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 = {}
def test_cohesive_energy(self):
mpr = MPRester()
if not mpr.api_key:
raise SkipTest(
"Materials Project API key not set; Skipping cohesive energy test"
)
df_cohesive_energy = CohesiveEnergy().featurize_dataframe(
self.df, col_id="composition")
self.assertAlmostEqual(df_cohesive_energy["cohesive energy"][0], 5.179,
2)
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 __init__(self,normalize_formula=False):
self.normalize_formula = normalize_formula
# don't need ValenceOrbital - valence counts etc. covered in ElementProperty.from_preset('magpie')
# self.ValenceOrbital = ValenceOrbital()
self.AtomicOrbitals = AtomicOrbitalsMod()
self.CohesiveEnergy = CohesiveEnergy()
self.BandCenter = BandCenter()
self.ValenceOrbitalEnergy = ValenceOrbitalEnergy()
# ElementProperty featurizer with magpie properties plus additional properties
self.ElementProperty = ElementProperty.from_preset('magpie')
self.ElementProperty.features += ['BoilingT',
'BulkModulus', 'ShearModulus',
'Density','MolarVolume',
'FusionEnthalpy','HeatVaporization',
'Polarizability',
'ThermalConductivity']
# range, min, max are irrelevant inside the ternary
# self.ElementProperty.stats = ['mean', 'avg_dev','mode']
# check matminer featurizers
self.check_matminer_featurizers()
def _extract_features(self, df_input):
"""
Extract features using Matminer from the 'structure' column in
df_input
Args:
df_input (DataFrame): Pandas DataFrame whcih conatains features
from Materials Project Database of the input samples
Returns:
df_extracted (DataFrame): Pandas DataFrame which contains
features of input samples extracted using Matminer
"""
# Dropping the 'theoretical' column
df_input.drop(columns=["theoretical"], inplace=True)
# Extracting the features
dfeat = DensityFeatures()
symmfeat = GlobalSymmetryFeatures()
mfeat = Meredig()
cefeat = CohesiveEnergy()
df_input["density"] = df_input.structure.apply(
lambda x: dfeat.featurize(x)[0])
df_input["vpa"] = df_input.structure.apply(
lambda x: dfeat.featurize(x)[1])
df_input["packing fraction"] = df_input.structure.apply(
lambda x: dfeat.featurize(x)[2])
df_input["spacegroup_num"] = df_input.structure.apply(
lambda x: symmfeat.featurize(x)[0])
df_input["cohesive_energy"] = df_input.apply(
lambda x: cefeat.featurize(
x.structure.composition,
formation_energy_per_atom=x.formation_energy_per_atom,
)[0],
axis=1,
)
df_input["mean AtomicWeight"] = df_input.structure.apply(
lambda x: mfeat.featurize(x.composition)[-17])
df_input["range AtomicRadius"] = df_input.structure.apply(
lambda x: mfeat.featurize(x.composition)[-12])
df_input["mean AtomicRadius"] = df_input.structure.apply(
lambda x: mfeat.featurize(x.composition)[-11])
df_input["range Electronegativity"] = df_input.structure.apply(
lambda x: mfeat.featurize(x.composition)[-10])
df_input["mean Electronegativity"] = df_input.structure.apply(
lambda x: mfeat.featurize(x.composition)[-9])
# Drop 'structure' column
df_input.drop(columns=["structure"], inplace=True)
# ignore compounds that failed to featurize
df_extracted = df_input.fillna(
df_input.mean()).query("cohesive_energy > 0.0")
# Re-arranging the 'PU Label' column
pu_label = df_extracted["PU_label"]
df_extracted = df_extracted.drop(["PU_label"], axis=1)
df_extracted["PU_label"] = pu_label
# Drop the icsd_ids column
df_extracted.drop(columns=["icsd_ids"], inplace=True)
return df_extracted
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()
def AddFeatures(df): # Add features by Matminer
from matminer.featurizers.conversions import StrToComposition
df = StrToComposition().featurize_dataframe(df, "formula")
from matminer.featurizers.composition import ElementProperty
ep_feat = ElementProperty.from_preset(preset_name="magpie")
df = ep_feat.featurize_dataframe(
df, col_id="composition"
) # input the "composition" column to the featurizer
from matminer.featurizers.conversions import CompositionToOxidComposition
from matminer.featurizers.composition import OxidationStates
df = CompositionToOxidComposition().featurize_dataframe(df, "composition")
os_feat = OxidationStates()
df = os_feat.featurize_dataframe(df, "composition_oxid")
from matminer.featurizers.composition import ElectronAffinity
ea_feat = ElectronAffinity()
df = ea_feat.featurize_dataframe(df,
"composition_oxid",
ignore_errors=True)
from matminer.featurizers.composition import BandCenter
bc_feat = BandCenter()
df = bc_feat.featurize_dataframe(df,
"composition_oxid",
ignore_errors=True)
from matminer.featurizers.composition import CohesiveEnergy
ce_feat = CohesiveEnergy()
df = ce_feat.featurize_dataframe(df,
"composition_oxid",
ignore_errors=True)
from matminer.featurizers.composition import Miedema
m_feat = Miedema()
df = m_feat.featurize_dataframe(df, "composition_oxid", ignore_errors=True)
from matminer.featurizers.composition import TMetalFraction
tmf_feat = TMetalFraction()
df = tmf_feat.featurize_dataframe(df,
"composition_oxid",
ignore_errors=True)
from matminer.featurizers.composition import ValenceOrbital
vo_feat = ValenceOrbital()
df = vo_feat.featurize_dataframe(df,
"composition_oxid",
ignore_errors=True)
from matminer.featurizers.composition import YangSolidSolution
yss_feat = YangSolidSolution()
df = yss_feat.featurize_dataframe(df,
"composition_oxid",
ignore_errors=True)
from matminer.featurizers.structure import GlobalSymmetryFeatures
# This is the border between compositional features and structural features. Comment out the following featurizers to use only compostional features.
gsf_feat = GlobalSymmetryFeatures()
df = gsf_feat.featurize_dataframe(df, "structure", ignore_errors=True)
from matminer.featurizers.structure import StructuralComplexity
sc_feat = StructuralComplexity()
df = sc_feat.featurize_dataframe(df, "structure", ignore_errors=True)
from matminer.featurizers.structure import ChemicalOrdering
co_feat = ChemicalOrdering()
df = co_feat.featurize_dataframe(df, "structure", ignore_errors=True)
from matminer.featurizers.structure import MaximumPackingEfficiency
mpe_feat = MaximumPackingEfficiency()
df = mpe_feat.featurize_dataframe(df, "structure", ignore_errors=True)
from matminer.featurizers.structure import MinimumRelativeDistances
mrd_feat = MinimumRelativeDistances()
df = mrd_feat.featurize_dataframe(df, "structure", ignore_errors=True)
from matminer.featurizers.structure import StructuralHeterogeneity
sh_feat = StructuralHeterogeneity()
df = sh_feat.featurize_dataframe(df, "structure", ignore_errors=True)
from matminer.featurizers.structure import SiteStatsFingerprint
from matminer.featurizers.site import AverageBondLength
from pymatgen.analysis.local_env import CrystalNN
bl_feat = SiteStatsFingerprint(
AverageBondLength(CrystalNN(search_cutoff=20)))
df = bl_feat.featurize_dataframe(df, "structure", ignore_errors=True)
from matminer.featurizers.site import AverageBondAngle
ba_feat = SiteStatsFingerprint(
AverageBondAngle(CrystalNN(search_cutoff=20)))
df = ba_feat.featurize_dataframe(df, "structure", ignore_errors=True)
from matminer.featurizers.site import BondOrientationalParameter
bop_feat = SiteStatsFingerprint(BondOrientationalParameter())
df = bop_feat.featurize_dataframe(df, "structure", ignore_errors=True)
from matminer.featurizers.site import CoordinationNumber
cn_feat = SiteStatsFingerprint(CoordinationNumber())
df = cn_feat.featurize_dataframe(df, "structure", ignore_errors=True)
from matminer.featurizers.structure import DensityFeatures
df_feat = DensityFeatures()
df = df_feat.featurize_dataframe(df, "structure", ignore_errors=True)
return (df)
#df = structural_heterogeneity.featurize_dataframe(df, 'structures',ignore_errors=False)
#convert structure to composition
from matminer.featurizers.conversions import StructureToComposition
structures_to_compositions = StructureToComposition()
df = structures_to_compositions.featurize_dataframe(df, 'structures')
#convert composition to oxidcomposition
from matminer.featurizers.conversions import CompositionToOxidComposition
OxidCompositions = CompositionToOxidComposition()
print(OxidCompositions.feature_labels())
df = OxidCompositions.featurize_dataframe(df, 'composition')
#CohesiveEnergy
from matminer.featurizers.composition import CohesiveEnergy
cohesive_energy = CohesiveEnergy()
cohesive_energy.set_n_jobs(28)
labels.append(cohesive_energy.feature_labels())
df = cohesive_energy.featurize_dataframe(df,
'composition',
ignore_errors=True)
#ValenceOrbital
from matminer.featurizers.composition import ValenceOrbital
valence_orbital = ValenceOrbital()
valence_orbital.set_n_jobs(28)
labels.append(valence_orbital.feature_labels())
df = valence_orbital.featurize_dataframe(df,
'composition',
ignore_errors=True)
def test_cohesive_energy(self):
df_cohesive_energy = CohesiveEnergy().featurize_dataframe(
self.df, col_id="composition")
self.assertAlmostEqual(df_cohesive_energy["Cohesive Energy"][0],
-18.24568582)
class GenericFeaturizer(BaseFeaturizer):
"""
Featurizer to use generic properties available in matminer featurizers; no features from BCA class utilized
"""
def __init__(self,normalize_formula=False):
self.normalize_formula = normalize_formula
# don't need ValenceOrbital - valence counts etc. covered in ElementProperty.from_preset('magpie')
# self.ValenceOrbital = ValenceOrbital()
self.AtomicOrbitals = AtomicOrbitalsMod()
self.CohesiveEnergy = CohesiveEnergy()
self.BandCenter = BandCenter()
self.ValenceOrbitalEnergy = ValenceOrbitalEnergy()
# ElementProperty featurizer with magpie properties plus additional properties
self.ElementProperty = ElementProperty.from_preset('magpie')
self.ElementProperty.features += ['BoilingT',
'BulkModulus', 'ShearModulus',
'Density','MolarVolume',
'FusionEnthalpy','HeatVaporization',
'Polarizability',
'ThermalConductivity']
# range, min, max are irrelevant inside the ternary
# self.ElementProperty.stats = ['mean', 'avg_dev','mode']
# check matminer featurizers
self.check_matminer_featurizers()
def featurize(self,composition):
# use BCA just to get composition and metal_composition
bca = BCA(composition,'ionic_radius',self.normalize_formula)
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 = ao_features + ce_features + bc_features + ve_features + ep_features
return mm_features
def feature_labels(self):
"""
Feature labels for matminer-derived features
"""
labels = [
#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 += [f'M {l}' for l in self.ElementProperty.feature_labels()]
labels += [f'BCA {l}' for l in self.ElementProperty.feature_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_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.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')
def citations(self):
featurizers = [self.AtomicOrbitals, self.CohesiveEnergy, self.BandCenter, self.ValenceOrbitalEnergy]
citations = sum([f.citations() for f in featurizers],[])
# add pymatgen citation
citations += [
"@article{Ong2012b,"
"author = {Ong, Shyue Ping and Richards, William Davidson and Jain, Anubhav and Hautier, Geoffroy and Kocher, Michael and Cholia, Shreyas and Gunter, Dan and Chevrier, Vincent L. and Persson, Kristin A. and Ceder, Gerbrand},"
"doi = {10.1016/j.commatsci.2012.10.028},"
"file = {:Users/shyue/Mendeley Desktop/Ong et al/Computational Materials Science/2013 - Ong et al. - Python Materials Genomics (pymatgen) A robust, open-source python library for materials analysis.pdf:pdf;:Users/shyue/Mendeley Desktop/Ong et al/Computational Materials Science/2013 - Ong et al. - Python Materials Genomics (pymatgen) A robust, open-source python library for materials analysis(2).pdf:pdf},"
"issn = {09270256},"
"journal = {Computational Materials Science},"
"month = feb,"
"pages = {314--319},"
"title = {{Python Materials Genomics (pymatgen): A robust, open-source python library for materials analysis}},"
"url = {http://linkinghub.elsevier.com/retrieve/pii/S0927025612006295},"
"volume = {68},"
"year = {2013}"
"}"
]
return list(np.unique(citations))
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],[])))