Atomik

Note: This library is no longer developed nor maintained. Use Reaktoro instead (https://reaktoro.org).

Atomik is a C++17 library that implements classes such as Element, Elements, Substance, Substances, Formula, and others to be used in libraries of the Reaktoro Project.

Overview

Below we present a few use cases in which Atomik library can be helpful.

Using class Formula to parse chemical formulas

Given chemical formulas such as H2O, CO2, CaCO3, (CaMg)(CO3)2, Atomik can help you parsing them into lists of element symbols and coefficients. See example below:

// C++ includes
#include <iostream>
using namespace std;

// Atomik includes
#include <Atomik/Atomik.hpp>
using namespace Atomik;

int main()
{
    Formula formula("CaCO3");

    cout << "The elemental composition of CaCO3 is:" << endl;
    for(auto symbol : formula.symbols())
        cout << symbol << ": " << formula.coefficient(symbol) << endl;
}

Note: Formula can parse any chemical formula and the elements might not even exist, such as AaBb2. The requirements are that the element symbols in your formula:

• start with an uppercase letter and continue with lowercase letters only (e.g., A, Bb, Ccx are valid names, but not AaB!);
• has no digits (i.e., Aa2 not allowed - I guess you know why!); and
• when needed, parenthesis need to be consistent (e.g., Ca(CO3) and (Ca)((CO3)) are both valid formulas, but not Ca)(CO3!).

Using class Substance to obtain certain properties from their chemical formulas

A Formula object only has element symbols, which are strings such as "H", "O", "Ca", and so forth. A Substance object, on the other hand, will use a given chemical formula to create Element objects from a default Elements object (a collection of Element objects initialized based on 120 elements of the ) be incontain We can also create Substance objects from given chemical formulas and compute their molar masses, determine their electric charges, the elements that compose it, and so forth:

Substance substance("CO3--"); // or CO3-2 if you prefer!

cout << "The molar mass of CaCO3 is (in kg/mol)" << endl;
cout << substance.molarMass() << endl;

cout << "The electric charge of CO3-- is" << endl;
cout << substance.charge() << endl;

The above example of constructing a Substance object is identical to:

Elements elementdb = Elements::PeriodicTable();
Substance substance("CO3--", elementdb);

The static member method Elements::PeriodicTable() returns an Elements objects initialized with Element instances as show here. If you want to use customized elements (for example, Aa and Bb), then you can do:

Elements elementdb;

Element elementAa({
    .symbol = "Aa",
    .name = "Aa",
    .atomicNumber = 0,
    .atomicWeight = 123.4,
    .electronegativity = 0.123,
    .tags = {"my-strange-element" }
});

Element elementBb({
    .symbol = "Bb",
    .name = "Bb",
    .atomicNumber = 0,
    .atomicWeight = 321.0,
    .electronegativity = 0.321,
    .tags = {"my-strange-element" }
});

elementdb.append(elementAa);
elementdb.append(elementBb);

Substance substance("AaBb2", elementdb);

Using Substances objects

The Substances class is a convenient class to manage a collection of Substance objects and create other substance collections by using its rich selection of filter methods as shown below:

// Initialize a Substances object from some database of substances
Substances substances = /* initialize from some database */;

// Filter all substances with tag "aqueous" and composed by some given elements
Substances aqueous = substances.tagged("aqueous").containing("H C O Na Cl Z");  // Z below is the name of the electric charge element!

// Filter all substances with given unique names
Substances gaseous = substances.withNames("H2O(g) CO2(g) CH4(g)");

Installation

Installation of Atomik using CMake is greatly simplified if conda is available in your system. We recommend you to install a Python 3.x (64-bit) installer of Miniconda to give you access to the conda application.

Once you have installed conda, append the conda-forge channel so that we can have access to a rich collection of packages in addition to the default channel:

conda config --append channels conda-forge

The next step is to install conda-devenv to create a conda development environment containing all required library dependencies of Atomik.

conda install conda-devenv

After this, you should execute:

conda activate atomik

to activate the create conda environment.

It's now time to download Atomik from GitHub:

git clone https://github.com/reaktoro/atomik.git

and then start the build & install task by executing:

cmake -P install

This will install Atomik header, library, and cmake configuration files in your created conda environment, and not in your system. If you wish to install Atomik in a different location, use:

cmake -DPREFIX=/home/user/other -P install

License

Copyright (C) 2018-2019 Allan Leal and Reaktoro Contributors

This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version.

This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.

You should have received a copy of the GNU Lesser General Public License along with this library. If not, see http://www.gnu.org/licenses/.

Contact us

Do you have a question or want to report a bug or any other issue? Please create a GitHub Issue and let us know.

Appendix

Elements from Elements::PeriodicTable()

The table below shows the attributes of the elements that are used in the static member method Elements::PeriodicTable().

Note: The only difference from the standard periodic table is the addition of element Z, which denotes an element representative of electric charges. This has been added for convenience reasons, to allow, for example, Formula to determine the charge of chemical formulas such as HCO3- or Fe+3 (alternatively Fe+++).

Symbol	Name	Atomic Number	Atomic Weight (kg/mol)	Electronegativity
Z	Charge	0	0.000000000	0.00
H	Hydrogen	1	0.001007940	2.20
He	Helium	2	0.004002602	0.00
Li	Lithium	3	0.006941000	0.98
Be	Beryllium	4	0.009012180	1.57
B	Boron	5	0.010811000	2.04
C	Carbon	6	0.012011000	2.55
N	Nitrogen	7	0.014006740	3.04
O	Oxygen	8	0.015999400	3.44
F	Fluorine	9	0.018998403	3.98
Ne	Neon	10	0.020179700	0.00
Na	Sodium	11	0.022989768	0.93
Mg	Magnesium	12	0.024305000	1.31
Al	Aluminum	13	0.026981539	1.61
Si	Silicon	14	0.028085500	1.90
P	Phosphorus	15	0.030973762	2.19
S	Sulfur	16	0.032066000	2.58
Cl	Chlorine	17	0.035452700	3.16
Ar	Argon	18	0.039948000	0.00
K	Potassium	19	0.039098300	0.82
Ca	Calcium	20	0.040078000	1.00
Sc	Scandium	21	0.044955910	1.36
Ti	Titanium	22	0.047880000	1.54
V	Vanadium	23	0.050941500	1.63
Cr	Chromium	24	0.051996100	1.66
Mn	Manganese	25	0.054938050	1.55
Fe	Iron	26	0.055847000	1.83
Co	Cobalt	27	0.058933200	1.88
Ni	Nickel	28	0.058693400	1.91
Cu	Copper	29	0.063546000	1.90
Zn	Zinc	30	0.065390000	1.65
Ga	Gallium	31	0.069723000	1.81
Ge	Germanium	32	0.072610000	2.01
As	Arsenic	33	0.074921590	2.18
Se	Selenium	34	0.078960000	2.55
Br	Bromine	35	0.079904000	2.96
Kr	Krypton	36	0.083800000	0.00
Rb	Rubidium	37	0.085467800	0.82
Sr	Strontium	38	0.087620000	0.95
Y	Yttrium	39	0.088905850	1.22
Zr	Zirconium	40	0.091224000	1.33
Nb	Niobium	41	0.092906380	1.60
Mo	Molybdenum	42	0.095940000	2.16
Tc	Technetium	43	0.097907200	1.90
Ru	Ruthenium	44	0.101070000	2.20
Rh	Rhodium	45	0.102905500	2.28
Pd	Palladium	46	0.106420000	2.20
Ag	Silver	47	0.107868200	1.93
Cd	Cadmium	48	0.112411000	1.69
In	Indium	49	0.114818000	1.78
Sn	Tin	50	0.118710000	1.96
Sb	Antimony	51	0.121760000	2.05
Te	Tellurium	52	0.127600000	2.10
I	Iodine	53	0.126904470	2.66
Xe	Xenon	54	0.131290000	0.00
Cs	Cesium	55	0.132905430	0.79
Ba	Barium	56	0.137327000	0.89
La	Lanthanum	57	0.138905500	1.10
Ce	Cerium	58	0.140115000	1.12
Pr	Praseodymium	59	0.140907650	1.13
Nd	Neodymium	60	0.144240000	1.14
Pm	Promethium	61	0.144912700	0.00
Sm	Samarium	62	0.150360000	1.17
Eu	Europium	63	0.151965000	0.00
Gd	Gadolinium	64	0.157250000	1.20
Tb	Terbium	65	0.158925340	1.20
Dy	Dysprosium	66	0.162500000	0.00
Ho	Holmium	67	0.164930320	1.23
Er	Erbium	68	0.167260000	1.24
Tm	Thulium	69	0.168934210	1.25
Yb	Ytterbium	70	0.173040000	1.10
Lu	Lutetium	71	0.174967000	1.27
Hf	Hafnium	72	0.178490000	1.30
Ta	Tantalum	73	0.180947900	1.50
W	Tungsten	74	0.183840000	1.70
Re	Rhenium	75	0.186207000	1.90
Os	Osmium	76	0.190230000	2.20
Ir	Iridium	77	0.192220000	2.20
Pt	Platinum	78	0.195080000	2.28
Au	Gold	79	0.196966540	2.54
Hg	Mercury	80	0.200590000	2.00
Tl	Thallium	81	0.204383300	1.62
Pb	Lead	82	0.207200000	1.80
Bi	Bismuth	83	0.208980370	2.02
Po	Polonium	84	0.208982400	2.00
At	Astatine	85	0.209987100	2.20
Rn	Radon	86	0.222017600	0.00
Fr	Francium	87	0.223019700	0.70
Ra	Radium	88	0.226025400	0.90
Ac	Actinium	89	0.227027800	1.10
Th	Thorium	90	0.232038100	1.30
Pa	Protactinium	91	0.231035880	1.50
U	Uranium	92	0.238028900	1.38
Np	Neptunium	93	0.237048000	1.36
Pu	Plutonium	94	0.244064200	1.28
Am	Americium	95	0.243061400	1.30
Cm	Curium	96	0.247070300	1.30
Bk	Berkelium	97	0.247070300	1.30
Cf	Californium	98	0.251079600	1.30
Es	Einsteinium	99	0.252083000	1.30
Fm	Fermium	100	0.257095100	1.30
Md	Mendelevium	101	0.258100000	1.30
No	Nobelium	102	0.259100900	1.30
Lr	Lawrencium	103	0.262110000	0.00
Rf	Rutherfordium	104	0.261000000	0.00
Db	Dubnium	105	0.262000000	0.00
Sg	Seaborgium	106	0.266000000	0.00
Bh	Bohrium	107	0.264000000	0.00
Hs	Hassium	108	0.269000000	0.00
Mt	Meitnerium	109	0.268000000	0.00
Ds	Darmstadtium	110	0.269000000	0.00
Rg	Roentgenium	111	0.272000000	0.00
Cn	Copernicium	112	0.277000000	0.00
Nh	Nihonium	113	0.000000000	0.00
Fl	Flerovium	114	0.289000000	0.00
Mc	Moscovium	115	0.000000000	0.00
Lv	Livermorium	116	0.000000000	0.00
Ts	Tennessine	117	0.000000000	0.00
Og	Oganesson	118	0.000000000	0.00