molecule.plot_diagonalized_kernel#

molecule.plot_diagonalized_kernel(kernel, mol_p=None, mol_m=None, fukui_type='0', number_plotted_eigenvectors=100, try_reading=True, save=True, plotting_method='isodensity', number_isodensities=10, opacity=0.8, factor=1, with_radius=True, opacity_radius=1, factor_radius=.3, cutoff=.2, screenshot_button=True, window_size_screenshot=(1000, 1000), grid_points=(80, 80, 80), delta=5)#

Calculate and diagonalize a kernel. The available kernels are : “linear_response_function” and “softness_kernel” Only the eigenmodes are computed using a method that does not calculate the whole kernel. All the computations will be done on the atomic grids.

The eigenmodes will also be computed on the atomic grids. One might consider using plot_on_atomic_grid for visualization

By default the eigenmodes will also be plotted on the representative grid using the calculations on the atomic grids. If one wants not to do the plot, putting number_plotted_eigenvectors to 0 will not produce any plot.

For the softness kernel as it is calculated using the Parr-Berkowitz relation, the fukui functions need to be computed. For that, a calculation adding (mol_p) or removing an electron (mol_m) needs to be done with the same geometry.

Parameters:

  • kernel (str) – The kernel to be diagonalized and plotted

  • mol_p (molecule, optional) – The molecule with an electron added. Needed for calculating the softness kernel with a fukui_type of “0” or “+”

  • mol_m (molecule, optional) – The molecule with an electron removed. Needed for calculating the softness kernel with a fukui_type of “0” or “-”

  • fukui_type (molecule, optional) – The type of fukui function used to calculate the softness kernel. The available types are “0”, “+” or “-”

  • number_plotted_eigenvectors (int, optional) – The Number of eigenvectors to be plotted. If 0, no plot will be produced. By default 100

  • try_reading (bool, optional) – If the eigenmodes were calculated and saved before, try reading them from the rgmol folder. If False, the computation will be remade. True by default

  • save (bool, optional) – The eigenmodes, eigenvalues and contributions of transition densities will be save in the folder rgmol that will be created where the molecule file is located

  • opacity (float, optional) – The opacity of the plot. By default .5

  • factor (float, optional) – The factor by which the plotted_property will be multiplied. By default 1

  • with_radius (bool, optional) – Chose to show the radius and the bonds between the atoms or not. By default True

  • opacity_radius (float, optional) – The opacity of the radius plot. By default .8

  • factor_radius (float, optional) – The factor by which the radius will be multiplied. By default .3

  • cutoff (float, optional) – The initial cutoff of the isodensity plot for the isodensity plotting method. By default .2

  • screenshot_button (bool, optional) – Adds a screenshot button. True by default

  • window_size_screenshot (tuple, optional) – The size of the screenshots. By default (1000,1000)

  • grid_points (list of 3, optional) – The number of points for the representative grid in each dimension. By default (80,80,80)

  • delta (float, optional) – The length added in all directions for the construction of the representative grid. By default 5

Returns:

None – The plotter should display when using this function and all the properties will be sorted inside the molecule.properties