"""Modules related to chemistry of periodic-table elements."""
import os
import json
import numpy as np
el_chem_json_file = str(os.path.join(
os.path.dirname(__file__), "Elements.json"))
el_chem_json = open(el_chem_json_file, "r")
chem_data = json.load(el_chem_json)
el_chem_json.close()
el_chrg_json_file = str(os.path.join(
os.path.dirname(__file__), "element_charge.json"))
el_chrg_json = open(el_chrg_json_file, "r")
chrg_data = json.load(el_chrg_json)
el_chrg_json.close()
[docs]def get_descrp_arr_name(elm="Al"):
"""
Get chemical descriptors for an element.
Can be used in JARVIS-ML.
Args:
elm: element name
Returns:
arr: array value
"""
arr = []
try:
dat = chem_data
d = dat[elm]
arr = []
for k, v in d.items():
arr.append(k)
except Exception:
pass
return arr
[docs]class Specie(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
"""
def __init__(self, symbol=""):
"""Initialize with periodic table element."""
self.symbol = symbol
self._data = chem_data
@property
def Z(self):
"""Get atomic number."""
return self.element_property("Z")
@property
def atomic_mass(self):
"""Get atomic mass."""
return self.element_property("atom_mass")
@property
def get_chgdescrp_arr(self):
"""
Get charge descriptors for an element.
Gives 378 array data.
Args:
elm: element name
Returns:
arr: array value
"""
arr = []
# try:
arr = chrg_data[self.symbol][0][1]
# except:
# pass
return arr
@property
def get_descrp_arr(self):
"""
Get chemical descriptors for an element.
Gives 438 array data.
Args:
elm: element name
Returns:
arr: array value
"""
arr = []
d = chem_data[self.symbol]
arr = []
for k, v in d.items():
arr.append(v)
arr = np.array(arr).astype(float)
return arr
@property
def atomic_rad(self):
"""Get atomic radii."""
return self.element_property("atom_rad")
[docs] def element_property(self, key=""):
"""
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",
]
"""
val = np.nan
try:
val = self._data[self.symbol][key]
except Exception:
pass
return val
"""
if __name__ == "__main__":
el = Specie("Al")
#print(el.get_chgdescrp_arr)
print(len(el.get_descrp_arr))
#print (get_descrp_arr_name())
"""