/* * File: periodcTable.cpp * Author: flong * * Created on July 29, 2012, 11:22 PM */ #include "periodicTable.h" namespace LIBMOL { PeriodicTable::PeriodicTable() { matTypes[1] = "H"; // H matTypes[2] = "Non-Metal"; // C, N, O, P, S, Se matTypes[3] = "Alkali-Metals"; // Li, Na, K, Rb, Cs, Fr matTypes[4] = "Alkaline-earth-Metals"; // Be, Mg, Ca, Sr, Ba, Ra matTypes[5] = "Transition-Metals"; // Fe, Cu, Au, Mn, Ni etc matTypes[6] = "Other-Metal"; // Al, Ga, In, Sn, Tl, Pb, Bi, etc. matTypes[7] = "Semimetallics"; // B, Si, Ge, As, Sb, Te, Po matTypes[8] = "Halogens"; // F, Cl, Br, I, At matTypes[9] = "Rare-Earth"; // La, Ce etc. matTypes[10] = "Inert-Gases"; // He, Ne, Ar, Kr, Xe, Rn /* For each element, the following properties are listed: * 1. row # in the periodic table * 2. group # (general groups include the transition metal * 3. material type, such as metal, non-metal, rare-earth etc * 4. atomic number., (indication of the weight) * 5. default valence. * 6. default oxidation number. If it is 0, then it has no default value and * needs to to be decided on-fly * * Unknown = -1 */ // Some of covalent radii for non-organic elements are from "Dalton Trans., 2008, 2832–2838, // Covalent radii revisited, by Beatriz Cordero at el" // // Hydrogen elements["H"]["row"] = 1; elements["H"]["group"] = 1; elements["H"]["matType"] = 1; elements["H"]["atomNum"] = 1; elements["H"]["val"] = 1; elemProps["H"]["vdw"] = 1.20; elemProps["H"]["cova"] = 0.32; elemProps["H"]["ionM-"] = 0.23; elemProps["H"]["ionM+"] = 0.23; elements["D"]["row"] = 1; elements["D"]["group"] = 1; elements["D"]["matType"] = 1; elements["D"]["atomNum"] = 1; elements["D"]["val"] = 1; elemProps["D"]["vdw"] = 1.20; elemProps["D"]["cova"] = 0.32; elemProps["D"]["ionM-"] = 0.23; elemProps["D"]["ionM+"] = 0.23; // Organic set or Non-metal elements["C"]["row"] = 2; elements["C"]["group"] = 14; elements["C"]["matType"] = 2; elements["C"]["atomNum"] = 6; elements["C"]["val"] = 4; elemProps["C"]["vdw"] = 1.70; elemProps["C"]["cova"] = 0.76; //0.85; // 0.76; elemProps["C"]["ionM-"] = 0.30; elements["N"]["row"] = 2; elements["N"]["group"] = 15; elements["N"]["matType"] = 2; elements["N"]["atomNum"] = 7; elements["N"]["val"] = 3; elemProps["N"]["vdw"] = 1.55; elemProps["N"]["cova"] = 0.71; elemProps["N"]["ionM-"] = 1.32; elemProps["N"]["ionM+"] = 0.30; elements["O"]["row"] = 2; elements["O"]["group"] = 16; elements["O"]["matType"] = 2; elements["O"]["atomNum"] = 8; elements["O"]["val"] = 2; elemProps["O"]["vdw"] = 1.52; elemProps["O"]["cova"] = 0.68; elemProps["O"]["ionM-"] = 1.26; elements["P"]["row"] = 3; elements["P"]["group"] = 15; elements["P"]["matType"] = 2; elements["P"]["atomNum"] = 15; elements["P"]["val"] = 5; elemProps["P"]["vdw"] = 1.52; elemProps["P"]["vdw"] = 1.80; elemProps["P"]["cova"] = 1.05; elemProps["P"]["ionM+"] = 0.58; //elemProps["P5+"]["cova"] = 0.52; elements["S"]["row"] = 3; elements["S"]["group"] = 16; elements["S"]["matType"] = 2; elements["S"]["atomNum"] = 16; elements["S"]["val"] = 6; elemProps["S"]["vdw"] = 1.80; elemProps["S"]["vdw"] = 1.80; elemProps["S"]["cova"] = 1.02; elemProps["S"]["ionM-"] = 1.70; elemProps["S"]["ionM+"] = 0.51; //elemProps["S6+"]["cova"] = 0.43; elements["Se"]["row"] = 4; elements["Se"]["group"] = 16; elements["Se"]["matType"] = 2; elements["Se"]["atomNum"] = 34; elements["Se"]["val"] = 6; elemProps["Se"]["vdw"] = 1.90; elemProps["Se"]["cova"] = 1.16; elemProps["Se"]["ionM-"] = 1.84; elemProps["Se"]["ionM+"] = 0.64; //elemProps["Se6+"]["cova"] = 0.56; elements["B"]["row"] = 2; elements["B"]["group"] = 13; elements["B"]["matType"] = 7; elements["B"]["atomNum"] = 5; elements["B"]["val"] = 3; //elements["B"]["vdw"] = 1.85; //elements["B"]["cova"] = 0.83; elemProps["B"]["vdw"] = 1.85; elemProps["B"]["cova"] = 0.83; elemProps["B"]["ionM+"] = 0.41; // Halogens elements["F"]["row"] = 2; elements["F"]["group"] = 17; elements["F"]["matType"] = 8; elements["F"]["atomNum"] = 9; elements["F"]["val"] = 1; //elements["F"]["vdw"] = 1.47; //elements["F"]["cova"] = 0.64; elemProps["F"]["vdw"] = 1.47; elemProps["F"]["cova"] = 0.57; elemProps["F"]["ionM-"] = 1.19; elemProps["F"]["ionM+"] = 0.22; elements["Cl"]["row"] = 3; elements["Cl"]["group"] = 17; elements["Cl"]["matType"] = 8; elements["Cl"]["atomNum"] = 17; elements["Cl"]["val"] = 1; //elements["Cl"]["vdw"] = 1.75; //elements["Cl"]["cova"] = 0.99; elemProps["Cl"]["vdw"] = 1.75; elemProps["Cl"]["cova"] = 0.99; elemProps["Cl"]["ionM-"] = 1.67; elements["Br"]["row"] = 4; elements["Br"]["group"] = 17; elements["Br"]["matType"] = 8; elements["Br"]["atomNum"] = 35; elements["Br"]["val"] = 1; //elements["Br"]["vdw"] = 1.85; //elements["Br"]["cova"] = 1.21; elemProps["Br"]["vdw"] = 1.85; elemProps["Br"]["cova"] = 1.14; elemProps["Br"]["ionM-"] = 1.96; elements["I"]["row"] = 5; elements["I"]["group"] = 17; elements["I"]["matType"] = 8; elements["I"]["atomNum"] = 53; elements["I"]["val"] = 1; //elements["I"]["vdw"] = 1.98; //elements["I"]["cova"] = 1.40; elemProps["I"]["vdw"] = 1.98; elemProps["I"]["cova"] = 1.33; elemProps["I"]["ionM-"] = 2.06; elements["At"]["row"] = 6; elements["At"]["group"] = 17; elements["At"]["matType"] = 8; elements["At"]["atomNum"] = 85; elements["At"]["val"] = 1; //elements["At"]["vdw"] = 2.00; //elements["At"]["cova"] = 1.50; elemProps["At"]["vdw"] = 2.00; elemProps["At"]["cova"] = 1.50; elemProps["At"]["ionM-"] = 0.76; // Alkali-Metals elements["Li"]["row"] = 2; elements["Li"]["group"] = 1; elements["Li"]["matType"] = 3; elements["Li"]["atomNum"] = 3; elements["Li"]["val"] = 1; //elements["Li"]["vdw"] = 1.82; //elements["Li"]["cova"] = 0.68; elemProps["Li"]["vdw"] = 1.82; elemProps["Li"]["cova"] = 1.28; elemProps["Li"]["ionM+"] = 0.73; elements["Na"]["row"] = 3; elements["Na"]["group"] = 1; elements["Na"]["matType"] = 3; elements["Na"]["atomNum"] = 11; elements["Na"]["val"] = 1; //elements["Na"]["vdw"] = 2.27; //elements["Na"]["cova"] = 0.97; elemProps["Na"]["vdw"] = 2.27; elemProps["Na"]["cova"] = 1.66; // 1.13; elemProps["Na"]["ionM+"] = 1.13; elements["K"]["row"] = 4; elements["K"]["group"] = 1; elements["K"]["matType"] = 3; elements["K"]["atomNum"] = 19; elements["K"]["val"] = 1; //elements["K"]["vdw"] = 2.75; //elements["K"]["cova"] = 1.33; elemProps["K"]["vdw"] = 2.75; elemProps["K"]["cova"] = 2.03; elemProps["K"]["ionM+"] = 1.52; elements["Rb"]["row"] = 5; elements["Rb"]["group"] = 1; elements["Rb"]["matType"] = 3; elements["Rb"]["atomNum"] = 37; elements["Rb"]["val"] = 1; //elements["Rb"]["vdw"] = 2.00; //elements["Rb"]["cova"] = 1.47; elemProps["Rb"]["vdw"] = 2.00; elemProps["Rb"]["cova"] = 1.48; elemProps["Rb"]["ionM+"] = 1.48; elements["Cs"]["row"] = 6; elements["Cs"]["group"] = 1; elements["Cs"]["matType"] = 3; elements["Cs"]["atomNum"] = 55; elements["Cs"]["val"] = 1; elements["Cs"]["vdw"] = 2.00; //elements["Cs"]["cova"] = 1.67; //elemProps["Cs"]["vdw"] = 2.00; elemProps["Cs"]["cova"] = 1.67; elemProps["Cs"]["ionM+"] = 1.81; elements["Fr"]["row"] = 7; elements["Fr"]["group"] = 1; elements["Fr"]["matType"] = 3; elements["Fr"]["atomNum"] = 87; elements["Fr"]["val"] = 1; //elements["Fr"]["vdw"] = 2.00; //elements["Fr"]["cova"] = 1.50; elemProps["Fr"]["vdw"] = 2.00; // need to find out it elemProps["Fr"]["cova"] = 1.50; elemProps["Fr"]["ionM+"] = 1.94; // Alkaline-earth-Metals elements["Be"]["row"] = 2; elements["Be"]["group"] = 2; elements["Be"]["matType"] = 4; elements["Be"]["atomNum"] = 4; elements["Be"]["val"] = 2; //elements["Be"]["vdw"] = 2.00; //elements["Be"]["cova"] = 0.35; elemProps["Be"]["vdw"] = 2.00; elemProps["Be"]["cova"] = 0.96; elemProps["Be"]["ionM+"] = 0.41; elements["Mg"]["row"] = 3; elements["Mg"]["group"] = 2; elements["Mg"]["matType"] = 4; elements["Mg"]["atomNum"] = 12; elements["Mg"]["val"] = 2; //elements["Mg"]["vdw"] = 1.73; //elements["Mg"]["cova"] = 1.10; elemProps["Mg"]["vdw"] = 1.73; elemProps["Mg"]["cova"] = 1.41; elemProps["Mg"]["ionM+"] = 0.71; elements["Ca"]["row"] = 4; elements["Ca"]["group"] = 2; elements["Ca"]["matType"] = 4; elements["Ca"]["atomNum"] = 20; elements["Ca"]["val"] = 2; //elements["Ca"]["vdw"] = 2.00; //elements["Ca"]["cova"] = 0.99; elemProps["Ca"]["vdw"] = 2.00; elemProps["Ca"]["cova"] = 1.76; elemProps["Ca"]["ionM+"] = 1.14; elements["Sr"]["row"] = 5; elements["Sr"]["group"] = 2; elements["Sr"]["matType"] = 4; elements["Sr"]["atomNum"] = 38; elements["Sr"]["val"] = 2; //elements["Sr"]["vdw"] = 2.19; //elements["Sr"]["cova"] = 1.12; elemProps["Sr"]["vdw"] = 2.19; // elemProps["Sr"]["cova"] = 1.92; elemProps["Sr"]["cova"] = 1.85; elemProps["Sr"]["ionM+"] = 1.32; elements["Ba"]["row"] = 6; elements["Ba"]["group"] = 2; elements["Ba"]["matType"] = 4; elements["Ba"]["atomNum"] = 56; elements["Ba"]["val"] = 2; //elements["Ba"]["vdw"] = 2.53; //elements["Ba"]["cova"] = 1.34; elemProps["Ba"]["vdw"] = 2.53; elemProps["Ba"]["cova"] = 1.98; elemProps["Ba"]["ionM+"] = 1.49; elements["Ra"]["row"] = 7; elements["Ra"]["group"] = 2; elements["Ra"]["matType"] = 4; elements["Ra"]["atomNum"] = 88; elements["Ra"]["val"] = 2; //elements["Ra"]["vdw"] = 2.15; //elements["Ra"]["cova"] = 1.90; elemProps["Ra"]["vdw"] = 2.15; elemProps["Ra"]["cova"] = 1.90; elemProps["Ra"]["ionM+"] = 1.62; // Transition-Metals elements["Sc"]["row"] = 4; elements["Sc"]["group"] = 3; elements["Sc"]["matType"] = 5; elements["Sc"]["atomNum"] = 21; elements["Sc"]["val"] = 3; //elements["Sc"]["vdw"] = 1.60; //elements["Sc"]["cova"] = 1.44; elemProps["Sc"]["vdw"] = 1.60; elemProps["Sc"]["cova"] = 1.70; elemProps["Sc"]["ionM+"] = 0.885; elements["Y"]["row"] = 5; elements["Y"]["group"] = 3; elements["Y"]["matType"] = 5; elements["Y"]["atomNum"] = 39; elements["Y"]["val"] = 3; //elements["Y"]["vdw"] = 1.80; //elements["Y"]["cova"] = 1.78; elemProps["Y"]["vdw"] = 1.80; elemProps["Y"]["cova"] = 1.90; elemProps["Y"]["ionM+"] = 1.04; elements["Ti"]["row"] = 4; elements["Ti"]["group"] = 4; elements["Ti"]["matType"] = 5; elements["Ti"]["atomNum"] = 22; elements["Ti"]["val"] = 4; //elements["Ti"]["vdw"] = 1.40; //elements["Ti"]["cova"] = 1.47; elemProps["Ti"]["vdw"] = 1.40; elemProps["Ti"]["cova"] = 1.60; elemProps["Ti"]["ionM+"] = 0.86; //elemProps["Ti3+"]["cova"] = 0.67; //elemProps["Ti4+"]["cova"] = 0.61; elements["Zr"]["row"] = 5; elements["Zr"]["group"] = 4; elements["Zr"]["matType"] = 5; elements["Zr"]["atomNum"] = 40; elements["Zr"]["val"] = 4; //elements["Zr"]["vdw"] = 1.55; //elements["Zr"]["cova"] = 1.56; elemProps["Zr"]["vdw"] = 1.55; elemProps["Zr"]["cova"] = 1.75; elemProps["Zr"]["ionM+"] = 0.72; elements["Hf"]["row"] = 6; elements["Hf"]["group"] = 4; elements["Hf"]["matType"] = 5; elements["Hf"]["atomNum"] = 72; elements["Hf"]["val"] = 4; //elements["Hf"]["vdw"] = 1.55; //elements["Hf"]["cova"] = 1.57; elemProps["Hf"]["vdw"] = 1.55; elemProps["Hf"]["cova"] = 1.75; elemProps["Hf"]["ionM+"] = 0.85; elements["Rf"]["row"] = 7; elements["Rf"]["group"] = 4; elements["Rf"]["matType"] = 5; elements["Rf"]["atomNum"] = 104; elements["Rf"]["val"] = 4; elemProps["Rf"]["vdw"] = 1.60; // need to find it out elemProps["Rf"]["cova"] = 1.21; elemProps["Rf"]["ionM+"] = 0.85; elements["V"]["row"] = 4; elements["V"]["group"] = 5; elements["V"]["matType"] = 5; elements["V"]["atomNum"] = 23; elements["V"]["val"] = 5; //elements["V"]["vdw"] = 1.35; //elements["V"]["cova"] = 1.33; elemProps["V"]["vdw"] = 1.35; elemProps["V"]["cova"] = 1.43; //1.53; elemProps["V"]["ionM+"] = 0.60; // 0.68; //elemProps["V3+"]["cova"] = 0.78; //elemProps["V4+"]["cova"] = 0.72; elements["Nb"]["row"] = 5; elements["Nb"]["group"] = 5; elements["Nb"]["matType"] = 5; elements["Nb"]["atomNum"] = 41; elements["Nb"]["val"] = 5; //elements["Nb"]["vdw"] = 1.45; //elements["Nb"]["cova"] = 1.48; elemProps["Nb"]["vdw"] = 1.45; elemProps["Nb"]["cova"] = 1.64; elemProps["Nb"]["ionM+"] = 0.62; //elemProps["Nb4+"]["cova"] = 0.82; //elemProps["Nb5+"]["cova"] = 0.78; elements["Ta"]["row"] = 6; elements["Ta"]["group"] = 5; elements["Ta"]["matType"] = 5; elements["Ta"]["atomNum"] = 73; elements["Ta"]["val"] = 5; //elements["Ta"]["vdw"] = 1.45; //elements["Ta"]["cova"] = 1.43; elemProps["Ta"]["vdw"] = 1.45; elemProps["Ta"]["cova"] = 1.70; elemProps["Ta"]["ionM+"] = 0.78; //elemProps["Ta4+"]["cova"] = 0.82; //elemProps["Ta5+"]["cova"] = 0.78; elements["Db"]["row"] = 7; elements["Db"]["group"] = 5; elements["Db"]["matType"] = 5; elements["Db"]["atomNum"] = 105; elements["Db"]["val"] = 5; //elements["Db"]["vdw"] = 1.45; //elements["Db"]["cova"] = 1.50; elemProps["Db"]["vdw"] = 1.45; // need to find it out elemProps["Db"]["cova"] = 1.50; elemProps["Db"]["ionM+"] = 0.78; elements["Cr"]["row"] = 4; elements["Cr"]["group"] = 6; elements["Cr"]["matType"] = 5; elements["Cr"]["atomNum"] = 24; elements["Cr"]["val"] = 6; //elements["Cr"]["vdw"] = 1.40; //elements["Cr"]["cova"] = 1.35; elemProps["Cr"]["vdw"] = 1.40; elemProps["Cr"]["cova"] = 1.39; elemProps["Cr"]["ionM+"] = 0.87; //elemProps["Cr3+"]["cova"] = 0.76; //elemProps["Cr4+"]["cova"] = 0.69; //elemProps["Cr5+"]["cova"] = 0.63; //elemProps["Cr6+"]["cova"] = 0.58; elements["Mo"]["row"] = 5; elements["Mo"]["group"] = 6; elements["Mo"]["matType"] = 5; elements["Mo"]["atomNum"] = 42; elements["Mo"]["val"] = 6; //elements["Mo"]["vdw"] = 1.45; //elements["Mo"]["cova"] = 1.47; elemProps["Mo"]["vdw"] = 1.45; elemProps["Mo"]["cova"] = 1.29; //1.39; elemProps["Mo"]["ionM+"] = 0.69; //elemProps["Mo4+"]["cova"] = 0.79; //elemProps["Mo5+"]["cova"] = 0.75; //elemProps["Mo6+"]["cova"] = 0.73; elements["W"]["row"] = 6; elements["W"]["group"] = 6; elements["W"]["matType"] = 5; elements["W"]["atomNum"] = 74; elements["W"]["val"] = 6; //elements["W"]["vdw"] = 1.85; //elements["W"]["cova"] = 1.21; elemProps["W"]["vdw"] = 1.35; elemProps["W"]["cova"] = 1.62; elemProps["W"]["ionM+"] = 0.80; //elemProps["W5+"]["cova"] = 0.76; //elemProps["W6+"]["cova"] = 0.74; elements["Sg"]["row"] = 7; elements["Sg"]["group"] = 6; elements["Sg"]["matType"] = 5; elements["Sg"]["atomNum"] = 106; elements["Sg"]["val"] = 6; //elements["Sg"]["vdw"] = 1.35; //elements["Sg"]["cova"] = 1.50; elemProps["Sg"]["vdw"] = 1.35; elemProps["Sg"]["cova"] = 1.50; elemProps["Sg"]["ionM+"] = 0.79; elements["Mn"]["row"] = 4; elements["Mn"]["group"] = 7; elements["Mn"]["matType"] = 5; elements["Mn"]["atomNum"] = 25; elements["Mn"]["val"] = 7; //elements["Mn"]["vdw"] = 1.40; //elements["Mn"]["cova"] = 1.35; elemProps["Mn"]["vdw"] = 1.40; elemProps["Mn"]["cova"] = 1.39; elemProps["Mn"]["ionM+"] = 0.81; //elemProps["Mn4+"]["cova"] = 0.72; //elemProps["Mn5+"]["cova"] = 0.67; //elemProps["Mn6+"]["cova"] = 0.47; //elemProps["Mn7+"]["cova"] = 0.40; elements["Tc"]["row"] = 5; elements["Tc"]["group"] = 7; elements["Tc"]["matType"] = 5; elements["Tc"]["atomNum"] = 43; elements["Tc"]["val"] = 7; //elements["Tc"]["vdw"] = 1.35; //elements["Tc"]["cova"] = 1.35; elemProps["Tc"]["vdw"] = 1.35; elemProps["Tc"]["cova"] = 1.47; elemProps["Tc"]["ionM+"] = 0.79; //elemProps["Tc5+"]["cova"] = 0.64; //elemProps["Tc7+"]["cova"] = 0.70; elements["Re"]["row"] = 6; elements["Re"]["group"] = 7; elements["Re"]["matType"] = 5; elements["Re"]["atomNum"] = 75; elements["Re"]["val"] = 7; //elements["Re"]["vdw"] = 1.35; //elements["Re"]["cova"] = 1.35; elemProps["Re"]["vdw"] = 1.35; elemProps["Re"]["cova"] = 1.51; elemProps["Re"]["ionM+"] = 0.77; //elemProps["Re5+"]["cova"] = 0.72; //elemProps["Re6+"]["cova"] = 0.69; //elemProps["Re7+"]["cova"] = 0.67; elements["Bh"]["row"] = 7; elements["Bh"]["group"] = 7; elements["Bh"]["matType"] = 5; elements["Bh"]["atomNum"] = 107; elements["Bh"]["val"] = 7; //elements["Bh"]["vdw"] = 1.35; //elements["Bh"]["cova"] = 1.50; elemProps["Bh"]["vdw"] = 1.35; // Need to find it out elemProps["Bh"]["cova"] = 1.50; elemProps["Bh"]["ionM+"] = 0.77; elements["Fe"]["row"] = 4; elements["Fe"]["group"] = 8; elements["Fe"]["matType"] = 5; elements["Fe"]["atomNum"] = 26; elements["Fe"]["val"] = 6; //elements["Fe"]["vdw"] = 1.40; //elements["Fe"]["cova"] = 1.34; elemProps["Fe"]["vdw"] = 1.40; elemProps["Fe"]["cova"] = 1.32; elemProps["Fe"]["ionM+"] = 0.85; //elemProps["Fe3+"]["cova"] = 0.69; //elemProps["Fe4+"]["cova"] = 0.725; //elemProps["Fe6+"]["cova"] = 0.39; elements["Ru"]["row"] = 5; elements["Ru"]["group"] = 8; elements["Ru"]["matType"] = 5; elements["Ru"]["atomNum"] = 44; elements["Ru"]["val"] = 8; //elements["Ru"]["vdw"] = 1.30; //elements["Ru"]["cova"] = 1.40; elemProps["Ru"]["vdw"] = 1.30; elemProps["Ru"]["cova"] = 1.46; elemProps["Ru"]["ionM+"] = 0.82; //elemProps["Ru4+"]["cova"] = 0.76; //elemProps["Ru5+"]["cova"] = 0.705; //elemProps["Ru7+"]["cova"] = 0.52; //elemProps["Ru8+"]["cova"] = 0.50; elements["Os"]["row"] = 6; elements["Os"]["group"] = 8; elements["Os"]["matType"] = 5; elements["Os"]["atomNum"] = 76; elements["Os"]["val"] = 8; //elements["Os"]["vdw"] = 1.30; //elements["Os"]["cova"] = 1.37; elemProps["Os"]["vdw"] = 1.30; elemProps["Os"]["cova"] = 1.44; elemProps["Os"]["ionM+"] = 0.77; //elemProps["Os5+"]["cova"] = 0.715; //elemProps["Os6+"]["cova"] = 0.685; //elemProps["Os7+"]["cova"] = 0.665; //elemProps["Os8+"]["cova"] = 0.53; elements["Hs"]["row"] = 7; elements["Hs"]["group"] = 8; elements["Hs"]["matType"] = 5; elements["Hs"]["atomNum"] = 108; elements["Hs"]["val"] = 8; //elements["Hs"]["vdw"] = 1.30; //elements["Hs"]["cova"] = 1.50; elemProps["Hs"]["vdw"] = 1.30; // Need to find it out elemProps["Hs"]["cova"] = 1.50; elemProps["Hs"]["ionM+"] = 0.805; elements["Co"]["row"] = 4; elements["Co"]["group"] = 9; elements["Co"]["matType"] = 5; elements["Co"]["atomNum"] = 27; elements["Co"]["val"] = 5; //elements["Co"]["vdw"] = 1.35; //elements["Co"]["cova"] = 1.33; elemProps["Co"]["vdw"] = 1.35; elemProps["Co"]["cova"] = 1.33; // 1.26 elemProps["Co"]["ionM+"] = 0.885; //elemProps["Co3+"]["cova"] = 0.75; //elemProps["Co4+"]["cova"] = 0.67; elements["Rh"]["row"] = 5; elements["Rh"]["group"] = 9; elements["Rh"]["matType"] = 5; elements["Rh"]["atomNum"] = 45; //elements["Rh"]["val"] = 6; //elements["Rh"]["vdw"] = 1.35; elemProps["Rh"]["vdw"] = 1.35; elemProps["Rh"]["cova"] = 1.42; elemProps["Rh"]["ionM+"] = 0.805; //elemProps["Rh4+"]["cova"] = 0.74; //elemProps["Rh5+"]["cova"] = 0.69; elements["Ir"]["row"] = 6; elements["Ir"]["group"] = 9; elements["Ir"]["matType"] = 5; elements["Ir"]["atomNum"] = 77; elements["Ir"]["val"] = 8; //elements["Ir"]["vdw"] = 1.35; //elements["Ir"]["cova"] = 1.32; elemProps["Ir"]["vdw"] = 1.35; elemProps["Ir"]["ionM+"] = 0.82; elemProps["Ir"]["cova"] = 1.41; //elemProps["Ir5+"]["cova"] = 0.71; elements["Mt"]["row"] = 7; elements["Mt"]["group"] = 9; elements["Mt"]["matType"] = 5; elements["Mt"]["atomNum"] = 109; elements["Mt"]["val"] = -1; //elements["Mt"]["vdw"] = 1.35; //elements["Mt"]["cova"] = 1.21; elemProps["Mt"]["vdw"] = 1.35; // Need to find it out elemProps["Mt"]["cova"] = 1.21; elemProps["Mt"]["ionM+"] = 0.82; elements["Ni"]["row"] = 4; elements["Ni"]["group"] = 10; elements["Ni"]["matType"] = 5; elements["Ni"]["atomNum"] = 28; elements["Ni"]["val"] = 4; //elements["Ni"]["vdw"] = 1.63; //elements["Ni"]["cova"] = 1.50; elemProps["Ni"]["vdw"] = 1.63; elemProps["Ni"]["cova"] = 1.24; elemProps["Ni"]["ionM+"] = 0.83; //elemProps["Ni3+"]["cova"] = 0.70; //elemProps["Ni4+"]["cova"] = 0.62; elements["Pd"]["row"] = 5; elements["Pd"]["group"] = 10; elements["Pd"]["matType"] = 5; elements["Pd"]["atomNum"] = 46; elements["Pd"]["val"] = 4; //elements["Pd"]["vdw"] = 1.63; //elements["Pd"]["cova"] = 1.50; elemProps["Pd"]["vdw"] = 1.63; elemProps["Pd"]["cova"] = 1.39; //1.50; //1.39; elemProps["Pd"]["ionM+"] = 0.73; //elemProps["Pd2+"]["cova"] = 1.00; //elemProps["Pd3+"]["cova"] = 0.90; //elemProps["Pd4+"]["cova"] = 0.755; elements["Pt"]["row"] = 6; elements["Pt"]["group"] = 10; elements["Pt"]["matType"] = 5; elements["Pt"]["atomNum"] = 78; elements["Pt"]["val"] = 6; //elements["Pt"]["vdw"] = 1.72; //elements["Pt"]["cova"] = 1.50; elemProps["Pt"]["vdw"] = 1.72; elemProps["Pt"]["cova"] = 1.60; // 1.36; elemProps["Pt"]["ionM+"] = 0.94; //elemProps["Pt4+"]["cova"] = 0.765; //elemProps["Pt5+"]["cova"] = 0.71; elements["Ds"]["row"] = 7; elements["Ds"]["group"] = 10; elements["Ds"]["matType"] = 5; elements["Ds"]["atomNum"] = 110; elements["Ds"]["val"] = -1; //elements["Ds"]["vdw"] = 1.75; //elements["Ds"]["cova"] = 1.50; elemProps["Ds"]["vdw"] = 1.75; elemProps["Ds"]["cova"] = 1.50; elemProps["Ds"]["ionM+"] = 0.94; elements["Cu"]["row"] = 4; elements["Cu"]["group"] = 11; elements["Cu"]["matType"] = 5; elements["Cu"]["atomNum"] = 29; elements["Cu"]["val"] = 2; //elements["Cu"]["vdw"] = 1.40; //elements["Cu"]["cova"] = 1.52; elemProps["Cu"]["vdw"] = 1.40; elemProps["Cu"]["cova"] = 1.20; // 1.32; elemProps["Cu"]["ionM+"] = 0.91; //elemProps["Cu2+"]["cova"] = 0.87; //elemProps["Cu3+"]["cova"] = 0.68; elements["Ag"]["row"] = 5; elements["Ag"]["group"] = 11; elements["Ag"]["matType"] = 5; elements["Ag"]["atomNum"] = 47; elements["Ag"]["val"] = 4; //elements["Ag"]["vdw"] = 1.72; //elements["Ag"]["cova"] = 1.59; elemProps["Ag"]["vdw"] = 1.72; elemProps["Ag"]["cova"] = 1.25;//1.45; elemProps["Ag"]["ionM+"] = 1.29; //elemProps["Ag2+"]["cova"] = 1.08; //elemProps["Ag3+"]["cova"] = 0.89; elements["Au"]["row"] = 6; elements["Au"]["group"] = 11; elements["Au"]["matType"] = 5; elements["Au"]["atomNum"] = 79; elements["Au"]["val"] = 5; //elements["Au"]["vdw"] = 1.66; //elements["Au"]["cova"] = 1.50; elemProps["Au"]["vdw"] = 1.66; elemProps["Au"]["cova"] = 1.37; elemProps["Au"]["ionM+"] = 1.51; //elemProps["Au3+"]["cova"] = 0.99; //elemProps["Au5+"]["cova"] = 0.71; elements["Rg"]["row"] = 7; elements["Rg"]["group"] = 11; elements["Rg"]["matType"] = 5; elements["Rg"]["atomNum"] = 111; elements["Rg"]["val"] = -1; //elements["Rg"]["vdw"] = 1.66; //elements["Rg"]["cova"] = 1.50; elemProps["Rg"]["vdw"] = 1.66; // Need to find it out elemProps["Rg"]["cova"] = 1.50; elemProps["Rg"]["ionM+"] = 0.94; elements["Zn"]["row"] = 4; elements["Zn"]["group"] = 12; elements["Zn"]["matType"] = 5; elements["Zn"]["atomNum"] = 30; elements["Zn"]["val"] = 2; //elements["Zn"]["vdw"] = 1.39; //elements["Zn"]["cova"] = 1.45; elemProps["Zn"]["vdw"] = 1.39; elemProps["Zn"]["cova"] = 1.18; elemProps["Zn"]["ionM+"] = 0.88; elements["Cd"]["row"] = 5; elements["Cd"]["group"] = 12; elements["Cd"]["matType"] = 5; elements["Cd"]["atomNum"] = 48; elements["Cd"]["val"] = 2; //elements["Cd"]["vdw"] = 1.58; //elements["Cd"]["cova"] = 1.69; elemProps["Cd"]["vdw"] = 1.58; elemProps["Cd"]["cova"] = 1.69; // 1.44; elemProps["Cd"]["ionM+"] = 1.09; elements["Hg"]["row"] = 6; elements["Hg"]["group"] = 12; elements["Hg"]["matType"] = 5; elements["Hg"]["atomNum"] = 80; elements["Hg"]["val"] = 2; //elements["Hg"]["vdw"] = 155; //elements["Hg"]["cova"] = 1.70; elemProps["Hg"]["vdw"] = 1.55; elemProps["Hg"]["cova"] = 1.70; // 1.32; elemProps["Hg"]["ionM+"] = 1.33; //elemProps["Hg2+"]["cova"] = 1.16; elements["Cn"]["row"] = 7; elements["Cn"]["group"] = 12; elements["Cn"]["matType"] = 5; elements["Cn"]["atomNum"] = 112; elements["Cn"]["val"] = -1; elemProps["Cn"]["vdw"] = 1.58; // Need to find it out elemProps["Cn"]["cova"] = 1.58; // Need to find it out // Other-Metal elements["Al"]["row"] = 3; elements["Al"]["group"] = 13; elements["Al"]["matType"] = 6; elements["Al"]["atomNum"] = 13; elements["Al"]["val"] = 3; //elements["Al"]["vdw"] = 1.25; //elements["Al"]["cova"] = 1.35; elemProps["Al"]["vdw"] = 1.25; elemProps["Al"]["cova"] = 1.21; elemProps["Al"]["ionM+"] = 0.675; elements["Ga"]["row"] = 4; elements["Ga"]["group"] = 13; elements["Ga"]["matType"] = 6; elements["Ga"]["atomNum"] = 31; elements["Ga"]["val"] = 3; //elements["Ga"]["vdw"] = 1.87; //elements["Ga"]["cova"] = 1.22; elemProps["Ga"]["vdw"] = 1.87; elemProps["Ga"]["cova"] = 1.22; elemProps["Ga"]["ionM+"] = 0.76; elements["In"]["row"] = 5; elements["In"]["group"] = 13; elements["In"]["matType"] = 6; elements["In"]["atomNum"] = 49; elements["In"]["val"] = 3; //elements["In"]["vdw"] = 1.93; //elements["In"]["cova"] = 1.63; elemProps["In"]["vdw"] = 1.93; elemProps["In"]["cova"] = 1.42; elemProps["In"]["ionM+"] = 0.94; elements["Ti"]["row"] = 6; elements["Ti"]["group"] = 13; elements["Ti"]["matType"] = 6; elements["Ti"]["atomNum"] = 81; elements["Ti"]["val"] = 3; //elements["Ti"]["vdw"] = 1.40; //elements["Ti"]["cova"] = 1.47; elemProps["Ti"]["vdw"] = 1.40; elemProps["Ti"]["cova"] = 1.60; elemProps["Ti"]["ionM+"] = 1.00; //elemProps["Ti3+"]["cova"] = 0.81; //elemProps["Ti4+"]["cova"] = 0.745; elements["Sn"]["row"] = 5; elements["Sn"]["group"] = 14; elements["Sn"]["matType"] = 6; elements["Sn"]["atomNum"] = 50; elements["Sn"]["val"] = 4; //elements["Sn"]["vdw"] = 2.17; //elements["Sn"]["cova"] = 1.46; elemProps["Sn"]["vdw"] = 2.17; elemProps["Sn"]["cova"] = 1.39; elemProps["Sn"]["ionM+"] = 0.83; elements["Pb"]["row"] = 6; elements["Pb"]["group"] = 14; elements["Pb"]["matType"] = 6; elements["Pb"]["atomNum"] = 82; elements["Pb"]["val"] = 4; //elements["Pb"]["vdw"] = 2.02; //elements["Pb"]["cova"] = 1.54; elemProps["Pb"]["vdw"] = 2.02; elemProps["Pb"]["cova"] = 1.46; elemProps["Pb"]["ionM+"] = 1.33; //elemProps["Pb+4"]["cova"] = 0.915; elements["Bi"]["row"] = 6; elements["Bi"]["group"] = 15; elements["Bi"]["matType"] = 6; elements["Bi"]["atomNum"] = 83; elements["Bi"]["val"] = 5; //elements["Bi"]["vdw"] = 1.80; //elements["Bi"]["cova"] = 1.54; elemProps["Bi"]["vdw"] = 1.80; elemProps["Bi"]["cova"] = 1.42; //1.48; elemProps["Bi"]["ionM+"] = 1.07; // Semimetallics elements["Si"]["row"] = 3; elements["Si"]["group"] = 14; elements["Si"]["matType"] = 7; elements["Si"]["atomNum"] = 14; elements["Si"]["val"] = 4; //elements["Si"]["vdw"] = 2.10; //elements["Si"]["cova"] = 1.20; elemProps["Si"]["vdw"] = 2.10; elemProps["Si"]["cova"] = 1.20; elemProps["Si"]["ionM+"] = 0.54; elements["Ge"]["row"] = 4; elements["Ge"]["group"] = 14; elements["Ge"]["matType"] = 7; elements["Ge"]["atomNum"] = 32; elements["Ge"]["val"] = 4; //elements["Ge"]["vdw"] = 2.10; //elements["Ge"]["cova"] = 1.17; elemProps["Ge"]["vdw"] = 2.10; elemProps["Ge"]["cova"] = 1.20; elemProps["Ge"]["ionM+"] = 0.87; //elemProps["Ge4+"]["cova"] = 0.67; elements["As"]["row"] = 4; elements["As"]["group"] = 15; elements["As"]["matType"] = 7; elements["As"]["atomNum"] = 33; elements["As"]["val"] = 5; //elements["As"]["vdw"] = 1.85; //elements["As"]["cova"] = 1.21; elemProps["As"]["vdw"] = 1.85; elemProps["As"]["cova"] = 1.21; // 1.11; elemProps["As"]["ionM+"] = 0.72; //elemProps["As5+"]["cova"] = 0.60; elements["Sb"]["row"] = 5; elements["Sb"]["group"] = 15; elements["Sb"]["matType"] = 7; elements["Sb"]["atomNum"] = 51; elements["Sb"]["val"] = 5; //elements["Sb"]["vdw"] = 1.85; //elements["Sb"]["cova"] = 1.21; elemProps["Sb"]["vdw"] = 1.80; elemProps["Sb"]["cova"] = 1.39; elemProps["Sb"]["ionM+"] = 0.90; //elemProps["Sb5+"]["cova"] = 0.74; elements["Te"]["row"] = 5; elements["Te"]["group"] = 16; elements["Te"]["matType"] = 7; elements["Te"]["atomNum"] = 52; elements["Te"]["val"] = 6; //elements["Te"]["vdw"] = 2.06; //elements["Te"]["cova"] = 1.47; elemProps["Te"]["vdw"] = 2.06; elemProps["Te"]["cova"] = 1.38; elemProps["Te"]["ionM-"] = 2.07; elemProps["Te"]["ionM+"] = 1.11; //elemProps["Te5+"]["cova"] = 0.70; elements["Po"]["row"] = 6; elements["Po"]["group"] = 16; elements["Po"]["matType"] = 7; elements["Po"]["atomNum"] = 84; elements["Po"]["val"] = 6; //elements["Po"]["vdw"] = 1.85; //elements["Po"]["cova"] = 1.60; elemProps["Po"]["vdw"] = 2.00; elemProps["Po"]["cova"] = 1.40; elemProps["Po"]["ionM+"] = 1.08; //elemProps["Po6+"]["cova"] = 0.81; // Rare earth metals elements["La"]["row"] = 6; elements["La"]["group"] = 3; elements["La"]["matType"] = 9; elements["La"]["atomNum"] = 57; elements["La"]["val"] = 3; //elements["Po"]["vdw"] = 1.85; //elements["Po"]["cova"] = 1.60; elemProps["La"]["vdw"] = 1.87; //atom radius elemProps["La"]["cova"] = 2.07; elemProps["La"]["ionM+"] = 1.08; elements["Ce"]["row"] = 6; elements["Ce"]["group"] = 3; elements["Ce"]["matType"] = 9; elements["Ce"]["atomNum"] = 58; elements["Ce"]["val"] = 4; //elements["Po"]["vdw"] = 1.85; //elements["Po"]["cova"] = 1.60; elemProps["Ce"]["vdw"] = 1.82; //atom radius elemProps["Ce"]["cova"] = 2.04; elemProps["Ce"]["ionM+"] = 1.08; elements["Pr"]["row"] = 6; elements["Pr"]["group"] = 3; elements["Pr"]["matType"] = 9; elements["Pr"]["atomNum"] = 59; elements["Pr"]["val"] = 4; //elements["Po"]["vdw"] = 1.85; //elements["Po"]["cova"] = 1.60; elemProps["Pr"]["vdw"] = 1.82; //atom radius elemProps["Pr"]["cova"] = 2.03; elemProps["Pr"]["ionM+"] = 1.08; elements["Nd"]["row"] = 6; elements["Nd"]["group"] = 3; elements["Nd"]["matType"] = 9; elements["Nd"]["atomNum"] = 60; elements["Nd"]["val"] = 3; //elements["Po"]["vdw"] = 1.85; //elements["Po"]["cova"] = 1.60; elemProps["Nd"]["vdw"] = 1.81; //atom radius elemProps["Nd"]["cova"] = 2.01; elemProps["Nd"]["ionM+"] = 1.08; elements["Pm"]["row"] = 6; elements["Pm"]["group"] = 3; elements["Pm"]["matType"] = 9; elements["Pm"]["atomNum"] = 61; elements["Pm"]["val"] = 2; //elements["Po"]["vdw"] = 1.85; //elements["Po"]["cova"] = 1.60; elemProps["Pm"]["vdw"] = 1.59; elemProps["Pm"]["cova"] = 1.87; elemProps["Pm"]["ionM+"] = 1.08; elements["Sm"]["row"] = 6; elements["Sm"]["group"] = 3; elements["Sm"]["matType"] = 9; elements["Sm"]["atomNum"] = 62; elements["Sm"]["val"] = 3; //elements["Po"]["vdw"] = 1.85; //elements["Po"]["cova"] = 1.60; elemProps["Sm"]["vdw"] = 1.59; elemProps["Sm"]["cova"] = 1.87; elemProps["Sm"]["ionM+"] = 1.08; elements["Eu"]["row"] = 6; elements["Eu"]["group"] = 3; elements["Eu"]["matType"] = 9; elements["Eu"]["atomNum"] = 63; elements["Eu"]["val"] = 6; //elements["Po"]["vdw"] = 1.85; //elements["Po"]["cova"] = 1.60; elemProps["Eu"]["vdw"] = 1.59; elemProps["Eu"]["cova"] = 1.87; elemProps["Eu"]["ionM+"] = 1.08; elements["Gd"]["row"] = 6; elements["Gd"]["group"] = 3; elements["Gd"]["matType"] = 9; elements["Gd"]["atomNum"] = 64; elements["Gd"]["val"] = 3; elemProps["Gd"]["vdw"] = 1.80; elemProps["Gd"]["cova"] = 1.96; elemProps["Gd"]["ionM+"] = 1.08; elements["Tb"]["row"] = 6; elements["Tb"]["group"] = 3; elements["Tb"]["matType"] = 9; elements["Tb"]["atomNum"] = 65; elements["Tb"]["val"] = 4; elemProps["Tb"]["vdw"] = 1.77; elemProps["Tb"]["cova"] = 1.94; elemProps["Tb"]["ionM+"] = 1.08; elements["Dy"]["row"] = 6; elements["Dy"]["group"] = 3; elements["Dy"]["matType"] = 9; elements["Dy"]["atomNum"] = 66; elements["Dy"]["val"] = 3; elemProps["Dy"]["vdw"] = 1.78; elemProps["Dy"]["cova"] = 1.94; elemProps["Dy"]["ionM+"] = 1.08; elements["Ho"]["row"] = 6; elements["Ho"]["group"] = 3; elements["Ho"]["matType"] = 9; elements["Ho"]["atomNum"] = 67; elements["Ho"]["val"] = 3; elemProps["Ho"]["vdw"] = 1.76; elemProps["Ho"]["cova"] = 1.92; elemProps["Ho"]["ionM+"] = 1.08; elements["Er"]["row"] = 6; elements["Er"]["group"] = 3; elements["Er"]["matType"] = 9; elements["Er"]["atomNum"] = 68; elements["Er"]["val"] = 3; elemProps["Er"]["vdw"] = 1.76; elemProps["Er"]["cova"] = 1.89; elemProps["Er"]["ionM+"] = 1.08; elements["Tm"]["row"] = 6; elements["Tm"]["group"] = 3; elements["Tm"]["matType"] = 9; elements["Tm"]["atomNum"] = 69; elements["Tm"]["val"] = 3; elemProps["Tm"]["vdw"] = 1.76; elemProps["Tm"]["cova"] = 1.90; elemProps["Tm"]["ionM+"] = 1.08; elements["Yb"]["row"] = 6; elements["Yb"]["group"] = 3; elements["Yb"]["matType"] = 9; elements["Yb"]["atomNum"] = 70; elements["Yb"]["val"] = 1; elemProps["Yb"]["vdw"] = 1.76; elemProps["Yb"]["cova"] = 1.87; elemProps["Yb"]["ionM+"] = 1.08; elements["Lu"]["row"] = 6; elements["Lu"]["group"] = 3; elements["Lu"]["matType"] = 9; elements["Lu"]["atomNum"] = 71; elements["Lu"]["val"] = 1; elemProps["Lu"]["vdw"] = 1.74; elemProps["Lu"]["cova"] = 1.87; elemProps["Lu"]["ionM+"] = 1.08; elements["Ac"]["row"] = 7; elements["Ac"]["group"] = 3; elements["Ac"]["matType"] = 9; elements["Ac"]["atomNum"] = 89; elements["Ac"]["val"] = 3; elemProps["Ac"]["vdw"] = 1.76; elemProps["Ac"]["cova"] = 2.15; elemProps["Ac"]["ionM+"] = 1.08; elements["Th"]["row"] = 7; elements["Th"]["group"] = 3; elements["Th"]["matType"] = 9; elements["Th"]["atomNum"] = 90; elements["Th"]["val"] = 4; elemProps["Th"]["vdw"] = 1.80; elemProps["Th"]["cova"] = 2.06; elemProps["Th"]["ionM+"] = 1.08; elements["Pa"]["row"] = 7; elements["Pa"]["group"] = 3; elements["Pa"]["matType"] = 9; elements["Pa"]["atomNum"] = 91; elements["Pa"]["val"] = 4; elemProps["Pa"]["vdw"] = 1.63; elemProps["Pa"]["cova"] = 2.00; elemProps["Pa"]["ionM+"] = 1.08; elements["U"]["row"] = 7; elements["U"]["group"] = 3; elements["U"]["matType"] = 9; elements["U"]["atomNum"] = 92; elements["U"]["val"] = 6; elemProps["U"]["vdw"] = 1.86; elemProps["U"]["cova"] = 1.96; elemProps["U"]["ionM+"] = 1.08; elements["Np"]["row"] = 7; elements["Np"]["group"] = 3; elements["Np"]["matType"] = 9; elements["Np"]["atomNum"] = 93; elements["Np"]["val"] = 4; elemProps["Np"]["vdw"] = 1.55; elemProps["Np"]["cova"] = 1.90; elemProps["Np"]["ionM+"] = 1.08; elements["Pu"]["row"] = 7; elements["Pu"]["group"] = 3; elements["Pu"]["matType"] = 9; elements["Pu"]["atomNum"] = 94; elements["Pu"]["val"] = 6; elemProps["Pu"]["vdw"] = 1.59; elemProps["Pu"]["cova"] = 1.87; elemProps["Pu"]["ionM+"] = 1.08; elements["Am"]["row"] = 7; elements["Am"]["group"] = 3; elements["Am"]["matType"] = 9; elements["Am"]["atomNum"] = 95; elements["Am"]["val"] = 6; elemProps["Am"]["vdw"] = 1.73; elemProps["Am"]["cova"] = 1.80; elemProps["Am"]["ionM+"] = 1.08; elements["Cm"]["row"] = 7; elements["Cm"]["group"] = 3; elements["Cm"]["matType"] = 9; elements["Cm"]["atomNum"] = 96; elements["Cm"]["val"] = 4; elemProps["Cm"]["vdw"] = 1.74; elemProps["Cm"]["cova"] = 1.69; elemProps["Cm"]["ionM+"] = 1.08; elements["Bk"]["row"] = 7; elements["Bk"]["group"] = 3; elements["Bk"]["matType"] = 9; elements["Bk"]["atomNum"] = 97; elements["Bk"]["val"] = 4; elemProps["Bk"]["vdw"] = 1.70; elemProps["Bk"]["cova"] = 1.80; elemProps["Bk"]["ionM+"] = 1.08; // The following are rare-earth synthetic elements // where atom, vdw and covalent radii are not available // Put those props here just as position holders elements["Cf"]["row"] = 7; elements["Cf"]["group"] = 3; elements["Cf"]["matType"] = 9; elements["Cf"]["atomNum"] = 98; elements["Cf"]["val"] = 4; elemProps["Cf"]["vdw"] = 1.73; // not sure elemProps["Cf"]["cova"] = 1.80; // not sure elemProps["Cf"]["ionM+"] = 1.08; elements["Es"]["row"] = 7; elements["Es"]["group"] = 3; elements["Es"]["matType"] = 9; elements["Es"]["atomNum"] = 99; elements["Es"]["val"] = 3; elemProps["Es"]["vdw"] = 1.73; // not sure elemProps["Es"]["cova"] = 1.80; // not sure elemProps["Es"]["ionM+"] = 1.08; elements["Fm"]["row"] = 7; elements["Fm"]["group"] = 3; elements["Fm"]["matType"] = 9; elements["Fm"]["atomNum"] = 100; elements["Fm"]["val"] = 3; elemProps["Fm"]["vdw"] = 1.73; // not sure elemProps["Fm"]["cova"] = 1.80; // not sure elemProps["Fm"]["ionM+"] = 1.08; elements["Md"]["row"] = 7; elements["Md"]["group"] = 3; elements["Md"]["matType"] = 9; elements["Md"]["atomNum"] = 101; elements["Md"]["val"] = 3; elemProps["Md"]["vdw"] = 1.73; // not sure elemProps["Md"]["cova"] = 1.80; // not sure elemProps["Md"]["ionM+"] = 1.08; elements["No"]["row"] = 7; elements["No"]["group"] = 3; elements["No"]["matType"] = 9; elements["No"]["atomNum"] = 102; elements["No"]["val"] = 3; elemProps["No"]["vdw"] = 1.73; // not sure elemProps["No"]["cova"] = 1.80; // not sure elemProps["No"]["ionM+"] = 1.08; elements["Lr"]["row"] = 7; elements["Lr"]["group"] = 3; elements["Lr"]["matType"] = 9; elements["Lr"]["atomNum"] = 103; elements["Lr"]["val"] = 3; elemProps["Lr"]["vdw"] = 1.73; // not sure elemProps["Lr"]["cova"] = 1.80; // not sure elemProps["Lr"]["ionM+"] = 1.08; //Organic elements which have multiple valences extraValences["P"].push_back(3); extraValences["N"].push_back(5); extraValences["S"].push_back(4); extraValences["S"].push_back(6); extraValences["Se"].push_back(2); extraValences["Se"].push_back(4); extraValences["I"].push_back(3); extraValences["I"].push_back(5); extraValences["Br"].push_back(3); extraValences["Br"].push_back(5); extraValences["Br"].push_back(7); extraValences["B"].push_back(4); extraValences["B"].push_back(5); extraValences["B"].push_back(6); // Other elements which have multiple valences extraValences["Cu"].push_back(1); extraValences["Hg"].push_back(1); for (std::map >::iterator iEl=elements.begin(); iEl!=elements.end(); iEl++) { if (iEl->second["group"]==1) { iEl->second["oxiNum"]= 1; } else if (iEl->second["group"]==2) { iEl->second["oxiNum"]=2; } else if (iEl->first == "O") { iEl->second["oxiNum"] = 2; } else if (iEl->first =="F") { iEl->second["oxiNum"]=1; } else { // Oxidation number of the rest of elements // are decided on-fly iEl->second["oxiNum"]=0; } // lone-pair electrons if (iEl->first == "N") { iEl->second["pairedVE"] = 2; } else if (iEl->first=="S") { iEl->second["pairedVE"] = 4; } else if (iEl->first=="P") { iEl->second["pairedVE"] = 2; } else if (iEl->first=="Cl" || iEl->first=="Br" || iEl->first=="I" || iEl->first=="At") { iEl->second["pairedVE"] = 6; } else { // for metal and C atoms, set number of default lone-pair // electrons to zero iEl->second["pairedVE"] = 0; } } // Hydrogen electronConf["H"].push_back(std::make_pair ("1s",1)); // Organic set or Non-metal electronConf["C"].push_back(std::make_pair ("2s",2)); electronConf["C"].push_back(std::make_pair ("2p",2)); electronConf["N"].push_back(std::make_pair ("2s",2)); electronConf["N"].push_back(std::make_pair ("2p",3)); electronConf["O"].push_back(std::make_pair ("2s",2)); electronConf["O"].push_back(std::make_pair ("2p",4)); electronConf["P"].push_back(std::make_pair ("3s",2)); electronConf["P"].push_back(std::make_pair ("3p",3)); electronConf["S"].push_back(std::make_pair ("3s",2)); electronConf["S"].push_back(std::make_pair ("3p",4)); electronConf["Se"].push_back(std::make_pair ("4s",2)); electronConf["Se"].push_back(std::make_pair ("3d",10)); electronConf["Se"].push_back(std::make_pair ("4p",4)); // Halogens electronConf["F"].push_back(std::make_pair ("2s",2)); electronConf["F"].push_back(std::make_pair ("2p",5)); electronConf["Cl"].push_back(std::make_pair ("3s",2)); electronConf["Cl"].push_back(std::make_pair ("3p",5)); electronConf["Br"].push_back(std::make_pair ("4s",2)); electronConf["Br"].push_back(std::make_pair ("4p",5)); electronConf["I"].push_back(std::make_pair ("5s",2)); electronConf["I"].push_back(std::make_pair ("5p",5)); electronConf["At"].push_back(std::make_pair ("6s",2)); electronConf["At"].push_back(std::make_pair ("6p",5)); // Alkali-Metals electronConf["Li"].push_back(std::make_pair ("2s",1)); electronConf["Na"].push_back(std::make_pair ("3s",1)); electronConf["K"].push_back(std::make_pair ("4s",1)); electronConf["Rb"].push_back(std::make_pair ("5s",1)); electronConf["Cs"].push_back(std::make_pair ("6s",1)); electronConf["Fr"].push_back(std::make_pair ("7s",1)); // Alkaline-earth-Metals electronConf["Be"].push_back(std::make_pair ("2s",2)); electronConf["Mg"].push_back(std::make_pair ("3s",2)); electronConf["Ca"].push_back(std::make_pair ("4s",2)); electronConf["Sr"].push_back(std::make_pair ("5s",2)); electronConf["Ba"].push_back(std::make_pair ("6s",2)); electronConf["Ra"].push_back(std::make_pair ("7s",2)); // Transition-Metals electronConf["Sc"].push_back(std::make_pair ("3d",1)); electronConf["Y"].push_back(std::make_pair ("4d",1)); electronConf["Ti"].push_back(std::make_pair ("3d",2)); electronConf["Zr"].push_back(std::make_pair ("4d",2)); electronConf["Hf"].push_back(std::make_pair ("5d",2)); electronConf["Rf"].push_back(std::make_pair ("6d",2)); electronConf["V"].push_back(std::make_pair ("3d",3)); electronConf["Nb"].push_back(std::make_pair ("5s",1)); electronConf["Nb"].push_back(std::make_pair ("4d",4)); electronConf["Ta"].push_back(std::make_pair ("5d",3)); electronConf["Db"].push_back(std::make_pair ("6d",3)); electronConf["Cr"].push_back(std::make_pair ("4s",1)); electronConf["Cr"].push_back(std::make_pair ("3d",5)); electronConf["Mo"].push_back(std::make_pair ("5s",1)); electronConf["Mo"].push_back(std::make_pair ("4d",5)); electronConf["W"].push_back(std::make_pair ("5d",4)); electronConf["Sg"].push_back(std::make_pair ("6d",4)); electronConf["Mn"].push_back(std::make_pair ("3d",5)); electronConf["Tc"].push_back(std::make_pair ("4d",5)); electronConf["Re"].push_back(std::make_pair ("5d",5)); electronConf["Bh"].push_back(std::make_pair ("6d",5)); electronConf["Fe"].push_back(std::make_pair ("3d",6)); electronConf["Fe"].push_back(std::make_pair ("4s",2)); electronConf["Ru"].push_back(std::make_pair ("5s",1)); electronConf["Ru"].push_back(std::make_pair ("4d",7)); electronConf["Os"].push_back(std::make_pair ("5d",6)); electronConf["Hs"].push_back(std::make_pair ("6d",6)); electronConf["Co"].push_back(std::make_pair ("3d",7)); electronConf["Rh"].push_back(std::make_pair ("5s",1)); electronConf["Rh"].push_back(std::make_pair ("4d",8)); electronConf["Ir"].push_back(std::make_pair ("5d",7)); electronConf["Mt"].push_back(std::make_pair ("6d",7)); electronConf["Ni"].push_back(std::make_pair ("3d",8)); electronConf["Pd"].push_back(std::make_pair ("4d",10)); electronConf["Pt"].push_back(std::make_pair ("6s",1)); electronConf["Pt"].push_back(std::make_pair ("5d",9)); electronConf["Ds"].push_back(std::make_pair ("7s",1)); electronConf["Ds"].push_back(std::make_pair ("6d",9)); electronConf["Cu"].push_back(std::make_pair ("4s",1)); electronConf["Cu"].push_back(std::make_pair ("3d",10)); electronConf["Ag"].push_back(std::make_pair ("5s",1)); electronConf["Ag"].push_back(std::make_pair ("4d",10)); electronConf["Au"].push_back(std::make_pair ("6s",1)); electronConf["Au"].push_back(std::make_pair ("5d",10)); electronConf["Rg"].push_back(std::make_pair ("7s",1)); electronConf["Rg"].push_back(std::make_pair ("6d",10)); electronConf["Zn"].push_back(std::make_pair ("4s",2)); electronConf["Zn"].push_back(std::make_pair ("3d",10)); electronConf["Cd"].push_back(std::make_pair ("5s",2)); electronConf["Cd"].push_back(std::make_pair ("4d",10)); electronConf["Hg"].push_back(std::make_pair ("6s",2)); electronConf["Hg"].push_back(std::make_pair ("5d",10)); electronConf["Cn"].push_back(std::make_pair ("7s",2)); electronConf["Cn"].push_back(std::make_pair ("6d",10)); // Other-Metal electronConf["Al"].push_back(std::make_pair ("3s",2)); electronConf["Al"].push_back(std::make_pair ("3p",1)); electronConf["Ga"].push_back(std::make_pair ("4s",2)); electronConf["Ga"].push_back(std::make_pair ("4p",1)); electronConf["In"].push_back(std::make_pair ("5s",2)); electronConf["In"].push_back(std::make_pair ("4d",10)); electronConf["In"].push_back(std::make_pair ("5p",1)); electronConf["Ti"].push_back(std::make_pair ("4f",14)); electronConf["Ti"].push_back(std::make_pair ("5d",10)); electronConf["Ti"].push_back(std::make_pair ("6p",1)); electronConf["Sn"].push_back(std::make_pair ("5s",2)); electronConf["Sn"].push_back(std::make_pair ("4d",10)); electronConf["Sn"].push_back(std::make_pair ("5p",2)); electronConf["Pb"].push_back(std::make_pair ("6s",2)); electronConf["Pb"].push_back(std::make_pair ("4f",14)); electronConf["Pb"].push_back(std::make_pair ("5d",10)); electronConf["Pb"].push_back(std::make_pair ("6p",2)); electronConf["Bi"].push_back(std::make_pair ("6s",2)); electronConf["Bi"].push_back(std::make_pair ("4f",14)); electronConf["Bi"].push_back(std::make_pair ("5d",10)); electronConf["Bi"].push_back(std::make_pair ("6p",3)); // Semimetallics electronConf["B"].push_back(std::make_pair ("2s",2)); electronConf["B"].push_back(std::make_pair ("2p",1)); electronConf["Si"].push_back(std::make_pair ("3s",2)); electronConf["Si"].push_back(std::make_pair ("3p",2)); electronConf["Ge"].push_back(std::make_pair ("4s",2)); electronConf["Ge"].push_back(std::make_pair ("3d",10)); electronConf["Ge"].push_back(std::make_pair ("4p",2)); electronConf["As"].push_back(std::make_pair ("4s",2)); electronConf["As"].push_back(std::make_pair ("3d",10)); electronConf["As"].push_back(std::make_pair ("4p",3)); electronConf["Sb"].push_back(std::make_pair ("5s",2)); electronConf["Sb"].push_back(std::make_pair ("4d",10)); electronConf["Sb"].push_back(std::make_pair ("5p",3)); electronConf["Te"].push_back(std::make_pair ("5s",2)); electronConf["Te"].push_back(std::make_pair ("4d",10)); electronConf["Te"].push_back(std::make_pair ("5p",4)); electronConf["Po"].push_back(std::make_pair ("6s",2)); electronConf["Po"].push_back(std::make_pair ("4f",14)); electronConf["Po"].push_back(std::make_pair ("5d",10)); electronConf["Po"].push_back(std::make_pair ("6p",4)); // Electronegativity of atoms, Allen scale // Allen, L.C., J. Am. Chem. Soc., 111, 9003, 1989 // Unknown = -1.0 // Hydrogen electronegativities["H"] = 2.300; // Organic set or Non-metal electronegativities["C"] = 2.544; electronegativities["N"] = 3.066; electronegativities["O"] = 3.610; electronegativities["P"] = 2.253; electronegativities["S"] = 2.589; electronegativities["Se"] = 2.434; // Halogens electronegativities["F"] = 4.193; electronegativities["Cl"] = 2.869; electronegativities["Br"] = 2.685; electronegativities["I"] = 2.359; electronegativities["At"] = 2.39; // Alkali-Metals electronegativities["Li"] = 0.912; electronegativities["Na"] = 0.869; electronegativities["K"] = 0.734; electronegativities["Rb"] = 0.706; electronegativities["Cs"] = 0.659; electronegativities["Fr"] = 0.67; // Alkaline-earth-Metals electronegativities["Be"] = 1.576; electronegativities["Mg"] = 1.293; electronegativities["Ca"] = 1.034; electronegativities["Sr"] = 0.963; electronegativities["Ba"] = 0.881; electronegativities["Ra"] = 0.89; // Transition-Metals electronegativities["Sc"] = 1.19; electronegativities["Y"] = 1.12; electronegativities["Ti"] = 1.38; electronegativities["Zr"] = 1.32; electronegativities["Hf"] = 1.16; electronegativities["Rf"] = -1.0; electronegativities["V"] = 1.53; electronegativities["Nb"] = 1.41; electronegativities["Ta"] = 1.34; electronegativities["Db"] = -1.0; electronegativities["Cr"] = 1.65; electronegativities["Mo"] = 1.47; electronegativities["W"] = 1.47; electronegativities["Sg"] = -1.0; electronegativities["Mn"] = 1.75; electronegativities["Tc"] = 1.51; electronegativities["Re"] = 1.60; electronegativities["Bh"] = -1.0; electronegativities["Fe"] = 1.80; electronegativities["Ru"] = 1.54; electronegativities["Os"] = 1.65; electronegativities["Hs"] = -1.0; electronegativities["Co"] = 1.84; electronegativities["Rh"] = 1.56; electronegativities["Ir"] = 1.68; electronegativities["Mt"] = -1.0; electronegativities["Ni"] = 1.88; electronegativities["Pd"] = 1.59; electronegativities["Pt"] = 1.72; electronegativities["Ds"] = -1.0; electronegativities["Cu"] = 1.85; electronegativities["Ag"] = 1.87; electronegativities["Au"] = 1.92; electronegativities["Rg"] = -1.0; electronegativities["Zn"] = 1.59; electronegativities["Cd"] = 1.52; electronegativities["Hg"] = 1.76; electronegativities["Cn"] = -1.0; // Other-Metal electronegativities["Al"] = 1.613; electronegativities["Ga"] = 1.756; electronegativities["In"] = 1.656; electronegativities["Ti"] = 1.789; electronegativities["Sn"] = 1.824; electronegativities["Pb"] = 1.854; electronegativities["Bi"] = 2.01; // Semimetallics electronegativities["B"] = 2.051; electronegativities["Si"] = 1.916; electronegativities["Ge"] = 1.994; electronegativities["As"] = 2.211; electronegativities["Sb"] = 1.984; electronegativities["Te"] = 2.158; electronegativities["Po"] = 2.190; } PeriodicTable::~PeriodicTable() { } void PeriodicTable::compareIdealDists(std::map > > & tAllowedRangeDists, double tDelta) { // This function is for metal related bonds //std::ofstream compTab("idealComp.table"); tDelta = tDelta/10.0; std::vector metTab, metLoidTab; initMetalTab(metTab); initMetalloidTab(metLoidTab); for (std::map >::iterator iProp1=elemProps.begin(); iProp1 != elemProps.end(); iProp1++) { ID elem1 = iProp1->first; if (isMetal(metTab, elem1) || isMetalloid(metLoidTab, elem1)) { for (std::map >::iterator iProp2=elemProps.begin(); iProp2 != elemProps.end(); iProp2++) { double d1=0.0, d2=0.0, dI=0; ID elem2 = iProp2->first; if (isMetal(metTab, elem2)) { if (elemProps[elem2].find("ionM-") !=elemProps[elem2].end()) { dI = elemProps[elem1]["ionM+"] + elemProps[elem2]["ionM-"]; } else { dI = elemProps[elem1]["ionM+"] + elemProps[elem2]["ionM+"]; } } else { if (elemProps[elem1].find("cova") !=elemProps[elem1].end() && elemProps[elem2].find("cova") !=elemProps[elem2].end()) { d1 = elemProps[elem1]["cova"] + elemProps[elem2]["cova"]; } if (elemProps[elem1].find("ionM+") !=elemProps[elem1].end() && elemProps[elem2].find("ionM-") !=elemProps[elem2].end()) { d2 = elemProps[elem1]["ionM+"] + elemProps[elem2]["ionM-"]; } /* if(elem1.find("Mo")!=std::string::npos && elem2.find("N")!=std::string::npos) { std::cout << "elem1 " << elem1 << " " << elem2 << std::endl; std::cout << " d1 " << d1 << std::endl; std::cout << " d2 " << d2 << std::endl; } */ if (d1 >= d2) { dI = d1; } else { dI = d2; } } if (dI !=0) { tAllowedRangeDists[elem1][elem2]["max"]= dI*(1+tDelta); tAllowedRangeDists[elem1][elem2]["min"]= dI*(1-tDelta); } else { std::cout << "The distance range between elements " << elem1 << " and " << elem2 << " is not determined " << std::endl; } } } } /* for (std::map > >::iterator iR1=tAllowedRangeDists.begin(); iR1 != tAllowedRangeDists.end(); iR1++) { for (std::map >::iterator iR2=iR1->second.begin(); iR2 !=iR1->second.end(); iR2++) { std::cout << iR1->first << "\t" << iR2->first << "\t" << iR2->second["min"] << "\t" << iR2->second["max"] << "\n"; } } */ } void PeriodicTable::construAtomIdealDists(std::map > >& tAllowedRangeDists, double tDelta) { const double dS = 1.0, dL=2.0, dDiff=0.5; // Try use electro-negative to decide the ideal pair distances. for (std::map >::iterator iProp1=elemProps.begin(); iProp1 != elemProps.end(); iProp1++) { ID elem1 = iProp1->first; for (std::map >::iterator iProp2=elemProps.begin(); iProp2 != elemProps.end(); iProp2++) { ID elem2 = iProp2->first; double dIon, dCova, dMax, dIdeal=0.0; if (electronegativities.find(elem1) !=electronegativities.end() && electronegativities.find(elem2) !=electronegativities.end()) { // dIon if(electronegativities[elem1] <= electronegativities[elem2]) { if (elemProps[elem2].find("ionM-") !=elemProps[elem2].end() && elemProps[elem1].find("ionM+") !=elemProps[elem1].end()) { dIon=elemProps[elem1]["ionM+"] +elemProps[elem2]["ionM-"]; } else { dIon = elemProps[elem1]["cova"] +elemProps[elem2]["cova"]; } } else { if (elemProps[elem1].find("ionM-") !=elemProps[elem1].end() && elemProps[elem2].find("ionM+") !=elemProps[elem2].end()) { dIon=elemProps[elem1]["ionM-"] +elemProps[elem2]["ionM+"]; } else { dIon = elemProps[elem1]["cova"] +elemProps[elem2]["cova"]; } } // dCova dCova = elemProps[elem1]["cova"] +elemProps[elem2]["cova"]; // dMax if (dIon >= dCova) { dMax = dIon; } else { dMax = dCova; } if (electronegativities[elem1] <= dS && electronegativities[elem2] <= dS) { dIdeal = dMax; } else if (electronegativities[elem1] >= dL && electronegativities[elem2] >= dL) { dIdeal = dCova; } else { double diffNE = fabs(electronegativities[elem1] -electronegativities[elem2]); if (diffNE<= dDiff) { dIdeal = dCova; } else { dIdeal = dIon; } } if (dIdeal !=0.0) { tAllowedRangeDists[elem1][elem2]["max"] =dIdeal*(1+tDelta); tAllowedRangeDists[elem1][elem2]["min"] = dIdeal*(1-tDelta); } else { std::cout << "The distance range between elements " << elem1 << " and " << elem2 << " is not determined " << std::endl; } } else { // dCova dCova = elemProps[elem1]["cova"] +elemProps[elem2]["cova"]; } } } } }