def __init__(self,
slab,
n_top,
blmin,
number_of_variable_cell_vectors=0,
p1=1,
p2=0.05,
minfrac=None,
cellbounds=None,
test_dist_to_slab=True,
use_tags=False,
rng=np.random,
verbose=False):
OffspringCreator.__init__(self, verbose, rng=rng)
self.slab = slab
self.n_top = n_top
self.blmin = blmin
assert number_of_variable_cell_vectors in range(4)
self.number_of_variable_cell_vectors = number_of_variable_cell_vectors
self.p1 = p1
self.p2 = p2
self.minfrac = minfrac
self.cellbounds = cellbounds
self.test_dist_to_slab = test_dist_to_slab
self.use_tags = use_tags
self.scaling_volume = None
self.descriptor = 'CutAndSplicePairing'
self.min_inputs = 2
def __init__(self, element_pool, verbose=False, num_muts=1):
OffspringCreator.__init__(self, verbose, num_muts=num_muts)
self.descriptor = 'FullElementMutation'
if not isinstance(element_pool[0], (list, np.ndarray)):
self.element_pools = [element_pool]
else:
self.element_pools = element_pool
def __init__(self, slab, n_top, blmin, verbose=False):
OffspringCreator.__init__(self, verbose)
self.blmin = blmin
self.slab = slab
self.n_top = n_top
self.descriptor = 'CutAndSplicePairing'
self.min_inputs = 2
def __init__(self, element_pool, verbose=False, num_muts=1):
OffspringCreator.__init__(self, verbose, num_muts=num_muts)
self.descriptor = 'FullElementMutation'
if not isinstance(element_pool[0], (list, np.ndarray)):
self.element_pools = [element_pool]
else:
self.element_pools = element_pool
def __init__(self, blmin, n_top, reflect=False, verbose=False):
OffspringCreator.__init__(self, verbose)
self.blmin = blmin
self.n_top = n_top
self.reflect = reflect
self.descriptor = 'MirrorMutation'
self.min_inputs = 1
def __init__(self, element_pool, max_diff_elements,
min_percentage_elements, verbose):
OffspringCreator.__init__(self, verbose)
if not isinstance(element_pool[0], (list, np.ndarray)):
self.element_pools = [element_pool]
else:
self.element_pools = element_pool
if max_diff_elements is None:
self.max_diff_elements = [None for _ in self.element_pools]
elif isinstance(max_diff_elements, int):
self.max_diff_elements = [max_diff_elements]
else:
self.max_diff_elements = max_diff_elements
assert len(self.max_diff_elements) == len(self.element_pools)
if min_percentage_elements is None:
self.min_percentage_elements = [0 for _ in self.element_pools]
elif isinstance(min_percentage_elements, (int, float)):
self.min_percentage_elements = [min_percentage_elements]
else:
self.min_percentage_elements = min_percentage_elements
assert len(self.min_percentage_elements) == len(self.element_pools)
self.min_inputs = 2
def __init__(self, slab, n_top, blmin, verbose=False):
OffspringCreator.__init__(self, verbose)
self.blmin = blmin
self.slab = slab
self.n_top = n_top
self.descriptor = 'CutAndSplicePairing'
self.min_inputs = 2
def __init__(self,
element_pool,
max_diff_elements,
min_percentage_elements,
verbose,
rng=np.random):
OffspringCreator.__init__(self, verbose, rng=rng)
if not isinstance(element_pool[0], (list, np.ndarray)):
self.element_pools = [element_pool]
else:
self.element_pools = element_pool
if max_diff_elements is None:
self.max_diff_elements = [None for _ in self.element_pools]
elif isinstance(max_diff_elements, int):
self.max_diff_elements = [max_diff_elements]
else:
self.max_diff_elements = max_diff_elements
assert len(self.max_diff_elements) == len(self.element_pools)
if min_percentage_elements is None:
self.min_percentage_elements = [0 for _ in self.element_pools]
elif isinstance(min_percentage_elements, (int, float)):
self.min_percentage_elements = [min_percentage_elements]
else:
self.min_percentage_elements = min_percentage_elements
assert len(self.min_percentage_elements) == len(self.element_pools)
self.min_inputs = 2
def __init__(self, blmin, n_top, reflect=False, verbose=False):
OffspringCreator.__init__(self, verbose)
self.blmin = blmin
self.n_top = n_top
self.reflect = reflect
self.descriptor = 'MirrorMutation'
self.min_inputs = 1
def test_add_candidates():
import pytest
from ase.build import fcc111
from ase.ga.data import PrepareDB
from ase.ga.data import DataConnection
from ase.ga.offspring_creator import OffspringCreator
from ase.ga import set_raw_score
import os
db_file = 'gadb.db'
if os.path.isfile(db_file):
os.remove(db_file)
db = PrepareDB(db_file)
slab1 = fcc111('Ag', size=(2, 2, 2))
db.add_unrelaxed_candidate(slab1)
slab2 = fcc111('Cu', size=(2, 2, 2))
set_raw_score(slab2, 4)
db.add_relaxed_candidate(slab2)
assert slab2.info['confid'] == 3
db = DataConnection(db_file)
assert db.get_number_of_unrelaxed_candidates() == 1
slab3 = db.get_an_unrelaxed_candidate()
old_confid = slab3.info['confid']
slab3[0].symbol = 'Au'
db.add_unrelaxed_candidate(slab3, 'mutated: Parent {0}'.format(old_confid))
new_confid = slab3.info['confid']
# confid should update when using add_unrelaxed_candidate
assert old_confid != new_confid
slab3[1].symbol = 'Au'
db.add_unrelaxed_step(slab3, 'mutated: Parent {0}'.format(new_confid))
# confid should not change when using add_unrelaxed_step
assert slab3.info['confid'] == new_confid
with pytest.raises(AssertionError):
db.add_relaxed_step(slab3)
set_raw_score(slab3, 3)
db.add_relaxed_step(slab3)
slab4 = OffspringCreator.initialize_individual(slab1,
fcc111('Au', size=(2, 2, 2)))
set_raw_score(slab4, 67)
db.add_relaxed_candidate(slab4)
assert slab4.info['confid'] == 7
more_slabs = []
for m in ['Ni', 'Pd', 'Pt']:
slab = fcc111(m, size=(2, 2, 2))
slab = OffspringCreator.initialize_individual(slab1, slab)
set_raw_score(slab, sum(slab.get_masses()))
more_slabs.append(slab)
db.add_more_relaxed_candidates(more_slabs)
assert more_slabs[1].info['confid'] == 9
os.remove(db_file)
def __init__(self, adsorbate, adsorption_sites=None, num_muts=1):
OffspringCreator.__init__(self, num_muts=num_muts)
self.adsorbate = self.convert_adsorbate(adsorbate)
self.adsorbate_set = set(self.adsorbate.get_chemical_symbols())
if adsorption_sites is None:
raise NotImplementedError
self.adsorption_sites = adsorption_sites
self.descriptor = 'AdsorbateOperator'
def __init__(self, blmin, n_top, rattle_strength=0.8,
rattle_prop=0.4, verbose=False):
OffspringCreator.__init__(self, verbose)
self.blmin = blmin
self.n_top = n_top
self.rattle_strength = rattle_strength
self.rattle_prop = rattle_prop
self.descriptor = 'RattleMutation'
def __init__(self, adsorbate, adsorption_sites=None, num_muts=1):
OffspringCreator.__init__(self, num_muts=num_muts)
self.adsorbate = self.convert_adsorbate(adsorbate)
self.adsorbate_set = set(self.adsorbate.get_chemical_symbols())
if adsorption_sites is None:
raise NotImplementedError
self.adsorption_sites = adsorption_sites
self.descriptor = 'AdsorbateOperator'
def __init__(self,
blmin,
n_top,
rattle_prop=0.4,
verbose=False,
descriptor='RattleMutation_new'):
OffspringCreator.__init__(self, verbose)
self.blmin = blmin
self.n_top = n_top
self.rattle_prop = rattle_prop
self.descriptor = descriptor
self.min_inputs = 1
def __init__(self,
blmin,
n_top,
rattle_strength=0.8,
rattle_prop=0.4,
verbose=False):
OffspringCreator.__init__(self, verbose)
self.blmin = blmin
self.n_top = n_top
self.rattle_strength = rattle_strength
self.rattle_prop = rattle_prop
self.descriptor = 'RattleMutation'
def __init__(self,
blmin,
n_top,
probability=0.33,
verbose=False,
descriptor='PermutationMutation'):
OffspringCreator.__init__(self, verbose)
self.blmin = blmin
self.n_top = n_top
self.probability = probability
self.descriptor = descriptor
self.min_inputs = 1
def __init__(self, verbose=False, num_muts=1,
allowed_compositions=None,
distribution_correction_function=None,
element_pools=None):
OffspringCreator.__init__(self, verbose, num_muts=num_muts)
self.allowed_compositions = allowed_compositions
self.element_pools = element_pools
if distribution_correction_function is None:
self.dcf = dummy_func
else:
self.dcf = distribution_correction_function
def __init__(self,
blmin,
cellbounds=None,
stddev=0.7,
use_tags=False,
verbose=False):
OffspringCreator.__init__(self, verbose)
self.blmin = blmin
self.cellbounds = cellbounds
self.stddev = stddev
self.use_tags = use_tags
self.scaling_volume = None
self.descriptor = 'StrainMutation'
self.min_inputs = 1
def __init__(self,
n_top,
probability=0.33,
test_dist_to_slab=True,
use_tags=False,
blmin=None,
verbose=False):
OffspringCreator.__init__(self, verbose)
self.n_top = n_top
self.probability = probability
self.test_dist_to_slab = test_dist_to_slab
self.use_tags = use_tags
self.blmin = blmin
self.descriptor = 'PermutationMutation'
self.min_inputs = 1
def __init__(self,
blmin,
n_top,
rattle_strength=0.8,
rattle_prop=0.4,
min_z=None,
verbose=False,
descriptor='RattleMutation'):
OffspringCreator.__init__(self, verbose)
self.blmin = blmin
self.n_top = n_top
self.rattle_strength = rattle_strength
self.rattle_prop = rattle_prop
self.min_z = min_z
self.descriptor = descriptor
self.min_inputs = 1
def __init__(self,
slab,
n_top,
blmin,
n_clusters,
n_parents=3,
r_cut=11.9,
verbose=False):
OffspringCreator.__init__(self, verbose)
self.slab = slab
self.n_top = n_top
self.blmin = blmin
self.n_clusters = n_clusters
self.r_cut = r_cut
self.descriptor = 'ClusterDistanceMutation'
self.min_inputs = n_parents
def __init__(self,
blmin,
n_top=None,
fraction=0.33,
tags=None,
min_angle=1.57,
test_dist_to_slab=True,
verbose=False):
OffspringCreator.__init__(self, verbose)
self.blmin = blmin
self.n_top = n_top
self.fraction = fraction
self.tags = tags
self.min_angle = min_angle
self.test_dist_to_slab = test_dist_to_slab
self.descriptor = 'RotationalMutation'
self.min_inputs = 1
def __init__(self,
blmin,
n_top,
rattle_strength=0.8,
rattle_prop=0.4,
test_dist_to_slab=True,
use_tags=False,
verbose=False):
OffspringCreator.__init__(self, verbose)
self.blmin = blmin
self.n_top = n_top
self.rattle_strength = rattle_strength
self.rattle_prop = rattle_prop
self.test_dist_to_slab = test_dist_to_slab
self.use_tags = use_tags
self.descriptor = 'RattleMutation'
self.min_inputs = 1
def __init__(self,
blmin,
cellbounds=None,
stddev=0.7,
number_of_variable_cell_vectors=3,
use_tags=False,
rng=np.random,
verbose=False):
OffspringCreator.__init__(self, verbose, rng=rng)
self.blmin = blmin
self.cellbounds = cellbounds
self.stddev = stddev
self.number_of_variable_cell_vectors = number_of_variable_cell_vectors
self.use_tags = use_tags
self.scaling_volume = None
self.descriptor = 'StrainMutation'
self.min_inputs = 1
def initialize_individual(cls, parent, indi=None):
indi = OffspringCreator.initialize_individual(parent, indi=indi)
if 'unrelaxed_adsorbates' in parent.info['data']:
unrelaxed = list(parent.info['data']['unrelaxed_adsorbates'])
else:
unrelaxed = []
indi.info['data']['unrelaxed_adsorbates'] = unrelaxed
return indi
def initialize_individual(cls, parent, indi=None):
indi = OffspringCreator.initialize_individual(parent, indi=indi)
if 'unrelaxed_adsorbates' in parent.info['data']:
unrelaxed = list(parent.info['data']['unrelaxed_adsorbates'])
else:
unrelaxed = []
indi.info['data']['unrelaxed_adsorbates'] = unrelaxed
return indi
def __init__(self,
blmin,
n_top=None,
p1=1.,
p2=0.05,
minfrac=None,
cellbounds=None,
use_tags=False,
test_dist_to_slab=True,
verbose=False):
OffspringCreator.__init__(self, verbose)
self.blmin = blmin
self.n_top = n_top
self.p1 = p1
self.p2 = p2
self.minfrac = minfrac
self.cellbounds = cellbounds
self.use_tags = use_tags
self.test_dist_to_slab = test_dist_to_slab
self.scaling_volume = None
self.descriptor = 'CutAndSplicePairing'
self.min_inputs = 1
def __init__(self,
blmin,
bounds=[0.5, 2.0],
calculator=BondElectroNegativityModel,
rcut=10.,
used_modes_file='used_modes.json',
use_tags=False,
verbose=False):
OffspringCreator.__init__(self, verbose)
self.blmin = blmin
self.bounds = bounds
self.calc = calculator
self.rcut = rcut
self.used_modes_file = used_modes_file
self.use_tags = use_tags
self.descriptor = 'SoftMutation'
self.used_modes = {}
if self.used_modes_file is not None:
try:
self.read_used_modes(self.used_modes_file)
except IOError:
# file doesn't exist (yet)
pass
def __init__(self, num_muts):
OffspringCreator.__init__(self)
self.descriptor = 'Mutation'
self.num_muts = num_muts
def __init__(self, n_top, probability=0.33, verbose=False):
OffspringCreator.__init__(self, verbose)
self.n_top = n_top
self.probability = probability
self.descriptor = 'PermutationMutation'
def __init__(self, n_top, probability=0.33, verbose=False):
OffspringCreator.__init__(self, verbose)
self.n_top = n_top
self.probability = probability
self.descriptor = 'PermutationMutation'
def __init__(self):
OffspringCreator.__init__(self)
self.descriptor = 'Crossover'
def finalize_individual(self, indi):
atoms_string = ''.join(indi.get_chemical_symbols())
indi.info['key_value_pairs']['atoms_string'] = atoms_string
return OffspringCreator.finalize_individual(self, indi)
def __init__(self, adsorbate):
OffspringCreator.__init__(self)
self.adsorbate = self.convert_adsorbate(adsorbate)
self.descriptor = 'AdsorbateOperator'
def __init__(self, adsorbate):
OffspringCreator.__init__(self)
self.adsorbate = self.convert_adsorbate(adsorbate)
self.descriptor = 'AdsorbateOperator'
def __init__(self, num_muts=1, rng=np.random):
OffspringCreator.__init__(self, num_muts=num_muts, rng=rng)
self.descriptor = 'Mutation'
self.min_inputs = 1
def __init__(self, rng=np.random):
OffspringCreator.__init__(self, rng=rng)
self.descriptor = 'Crossover'
self.min_inputs = 2
def __init__(self):
OffspringCreator.__init__(self)
self.descriptor = 'Crossover'
def __init__(self):
OffspringCreator.__init__(self)
self.descriptor = "Crossover"
self.min_inputs = 2
def __init__(self, num_muts):
OffspringCreator.__init__(self)
self.descriptor = 'Mutation'
self.num_muts = num_muts
slab3[0].symbol = 'Au'
db.add_unrelaxed_candidate(slab3, 'mutated: Parent {0}'.format(old_confid))
new_confid = slab3.info['confid']
# confid should update when using add_unrelaxed_candidate
assert old_confid != new_confid
slab3[1].symbol = 'Au'
db.add_unrelaxed_step(slab3, 'mutated: Parent {0}'.format(new_confid))
# confid should not change when using add_unrelaxed_step
assert slab3.info['confid'] == new_confid
with must_raise(AssertionError):
db.add_relaxed_step(slab3)
set_raw_score(slab3, 3)
db.add_relaxed_step(slab3)
slab4 = OffspringCreator.initialize_individual(slab1,
fcc111('Au', size=(2, 2, 2)))
set_raw_score(slab4, 67)
db.add_relaxed_candidate(slab4)
assert slab4.info['confid'] == 7
more_slabs = []
for m in ['Ni', 'Pd', 'Pt']:
slab = fcc111(m, size=(2, 2, 2))
slab = OffspringCreator.initialize_individual(slab1, slab)
set_raw_score(slab, sum(slab.get_masses()))
more_slabs.append(slab)
db.add_more_relaxed_candidates(more_slabs)
assert more_slabs[1].info['confid'] == 9
os.remove(db_file)
