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prep

Prepration for runners.

logger module-attribute 

logger = getLogger(__name__)

calc_cleanup 

calc_cleanup(
    atoms: Atoms | None,
    tmpdir: Path | str,
    job_results_dir: Path | str,
) -> None

Perform cleanup operations for a calculation, including gzipping files, copying files back to the original directory, and removing the tmpdir.

Parameters:

  • atoms (Atoms | None) –

    The Atoms object after the calculation. Must have a calculator attached.

  • tmpdir (Path | str) –

    The path to the tmpdir, where the calculation will be run. It will be deleted after the calculation is complete.

  • job_results_dir (Path | str) –

    The path to the job_results_dir, where the files will ultimately be stored.

Returns:

  • None –
Source code in quacc/runners/prep.py 
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def calc_cleanup(
    atoms: Atoms | None, tmpdir: Path | str, job_results_dir: Path | str
) -> None:
    """
    Perform cleanup operations for a calculation, including gzipping files, copying
    files back to the original directory, and removing the tmpdir.

    Parameters
    ----------
    atoms
        The Atoms object after the calculation. Must have a calculator
        attached.
    tmpdir
        The path to the tmpdir, where the calculation will be run. It will be
        deleted after the calculation is complete.
    job_results_dir
        The path to the job_results_dir, where the files will ultimately be
        stored.

    Returns
    -------
    None
    """
    job_results_dir, tmpdir = Path(job_results_dir), Path(tmpdir)

    # Safety check
    if "tmp-" not in str(tmpdir):
        msg = f"{tmpdir} does not appear to be a tmpdir... exiting for safety!"
        raise ValueError(msg)

    # Reset the calculator's directory
    if atoms is not None:
        atoms.calc.directory = job_results_dir

    # Gzip files in tmpdir
    if SETTINGS.GZIP_FILES:
        gzip_dir(tmpdir)

    # Move files from tmpdir to job_results_dir
    if SETTINGS.CREATE_UNIQUE_DIR:
        move(tmpdir, job_results_dir)
    else:
        for file_name in os.listdir(tmpdir):
            move(tmpdir / file_name, job_results_dir / file_name)
        rmtree(tmpdir)
    logger.info(f"Calculation results stored at {job_results_dir}")

    # Remove symlink to tmpdir
    if os.name != "nt" and SETTINGS.SCRATCH_DIR:
        symlink_path = SETTINGS.RESULTS_DIR / f"symlink-{tmpdir.name}"
        symlink_path.unlink(missing_ok=True)

calc_setup 

calc_setup(
    atoms: Atoms | None,
    copy_files: (
        SourceDirectory
        | dict[SourceDirectory, Filenames]
        | None
    ) = None,
) -> tuple[Path, Path]

Perform staging operations for a calculation, including copying files to the scratch directory, setting the calculator's directory, decompressing files, and creating a symlink to the scratch directory.

Parameters:

  • atoms (Atoms | None) –

    The Atoms object to run the calculation on. Must have a calculator attached.

  • copy_files (SourceDirectory | dict[SourceDirectory, Filenames] | None, default: None ) –

    Files to copy (and decompress) from source to the runtime directory.

Returns:

  • Path –

    The path to the unique tmpdir, where the calculation will be run. It will be deleted after the calculation is complete. By default, this will be located within the SETTINGS.SCRATCH_DIR, but if that is not set, it will be located within the SETTINGS.RESULTS_DIR. For conenience, a symlink to this directory will be made in the SETTINGS.RESULTS_DIR.

  • Path –

    The path to the results_dir, where the files will ultimately be stored. By defualt, this will be the SETTINGS.RESULTS_DIR, but if SETTINGS.CREATE_UNIQUE_DIR is set, it will be a unique directory within the SETTINGS.RESULTS_DIR.

Source code in quacc/runners/prep.py 
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def calc_setup(
    atoms: Atoms | None,
    copy_files: SourceDirectory | dict[SourceDirectory, Filenames] | None = None,
) -> tuple[Path, Path]:
    """
    Perform staging operations for a calculation, including copying files to the scratch
    directory, setting the calculator's directory, decompressing files, and creating a
    symlink to the scratch directory.

    Parameters
    ----------
    atoms
        The Atoms object to run the calculation on. Must have a calculator
        attached.
    copy_files
        Files to copy (and decompress) from source to the runtime directory.

    Returns
    -------
    Path
        The path to the unique tmpdir, where the calculation will be run. It will be
        deleted after the calculation is complete. By default, this will be
        located within the `SETTINGS.SCRATCH_DIR`, but if that is not set, it will
        be located within the `SETTINGS.RESULTS_DIR`. For conenience, a symlink
        to this directory will be made in the `SETTINGS.RESULTS_DIR`.
    Path
        The path to the results_dir, where the files will ultimately be stored.
        By defualt, this will be the `SETTINGS.RESULTS_DIR`, but if
        `SETTINGS.CREATE_UNIQUE_DIR` is set, it will be a unique directory
        within the `SETTINGS.RESULTS_DIR`.
    """
    # Create a tmpdir for the calculation
    tmpdir_base = SETTINGS.SCRATCH_DIR or SETTINGS.RESULTS_DIR
    tmpdir = make_unique_dir(base_path=tmpdir_base, prefix="tmp-quacc-")
    logger.info(f"Calculation will run at {tmpdir}")

    # Set the calculator's directory
    if atoms is not None:
        atoms.calc.directory = tmpdir

    # Define the results directory
    job_results_dir = SETTINGS.RESULTS_DIR
    if SETTINGS.CREATE_UNIQUE_DIR:
        job_results_dir /= f"{tmpdir.name.split('tmp-')[-1]}"

    # Create a symlink to the tmpdir
    if os.name != "nt" and SETTINGS.SCRATCH_DIR:
        symlink_path = SETTINGS.RESULTS_DIR / f"symlink-{tmpdir.name}"
        symlink_path.symlink_to(tmpdir, target_is_directory=True)

    # Copy files to tmpdir and decompress them if needed
    if copy_files:
        if isinstance(copy_files, (str, Path)):
            copy_files = {copy_files: "*"}

        for source_directory, filenames in copy_files.items():
            if source_directory is not None:
                copy_decompress_files(source_directory, filenames, tmpdir)

    return tmpdir, job_results_dir

terminate 

terminate(
    tmpdir: Path | str, exception: Exception
) -> Exception

Terminate a calculation and move files to a failed directory.

Parameters:

  • tmpdir (Path | str) –

    The path to the tmpdir, where the calculation was run.

  • exception (Exception) –

    The exception that caused the calculation to fail.

Raises:

  • Exception –

    The exception that caused the calculation to fail.

Source code in quacc/runners/prep.py 
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def terminate(tmpdir: Path | str, exception: Exception) -> Exception:
    """
    Terminate a calculation and move files to a failed directory.

    Parameters
    ----------
    tmpdir
        The path to the tmpdir, where the calculation was run.
    exception
        The exception that caused the calculation to fail.

    Raises
    -------
    Exception
        The exception that caused the calculation to fail.
    """
    job_failed_dir = tmpdir.with_name(tmpdir.name.replace("tmp-", "failed-"))
    tmpdir.rename(job_failed_dir)

    msg = f"Calculation failed! Files stored at {job_failed_dir}"
    logging.info(msg)

    if os.name != "nt" and SETTINGS.SCRATCH_DIR:
        old_symlink_path = SETTINGS.RESULTS_DIR / f"symlink-{tmpdir.name}"
        symlink_path = SETTINGS.RESULTS_DIR / f"symlink-{job_failed_dir.name}"
        old_symlink_path.unlink(missing_ok=True)
        symlink_path.symlink_to(job_failed_dir, target_is_directory=True)

    raise exception