sisl.io.orca.txtSileORCA

class sisl.io.orca.txtSileORCA(filename, *args, **kwargs)

Bases: SileORCA

Output from the ORCA property.txt file

Plotting

plot

Plotting functions for the txtSileORCA class.

plot.geometry(*[, axes, atoms, ...])

Calls read_geometry and creates a GeometryPlot from its output.

Methods

base_directory([relative_to])

Retrieve the base directory of the file, relative to the path relative_to

close()

dir_file([filename, filename_base])

File of the current Sile

read(*args, **kwargs)

Generic read method which should be overloaded in child-classes

read_electrons()

Read number of electrons (alpha, beta)

read_energy([units])

Reads the energy blocks

read_geometry()

Reads the geometry from ORCA property.txt file

read_gtensor()

Reads electronic g-tensor data from the EPRNMR_GTensor block

read_hyperfine_coupling([units])

Reads hyperfine couplings from the EPRNMR_ATensor block

write(*args, **kwargs)

Generic write method which should be overloaded in child-classes

Attributes

base_file

File of the current Sile

file

File of the current Sile

na

Number of atoms

no

Number of orbitals (basis functions)
base_directory(relative_to='.')

Retrieve the base directory of the file, relative to the path relative_to

close()
dir_file(filename=None, filename_base='')

File of the current Sile

plot.geometry(*, axes: Axes = ['x', 'y', 'z'], atoms: AtomsIndex = None, atoms_style: Sequence[AtomsStyleSpec] = [], atoms_scale: float = 1.0, atoms_colorscale: Colorscale | None = None, drawing_mode: Literal['scatter', 'balls', None] = None, bind_bonds_to_ats: bool = True, points_per_bond: int = 20, bonds_style: StyleSpec = {}, bonds_scale: float = 1.0, bonds_colorscale: Colorscale | None = None, show_atoms: bool = True, show_bonds: bool = True, show_cell: Literal['box', 'axes', False] = 'box', cell_style: StyleSpec = {}, nsc: tuple[int, int, int] = (1, 1, 1), atoms_ndim_scale: tuple[float, float, float] = (16, 16, 1), bonds_ndim_scale: tuple[float, float, float] = (1, 1, 10), dataaxis_1d: np.ndarray | Callable | None = None, arrows: Sequence[AtomArrowSpec] = (), backend='plotly') → GeometryPlot

Calls read_geometry and creates a GeometryPlot from its output.

Parameters:

  • axes – The axes to project the geometry to.

  • atoms – The atoms to plot. If None, all atoms are plotted.

  • atoms_style – List of style specifications for the atoms. See the showcase notebooks for examples.

  • atoms_scale – Scaling factor for the size of all atoms.

  • atoms_colorscale – Colorscale to use for the atoms in case the color attribute is an array of values. If None, the default colorscale is used for each backend.

  • drawing_mode – The method used to draw the atoms.

  • bind_bonds_to_ats – Whether to display only bonds between atoms that are being displayed.

  • points_per_bond – When the points are drawn using points instead of lines (e.g. in some frameworks to draw multicolor bonds), the number of points used per bond.

  • bonds_style – Style specification for the bonds. See the showcase notebooks for examples.

  • bonds_scale – Scaling factor for the width of all bonds.

  • bonds_colorscale – Colorscale to use for the bonds in case the color attribute is an array of values. If None, the default colorscale is used for each backend.

  • show_atoms – Whether to display the atoms.

  • show_bonds – Whether to display the bonds.

  • show_cell – Mode to display the cell. If False, the cell is not displayed.

  • cell_style – Style specification for the cell. See the showcase notebooks for examples.

  • nsc – Number of unit cells to display in each direction.

  • atoms_ndim_scale – Scaling factor for the size of the atoms for different dimensionalities (1D, 2D, 3D).

  • bonds_ndim_scale – Scaling factor for the width of the bonds for different dimensionalities (1D, 2D, 3D).

  • dataaxis_1d – Only meaningful for 1D plots. The data to plot on the Y axis.

  • arrows – List of arrow specifications to display. See the showcase notebooks for examples.

  • backend – The backend to use to generate the figure.

See also

GeometryPlot

The plot class used to generate the plot.

read_geometry

The method called to get the data.

read(*args, **kwargs)

Generic read method which should be overloaded in child-classes

Parameters:

kwargs – keyword arguments will try and search for the attribute read_<> and call it with the remaining **kwargs as arguments.

read_electrons() → tuple[float, float] | None[source]

Read number of electrons (alpha, beta)

Returns:

out (numpy.ndarray or list of numpy.ndarray) – alpha and beta electrons

Notes

This method defaults to return the first item(s).

This method enables slicing for handling multiple values (see [...|default]).

This is an optional handler enabling returning multiple elements if read_electrons[...|0] allows this.

>>> single = obj.read_electrons() # returns the default entry of read_electrons[...|0]

To retrieve the first two elements that read_electrons will return

>>> first_two = obj.read_electrons[:2]()

Retrieving the last two is done equivalently:

>>> last_two = obj.read_electrons[-2:]()

While one can store the sliced function tmp = obj.read_electrons[:] one will loose the slice after each call.

read_energy(units: sisl.typing.UnitsVar = 'eV') → PropertyDict[source]

Reads the energy blocks

Parameters:

units – selects units in the returned data

Notes

Energies written by ORCA have units of Ha.

Returns:

PropertyDict or list of PropertyDict – all data from the “DFT_Energy” and “VdW_Correction” blocks

Notes

This method defaults to return the first item(s).

This method enables slicing for handling multiple values (see [...|default]).

This is an optional handler enabling returning multiple elements if read_energy[...|0] allows this.

>>> single = obj.read_energy() # returns the default entry of read_energy[...|0]

To retrieve the first two elements that read_energy will return

>>> first_two = obj.read_energy[:2]()

Retrieving the last two is done equivalently:

>>> last_two = obj.read_energy[-2:]()

While one can store the sliced function tmp = obj.read_energy[:] one will loose the slice after each call.

read_geometry() → Geometry[source]

Reads the geometry from ORCA property.txt file

Returns:

Geometry or list of Geometry – the geometries contained

Notes

This method defaults to return the first item(s).

This method enables slicing for handling multiple values (see [...|default]).

This is an optional handler enabling returning multiple elements if read_geometry[...|0] allows this.

>>> single = obj.read_geometry() # returns the default entry of read_geometry[...|0]

To retrieve the first two elements that read_geometry will return

>>> first_two = obj.read_geometry[:2]()

Retrieving the last two is done equivalently:

>>> last_two = obj.read_geometry[-2:]()

While one can store the sliced function tmp = obj.read_geometry[:] one will loose the slice after each call.

read_gtensor() → PropertyDict[source]

Reads electronic g-tensor data from the EPRNMR_GTensor block

Returns:

PropertyDict – Electronic g-tensor

read_hyperfine_coupling(units: sisl.typing.UnitsVar = 'eV') → list[PropertyDict][source]

Reads hyperfine couplings from the EPRNMR_ATensor block

For a nucleus \(k\), the hyperfine interaction is usually written in terms of the symmetric \(3\times 3\) hyperfine tensor \(\mathbf A^{(k)}\) such that

\[H_{\mathrm{hfi}} = \mathbf{S} \cdot \mathbf A^{(k)} \mathbf{I}^{(k)}\]

where \(\mathbf{S}\) and \(\mathbf{I}^{(k)}\) represent the electron and nuclear spin operators, respectively.

For a study of hyperfine coupling in nanographenes using ORCA see [12].

Parameters:

units – selects units in the returned data

Notes

Hyperfine tensors written by ORCA have units of MHz.

Currently the fields of each PropertyDict contains:

  • ia: atomic index

  • species: species for atom

  • isotope: the atomic isotope

  • spin: spin multiplicity

  • prefactor: prefactor defined in output

  • tensor: the \(\mathbf A^{(k)}\) tensor

  • vectors: eigenvectors

  • eigenvalues: eigenvalues

  • iso: Fermi contact

Returns:

list of PropertyDict – Hyperfine coupling data

write(*args, **kwargs)

Generic write method which should be overloaded in child-classes

Parameters:

**kwargs – keyword arguments will try and search for the attribute write_ and call it with the remaining **kwargs as arguments.

property base_file

File of the current Sile

property file

File of the current Sile

property na

Number of atoms

property no

Number of orbitals (basis functions)

plot

Plotting functions for the txtSileORCA class.