Data

Data objects contains the structured calculation data. When contained in a ProgramOutput, the concrete type depends on the requested CalcType.

qcdata.Data module-attribute

Data = Union[Files, StructuredData]

qcdata.SinglePointData

The computed data from a single point calculation.

Attributes:

Name	Type	Description
energy	float | None	The electronic energy of the structure in Hartrees.
gradient	SerializableNDArray | None	The gradient of the structure in Hartrees/Bohr.
hessian	SerializableNDArray | None	The hessian of the structure in Hartrees/Bohr^2.
nuclear_repulsion_energy	float | None	The nuclear repulsion energy of the structure in Hartrees.
wavefunction	Wavefunction | None	Wavefunction data from the calculation.
freqs_wavenumber	list[float]	The frequencies of the structure in wavenumbers.
normal_modes_cartesian	SerializableNDArray | None	3D n_vibmodes x n_atoms x 3 array containing un-mass-weighted Cartesian displacements of each normal mode in Bohr.
gibbs_free_energy	float | None	Gibbs free energy (i.e. thermochemical analysis) in Hartrees of a system where translation / rotation / vibration degrees of freedom are approximated using ideal gas / rigid rotor / harmonic oscillator respectively.
scf_dipole_moment	list[float] | None	The x, y, z component of the dipole moment of the structure in units of e a0 (NOT Debye!).

return_result

return_result(
    calctype: CalcType,
) -> float | SerializableNDArray

Return the primary result of the calculation.

Source code in src/qcdata/models/data.py

def return_result(self, calctype: CalcType) -> float | SerializableNDArray:
    """Return the primary result of the calculation."""
    return getattr(self, calctype.value)

options: members: false

qcdata.OptimizationData

Computed data for an optimization (may be for a minimum or transition state).

Attributes:

Name	Type	Description
energies	ndarray	The energies for each step of the optimization.
structures	list[Structure]	The Structure objects for each step of the optimization.
final_structure	Structure	The final, optimized Structure.
trajectory	list['ProgramOutput[ProgramInput, SinglePointData] | ProgramOutput[ProgramInput, Files]']	The ProgramOutput objects for each step of the optimization.

energies property

energies: ndarray

The energies for each step of the optimization.

final_energy property

final_energy: float | None

The final energy in the optimization. Is np.nan if final calculation failed.

final_structure property

final_structure: Structure

The final Structure in the optimization.

structures property

structures: list[Structure]

The Structure objects for each step of the optimization.

save

save(
    filepath: Path | str,
    exclude_none: bool = True,
    exclude_unset: bool = True,
    indent: int = 4,
    **kwargs: dict[str, Any],
) -> None

Save an OptimizationOutput to a file.

Parameters:

Name	Type	Description	Default
filepath	Path | str	The path to save the molecule to.	required
exclude_none	bool	If True, attributes with a value of None will not be written to the file.	True
exclude_unset	bool	If True, attributes that have not been set will not be written to the file.	True
**kwargs	dict[str, Any]	Additional keyword arguments to pass to the json serializer.	{}

Note

If the filepath has a .xyz extension, the trajectory will be saved to a multi-structure xyz file.

Source code in src/qcdata/models/data.py

def save(
    self,
    filepath: Path | str,
    exclude_none: bool = True,
    exclude_unset: bool = True,
    indent: int = 4,
    **kwargs: dict[str, Any],
) -> None:
    """Save an OptimizationOutput to a file.

    Args:
        filepath: The path to save the molecule to.
        exclude_none: If True, attributes with a value of None will not be written
            to the file.
        exclude_unset: If True, attributes that have not been set will not be
            written to the file.
        **kwargs: Additional keyword arguments to pass to the json serializer.

    Note:
        If the filepath has a `.xyz` extension, the trajectory will be saved to a
        multi-structure `xyz` file.
    """
    filepath = Path(filepath)
    if filepath.suffix == ".xyz":
        filepath.write_text(self.to_xyz())
        return
    super().save(filepath, exclude_none, exclude_unset, indent, **kwargs)

to_xyz

to_xyz() -> str

Return the trajectory as an xyz string.

Source code in src/qcdata/models/data.py

def to_xyz(self) -> str:
    """Return the trajectory as an `xyz` string."""
    return to_multi_xyz(
        prog_output.input_data.structure for prog_output in self.trajectory
    )

options: members: - structures - final_structure - energies - final_energy - to_xyz - save

qcdata.ConformerSearchData

Data from a conformer search calculation.

Conformers and rotamers are sorted by energy.

Attributes:

Name	Type	Description
conformers	list[Structure]	The conformers found in the search.
conformer_energies	SerializableNDArray	The energies for each conformer.
rotamers	list[Structure]	The rotamers found in the search.
rotamer_energies	SerializableNDArray	The energies for each rotamer.

conformer_energies_relative property

conformer_energies_relative: ndarray

The relative energies for each conformer in the search.

rotamer_energies_relative property

rotamer_energies_relative: ndarray

The relative energies for each rotamer in the search.

conformers_filtered

conformers_filtered(
    threshold: float = 1.0, **rmsd_kwargs
) -> tuple[list[Structure], SerializableNDArray]

Moved since qcdata 0.15.0

This convenience method has moved to [qcinf.filter_conformers][] and this stub will be removed from qcdata in a future release.

from qcinf import filter_conformers

filtered_csr = filter_conformers(
    conformers=csr
    threshold=1.0,          # Bohr
    backend="qcinf",      # or "rdkit",
    **rmsd_kwargs,
)

Source code in src/qcdata/models/data.py

def conformers_filtered(
    self,
    threshold: float = 1.0,
    **rmsd_kwargs,
) -> tuple[list[Structure], SerializableNDArray]:
    """
    !!! warning "Moved since *qcdata* 0.15.0"
        This convenience method has moved to
        [`qcinf.filter_conformers`][qcinf.filter_conformers]
        and this stub will be **removed** from *qcdata* in a future release.

        ```python
        from qcinf import filter_conformers

        filtered_csr = filter_conformers(
            conformers=csr
            threshold=1.0,          # Bohr
            backend="qcinf",      # or "rdkit",
            **rmsd_kwargs,
        )
        ```
    """
    warnings.warn(
        "`ConformerSearchResults.conformers_filtered()` is deprecated. "
        "Install *qcinf* and use `qcinf.filter_conformers` instead.",
        DeprecationWarning,
        stacklevel=2,
    )
    raise NotImplementedError(
        "Method removed.  Replace with:\n\n"
        "    from qcinf import filter_conformers\n\n"
        "    filtered_csr = filter_conformers(\n"
        "        prog_output.results,\n"
        "        threshold=1.0,\n"
        "        backend='qcinf',\n"
        "        **rmsd_kwargs\n"
        "    )"
    )

qcdata.Wavefunction

The wavefunction for a single point calculation.

Attributes:

Name	Type	Description
scf_eigenvalues_a	SerializableNDArray | None	The SCF alpha-spin orbital eigenvalues.
scf_eigenvalues_b	SerializableNDArray | None	The SCF beta-spin orbital eigenvalues.
scf_occupations_a	SerializableNDArray | None	The SCF alpha-spin orbital occupations.
scf_occupations_b	SerializableNDArray | None	The SCF beta-spin orbital occupations.