def get_structure_properties(structure: Structure, mode: str = 'all') -> dict:
if mode == 'all':
featurizer = MultipleFeaturizer([
SiteStatsFingerprint.from_preset(
'CoordinationNumber_ward-prb-2017'),
StructuralHeterogeneity(),
ChemicalOrdering(),
DensityFeatures(),
MaximumPackingEfficiency(),
SiteStatsFingerprint.from_preset(
'LocalPropertyDifference_ward-prb-2017'),
StructureComposition(Stoichiometry()),
StructureComposition(ElementProperty.from_preset('magpie')),
StructureComposition(ValenceOrbital(props=['frac'])),
])
else:
# Calculate only those which do not need a Voronoi tesselation
featurizer = MultipleFeaturizer([
DensityFeatures(),
StructureComposition(Stoichiometry()),
StructureComposition(ElementProperty.from_preset('magpie')),
StructureComposition(ValenceOrbital(props=['frac'])),
])
X = featurizer.featurize(structure)
matminer_dict = dict(list(zip(featurizer.feature_labels(), X)))
matminer_dict['volume'] = structure.volume
return matminer_dict
def composition_featurizer(df_input: pd.DataFrame, **kwargs) -> pd.DataFrame:
"""Return a Pandas DataFrame with all compositional features"""
# generate the "composition" column
df_comp = StrToComposition().featurize_dataframe(df_input,
col_id="Compound")
# generate features based on elemental properites
ep_featurizer = ElementProperty.from_preset(preset_name="magpie")
ep_featurizer.featurize_dataframe(df_comp,
col_id="composition",
inplace=True)
# generate the "composition_oxid" column based on guessed oxidation states
CompositionToOxidComposition(
return_original_on_error=True, **kwargs).featurize_dataframe(
# ignore errors from non-integer stoichiometries
df_comp,
"composition",
ignore_errors=True,
inplace=True)
# correct oxidation states
df_comp = correct_comp_oxid(df_comp)
# generate features based on oxidation states
os_featurizer = OxidationStates()
os_featurizer.featurize_dataframe(df_comp,
"composition_oxid",
ignore_errors=True,
inplace=True)
# remove compounds with predicted oxidation states of 0
return df_comp[df_comp["minimum oxidation state"] != 0]
def test_elem_matminer(self):
df_elem = ElementProperty.from_preset("matminer").featurize_dataframe(self.df, col_id="composition")
self.assertAlmostEqual(df_elem["minimum melting_point"][0], 54.8, 1)
self.assertTrue(math.isnan(df_elem["maximum bulk_modulus"][0]))
self.assertAlmostEqual(df_elem["range X"][0], 1.61, 1)
self.assertAlmostEqual(df_elem["mean X"][0], 2.796, 1)
self.assertAlmostEqual(df_elem["maximum block"][0], 3, 1)
def test_elem_deml(self):
df_elem_deml = ElementProperty.from_preset("deml").featurize_dataframe(self.df, col_id="composition")
self.assertAlmostEqual(df_elem_deml["minimum atom_num"][0], 8)
self.assertAlmostEqual(df_elem_deml["maximum atom_num"][0], 26)
self.assertAlmostEqual(df_elem_deml["range atom_num"][0], 18)
self.assertAlmostEqual(df_elem_deml["mean atom_num"][0], 15.2)
self.assertAlmostEqual(df_elem_deml["std_dev atom_num"][0], 12.7279, 4)
def featurize_structures(self, featurizer=None, **kwargs):
"""
Featurizes the hypothetical structures available from
hypo_structures method. Hypothetical structures for which
featurization fails are removed and valid structures are
made available as valid_structures
Args:
featurizer (Featurizer): A MatMiner Featurizer.
Defaults to MultipleFeaturizer with PRB Ward
Voronoi descriptors.
**kwargs (dict): kwargs passed to featurize_many
method of featurizer.
Returns:
(pandas.DataFrame): features
"""
# Note the redundancy here is for pandas to work
if self.hypo_structures is None:
warnings.warn("No structures available. Generating structures.")
self.get_structures()
print("Generating features")
featurizer = featurizer if featurizer else MultipleFeaturizer([
SiteStatsFingerprint.from_preset("CoordinationNumber_ward-prb-2017"),
StructuralHeterogeneity(),
ChemicalOrdering(),
MaximumPackingEfficiency(),
SiteStatsFingerprint.from_preset("LocalPropertyDifference_ward-prb-2017"),
StructureComposition(Stoichiometry()),
StructureComposition(ElementProperty.from_preset("magpie")),
StructureComposition(ValenceOrbital(props=['frac'])),
StructureComposition(IonProperty(fast=True))
])
features = featurizer.featurize_many(
self.hypo_structures['structure'],
ignore_errors=True, **kwargs)
n_species, formula = [], []
for s in self.hypo_structures['structure']:
n_species.append(len(s.composition.elements))
formula.append(s.composition.formula)
self._features_df = pd.DataFrame.from_records(
features, columns=featurizer.feature_labels())
self._features_df.index = self.hypo_structures.index
self._features_df['N_species'] = n_species
self._features_df['Composition'] = formula
self._features_df['structure'] = self.hypo_structures['structure']
self.features = self._features_df.dropna(axis=0, how='any')
self.features = self.features.reindex(sorted(self.features.columns), axis=1)
self._valid_structure_labels = list(self.features.index)
self.valid_structures = self.hypo_structures.loc[self._valid_structure_labels]
print("{} out of {} structures were successfully featurized.".format(
self.features.shape[0], self._features_df.shape[0]))
return self.features
def _featurize(self, composition: "pymatgen.Composition"):
"""
Calculate chemical fingerprint from crystal composition.
Parameters
----------
composition: pymatgen.Composition object
Composition object.
Returns
-------
feats: np.ndarray
Vector of properties and statistics derived from chemical
stoichiometry. Some values may be NaN.
"""
try:
from matminer.featurizers.composition import ElementProperty
except ModuleNotFoundError:
raise ValueError("This class requires matminer to be installed.")
ep = ElementProperty.from_preset(self.data_source)
try:
feats = ep.featurize(composition)
except:
feats = []
return np.array(feats)
def __init__(self, pbar=False):
self.regressor = RandomForestRegressor(n_estimators=500, n_jobs=-1, verbose=3)
self.stc = StrToComposition()
ep = ElementProperty.from_preset("magpie")
ef = ElementFraction()
self.featurizer = MultipleFeaturizer([ep, ef])
self.pbar = pbar
def tran_feat_composition(
df,
var_formula="FORMULA",
preset_name="magpie",
append=True,
ignore_errors=True,
**kwargs,
):
r"""Featurize a dataset using matminer
Featurize chemical composition using matminer package.
Args:
df (DataFrame): Data to featurize
var_formula (string): Column in df with chemical formula; formula
given as string
append (bool): Append results to original columns?
preset_name (string): Matminer featurization preset
Kwargs:
ignore_errors (bool): Do not throw an error while parsing formulae; set to
True to return NaN's for invalid formulae.
Notes:
- A pre-processor and wrapper for matminer.featurizers.composition
References:
Ward, L., Dunn, A., Faghaninia, A., Zimmermann, N. E. R., Bajaj, S., Wang, Q., Montoya, J. H., Chen, J., Bystrom, K., Dylla, M., Chard, K., Asta, M., Persson, K., Snyder, G. J., Foster, I., Jain, A., Matminer: An open source toolkit for materials data mining. Comput. Mater. Sci. 152, 60-69 (2018).
Examples:
>>> import grama as gr
>>> from grama.tran import tf_feat_composition
>>> (
>>> gr.df_make(FORMULA=["C6H12O6"])
>>> >> gr.tf_feat_composition()
>>> )
"""
## Check invariants
## Featurize
featurizer = ElementProperty.from_preset(preset_name=preset_name)
df_res = StrToComposition().featurize_dataframe(
df[[var_formula]],
var_formula,
ignore_errors=ignore_errors,
)
df_res = featurizer.featurize_dataframe(
df_res,
col_id="composition",
ignore_errors=ignore_errors,
**kwargs,
)
df_res.drop(columns=[var_formula, "composition"], inplace=True)
## Concatenate as necessary
if append:
df_res = concat((df, df_res), axis=1)
return df_res
def _featurize(self, comp):
"""
Calculate chemical fingerprint from crystal composition.
Parameters
----------
comp : str
Reduced formula of crystal.
Returns
-------
feats: np.ndarray
Vector of properties and statistics derived from chemical
stoichiometry. Some values may be NaN.
"""
from pymatgen import Composition
from matminer.featurizers.composition import ElementProperty
# Get pymatgen Composition object
c = Composition(comp)
ep = ElementProperty.from_preset(self.data_source)
try:
feats = ep.featurize(c)
except:
feats = []
return np.array(feats)
def test_elem_matminer(self):
df_elem = ElementProperty.from_preset("matminer").featurize_dataframe(
self.df, col_id="composition")
self.assertAlmostEqual(df_elem["minimum melting_point"][0], 54.8, 1)
self.assertTrue(math.isnan(df_elem["maximum bulk_modulus"][0]))
self.assertAlmostEqual(df_elem["range X"][0], 1.61, 1)
self.assertAlmostEqual(df_elem["mean X"][0], 2.796, 1)
def featurize_composition(df: pd.DataFrame) -> pd.DataFrame:
""" Decorate input `pandas.DataFrame` of structures with composition
features from matminer.
Currently applies the set of all matminer composition features.
Args:
df (pandas.DataFrame): the input dataframe with `"structure"`
column containing `pymatgen.Structure` objects.
Returns:
pandas.DataFrame: the decorated DataFrame.
"""
logging.info("Applying composition featurizers...")
df = df.copy()
df['composition'] = df['structure'].apply(lambda s: s.composition)
featurizer = MultipleFeaturizer([ElementProperty.from_preset("magpie"),
AtomicOrbitals(),
BandCenter(),
# ElectronAffinity(), - This descriptor was not used in the paper preset
Stoichiometry(),
ValenceOrbital(),
IonProperty(),
ElementFraction(),
TMetalFraction(),
# CohesiveEnergy(), - This descriptor was not used in the paper preset
Miedema(),
YangSolidSolution(),
AtomicPackingEfficiency(),
])
df = featurizer.featurize_dataframe(df, "composition", multiindex=True, ignore_errors=True)
df.columns = df.columns.map('|'.join).str.strip('|')
ox_featurizer = MultipleFeaturizer([OxidationStates(),
ElectronegativityDiff()
])
df = CompositionToOxidComposition().featurize_dataframe(df, "Input Data|composition")
df = ox_featurizer.featurize_dataframe(df, "composition_oxid", multiindex=True, ignore_errors=True)
df = df.rename(columns={'Input Data': ''})
df.columns = df.columns.map('|'.join).str.strip('|')
_orbitals = {"s": 1, "p": 2, "d": 3, "f": 4}
df['AtomicOrbitals|HOMO_character'] = df['AtomicOrbitals|HOMO_character'].map(_orbitals)
df['AtomicOrbitals|LUMO_character'] = df['AtomicOrbitals|LUMO_character'].map(_orbitals)
df['AtomicOrbitals|HOMO_element'] = df['AtomicOrbitals|HOMO_element'].apply(
lambda x: -1 if not isinstance(x, str) else Element(x).Z
)
df['AtomicOrbitals|LUMO_element'] = df['AtomicOrbitals|LUMO_element'].apply(
lambda x: -1 if not isinstance(x, str) else Element(x).Z
)
df = df.replace([np.inf, -np.inf, np.nan], 0)
return clean_df(df)
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_elem(self):
df_elem = ElementProperty.from_preset("magpie").featurize_dataframe(self.df, col_id="composition")
self.assertAlmostEqual(df_elem["minimum Number"][0], 8)
self.assertAlmostEqual(df_elem["maximum Number"][0], 26)
self.assertAlmostEqual(df_elem["range Number"][0], 18)
self.assertAlmostEqual(df_elem["mean Number"][0], 15.2)
self.assertAlmostEqual(df_elem["avg_dev Number"][0], 8.64)
self.assertAlmostEqual(df_elem["mode Number"][0], 8)
def test_elem_megnet_el(self):
ep = ElementProperty.from_preset("megnet_el")
df_elem = ep.featurize_dataframe(self.df, col_id="composition")
self.assertAlmostEqual(df_elem["MEGNetElementData maximum embedding 1"].iloc[0], 0.127333, places=6)
self.assertAlmostEqual(df_elem["MEGNetElementData maximum embedding 1"].iloc[1], 0.127333, places=6)
self.assertAlmostEqual(df_elem["MEGNetElementData maximum embedding 11"].iloc[0], 0.160505, places=6)
self.assertAlmostEqual(df_elem["MEGNetElementData maximum embedding 11"].iloc[1], 0.160505, places=6)
self.assertTrue(ep.citations())
def magpie_feature(formula):
data = [formula]
df = pd.DataFrame(data, columns=["formula"])
df["composition"] = df["formula"].transform(str_to_composition)
ep_feat = ElementProperty.from_preset(preset_name="magpie")
df = ep_feat.featurize_dataframe(df, col_id="composition")
df.drop(labels=["composition"], axis=1, inplace=True)
return df.iloc[0, 1:].to_numpy()
def Magpie(formulas):
if isinstance(formulas, str):
formulas = [formulas]
ep_feat = ElementProperty.from_preset(preset_name="magpie")
df = pd.DataFrame({"formula": formulas})
df["composition"] = df["formula"].transform(str_to_composition)
df = ep_feat.featurize_dataframe(df, col_id="composition")
df.drop(labels=["composition", "formula"], axis=1, inplace=True)
return np.array(df).astype(np.float32)
def test_fere_corr(self):
df_fere_corr = ElementProperty(features=["FERE correction"],
stats=["minimum", "maximum", "range", "mean", "std_dev"],
data_source="deml")\
.featurize_dataframe(self.df, col_id="composition")
self.assertAlmostEqual(df_fere_corr["minimum FERE correction"][0], -0.15213431610903)
self.assertAlmostEqual(df_fere_corr["maximum FERE correction"][0], 0.23)
self.assertAlmostEqual(df_fere_corr["range FERE correction"][0], 0.382134316)
self.assertAlmostEqual(df_fere_corr["mean FERE correction"][0], 0.077146274)
self.assertAlmostEqual(df_fere_corr["std_dev FERE correction"][0], 0.270209766)
def test_elem_matscholar_el(self):
df_elem = ElementProperty.from_preset("matscholar_el").featurize_dataframe(self.df, col_id="composition")
self.assertAlmostEqual(df_elem["range matscholar_el_149"].iloc[0],
0.06827970966696739)
self.assertAlmostEqual(df_elem["range matscholar_el_149"].iloc[1],
0.06827970966696739)
self.assertAlmostEqual(df_elem["mean matscholar_el_18"].iloc[0],
-0.020534400502219795)
self.assertAlmostEqual(df_elem["mean matscholar_el_18"].iloc[1],
-0.02483355056028813)
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, data_source: str = 'matminer'):
"""
Parameters
----------
data_source: str of "matminer", "magpie" or "deml" (default "matminer")
Source for element property data.
"""
try:
from matminer.featurizers.composition import ElementProperty
except ModuleNotFoundError:
raise ImportError("This class requires matminer to be installed.")
self.data_source = data_source
self.ep_featurizer = ElementProperty.from_preset(self.data_source)
def similarity(_parents, target):
featurizer = MultipleFeaturizer([
SiteStatsFingerprint.from_preset("CoordinationNumber_ward-prb-2017"),
StructuralHeterogeneity(),
ChemicalOrdering(),
MaximumPackingEfficiency(),
SiteStatsFingerprint.from_preset(
"LocalPropertyDifference_ward-prb-2017"),
StructureComposition(Stoichiometry()),
StructureComposition(ElementProperty.from_preset("magpie")),
StructureComposition(ValenceOrbital(props=["frac"])),
StructureComposition(IonProperty(fast=True)),
])
# HACK celery doesn't work with multiprocessing (used by matminer)
try:
from celery import current_task
if current_task:
featurizer.set_n_jobs(1)
except ImportError:
pass
x_target = pd.DataFrame.from_records([featurizer.featurize(target)],
columns=featurizer.feature_labels())
x_parent = pd.DataFrame.from_records(
featurizer.featurize_many(_parents, ignore_errors=True, pbar=False),
columns=featurizer.feature_labels(),
)
nulls = x_parent[x_parent.isnull().any(axis=1)].index.values
x_parent.fillna(100000, inplace=True)
x_target = x_target.reindex(sorted(x_target.columns), axis=1)
x_parent = x_parent.reindex(sorted(x_parent.columns), axis=1)
with open(os.path.join(settings.rxn_files, "scaler2.pickle"), "rb") as f:
scaler = pickle.load(f)
with open(os.path.join(settings.rxn_files, "quantiles.pickle"), "rb") as f:
quantiles = pickle.load(f)
X = scaler.transform(x_parent.append(x_target))
D = [pairwise_distances(np.array([row, X[-1]]))[0, 1] for row in X[:-1]]
_res = []
for d in D:
_res.append(np.linspace(0, 1, 101)[np.abs(quantiles - d).argmin()])
_res = np.array(_res)
_res[nulls] = -1
return _res
def __init__(self, materials, descriptors, **kwargs):
"""
Calculates site-based descriptors (e.g., coordination numbers
with different near-neighbor finding approaches) for materials and
runs statistics analysis on selected descriptor types
(order parameter-based site fingerprints). The latter is
useful as a definition of a structure fingerprint
on the basis of local coordination information.
Furthermore, composition descriptors are calculated
(Magpie element property vector).
Args:
materials (Store): Store of materials documents.
descriptors (Store): Store of composition, site, and
structure descriptor data such
as tetrahedral order parameter or
fraction of being 8-fold coordinated.
mat_query (dict): dictionary to limit materials to be analyzed.
"""
self.materials = materials
self.descriptors = descriptors
# Set up all targeted site descriptors.
self.sds = {}
for nn in nn_target_classes:
nn_ = getattr(local_env, nn)
k = "cn_{}".format(nn)
self.sds[k] = CoordinationNumber(nn_(), use_weights="none")
k = "cn_wt_{}".format(nn)
self.sds[k] = CoordinationNumber(nn_(), use_weights="sum")
self.all_output_pieces = {"site_descriptors": [k for k in self.sds.keys()]}
self.sds["csf"] = CrystalNNFingerprint.from_preset("ops",
distance_cutoffs=None,
x_diff_weight=None)
self.all_output_pieces["statistics"] = ["csf"]
# Set up all targeted composition descriptors.
self.cds = {}
self.cds["magpie"] = ElementProperty.from_preset("magpie")
self.all_output_pieces["composition_descriptors"] = ["magpie"]
self.all_output_pieces["meta"] = ["atomate"]
super().__init__(source=materials,
target=descriptors,
ufn=self.calc,
projection=["structure"],
**kwargs)
def test_elem_deml(self):
df_elem_deml = ElementProperty.from_preset("deml").featurize_dataframe(
self.df, col_id="composition")
self.assertAlmostEqual(df_elem_deml["minimum atom_num"][0], 8)
self.assertAlmostEqual(df_elem_deml["maximum atom_num"][0], 26)
self.assertAlmostEqual(df_elem_deml["range atom_num"][0], 18)
self.assertAlmostEqual(df_elem_deml["mean atom_num"][0], 15.2)
self.assertAlmostEqual(df_elem_deml["std_dev atom_num"][0], 8.81816307)
#Charge dependent property
self.assertAlmostEqual(df_elem_deml["minimum magn_moment"][0], 0)
self.assertAlmostEqual(df_elem_deml["maximum magn_moment"][0], 5.2)
self.assertAlmostEqual(df_elem_deml["range magn_moment"][0], 5.2)
self.assertAlmostEqual(df_elem_deml["mean magn_moment"][0], 2.08)
self.assertAlmostEqual(df_elem_deml["std_dev magn_moment"][0],
2.547469332)
def test_composition_features(self):
comp = ElementProperty.from_preset("magpie")
f = StructureComposition(featurizer=comp)
# Test the fitting (should not crash)
f.fit([self.nacl, self.diamond])
# Test the features
features = f.featurize(self.nacl)
self.assertArrayAlmostEqual(comp.featurize(self.nacl.composition),
features)
# Test the citations/implementors
self.assertEqual(comp.citations(), f.citations())
self.assertEqual(comp.implementors(), f.implementors())
def test_composition_features(self):
comp = ElementProperty.from_preset("magpie")
f = StructureComposition(featurizer=comp)
# Test the fitting (should not crash)
f.fit([self.nacl, self.diamond])
# Test the features
features = f.featurize(self.nacl)
self.assertArrayAlmostEqual(comp.featurize(self.nacl.composition),
features)
# Test the citations/implementors
self.assertEqual(comp.citations(), f.citations())
self.assertEqual(comp.implementors(), f.implementors())
def __init__(self, materials, descriptors, mat_query=None, **kwargs):
"""
Calculates site-based descriptors (e.g., coordination numbers
with different near-neighbor finding approaches) for materials and
runs statistics analysis on selected descriptor types
(order parameter-based site fingerprints). The latter is
useful as a definition of a structure fingerprint
on the basis of local coordination information.
Furthermore, composition descriptors are calculated
(Magpie element property vector).
Args:
materials (Store): Store of materials documents.
descriptors (Store): Store of composition, site, and
structure descriptor data such
as tetrahedral order parameter or
fraction of being 8-fold coordinated.
mat_query (dict): dictionary to limit materials to be analyzed.
"""
self.materials = materials
self.descriptors = descriptors
self.mat_query = mat_query if mat_query else {}
# Set up all targeted site descriptors.
self.sds = {}
for nn in nn_target_classes:
nn_ = getattr(pymatgen.analysis.local_env, nn)
k = 'cn_{}'.format(nn)
self.sds[k] = CoordinationNumber(nn_(), use_weights='none')
k = 'cn_wt_{}'.format(nn)
self.sds[k] = CoordinationNumber(nn_(), use_weights='sum')
self.all_output_pieces = {
'site_descriptors': [k for k in self.sds.keys()]
}
self.sds['csf'] = CrystalNNFingerprint.from_preset(
'ops', distance_cutoffs=None, x_diff_weight=None)
self.all_output_pieces['statistics'] = ['csf']
# Set up all targeted composition descriptors.
self.cds = {}
self.cds["magpie"] = ElementProperty.from_preset('magpie')
self.all_output_pieces['composition_descriptors'] = ['magpie']
self.all_output_pieces['meta'] = ['atomate']
super().__init__(sources=[materials], targets=[descriptors], **kwargs)
def generate_data(name):
#这个函数作用，输入是指定的文件名，输出增加了gaps，is_daoti，以及其他共计145特征的完整向量矩阵
#name='test_plus_gaps.csv'
df=pd.read_csv(name,index_col=[0])
df['gaps']=-10.0
df_gap=pd.read_csv("gaps.csv",index_col = [0])
print(df_gap.index)
i=0
str_s=""
for j in range(len(df_gap.index)):
#先打印二者的id
# print(df.index[i])
str_s='mp-'+str(df_gap.index[j])
if(str_s==df.index[i]):
df.iloc[i,-1]=df_gap.iloc[j,0]
i=i+1
#print("确实一样")
print("合并完毕")
#同样的方法我们来建立不同的分类
df['is_daoti']=-2
for i in range(len(df.index)):
if(df.ix[i,-2]==0):
df.ix[i,-1]=1
else:
df.ix[i,-1]=0
print("分类feature建立完成")
#首先使用describe获得对于数据的整体把握
print(df.describe())
df.describe().to_csv('general_look_jie.csv')
#通过观察数据发现并没有什么异常之处
df=StrToComposition().featurize_dataframe(df,'full_formula',ignore_errors=True)
print(df.head())
#print(df['composition'])
ep_feat=ElementProperty.from_preset(preset_name='magpie')
df=ep_feat.featurize_dataframe(df,col_id='composition',ignore_errors=True)#将composition这一列作为特征化的输入
print(df.head())
#print(ep_feat.citations())
#df.to_csv("plus the composition.csv")
#以上这部分是将formula转化为composition并转化feature
df=CompositionToOxidComposition().featurize_dataframe(df,col_id='composition')#引入了氧化态的相关特征
os_feat=OxidationStates()
df=os_feat.featurize_dataframe(df,col_id='composition_oxid')
new_name='2d_vector_plus.csv'
df.to_csv(new_name)
def generate_data():
df = load_elastic_tensor()
df.to_csv('原始elastic数据.csv')
print(df.columns)
unwanted_columns = [
'volume', 'nsites', 'compliance_tensor', 'elastic_tensor',
'elastic_tensor_original', 'K_Voigt', 'G_Voigt', 'K_Reuss', 'G_Reuss'
]
df = df.drop(unwanted_columns, axis=1)
print(df.head())
df.to_csv('扔掉不需要的部分.csv')
#首先使用describe获得对于数据的整体把握
print(df.describe())
df.describe().to_csv('general_look.csv')
#通过观察数据发现并没有什么异常之处
df = StrToComposition().featurize_dataframe(df, 'formula')
print(df.head())
df.to_csv('引入composition.csv')
#下一步，我们需要其中一个特征化来增加一系列的特征算符
ep_feat = ElementProperty.from_preset(preset_name='magpie')
df = ep_feat.featurize_dataframe(
df, col_id='composition') #将composition这一列作为特征化的输入
print(df.head())
print(ep_feat.citations())
df.to_csv('将composition特征化后.csv')
#开始引入新的特征化算符吧
df = CompositionToOxidComposition().featurize_dataframe(
df, 'composition') #引入了氧化态的相关特征
os_feat = OxidationStates()
df = os_feat.featurize_dataframe(df, col_id='composition_oxid')
print(df.head())
df.to_csv('引入氧化态之后.csv')
#其实除了基于composition的特征之外还有很多其他的，比如基于结构的
df_feat = DensityFeatures()
df = df_feat.featurize_dataframe(df, 'structure')
print(df.head())
df.to_csv('引入结构中的密度.csv')
print(df_feat.feature_labels())
def test_featurizers():
df = pd.read_csv('test.csv', index_col=[0])
df = StrToComposition().featurize_dataframe(df, 'formula')
print(df.head())
#下一步，我们需要其中一个特征化来增加一系列的特征算符
ep_feat = ElementProperty.from_preset(preset_name='magpie')
df = ep_feat.featurize_dataframe(
df, col_id='composition') #将composition这一列作为特征化的输入
print(df.head())
print(ep_feat.citations())
#df.to_csv('将composition特征化后.csv')
#开始引入新的特征化算符吧
df = CompositionToOxidComposition().featurize_dataframe(
df, 'composition') #引入了氧化态的相关特征
os_feat = OxidationStates()
df = os_feat.featurize_dataframe(df, col_id='composition_oxid')
print(df.head())
df.to_csv('after_test.csv')
def test_exclude_by_users(self):
"""
Test custom args for featurizers to use.
"""
df = copy.copy(self.test_df.iloc[:self.limit])
target = "K_VRH"
exclude = ["ElementProperty"]
ep = ElementProperty.from_preset("matminer")
ep_feats = ep.feature_labels()
# Test to make sure excluded does not show up
af = AutoFeaturizer(exclude=exclude, preset="fast")
af.fit(df, target)
df = af.fit_transform(df, target)
self.assertTrue(af.auto_featurizer)
self.assertIn("ElementProperty", af.exclude)
self.assertFalse(any([f in df.columns for f in ep_feats]))
def test_elem_megnet_el(self):
ep = ElementProperty.from_preset("megnet_el")
df_elem = ep.featurize_dataframe(self.df, col_id="composition")
self.assertAlmostEqual(
df_elem["MEGNetElementData maximum embedding 1"].iloc[0],
0.127333,
places=6)
self.assertAlmostEqual(
df_elem["MEGNetElementData maximum embedding 1"].iloc[1],
0.127333,
places=6)
self.assertAlmostEqual(
df_elem["MEGNetElementData maximum embedding 11"].iloc[0],
0.160505,
places=6)
self.assertAlmostEqual(
df_elem["MEGNetElementData maximum embedding 11"].iloc[1],
0.160505,
places=6)
self.assertTrue(ep.citations())
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 test_featurizers_by_users(self):
df = copy.copy(self.test_df.iloc[:self.limit])
target = "K_VRH"
dn = DensityFeatures()
gsf = GlobalSymmetryFeatures()
featurizers = {"structure": [dn, gsf]}
af = AutoFeaturizer(featurizers=featurizers)
df = af.fit_transform(df, target)
# Ensure that the featurizers are not set automatically, metaselection
# is not used, exclude is None and featurizers not passed by the users
# are not used.
self.assertFalse(af.auto_featurizer)
self.assertTrue(af.exclude == [])
self.assertIn(dn, af.featurizers["structure"])
self.assertIn(gsf, af.featurizers["structure"])
ep = ElementProperty.from_preset("matminer")
ep_feats = ep.feature_labels()
self.assertFalse(any([f in df.columns for f in ep_feats]))