CHANGELOG.md

Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[0.7.6]

Fixed

• Fixed file extension for the optimizer trajectories, which should have been .json instead of .pckl

[0.7.5]

Changed

• Removed the atoms_info field from the AtomsSchema since this is already available in the database via Pymatgen's MSONAtoms serialization

[0.7.4]

Changed

• Only call jsanitize once before uploading to the Store

[0.7.3]

Added

• Added new Espresso recipes to perform electron-phonon calculations and Fourier interpolation of the phonon potential

Fixed

• Fixed potential issues with I/O settings and Espresso
• Fixed passing of custom decorators in the Espresso grid_phonon_flow

[0.7.2]

Changed

• Calculator executable commands are now str type instead of Path
• Removed slowconv from the default parameters of the ORCA recipes
• The Q-Chem calculator now uses the TaskDoc from emmet in its results attribute

Fixed

• Fixed user setting of logger level
• Fixed a glob-based issue with copy_decompress_files

[0.7.1]

Added

• Added an optional MP compatability checker for MP recipes
• Summaries for intermediate ASE optimization steps are now stored in the output schema for VASP and cclib-based recipes when store_intermediate_results=True
• Added a WRITE_PICKLE setting, which by default, will write out a .pkl file containing the result schema to the directory

Changed

• Updated ruff settings
• The Gaussian and ORCA static_job routines do a force calculation by default now

Fixed

• Fixed input file formatting for orcablocks in ORCA recipes

Removed

• Removed the CHDIR setting

[0.7.0]

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

[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

[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

[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

[0.6.7]

Added

• Added a store_intermediate_results 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

[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

[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

[0.6.4]

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

[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

[0.6.2]

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.
• Updated the "trajectory" entry in the OptSchema to be list[Atoms] instead of list[AtomsSchema]

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.
• Significant speedup in generating the OptSchema

[0.6.1]

Added

• Support for ONETEP recipes (@nekkrad)
• New Espresso recipe for ASE external relaxations (@tomdemeyere)

Fixed

• Fixed bug where autoamtic k-point schemes in VASP would return kpts as list[float] instead of list[int]
• VASP runs now respect the CHECK_CONVERGENCE global setting when set to False
• Fixed bug where the gamma-point only version of VASP was being called if kpts was None but kspacing was not None

Removed

• Removed the broken TRICs support with Sella
• Removed the covalent_to_db function

[0.6.0]

Added

• A new grid_phonon recipe in Espresso (@tomdemeyere)
• Preliminary support for the Prefect workflow engine, again, but this time without it breaking everything

Changed

• Raised the default logger level from WARNING to INFO

Fixed

• Codes calling Custodian can be used in Jupyter Notebooks
• Fixed an error in the Espresso phonon_flow when using the master branch of ASE
• Fixed a few erroneous type hints
• Fixed the typer depenendecy in pyproject.toml to be typer[all] like it was supposed to be
• Fixed a bug when passing decorator keyword arguments when using Dask

[0.5.2]

Changed

• ORCA and GULP recipes now use a more intuitive and concise list[str] input argument format instead of a dict format when overriding defaults

Fixed

• Fixed concurrency issues with Dask subflows

[0.5.1]

Added

• Adds a new ase_relax_job for ORCA
• Adds a new relax_job and post_processing_job for Quantum Espresso
• quacc.wflow_tools.customizers.strip_decorator and quacc.wflow_tools.customizers.redecorate are imported in the base __init__.py for easy user access
• The CLI now has color

Changed

• The test suite's SCRATCH_DIR and RESULTS_DIR are now fixed to a given location
• The default Espresso preset has been changed to "sssp_1.3.0_pbe_efficiency"
• To remove calculator defaults entirely, quacc.Remove is recommended in place of None
• The quacc.wflow_tools.customizers.strip_decorator function is recommended instead of calling .__wrapped__

Fixed

• Fixed Dask subflows that were calling .compute()
• Fixed various bugs in the Espresso calculator and recipes

[0.5.0]

Added

• Created a quacc.wflow_tools.customizers module to aid in customizing pre-made recipes.

Changed

• Overhauled how sub-jobs in recipes can be dynamically modified by the user to increase flexibility.
• Changed default fmax for quacc.recipes.mlp.core.relax_job to 0.05.
• Renamed the quacc.utils.dicts.merge_dicts function to ._recursive_dict_pair_merge to better reflect its functionality.
• Renamed the quacc.utils.dicts.merge_several_dicts function to .recursive_dict_merge to better reflect its functionality.

Fixed

• Increased support of ~/ throughout quacc file handling mechanisms
• Fixed an infinite recursion error when copy_decompress_files_from_dir was run in the current working directory.

[0.4.6]

Added

• The WORKFLOW_ENGINE quacc setting now accepts None.
• A DEBUG quacc setting as been added.

Changed

• The way to run complex, dynamic flows has been modified to rely on functools.partial() instead of kwargs. See the updated documentation.
• Refactored test suite

[0.4.5]

Added

• Added ML interatomic potential recipes

Changed

• ASE optimization log files and pickle files are written to disk by default
• Deprecated the old Q-Chem recipes and replaced them with the updated versions

Removed

• Officially drop support of the Prefect workflow engine

[0.4.4]

Added

• Added core Quantum ESPRESSO recipes and custom calculator. (@tomdemeyere)
• Added a new function, quacc.utils.files.copy_decompress_files_from_dir

Changed

• The copy_files kwarg in most recipes can now include a directory
• Renamed quacc.utils.files.copy_decompress to quacc.utils.files.copy_decompress_files

Fixed

• Quacc settings that are paths now have ~/ expanded in most cases

[0.4.3]

Added

• Added preliminary support for the Dask workflow engine via Dask Delayed and Dask Distributed.

Changed

• Renamed CREATE_UNIQUE_WORKDIR to CREATE_UNIQUE_DIR to better reflect its utility.
• The default for the SCRATCH_DIR setting is now None instead of ~/.quacc_scratch. In other words, the default is to not use a scratch directory. This should help with onboarding, and the ability to set it as None may be broadly of interest. Setting the SCRATCH_DIR to a given Path will still work as expected.
• Files are no longer recursively copied from SCRATCH_DIR to RESULTS_DIR. Instead, they are recursively moved. This should speed up I/O operations.

Fixed

• Fixed a missing phonopy_kwargs keyword argument in quacc.recipes.common.phonons

[0.4.2]

Added

• Added a Jenkins-based test suite that runs tests on HPC resources without mocking for Gaussian, GULP, ORCA, and VASP (minimal)
• Added a TBLite phonon recipe

Changed

• Changed the auto_kpts kwarg in the Vasp calculator to pmg_kpts
• Internal refactoring of recipes to have a separate _base.py module when appropriate
• Removed the unnecessary Atoms arg from the calc_setup function

Fixed

• Fixed slow initial import (3 s --> 1 s)
• Fixed a few broken type hints
• Fixed functional and basis set strings in Gaussian recipes
• Uses number of physical cores instead of logical cores as default for molecular DFT recipes

[0.4.1]

Changed

• Switched to using the PyPI release of NewtonNet (1.1).
• NewtonNet recipes don't run a Hessian calculation by default unless needed

Fixed

• Fixed circular import issue when running Q-Chem calculations.

Removed

• Removed unsupported qchem_internal_relax_job

[0.4.0]

Added

• Added quacc.recipes.common, including quacc.recipes.common.slabs, quacc.recipes.common.defects, and quacc.recipes.common.phonons
• Added phonopy schema in quacc.schemas.phonons
• Added EMT phonon workflow

Changed

• The method for specifying swaps to the default calculator arguments in recipes has been overhauled. In place of the previous calc_swaps: dict approach, additional parameters can be specified via the **kwargs. In practice, this means in recipes you can do scf = "diis", max_steps=100 instead of calc_swaps={"scf":"diis", "max_steps":100}, for instance.
• Moved quacc.runners.calc to quacc.runners.ase
• Moved quacc.runners.prep to quacc.schemas.prep
• Reduced code duplication across complex flows

[0.3.13]

Fixed

• Fixed support for the most recent version of ASE as of 11/2/2023

[0.3.12]

Added

• Added more type hints for input keyword arguments
• Added the quacc info command-line argument for error reporting

Changed

• Consolidated VASP INCAR co-pilot settings
• Internal refactoring of the Q-Chem and VASP calculators

Fixed

• All Path-based settings have .expanduser() applied

[0.3.11]

Changed

• Improved error handling

[0.3.10]

Changed

• DFTB+ MaxSccIterations set to 200 by default
• SCC errors in DFTB+ relaxations will be reported with higher priority than a relaxation error

[0.3.9]

Changed

• Changed prefix of scratch directories to have the datetime in it for easier debugging

Fixed

• DFTB+ recipes now won't crash when kpts=None for structures with PBCs

[0.3.8]

Changed

• Changed minimum version of Parsl

[0.3.7]

Added

• Added type-hinting for schemas

Changed

• Recipes now take Atoms instead of Atoms | dict as input
• Recipes no longer require the use of fetch_atoms
• Standardized schema fields

Removed

• Removed the fetch_atoms function

[0.3.6]

Fixed

• Fixed VASP recipes to always respect calc_swaps.
• Fixed setting multiple cores in Custodian for Q-Chem runs.

[0.3.5]

Added

• Added a new VibThermoSchema that merges the VibSchema and ThermoSchema as a convenience

Changed

• The output of recies no longer automatically removes blank lists/dicts/sets to maintain a consistent schema.
• The tblite freq_job and lj freq_job now use VibThermoSchema as the output
• Changed default SCRATCH_DIR from Path.cwd() / ".scratch" to Path("~/.scratch")

[0.3.4]

Added

• Added a new documentation section for worked examples on HPC.

Changed

• Updated the minimum required versions for Pymatgen and emmet-core to reflect Pydantic 2 update.
• Added symprec=1e-8 to the default parameters of VASP relaxation jobs.
• VASP bulk recipes now use "BulkSet" as the default preset instead of None.
• VASP slab recipes now use "SlabSet" as the default preset instead of None.

[0.3.3]

Fixed

• Fixed pip version conflict when installing Covalent dependencies.

[0.3.2]

Changed

• Migration to Pydantic 2 is complete, along with the corresponding dependencies.

[0.3.1]

Changed

• Pydantic field type validation has been improved.
• Moved quacc.utils.atoms/.slabs/.defects into quacc.atoms.core/.slabs/.defects
• Moved quacc.custodian to quacc.calculators.custodian
• Moved quacc.utils.thermo.ideal_gas to quacc.builders.thermo.run_ideal_gas
• Renamed quacc.schemas.ase.summarize_thermo to quacc.schemas.ase.summarize_ideal_gas_thermo

[0.3.0]

Changed

• Changed default SCRATCH_DIR from /tmp to Path.cwd() / .scratch
• Refactored decorator handling to be more concise
• Renamed [optimizers] extras to [sella]
• Moved quacc.utils.wflows into quacc.wflow_tools.decorators and quacc.wflow_tools.prefect
• Moved quacc.utils.db into quacc.wflow_tools.db
• Moved quacc.utils.calc to quacc.runners.ase
• Moved quacc.presets to quacc.calculators.presets

Fixed

• Fixed parsing of RESULTS_DIR and SCRATCH_DIR paths when they contain ~
• Symlinks are no longer created if RESULTS_DIR == SCRATCH_DIR since this is redundant
• If RESULTS_DIR or SCRATCH_DIR are not present, they will be automatically made

[0.2.8]

Changed

• Decorators are now applied at import time rather than at function-call time.

Fixed

• Fixed compatibility with FireWorks.
• Fixed I/O issue on Windows and NFS file systems where Sella optimizations would crash.

[0.2.7]

Added

• Added a freq_job recipe in Q-Chem (@samblau)
• Added support for TRICs in Sella calculations (@samblau)

Changed

• Refactored all recipes to prevent code duplication
• Set LREAL = False in VASP BulkSet.yaml

[0.2.6]

Added

• Add support for Path objects everywhere possible.

Changed

• Charge and spin multiplicity are now required arguments in molecular DFT calculators.
• Slab recipes now use make_slabs_from_bulk instead of make_max_slabs_from_bulk
• Use the logging module when warnings do not need to be immediately addressed.
• Functions are no longer used as kwargs in recipes to help with (de)serialization in certain workflow engines.

Removed

• Removed make_max_slabs_from_bulk function.

[0.2.5]

Added

• Added support for the Redun workflow engine.
• Added a simple CLI for (un)setting YAML config parameters.

Changed

• Internal refactoring of the Vasp calculator.

Removed

• Removed the demonstration Jobflow EMT slab recipe.

[0.2.4]

Changed

• Updated VASP co-pilot rules and BulkSet.yaml in accordance with recent MP benchmarking (#849).
• Moved fetch_atoms to quacc.schemas.

Fixed

• VASP: Fixed a scenario where SIGMA was set to 0.05 if the user provided SIGMA > 0.05. This was supposed to happen when ISMEAR = 0 but was previously done when ISMEAR = -5, which is not influenced by SIGMA.
• Fixed mp_metagga_relax_flow to use a #!Python @flow decorator instead of #!Python @job
• Fixed the Q-Chem Quasi-IRC job to run as one #!Python @job instead of two.

[0.2.3]

Added

• Added new defect EMT workflows (@rwexler)
• Added new defect utilities (@rwexler)
• Added a custom Q-Chem calculator based on Pymatgen and Custodian. (@samblau)
• Added Q-chem core recipes. (@samblau)
• Added the ability to pass option run_kwargs to the .run() method of the ASE optimizers.

Changed

• Removed the need to call ct.dispatch when launching Covalent workflows.
• Renamed quacc.util to quacc.utils
• Refactored and standardized the NewtonNet recipes to match the other recipes

Fixed

• The WORKFLOW_ENGINE setting can now be set dynamically, as expected.

[0.2.2]

Changed

• Changed package handling in pyproject.toml to better handle pip installs.

[0.2.1]

Added

• Added NewtonNet recipes and better sella support (@kumaranu)

Changed

• Standardized relax_cell to be False by default for all recipes.
• Update the default SIGMA and ISMEAR in MPScanSet to match the new values to be used in Atomate2.

Fixed

• Fixed a bug on Windows where the trajectory file would not be closed after a relaxation, causing permission errors.

Removed

• Removed atomate2 as a dependency.
• Removed experimental Prefect support.

[0.2.0]

Added

• Added a quacc global setting, WORKFLOW_ENGINE, to set the workflow manager.
• Added support for the new covalent-hpc-plugin in pyproject.toml.

Changed

• Quacc recipes are now decorated with generic #!Python @job, #!Python @subflow, or #!Python @flow decorators to be workflow engine-agnostic.
• Covalent is now an optional dependency to allow the base quacc package to be dependency-light.
• Default VASP pseudopotentials changed to setups_pbe54.yaml.
• Changed quacc.recipes.emt.jobflow and quacc.recipes.emt.prefect to quacc.recipes.emt._jobflow and quacc.recipes.emt._prefect

Fixed

• Set LMAXMIX based on the Z value, not the s/p/d/f-block type.
• Do not set automatically LMAXTAU to 8 for f-containing elements in Vasp calculator.

Removed

• Removed quacc.recipes.emt.parsl since it is now obsolete.
• Removed quacc config command-line option.

[0.1.3]

Added

• Added a PRIMARY_STORE quacc setting that, when specified, will automatically store all results in the specified Maggma store.

Changed

• The trajectory is now stored in quacc.schemas.cclib.summarize_run.
• By default, results are now stored in a fixed RESULTS_DIR, which defaults to the current working directory.

Fixed

• Fix path-related issues when running in local multi-threaded mode.
• Psi4 recipes now use uks for unrestricted calculations instead of uhf.

[0.1.2]

Added

• Added support for Prefect.
• Added quacc.wflow_tools module.

Changed

• Made slab-related kwargs more consistent, such as by changing slab_relax_electron/slab_relax_app to just slab_relax regardless of workflow manager.

[0.1.1]

Added

• Added this CHANGELOG.md file.
• Added the quacc.recipes.emt.parsl module.
• Added a CLI for quacc along with a quacc config option to configure Covalent appropriately upon install.
• Added generic type hints for schemas.
• Added a CREATE_UNIQUE_DIR global setting to have quacc automatically make a unique working directory for each calculation.
• Added CHECK_CONVERGENCE to global settings.

Changed

• The quacc directory is now found in a src basefolder.
• All recipes now support the Atoms object being passed in as an AtomsSchema.
• The slab_relax_job kwarg in recipes.emt.slabs and recipes.vasp.slabs workflows can no longer be set to None, as there are few situations where this would be desired.
• Class-based recipes have been converted to functions since they don't save state or have inheritance.

Docs

• Switched the docs from Furo to Material for MkDocs.
• Expanded upon Parsl documentation.
• Modified tutorials and added example configs for Slurm.

Fixed

• Temporary directories are cleaned up after the run is completed.

Removed

• Removed quacc.recipes.vasp.jobflow module to prioritize Covalent and Parsl.

[0.1.0]

See https://github.com/quantum-accelerators/quacc/releases/tag/v0.1.0 for more details.

[0.0.6]

See https://github.com/quantum-accelerators/quacc/releases/tag/v0.0.6 for more details.

[0.0.5]

See https://github.com/quantum-accelerators/quacc/releases/tag/v0.0.5 for more details.

[0.0.4]

See https://github.com/quantum-accelerators/quacc/releases/tag/v0.0.4 for more details.

[0.0.3]

See https://github.com/quantum-accelerators/quacc/releases/tag/v0.0.3 for more details.

[0.0.2]

See https://github.com/quantum-accelerators/quacc/releases/tag/v0.0.2 for more details.

[0.0.1]

See https://github.com/quantum-accelerators/quacc/releases/tag/v0.0.1 for more details.