visualize_3d

_eval_density(coords: ndarray, mol: Mole, dm: ndarray) → ndarray

Evaluate the electron density at the given coordinates.

Parameters:

• coords – The coordinates to evaluate the density at, shape (n, 3).

• mol – The molecule.

• dm – The density matrix.

Returns:

The electron density at the given coordinates, shape (n).

_eval_orbital(coords: ndarray, mol: Mole, coeff: ndarray) → ndarray

Evaluate an orbital at the given coordinates.

Parameters:

• coords – The coordinates to evaluate the orbital at, shape (n, 3).

• mol – The molecule.

Returns:

The orbital at the given coordinates, shape (n).

_fix_cube_data(cube_data: str) → str

Fix a cube file string produced by pyscf. Undoes a pyscf bug by adding spaces where needed: e.g. replace incorrect lines like “-2.52899E-114-1.81539E-116-9.75640E-119-3.92559E-121-1.18255E-123-2.66702E-126” with “-2.52899E-114 -1.81539E-116 -9.75640E-119 -3.92559E-121 -1.18255E-123 -2.66702E-126”.

Parameters:

cube_data – The cube data to fix.

Returns:

The fixed cube data.

find_isosurface_value(cube_array: ndarray, quantile: float | ndarray = 0.9, p: int = 2) → float | ndarray

Find an isosurface value for a cube array, such that the isosurface contains a given fraction of the total mass. The mass is computed as the sum of the absolute values of the cube array raised to the power p.

Parameters:

• cube_array – The cube array.

• quantile – The fraction (or array of fractions) of the total mass to be contained in the isosurface.

• p – The power to raise the cube array to. Use p=1 for electron density and p=2 for orbitals.

Returns:

The isosurface value.

get_local_frames_mesh_dict(origins: ndarray, bases: ndarray, scale: float = 1, axes_radius_scale: float = 0.03, cone_scale: float = 2.0, cone_aspect_ratio: float = 2, resolution: int = 20) → dict

Create a mesh dict for a set of local frames, given by their origin and basis vectors.

Parameters:

• origins – The origins of the local frames, shape (n, 3).

• bases – The basis vectors of the local frames, shape (n, 3=n_vectors, 3=n_axes).

• scale – The scale of the local frames.

• axes_radius_scale – The radius of the cylinders representing the axes.

• cone_scale – The scale of the cones representing the axes.

• cone_aspect_ratio – The aspect ratio of the cones representing the axes.

• resolution – The resolution of the cylinders and cones.

Returns:

A dictionary with keyword arguments to pass to pyvista.Plotter.add_mesh().

get_sticks_mesh_dict(mol: Mole, bond_radius: float = 0.2, atom_radius: float = None, resolution=20) → dict

Create a ‘sticks’ representation for a pyscf molecule. By choosing a larger atom_radius, one can make this look like balls-and-sticks.

Parameters:

• mol – The molecule.

• bond_radius – The radius of the cylinders representing the bonds.

• atom_radius – The radius of the spheres representing the atoms. If None, use bond_radius.

• resolution – The resolution of the cylinders and spheres.

Returns:

A dictionary with keyword arguments to pass to pyvista.Plotter.add_mesh.

plot_density(cube: DataCube = None, mode: str = 'auto', plot_molecule: bool = True, isosurface_quantile: float = None, isosurface_opacity: float = 0.4, plotter: Plotter = None, figsize: tuple[int, int] = None, title: str = None, cmap: str = None)

Plot an electron density using pyvista. By default, the orbital is plotted as a volume.

Parameters:

• cube – The DataCube.

• mode – The mode to use for plotting. Must be one of ‘volume’, ‘isosurface’, ‘nested_isosurfaces’.

• plot_molecule – Whether to plot the molecule.

• isosurface_quantile – For mode ‘isosurface’, the quantile of the total mass to be contained in the isosurface. Defaults to 0.9.

• isosurface_opacity – For mode ‘isosurface’, the opacity of the isosurface.

• plotter – A pyvista plotter to use. If None, a new plotter is created.

• figsize – The figure size in inches.

• title – The title of the plot.

• cmap – The colormap to use.

Returns:

The pyvista plotter.

plot_molecule(mol: Mole, plotter: Plotter = None, figsize: tuple[int, int] = None, title: str = None) → Plotter

Plot molecule.

Parameters:

• mol – The pyscf molecule.

• plotter – A pyvista plotter to use. If None, a new plotter is created.

• figsize – The figure size in inches.

• title – The title of the plot.

Returns:

The pyvista plotter.

plot_orbital(cube: DataCube, mode: str = 'auto', plot_molecule: bool = True, isosurface_quantile: float = None, plotter: Plotter = None, figsize: tuple[int, int] = None, title: str = None) → Plotter

Plot an electron orbital using pyvista. By default, the orbital is plotted as a volume.

Parameters:

• cube – The DataCube.

• mode – The mode to use for plotting. Must be one of ‘volume’, ‘isosurface’, ‘nested_isosurfaces’.

• plot_molecule – Whether to plot the molecule.

• isosurface_quantile – The quantile of the total mass to be contained in the isosurface, for mode ‘isosurface’. Defaults to 0.9.

• plotter – A pyvista plotter to use. If None, a new plotter is created.

• figsize – The figure size in inches.

• title – The title of the plot.

Returns:

The pyvista plotter.

visualize_density(mol: Mole, density_matrix: ndarray, resolution: float = 0.3, margin: float = 3.0, **plot_density_kwargs)

Visualize the electron density with the corresponding molecule.

Parameters:

• mol – The molecule.

• density_matrix – The density matrix in the atomic orbital basis.

• resolution – The resolution of the cube file.

• margin – The margin of the cube file.

• plot_density_kwargs – Keyword arguments to pass to plot_density.

Returns:

The pyvista plotter.

visualize_orbital(mol: Mole, coeff: ndarray, resolution: float = 0.3, margin: float = 3.0, **plot_orbital_kwargs)

Visualize an orbital together with the molecule it belongs to.

Parameters:

• mol – The molecule.

• coeff – The orbital coefficients.

• resolution – The resolution of the cube file.

• margin – The margin of the cube file.

• plot_orbital_kwargs – Keyword arguments to pass to plot_orbital.

Returns:

The pyvista plotter.