Update atomic weights with 2018 IUPAC/CIAAW data
Use data from the periodic table at http://www.ciaaw.org/atomic-weights.htm and https://iupac.org/wp-content/uploads/2018/12/IUPAC_Periodic_Table-01Dec18.pdf Elements without any atomic weight in either table do not have a stable isotope. These are deleted from elements.xml and have their atomic weight set to -1.0 in Elements.cpp. Add elements after plutonium that were not previously listed. None of these elements have stable isotopes. These elements are retained/added so their symbols, names, and atomic numbers can still be retrieved and the mapping of atomic number to index - 1 in the struct is maintained. Modify the element weight lookup functions to throw errors when an element with no weight is requested (i.e., the weight is -1.0 in the struct).
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Bryan W. Weber
Ray Speth
parent
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commit
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2 changed files with 507 additions and 529 deletions
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@ -4,7 +4,7 @@
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*/
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// This file is part of Cantera. See License.txt in the top-level directory or
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// at http://www.cantera.org/license.txt for license and copyright information.
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// at https://cantera.org/license.txt for license and copyright information.
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#include "cantera/thermo/Elements.h"
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#include "cantera/base/ctml.h"
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@ -16,7 +16,17 @@ namespace Cantera
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{
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/*! Database for atomic weights
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* Values are taken from the 1989 Standard Atomic Weights, CRC
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* Values are used from CIAAW. Atomic weights of the elements 2017
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* when a single value is given. Available online at
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* http://www.ciaaw.org/atomic-weights.htm
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*
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* When a range of values is given in the CIAAW table, the "conventional
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* atomic weight" from the IUPAC Periodic Table is used. Available
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* online at https://iupac.org/wp-content/uploads/2018/12/IUPAC_Periodic_Table-01Dec18.pdf
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*
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* If no value is given in either source, it is because no stable isotopes of
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* that element are known and the atomic weight of that element is listed here
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* as -1.0
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*
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* units = kg / kg-mol (or equivalently gm / gm-mol)
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*
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@ -25,11 +35,16 @@ namespace Cantera
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struct atomicWeightData {
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string symbol; //!< Element symbol, first letter capitalized
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string fullName; //!< Element full name, first letter lowercase
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double atomicWeight; //!< Element atomic weight in kg / kg-mol
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double atomicWeight; //!< Element atomic weight in kg / kg-mol, if known. -1 if no stable isotope
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};
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/*! Database for named isotopic weights
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* Values are taken from the 1989 Standard Atomic Weights, CRC
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* Values are used from
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* Kim S, Chen J, Cheng T, Gindulyte A, He J, He S, Li Q, Shoemaker BA,
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* Thiessen PA, Yu B, Zaslavsky L, Zhang J, Bolton EE. PubChem 2019
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* update: improved access to chemical data. Nucleic Acids Res. 2019
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* Jan 8; 47(D1):D1102-1109. doi:10.1093/nar/gky1033.
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* [PubMed PMID:30371825]
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*
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* units = kg / kg-mol (or equivalently gm / gm-mol)
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*
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@ -46,106 +61,130 @@ struct isotopeWeightData {
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* @var static struct atomicWeightData atomicWeightTable[]
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* \brief atomicWeightTable is a vector containing the atomic weights database.
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*
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* atomicWeightTable[] is a static function with scope limited to this file.
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* atomicWeightTable[] is a static variable with scope limited to this file.
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* It can only be referenced via the functions in this file.
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*
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* The size of the table is given by the initial instantiation.
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*/
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static struct atomicWeightData atomicWeightTable[] = {
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{"H", "hydrogen", 1.00794},
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{"H", "hydrogen", 1.008},
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{"He", "helium", 4.002602},
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{"Li", "lithium", 6.941 },
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{"Be", "beryllium", 9.012182},
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{"B", "boron", 10.811 },
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{"Li", "lithium", 6.94},
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{"Be", "beryllium", 9.0121831},
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{"B", "boron", 10.81},
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{"C", "carbon", 12.011 },
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{"N", "nitrogen", 14.00674},
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{"O", "oxygen", 15.9994 },
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{"F", "fluorine", 18.9984032},
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{"N", "nitrogen", 14.007},
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{"O", "oxygen", 15.999 },
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{"F", "fluorine", 18.998403163},
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{"Ne", "neon", 20.1797 },
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{"Na", "sodium", 22.98977},
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{"Mg", "magnesium", 24.3050 },
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{"Al", "aluminum", 26.98154},
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{"Si", "silicon", 28.0855 },
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{"P", "phosphorus", 30.97376},
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{"S", "sulfur", 32.066 },
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{"Cl", "chlorine", 35.4527 },
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{"Ar", "argon", 39.948 },
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{"Na", "sodium", 22.98976928},
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{"Mg", "magnesium", 24.305 },
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{"Al", "aluminum", 26.9815384},
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{"Si", "silicon", 28.085 },
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{"P", "phosphorus", 30.973761998},
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{"S", "sulfur", 32.06 },
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{"Cl", "chlorine", 35.45 },
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{"Ar", "argon", 39.95 },
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{"K", "potassium", 39.0983 },
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{"Ca", "calcium", 40.078 },
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{"Sc", "scandium", 44.95591},
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{"Ti", "titanium", 47.88 },
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{"Sc", "scandium", 44.955908},
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{"Ti", "titanium", 47.867 },
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{"V", "vanadium", 50.9415 },
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{"Cr", "chromium", 51.9961 },
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{"Mn", "manganese", 54.9381 },
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{"Fe", "iron", 55.847 },
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{"Co", "cobalt", 58.9332 },
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{"Ni", "nickel", 58.69 },
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{"Mn", "manganese", 54.938043 },
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{"Fe", "iron", 55.845 },
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{"Co", "cobalt", 58.933194 },
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{"Ni", "nickel", 58.6934 },
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{"Cu", "copper", 63.546 },
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{"Zn", "zinc", 65.39 },
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{"Zn", "zinc", 65.38 },
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{"Ga", "gallium", 69.723 },
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{"Ge", "germanium", 72.61 },
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{"As", "arsenic", 74.92159},
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{"Se", "selenium", 78.96 },
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{"Ge", "germanium", 72.630 },
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{"As", "arsenic", 74.921595},
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{"Se", "selenium", 78.971 },
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{"Br", "bromine", 79.904 },
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{"Kr", "krypton", 83.80 },
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{"Kr", "krypton", 83.798 },
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{"Rb", "rubidium", 85.4678 },
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{"Sr", "strontium", 87.62 },
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{"Y", "yttrium", 88.90585},
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{"Y", "yttrium", 88.90584},
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{"Zr", "zirconium", 91.224 },
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{"Nb", "nobelium", 92.90638},
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{"Mo", "molybdenum", 95.94 },
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{"Tc", "technetium", 97.9072 },
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{"Nb", "nobelium", 92.90637},
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{"Mo", "molybdenum", 95.95 },
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{"Tc", "technetium", -1.0 },
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{"Ru", "ruthenium", 101.07 },
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{"Rh", "rhodium", 102.9055 },
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{"Rh", "rhodium", 102.90549 },
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{"Pd", "palladium", 106.42 },
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{"Ag", "silver", 107.8682 },
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{"Cd", "cadmium", 112.411 },
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{"In", "indium", 114.82 },
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{"Cd", "cadmium", 112.414 },
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{"In", "indium", 114.818 },
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{"Sn", "tin", 118.710 },
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{"Sb", "antimony", 121.75 },
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{"Te", "tellurium", 127.6 },
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{"Sb", "antimony", 121.760 },
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{"Te", "tellurium", 127.60 },
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{"I", "iodine", 126.90447},
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{"Xe", "xenon", 131.29 },
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{"Cs", "cesium", 132.90543},
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{"Xe", "xenon", 131.293 },
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{"Cs", "cesium", 132.90545196},
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{"Ba", "barium", 137.327 },
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{"La", "lanthanum", 138.9055 },
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{"Ce", "cerium", 140.115 },
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{"Pr", "praseodymium", 140.90765},
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{"Nd", "neodymium", 144.24 },
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{"Pm", "promethium", 144.9127 },
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{"La", "lanthanum", 138.90547 },
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{"Ce", "cerium", 140.116 },
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{"Pr", "praseodymium", 140.90766},
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{"Nd", "neodymium", 144.242 },
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{"Pm", "promethium", -1.0 },
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{"Sm", "samarium", 150.36 },
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{"Eu", "europium", 151.965 },
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{"Eu", "europium", 151.964 },
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{"Gd", "gadolinium", 157.25 },
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{"Tb", "terbium", 158.92534},
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{"Dy", "dysprosium", 162.50 },
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{"Ho", "holmium", 164.93032},
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{"Er", "erbium", 167.26 },
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{"Tm", "thulium", 168.93421},
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{"Yb", "ytterbium", 173.04 },
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{"Lu", "lutetium", 174.967 },
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{"Tb", "terbium", 158.925354},
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{"Dy", "dysprosium", 162.500 },
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{"Ho", "holmium", 164.930328},
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{"Er", "erbium", 167.259 },
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{"Tm", "thulium", 168.934218},
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{"Yb", "ytterbium", 173.045 },
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{"Lu", "lutetium", 174.9668 },
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{"Hf", "hafnium", 178.49 },
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{"Ta", "tantalum", 180.9479 },
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{"W", "tungsten", 183.85 },
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{"Ta", "tantalum", 180.94788 },
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{"W", "tungsten", 183.84 },
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{"Re", "rhenium", 186.207 },
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{"Os", "osmium", 190.2 },
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{"Ir", "iridium", 192.22 },
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{"Pt", "platinum", 195.08 },
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{"Au", "gold", 196.96654},
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{"Hg", "mercury", 200.59 },
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{"Tl", "thallium", 204.3833 },
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{"Os", "osmium", 190.23 },
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{"Ir", "iridium", 192.217 },
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{"Pt", "platinum", 195.084 },
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{"Au", "gold", 196.966570},
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{"Hg", "mercury", 200.592 },
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{"Tl", "thallium", 204.38 },
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{"Pb", "lead", 207.2 },
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{"Bi", "bismuth", 208.98037},
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{"Po", "polonium", 208.9824 },
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{"At", "astatine", 209.9871 },
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{"Rn", "radon", 222.0176 },
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{"Fr", "francium", 223.0197 },
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{"Ra", "radium", 226.0254 },
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{"Ac", "actinium", 227.0279 },
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{"Th", "thorium", 232.0381 },
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{"Bi", "bismuth", 208.98040},
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{"Po", "polonium", -1.0 },
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{"At", "astatine", -1.0 },
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{"Rn", "radon", -1.0 },
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{"Fr", "francium", -1.0 },
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{"Ra", "radium", -1.0 },
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{"Ac", "actinium", -1.0 },
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{"Th", "thorium", 232.0377 },
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{"Pa", "protactinium", 231.03588},
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{"U", "uranium", 238.0508 },
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{"Np", "neptunium", 237.0482 },
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{"Pu", "plutonium", 244.0482 },
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{"U", "uranium", 238.02891 },
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{"Np", "neptunium", -1.0 },
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{"Pu", "plutonium", -1.0 },
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{"Am", "americium", -1.0 },
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{"Cm", "curium", -1.0 },
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{"Bk", "berkelium", -1.0 },
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{"Cf", "californium", -1.0 },
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{"Es", "einstiunium", -1.0 },
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{"Fm", "fermium", -1.0 },
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{"Md", "mendelevium", -1.0 },
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{"No", "nobelium", -1.0 },
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{"Lr", "lawrencium", -1.0 },
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{"Rf", "rutherfordium", -1.0 },
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{"Db", "dubnium", -1.0 },
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{"Sg", "seaborgium", -1.0 },
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{"Bh", "bohrium", -1.0 },
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{"Hs", "hassium", -1.0 },
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{"Mt", "meitnerium", -1.0 },
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{"Ds", "darmstadtium", -1.0 },
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{"Rg", "roentgenium", -1.0 },
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{"Cn", "copernicium", -1.0 },
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{"Nh", "nihonium", -1.0 },
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{"Gl", "flerovium", -1.0 },
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{"Mc", "moscovium", -1.0 },
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{"Lv", "livermorium", -1.0 },
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{"Ts", "tennessine", -1.0 },
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{"Og", "oganesson", -1.0 },
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};
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/*!
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@ -158,8 +197,15 @@ static struct atomicWeightData atomicWeightTable[] = {
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* The size of the table is given by the initial instantiation.
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*/
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static struct isotopeWeightData isotopeWeightTable[] = {
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{"D", "deuterium", 2.0, 1},
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{"Tr", "tritium", 3.0, 1},
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// National Center for Biotechnology Information. PubChem Database.
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// Deuterium, CID=24523, https://pubchem.ncbi.nlm.nih.gov/compound/Deuterium
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// (accessed on Aug. 7, 2019)
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{"D", "deuterium", 2.014102, 1},
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// National Center for Biotechnology Information. PubChem Database.
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// Tritium, CID=24824, https://pubchem.ncbi.nlm.nih.gov/compound/Tritium
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// (accessed on Aug. 7, 2019)
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{"Tr", "tritium", 3.0160495, 1},
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{"E", "electron", 0.000545, 0},
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};
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@ -167,15 +213,24 @@ double getElementWeight(const std::string& ename)
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{
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int numElements = numElementsDefined();
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int numIsotopes = numIsotopesDefined();
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double elementWeight = 0.0;
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string symbol = trimCopy(ename);
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string name = toLowerCopy(symbol);
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for (int i = 0; i < numElements; i++) {
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if (symbol == atomicWeightTable[i].symbol) {
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return atomicWeightTable[i].atomicWeight;
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elementWeight = atomicWeightTable[i].atomicWeight;
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break;
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} else if (name == atomicWeightTable[i].fullName) {
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return atomicWeightTable[i].atomicWeight;
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elementWeight = atomicWeightTable[i].atomicWeight;
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break;
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}
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}
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if (elementWeight > 0.0) {
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return elementWeight;
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} else if (elementWeight < 0.0) {
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throw CanteraError("getElementWeight",
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"element has no stable isotopes: " + ename);
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}
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for (int i = 0; i < numIsotopes; i++) {
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if (symbol == isotopeWeightTable[i].symbol) {
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return isotopeWeightTable[i].atomicWeight;
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@ -192,7 +247,13 @@ double getElementWeight(int atomicNumber)
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if (atomicNumber > num || atomicNumber < 1) {
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throw IndexError("getElementWeight", "atomicWeightTable", atomicNumber, num);
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}
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return atomicWeightTable[atomicNumber - 1].atomicWeight;
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double elementWeight = atomicWeightTable[atomicNumber - 1].atomicWeight;
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if (elementWeight < 0.0) {
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string ename = getElementName(atomicNumber);
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throw CanteraError("getElementWeight",
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"element has no stable isotopes: " + ename);
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}
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return elementWeight;
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}
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string getElementSymbol(const std::string& ename)
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