HTSTParameters¶
- class HTSTParameters(assumed_prefactor=None, minimum_displacement=None, finite_difference=None, finite_difference_method=None, spline_estimate=None, dynamical_matrix_processes_per_displacement=1)¶
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
dynamical_matrix_processes_per_displacement (int) – The number of processes assigned to calculating a single displacement Default: 1 process per displacement.
- uniqueString()¶
Return a unique string representing the state of the object.
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,
)
Notes¶
These parameters are normally passed to the
AdaptiveKineticMonteCarlo
class. For more details on harmonic
transition state theory, see the HTSTEvent
class.