Skip to content

qchem_custodian

Custodian handlers for QChem.

has_ob module-attribute 

has_ob = bool(find_spec('openbabel'))

run_custodian 

run_custodian(
    qchem_cmd: str | DefaultSetting = QuaccDefault,
    qchem_cores: int | DefaultSetting = QuaccDefault,
    qchem_local_scratch: (
        str | Path | DefaultSetting
    ) = QuaccDefault,
    qchem_use_error_handlers: (
        bool | DefaultSetting
    ) = QuaccDefault,
    qchem_custodian_max_errors: (
        int | DefaultSetting
    ) = QuaccDefault,
    qchem_nbo_exe: (
        str | Path | DefaultSetting
    ) = QuaccDefault,
    directory: str | Path | None = None,
) -> list[list[dict]]

Function to run QChem Custodian.

Parameters:

  • qchem_cmd (str | DefaultSetting, default: QuaccDefault ) –

    Q-Chem command. Defaults to "qchem" in settings.

  • qchem_cores (int | DefaultSetting, default: QuaccDefault ) –

    Number of cores to use for the Q-Chem calculation.

  • qchem_local_scratch (str | Path | DefaultSetting, default: QuaccDefault ) –

    Compute-node local scratch directory in which Q-Chem should perform IO. Defaults to /tmp in settings.

  • qchem_use_error_handlers (bool | DefaultSetting, default: QuaccDefault ) –

    Whether or not to employ error handlers. Defaults to True in settings.

  • qchem_custodian_max_errors (int | DefaultSetting, default: QuaccDefault ) –

    Maximum number of errors to allow before stopping the run. Defaults to 5 in settings.

  • qchem_nbo_exe (str | Path | DefaultSetting, default: QuaccDefault ) –

    The full path to the NBO executable.

  • directory (str | Path | None, default: None ) –

    The runtime directory.

Returns:

Source code in quacc/calculators/qchem/qchem_custodian.py 
 21
 22
 23
 24
 25
 26
 27
 28
 29
 30
 31
 32
 33
 34
 35
 36
 37
 38
 39
 40
 41
 42
 43
 44
 45
 46
 47
 48
 49
 50
 51
 52
 53
 54
 55
 56
 57
 58
 59
 60
 61
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
@requires(
    has_ob, "Openbabel must be installed. Try conda install -c conda-forge openbabel"
)
def run_custodian(
    qchem_cmd: str | DefaultSetting = QuaccDefault,
    qchem_cores: int | DefaultSetting = QuaccDefault,
    qchem_local_scratch: str | Path | DefaultSetting = QuaccDefault,
    qchem_use_error_handlers: bool | DefaultSetting = QuaccDefault,
    qchem_custodian_max_errors: int | DefaultSetting = QuaccDefault,
    qchem_nbo_exe: str | Path | DefaultSetting = QuaccDefault,
    directory: str | Path | None = None,
) -> list[list[dict]]:
    """
    Function to run QChem Custodian.

    Parameters
    ----------
    qchem_cmd
        Q-Chem command. Defaults to "qchem" in settings.
    qchem_cores
        Number of cores to use for the Q-Chem calculation.
    qchem_local_scratch
        Compute-node local scratch directory in which Q-Chem should perform IO.
        Defaults to /tmp in settings.
    qchem_use_error_handlers
        Whether or not to employ error handlers. Defaults to True in settings.
    qchem_custodian_max_errors
        Maximum number of errors to allow before stopping the run. Defaults to 5
        in settings.
    qchem_nbo_exe
        The full path to the NBO executable.
    directory
        The runtime directory.

    Returns
    -------
    list[list[dict]]
        Lists of lists of errors.
    """
    # Adapted from atomate.qchem.firetasks.run_calc
    from custodian.custodian import Custodian
    from custodian.qchem.handlers import QChemErrorHandler
    from custodian.qchem.jobs import QCJob

    settings = get_settings()

    # Set defaults
    qchem_cores = (
        settings.QCHEM_NUM_CORES if qchem_cores == QuaccDefault else qchem_cores
    )
    qchem_cmd = settings.QCHEM_CMD if qchem_cmd == QuaccDefault else qchem_cmd
    qchem_local_scratch = (
        settings.QCHEM_LOCAL_SCRATCH
        if qchem_local_scratch == QuaccDefault
        else qchem_local_scratch
    )
    qchem_use_error_handlers = (
        settings.QCHEM_USE_ERROR_HANDLERS
        if qchem_use_error_handlers == QuaccDefault
        else qchem_use_error_handlers
    )
    qchem_custodian_max_errors = (
        settings.QCHEM_CUSTODIAN_MAX_ERRORS
        if qchem_custodian_max_errors == QuaccDefault
        else qchem_custodian_max_errors
    )
    qchem_nbo_exe = (
        settings.QCHEM_NBO_EXE if qchem_nbo_exe == QuaccDefault else qchem_nbo_exe
    )

    # Error handlers for Q-Chem
    handlers = [QChemErrorHandler()] if qchem_use_error_handlers else []

    # Run Q-Chem
    jobs = [
        QCJob(
            qchem_command=qchem_cmd,
            max_cores=qchem_cores,
            calc_loc=str(qchem_local_scratch),
            nboexe=str(qchem_nbo_exe),
        )
    ]

    c = Custodian(
        handlers,
        jobs,
        max_errors=qchem_custodian_max_errors,
        terminate_on_nonzero_returncode=False,
        directory=directory,
    )

    return c.run()