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).