jarvis.core.specie
¶
Modules related to chemistry of periodic-table elements.
Module Contents¶
Classes¶
Specie object for chemistry information. |
Functions¶
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Get chemical descriptors for an element. |
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Get specific node features for an element. |
Get the json and key data from Specie. |
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Get OneHotEncoded features with digitized features. |
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Get OneHotEncoded features. |
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Convert atomic number array to atomic symbols. |
Attributes¶
- jarvis.core.specie.el_chem_json_file¶
- jarvis.core.specie.el_chem_json¶
- jarvis.core.specie.chem_data¶
- jarvis.core.specie.chem_data_magpie¶
- jarvis.core.specie.el_chrg_json_file¶
- jarvis.core.specie.el_chrg_json¶
- jarvis.core.specie.chrg_data¶
- jarvis.core.specie.cgcnn_feature_json¶
- jarvis.core.specie.get_descrp_arr_name(elm='Al')[source]¶
Get chemical descriptors for an element.
Can be used in JARVIS-ML.
Args:
elm: element name
- Returns:
arr: array value
- class jarvis.core.specie.Specie(symbol='', source='cfid')[source]¶
Bases:
object
Specie object for chemistry information.
Used in defining chemistry of a material.
>>> el = Specie('Al') >>> el.Z 13 >>> round(el.atomic_mass,2) 26.98 >>> el.symbol 'Al' >>> round(el.get_chgdescrp_arr[1],2) 12.17 >>> round(el.get_descrp_arr[1],2) 2792.11 >>> el = Specie('asdfg') >>> el.element_property("asdfg") nan
- property Z¶
Get atomic number.
- property atomic_mass¶
Get atomic mass.
- property get_chgdescrp_arr¶
Get charge descriptors for an element.
Gives 378 array data.
Args:
elm: element name
- Returns:
arr: array value
- property get_descrp_arr¶
Get chemical descriptors for an element.
Gives 438 array data.
Args:
elm: element name
- Returns:
arr: array value
- property atomic_rad¶
Get atomic radii.
- property X¶
Get electronegativity.
- element_property(key='')[source]¶
Get element property from the list of keys.
These 84 keys are: keys = [
“is_halogen”, “row”, “GV”, “nfunfill”, “C-9”, “C-8”, “C-7”, “C-6”, “C-5”, “C-4”, “C-3”, “C-2”, “C-1”, “C-0”, “me1”, “me3”, “me2”, “max_oxid_s”, “npvalence”, “mp”, “first_ion_en”, “ndunfill”, “op_eg”, “jv_enp”, “nfvalence”, “polzbl”, “oq_bg”, “atom_rad”, “atom_mass”, “is_alkali”, “C-13”, “C-12”, “C-11”, “C-10”, “C-17”, “C-16”, “C-15”, “C-14”, “C-19”, “C-18”, “voro_coord”, “is_noble_gas”, “e1”, “e3”, “e2”, “is_lanthanoid”, “ndvalence”, “KV”, “min_oxid_s”, “nsunfill”, “C-26”, “X”, “is_actinoid”, “C-28”, “C-29”, “C-27”, “C-24”, “C-25”, “C-22”, “C-23”, “C-20”, “C-21”, “avg_ion_rad”, “nsvalence”, “is_metalloid”, “elec_aff”, “coulmn”, “mol_vol”, “bp”, “C-31”, “C-30”, “C-33”, “C-32”, “C-35”, “C-34”, “is_transition_metal”, “block”, “therm_cond”, “Z”, “is_alkaline”, “npunfill”, “oq_enp”, “mop_eg”, “hfus”,
]
- jarvis.core.specie.BASIC_FEATURES = ['Z', 'coulmn', 'row', 'X', 'atom_rad', 'nsvalence', 'npvalence', 'ndvalence', 'nfvalence',...¶
- jarvis.core.specie.get_node_attributes(species, atom_features='atomic_number')[source]¶
Get specific node features for an element.
- jarvis.core.specie.keys = ['is_halogen', 'row', 'GV', 'nfunfill', 'C-9', 'C-8', 'C-7', 'C-6', 'C-5', 'C-4', 'C-3', 'C-2',...¶
- jarvis.core.specie.get_digitized_feats_hot_encoded(feature_names=keys, filename='feats_encoded.json')[source]¶
Get OneHotEncoded features with digitized features.
- jarvis.core.specie.get_feats_hot_encoded(feature_names=keys, filename='feats_encoded.json')[source]¶
Get OneHotEncoded features.
- jarvis.core.specie.info_z¶