sisl.io.orca.txtSileORCA

class sisl.io.orca.txtSileORCA

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=['x', 'y', 'z'], atoms=None, atoms_style=[], atoms_scale=1.0, atoms_colorscale=None, drawing_mode=None, bind_bonds_to_ats=True, points_per_bond=20, bonds_style={}, bonds_scale=1.0, bonds_colorscale=None, show_atoms=True, show_bonds=True, show_cell='box', cell_style={}, nsc=(1, 1, 1), atoms_ndim_scale=(16, 16, 1), bonds_ndim_scale=(1, 1, 10), dataaxis_1d=None, arrows=(), backend='plotly')

Calls read_geometry and creates a GeometryPlot from its output.

Parameters:

axes (Axes) – The axes to project the geometry to.
atoms (AtomsIndex) – The atoms to plot. If None, all atoms are plotted.
atoms_style (Sequence[AtomsStyleSpec]) – List of style specifications for the atoms. See the showcase notebooks for examples.
atoms_scale (float) – Scaling factor for the size of all atoms.
atoms_colorscale (Optional[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 (Literal['scatter', 'balls', None]) – The method used to draw the atoms.
bind_bonds_to_ats (bool) – Whether to display only bonds between atoms that are being displayed.
points_per_bond (int) – 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 (StyleSpec) – Style specification for the bonds. See the showcase notebooks for examples.
bonds_scale (float) – Scaling factor for the width of all bonds.
bonds_colorscale (Optional[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 (bool) – Whether to display the atoms.
show_bonds (bool) – Whether to display the bonds.
show_cell (Literal['box', 'axes', False]) – Mode to display the cell. If False, the cell is not displayed.
cell_style (StyleSpec) – Style specification for the cell. See the showcase notebooks for examples.
nsc (tuple[int, int, int]) – Number of unit cells to display in each direction.
atoms_ndim_scale (tuple[float, float, float]) – Scaling factor for the size of the atoms for different dimensionalities (1D, 2D, 3D).
bonds_ndim_scale (tuple[float, float, float]) – Scaling factor for the width of the bonds for different dimensionalities (1D, 2D, 3D).
dataaxis_1d (Optional[Union[np.ndarray, Callable]]) – Only meaningful for 1D plots. The data to plot on the Y axis.
arrows (Sequence[AtomArrowSpec]) – List of arrow specifications to display. See the showcase notebooks for examples.
backend – The backend to use to generate the figure.

Return type:

GeometryPlot

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()[source]

Read number of electrons (alpha, beta)

Returns:: out – alpha and beta electrons
Return type:: numpy.ndarray or list of numpy.ndarray

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='eV')[source]

Reads the energy blocks

Parameters:: units (str | Mapping[str, str] | Sequence[str]) – selects units in the returned data
Return type:: PropertyDict

Notes

Energies written by ORCA have units of Ha.

Returns:: all data from the “DFT_Energy” and “VdW_Correction” blocks
Return type:: PropertyDict or list of PropertyDict
Parameters:: units (str | Mapping[str, str] | Sequence[str])

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()[source]

Reads the geometry from ORCA property.txt file

Returns:: the geometries contained
Return type:: Geometry or list of Geometry

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()[source]

Reads electronic g-tensor data from the EPRNMR_GTensor block

Returns:: Electronic g-tensor
Return type:: PropertyDict

read_hyperfine_coupling(units='eV')[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 (str | Mapping[str, str] | Sequence[str]) – selects units in the returned data
Return type:: list[PropertyDict]

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:: Hyperfine coupling data
Return type:: list of PropertyDict
Parameters:: units (str | Mapping[str, str] | Sequence[str])

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.