Resolve conflicts #93
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Bumps [chgnet](https://github.com/CederGroupHub/chgnet) from 0.3.4 to 0.3.5. - [Release notes](https://github.com/CederGroupHub/chgnet/releases) - [Commits](CederGroupHub/chgnet@v0.3.4...v0.3.5) --- updated-dependencies: - dependency-name: chgnet dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Bumps [pydantic](https://github.com/pydantic/pydantic) from 2.6.3 to 2.6.4. - [Release notes](https://github.com/pydantic/pydantic/releases) - [Changelog](https://github.com/pydantic/pydantic/blob/main/HISTORY.md) - [Commits](pydantic/pydantic@v2.6.3...v2.6.4) --- updated-dependencies: - dependency-name: pydantic dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Bumps [custodian](https://github.com/materialsproject/custodian) from 2024.2.15 to 2024.3.12. - [Release notes](https://github.com/materialsproject/custodian/releases) - [Changelog](https://github.com/materialsproject/custodian/blob/master/docs/changelog.md) - [Commits](materialsproject/custodian@v2024.2.15...v2024.3.12) --- updated-dependencies: - dependency-name: custodian dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Bumps [phonopy](https://phonopy.github.io/phonopy/) from 2.21.2 to 2.22.0. --- updated-dependencies: - dependency-name: phonopy dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Bumps [autodoc-pydantic](https://github.com/mansenfranzen/autodoc_pydantic) from 2.0.1 to 2.1.0. - [Changelog](https://github.com/mansenfranzen/autodoc_pydantic/blob/main/CHANGELOG.md) - [Commits](mansenfranzen/autodoc_pydantic@v2.0.1...v2.1.0) --- updated-dependencies: - dependency-name: autodoc-pydantic dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Bumps [pytest-cov](https://github.com/pytest-dev/pytest-cov) from 4.1.0 to 5.0.0. - [Changelog](https://github.com/pytest-dev/pytest-cov/blob/master/CHANGELOG.rst) - [Commits](pytest-dev/pytest-cov@v4.1.0...v5.0.0) --- updated-dependencies: - dependency-name: pytest-cov dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Bumps python-ulid from 2.2.0 to 2.3.0. --- updated-dependencies: - dependency-name: python-ulid dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Bumps [cclib](https://github.com/cclib/cclib) from 1.8 to 1.8.1. - [Release notes](https://github.com/cclib/cclib/releases) - [Commits](cclib/cclib@v1.8...v1.8.1) --- updated-dependencies: - dependency-name: cclib dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
By default the data is loaded by phonopy.load() instead of phonon.load(). Co-authored-by: Alex Ganose <utf@users.noreply.github.com>
…sproject#794) * move _ENV_PREFIX = "atomate2_" into module scope * construct env var name ATOMATE2_CONFIG_FILE from _ENV_PREFIX and use in warn/err msg use monkeypatch.setenv to restore env var after test * Add warning for non-existent non-default config file * test no warning if config path is default and file does not exist * test warning if config path is non-default and file does not exist
* add qchem files * remove __all__ * refactor * remove dead code in qchem/sets/core.py * delete solitary qchem/schemas/__init__.py * delete dead code in tests/qchem/jobs/test_core.py * remove dead code in tests/qchem/sets/test_core.py * refactored the InputSetGenerator to dataclass args * added the test for get_valid_paths in drones * increased test coverage for sets: * increased test coverage for input generators * increases coverage for .write_input and .from_directory * fixed linting * increased test coverage for plots and nbo * small changes to names of the QChem makers * correcting single_point maker name in tests * added a test for run functionality * fixed linting for test_run * increasing the test coverage for qche run.py * corrected error in test_run * deleted extra unnecessary files in test_dir --------- Co-authored-by: Janosh Riebesell <janosh.riebesell@gmail.com>
…ct#722) * FF MD fully implemented * change MD defaults to be NVT + Langevin dynamics * add md defaults that are as consistent with vasp implementation as possible * correct typing of langevin friction coeff * Add option to ForceFieldTaskDocument to store trajectory information as pmg object * Add tests, remove dependence on pickle for trajectory i/o * fix tests, update matgl dependence * rename MD forcefield class vars to be consistent with VASP MDSetGenerator * Add option to explicitly specify thermostat as ASE MolecularDynamics object * refactoring and add T/P schedule * implement T/P schedule and attach callback func * np.nan * np.nan * small fixes * pass ASE dynamics object instead of class, update docstring * add temp ramp test and make sure upper tria matrix cell * add stresses to trajeoctroy observer, add pressure schedule test * avoid `stresses` key not in taskdoc bug * Refactory TrajectoryObserver, add option to save trajectory as either pmg or ase trajectory objects, add test for trajectory parsing * Change decomposition to upper triangular cell only when Nose-Hoover requested * Fix failing tests * Change MD default TaskDoc ionic step to only store mandatory info * update pymatgen requirement because of CifParser deprecation * Significant refactor to all forcefield jobs. Use commmon ASE calc structure, allow loading via MontyDecoder. Add check in relaxation for force convergence, attr in Forcefield taskdoc * Fix forcefield utils test and lint * Add revert_dtype env for running forcefield relax and md jobs / undo removal * refactor nequip jobs, add md default for nequip * Add GAP and Nequip MD tests, fix arg / kwarg passing in MD * remove calculator_args / ase_calculator args, revert phonon job change * remove todo about adding magmoms to forcefield traj observer as that's now implemented * Remove comments, add option to seed rng for MB velocities, turn on ideal gas stress contribution only when MD trajectory outputs (temp / velocity) are stored * Ensure CHGNet and M3GNet relax / static makers convert stress to eV/A0**3; add tests for MD NVE ensemble and specifying MolecularDynamics object as input * fix M3GNet test related to outdated cached model * Fix dependencies, amend forcefield static option parsing * linting * try to fix ci tests caused by torch / dgl incompatibility * try to fix ci tests caused by torch / dgl incompatibility * Change: default time_step, units for time_step, initialization of temperature and velocity in TrajectoryObserver, snake case change * linting / pre-commit * revert default time_step units to fs * add missing forcefields to version check in forcefield task document * allow complex schur decomposition * more snake case * Decrease number of steps in tests for speed. Fix (?) temperature / pressure scheduling * linting * fix T/P schedule * linting * replace dunder __getattribute__ --> getattr in forcefield test_md --------- Co-authored-by: Yuan Chiang <qaqowotut@gmail.com> Co-authored-by: Yuan (Cyrus) Chiang <41962462+chiang-yuan@users.noreply.github.com> Co-authored-by: Janosh Riebesell <janosh.riebesell@gmail.com>
…e_compatible_result (materialsproject#791) * added dir_name to ForceFieldRelaxMaker and **task_document_kwargs to ForceFieldTaskDocument.from_ase_compatible_result * Simplify taskdoc update Co-authored-by: Janosh Riebesell <janosh.riebesell@gmail.com> * added docstring for task_doc_kwargs in force field schemas * changed the unit test for the force_field_task_doc attributes * fix linting --------- Co-authored-by: Janosh Riebesell <janosh.riebesell@gmail.com>
…roject#792) * added a way to set a flexible filename and extension for the phonon band structure and DOS new_plotter object. * replacing Si strcuture with si_strcuture fixture * implementing requested changes * change default filename_(bs|dos) extension to PDF * use frozenset for SUPPORTED_CODES * save filename_bs, filename_dos to tmp dir and simplify assert file exists * tweak comment --------- Co-authored-by: Janosh Riebesell <janosh.riebesell@gmail.com>
Bumps [monty](https://github.com/materialsvirtuallab/monty) from 2024.2.26 to 2024.3.31. - [Release notes](https://github.com/materialsvirtuallab/monty/releases) - [Changelog](https://github.com/materialsvirtuallab/monty/blob/master/docs/changelog.md) - [Commits](materialsvirtuallab/monty@v2024.2.26...v2024.3.31) --- updated-dependencies: - dependency-name: monty dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Janosh Riebesell <janosh.riebesell@gmail.com>
Bumps [phonopy](https://phonopy.github.io/phonopy/) from 2.22.0 to 2.22.1. --- updated-dependencies: - dependency-name: phonopy dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Janosh Riebesell <janosh.riebesell@gmail.com>
Bumps [ipython](https://github.com/ipython/ipython) from 8.22.2 to 8.23.0. - [Release notes](https://github.com/ipython/ipython/releases) - [Commits](ipython/ipython@8.22.2...8.23.0) --- updated-dependencies: - dependency-name: ipython dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Janosh Riebesell <janosh.riebesell@gmail.com>
Bumps [numpydoc](https://github.com/numpy/numpydoc) from 1.6.0 to 1.7.0. - [Release notes](https://github.com/numpy/numpydoc/releases) - [Changelog](https://github.com/numpy/numpydoc/blob/main/RELEASE.rst) - [Commits](numpy/numpydoc@v1.6.0...v1.7.0) --- updated-dependencies: - dependency-name: numpydoc dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Janosh Riebesell <janosh.riebesell@gmail.com>
Bumps [typing-extensions](https://github.com/python/typing_extensions) from 4.10.0 to 4.11.0. - [Release notes](https://github.com/python/typing_extensions/releases) - [Changelog](https://github.com/python/typing_extensions/blob/main/CHANGELOG.md) - [Commits](python/typing_extensions@4.10.0...4.11.0) --- updated-dependencies: - dependency-name: typing-extensions dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Bumps [python-ulid](https://github.com/mdomke/python-ulid) from 2.3.0 to 2.4.0.post0. - [Release notes](https://github.com/mdomke/python-ulid/releases) - [Changelog](https://github.com/mdomke/python-ulid/blob/main/CHANGELOG.rst) - [Commits](mdomke/python-ulid@2.3.0...2.4.0.post0) --- updated-dependencies: - dependency-name: python-ulid dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
davidwaroquiers
merged commit a27caaf
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davidwaroquiers:abinit_workflows
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Merge latest updates from main and resolve conflicts.