# for each structure in the database. The mode indices start at 3
# as the three lowest frequency modes are translational modes.
# Set up the relative probabilities for the different operators
operators = OperationSelector([4., 3., 3.], [pairing, softmut, strainmut])
# Relax the initial candidates
while da.get_number_of_unrelaxed_candidates() > 0:
a = da.get_an_unrelaxed_candidate()
relax(a, cellbounds=cellbounds)
da.add_relaxed_step(a)
cell = a.get_cell()
if not cellbounds.is_within_bounds(cell):
da.kill_candidate(a.info['confid'])
# Initialize the population
population_size = 20
population = Population(data_connection=da,
population_size=population_size,
comparator=comp,
logfile='log.txt',
use_extinct=True)
# Update the scaling volume used in some operators
# based on a number of the best candidates
current_pop = population.get_current_population()
strainmut.update_scaling_volume(current_pop, w_adapt=0.5, n_adapt=4)
pairing.update_scaling_volume(current_pop, w_adapt=0.5, n_adapt=4)
