ase_uhal.StructureSelector#

class ase_uhal.StructureSelector(bias_calc, threshold='adaptive', auto_resample=True, delay=10, mixing=0.1, thresh_mul=1.2)[source]#

Dynamics observer which decides whether to select a structure based on the score values of a trajectory

Selects a structure if the score is above some threshold, and if the previous and next scores are both lower

__init__(bias_calc, threshold='adaptive', auto_resample=True, delay=10, mixing=0.1, thresh_mul=1.2)[source]#
Parameters:

  • bias_calc (ase_uhal.HalCalculator object) – HAL calculator used to run dynamics

  • threshold (float or “adaptive” (default: “adaptive”)) – threshold for determining when peaks in the score should be detected “adaptive” computes a new threshold after each call, by mixing scores from each call to the observer (see delay, mixing, and thresh_mul for more details)

  • auto_resample (bool (default: False)) – Whether the biasing committee should be automatically resampled after every selection

  • delay (int (default: 10)) – When the threshold is determined automatically, don’t update it for this many calls (to allow mixing to settle on a reasonable value)

  • mixing (float (default: 0.1)) – Mixing strength when threshold is automatically determined mixed_score = (1-mixing) * mixed_score + mixing * new_score

  • thresh_mul (float (default: 1.2)) – Multiplier on the mixed score to determine the threshold threshold = thresh_mul * mixed_score

Methods

__init__(bias_calc[, threshold, ...])

reset_threshold()

Sets threshold to np.inf, resets the internal mixing state and the delay back to self.delay