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qzhu2017qzhu2017
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add mass to element
1 parent 6a09a74 commit eae8b57

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-131
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2 files changed

+135
-131
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‎pyxtal/database/element.py‎

Lines changed: 129 additions & 125 deletions
Original file line numberDiff line numberDiff line change
@@ -15,113 +15,113 @@ def __init__(self, input_value):
1515
self.input = input_value
1616

1717
# list with atomic number z, short name, full name, valence,
18-
# valence electrons, covalent radius, vdW radius, metallic radius
18+
# mass, valence electrons, covalent radius, vdW radius, metallic radius
1919
self.elements_list = [
20-
(1, "H", "Hydrogen", 1.0, 1, 0.31, 1.20, None),
21-
(2, "He", "Helium", 0.5, 2, 0.28, 1.40, None),
22-
(3, "Li", "Lithium", 1.0, 1, 1.28, 1.82, 1.52),
23-
(4, "Be", "Beryllium", 2.0, 2, 0.96, 1.53, 1.12),
24-
(5, "B", "Boron", 3.0, 3, 0.84, 1.92, None),
25-
(6, "C", "Carbon", 4.0, 4, 0.78, 1.70, None),
26-
(7, "N", "Nitrogen", 3.0, 5, 0.78, 1.55, None),
27-
(8, "O", "Oxygen", 2.0, 6, 0.70, 1.52, None),
28-
(9, "F", "Fluorine", 1.0, 7, 0.57, 1.47, None),
29-
(10, "Ne", "Neon", 0.5, 8, 0.58, 1.54, None),
30-
(11, "Na", "Sodium", 1.0, 1, 1.66, 2.27, 1.86),
31-
(12, "Mg", "Magnesium", 2.0, 2, 1.41, 1.73, 1.60),
32-
(13, "Al", "Aluminium", 3.0, 3, 1.21, 1.84, 1.43),
33-
(14, "Si", "Silicon", 4.0, 4, 1.11, 2.10, None),
34-
(15, "P", "Phosphorus", 3.0, 5, 1.07, 1.80, None),
35-
(16, "S", "Sulfur", 2.0, 6, 1.25, 1.80, None),
36-
(17, "Cl", "Chlorine", 1.0, 7, 1.02, 1.75, None),
37-
(18, "Ar", "Argon", 0.5, 8, 1.06, 1.88, None),
38-
(19, "K", "Potassium", 1.0, 1, 2.03, 2.75, 2.27),
39-
(20, "Ca", "Calcium", 2.0, 2, 1.76, 2.31, 1.97),
40-
(21, "Sc", "Scandium", 3.0, 3, 1.70, 2.11, 1.62),
41-
(22, "Ti", "Titanium", 4.0, 4, 1.60, 2.00, 1.47),
42-
(23, "V", "Vanadium", 4.0, 5, 1.53, 2.00, 1.34),
43-
(24, "Cr", "Chromium", 3.0, 6, 1.39, 2.00, 1.28),
44-
(25, "Mn", "Manganese", 4.0, 5, 1.39, 2.00, 1.27),
45-
(26, "Fe", "Iron", 3.0, 3, 1.32, 2.00, 1.26),
46-
(27, "Co", "Cobalt", 3.0, 3, 1.26, 2.00, 1.25),
47-
(28, "Ni", "Nickel", 2.0, 3, 1.24, 1.63, 1.24),
48-
(29, "Cu", "Copper", 2.0, 2, 1.32, 1.40, 1.28),
49-
(30, "Zn", "Zinc", 2.0, 2, 1.22, 1.39, 1.34),
50-
(31, "Ga", "Gallium", 3.0, 3, 1.22, 1.87, 1.35),
51-
(32, "Ge", "Germanium", 4.0, 4, 1.20, 2.11, None),
52-
(33, "As", "Arsenic", 3.0, 5, 1.19, 1.85, None),
53-
(34, "Se", "Selenium", 2.0, 6, 1.20, 1.90, None),
54-
(35, "Br", "Bromine", 1.0, 7, 1.20, 1.85, None),
55-
(36, "Kr", "Krypton", 0.5, 8, 1.16, 2.02, None),
56-
(37, "Rb", "Rubidium", 1.0, 1, 2.20, 3.03, 2.48),
57-
(38, "Sr", "Strontium", 2.0, 2, 1.95, 2.49, 2.15),
58-
(39, "Y", "Yttrium", 3.0, 3, 1.90, 2.00, 1.80),
59-
(40, "Zr", "Zirconium", 4.0, 4, 1.75, 2.00, 1.60),
60-
(41, "Nb", "Niobium", 5.0, 5, 1.64, 2.00, 1.46),
61-
(42, "Mo", "Molybdenum", 4.0, 6, 1.54, 2.00, 1.39),
62-
(43, "Tc", "Technetium", 4.0, 5, 1.47, 2.00, 1.36),
63-
(44, "Ru", "Ruthenium", 4.0, 3, 1.46, 2.00, 1.34),
64-
(45, "Rh", "Rhodium", 4.0, 3, 1.42, 1.63, 1.34),
65-
(46, "Pd", "Palladium", 4.0, 3, 1.39, 1.72, 1.37),
66-
(47, "Ag", "Silver", 1.0, 2, 1.45, 1.58, 1.44),
67-
(48, "Cd", "Cadmium", 2.0, 2, 1.44, 1.93, 1.51),
68-
(49, "In", "Indium", 3.0, 3, 1.42, 2.17, 1.67),
69-
(50, "Sn", "Tin", 4.0, 4, 1.39, 2.06, None),
70-
(51, "Sb", "Antimony", 3.0, 5, 1.39, 2.06, None),
71-
(52, "Te", "Tellurium", 2.0, 6, 1.38, 2.06, None),
72-
(53, "I", "Iodine", 1.0, 7, 1.39, 1.98, None),
73-
(54, "Xe", "Xenon", 0.5, 8, 1.40, 2.16, None),
74-
(55, "Cs", "Caesium", 1.0, 1, 2.44, 3.43, 2.65),
75-
(56, "Ba", "Barium", 2.0, 2, 2.15, 2.68, 2.22),
76-
(57, "La", "Lanthanum", 3.0, 3, 2.07, 2.10, 1.87),
77-
(58, "Ce", "Cerium", 4.0, 3, 2.04, 2.10, 1.818),
78-
(59, "Pr", "Praseodymium", 3.0, 3, 2.03, 2.10, 1.824),
79-
(60, "Nd", "Neodymium", 3.0, 3, 2.01, 2.10, 1.814),
80-
(61, "Pm", "Promethium", 3.0, 3, 1.99, 2.10, 1.834),
81-
(62, "Sm", "Samarium", 3.0, 3, 1.98, 2.10, 1.804),
82-
(63, "Eu", "Europium", 3.0, 3, 1.98, 2.10, 1.804),
83-
(64, "Gd", "Gadolinium", 3.0, 3, 1.96, 2.10, 1.804),
84-
(65, "Tb", "Terbium", 3.0, 3, 1.94, 2.10, 1.773),
85-
(66, "Dy", "Dysprosium", 3.0, 3, 1.92, 2.10, 1.781),
86-
(67, "Ho", "Holmium", 3.0, 3, 1.92, 2.10, 1.762),
87-
(68, "Er", "Erbium", 3.0, 3, 1.89, 2.10, 1.761),
88-
(69, "Tm", "Thulium", 3.0, 3, 1.90, 2.10, 1.759),
89-
(70, "Yb", "Ytterbium", 3.0, 3, 1.87, 2.10, 1.76),
90-
(71, "Lu", "Lutetium", 3.0, 3, 1.87, 2.10, 1.738),
91-
(72, "Hf", "Hafnium", 4.0, 3, 1.75, 2.10, 1.59),
92-
(73, "Ta", "Tantalum", 5.0, 3, 1.70, 2.10, 1.46),
93-
(74, "W", "Tungsten", 4.0, 3, 1.62, 2.10, 1.39),
94-
(75, "Re", "Rhenium", 4.0, 3, 1.51, 2.10, 1.37),
95-
(76, "Os", "Osmium", 4.0, 3, 1.44, 2.10, 1.35),
96-
(77, "Ir", "Iridium", 4.0, 3, 1.41, 2.10, 1.355),
97-
(78, "Pt", "Platinum", 4.0, 3, 1.36, 1.75, 1.385),
98-
(79, "Au", "Gold", 1.0, 3, 1.36, 1.66, 1.44),
99-
(80, "Hg", "Mercury", 2.0, 3, 1.32, 1.55, 1.51),
100-
(81, "Tl", "Thallium", 3.0, 3, 1.45, 1.96, 1.70),
101-
(82, "Pb", "Lead", 4.0, 4, 1.46, 2.02, None),
102-
(83, "Bi", "Bismuth", 3.0, 5, 1.48, 2.07, None),
103-
(84, "Po", "Polonium", 2.0, 6, 1.40, 1.97, None),
104-
(85, "At", "Astatine", 1.0, 7, 1.50, 2.02, None),
105-
(86, "Rn", "Radon", 0.5, 8, 1.50, 2.20, None),
106-
(87, "Fr", "Francium", 1.0, 1, 2.60, 3.48, None),
107-
(88, "Ra", "Radium", 2.0, 2, 2.21, 2.83, None),
108-
(89, "Ac", "Actinium", 3.0, 3, 2.15, 2.20, None),
109-
(90, "Th", "Thorium", 4.0, 3, 2.06, 2.20, 1.79),
110-
(91, "Pa", "Protactinium", 4.0, 3, 2.00, 2.20, 1.63),
111-
(92, "U", "Uranium", 4.0, 3, 1.96, 2.20, 1.56),
112-
(93, "Np", "Neptunium", 4.0, 3, 1.90, 2.20, 1.55),
113-
(94, "Pu", "Plutonium", 4.0, 3, 1.87, 2.20, 1.59),
114-
(95, "Am", "Americium", 4.0, 3, 1.80, 2.20, 1.73),
115-
(96, "Cm", "Curium", 4.0, 3, 1.69, 2.20, 1.74),
116-
(97, "Bk", "Berkelium", 4.0, 3, None, None, 1.70),
117-
(98, "Cf", "Californium", 4.0, 3, None, None, 1.86),
118-
(99, "Es", "Einsteinium", 4.0, 3, None, None, 1.86),
119-
(100, "Fm", "Fermium", 4.0, 3, None, None, None),
120-
(101, "Md", "Mendelevium", 4.0, 3, None, None, None),
121-
(102, "No", "Nobelium", 4.0, 3, None, None, None),
122-
(103, "Lr", "Lawrencium", 4.0, 3, None, None, None),
123-
(104, "Rf", "Rutherfordium", 4.0, 3, None, None, None),
124-
(105, "Db", "Dubnium", 2.0, 3, None, None, None),
20+
(1, "H", "Hydrogen", 1.008, 1.0, 1, 0.31, 1.20, None),
21+
(2, "He", "Helium", 4.0026, 0.5, 2, 0.28, 1.40, None),
22+
(3, "Li", "Lithium", 6.94, 1.0, 1, 1.28, 1.82, 1.52),
23+
(4, "Be", "Beryllium", 9.0122, 2.0, 2, 0.96, 1.53, 1.12),
24+
(5, "B", "Boron", 10.81, 3.0, 3, 0.84, 1.92, None),
25+
(6, "C", "Carbon", 12.011, 4.0, 4, 0.78, 1.70, None),
26+
(7, "N", "Nitrogen", 14.007, 3.0, 5, 0.78, 1.55, None),
27+
(8, "O", "Oxygen", 15.999, 2.0, 6, 0.70, 1.52, None),
28+
(9, "F", "Fluorine", 18.998, 1.0, 7, 0.57, 1.47, None),
29+
(10, "Ne", "Neon", 20.180, 0.5, 8, 0.58, 1.54, None),
30+
(11, "Na", "Sodium", 22.990, 1.0, 1, 1.66, 2.27, 1.86),
31+
(12, "Mg", "Magnesium", 24.305, 2.0, 2, 1.41, 1.73, 1.60),
32+
(13, "Al", "Aluminium", 26.982, 3.0, 3, 1.21, 1.84, 1.43),
33+
(14, "Si", "Silicon", 28.085, 4.0, 4, 1.11, 2.10, None),
34+
(15, "P", "Phosphorus", 30.974, 3.0, 5, 1.07, 1.80, None),
35+
(16, "S", "Sulfur", 32.06, 2.0, 6, 1.25, 1.80, None),
36+
(17, "Cl", "Chlorine", 35.45, 1.0, 7, 1.02, 1.75, None),
37+
(18, "Ar", "Argon", 39.948, 0.5, 8, 1.06, 1.88, None),
38+
(19, "K", "Potassium", 39.098, 1.0, 1, 2.03, 2.75, 2.27),
39+
(20, "Ca", "Calcium", 40.078, 2.0, 2, 1.76, 2.31, 1.97),
40+
(21, "Sc", "Scandium", 44.956, 3.0, 3, 1.70, 2.11, 1.62),
41+
(22, "Ti", "Titanium", 47.867, 4.0, 4, 1.60, 2.00, 1.47),
42+
(23, "V", "Vanadium", 50.942, 4.0, 5, 1.53, 2.00, 1.34),
43+
(24, "Cr", "Chromium", 51.996, 3.0, 6, 1.39, 2.00, 1.28),
44+
(25, "Mn", "Manganese", 54.938, 4.0, 5, 1.39, 2.00, 1.27),
45+
(26, "Fe", "Iron", 55.845, 3.0, 3, 1.32, 2.00, 1.26),
46+
(27, "Co", "Cobalt", 58.933, 3.0, 3, 1.26, 2.00, 1.25),
47+
(28, "Ni", "Nickel", 58.693, 2.0, 3, 1.24, 1.63, 1.24),
48+
(29, "Cu", "Copper", 63.546, 2.0, 2, 1.32, 1.40, 1.28),
49+
(30, "Zn", "Zinc", 65.38, 2.0, 2, 1.22, 1.39, 1.34),
50+
(31, "Ga", "Gallium", 69.723, 3.0, 3, 1.22, 1.87, 1.35),
51+
(32, "Ge", "Germanium", 72.63, 4.0, 4, 1.20, 2.11, None),
52+
(33, "As", "Arsenic", 74.922, 3.0, 5, 1.19, 1.85, None),
53+
(34, "Se", "Selenium", 78.96, 2.0, 6, 1.20, 1.90, None),
54+
(35, "Br", "Bromine", 79.904, 1.0, 7, 1.20, 1.85, None),
55+
(36, "Kr", "Krypton", 83.798, 0.5, 8, 1.16, 2.02, None),
56+
(37, "Rb", "Rubidium", 85.468, 1.0, 1, 2.20, 3.03, 2.48),
57+
(38, "Sr", "Strontium", 87.62, 2.0, 2, 1.95, 2.49, 2.15),
58+
(39, "Y", "Yttrium", 88.906, 3.0, 3, 1.90, 2.00, 1.80),
59+
(40, "Zr", "Zirconium", 91.224, 4.0, 4, 1.75, 2.00, 1.60),
60+
(41, "Nb", "Niobium", 92.906, 5.0, 5, 1.64, 2.00, 1.46),
61+
(42, "Mo", "Molybdenum", 95.95, 4.0, 6, 1.54, 2.00, 1.39),
62+
(43, "Tc", "Technetium", 98.0, 4.0, 5, 1.47, 2.00, 1.36),
63+
(44, "Ru", "Ruthenium", 101.07, 4.0, 3, 1.46, 2.00, 1.34),
64+
(45, "Rh", "Rhodium", 102.91, 4.0, 3, 1.42, 1.63, 1.34),
65+
(46, "Pd", "Palladium", 106.42, 4.0, 3, 1.39, 1.72, 1.37),
66+
(47, "Ag", "Silver", 107.87, 1.0, 2, 1.45, 1.58, 1.44),
67+
(48, "Cd", "Cadmium", 112.41, 2.0, 2, 1.44, 1.93, 1.51),
68+
(49, "In", "Indium", 114.82, 3.0, 3, 1.42, 2.17, 1.67),
69+
(50, "Sn", "Tin", 118.71, 4.0, 4, 1.39, 2.06, None),
70+
(51, "Sb", "Antimony", 121.76, 3.0, 5, 1.39, 2.06, None),
71+
(52, "Te", "Tellurium", 127.60, 2.0, 6, 1.38, 2.06, None),
72+
(53, "I", "Iodine", 126.90, 1.0, 7, 1.39, 1.98, None),
73+
(54, "Xe", "Xenon", 131.29, 0.5, 8, 1.40, 2.16, None),
74+
(55, "Cs", "Caesium", 132.91, 1.0, 1, 2.44, 3.43, 2.65),
75+
(56, "Ba", "Barium", 137.33, 2.0, 2, 2.15, 2.68, 2.22),
76+
(57, "La", "Lanthanum", 138.91, 3.0, 3, 2.07, 2.10, 1.87),
77+
(58, "Ce", "Cerium", 140.12, 4.0, 3, 2.04, 2.10, 1.818),
78+
(59, "Pr", "Praseodymium", 140.91, 3.0, 3, 2.03, 2.10, 1.824),
79+
(60, "Nd", "Neodymium", 144.24, 3.0, 3, 2.01, 2.10, 1.814),
80+
(61, "Pm", "Promethium", 145.0, 3.0, 3, 1.99, 2.10, 1.834),
81+
(62, "Sm", "Samarium", 150.36, 3.0, 3, 1.98, 2.10, 1.804),
82+
(63, "Eu", "Europium", 151.96, 3.0, 3, 1.98, 2.10, 1.804),
83+
(64, "Gd", "Gadolinium", 157.25, 3.0, 3, 1.96, 2.10, 1.804),
84+
(65, "Tb", "Terbium", 158.93, 3.0, 3, 1.94, 2.10, 1.773),
85+
(66, "Dy", "Dysprosium", 162.50, 3.0, 3, 1.92, 2.10, 1.781),
86+
(67, "Ho", "Holmium", 164.93, 3.0, 3, 1.92, 2.10, 1.762),
87+
(68, "Er", "Erbium", 167.26, 3.0, 3, 1.89, 2.10, 1.761),
88+
(69, "Tm", "Thulium", 168.93, 3.0, 3, 1.90, 2.10, 1.759),
89+
(70, "Yb", "Ytterbium", 173.05, 3.0, 3, 1.87, 2.10, 1.76),
90+
(71, "Lu", "Lutetium", 174.97, 3.0, 3, 1.87, 2.10, 1.738),
91+
(72, "Hf", "Hafnium", 178.49, 4.0, 3, 1.75, 2.10, 1.59),
92+
(73, "Ta", "Tantalum", 180.95, 5.0, 3, 1.70, 2.10, 1.46),
93+
(74, "W", "Tungsten", 183.84, 4.0, 3, 1.62, 2.10, 1.39),
94+
(75, "Re", "Rhenium", 186.21, 4.0, 3, 1.51, 2.10, 1.37),
95+
(76, "Os", "Osmium", 190.23, 4.0, 3, 1.44, 2.10, 1.35),
96+
(77, "Ir", "Iridium", 192.22, 4.0, 3, 1.41, 2.10, 1.355),
97+
(78, "Pt", "Platinum", 195.08, 4.0, 3, 1.36, 1.75, 1.385),
98+
(79, "Au", "Gold", 196.97, 1.0, 3, 1.36, 1.66, 1.44),
99+
(80, "Hg", "Mercury", 200.59, 2.0, 3, 1.32, 1.55, 1.51),
100+
(81, "Tl", "Thallium", 204.38, 3.0, 3, 1.45, 1.96, 1.70),
101+
(82, "Pb", "Lead", 207.2, 4.0, 4, 1.46, 2.02, None),
102+
(83, "Bi", "Bismuth", 208.98, 3.0, 5, 1.48, 2.07, None),
103+
(84, "Po", "Polonium", 209.0, 2.0, 6, 1.40, 1.97, None),
104+
(85, "At", "Astatine", 210.0, 1.0, 7, 1.50, 2.02, None),
105+
(86, "Rn", "Radon", 222.0, 0.5, 8, 1.50, 2.20, None),
106+
(87, "Fr", "Francium", 223.0, 1.0, 1, 2.60, 3.48, None),
107+
(88, "Ra", "Radium", 226.0, 2.0, 2, 2.21, 2.83, None),
108+
(89, "Ac", "Actinium", 227.0, 3.0, 3, 2.15, 2.20, None),
109+
(90, "Th", "Thorium", 232.04, 4.0, 3, 2.06, 2.20, 1.79),
110+
(91, "Pa", "Protactinium", 231.04, 4.0, 3, 2.00, 2.20, 1.63),
111+
(92, "U", "Uranium", 238.03, 4.0, 3, 1.96, 2.20, 1.56),
112+
(93, "Np", "Neptunium", 237.0, 4.0, 3, 1.90, 2.20, 1.55),
113+
(94, "Pu", "Plutonium", 244.0, 4.0, 3, 1.87, 2.20, 1.59),
114+
(95, "Am", "Americium", 243.0, 4.0, 3, 1.80, 2.20, 1.73),
115+
(96, "Cm", "Curium", 247.0, 4.0, 3, 1.69, 2.20, 1.74),
116+
(97, "Bk", "Berkelium", 247.0, 4.0, 3, None, None, 1.70),
117+
(98, "Cf", "Californium", 251.0, 4.0, 3, None, None, 1.86),
118+
(99, "Es", "Einsteinium", 252.0, 4.0, 3, None, None, 1.86),
119+
(100, "Fm", "Fermium", 257.0, 4.0, 3, None, None, None),
120+
(101, "Md", "Mendelevium", 258.0, 4.0, 3, None, None, None),
121+
(102, "No", "Nobelium", 259.0, 4.0, 3, None, None, None),
122+
(103, "Lr", "Lawrencium", 262.0, 4.0, 3, None, None, None),
123+
(104, "Rf", "Rutherfordium", 267.0, 4.0, 3, None, None, None),
124+
(105, "Db", "Dubnium", 270.0, 2.0, 3, None, None, None),
125125
]
126126
"""A list of atomic numbers, symbols, names, and other information, up
127127
to atomic number 105"""
@@ -226,21 +226,14 @@ def __init__(self, input_value):
226226
"""A list of scatter factors for the elements"""
227227

228228
self.z = None
229-
"""atomic number"""
230229
self.short_name = None
231-
"""atomic symbol"""
232230
self.long_name = None
233-
"""atomic name"""
231+
self.mass = None
234232
self.valence = None
235-
"""valence value"""
236233
self.valence_electrons = None
237-
"""number of valence electrons"""
238234
self.covalent_radius = None
239-
"""atomic radius used for distance checking within crystals"""
240235
self.vdw_radius = None
241-
"""atomic radius used for volume estimation within crystals"""
242236
self.metallic_radius = None
243-
"""atomic radius used for distance checking within metallic crystals"""
244237

245238
pos = None
246239

@@ -276,11 +269,12 @@ def __init__(self, input_value):
276269
self.long_name = None
277270

278271
if pos is not None:
279-
self.valence = self.elements_list[pos][3]
280-
self.valence_electrons = self.elements_list[pos][4]
281-
self.covalent_radius = self.elements_list[pos][5]
282-
self.vdw_radius = self.elements_list[pos][6]
283-
self.metallic_radius = self.elements_list[pos][7]
272+
self.mass = self.elements_list[pos][3]
273+
self.valence = self.elements_list[pos][4]
274+
self.valence_electrons = self.elements_list[pos][5]
275+
self.covalent_radius = self.elements_list[pos][6]
276+
self.vdw_radius = self.elements_list[pos][7]
277+
self.metallic_radius = self.elements_list[pos][8]
284278
if pos < len(self.sf):
285279
self.scatter = self.sf[pos]
286280

@@ -314,7 +308,6 @@ def get_sf(self, pos):
314308
els.append(el[pos])
315309
return els
316310

317-
# TODO: add docstrings for miscellaneous functions
318311
def all_z(self):
319312
return self.get_all(0)
320313

@@ -324,21 +317,24 @@ def all_short_names(self):
324317
def all_long_names(self):
325318
return self.get_all(2)
326319

327-
def all_valences(self):
320+
def all_masses(self):
328321
return self.get_all(3)
329322

330-
def all_valence_electrons(self):
323+
def all_valences(self):
331324
return self.get_all(4)
332325

333-
def all_covalent_radii(self):
326+
def all_valence_electrons(self):
334327
return self.get_all(5)
335328

336-
def all_vdw_radii(self):
329+
def all_covalent_radii(self):
337330
return self.get_all(6)
338331

339-
def all_metallic_radii(self):
332+
def all_vdw_radii(self):
340333
return self.get_all(7)
341334

335+
def all_metallic_radii(self):
336+
return self.get_all(8)
337+
342338
def get_sf(self):
343339
return self.get_sf()
344340

@@ -371,3 +367,11 @@ def number_from_specie(specie):
371367
print("Error: Invalid atomic symbol, name, or number.")
372368
return None
373369
return index
370+
371+
if __name__ == "__main__":
372+
el = Element("Fe")
373+
print(el.z)
374+
print(el.mass)
375+
print(el.covalent_radius)
376+
print(el.scatter)
377+
print(el.all_masses())

‎pyxtal/tolerance.py‎

Lines changed: 6 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -25,18 +25,18 @@ def __init__(self, *tuples, prototype="atomic", factor=1.0):
2525
self.prototype = prototype
2626
if prototype == "atomic":
2727
f *= 0.5
28-
attrindex = 5
28+
attrindex = 6
2929
self.radius_type = "covalent"
3030
elif prototype == "molecular":
31-
attrindex = 5
31+
attrindex = 7
3232
self.radius_type = "covalent"
3333
f *= 1.2
3434
elif prototype == "metallic":
35-
attrindex = 7
35+
attrindex = 8
3636
self.radius_type = "metallic"
3737
f *= 0.5
3838
elif prototype == "vdW":
39-
attrindex = 6
39+
attrindex = 7
4040
self.radius_type = "vdW"
4141
else:
4242
self.radius_type = "N/A"
@@ -48,9 +48,9 @@ def __init__(self, *tuples, prototype="atomic", factor=1.0):
4848
m.append([0.0])
4949
for tup2 in H.elements_list:
5050
# Get the appropriate atomic radii
51-
val1 = tup1[5] if tup1[attrindex] is None else tup1[attrindex]
51+
val1 = tup1[6] if tup1[attrindex] is None else tup1[attrindex]
5252
# FIXME this is suspicious but matches exactly the original code
53-
val2 = (tup1[5] if tup2[5] is not None else None) if tup2[attrindex] is None else tup2[attrindex]
53+
val2 = (tup1[6] if tup2[6] is not None else None) if tup2[attrindex] is None else tup2[attrindex]
5454

5555
if val1 is not None and val2 is not None:
5656
m[-1].append(f * (val1 + val2))

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