sith.energy_analysis package

Submodules

class sith.energy_analysis.jedi_analysis.JediAnalysis(structures_info)[source]

Bases: object

Object that executes JEDI analysis. For details about JEDI: T. Stauch and A. Dreuw (2016), Chem. Rev. 116

Parameters:

structures_info (sith.SITH) – object containing the necessary information for the energy analysis.

get_jedi_dq() → ndarray[source]

Populates delta_q taking the changes respect to the reference structure.

Returns:

  • (np.array) change in each degree of freedom respect to the reference

  • structure.

jedi_analysis()[source]

Performs the JEDI energy analysis, populates energies, and energies_percentage.

Returns:

  • (tuple) array of energies per structure per dof [#structures, #dofs],

  • array with predicted energy per structure [#structures].

Notes

Consists of the dot multiplication of the structure vectors and the Hessian matrix (analytical gradient of the harmonic potential energy surface) to produce both the total calculated change in energy between the reference structure and each structure (SITH.structure_energy) as well as the subdivision of that energy into each DOF (SITH.dof_energies).

class sith.energy_analysis.sith_analysis.SithAnalysis(structures_info)[source]

Bases: object

Tool to compute the energy distribution analysis using numerical integration.

Parameters:

structures_info (sith.SITH) – object containing the necessary information for the energy analysis.

get_sith_dq()[source]

Populates delta_q taking the changes respect to the consecutive strutures. Namely \(\Delta q_i = q_i - q_{i-1}\) and \(\Delta q_0 = 0\).

Returns:

  • (np.array) change in each degree of freedom respect to the optimized

  • structure.

rectangle_integration()[source]

Numerical integration using rectangle rule algorithm.

Returns:

  • (tuple) [energies, total_ener] energies computed by SITH

  • method.

simpson_integration()[source]

Numerical integration using Simpson algorithm.

Returns:

  • (tuple) [energies, total_ener] energies computed by SITH

  • method.

trapezoid_integration()[source]

Numerical integration using trapezoid rule algorithm.

Returns:

  • (tuple) [energies, total_ener] energies computed by SITH

  • method.

Module contents