class PerovskiteProperty(BaseFeaturizer):
"""
Class to calculate perovskite features. Includes custom features from the Perovskite class and generic features from ElementProperty,
AtomicOrbitals, ValenceOrbital, and CohesiveEnergy matminer featurizers.
Options for initializing:
ordered_formula_featurizer(): for featurizing ordered formulas
cation_site_featurizer(): for featurizing unordered formulas based on user-provided cation site assignments
from_preset(): load a preset
The class can also be called manually, but be aware that different parameter sets are required for an ordered formula featurizer instance than for a cation site featurizer instance.
Parameters:
-----------
cation_site: dict of site assignments for cations, i.e. {el:site}. Elements not in cation_site are assumed to be anions on X-site
site_ox_lim: dict of oxidation state limits for each site, i.e. {site:[min,max]}. Elements on sites are limited to oxidation states within these limits
site_base_ox: dict of base oxidation state for each site, i.e. {site:ox}. Used for determining aliovalent ions and acceptor/donor dopants
ordered_formulas: if True, determine cation site assignments from order
A_site_occupancy: Number of atoms on A site. Used when ordered_formulas is True
anions: list of anions. Used when ordered_formulas is True
Parameters for ordered formula featurizer: site_ox_lim, site_base_ox, A_site_occupancy, anions
Parameters for cation site featurizer: cation_site, site_ox_lim, site_base_ox
"""
def __init__(self,
cation_site=None,
site_ox_lim={
'A': [0, 10],
'B': [0, 10],
'X': [-10, 0]
},
site_base_ox={
'A': 2,
'B': 4,
'X': -2
},
ordered_formulas=False,
A_site_occupancy=1,
anions=None):
if cation_site is None and ordered_formulas is False:
raise ValueError(
'Either cation sites must be assigned, or formulas must be ordered. Otherwise site assignments can not be determined'
)
self.cation_site = cation_site
self.site_ox_lim = site_ox_lim
self.site_base_ox = site_base_ox
self.ordered_formulas = ordered_formulas
self.A_site_occupancy = A_site_occupancy
self.anions = anions
#matminer featurizers
self.ValenceOrbital = ValenceOrbital()
self.AtomicOrbitals = AtomicOrbitalsMod()
self.CohesiveEnergy = CohesiveEnergy()
#custom ElementProperty featurizer
elemental_properties = [
'BoilingT', 'MeltingT', 'BulkModulus', 'ShearModulus', 'Row',
'Column', 'Number', 'MendeleevNumber', 'SpaceGroupNumber',
'Density', 'MolarVolume', 'FusionEnthalpy', 'HeatVaporization',
'NsUnfilled', 'NpUnfilled', 'NdUnfilled', 'NfUnfilled',
'Polarizability', 'ThermalConductivity'
]
self.ElementProperty = ElementProperty(
data_source='magpie',
features=elemental_properties,
stats=["mean", "std_dev", "range"])
self.check_matminer_featurizers()
self.featurize_options = {}
@classmethod
def from_preset(cls, preset_name):
"""
Initialize from preset
Parameters:
-----------
preset_name: name of preset to load. Currently accepts 'BCFZY'
"""
if preset_name == 'BCFZY':
#Ba(Co,Fe,Zr,Y)O_3-d system
cation_site = {
'Ba': 'A',
'Co': 'B',
'Fe': 'B',
'Zr': 'B',
'Y': 'B'
}
site_ox_lim = {'A': [2, 2], 'B': [2, 4], 'X': [-2, -2]}
site_base_ox = {'A': 2, 'B': 4, 'X': -2}
else:
raise ValueError("Invalid preset_name specified!")
return cls(cation_site, site_ox_lim, site_base_ox)
@classmethod
def ordered_formula_featurizer(cls,
A_site_occupancy=1,
anions=None,
site_ox_lim={
'A': [0, 10],
'B': [0, 10],
'X': [-10, 0]
},
site_base_ox={
'A': 2,
'B': 4,
'X': -2
}):
"""
Convenience method for instantiating a featurizer for ordered formulas
"""
return cls(cation_site=None,
site_ox_lim=site_ox_lim,
site_base_ox=site_base_ox,
ordered_formulas=True,
A_site_occupancy=A_site_occupancy,
anions=anions)
@classmethod
def cation_site_featurizer(cls,
cation_site,
site_ox_lim={
'A': [0, 10],
'B': [0, 10],
'X': [-10, 0]
},
site_base_ox={
'A': 2,
'B': 4,
'X': -2
}):
"""
Convenience method for instantiating a featurizer for unordered formulas, based on site assignments
"""
return cls(cation_site, site_ox_lim, site_base_ox)
@property
def ElementProperty_custom_labels(self):
"""
Generate custom labels for ElementProperty featurizer that follow same naming convention as Perovskite class
"""
elemental_property_label_map = {
'BoilingT': 'boil_temp',
'MeltingT': 'melt_temp',
'BulkModulus': 'bulk_mod',
'ShearModulus': 'shear_mod',
'Row': 'row',
'Column': 'column',
'Number': 'number',
'MendeleevNumber': 'mendeleev',
'SpaceGroupNumber': 'space_group',
'Density': 'density',
'MolarVolume': 'molar_vol',
'FusionEnthalpy': 'H_fus',
'HeatVaporization': 'H_vap',
'NsUnfilled': 'valence_unfilled_s',
'NpUnfilled': 'valence_unfilled_p',
'NdUnfilled': 'valence_unfilled_d',
'NfUnfilled': 'valence_unfilled_f',
'Polarizability': 'polarizability',
'ThermalConductivity': 'sigma_therm'
}
element_property_labels = list(
map(elemental_property_label_map.get,
self.ElementProperty.features))
labels = []
for attr in element_property_labels:
for stat in self.ElementProperty.stats:
if stat == 'std_dev':
stat = 'std'
labels.append(f'{attr}_{stat}')
return labels
@property
def ElementProperty_categories(self):
"""
Generate categories for ElementProperty featurizer
"""
elemental_property_category_map = {
'BoilingT': 'elemental',
'MeltingT': 'elemental',
'BulkModulus': 'elemental',
'ShearModulus': 'elemental',
'Row': 'periodic',
'Column': 'periodic',
'Number': 'periodic',
'MendeleevNumber': 'periodic',
'SpaceGroupNumber': 'periodic',
'Density': 'elemental',
'MolarVolume': 'elemental',
'FusionEnthalpy': 'elemental',
'HeatVaporization': 'elemental',
'NsUnfilled': 'electronic',
'NpUnfilled': 'electronic',
'NdUnfilled': 'electronic',
'NfUnfilled': 'electronic',
'Polarizability': 'elemental',
'ThermalConductivity': 'elemental'
}
element_property_categories = list(
map(elemental_property_category_map.get,
self.ElementProperty.features))
categories = []
for ep_cat in element_property_categories:
for stat in self.ElementProperty.stats:
categories.append(ep_cat)
return categories
@property
def ElementProperty_units(self):
"""
Generate units for ElementProperty featurizer
"""
elemental_property_unit_map = {
'BoilingT': 'temp',
'MeltingT': 'temp',
'BulkModulus': 'pressure',
'ShearModulus': 'pressure',
'Row': 'none',
'Column': 'none',
'Number': 'none',
'MendeleevNumber': 'none',
'SpaceGroupNumber': 'none',
'Density': 'density',
'MolarVolume': 'volume',
'FusionEnthalpy': 'energy',
'HeatVaporization': 'energy',
'NsUnfilled': 'none',
'NpUnfilled': 'none',
'NdUnfilled': 'none',
'NfUnfilled': 'none',
'Polarizability':
'polarizability', #complex units - doesn't matter
'ThermalConductivity': 'therm'
} #complex units - doesn't matter
element_property_units = list(
map(elemental_property_unit_map.get,
self.ElementProperty.features))
units = []
for ep_unit in element_property_units:
for stat in self.ElementProperty.stats:
units.append(ep_unit)
return units
def ElementProperty_label_check(self):
"""
Check that ElementProperty feature labels are as expected
If not, features may not align with feature labels
"""
#ElementProperty.feature_labels() code as of 2/17/19
labels = []
for attr in self.ElementProperty.features:
src = self.ElementProperty.data_source.__class__.__name__
for stat in self.ElementProperty.stats:
labels.append("{} {} {}".format(src, stat, attr))
if labels != self.ElementProperty.feature_labels():
raise Exception('ElementProperty features or labels have changed')
def set_featurize_options(
self,
sites,
ox_stats=['min', 'max', 'mean', 'median', 'std', 'range'],
ep_stats=["mean", "std_dev", "range"],
radius_type='ionic_radius',
normalize_formula=True,
silent=True,
categories=None):
"""
Set options for featurization. Since these options should be the same for all compositions in a batch, set for the featurizer instance rather than passing as args to featurize()
so that they do not have to be duplicated in every row of a DataFrame when calling featurize_dataframe().
Since these options change the number and meaning of features returned, it's also safest to set for the whole instance for consistency.
Parameters:
-----------
sites: list or string of sites to featurize. Any combination of 'A', 'B', 'X', and/or 'comp' accepted.
Composition-level, oxidation-state-dependent features are always calculated by the Perovskite class. Passing '' or [] will return only these features.
Specifying 'A','B', and/or 'X' sites will calculate site-level features for these sites (oxidation-state independent and dependent features, and matminer features).
Including 'comp' will calculate oxidation-state-independent features and matminer features for the full composition.
ox_stats: list of aggregate functions to apply to oxidation state combinations for feature generation using Perovskite class.
Options: 'min','max','mean','median','std','range'
ep_stats: ElementProperty stats. Options: "minimum", "maximum", "range", "mean", "avg_dev", "mode"
radius_type: Shannon radius type to use in features. Accepts 'crystal_radius' or 'ionic_radius'
normalize_formula: if True, normalize formula such that higher occupancy cation site has one formula unit (applies to Perovskite class only)
silent: if False, print informational messages from Perovksite class
categories: list of feature categories to return. If None, return all. Options: 'bonding','structure','charge','composition','electronic','elemental','periodic'
"""
feat_options = dict(sites=sites,
ox_stats=ox_stats,
radius_type=radius_type,
normalize_formula=normalize_formula,
silent=silent)
self.featurize_options.update(feat_options)
self.ElementProperty.stats = ep_stats
def featurize(self, formula):
"""
Calculate features
Parameters:
-----------
formula: chemical formula string
Returns: list of feature values
"""
if self.featurize_options == {}:
raise Exception(
'Featurize options have not been set. Use set_featurize_options before featurizing'
)
if self.ordered_formulas is True:
pvsk = Perovskite.from_ordered_formula(
formula,
self.A_site_occupancy,
self.anions,
site_ox_lim=self.site_ox_lim,
site_base_ox=self.site_base_ox,
radius_type=self.featurize_options['radius_type'],
silent=self.featurize_options['silent'])
elif self.ordered_formulas is False:
pvsk = Perovskite(formula, self.cation_site, self.site_ox_lim,
self.site_base_ox,
self.featurize_options['radius_type'],
self.featurize_options['normalize_formula'],
self.featurize_options['silent'])
pvsk_features = pvsk.featurize(self.featurize_options['sites'],
self.featurize_options['ox_stats'])
mm_features = []
for site in self.featurize_options['sites']:
vo_features = self.ValenceOrbital.featurize(
pvsk.site_composition[site]
) #avg and frac s, p , d, f electrons
vo_features += [sum(vo_features[0:3])
] #avg total valence electrons
ao_features = self.AtomicOrbitals.featurize(
pvsk.site_composition[site]
) #H**O and LUMO character and energy levels (from atomic orbitals)
ao_features = [
ao_features[i] for i in range(len(ao_features))
if i not in (0, 1, 3, 4)
] #exclude HOMO_character,HOMO_element, LUMO_character, LUMO_element - categoricals
ce_features = self.CohesiveEnergy.featurize(
pvsk.site_composition[site], formation_energy_per_atom=1e-10
) #avg elemental cohesive energy
ep_features = self.ElementProperty.featurize(
pvsk.site_composition[site]) #elemental property features
mm_features += vo_features + ao_features + ce_features + ep_features
features = list(pvsk_features) + mm_features
return features
@property
def matminer_labels(self):
"""
Feature labels for matminer-derived features
"""
labels = [
#ValenceOrbital labels
'valence_elec_s_mean',
'valence_elec_p_mean',
'valence_elec_d_mean',
'valence_elec_f_mean',
'valence_elec_s_frac',
'valence_elec_p_frac',
'valence_elec_d_frac',
'valence_elec_f_frac',
'valence_elec_tot_mean',
#AtomicOrbitals labels
#'HOMO_character',
'HOMO_energy',
#'LUMO_character',
'LUMO_energy',
'AO_gap',
#CohesiveEnergy labels
'cohesive_energy_mean'
]
#ElementProperty labels
labels += self.ElementProperty_custom_labels
return labels
@property
def matminer_categories(self):
"""
Feature categories for matminer-derived features
"""
categories = [
#ValenceOrbital categories
'electronic',
'electronic',
'electronic',
'electronic',
'electronic',
'electronic',
'electronic',
'electronic',
'electronic',
#AtomicOrbitals categories
#'HOMO_character',
'electronic',
#'LUMO_character',
'electronic',
'electronic',
#CohesiveEnergy categories
'bonding'
]
#ElementProperty categories
categories += self.ElementProperty_categories
return categories
@property
def matminer_units(self):
"""
Feature units for matminer-derived features
"""
units = [
#ValenceOrbital units
'none',
'none',
'none',
'none',
'none',
'none',
'none',
'none',
'none',
#AtomicOrbitals units
#'HOMO_character',
'energy',
#'LUMO_character',
'energy',
'energy',
#CohesiveEnergy units
'energy'
]
#ElementProperty units
units += self.ElementProperty_units
return units
def feature_labels(self):
"""
Get list of feature labels
"""
try:
pvsk_labels = Perovskite.from_preset(
'BaCoO3', 'BCFZY',
silent=True).feature_labels(self.featurize_options['sites'],
self.featurize_options['ox_stats'])
except KeyError:
raise Exception(
'Featurize options have not been set. Use set_featurize_options before accessing feature labels'
)
mm_labels = []
for site in self.featurize_options['sites']:
if site == 'comp':
site_label = 'comp'
else:
site_label = f'{site}site'
mm_labels += [
f'{site_label}_{label}' for label in self.matminer_labels
]
return pvsk_labels + mm_labels
def feature_categories(self):
"""
Get list of feature categories. For quick filtering
"""
try:
pvsk_categories = Perovskite.from_preset(
'BaCoO3', 'BCFZY', silent=True).feature_categories(
self.featurize_options['sites'],
self.featurize_options['ox_stats'])
except KeyError:
raise Exception(
'Featurize options have not been set. Use set_featurize_options before accessing feature labels'
)
mm_categories = []
for site in self.featurize_options['sites']:
mm_categories += self.matminer_categories
return pvsk_categories + mm_categories
def feature_units(self):
"""
Get list of feature labels. For dimensional analysis
"""
try:
pvsk_units = Perovskite.from_preset(
'BaCoO3', 'BCFZY',
silent=True).feature_units(self.featurize_options['sites'],
self.featurize_options['ox_stats'])
except KeyError:
raise Exception(
'Featurize options have not been set. Use set_featurize_options before accessing feature labels'
)
mm_units = []
for site in self.featurize_options['sites']:
mm_units += self.matminer_units
return pvsk_units + mm_units
def check_matminer_featurizers(self):
"""
Check that features and feature order for matminer featurizers are as expected
If features or feature order have changed, featurize() may return unexpected features that do not align with feature_labels()
"""
#verify that matminer feature labels haven't changed
if self.ValenceOrbital.feature_labels() != [
'avg s valence electrons', 'avg p valence electrons',
'avg d valence electrons', 'avg f valence electrons',
'frac s valence electrons', 'frac p valence electrons',
'frac d valence electrons', 'frac f valence electrons'
]:
raise Exception('ValenceOrbital features or labels have changed')
if self.AtomicOrbitals.feature_labels() != [
'HOMO_character', 'HOMO_element', 'HOMO_energy',
'LUMO_character', 'LUMO_element', 'LUMO_energy', 'gap_AO'
]:
raise Exception('AtomicOrbitals features or labels have changed')
if self.CohesiveEnergy.feature_labels() != ['cohesive energy']:
raise Exception('CohesiveEnergy features or labels have changed')
self.ElementProperty_label_check()
class BCA_Featurizer(BaseFeaturizer):
def __init__(self,radius_type='ionic_radius',normalize_formula=False):
self.radius_type = radius_type
self.normalize_formula = normalize_formula
self.ValenceOrbital = ValenceOrbital()
self.AtomicOrbitals = AtomicOrbitalsMod()
self.CohesiveEnergy = CohesiveEnergy()
self.BandCenter = BandCenter()
self.ValenceOrbitalEnergy = ValenceOrbitalEnergy()
#custom ElementProperty featurizer
elemental_properties = ['BoilingT', 'MeltingT',
'BulkModulus', 'ShearModulus',
'Row', 'Column', 'Number', 'MendeleevNumber', 'SpaceGroupNumber',
'Density','MolarVolume',
'FusionEnthalpy','HeatVaporization',
'Polarizability',
'ThermalConductivity']
self.ElementProperty = ElementProperty(data_source='magpie',features=elemental_properties,
stats=["mean", "std_dev"])
#check matminer featurizers
self.check_matminer_featurizers()
def featurize(self,composition):
bca = BCA(composition,self.radius_type,self.normalize_formula)
bca_features = bca.featurize()
vo_features = self.ValenceOrbital.featurize(bca.metal_composition) #avg and frac s, p , d, f electrons for metals
vo_features += [sum(vo_features[0:3])] #avg total valence electrons for metals
ao_features = self.AtomicOrbitals.featurize(bca.metal_composition) #H**O and LUMO character and energy levels for metals from atomic orbitals)
ao_features = [ao_features[i] for i in range(len(ao_features)) if i not in (0,1,3,4)]#exclude HOMO_character,HOMO_element, LUMO_character, LUMO_element - categoricals
ce_features = self.CohesiveEnergy.featurize(bca.metal_composition,formation_energy_per_atom=1e-10) #avg metal elemental cohesive energy
bc_features = self.BandCenter.featurize(bca.metal_composition) + self.BandCenter.featurize(bca.composition)
ve_features = self.ValenceOrbitalEnergy.featurize(bca.metal_composition) + self.ValenceOrbitalEnergy.featurize(bca.composition)
ep_features = self.ElementProperty.featurize(bca.metal_composition) + self.ElementProperty.featurize(bca.composition)
mm_features = vo_features + ao_features + ce_features + bc_features + ve_features + ep_features
return list(bca_features.values()) + mm_features
@property
def ElementProperty_custom_labels(self):
"""
Generate custom labels for ElementProperty featurizer that follow same naming convention as Perovskite class
"""
elemental_property_label_map = {'BoilingT':'boil_temp','MeltingT':'melt_temp',
'BulkModulus':'bulk_mod','ShearModulus':'shear_mod',
'Row':'row','Column':'column','Number':'number','MendeleevNumber':'mendeleev','SpaceGroupNumber':'space_group',
'Density':'density','MolarVolume':'molar_vol',
'FusionEnthalpy':'H_fus','HeatVaporization':'H_vap',
'Polarizability':'polarizability',
'ThermalConductivity':'sigma_therm'}
element_property_labels = list(map(elemental_property_label_map.get,self.ElementProperty.features))
labels = []
for attr in element_property_labels:
for stat in self.ElementProperty.stats:
if stat=='std_dev':
stat = 'std'
labels.append(f'M_{attr}_{stat}')
for attr in element_property_labels:
for stat in self.ElementProperty.stats:
if stat=='std_dev':
stat = 'std'
labels.append(f'BCA_{attr}_{stat}')
return labels
@property
def ElementProperty_units(self):
"""
Generate units for ElementProperty featurizer that follow same naming convention as Perovskite class
"""
elemental_property_unit_map = {'BoilingT':'temperature','MeltingT':'temperature',
'BulkModulus':'pressure','ShearModulus':'pressure',
'Row':'none','Column':'none','Number':'none','MendeleevNumber':'none','SpaceGroupNumber':'none',
'Density':'density','MolarVolume':'volume',
'FusionEnthalpy':'energy','HeatVaporization':'energy',
'Polarizability':'polarizability',
'ThermalConductivity':'therm'}
element_property_units = list(map(elemental_property_unit_map.get,self.ElementProperty.features))
units = []
for ep_unit in element_property_units:
for stat in self.ElementProperty.stats:
units.append(ep_unit)
return units*2
def ElementProperty_label_check(self):
"""
Check that ElementProperty feature labels are as expected
If not, features may not align with feature labels
"""
#ElementProperty.feature_labels() code as of 1/24/20
labels = []
for attr in self.ElementProperty.features:
src = self.ElementProperty.data_source.__class__.__name__
for stat in self.ElementProperty.stats:
labels.append("{} {} {}".format(src, stat, attr))
if labels!=self.ElementProperty.feature_labels():
raise Exception('ElementProperty features or labels have changed')
@property
def matminer_labels(self):
"""
Feature labels for matminer-derived features
"""
labels = [
#ValenceOrbital labels
'M_ValenceElec_s_mean',
'M_ValenceElec_p_mean',
'M_ValenceElec_d_mean',
'M_ValenceElec_f_mean',
'M_ValenceElec_s_frac',
'M_ValenceElec_p_frac',
'M_ValenceElec_d_frac',
'M_ValenceElec_f_frac',
'M_ValenceElec_tot_mean',
#AtomicOrbitals labels
#'M_HOMO_character',
'M_HOMO_energy',
#'M_LUMO_character',
'M_LUMO_energy',
'M_AO_gap',
#CohesiveEnergy labels
'M_cohesive_energy_mean',
#BandCenter labels
'M_BandCenter',
'BCA_BandCenter',
#ValenceOrbitalEnergy labels
'M_ValenceEnergy_mean',
'BCA_ValenceEnergy_mean'
]
labels += self.ElementProperty_custom_labels
return labels
@property
def matminer_units(self):
"""
Feature units for matminer-derived features
"""
units = [
#ValenceOrbital units
'none',
'none',
'none',
'none',
'none',
'none',
'none',
'none',
'none',
#AtomicOrbitals units
#'M_HOMO_character',
'energy',
#'M_LUMO_character',
'energy',
'energy',
#CohesiveEnergy units
'energy',
#BandCenter units
'energy',
'energy',
#ValenceOrbitalEnergy units
'energy',
'energy'
]
units += self.ElementProperty_units
return units
def feature_labels(self):
bca_feature_labels = list(BCA(mg.Composition('BaO'),self.radius_type,self.normalize_formula).featurize().keys())
return bca_feature_labels + self.matminer_labels
def feature_units(self):
bca_units = BCA(mg.Composition('BaO')).feature_units()
return bca_units + self.matminer_units
def check_matminer_featurizers(self):
"""
Check that features and feature order for matminer featurizers are as expected
If features or feature order have changed, featurize() may return unexpected features that do not align with feature_labels()
"""
#verify that matminer feature labels haven't changed
if self.ValenceOrbital.feature_labels() != ['avg s valence electrons',
'avg p valence electrons',
'avg d valence electrons',
'avg f valence electrons',
'frac s valence electrons',
'frac p valence electrons',
'frac d valence electrons',
'frac f valence electrons']:
raise Exception('ValenceOrbital features or labels have changed')
if self.AtomicOrbitals.feature_labels() != ['HOMO_character',
'HOMO_element',
'HOMO_energy',
'LUMO_character',
'LUMO_element',
'LUMO_energy',
'gap_AO']:
raise Exception('AtomicOrbitals features or labels have changed')
if self.CohesiveEnergy.feature_labels() != ['cohesive energy']:
raise Exception('CohesiveEnergy features or labels have changed')
if self.BandCenter.feature_labels() != ['band center']:
raise Exception('BandCenter features or labels have changed')
self.ElementProperty_label_check()
def citations(self):
featurizers = [self.ValenceOrbital, self.AtomicOrbitals, self.CohesiveEnergy, self.BandCenter, self.ValenceOrbitalEnergy, BCA(mg.Composition('BaO'))]
return list(np.unique(sum([f.citations() for f in featurizers],[])))