v0.7.0: The multi 🧵 release

Summary

After countless PRs to upstream codes and some messing around with the innards of quacc, you can now run multiple @jobs in a single Python process. This was historically not possible because quacc had to make os.chdir calls to the calculation working directory, which breaks thread safety. These calls to os.chdir have now been successfully removed with proper directory handling in ASE and Custodian, and the removal of all relative paths in quacc.

Of course, there are several other additions and bugfixes, as outlined below.

Changelog

Added

• Added a non_scf_job for VASP

Changed

• There are no more os.chdir calls to ensure thread safety
• Use pymatgen.io.ase.MSONAtoms to make MSONable Atoms
• Changed default NEDOS value from 5001 to 3001 for VASP static jobs (10x the default)

Fixed

• Fixed multithreaded @task distribution with VASP and Q-Chem
• Fixed a bug where, with Prefect, the State would raise an indexing error when passing around deferred dict entries
• Fixed a bug when job_parameters and job_decorators are both passed to customize_funcs()
• Raise a ValueError when the user provides SCRATCH_DIR or RESULTS_DIR as a relative path

PRs

• Fix psi4 test suite by @Andrew-S-Rosen in #1856
• More docs cleanup by @Andrew-S-Rosen in #1857
• Clarify recipe docs by @Andrew-S-Rosen in #1859
• Update pyproject.toml by @Andrew-S-Rosen in #1860
• Fix None job_params in grid_phonon_flow by @Andrew-S-Rosen in #1862
• Add more customize_funcs tests by @Andrew-S-Rosen in #1863
• Raise a ValueError if RESULTS_DIR or SCRATCH_DIR is relative by @Andrew-S-Rosen in #1861
• Bump covalent-slurm-plugin from 0.16.0rc0 to 0.18.0 by @dependabot in #1869
• Bump parsl[monitoring] from 2024.2.26 to 2024.3.4 by @dependabot in #1868
• Bump prefect from 2.16.1 to 2.16.3 by @dependabot in #1870
• Patch __getitem__ method on Prefect State by @Andrew-S-Rosen in #1871
• Change NEDOS from 5001 to 3001 in VASP static_job by @Andrew-S-Rosen in #1867
• Streamline MSONAtoms by @Andrew-S-Rosen in #1873
• non_scf_job for vasp calculations by @yw-fang in #1840
• Update NEDOS in VASP static job by @Andrew-S-Rosen in #1874
• Don't call a subprocess with Q-Chem Custodian by @Andrew-S-Rosen in #1851
• Don't call a subprocess with VASP custodian by @Andrew-S-Rosen in #1850
• Set CHDIR to False by @Andrew-S-Rosen in #1875

New Contributors

• @yw-fang made their first contribution in #1840

Full Changelog: v0.6.10...v0.7.0

v0.6.10

[0.6.10]

Fixed

• Fixed pickle-ability of the schemas
• Fixed multithreaded @task distribution with GULP, Espresso, and common phonon flow recipes
• Fixed concurrency issues with VASP/Q-Chem due to refactoring

Removed

• Removed the quacc.schemas.atoms._quacc_sanitize function

What's Changed

• Make ESPRESSO compatible with chdir: False by @tomdemeyere in #1822
• ESPRESSO: fix failing dask tests when CHDIR: False by @tomdemeyere in #1825
• Bump sella by @Andrew-S-Rosen in #1827
• Fix pickle serializability by @Andrew-S-Rosen in #1828
• Get rid of _quacc_sanitize function by @Andrew-S-Rosen in #1829
• Refactor NewtonNet vibthermo by @Andrew-S-Rosen in #1830
• Refactor schemas by @Andrew-S-Rosen in #1831
• Refactor phonopy schema by @Andrew-S-Rosen in #1832
• Bump emmet-core from 0.78.6 to 0.78.7 by @dependabot in #1836
• Update Covalent docs by @Andrew-S-Rosen in #1839
• Fix self assignment for command in VASP calculator by @Andrew-S-Rosen in #1842
• Add script support for custodian by @Andrew-S-Rosen in #1846
• Remove unnecessary test by @Andrew-S-Rosen in #1847
• Revert custodian subprocess in Q-Chem by @Andrew-S-Rosen in #1844
• Fix Q-Chem mocking for multithreading by @Andrew-S-Rosen in #1848
• Fix multithreading support in qchem by @Andrew-S-Rosen in #1849
• Revert custodian subprocess in VASP by @Andrew-S-Rosen in #1843
• Streamline the documentation by @Andrew-S-Rosen in #1841
• Add Dask details to executor documentation by @Andrew-S-Rosen in #1853
• Add Prefect documentation by @Andrew-S-Rosen in #1854

Full Changelog: v0.6.9...v0.6.10

v0.6.9

[0.6.9]

Added

• Added MP compatability corrections in VASP MP recipes
• Added various phonon recipes for Espresso
• Added various DOS recipes for Espresso

Fixed

• Fixed a rare edge case where final magmoms would not be moved to initial magmoms of next run in MP VASP recipes

What's Changed

• Better thread safety in tests by @Andrew-S-Rosen in #1805
• Fix thread safety of q-chem tests by @Andrew-S-Rosen in #1806
• Fix thread safety in q-chem test by @Andrew-S-Rosen in #1808
• Bump emmet-core from 0.78.0 to 0.78.6 by @dependabot in #1809
• Bump prefect from 2.16.0 to 2.16.1 by @dependabot in #1810
• Espresso Bands job and flow by @Nekkrad in #1701
• Bump pymatgen from 2024.2.23 to 2024.3.1 by @dependabot in #1812
• Revert "Bump pymatgen from 2024.2.23 to 2024.3.1" by @Andrew-S-Rosen in #1813
• Store eigenvectors in phonopy run by @Andrew-S-Rosen in #1815
• Stricter magmom handler and tests by @Andrew-S-Rosen in #1816
• Add more monty.dev.requires decorators by @Andrew-S-Rosen in #1817
• Espresso: faster tests by @tomdemeyere in #1819
• Bump pymatgen and shakenbreak by @Andrew-S-Rosen in #1814
• Espresso: q2r and matdyn jobs by @tomdemeyere in #1789
• Apply MP corrections in MP recipes by @Andrew-S-Rosen in #1820

Full Changelog: v0.6.8...v0.6.9

v.0.6.8

[0.6.8]

Added

• Added an option to prevent os.chdir calls for multithread safety
• Added a common elastic calculation

Changed

• Switched to ruff for formatting, replacing the need for black and isort
• Changed VASP double relaxes to be flows and not jobs
• Changed the behavior of quacc.utils.files.copy_decompress_files

Fixed

• Fixed copy_files handling with workflow engines
• Fixed MP VASP double relaxes, where the same relaxation was done twice by mistake
• Fixed use of **calc_kwargs in MP flow recipes

What's Changed

• style: format code with Black, isort and Prettier by @deepsource-autofix in #1745
• Add more MP VASP tests by @Andrew-S-Rosen in #1746
• Fix MP double-relax by @Andrew-S-Rosen in #1748
• Refactor VASP mocked tests by @Andrew-S-Rosen in #1750
• Bump pymatgen from 2024.2.20 to 2024.2.23 by @dependabot in #1751
• Bump pymatgen-analysis-defects from 2024.2.9 to 2024.2.24 by @dependabot in #1754
• Bump maggma from 0.63.2 to 0.63.3 by @dependabot in #1753
• Bump dask[distributed] from 2024.2.0 to 2024.2.1 by @dependabot in #1755
• Bump pydantic from 2.6.1 to 2.6.2 by @dependabot in #1756
• Bump prefect from 2.15.0 to 2.16.0 by @dependabot in #1758
• Bump parsl[monitoring] from 2024.2.12 to 2024.2.19 by @dependabot in #1757
• Bump dask-jobqueue from 0.8.2 to 0.8.5 by @dependabot in #1752
• Bump monty from 2024.2.2 to 2024.2.26 by @dependabot in #1764
• Set an upper bound on jax version with sella by @Andrew-S-Rosen in #1766
• Fix jax version by @Andrew-S-Rosen in #1767
• style: format code with Black, isort and Prettier by @deepsource-autofix in #1768
• style: format code with Black, isort and Prettier by @deepsource-autofix in #1769
• Fix docstring by @Andrew-S-Rosen in #1772
• Common flow for elastic constants calculations by @Nekkrad in #1762
• style: format code with Black, isort and Prettier by @deepsource-autofix in #1775
• Allow for thread-safe execution by @Andrew-S-Rosen in #1780
• Use .to_ase_atoms() by @Andrew-S-Rosen in #1782
• style: format code with Black, isort and Prettier by @deepsource-autofix in #1788
• Refactor and streamline copy_files handling by @Andrew-S-Rosen in #1759
• Modify VASP double relaxes to be a flow by @Andrew-S-Rosen in #1786
• Create .pre-commit-config.yaml by @Andrew-S-Rosen in #1793
• Fix double_relax_flow by @Andrew-S-Rosen in #1794
• Bump emmet by @Andrew-S-Rosen in #1795
• Bump parsl[monitoring] from 2024.2.19 to 2024.2.26 by @dependabot in #1797
• Bump covalent-cloud from 0.40.1 to 0.45.1 by @dependabot in #1799
• Bump maggma from 0.63.3 to 0.63.4 by @dependabot in #1800
• Bump pydantic from 2.6.2 to 2.6.3 by @dependabot in #1798
• Bump emmet-core from 0.77.1 to 0.78.0 by @dependabot in #1802
• Clean up conftest.py imports by @Andrew-S-Rosen in #1803

Full Changelog: v0.6.7...v0.6.8

v0.6.7

Summary

Added

• Added a store_intermediate_files keyword option to quacc.runners.ase.run_opt() to allow for storing of the logfiles in intermediate geometry optimization steps.
• Added support for Pymatgen-based input sets in VASP jobs
• Added an MP meta-GGA VASP static job
• Added MP GGA relax job, MP GGA static job, and MP GGA relax flow
• Added a validity checker on CLI parameters

Changed

• Changed the default ASE optimizer from FIRE to BFGS for most recipes
• Changed the VASP DoubleRelaxSchema to be consistent between flows
• Refactored VASP and Q-Chem execution commands in custom calculators

Fixed

• Fixed dir_name in VASP output schema
• Fixed auto-detection of the Prefect workflow engine in settings
• Fixed compatability of MP meta-GGA workflow with that in atomate2

What's Changed

• Add test for copy_decompress_files_from_dir by @Andrew-S-Rosen in #1699
• bump matgl by @Andrew-S-Rosen in #1703
• Update hpc_tests.sh by @Andrew-S-Rosen in #1705
• Check for MutableMapping, not dict in utils by @Andrew-S-Rosen in #1706
• Stricter matches on raised errors in test suite by @Andrew-S-Rosen in #1707
• Add an option to store intermediate log files during ASE opt by @Andrew-S-Rosen in #1711
• Use a (mostly) consistent default ASE optimizer by @Andrew-S-Rosen in #1712
• Streamline opt params by @Andrew-S-Rosen in #1713
• Support Pymatgen-style VASP input sets by @Andrew-S-Rosen in #1649
• Add a validity checker on CLI parameters by @Andrew-S-Rosen in #1717
• Add support for MP GGA Workflows by @Andrew-S-Rosen in #1719
• Bump parsl[monitoring] from 2024.2.5 to 2024.2.12 by @dependabot in #1720
• Bump custodian from 2023.10.9 to 2024.2.15 by @dependabot in #1721
• Bump maggma from 0.62.1 to 0.63.2 by @dependabot in #1722
• Bump phonopy from 2.21.0 to 2.21.1 by @dependabot in #1723
• Bump pydantic-settings from 2.1.0 to 2.2.0 by @dependabot in #1726
• Bump shakenbreak from 3.2.3 to 3.3.0 by @dependabot in #1724
• Bump prefect from 2.14.21 to 2.15.0 by @dependabot in #1725
• Add more pydantic-settings tests by @Andrew-S-Rosen in #1727
• Bump pydantic-settings from 2.2.0 to 2.2.1 by @dependabot in #1731
• Bump phonopy from 2.21.1 to 2.21.2 by @dependabot in #1730
• Fix and add tests for dir_name by @Andrew-S-Rosen in #1736
• style: format code with Black, isort and Prettier by @deepsource-autofix in #1738
• style: format code with Black, isort and Prettier by @deepsource-autofix in #1739
• Bump pymatgen by @Andrew-S-Rosen in #1741
• Refactor subprocess calls in VASP by @Andrew-S-Rosen in #1737
• Refactor subprocess calls for Q-Chem by @Andrew-S-Rosen in #1740

Full Changelog: v0.6.6...v0.6.7

v0.6.6

[0.6.6]

Fixed

• Using environment variables to set a setting to None now works as expected
• Overall, more intuitive and robust handling of settings across the various input methods

Full Changelog: v0.6.5...v0.6.6

v0.6.5

[0.6.5]

Added

• PDOS jobs and flows for Espresso

Changed

• Modified the Espresso results schema to be DB-compatible
• The PRIMARY_STORE setting has changed to STORE and is now formatted more intuitively
• Uses 2024 stable release of black

Fixed

• Fixed usage of MontyStore as the data store option

Removed

• Removed the deprecated "q-chem legacy" recipes

v0.6.4

Added

• Added a supercell_matrix keyword argument to the phonon recipes.
• More data is now generated, parsed, and stored in phonon workflows, including total DOS and the automatically generated band structure

Changed

• The seekpath dependency is now required for phonon workflows, as reflected in the quacc[phonons] optional dependencies
• Changed the min_length: float | None keyword argument in phonon flows to min_lengths: float | tuple[float, float, float] | None for greater flexibility. The default value is now set to 20.0 instead of 15.0 as well.

Fixed

• Fixed occasional edge cases where the charge/spin multiplicity checker would raise a ValueError in generating the RunSchema
• Fixed phonon flow with MACE-MP-0 when dispersion=True

v0.6.3

[0.6.3]

Added

• Added phonon job for MLPs
• Added an ASE relax job recipe for ONETEP
• Added a non-SCF job for Quantum Espresso
• Added a DOS job for Quantum Espresso
• Added a DOS flow for Quantum Espresso

Changed

• Redesigned the common_phonon_flow to accept new keyword arguments that enable symmetry reduction. A pre-relaxation step is now also carried out by default.

Fixed

• Ensures the "restart" keyword argument is not set when a SciPy optimizer is used
• Fixed the ONETEP_CMD setting to be str instead of Path when used to instantiate the calculator
• Quantum Espresso restarts are now disabled between steps in ASE relaxations
• Various bug fixes for the Espresso grid_phonon_flow
• Fixed redundant Structure info in the RunSchema

v0.6.2

Changed

• The CREATE_UNIQUE_DIR setting is now set to True by default.
• The temporary directory name and its symlink have been slightly updated to have "tmp-" and "symlink-" at the front of the name instead of the end for easier file navigation.

Fixed

• Fixed an occasional race condition that occurs when running concurrent calculations in multi-threaded mode
• The temporary directory made when a @job runs now has a name consistent with the folder where the results will ultimately be stored.