plot_density_slices

This module plots slices of the density of the orbitals of the kohn sham calculation and of the density after density fitting.

Manual of the interactive plots:

  • m : change plotting mode between different metrics

  • n : toggle between comparing different metrics and different basis sets

  • b : toggle contour lines

  • Arrow keys : move the view on the x-y axis

  • x/y : move the view along the z axis

  • c/v : decrease/increase the colour range of the plots

  • k/l : zoom out/in

  • ä/ö : change the basis set on which the df options are compare. (Or vice versa)

  • w/e : rotate around x-axis

  • r/t : rotate around z-axis

  • z/u : rotate around y-axis

  • o/i : decrease/increase the resolution of the plots by a factor of 2

  • p/ü : change the orbit which is shown in the kohn_sham plot (0 shows the total density)

  • d/g : change index of atom which is being shown

  • h/j : increase/decrease the shown scf iteration

  • ,/. : show different density basis functions

  • 0,1 : Show different l basis functions

  • 8 : toggle different initial guesses to subtract from the plot

  • 9 : toggle different annotation methods to display the position of the nuclei

  • q : quit

  • s : save image

  • f : toggle fullscreen

_save_additional_data_callback(envs: dict) → None[source]

Save the data of each iteration in the chkfile. Modified version to provide additional data for tests.

Parameters:

envs – Dictionary with the local environment variables of the iteration.

Returns:

None

rotate_molecule2_onto_plane(mol_ks: Mole) → Tuple[ndarray, ndarray][source]

Rotate a molecule onto the plane of most symmetry by just rotating the 3 heaviest atoms into a plane.

Parameters:

mol_ks (gto.Mole) – the molecule we want to rotate

Returns:

offset (np.ndarray) The offset of the center of the molecule to the origin rotation matrix (np.ndarray) Rotation matrix to rotate the molecules symmetry axis onto the x-y plane

rotate_molecule_pca(mol_ks: Mole) → Tuple[ndarray, ndarray][source]

Rotate a molecule onto the plane of most symmetry using PCA.

Parameters:

mol_ks (gto.Mole) – the molecule we want to rotate

Returns:

offset (np.ndarray) The offset of the center of the molecule to the origin rotation matrix (np.ndarray) Rotation matrix to rotate the molecules symmetry axis onto the x-y plane