molecule.plot_transition_density#

molecule.plot_transition_density(grid_points=(80, 80, 80), delta=5, opacity=0.8, factor=1, with_radius=True, opacity_radius=1, factor_radius=.3, cutoff=.2, screenshot_button=True, window_size_screenshot=(1000, 1000))#

Plot the Transition Densities of a molecule. All the AOs and the MOs will be calculated on the grid if they were not calculated. Because no calculations are truly done, the electron density will be calculated on the representative grid. The representative grid is a cubic grid around the molecule. The delta defines the length to be added to the extremities of the position of the atoms. The order of the Atomic Orbitals is defined in the molden file

Parameters:

  • 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

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

  • 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 – The initial cutoff of the isodensity plot. 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)

Returns:

None – The plotter should display when using this function

Notes

The transition densities are defined as :

\(\rho_0^k = \sum_i c_i (Occ_i(r) * Virt_i(r))\)
With the sum being on all the transitions of the excitation, \(Occ_i(r)\) and \(Virt_i(r)\) being respectively the occupied and the virtual molecular orbitals considered in the transition, and \(c_i\) the coefficient of the transition.

Examples

For a TD-DFT calculation output :

STATE 1: E= 0.148431 au 4.039 eV
18a -> 20a : 0.5000 (c= 0.7071)
19a -> 21a : 0.5000 (c= -0.7071)
The transition density will be :
\(\rho_0^1 = c_1 (\psi_{18}(r) * \psi_{20}(r)) + c_2 (\psi_{19}(r) * \psi_{21}(r))\)
with \(c_1 = 0.7071\) and \(c_2 = -0.7071\)