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, 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).