
github: https://github.com/Zhuoying
affiliation: Lawrence Berkeley National Laboratory
- given-names: Matthew
family-names: Horton
github: https://github.com/mkhorton
affiliation: Microsoft Research
orcid: 0000-0001-7777-8871
- given-names: Hrushikesh
family-names: Sahasrabuddhe
github: https://github.com/hrushikesh-s
affiliation: University of California, Berkeley
- given-names: Aaron
family-names: Kaplan
github: https://github.com/esoteric-ephemera
affiliation: Lawrence Berkeley National Laboratory
- given-names: Jonathan
family-names: Schmidt
github: https://github.com/JonathanSchmidt1
affiliation: ETH Zurich
- given-names: Christina
family-names: Ertural
github: https://github.com/QuantumChemist
affiliation: Federal Institute for Materials Research and Testing (BAM)
- given-names: Ryan
family-names: Kingsbury
github: https://github.com/rkingsbury
affiliation: Princeton University
- given-names: Matt
family-names: McDermott
github: https://github.com/mattmcdermott
affiliation: Lawrence Berkeley National Laboratory
- given-names: Rhys
family-names: Goodall
github: https://github.com/CompRhys
affiliation: Chemix.ai
- given-names: Alexander
family-names: Bonkowski
github: https://github.com/ab5424
affiliation: RWTH Aachen University
- given-names: Thomas
family-names: Purcell
github: https://github.com/tpurcell90
affiliation: Fritz Haber Institute
- given-names: Daniel
family-names: Zügner
github: https://github.com/danielzuegner
affiliation: Microsoft Research
- given-names: Ji
family-names: Qi
github: https://github.com/JiQi535
affiliation: University of California, San Diego
version: 0.0.13
date-released: 2024-01-08
repository-code: https://github.com/materialsproject/atomate2
license: cc-by-4.0
license-url: https://github.com/materialsproject/atomate2/blob/main/LICENSE
type: software
7 changes: 7 additions & 0 deletions docs/about/contributors.md
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Expand Up @@ -103,6 +103,13 @@ University of Arizona
[tpurcell90]: https://github.com/tpurcell90
[0000-0003-4564-7206]: https://orcid.org/0000-0003-4564-7206

**Andrei Sobolev** [![gh]][ansobolev] [![orc]][0000-0001-5086-6601] \
Software Scientist \
MS1P e.V.

[ansobolev]: https://github.com/ansobolev
[0000-0001-5086-6601]: https://orcid.org/0000-0001-5086-6601

**Alexander Bonkowski** [![gh]][ab5424] [![orc]][0000-0002-0525-4742] \
PhD student in Chemistry \
RWTH Aachen University
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Expand Up @@ -114,7 +114,7 @@ atm dev vasp-test-data WF_NAME
```

You should change WF_NAME to be a name for the workflow. Note, WF_NAME should not
contain spaces or punctuation. For example, the elastic constant workflow test data was generated using `atm` dev vasp-test-data Si_elastic`.
contain spaces or punctuation. For example, the elastic constant workflow test data was generated using `atm dev vasp-test-data Si_elastic`.

This will generate a folder in the current directory called "WF_NAME" that contains
the folders in the correct format.
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13 changes: 13 additions & 0 deletions docs/user/codes/vasp.md
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Expand Up @@ -232,6 +232,12 @@ converted into a dynamical matrix. To correct for polarization effects, a correc
dynamical matrix based on BORN charges can be performed. Finally, phonon densities of states,
phonon band structures and thermodynamic properties are computed.

```{warning}
The current implementation of the workflow does not consider the initial magnetic moments
for the determination of the symmetry of the structure; therefore, they are removed from the structure.
```


```{note}
It is heavily recommended to symmetrize the structure before passing it to
this flow. Otherwise, a different space group might be detected and too
Expand All @@ -258,6 +264,13 @@ VASP_CMD: <<VASP_CMD>>
LOBSTER_CMD: <<LOBSTER_CMD>>
```
```{note}
A LOBSTER workflow with settings compatible to LOBSTER database (Naik, A.A., et al. Sci Data 10, 610 (2023). https://doi.org/10.1038/s41597-023-02477-5 , currently being integrated into Materials Project) is also available now,
which could be used by simply importing from atomate2.vasp.flows.mp > MPVaspLobsterMaker
instead of VaspLobsterMaker. Rest of the things to execute the workflow stays same as
shown below.
```

The corresponding flow could, for example, be started with the following code:

```py
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2 changes: 1 addition & 1 deletion docs/user/fireworks.md
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Expand Up @@ -46,7 +46,7 @@ lpad = LaunchPad.auto_load()
lpad.add_wf(wf)
```

Additional details about interfacing Jobflow-based packages with FireWorks can be found in the [Running Jobflow with FireWorks](fw_guide) guide.
Additional details about interfacing Jobflow-based packages with FireWorks can be found in the [Running Jobflow with FireWorks][fw_guide] guide.

[fireworks]: https://materialsproject.github.io/fireworks/
[fireworks_instructions]: https://materialsproject.github.io/jobflow/install_fireworks.html
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