# -*- coding: utf-8 -*-
# Copyright (c) 2016-2017, Zhijiang Yao, Jie Dong and Dongsheng Cao
# All rights reserved.
# This file is part of the PyBioMed.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the PyBioMed source tree.
"""
You can freely use and distribute it. If you hava
any problem, you could contact with us timely!
Authors: Zhijiang Yao and Dongsheng Cao.
Date: 2016.06.04
Email: gadsby@163.com
Z: atomic number
L: principal quantum number
Zv: number of valence electrons
Rv: van der Waals atomic radius
Rc: covalent radius
m: atomic mass
V: van der Waals vloume
En: Sanderson electronegativity
alapha: atomic polarizability (10e-24 cm3)
IP: ionization potential (eV)
EA: electron affinity (eV)
"""
################################################################################
AtomProperty = {
"H": {
"Z": 1,
"L": 1,
"Zv": 1,
"Rv": 1.17,
"Rc": 0.37,
"m": 1.01,
"V": 6.71,
"En": 2.59,
"alapha": 0.67,
"IP": 13.598,
"EA": 0.754,
},
"Li": {
"Z": 3,
"L": 2,
"Zv": 1,
"Rv": 1.82,
"Rc": 1.34,
"m": 6.94,
"V": 25.25,
"En": 0.89,
"alapha": 24.3,
"IP": 5.392,
"EA": 0.618,
},
"Be": {
"Z": 4,
"L": 2,
"Zv": 2,
"Rv": 0.0,
"Rc": 0.90,
"m": 9.01,
"V": 0.0,
"En": 1.81,
"alapha": 5.60,
"IP": 9.323,
"EA": 0.0,
},
"B": {
"Z": 5,
"L": 2,
"Zv": 3,
"Rv": 1.62,
"Rc": 0.82,
"m": 10.81,
"V": 17.88,
"En": 2.28,
"alapha": 3.03,
"IP": 8.298,
"EA": 0.277,
},
"C": {
"Z": 6,
"L": 2,
"Zv": 4,
"Rv": 1.75,
"Rc": 0.77,
"m": 12.01,
"V": 22.45,
"En": 2.75,
"alapha": 1.76,
"IP": 11.260,
"EA": 1.263,
},
"N": {
"Z": 7,
"L": 2,
"Zv": 5,
"Rv": 1.55,
"Rc": 0.75,
"m": 14.01,
"V": 15.60,
"En": 3.19,
"alapha": 1.10,
"IP": 14.534,
"EA": 0.0,
},
"O": {
"Z": 8,
"L": 2,
"Zv": 6,
"Rv": 1.40,
"Rc": 0.73,
"m": 16.00,
"V": 11.49,
"En": 3.65,
"alapha": 0.80,
"IP": 13.618,
"EA": 1.461,
},
"F": {
"Z": 9,
"L": 2,
"Zv": 7,
"Rv": 1.30,
"Rc": 0.71,
"m": 19.00,
"V": 9.20,
"En": 4.00,
"alapha": 0.56,
"IP": 17.423,
"EA": 3.401,
},
"Na": {
"Z": 11,
"L": 3,
"Zv": 1,
"Rv": 2.27,
"Rc": 1.54,
"m": 22.99,
"V": 49.00,
"En": 0.56,
"alapha": 23.6,
"IP": 5.139,
"EA": 0.548,
},
"Mg": {
"Z": 12,
"L": 3,
"Zv": 2,
"Rv": 1.73,
"Rc": 1.30,
"m": 24.31,
"V": 21.69,
"En": 1.32,
"alapha": 10.6,
"IP": 7.646,
"EA": 0.0,
},
"Al": {
"Z": 13,
"L": 3,
"Zv": 3,
"Rv": 2.06,
"Rc": 1.18,
"m": 26.98,
"V": 36.51,
"En": 1.71,
"alapha": 6.80,
"IP": 5.986,
"EA": 0.441,
},
"Si": {
"Z": 14,
"L": 3,
"Zv": 4,
"Rv": 1.97,
"Rc": 1.11,
"m": 28.09,
"V": 31.98,
"En": 2.14,
"alapha": 5.38,
"IP": 8.152,
"EA": 1.385,
},
"P": {
"Z": 15,
"L": 3,
"Zv": 5,
"Rv": 1.85,
"Rc": 1.06,
"m": 30.97,
"V": 26.52,
"En": 2.52,
"alapha": 3.63,
"IP": 10.487,
"EA": 0.747,
},
"S": {
"Z": 16,
"L": 3,
"Zv": 6,
"Rv": 1.80,
"Rc": 1.02,
"m": 32.07,
"V": 24.43,
"En": 2.96,
"alapha": 2.90,
"IP": 10.360,
"EA": 2.077,
},
"Cl": {
"Z": 17,
"L": 3,
"Zv": 7,
"Rv": 1.75,
"Rc": 0.99,
"m": 35.45,
"V": 22.45,
"En": 3.48,
"alapha": 2.18,
"IP": 12.968,
"EA": 3.613,
},
"K": {
"Z": 19,
"L": 4,
"Zv": 1,
"Rv": 2.75,
"Rc": 1.96,
"m": 39.10,
"V": 87.11,
"En": 0.45,
"alapha": 43.4,
"IP": 4.341,
"EA": 0.501,
},
"Ca": {
"Z": 20,
"L": 4,
"Zv": 2,
"Rv": 0.0,
"Rc": 1.74,
"m": 40.08,
"V": 0.0,
"En": 0.95,
"alapha": 22.8,
"IP": 6.113,
"EA": 0.018,
},
"Cr": {
"Z": 24,
"L": 4,
"Zv": 6,
"Rv": 2.20,
"Rc": 1.27,
"m": 52.00,
"V": 44.60,
"En": 1.66,
"alapha": 11.60,
"IP": 6.767,
"EA": 0.666,
},
"Mn": {
"Z": 25,
"L": 4,
"Zv": 7,
"Rv": 2.18,
"Rc": 1.39,
"m": 54.94,
"V": 43.40,
"En": 2.20,
"alapha": 9.40,
"IP": 7.434,
"EA": 0.0,
},
"Fe": {
"Z": 26,
"L": 4,
"Zv": 8,
"Rv": 2.14,
"Rc": 1.25,
"m": 55.85,
"V": 41.05,
"En": 2.20,
"alapha": 8.40,
"IP": 7.902,
"EA": 1.151,
},
"Co": {
"Z": 27,
"L": 4,
"Zv": 9,
"Rv": 2.03,
"Rc": 1.26,
"m": 58.93,
"V": 35.04,
"En": 2.56,
"alapha": 7.50,
"IP": 7.881,
"EA": 0.662,
},
"Ni": {
"Z": 28,
"L": 4,
"Zv": 10,
"Rv": 1.60,
"Rc": 1.21,
"m": 58.69,
"V": 17.16,
"En": 1.94,
"alapha": 6.80,
"IP": 7.640,
"EA": 1.156,
},
"Cu": {
"Z": 29,
"L": 4,
"Zv": 11,
"Rv": 1.40,
"Rc": 1.38,
"m": 63.55,
"V": 11.49,
"En": 1.95,
"alapha": 6.10,
"IP": 7.723,
"EA": 1.235,
},
"Zn": {
"Z": 30,
"L": 4,
"Zv": 12,
"Rv": 1.39,
"Rc": 1.31,
"m": 65.39,
"V": 11.25,
"En": 2.23,
"alapha": 7.10,
"IP": 9.394,
"EA": 0.0,
},
"Ga": {
"Z": 31,
"L": 4,
"Zv": 3,
"Rv": 1.87,
"Rc": 1.26,
"m": 69.72,
"V": 27.39,
"En": 2.42,
"alapha": 8.12,
"IP": 5.999,
"EA": 0.300,
},
"Ge": {
"Z": 32,
"L": 4,
"Zv": 4,
"Rv": 1.90,
"Rc": 1.22,
"m": 72.61,
"V": 28.73,
"En": 2.62,
"alapha": 6.07,
"IP": 7.900,
"EA": 1.233,
},
"As": {
"Z": 33,
"L": 4,
"Zv": 5,
"Rv": 1.85,
"Rc": 1.19,
"m": 74.92,
"V": 26.52,
"En": 2.82,
"alapha": 4.31,
"IP": 9.815,
"EA": 0.810,
},
"Se": {
"Z": 34,
"L": 4,
"Zv": 6,
"Rv": 1.90,
"Rc": 1.16,
"m": 78.96,
"V": 28.73,
"En": 3.01,
"alapha": 3.73,
"IP": 9.752,
"EA": 2.021,
},
"Br": {
"Z": 35,
"L": 4,
"Zv": 7,
"Rv": 1.95,
"Rc": 1.14,
"m": 79.90,
"V": 31.06,
"En": 3.22,
"alapha": 3.05,
"IP": 11.814,
"EA": 3.364,
},
"Rb": {
"Z": 37,
"L": 5,
"Zv": 1,
"Rv": 0.0,
"Rc": 2.11,
"m": 85.47,
"V": 0.0,
"En": 0.31,
"alapha": 47.3,
"IP": 4.177,
"EA": 0.486,
},
"Sr": {
"Z": 38,
"L": 5,
"Zv": 2,
"Rv": 0.0,
"Rc": 1.92,
"m": 87.62,
"V": 0.0,
"En": 0.72,
"alapha": 27.6,
"IP": 5.695,
"EA": 0.110,
},
"Mo": {
"Z": 42,
"L": 5,
"Zv": 6,
"Rv": 2.00,
"Rc": 1.45,
"m": 95.94,
"V": 33.51,
"En": 1.15,
"alapha": 12.80,
"IP": 7.092,
"EA": 0.746,
},
"Ag": {
"Z": 47,
"L": 5,
"Zv": 11,
"Rv": 1.72,
"Rc": 1.53,
"m": 107.87,
"V": 21.31,
"En": 1.83,
"alapha": 7.20,
"IP": 7.576,
"EA": 1.302,
},
"Cd": {
"Z": 48,
"L": 5,
"Zv": 12,
"Rv": 1.58,
"Rc": 1.48,
"m": 112.41,
"V": 16.52,
"En": 1.98,
"alapha": 7.20,
"IP": 8.994,
"EA": 0.0,
},
"In": {
"Z": 49,
"L": 5,
"Zv": 3,
"Rv": 1.93,
"Rc": 1.44,
"m": 114.82,
"V": 30.11,
"En": 2.14,
"alapha": 10.20,
"IP": 5.786,
"EA": 0.300,
},
"Sn": {
"Z": 50,
"L": 5,
"Zv": 4,
"Rv": 2.22,
"Rc": 1.41,
"m": 118.71,
"V": 45.83,
"En": 2.30,
"alapha": 7.70,
"IP": 7.344,
"EA": 1.112,
},
"Sb": {
"Z": 51,
"L": 5,
"Zv": 5,
"Rv": 2.10,
"Rc": 1.38,
"m": 121.76,
"V": 38.79,
"En": 2.46,
"alapha": 6.60,
"IP": 8.64,
"EA": 1.07,
},
"Te": {
"Z": 52,
"L": 5,
"Zv": 6,
"Rv": 2.06,
"Rc": 1.35,
"m": 127.60,
"V": 36.62,
"En": 2.62,
"alapha": 5.50,
"IP": 9.01,
"EA": 1.971,
},
"I": {
"Z": 53,
"L": 5,
"Zv": 7,
"Rv": 2.10,
"Rc": 1.33,
"m": 126.90,
"V": 38.79,
"En": 2.78,
"alapha": 5.35,
"IP": 10.451,
"EA": 3.059,
},
"Gd": {
"Z": 64,
"L": 6,
"Zv": 10,
"Rv": 2.59,
"Rc": 1.79,
"m": 157.25,
"V": 72.78,
"En": 2.00,
"alapha": 23.50,
"IP": 6.15,
"EA": 0.50,
},
"Pt": {
"Z": 78,
"L": 6,
"Zv": 10,
"Rv": 1.75,
"Rc": 1.28,
"m": 195.08,
"V": 22.45,
"En": 2.28,
"alapha": 6.50,
"IP": 9.00,
"EA": 2.128,
},
"Au": {
"Z": 79,
"L": 6,
"Zv": 11,
"Rv": 1.66,
"Rc": 1.44,
"m": 196.97,
"V": 19.16,
"En": 2.65,
"alapha": 5.80,
"IP": 9.226,
"EA": 2.309,
},
"Hg": {
"Z": 80,
"L": 6,
"Zv": 12,
"Rv": 1.55,
"Rc": 1.49,
"m": 200.59,
"V": 15.60,
"En": 2.20,
"alapha": 5.70,
"IP": 10.438,
"EA": 0.0,
},
"Tl": {
"Z": 81,
"L": 6,
"Zv": 3,
"Rv": 1.96,
"Rc": 1.48,
"m": 204.38,
"V": 31.54,
"En": 2.25,
"alapha": 7.60,
"IP": 6.108,
"EA": 0.200,
},
"Pb": {
"Z": 82,
"L": 6,
"Zv": 4,
"Rv": 2.02,
"Rc": 1.47,
"m": 207.20,
"V": 34.53,
"En": 2.29,
"alapha": 6.80,
"IP": 7.417,
"EA": 0.364,
},
"Bi": {
"Z": 83,
"L": 6,
"Zv": 5,
"Rv": 2.10,
"Rc": 1.46,
"m": 208.98,
"V": 38.79,
"En": 2.34,
"alapha": 7.40,
"IP": 7.289,
"EA": 0.946,
},
}
[docs]def GetAbsoluteAtomicProperty(element="C", propertyname="m"):
"""
Get the absolute property value with propertyname for the given atom.
"""
PropertyDic = AtomProperty[element]
return PropertyDic[propertyname]
[docs]def GetRelativeAtomicProperty(element="C", propertyname="m"):
"""
Get the absolute property value with propertyname for the given atom.
"""
CpropertyDic = AtomProperty["C"]
PropertyDic = AtomProperty[element]
return PropertyDic[propertyname] / (CpropertyDic[propertyname] + 0.0)
###############################################################################
if __name__ == "__main__":
for i, j in AtomProperty.items():
print(j)
print(GetAbsoluteAtomicProperty(element="S", propertyname="En"))
print(GetRelativeAtomicProperty(element="S", propertyname="En"))
