def mutate_and_relax(candidate, name, iteration, cnt_max, **kwargs):
print_output("__%s__" % name)
found = False
cnt = 0
while found is False and cnt < cnt_max:
candidate_backup = Structure(candidate)
candidate.mutate(**kwargs)
print_output("%s after mutation: " % name + str(candidate))
run_util.str_info(candidate)
if not candidate.is_geometry_valid():
print_output(" The geometry of %s is invalid." % name)
cnt += 1
# Rebuild the structure
candidate = candidate_backup
continue
if candidate not in blacklist:
name = "generation_%d_%s" % (iteration, name)
run_util.optimize(candidate, energy_function, params, name)
run_util.check_for_kill()
candidate.send_to_blacklist(blacklist)
print_output(str(candidate)+":, energy: "+str(float(
candidate))+", is temporary added to the population")
run_util.relax_info(candidate)
found = True
population.append(candidate)
else:
print_output("Geomerty of "+str(candidate)+" is fine, but already "
"known.")
cnt += 1
candidate = candidate_backup
if cnt == cnt_max:
raise Exception("The allowed number of trials for generating"
" a unique child has been exceeded.")
def mutate_and_relax(candidate, name, iteration, cnt_max, **kwargs):
print_output("__%s__" % name)
found = False
cnt = 0
while found is False and cnt < cnt_max:
candidate_backup = Structure(candidate)
candidate.mutate(**kwargs)
print_output("%s after mutation: " % name + str(candidate))
run_util.str_info(candidate)
if not candidate.is_geometry_valid():
print_output(" The geometry of %s is invalid." % name)
cnt += 1
# Rebuild the structure
candidate = candidate_backup
continue
if candidate not in blacklist:
name = "generation_%d_%s" % (iteration, name)
run_util.optimize(candidate, energy_function, params, name)
run_util.check_for_kill()
candidate.send_to_blacklist(blacklist)
print_output(
str(candidate) + ":, energy: " + str(float(candidate)) +
", is temporary added to the population")
run_util.relax_info(candidate)
found = True
population.append(candidate)
else:
print_output("Geomerty of " + str(candidate) +
" is fine, but already "
"known.")
cnt += 1
candidate = candidate_backup
if cnt == cnt_max:
raise Exception("The allowed number of trials for generating"
" a unique child has been exceeded.")
cnt += 1
continue
else:
child1, child2 = Structure(parent1), Structure(parent2)
print_output("No crossover was performed. Children are copies of "
"parents: " + str(child1) + (": ") + str(child1) +
(", ") + str(child2) + (": ") + str(child2))
# Delete inherited attributes.
for child in child1, child2:
attr_list = ["initial_sdf_string", "energy"]
for attr in attr_list:
delattr(child, attr)
for dof in child.dof:
delattr(dof, "initial_values")
run_util.str_info(child1)
run_util.str_info(child2)
try:
mutate_and_relax(child1, "child1", iteration, cnt_max, **linked_params)
except Exception as exc:
print_output(exc)
sys.exit(0)
try:
mutate_and_relax(child2, "child2", iteration, cnt_max, **linked_params)
except Exception as exc:
print_output(exc)
sys.exit(0)
population.sort()
print_output("Sorted population: " +
', '.join([str(v) for v in population]))
cnt += 1
continue
else:
child1, child2 = Structure(parent1), Structure(parent2)
print_output("No crossover was performed. Children are copies of "
"parents: " + str(child1) + (": ") + str(child1) +
(", ") + str(child2) + (": ") + str(child2))
# Delete inherited attributes.
for child in child1, child2:
attr_list = ["initial_sdf_string", "energy"]
for attr in attr_list:
delattr(child, attr)
for dof in child.dof:
delattr(dof, "initial_values")
run_util.str_info(child1)
run_util.str_info(child2)
try:
mutate_and_relax(child1, "child1", iteration, cnt_max, **linked_params)
except Exception as exc:
print_output(exc)
sys.exit(0)
try:
mutate_and_relax(child2, "child2", iteration, cnt_max, **linked_params)
except Exception as exc:
print_output(exc)
sys.exit(0)
population.sort()
print_output("Sorted population: " + ', '.join([
str(v) for v in population]))
