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const.py
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const.py
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"""Holds constants"""
import os
from AaronTools.utils.decorators import classproperty
HOME = os.path.expanduser("~")
if "AARONLIB" in os.environ:
AARONLIB = os.path.abspath(os.environ["AARONLIB"])
else:
AARONLIB = os.path.join(HOME, "Aaron_libs")
AARONTOOLS = os.path.dirname(os.path.abspath(__file__))
CONNECTIVITY_THRESHOLD = 0.5
D_CUTOFF = 0.35
RMSD_CUTOFF = 0.15
ELEMENTS = [
"Bq",
"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",
"Nh",
"Fl",
"Mc",
"Lv",
"Ts",
"Og",
"X",
]
TMETAL = {
"Sc": 1.44,
"Ti": 1.32,
"V": 1.22,
"Cr": 1.18,
"Mn": 1.17,
"Fe": 1.17,
"Co": 1.16,
"Ni": 1.15,
"Cu": 1.17,
"Zn": 1.25,
"Y": 1.62,
"Zr": 1.45,
"Nb": 1.34,
"Mo": 1.30,
"Tc": 1.27,
"Ru": 1.25,
"Rh": 1.25,
"Pd": 1.28,
"Ag": 1.34,
"Cd": 1.48,
"La": 1.69,
"Lu": 1.60,
"Hf": 1.44,
"Ta": 1.34,
"W": 1.30,
"Re": 1.28,
"Os": 1.26,
"Ir": 1.27,
"Pt": 1.30,
"Au": 1.34,
"Hg": 1.49,
}
METAL = [
"Li",
"Be",
"Na",
"Mg",
"K",
"Ca",
"Rb",
"Sr",
"Cs",
"Ba",
"Fr",
"Ra",
"Al",
"Ga",
"In",
"Sn",
"Tl",
"Pb",
"Bi",
"Nh",
"Fl",
"Mc",
"Lv",
"La",
"Ce",
"Pr",
"Nd",
"Pm",
"Sm",
"Eu",
"Gd",
"Tb",
"Dy",
"Ho",
"Er",
"Tm",
"Yb",
"Lu",
"Ac",
"Th",
"Pa",
"U",
"Np",
"Pu",
"Am",
"Cm",
"Bk",
"Cf",
"Es",
"Fm",
"Md",
"No",
"Lr",
] + list(TMETAL.keys())
# DOI 10.1039/B801115J
RADII = {
"H": 0.31,
"He": 0.28,
"Li": 1.28,
"Be": 0.96,
"B": 0.84,
"C": 0.76,
"N": 0.71,
"O": 0.66,
"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,
"Ar": 1.06,
"K": 2.03,
"Ca": 1.74,
"Sc": 1.44,
"Ti": 1.32,
"V": 1.22,
"Cr": 1.18,
"Mn": 1.17,
"Fe": 1.17,
"Co": 1.16,
"Ni": 1.15,
"Cu": 1.17,
"Zn": 1.25,
"Ga": 1.26,
"Ge": 1.22,
"As": 1.20,
"Se": 1.16,
"Br": 1.14,
"Kr": 1.12,
"Rb": 2.16,
"Sr": 1.91,
"Y": 1.62,
"Zr": 1.45,
"Nb": 1.34,
"Mo": 1.30,
"Tc": 1.27,
"Ru": 1.25,
"Rh": 1.25,
"Pd": 1.28,
"Ag": 1.34,
"Cd": 1.48,
"In": 1.44,
"Sn": 1.41,
"Sb": 1.40,
"Te": 1.36,
"I": 1.33,
"Xe": 1.31,
"Cs": 2.35,
"Ba": 1.98,
"La": 1.69,
"Lu": 1.60,
"Hf": 1.44,
"Ta": 1.34,
"W": 1.30,
"Re": 1.28,
"Os": 1.26,
"Ir": 1.27,
"Pt": 1.30,
"Au": 1.34,
"Hg": 1.49,
"Tl": 1.48,
"Pb": 1.47,
"Bi": 1.46,
"Ce": 1.63,
"Pr": 1.76,
"Nd": 1.74,
"Pm": 1.73,
"Sm": 1.72,
"Eu": 1.68,
"Gd": 1.69,
"Tb": 1.68,
"Dy": 1.67,
"Ho": 1.66,
"Er": 1.65,
"Tm": 1.64,
"Yb": 1.70,
"Lu": 1.62,
"Th": 1.75,
"Pa": 1.69,
"U": 1.70,
"Np": 1.71,
"Pu": 1.72,
"Am": 1.66,
"Cm": 1.66,
"Bk": 1.68,
"Cf": 1.68,
"Es": 1.65,
"Fm": 1.67,
"Md": 1.73,
"No": 1.76,
"Lr": 1.61,
"X": 0,
}
CONNECTIVITY = {
"H": 1,
"B": 4,
"C": 4,
"N": 4,
"O": 4,
"F": 4,
"Si": 6,
"Rh": 6,
"Fe": 6,
"Ni": 6,
"Cu": 6,
"Ru": 6,
"Pd": 6,
"Ir": 6,
"P": 4,
"S": 4,
"Cl": 4,
"I": 6,
"Br": 6,
"X": 1000,
"Pt": 6,
"Au": 6,
}
SATURATION = {
"H": 1,
"B": 3,
"C": 4,
"N": 3,
"O": 2,
"F": 1,
"Si": 6,
"P": 4,
"S": 4,
"Cl": 1,
"I": 1,
"Br": 1,
"X": 1000,
}
ELECTRONEGATIVITY = {
"H": 2.20,
"He": None,
"Li": 0.98,
"Be": 1.57,
"B": 2.04,
"C": 2.55,
"N": 3.04,
"O": 3.44,
"F": 3.98,
"Ne": None,
"Na": 0.93,
"Mg": 1.31,
"Al": 1.61,
"Si": 1.90,
"P": 2.19,
"S": 2.58,
"Cl": 3.16,
"Ar": None,
"K": 0.82,
"Ca": 1.00,
"Sc": 1.36,
"Ti": 1.54,
"V": 1.63,
"Cr": 1.66,
"Mn": 1.55,
"Fe": 1.83,
"Co": 1.88,
"Ni": 1.91,
"Cu": 1.90,
"Zn": 1.65,
"Ga": 1.81,
"Ge": 2.01,
"As": 2.18,
"Se": 2.55,
"Br": 2.96,
"Kr": 3.00,
"Rb": 0.82,
"Sr": 0.95,
"Y": 1.22,
"Zr": 1.33,
"Nb": 1.6,
"Mo": 2.16,
"Tc": 1.9,
"Ru": 2.2,
"Rh": 2.28,
"Pd": 2.20,
"Ag": 1.93,
"Cd": 1.69,
"In": 1.78,
"Sn": 1.96,
"Sb": 2.05,
"Te": 2.1,
"I": 2.66,
"Xe": 2.6,
"Cs": 0.79,
"Ba": 0.89,
"La": 1.10,
"Ce": 1.12,
"Pr": 1.13,
"Nd": 1.14,
"Pm": None,
"Sm": 1.17,
"Eu": None,
"Gd": 1.20,
"Tb": None,
"Dy": 1.22,
"Ho": 1.23,
"Er": 1.24,
"Tm": 1.25,
"Yb": None,
"Lu": 1.27,
"Hf": 1.3,
"Ta": 1.5,
"W": 2.36,
"Re": 1.9,
"Os": 2.2,
"Ir": 2.20,
"Pt": 2.28,
"Au": 2.54,
"Hg": 2.00,
"Tl": 1.62,
"Pb": 2.33,
"Bi": 2.02,
"Po": 2.0,
"At": 2.2,
"Rn": None,
"Fr": 0.7,
"Ra": 0.9,
"Ac": 1.1,
"Th": 1.3,
"Pa": 1.5,
"U": 1.38,
"Np": 1.36,
"Pu": 1.28,
"Am": 1.3,
"Cm": 1.3,
"Bk": 1.3,
"Cf": 1.3,
"Es": 1.3,
"Fm": 1.3,
"Md": 1.3,
"No": 1.3,
}
MASS = {
"X": 0.0,
"H": 1.00782503207,
"He": 4.00260325415,
"Li": 7.016004548,
"Be": 9.012182201,
"B": 11.009305406,
"C": 12.0,
"N": 14.00307400478,
"O": 15.99491461956,
"F": 18.998403224,
"Ne": 19.99244017542,
"Na": 22.98976928087,
"Mg": 23.985041699,
"Al": 26.981538627,
"Si": 27.97692653246,
"P": 30.973761629,
"S": 31.972070999,
"Cl": 34.968852682,
"Ar": 39.96238312251,
"K": 38.963706679,
"Ca": 39.962590983,
"Sc": 44.955911909,
"Ti": 47.947946281,
"V": 50.943959507,
"Cr": 51.940507472,
"Mn": 54.938045141,
"Fe": 55.934937475,
"Co": 58.933195048,
"Ni": 57.935342907,
"Cu": 62.929597474,
"Zn": 63.929142222,
"Ga": 68.925573587,
"Ge": 73.921177767,
"As": 74.921596478,
"Se": 79.916521271,
"Br": 78.918337087,
"Kr": 85.910610729,
"Rb": 84.911789737,
"Sr": 87.905612124,
"Y": 88.905848295,
"Zr": 89.904704416,
"Nb": 92.906378058,
"Mo": 97.905408169,
"Tc": 98.906254747,
"Ru": 101.904349312,
"Rh": 102.905504292,
"Pd": 105.903485715,
"Ag": 106.90509682,
"Cd": 113.90335854,
"In": 114.903878484,
"Sn": 119.902194676,
"Sb": 120.903815686,
"Te": 129.906224399,
"I": 126.904472681,
"Xe": 131.904153457,
"Cs": 132.905451932,
"Ba": 137.905247237,
"La": 138.906353267,
"Lu": 174.940771819,
"Hf": 179.946549953,
"Ta": 180.947995763,
"W": 183.950931188,
"Re": 186.955753109,
"Os": 191.96148069,
"Ir": 192.96292643,
"Pt": 194.964791134,
"Au": 196.966568662,
"Hg": 201.970643011,
"Tl": 204.974427541,
"Pb": 207.976652071,
"Bi": 208.980398734,
}
EIJ = {
"CC": 0.1500,
"CN": 0.1549,
"NC": 0.1549,
"CO": 0.1732,
"OC": 0.1732,
"CP": 0.1732,
"PC": 0.1732,
"CS": 0.1732,
"SC": 0.1732,
"CH": 0.0548,
"HC": 0.0548,
"CFe": 0.0387,
"FeC": 0.0387,
"CF": 0.1095,
"FC": 0.1095,
"CCl": 0.2035,
"ClC": 0.2035,
"CBr": 0.2416,
"BrC": 0.2416,
"CI": 0.2877,
"IC": 0.2877,
"CMg": 0.3623,
"MgC": 0.3623,
"CZn": 0.2872,
"ZnC": 0.2872,
"CCa": 0.2872,
"CaC": 0.2872,
"NC": 0.1549,
"CN": 0.1549,
"NN": 0.1600,
"NO": 0.1789,
"ON": 0.1789,
"NP": 0.1789,
"PN": 0.1789,
"NS": 0.1789,
"SN": 0.1789,
"NH": 0.0566,
"HN": 0.0566,
"NFe": 0.0400,
"FeN": 0.0400,
"NF": 0.1131,
"FN": 0.1131,
"NCl": 0.2101,
"ClN": 0.2101,
"NBr": 0.2495,
"BrN": 0.2495,
"NI": 0.2972,
"IN": 0.2972,
"NMg": 0.3742,
"MgN": 0.3742,
"NZn": 0.2966,
"ZnN": 0.2966,
"NCa": 0.2966,
"CaN": 0.2966,
"OC": 0.1732,
"CO": 0.1732,
"ON": 0.1789,
"NO": 0.1789,
"OO": 0.2000,
"OP": 0.2000,
"PO": 0.2000,
"OS": 0.2000,
"SO": 0.2000,
"OH": 0.0632,
"HO": 0.0632,
"OFe": 0.0447,
"FeO": 0.0447,
"OF": 0.1265,
"FO": 0.1265,
"OCl": 0.2349,
"ClO": 0.2349,
"OBr": 0.2789,
"BrO": 0.2789,
"OI": 0.3323,
"IO": 0.3323,
"OMg": 0.4183,
"MgO": 0.4183,
"OZn": 0.3317,
"ZnO": 0.3317,
"OCa": 0.3317,
"CaO": 0.3317,
"PC": 0.1732,
"CP": 0.1732,
"PN": 0.1789,
"NP": 0.1789,
"PO": 0.2000,
"OP": 0.2000,
"PP": 0.2000,
"PS": 0.2000,
"SP": 0.2000,
"PH": 0.0632,
"HP": 0.0632,
"PFe": 0.0447,
"FeP": 0.0447,
"PF": 0.1265,
"FP": 0.1265,
"PCl": 0.2349,
"ClP": 0.2349,
"PBr": 0.2789,
"BrP": 0.2789,
"PI": 0.3323,
"IP": 0.3323,
"PMg": 0.4183,
"MgP": 0.4183,
"PZn": 0.3317,
"ZnP": 0.3317,
"PCa": 0.3317,
"CaP": 0.3317,
"SC": 0.1732,
"CS": 0.1732,
"SN": 0.1789,
"NS": 0.1789,
"SO": 0.2000,
"OS": 0.2000,
"SP": 0.2000,
"PS": 0.2000,
"SS": 0.2000,
"SH": 0.0632,
"HS": 0.0632,
"SFe": 0.0447,
"FeS": 0.0447,
"SF": 0.1265,
"FS": 0.1265,
"SCl": 0.2349,
"ClS": 0.2349,
"SBr": 0.2789,
"BrS": 0.2789,
"SI": 0.3323,
"IS": 0.3323,
"SMg": 0.4183,
"MgS": 0.4183,
"SZn": 0.3317,
"ZnS": 0.3317,
"SCa": 0.3317,
"CaS": 0.3317,
"HC": 0.0548,
"CH": 0.0548,
"HN": 0.0566,
"NH": 0.0566,
"HO": 0.0632,
"OH": 0.0632,
"HP": 0.0632,
"PH": 0.0632,
"HS": 0.0632,
"SH": 0.0632,
"HH": 0.0200,
"HFe": 0.0141,
"FeH": 0.0141,
"HF": 0.0400,
"FH": 0.0400,
"HCl": 0.0743,
"ClH": 0.0743,
"HBr": 0.0882,
"BrH": 0.0882,
"HI": 0.1051,
"IH": 0.1051,
"HMg": 0.1323,
"MgH": 0.1323,
"HZn": 0.1049,
"ZnH": 0.1049,
"HCa": 0.1049,
"CaH": 0.1049,
"FeC": 0.0387,
"CFe": 0.0387,
"FeN": 0.0400,
"NFe": 0.0400,
"FeO": 0.0447,
"OFe": 0.0447,
"FeP": 0.0447,
"PFe": 0.0447,
"FeS": 0.0447,
"SFe": 0.0447,
"FeH": 0.0141,
"HFe": 0.0141,
"FeFe": 0.0100,
"FeF": 0.0283,
"FFe": 0.0283,
"FeCl": 0.0525,
"ClFe": 0.0525,
"FeBr": 0.0624,
"BrFe": 0.0624,
"FeI": 0.0743,
"IFe": 0.0743,
"FeMg": 0.0935,
"MgFe": 0.0935,
"FeZn": 0.0742,
"ZnFe": 0.0742,
"FeCa": 0.0742,
"CaFe": 0.0742,
"FC": 0.1095,
"CF": 0.1095,
"FN": 0.1131,
"NF": 0.1131,
"FO": 0.1265,
"OF": 0.1265,
"FP": 0.1265,
"PF": 0.1265,
"FS": 0.1265,
"SF": 0.1265,
"FH": 0.0400,
"HF": 0.0400,
"FFe": 0.0283,
"FeF": 0.0283,
"FF": 0.0800,
"FCl": 0.1486,
"ClF": 0.1486,
"FBr": 0.1764,
"BrF": 0.1764,
"FI": 0.2101,
"IF": 0.2101,
"FMg": 0.2646,
"MgF": 0.2646,
"FZn": 0.2098,
"ZnF": 0.2098,
"FCa": 0.2098,
"CaF": 0.2098,
"ClC": 0.2035,
"CCl": 0.2035,
"ClN": 0.2101,
"NCl": 0.2101,
"ClO": 0.2349,
"OCl": 0.2349,
"ClP": 0.2349,
"PCl": 0.2349,
"ClS": 0.2349,
"SCl": 0.2349,
"ClH": 0.0743,
"HCl": 0.0743,
"ClFe": 0.0525,
"FeCl": 0.0525,
"ClF": 0.1486,
"FCl": 0.1486,
"ClCl": 0.2760,
"ClBr": 0.3277,
"BrCl": 0.3277,
"ClI": 0.3903,
"ICl": 0.3903,
"ClMg": 0.4914,
"MgCl": 0.4914,
"ClZn": 0.3896,
"ZnCl": 0.3896,
"ClCa": 0.3896,
"CaCl": 0.3896,
"BrC": 0.2416,
"CBr": 0.2416,
"BrN": 0.2495,
"NBr": 0.2495,
"BrO": 0.2789,
"OBr": 0.2789,
"BrP": 0.2789,
"PBr": 0.2789,
"BrS": 0.2789,
"SBr": 0.2789,
"BrH": 0.0882,
"HBr": 0.0882,
"BrFe": 0.0624,
"FeBr": 0.0624,
"BrF": 0.1764,
"FBr": 0.1764,
"BrCl": 0.3277,
"ClBr": 0.3277,
"BrBr": 0.3890,
"BrI": 0.4634,
"IBr": 0.4634,
"BrMg": 0.5834,
"MgBr": 0.5834,
"BrZn": 0.4625,
"ZnBr": 0.4625,
"BrCa": 0.4625,
"CaBr": 0.4625,
"IC": 0.2877,
"CI": 0.2877,
"IN": 0.2972,
"NI": 0.2972,
"IO": 0.3323,
"OI": 0.3323,
"IP": 0.3323,
"PI": 0.3323,
"IS": 0.3323,
"SI": 0.3323,
"IH": 0.1051,
"HI": 0.1051,
"IFe": 0.0743,
"FeI": 0.0743,
"IF": 0.2101,
"FI": 0.2101,
"ICl": 0.3903,
"ClI": 0.3903,
"IBr": 0.4634,
"BrI": 0.4634,
"II": 0.5520,
"IMg": 0.6950,
"MgI": 0.6950,
"IZn": 0.5510,
"ZnI": 0.5510,
"ICa": 0.5510,
"CaI": 0.5510,
"MgC": 0.3623,
"CMg": 0.3623,
"MgN": 0.3742,
"NMg": 0.3742,
"MgO": 0.4183,
"OMg": 0.4183,
"MgP": 0.4183,
"PMg": 0.4183,
"MgS": 0.4183,
"SMg": 0.4183,
"MgH": 0.1323,
"HMg": 0.1323,
"MgFe": 0.0935,
"FeMg": 0.0935,
"MgF": 0.2646,
"FMg": 0.2646,
"MgCl": 0.4914,
"ClMg": 0.4914,
"MgBr": 0.5834,
"BrMg": 0.5834,
"MgI": 0.6950,
"IMg": 0.6950,
"MgMg": 0.8750,
"MgZn": 0.6937,
"ZnMg": 0.6937,
"MgCa": 0.6937,
"CaMg": 0.6937,
"ZnC": 0.2872,
"CZn": 0.2872,
"ZnN": 0.2966,
"NZn": 0.2966,
"ZnO": 0.3317,
"OZn": 0.3317,
"ZnP": 0.3317,
"PZn": 0.3317,
"ZnS": 0.3317,
"SZn": 0.3317,
"ZnH": 0.1049,
"HZn": 0.1049,
"ZnFe": 0.0742,
"FeZn": 0.0742,
"ZnF": 0.2098,
"FZn": 0.2098,
"ZnCl": 0.3896,
"ClZn": 0.3896,
"ZnBr": 0.4625,
"BrZn": 0.4625,
"ZnI": 0.5510,
"IZn": 0.5510,
"ZnMg": 0.6937,
"MgZn": 0.6937,
"ZnZn": 0.5500,
"ZnCa": 0.5500,
"CaZn": 0.5500,
"CaC": 0.2872,
"CCa": 0.2872,
"CaN": 0.2966,
"NCa": 0.2966,
"CaO": 0.3317,
"OCa": 0.3317,
"CaP": 0.3317,
"PCa": 0.3317,
"CaS": 0.3317,
"SCa": 0.3317,
"CaH": 0.1049,
"HCa": 0.1049,
"CaFe": 0.0742,
"FeCa": 0.0742,
"CaF": 0.2098,
"FCa": 0.2098,
"CaCl": 0.3896,
"ClCa": 0.3896,
"CaBr": 0.4625,
"BrCa": 0.4625,
"CaI": 0.5510,
"ICa": 0.5510,
"CaMg": 0.6937,
"MgCa": 0.6937,
"CaZn": 0.5500,
"ZnCa": 0.5500,
"CaCa": 0.5500,
"X": 0,
}
RIJ = {
"CC": 4.00,
"CN": 3.75,
"NC": 3.75,
"CO": 3.60,
"OC": 3.60,
"CP": 4.10,
"PC": 4.10,
"CS": 4.00,
"SC": 4.00,
"CH": 3.00,
"HC": 3.00,
"CFe": 2.65,
"FeC": 2.65,
"CF": 3.54,
"FC": 3.54,
"CCl": 4.04,
"ClC": 4.04,
"CBr": 4.17,
"BrC": 4.17,
"CI": 4.36,
"IC": 4.36,
"CMg": 2.65,
"MgC": 2.65,
"CZn": 2.74,
"ZnC": 2.74,
"CCa": 2.99,
"CaC": 2.99,
"NC": 3.75,
"CN": 3.75,
"NN": 3.50,
"NO": 3.35,
"ON": 3.35,
"NP": 3.85,
"PN": 3.85,
"NS": 3.75,
"SN": 3.75,
"NH": 2.75,
"HN": 2.75,
"NFe": 2.40,
"FeN": 2.40,
"NF": 3.29,
"FN": 3.29,
"NCl": 3.79,
"ClN": 3.79,
"NBr": 3.92,
"BrN": 3.92,
"NI": 4.11,
"IN": 4.11,
"NMg": 2.40,
"MgN": 2.40,
"NZn": 2.49,
"ZnN": 2.49,
"NCa": 2.74,
"CaN": 2.74,
"OC": 3.60,
"CO": 3.60,
"ON": 3.35,
"NO": 3.35,
"OO": 3.20,
"OP": 3.70,
"PO": 3.70,
"OS": 3.60,
"SO": 3.60,
"OH": 2.60,