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atomic.py
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atomic.py
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MASS = {
"H": 1.00794,
"He": 4.002602,
"Li": 6.941,
"Be": 9.012182,
"B": 10.811,
"C": 12.0107,
"N": 14.0067,
"O": 15.9994,
"F": 18.9984032,
"Ne": 20.1797,
"Na": 22.98976928,
"Mg": 24.3050,
"Al": 26.9815386,
"Si": 28.0855,
"P": 30.973762,
"S": 32.065,
"Cl": 35.453,
"Ar": 39.948,
"K": 39.0983,
"Ca": 40.078,
"Sc": 44.955912,
"Ti": 47.867,
"V": 50.9415,
"Cr": 51.9961,
"Mn": 54.938045,
"Fe": 55.845,
"Co": 58.933195,
"Ni": 58.6934,
"Cu": 63.546,
"Zn": 65.38,
"Ga": 69.723,
"Ge": 72.64,
"As": 74.92160,
"Se": 78.96,
"Br": 79.904,
"Kr": 83.798,
"Rb": 85.4678,
"Sr": 87.62,
"Y": 88.90585,
"Zr": 91.224,
"Nb": 92.90638,
"Mo": 95.96,
"Tc": 98,
"Ru": 101.07,
"Rh": 102.90550,
"Pd": 106.42,
"Ag": 107.8682,
"Cd": 112.411,
"In": 114.818,
"Sn": 118.710,
"Sb": 121.760,
"Te": 127.60,
"I": 126.90447,
"Xe": 131.293,
"Cs": 132.9054519,
"Ba": 137.327,
"La": 138.90547,
"Ce": 140.116,
"Pr": 140.90765,
"Nd": 144.242,
"Pm": 145,
"Sm": 150.36,
"Eu": 151.964,
"Gd": 157.25,
"Tb": 158.92535,
"Dy": 162.500,
"Ho": 164.93032,
"Er": 167.259,
"Tm": 168.93421,
"Yb": 173.054,
"Lu": 174.9668,
"Hf": 178.49,
"Ta": 180.94788,
"W": 183.84,
"Re": 186.207,
"Os": 190.23,
"Ir": 192.217,
"Pt": 195.084,
"Au": 196.966569,
"Hg": 200.59,
"Tl": 204.3833,
"Pb": 207.2,
"Bi": 208.98040,
"Po": 209,
"At": 210,
"Rn": 222,
"Fr": 223,
"Ra": 226,
"Ac": 227,
"Th": 232.03806,
"Pa": 231.03588,
"U": 238.02891,
"Np": 237,
"Pu": 244,
"Am": 243,
"Cm": 247,
"Bk": 247,
"Cf": 251,
"Es": 252,
"Fm": 257,
"Md": 258,
"No": 259,
"Lr": 262,
"Rf": 265,
"Db": 268,
"Sg": 271,
"Bh": 272,
"Hs": 270,
"Mt": 276,
"Ds": 281,
"Rg": 280,
"Cn": 285,
"Uut": 284,
"Uuq": 289,
"Uup": 288,
"Uuh": 293,
"Uuo": 294}
# If this is a nice list we can just .index or [slice] to get atomic numbers
ATOMIC_NUMBER = [
"ZERO", "H", "He", "Li", "Be", "B", "C", "N", "O", "F", "Ne", "Na", "Mg",
"Al", "Si", "P", "S", "Cl", "Ar", "K", "Ca", "Sc", "Ti", "V", "Cr", "Mn",
"Fe", "Co", "Ni", "Cu", "Zn", "Ga", "Ge", "As", "Se", "Br", "Kr", "Rb",
"Sr", "Y", "Zr", "Nb", "Mo", "Tc", "Ru", "Rh", "Pd", "Ag", "Cd", "In",
"Sn", "Sb", "Te", "I", "Xe", "Cs", "Ba", "La", "Ce", "Pr", "Nd", "Pm",
"Sm", "Eu", "Gd", "Tb", "Dy", "Ho", "Er", "Tm", "Yb", "Lu", "Hf", "Ta",
"W", "Re", "Os", "Ir", "Pt", "Au", "Hg", "Tl", "Pb", "Bi", "Po", "At",
"Rn", "Fr", "Ra", "Ac", "Th", "Pa", "U", "Np", "Pu", "Am", "Cm", "Bk",
"Cf", "Es", "Fm", "Md", "No", "Lr", "Rf", "Db", "Sg", "Bh", "Hs", "Mt",
"Ds", "Rg", "Cn", "Uut", "Uuq", "Uup", "Uuh", "Uuo"]
COVALENT_RADII = {
# Covalent radii revisited -- DOI:10.1039/B801115J
"H": 0.25, ## 0.31 !! temporary for methyl
"He": 0.28,
"Li": 1.8,
"Be": 0.96,
"B": 0.84,
"C": 0.76, # for sp3; sp2 = 0.73; sp = 0.69
"C_1": 0.69,
"C_2": 0.73,
"C_R": 0.73,
"C_3": 0.76,
"N": 0.71,
"O": 0.66, ## 0.66 !! temporary for ZIFs 0.3 used
"F": 0.57,
"Ne": 0.58,
"Na": 1.66,
"Mg": 1.41,
"Al": 1.21,
"Si": 1.11,
"P": 1.07,
"S": 1.05,
"Cl": 1.02, ## 0.31 used for ZIFs !! temporary for ZIFs, 1.02 is correct
"Ar": 1.06,
"K": 2.03,
"Ca": 1.76,
"Sc": 1.7,
"Ti": 1.6,
"V": 1.53,
"Cr": 1.39,
"Mn": 1.61, # low spin = 1.39
"Fe": 1.52, # low spin = 1.32
"Co": 1.5, # low spin = 1.26
"Ni": 1.24,
"Cu": 1.32,
"Zn": 1.22,
"Ga": 1.22,
"Ge": 1.2,
"As": 1.19,
"Se": 1.2,
"Br": 1.2,
"Kr": 1.16,
"Rb": 2.2,
"Sr": 1.95,
"Y": 1.9,
"Zr": 1.5, # 1.75 !! temporarily added to correct the UIO cluster bonding problem
"Nb": 1.64,
"Mo": 1.54,
"Tc": 1.47,
"Ru": 1.46,
"Rh": 1.42,
"Pd": 1.39,
"Ag": 1.45,
"Cd": 1.44,
"In": 1.42,
"Sn": 1.39,
"Sb": 1.39,
"Te": 1.38,
"I": 1.39,
"Xe": 1.4,
"Cs": 2.44,
"Ba": 2.15,
"La": 2.07,
"Ce": 2.04,
"Pr": 2.03,
"Nd": 2.01,
"Pm": 1.99,
"Sm": 1.98,
"Eu": 1.98,
"Gd": 1.96,
"Tb": 1.94,
"Dy": 1.92,
"Ho": 1.92,
"Er": 1.89,
"Tm": 1.9,
"Yb": 1.87,
"Lu": 1.87,
"Hf": 1.75,
"Ta": 1.7,
"W": 1.62,
"Re": 1.51,
"Os": 1.44,
"Ir": 1.41,
"Pt": 1.36,
"Au": 1.36,
"Hg": 1.32,
"Tl": 1.45,
"Pb": 1.46,
"Bi": 1.48,
"Po": 1.4,
"At": 1.5,
"Rn": 1.5,
"Fr": 2.6,
"Ra": 2.21,
"Ac": 2.15,
"Th": 2.06,
"Pa": 2,
"U": 1.96,
"Np": 1.9,
"Pu": 1.87,
"Am": 1.8,
"Cm": 1.69,
}
METALS = [3, 4, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,
37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 55, 56, 57,
58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74,
75, 76, 77, 78, 79, 80, 81, 82, 83, 87, 88, 89, 90, 91, 92, 93, 94,
95, 96, 97, 98, 99, 100, 101, 102, 103]