jarvis.core.specie

Modules related to chemistry of periodic-table elements.

Module Contents

Classes

Specie

Specie object for chemistry information.

Functions

get_descrp_arr_name(elm='Al')

Get chemical descriptors for an element.

get_node_attributes(species, atom_features='atomic_number')

Get specific node features for an element.

get_specie_data()

Get the json and key data from Specie.

get_digitized_feats_hot_encoded(feature_names=keys, filename='feats_encoded.json')

Get OneHotEncoded features with digitized features.

get_feats_hot_encoded(feature_names=keys, filename='feats_encoded.json')

Get OneHotEncoded features.

atomic_numbers_to_symbols(numbers=[1, 2, 3, 4])

Convert atomic number array to atomic symbols.

Attributes

el_chem_json_file

el_chem_json

chem_data

chem_data_magpie

el_chrg_json_file

el_chrg_json

chrg_data

cgcnn_feature_json

BASIC_FEATURES

keys

info_z

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(self)

Get atomic number.

property atomic_mass(self)

Get atomic mass.

property get_chgdescrp_arr(self)

Get charge descriptors for an element.

Gives 378 array data.

Args:

elm: element name

Returns:

arr: array value

property get_descrp_arr(self)

Get chemical descriptors for an element.

Gives 438 array data.

Args:

elm: element name

Returns:

arr: array value

property atomic_rad(self)

Get atomic radii.

property X(self)

Get electronegativity.

element_property(self, 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_specie_data()[source]

Get the json and key data from Specie.

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
jarvis.core.specie.atomic_numbers_to_symbols(numbers=[1, 2, 3, 4])[source]

Convert atomic number array to atomic symbols.