def add_cs_features(df,rdf_flag=False):
df["composition"] = str_to_composition(df["pretty_formula"])
df["composition_oxid"] = composition_to_oxidcomposition(df["composition"])
df["structure"] = dict_to_object(df["structure"])
vo = ValenceOrbital()
df = vo.featurize_dataframe(df,"composition")
ox = OxidationStates()
df = ox.featurize_dataframe(df, "composition_oxid")
# structure features
den = DensityFeatures()
df = den.featurize_dataframe(df, "structure")
if rdf_flag:
rdf = RadialDistributionFunction(cutoff=15.0,bin_size=0.2)
df = rdf.featurize_dataframe(df, "structure")
return df
# -- start F7
from matminer.featurizers.composition import ElectronAffinity
ela_feat = ElectronAffinity()
fdf = ela_feat.featurize_dataframe(fdf,
col_id='composition',
ignore_errors=True)
# -- end F7
# -- start F9
from matminer.featurizers.composition import ValenceOrbital
vlo_feat = ValenceOrbital()
fdf = vlo_feat.featurize_dataframe(fdf,
col_id='composition',
ignore_errors=True)
# -- end F9
# -- start F10
from matminer.featurizers.composition import IonProperty
iop_feat = IonProperty()
fdf = iop_feat.featurize_dataframe(fdf,
col_id='composition',
ignore_errors=True)
# -- end F10
# -- start F12
from matminer.featurizers.composition import TMetalFraction
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)
#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)
#AtomicOrbital
from matminer.featurizers.composition import AtomicOrbitals
atomic_orbitals = AtomicOrbitals()
atomic_orbitals.set_n_jobs(28)
labels.append(atomic_orbitals.feature_labels())
df = atomic_orbitals.featurize_dataframe(df,
'composition',
ignore_errors=True)
#ElectronegativityDiff
from matminer.featurizers.composition import ElectronegativityDiff
electronegativity_diff = ElectronegativityDiff()
electronegativity_diff.set_n_jobs(28)