class DopingFermi(BaseFeaturizer):
"""
The fermi level (w.r.t. selected reference energy) associated with a
specified carrier concentration (1/cm3) and temperature. This featurizar
requires the total density of states and structure. The Structure
as dos.structure (e.g. in CompleteDos) is required by FermiDos class.
Args:
dopings ([float]): list of doping concentrations 1/cm3. Note that a
negative concentration is treated as electron majority carrier
(n-type) and positive for holes (p-type)
eref (str or int or float): energy alignment reference. Defaults
to midgap (equilibrium fermi). A fixed number can also be used.
str options: "midgap", "vbm", "cbm", "dos_fermi", "band_center"
T (float): absolute temperature in Kelvin
return_eref: if True, instead of aligning the fermi levels based
on eref, it (eref) will be explicitly returned as a feature
Returns (featurize returns [float] and featurize_labels returns [str]):
examples:
fermi_c-1e+20T300 (float): the fermi level for the electron
concentration of 1e20 and the temperature of 300K.
fermi_c1e+18T600 (float): the fermi level for the hole concentration
of 1e18 and the temperature of 600K.
midgap eref (float): if return_eref==True then eref (midgap here)
energy is returned. In this case other fermi levels returned are
absolute as opposed to relative to eref (i.e. if not return_eref)
"""
def __init__(self, dopings=None, eref="midgap", T=300, return_eref=False):
self.dopings = dopings or [-1e20, 1e20]
self.eref = eref
self.T = T
self.return_eref = return_eref
self.BC = BandCenter()
def featurize(self, dos, bandgap=None):
"""
Args:
dos (pymatgen Dos, CompleteDos or FermiDos):
bandgap (float): for example the experimentally measured band gap
or one that is calculated via more accurate methods than the
one used to generate dos. dos will be scissored to have the
same electronic band gap as bandgap.
Returns ([float]): features are fermi levels in eV at the given
concentrations and temperature + eref in eV if return_eref
"""
dos = FermiDos(dos, bandgap=bandgap)
feats = []
eref = 0.0
for c in self.dopings:
fermi = dos.get_fermi(c=c, T=self.T, nstep=50)
if isinstance(self.eref, str):
if self.eref == "dos_fermi":
eref = dos.efermi
elif self.eref in ["midgap", "vbm", "cbm"]:
ecbm, evbm = dos.get_cbm_vbm()
if self.eref == "midgap":
eref = (evbm + ecbm) / 2.0
elif self.eref == "vbm":
eref = evbm
elif self.eref == "cbm":
eref = ecbm
elif self.eref == "band center":
eref = self.BC.featurize(dos.structure.composition)[0]
else:
raise ValueError('Unsupported "eref": {}'.format(
self.eref))
else:
eref = self.eref
if not self.return_eref:
fermi -= eref
feats.append(fermi)
if self.return_eref:
feats.append(eref)
return feats
def feature_labels(self):
"""
Returns ([str]): list of names of the features generated by featurize
example: "fermi_c-1e+20T300" that is the fermi level for the
electron concentration of 1e20 (c-1e+20) and temperature of 300K.
"""
labels = []
for c in self.dopings:
labels.append("fermi_c{}T{}".format(c, self.T))
if self.return_eref:
labels.append("{} eref".format(self.eref))
return labels
def implementors(self):
return ["Alireza Faghaninia"]
def citations(self):
return []
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 DopingFermi(BaseFeaturizer):
"""
The fermi level (w.r.t. selected reference energy) associated with a
specified carrier concentration (1/cm3) and temperature. This featurizar
requires the total density of states and structure. The Structure
as dos.structure (e.g. in CompleteDos) is required by FermiDos class.
Args:
dopings ([float]): list of doping concentrations 1/cm3. Note that a
negative concentration is treated as electron majority carrier
(n-type) and positive for holes (p-type)
eref (str or int or float): energy alignment reference. Defaults
to midgap (equilibrium fermi). A fixed number can also be used.
str options: "midgap", "vbm", "cbm", "dos_fermi", "band_center"
T (float): absolute temperature in Kelvin
return_eref: if True, instead of aligning the fermi levels based
on eref, it (eref) will be explicitly returned as a feature
Returns (featurize returns [float] and featurize_labels returns [str]):
examples:
fermi_c-1e+20T300 (float): the fermi level for the electron
concentration of 1e20 and the temperature of 300K.
fermi_c1e+18T600 (float): fermi level for the hole concentration
of 1e18 and the temperature of 600K.
midgap eref (float): if return_eref==True then eref (midgap here)
energy is returned. In this case, fermi levels are absolute as
opposed to relative to eref (i.e. if not return_eref)
"""
def __init__(self, dopings=None, eref="midgap", T=300, return_eref=False):
self.dopings = dopings or [-1e20, 1e20]
self.eref = eref
self.T = T
self.return_eref = return_eref
self.BC = BandCenter()
def featurize(self, dos, bandgap=None):
"""
Args:
dos (pymatgen Dos, CompleteDos or FermiDos):
bandgap (float): for example the experimentally measured band gap
or one that is calculated via more accurate methods than the
one used to generate dos. dos will be scissored to have the
same electronic band gap as bandgap.
Returns ([float]): features are fermi levels in eV at the given
concentrations and temperature + eref in eV if return_eref
"""
dos = FermiDos(dos, bandgap=bandgap)
feats = []
eref = 0.0
for c in self.dopings:
fermi = dos.get_fermi(c=c, T=self.T, nstep=50)
if isinstance(self.eref, str):
if self.eref == "dos_fermi":
eref = dos.efermi
elif self.eref in ["midgap", "vbm", "cbm"]:
ecbm, evbm = dos.get_cbm_vbm()
if self.eref == "midgap":
eref = (evbm + ecbm) / 2.0
elif self.eref == "vbm":
eref = evbm
elif self.eref == "cbm":
eref = ecbm
elif self.eref == "band center":
eref = self.BC.featurize(dos.structure.composition)[0]
else:
raise ValueError('Unsupported "eref": {}'.format(self.eref))
else:
eref = self.eref
if not self.return_eref:
fermi -= eref
feats.append(fermi)
if self.return_eref:
feats.append(eref)
return feats
def feature_labels(self):
"""
Returns ([str]): list of names of the features generated by featurize
example: "fermi_c-1e+20T300" that is the fermi level for the
electron concentration of 1e20 (c-1e+20) and temperature of 300K.
"""
labels = []
for c in self.dopings:
labels.append("fermi_c{}T{}".format(c, self.T))
if self.return_eref:
labels.append("{} eref".format(self.eref))
return labels
def implementors(self):
return ["Alireza Faghaninia"]
def citations(self):
return []
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],[])))
