Merge branch 'main' into aims_magnetic_test_unskip

Author: esoteric-ephemera

.github/workflows/docs.yml

@@ -33,6 +33,7 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
+          pip install "setuptools==77.0.3"
           pip install .[strict,docs]
 
       - name: Copy tutorials

.github/workflows/testing.yml

@@ -58,16 +58,16 @@ jobs:
 
       - name: Install conda dependencies
         run: |
-          micromamba install -n a2 -c conda-forge enumlib packmol bader openbabel openff-toolkit==0.16.2 openff-interchange==0.3.22 --yes
+          micromamba install -n a2 -c conda-forge enumlib packmol bader --yes
 
       - name: Install dependencies
         run: |
           micromamba activate a2
           python -m pip install --upgrade pip
           mkdir -p ~/.abinit/pseudos
           cp -r tests/test_data/abinit/pseudos/ONCVPSP-PBE-SR-PDv0.4 ~/.abinit/pseudos
-          uv pip install .[strict,strict-forcefields,tests,abinit]
-          uv pip install torch-runstats
+          uv pip install .[strict,strict-forcefields,tests,abinit,approxneb]
+          uv pip install torch-runstats torch_dftd
           uv pip install --no-deps nequip==0.5.6
 
       - name: Install pymatgen from master if triggered by pymatgen repo dispatch
@@ -87,7 +87,7 @@ jobs:
         # However this `splitting-algorithm` means that tests cannot depend sensitively on the order they're executed in.
         run: |
           micromamba activate a2
-          pytest --splits 3 --group ${{ matrix.split }} --durations-path tests/.pytest-split-durations --splitting-algorithm least_duration --ignore=tests/ase --cov=atomate2 --cov-report=xml
+          pytest --splits 3 --group ${{ matrix.split }} --durations-path tests/.pytest-split-durations --splitting-algorithm least_duration --ignore=tests/ase --ignore=tests/openff_md --ignore=tests/openmm_md --cov=atomate2 --cov-report=xml
 
 
       - uses: codecov/codecov-action@v1
@@ -97,6 +97,62 @@ jobs:
           name: coverage${{ matrix.split }}
           file: ./coverage.xml
 
+  test-openff:
+    # prevent this action from running on forks
+    if: github.repository == 'materialsproject/atomate2'
+
+    services:
+      local_mongodb:
+        image: mongo:4.0
+        ports:
+          - 27017:27017
+
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0} # enables conda/mamba env activation by reading bash profile
+    strategy:
+      matrix:
+        python-version: ["3.10","3.11","3.12"]
+
+    steps:
+      - name: Check out repo
+        uses: actions/checkout@v4
+
+      - name: Set up micromamba
+        uses: mamba-org/setup-micromamba@main
+
+      - name: Create mamba environment
+        run: |
+          micromamba create -n a2 python=${{ matrix.python-version }} --yes
+
+      - name: Install uv
+        run: micromamba run -n a2 pip install uv
+
+      - name: Install conda dependencies
+        run: |
+          micromamba install -n a2 -c conda-forge enumlib packmol bader openbabel openff-toolkit==0.16.2 openff-interchange==0.3.22 --yes
+
+      - name: Install dependencies
+        run: |
+          micromamba activate a2
+          python -m pip install --upgrade pip
+          uv pip install .[strict-openff,tests]
+
+      - name: Install pymatgen from master if triggered by pymatgen repo dispatch
+        if: github.event_name == 'repository_dispatch' && github.event.action == 'pymatgen-ci-trigger'
+        run: |
+          micromamba activate a2
+          uv pip install --upgrade 'git+https://github.com/materialsproject/pymatgen@${{ github.event.client_payload.pymatgen_ref }}'
+
+      - name: Test split ${{ matrix.split }}
+        env:
+          MP_API_KEY: ${{ secrets.MP_API_KEY }}
+
+        run: |
+          micromamba activate a2
+          pytest tests/{openff_md,openmm_md}
+
   test-notebooks-and-ase:
     # prevent this action from running on forks
     if: github.repository == 'materialsproject/atomate2'
@@ -143,12 +199,15 @@ jobs:
           micromamba activate a2
           python -m pip install --upgrade pip
           uv pip install .[strict,tests]
+          uv pip install tblite>=0.4.0
 
       - name: Install pymatgen from master if triggered by pymatgen repo dispatch
         if: github.event_name == 'repository_dispatch' && github.event.action == 'pymatgen-ci-trigger'
         run: uv pip install --upgrade 'git+https://github.com/materialsproject/pymatgen@${{ github.event.client_payload.pymatgen_ref }}'
 
       - name: Test Notebooks
+        env:
+          MP_API_KEY: ${{ secrets.MP_API_KEY }}
         run: |
           micromamba activate a2
           pytest --nbmake ./tutorials --ignore=./tutorials/openmm_tutorial.ipynb --ignore=./tutorials/force_fields
@@ -262,7 +321,7 @@ jobs:
         run: sphinx-build docs docs_build
 
   automerge:
-    needs: [lint, test-non-ase, test-notebooks-and-ase, test-force-field-notebook, docs]
+    needs: [docs, lint, test-force-field-notebook, test-non-ase, test-notebooks-and-ase, test-openff]
     runs-on: ubuntu-latest
 
     permissions:

CHANGELOG.md

@@ -1,5 +1,55 @@
 # 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 🐛

CODE_OF_CONDUCT.md

@@ -35,12 +35,18 @@ This Code of Conduct applies both within project spaces and in public spaces
 when an individual is representing the project or its community.
 
 Instances of abusive, harassing, or otherwise unacceptable behavior may be
-reported by contacting a project maintainer at [INSERT EMAIL ADDRESS]. All
-complaints will be reviewed and investigated and will result in a response that
-is deemed necessary and appropriate to the circumstances. Maintainers are
-obligated to maintain confidentiality with regard to the reporter of an
-incident.
-
+reported by contacting a project maintainer at conduct@materialsproject.org. All
+complaints will be reviewed and investigated by a Materials Project staff member
+and will result in a response that
+is deemed necessary and appropriate to the circumstances.
+
+Project maintainers and Materials Project staff members are obligated to
+maintain confidentiality with regard to the reporter of an incident to the extent
+possible by law and institutional policy. Community members should be aware that
+Materials Project staff members are subject to Lawrence Berkeley National Laboratory's
+[harassment and discrimination policies](https://diversity.lbl.gov/harassment-discrimination-policies/),
+which require that reports of sexual violence or harassment (as defined in the policy)
+be reported to the institution.
 
 This Code of Conduct is adapted from the [Contributor Covenant][homepage],
 version 1.3.0, available at https://www.contributor-covenant.org/version/1/3/0/code-of-conduct.html

README.md

@@ -4,16 +4,17 @@
 [![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)
+[![Zenodo](https://img.shields.io/badge/DOI-10.5281/zenodo.10677080-blue?logo=Zenodo&logoColor=white)](https://doi.org/10.5281/zenodo.15603088)
 [![This project supports Python 3.10+](https://img.shields.io/badge/Python-3.10+-blue.svg?logo=python&logoColor=white)](https://python.org/downloads)
+[![PyPI](https://img.shields.io/pypi/dm/atomate2.svg?maxAge=2592000)](https://pypi.python.org/pypi/atomate2)
 
 [Documentation][docs] | [PyPI][pypi] | [GitHub][github]
 
 Atomate2 is a free, open-source software for performing complex materials science
 workflows using simple Python functions. Features of atomate2 include
 
 - It is built on open-source libraries: [pymatgen], [custodian], [jobflow], and
-  [FireWorks].
+  [jobflow-remote] or [FireWorks].
 - A library of "standard" workflows to compute a wide variety of desired materials
   properties.
 - The ability scale from a single material, to 100 materials, or 100,000 materials.
@@ -81,8 +82,8 @@ See the [installation] steps for details how to set all of this up.
 
 In this example, we execute the workflow immediately. In many cases, you might want
 to perform calculations on several materials simultaneously. To achieve this, all
-atomate2 workflows can be run using the [FireWorks] software. See the
-[documentation][atomate2_fireworks] for more details.
+atomate2 workflows can be run using the [jobflow-remote] or [FireWorks] software. See the
+[jobflow-remote-specific documentation][atomate2-jobflow-remote] or [fireworks-specific documentation][atomate2_fireworks] for more details.
 
 ## Installation
 
@@ -98,6 +99,14 @@ started:
 - [Using atomate2 with FireWorks][atomate2_fireworks]
 - [Overview of key concepts][key-concepts]
 - [List of VASP workflows][vasp_workflows]
+- [Executable tutorials for different workflows][tutorials]
+
+In March 2025, the first dedicated school on atomate2 (including the workflow language jobflow and the workflow manager jobflow-remote) took place, and one can access the video material here:
+
+- [Jobflow and Jobflow-remote][videotutorial1]
+- [atomate2][videotutorial2]
+- [Advanced Workflows in atomate2: Part 1][videotutorial3]
+- [Advanced Workflows in atomate2: Part 2][videotutorial4]
 
 ## Need help?
 
@@ -125,22 +134,24 @@ A full list of contributors can be found [here][contributors].
 
 ## Citing atomate2
 
-A journal submission of `atomate2` is undergoing peer review. In the meantime, please cite the [ChemRxiv preprint](https://chemrxiv.org/engage/chemrxiv/article-details/678e76a16dde43c9085c75e9):
+If you use atomate2, please cite the [following article](https://doi.org/10.1039/D5DD00019J):
 
 ```bib
 @article{ganose2025_atomate2,
-    title        = {Atomate2: Modular Workflows for Materials Science},
-    author       = {Ganose, Alex M. and Sahasrabuddhe, Hrushikesh and Asta, Mark and Beck, Kevin and Biswas, Tathagata and Bonkowski, Alexander and Bustamante, Joana and Chen, Xin and Chiang, Yuan and Chrzan, Daryl and Clary, Jacob and Cohen, Orion and Ertural, Christina and Gallant, Max and George, Janine and Gerits, Sophie and Goodall, Rhys and Guha, Rishabh and Hautier, Geoffroy and Horton, Matthew and Kaplan, Aaron and Kingsbury, Ryan and Kuner, Matthew and Li, Bryant and Linn, Xavier and McDermott, Matthew and Mohanakrishnan, Rohith Srinivaas and Naik, Aakash and Neaton, Jeffrey and Persson, Kristin and Petretto, Guido and Purcell, Thomas and Ricci, Francesco and Rich, Benjamin and Riebesell, Janosh and Rignanese, Gian-Marco and Rosen, Andrew and Scheffler, Matthias and Schmidt, Jonathan and Shen, Jimmy-Xuan and Sobolev, Andrei and Sundararaman, Ravishankar and Tezak, Cooper and Trinquet, Victor and Varley, Joel and Vigil-Fowler, Derek and Wang, Duo and Waroquiers, David and Wen, Mingjian and Yang, Han and Zheng, Hui and Zheng, Jiongzhi and Zhu, Zhuoying and Jain, Anubhav},
-    year         = 2025,
-    journal      = {ChemRxiv},
-    url          = {https://chemrxiv.org/engage/chemrxiv/article-details/678e76a16dde43c9085c75e9},
-    urldate      = {2025-01-22},
+	title = {Atomate2: modular workflows for materials science},
+	author = {Ganose, Alex M. and Sahasrabuddhe, Hrushikesh and Asta, Mark and Beck, Kevin and Biswas, Tathagata and Bonkowski, Alexander and Bustamante, Joana and Chen, Xin and Chiang, Yuan and Chrzan, Daryl C. and Clary, Jacob and Cohen, Orion A. and Ertural, Christina and Gallant, Max C. and George, Janine and Gerits, Sophie and Goodall, Rhys E. A. and Guha, Rishabh D. and Hautier, Geoffroy and Horton, Matthew and Inizan, T. J. and Kaplan, Aaron D. and Kingsbury, Ryan S. and Kuner, Matthew C. and Li, Bryant and Linn, Xavier and McDermott, Matthew J. and Mohanakrishnan, Rohith Srinivaas and Naik, Aakash N. and Neaton, Jeffrey B. and Parmar, Shehan M. and Persson, Kristin A. and Petretto, Guido and Purcell, Thomas A. R. and Ricci, Francesco and Rich, Benjamin and Riebesell, Janosh and Rignanese, Gian-Marco and Rosen, Andrew S. and Scheffler, Matthias and Schmidt, Jonathan and Shen, Jimmy-Xuan and Sobolev, Andrei and Sundararaman, Ravishankar and Tezak, Cooper and Trinquet, Victor and Varley, Joel B. and Vigil-Fowler, Derek and Wang, Duo and Waroquiers, David and Wen, Mingjian and Yang, Han and Zheng, Hui and Zheng, Jiongzhi and Zhu, Zhuoying and Jain, Anubhav},
+	year = {2025},
+	journal = {Digital Discovery},
+	doi = {10.1039/D5DD00019J},
+	url = {https://doi.org/10.1039/D5DD00019J},
+	urldate = {2025-07-01},
 }
 ```
 
 [pymatgen]: https://pymatgen.org
 [fireworks]: https://materialsproject.github.io/fireworks/
 [jobflow]: https://materialsproject.github.io/jobflow/
+[jobflow-remote]: https://github.com/Matgenix/jobflow-remote
 [custodian]: https://materialsproject.github.io/custodian/
 [VASP]: https://www.vasp.at
 [AMSET]: https://hackingmaterials.lbl.gov/amset/
@@ -154,11 +165,17 @@ A journal submission of `atomate2` is undergoing peer review. In the meantime, p
 [running-workflows]: https://materialsproject.github.io/atomate2/user/running-workflows.html
 [key-concepts]: https://materialsproject.github.io/atomate2/user/key_concepts_overview.html#key-concepts-in-atomate2-job-flow-makers-inputset-taskdocument-and-builder
 [atomate2_fireworks]: https://materialsproject.github.io/atomate2/user/fireworks.html
+[atomate2-jobflow-remote]: https://materialsproject.github.io/atomate2/user/jobflow-remote.html
 [vasp_workflows]: https://materialsproject.github.io/atomate2/user/codes/vasp.html
+[tutorials]: https://materialsproject.github.io/atomate2/tutorials/tutorials.html
 [RelaxBandStructure]: https://materialsproject.github.io/atomate2/user/codes/vasp.html#relax-and-band-structure
 [Lobster]: http://www.cohp.de
 [lobsterpy]: https://github.com/JaGeo/LobsterPy
 [phonopy]: https://github.com/phonopy/phonopy
 [docs]: https://materialsproject.github.io/atomate2/
 [github]: https://github.com/materialsproject/atomate2
 [pypi]: https://pypi.org/project/atomate2
+[videotutorial1]: https://lhumos.org/collection/0/680bb4d7e4b0f0d2028027ce
+[videotutorial2]: https://lhumos.org/collection/0/680bb4d3e4b0f0d2028027c9
+[videotutorial3]: https://lhumos.org/collection/0/680bb4d0e4b0f0d2028027c5
+[videotutorial4]: https://lhumos.org/collection/0/680bb4c7e4b0f0d2028027c1