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‎CHANGELOG.md

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# Change log
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## v0.0.21
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### Bug Fixes 🐛
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* switch to CONTCAR read for LOBSTERTaskDoc by @naik-aakash in https://github.com/materialsproject/atomate2/pull/1204
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* 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
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* Remove walrus operator to avoid unassigned vmax by @Jonas-Finkler in https://github.com/materialsproject/atomate2/pull/1203
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### Enhancements 🛠
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* add file output xyz file including final atoms object to ase and forcefield jobs by @JaGeo in https://github.com/materialsproject/atomate2/pull/1206
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### Documentation 📖
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* Add video tutorials to README by @JaGeo in https://github.com/materialsproject/atomate2/pull/1191
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* be more concrete for tutorial video names in readme by @JaGeo in https://github.com/materialsproject/atomate2/pull/1192
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* Adding download statistics to readme by @JaGeo in https://github.com/materialsproject/atomate2/pull/1209
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## New Contributors
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* @Jonas-Finkler made their first contribution in https://github.com/materialsproject/atomate2/pull/1203
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**Full Changelog**: https://github.com/materialsproject/atomate2/compare/v0.0.20...v0.0.21
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## v0.0.20
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### Enhancements 🛠
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* Add MatPES forcefields by @esoteric-ephemera in https://github.com/materialsproject/atomate2/pull/1158
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* Add `DynamicOpenMMFlowMaker` for dynamic OpenMM Simulations by @shehan807 in https://github.com/materialsproject/atomate2/pull/1115
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* atomate2 / OpenMM OPLS-AA Enhancements by @shehan807 in https://github.com/materialsproject/atomate2/pull/1111
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* Add updated MP workflows + cleanup by @esoteric-ephemera in https://github.com/materialsproject/atomate2/pull/1139
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### Documentation 📖
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* Improve documentation LOBSTER and PHONON workflow by @JaGeo in https://github.com/materialsproject/atomate2/pull/1117
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* Add key concept tutorial to tutorial list in README by @QuantumChemist in https://github.com/materialsproject/atomate2/pull/1120
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* Fixing headline levels in key_concepts_overview.md by @QuantumChemist in https://github.com/materialsproject/atomate2/pull/1121
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* try to fix the doc by @JaGeo in https://github.com/materialsproject/atomate2/pull/1125
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* Added code snippets for Grüneisen, QHA and EOS wfs documentation by @QuantumChemist in https://github.com/materialsproject/atomate2/pull/1130
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* a few improvements for the tutorials by @QuantumChemist in https://github.com/materialsproject/atomate2/pull/1132
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* Update tutorials.md by @JaGeo in https://github.com/materialsproject/atomate2/pull/1138
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* Electrode workflow and documentation improvements by @esoteric-ephemera in https://github.com/materialsproject/atomate2/pull/1055
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* Update index.md by @JaGeo in https://github.com/materialsproject/atomate2/pull/1155
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### House-Keeping 🧹
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* More CI fixes by @esoteric-ephemera in https://github.com/materialsproject/atomate2/pull/1141
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### Other Changes
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* Pin MACE calculator version, add missing metadata to AseStructureTaskDoc by @esoteric-ephemera in https://github.com/materialsproject/atomate2/pull/1119
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* Tutorials for QHA and Grüneisen workflows by @JaGeo in https://github.com/materialsproject/atomate2/pull/1122
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* add more headlines to tutorials and fix a typo by @JaGeo in https://github.com/materialsproject/atomate2/pull/1126
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* Minor update to tutorials by @naik-aakash in https://github.com/materialsproject/atomate2/pull/1128
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* adjust example flow names by @QuantumChemist in https://github.com/materialsproject/atomate2/pull/1131
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* Aims phonon tutorials by @tpurcell90 in https://github.com/materialsproject/atomate2/pull/1136
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* fix gruneisen tutorial by @JaGeo in https://github.com/materialsproject/atomate2/pull/1142
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* fix link again for aims tutorial by @JaGeo in https://github.com/materialsproject/atomate2/pull/1143
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* Append name relax by @JaGeo in https://github.com/materialsproject/atomate2/pull/1150
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* add more info on jobflow-remote by @JaGeo in https://github.com/materialsproject/atomate2/pull/1154
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* Add example MP-compatible phase diagram tutorial by @esoteric-ephemera in https://github.com/materialsproject/atomate2/pull/1159
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## v0.0.19
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### Bug Fixes 🐛

‎README.md

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[![code coverage](https://img.shields.io/codecov/c/gh/materialsproject/atomate2)](https://codecov.io/gh/materialsproject/atomate2)
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[![pypi version](https://img.shields.io/pypi/v/atomate2?color=blue)](https://pypi.org/project/atomate2)
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![supported python versions](https://img.shields.io/pypi/pyversions/atomate2)
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[![Zenodo](https://img.shields.io/badge/DOI-10.5281/zenodo.10677081-blue?logo=Zenodo&logoColor=white)](https://zenodo.org/records/10677081)
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[![Zenodo](https://img.shields.io/badge/DOI-10.5281/zenodo.10677080-blue?logo=Zenodo&logoColor=white)](https://doi.org/10.5281/zenodo.15603088)
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[![This project supports Python 3.10+](https://img.shields.io/badge/Python-3.10+-blue.svg?logo=python&logoColor=white)](https://python.org/downloads)
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[![PyPI](https://img.shields.io/pypi/dm/atomate2.svg?maxAge=2592000)](https://pypi.python.org/pypi/atomate2)
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[Documentation][docs] | [PyPI][pypi] | [GitHub][github]
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- [Using atomate2 with FireWorks][atomate2_fireworks]
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- [Overview of key concepts][key-concepts]
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- [List of VASP workflows][vasp_workflows]
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- [Executable tutorials for different workflows][tutorials]
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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:
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- [Jobflow and Jobflow-remote][videotutorial1]
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- [atomate2][videotutorial2]
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- [Advanced Workflows in atomate2: Part 1][videotutorial3]
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- [Advanced Workflows in atomate2: Part 2][videotutorial4]
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## Need help?
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[atomate2_fireworks]: https://materialsproject.github.io/atomate2/user/fireworks.html
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[atomate2-jobflow-remote]: https://materialsproject.github.io/atomate2/user/jobflow-remote.html
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[vasp_workflows]: https://materialsproject.github.io/atomate2/user/codes/vasp.html
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[tutorials]: https://materialsproject.github.io/atomate2/tutorials/tutorials.html
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[RelaxBandStructure]: https://materialsproject.github.io/atomate2/user/codes/vasp.html#relax-and-band-structure
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[Lobster]: http://www.cohp.de
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[lobsterpy]: https://github.com/JaGeo/LobsterPy
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[phonopy]: https://github.com/phonopy/phonopy
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[docs]: https://materialsproject.github.io/atomate2/
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[github]: https://github.com/materialsproject/atomate2
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[pypi]: https://pypi.org/project/atomate2
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[videotutorial1]: https://lhumos.org/collection/0/680bb4d7e4b0f0d2028027ce
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[videotutorial2]: https://lhumos.org/collection/0/680bb4d3e4b0f0d2028027c9
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[videotutorial3]: https://lhumos.org/collection/0/680bb4d0e4b0f0d2028027c5
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[videotutorial4]: https://lhumos.org/collection/0/680bb4c7e4b0f0d2028027c1

‎pyproject.toml

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"PyYAML",
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"click",
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"custodian>=2025.4.14",
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"emmet-core>=0.84.3rc3",
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"emmet-core>=0.84.8",
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"jobflow>=0.1.11",
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"monty>=2024.12.10",
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"numpy",
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"python-ulid>=2.7",
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]
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forcefields = [
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"ase>=3.23.0",
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"ase>=3.25.0",
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"calorine>=3.0",
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"chgnet>=0.2.2",
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"mace-torch>=0.3.3",
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"sevenn>=0.9.3",
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"torchdata<=0.7.1", # TODO: remove when issue fixed
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]
65-
ase = ["ase>=3.23.0"]
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ase = ["ase>=3.25.0"]
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ase-ext = ["tblite>=0.3.0; platform_system=='Linux'"]
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openmm = [
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"mdanalysis>=2.8.0",
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"sphinx-copybutton==0.5.2",
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"sphinx==8.1.3",
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"sphinx_design==0.6.1",
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"jupyterlab==4.3.6",
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"jupyterlab==4.4.2",
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]
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dev = ["pre-commit>=2.12.1"]
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tests = [
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]
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strict = [
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"PyYAML==6.0.2",
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"ase==3.24.0",
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"ase==3.25.0",
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"cclib==1.8.1",
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"click==8.1.7",
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"click==8.2.0",
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"custodian==2025.4.14",
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"dscribe==2.1.1",
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"emmet-core==0.84.5",
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"ijson==3.3.0",
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"emmet-core==0.84.8",
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"ijson==3.4.0",
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"jobflow==0.1.19",
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"lobsterpy==0.4.9",
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"monty==2025.3.3",
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"mp-api==0.45.4",
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"mp-api==0.45.7",
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"numpy",
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"phonopy==2.30.1",
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"pydantic-settings==2.8.1",
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"pydantic-settings==2.9.1",
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"pydantic==2.11.3",
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"pymatgen-analysis-defects==2025.1.18",
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"pymatgen==2025.2.18",

‎src/atomate2/ase/jobs.py

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if self.steps < 0:
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logger.warning(
256256
"WARNING: A negative number of steps is not possible. "
257-
"Behavior may vary..."
257+
"Defaulting to a static calculation."
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)
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260260
relaxer = AseRelaxer(

‎src/atomate2/ase/utils.py

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from ase.constraints import FixSymmetry
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from ase.filters import FrechetCellFilter
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from ase.io import Trajectory as AseTrajectory
19+
from ase.io import write as ase_write
1920
from ase.optimize import BFGS, FIRE, LBFGS, BFGSLineSearch, LBFGSLineSearch, MDMin
2021
from ase.optimize.sciopt import SciPyFminBFGS, SciPyFminCG
2122
from monty.serialization import dumpfn
@@ -328,14 +329,18 @@ def relax(
328329
fmax: float = 0.1,
329330
steps: int = 500,
330331
traj_file: str = None,
332+
final_atoms_object_file: str | os.PathLike[str] = "final_atoms_object.xyz",
331333
interval: int = 1,
332334
verbose: bool = False,
333335
cell_filter: Filter = FrechetCellFilter,
336+
filter_kwargs: dict | None = None,
334337
**kwargs,
335338
) -> AseResult:
336339
"""
337340
Relax the molecule or structure.
338341
342+
If steps <= 1, this will perform a single-point calculation.
343+
339344
Parameters
340345
----------
341346
atoms : ASE Atoms, pymatgen Structure, or pymatgen Molecule
@@ -346,6 +351,8 @@ def relax(
346351
Max number of steps for relaxation.
347352
traj_file : str
348353
The trajectory file for saving.
354+
final_atoms_object_file: str | os.PathLike
355+
The final atoms object file for saving.
349356
interval : int
350357
The step interval for saving the trajectories.
351358
verbose : bool
@@ -363,19 +370,23 @@ def relax(
363370

364371
if isinstance(atoms, Structure | Molecule):
365372
atoms = self.ase_adaptor.get_atoms(atoms)
373+
374+
input_atoms = atoms.copy()
366375
if self.fix_symmetry:
367376
atoms.set_constraint(FixSymmetry(atoms, symprec=self.symprec))
368377
atoms.calc = self.calculator
369378
with contextlib.redirect_stdout(sys.stdout if verbose else io.StringIO()):
370379
obs = TrajectoryObserver(atoms)
371-
if self.relax_cell and (not is_mol):
372-
atoms = cell_filter(atoms)
373-
optimizer = self.opt_class(atoms, **kwargs)
374-
optimizer.attach(obs, interval=interval)
375380
t_i = time.perf_counter()
376-
optimizer.run(fmax=fmax, steps=steps)
377-
t_f = time.perf_counter()
381+
if steps > 1:
382+
if self.relax_cell and (not is_mol):
383+
atoms = cell_filter(atoms, **(filter_kwargs or {}))
384+
optimizer = self.opt_class(atoms, **kwargs)
385+
optimizer.attach(obs, interval=interval)
386+
optimizer.run(fmax=fmax, steps=steps)
378387
obs()
388+
t_f = time.perf_counter()
389+
379390
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380391
obs.save(traj_file)
381392
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389400
np.linalg.norm(traj.frame_properties[-1]["forces"][idx]) < abs(fmax)
390401
for idx in range(len(struct))
391402
)
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404+
if final_atoms_object_file is not None:
405+
if steps <= 1:
406+
write_atoms = input_atoms
407+
write_atoms.calc = self.calculator
408+
else:
409+
write_atoms = atoms
410+
ase_write(
411+
final_atoms_object_file, write_atoms, format="extxyz", append=True
412+
)
413+
392414
return AseResult(
393415
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394416
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‎src/atomate2/common/flows/mpmorph.py

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112112
*self.initial_strain, self.postprocessor.min_data_points
113113
)
114114
working_outputs = {
115-
"relax": {
116-
key: [] for key in ("energies", "volume", "stress", "pressure")
117-
}
115+
"relax": {key: [] for key in ("energy", "volume", "stress", "pressure")}
118116
}
119117

120118
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121119
# Fit EOS to running list of energies and volumes
122120
self.postprocessor.fit(working_outputs)
123121
working_outputs = dict(self.postprocessor.results)
124122
flow_output = {"working_outputs": working_outputs.copy(), "structure": None}
125-
for k in ("pressure", "energy"):
123+
for k in ("pressure",):
126124
working_outputs["relax"].pop(k, None)
127125

128126
# Stop flow here if EOS cannot be fit
129127
if (v0 := working_outputs.get("V0")) is None:
130128
return Response(output=flow_output, stop_children=True)
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# Check if equilibrium volume is in range of attempted volumes
133-
v0_in_range = (
134-
(vmin := working_outputs.get("Vmin"))
135-
<= v0
136-
<= (vmax := working_outputs.get("Vmax"))
137-
)
131+
vmin = working_outputs.get("Vmin")
132+
vmax = working_outputs.get("Vmax")
138133

139134
# Check if maximum number of refinement NVT runs is set,
140135
# and if so, if that limit has been reached
@@ -143,7 +138,7 @@ def make(
143138
)
144139

145140
# Successful fit: return structure at estimated equilibrium volume
146-
if v0_in_range or max_attempts_reached:
141+
if (vmin <= v0 <= vmax) or max_attempts_reached:
147142
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148143
flow_output["structure"].scale_lattice(v0) # type: ignore[attr-defined]
149144
return flow_output
@@ -162,19 +157,19 @@ def make(
162157
eos_jobs = []
163158
for index in range(len(deformation_matrices)):
164159
md_job = self.md_maker.make(
165-
structure=deformed_structures[index].final_structure,
160+
deformed_structures[index].final_structure,
166161
prev_dir=None,
167162
)
168163
relaxed_vol = len(working_outputs["relax"]["volume"])
169164
md_job.name = f"{self.name} {md_job.name} {relaxed_vol + 1}"
170165

171-
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166+
working_outputs["relax"]["energy"].append(md_job.output.output.energy)
172167
working_outputs["relax"]["volume"].append(md_job.output.structure.volume)
173168
working_outputs["relax"]["stress"].append(md_job.output.output.stress)
174169
eos_jobs.append(md_job)
175170

176171
recursive = self.make(
177-
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172+
structure,
178173
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179174
working_outputs=working_outputs,
180175
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@@ -262,14 +257,12 @@ def make(
262257
structure = convergence_flow.output["structure"]
263258

264259
self.production_md_maker.name = self.name + " production run"
265-
production_run = self.production_md_maker.make(
266-
structure=structure, prev_dir=prev_dir
267-
)
260+
production_run = self.production_md_maker.make(structure, prev_dir=prev_dir)
268261
flow_jobs.append(production_run)
269262

270263
if self.quench_maker:
271264
quench_flow = self.quench_maker.make(
272-
structure=production_run.output.structure,
265+
production_run.output.structure,
273266
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274267
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275268
flow_jobs += [quench_flow]
@@ -469,7 +462,7 @@ def make(self, structure: Structure, prev_dir: str | Path | None = None) -> Flow
469462
)
470463
if self.descent_method == "stepwise":
471464
md_job = self.call_md_maker(
472-
structure=structure,
465+
structure,
473466
temp=temp,
474467
prev_dir=prev_dir,
475468
)
@@ -478,13 +471,13 @@ def make(self, structure: Structure, prev_dir: str | Path | None = None) -> Flow
478471
self.descent_method == "linear with hold"
479472
): # TODO: Work in Progress; needs testing
480473
md_job_linear = self.call_md_maker(
481-
structure=structure,
474+
structure,
482475
temp=[temp, temp - self.quench_temperature_step], # type: ignore[arg-type]
483476
prev_dir=prev_dir,
484477
)
485478

486479
md_job = self.call_md_maker(
487-
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480+
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488481
temp=temp - self.quench_temperature_step,
489482
prev_dir=md_job_linear.output.dir_name,
490483
)

‎src/atomate2/forcefields/jobs.py

Lines changed: 10 additions & 2 deletions
Original file line numberDiff line numberDiff line change
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3838
MLFF.MACE_MP_0: {"model": "medium"},
3939
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4040
MLFF.MACE_MP_0B3: {"model": "medium-0b3"},
41-
MLFF.MATPES_PBE: {"architecture": "TensorNet", "version": "2025.1"},
42-
MLFF.MATPES_R2SCAN: {"architecture": "TensorNet", "version": "2025.1"},
41+
MLFF.MATPES_PBE: {
42+
"architecture": "TensorNet",
43+
"version": "2025.1",
44+
"stress_unit": "eV/A3",
45+
},
46+
MLFF.MATPES_R2SCAN: {
47+
"architecture": "TensorNet",
48+
"version": "2025.1",
49+
"stress_unit": "eV/A3",
50+
},
4351
}
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