HTST

Harmonic transition state theory.

Note that calculate_prefactor needs to be called before using any of the getter functions.

spirit.htst.calculate(p_state, idx_image_minimum, idx_image_sp, n_eigenmodes_keep=-1, sparse=False, idx_chain=-1)

Performs an HTST calculation and returns rate prefactor.

Note: this function must be called before any of the getters.

spirit.htst.get_eigenvalues_min(p_state, idx_chain=-1)

Returns the eigenvalues at the minimum with shape(2*nos).

spirit.htst.get_eigenvalues_sp(p_state, idx_chain=-1)

Returns the eigenvalues at the saddle point with shape(2*nos).

spirit.htst.get_eigenvectors_min(p_state, idx_chain=-1)

Returns a numpy array view to the eigenvectors at the minimum with shape(n_eigenmodes_keep, 2*nos).

spirit.htst.get_eigenvectors_sp(p_state, idx_chain=-1)

Returns a numpy array view to the eigenvectors at the saddle point with shape(n_eigenmodes_keep, 2*nos).

spirit.htst.get_info(p_state, idx_chain=-1)

Returns a set of HTST information:

  • the exponent of the temperature-dependence

  • me

  • Omega_0

  • s

  • zero mode volume at the minimum

  • zero mode volume at the saddle point

  • dynamical prefactor

  • full rate prefactor (without temperature dependent part)

spirit.htst.get_info_dict(p_state, idx_chain=-1)

Returns a set of HTST information in a dictionary:

  • the exponent of the temperature-dependence

  • me

  • Omega_0

  • s

  • zero mode volume at the minimum

  • zero mode volume at the saddle point

  • dynamical prefactor

  • full rate prefactor (without temperature dependent part)

spirit.htst.get_velocities(p_state, idx_chain=-1)

Returns the velocities perpendicular to the dividing surface with shape(2*nos).