HTSTParameters

class HTSTParameters(assumed_prefactor=None, minimum_displacement=None, finite_difference=None, finite_difference_method=None, spline_estimate=None)

This class stores parameters for the HTSTEvent calculation.

Parameters:
  • assumed_prefactor (PhysicalQuantity of type per Second) – A fixed value for the prefactors (both forward and reverse). If assumed_prefactor is None, then the vibrational frequencies at the minima and saddle point will be calculated.
    Default: None
  • minimum_displacement (PhysicalQuantity of type length) – The minimum distance that an atom must move during the reaction in order to be included in the prefactor calculation. If an atom moves further than this distance, it and its neighbors will be included in the dynamical matrix calculation that is needed for calculating the prefactor. Setting this value to zero will include all degrees of freedom. Setting this value to a larger number will reduce the amount of work needed to calculate the prefactor, but will decrease the accuracy. Note that this parameter is only used when assumed_prefactor is None.
    Default: 0.05 * Angstrom
  • finite_difference (PhysicalQuantity of type length) – The finite difference step size used when estimating the force constants needed to calculate the harmonic prefactor.
    Default: 0.01*Angstrom
  • finite_difference_method (Central | Forward) – The finite difference method to use when estimating the force constants needed to calculate the harmonic prefactor.
    Default: Central
  • spline_estimate (bool) – Obtain a rough estimate of the prefactor using a spline to obtain the vibrational frequency at the minimum in the direction of the saddle point. This requires that the NEB configuration has either had its update method called or has already been optimized so that the energy and forces of each image are available. This option is incompatible with assumed_prefactor.
    Default: False

Usage Examples

Calculate harmonic transition state theory prefactors using forward finite differences (finite_difference_method=Forward) with a small step length (finite_difference=1e-4*Angstrom) and include all atoms in the dynamical matrix calculation (minimum_displacement=0.0*Angstrom).

htst_parameters = HTSTParameters(
    finite_difference=1e-4*Angstrom,
    finite_difference_method=Forward,
    minimum_displacement=0.0*Angstrom,
    )

parameters.py

Notes

These parameters are normally passed to the AdaptiveKineticMonteCarlo class. For more details on harmonic transition state theory, see the HTSTEvent class.