Mendeleev.jl
A package for accessing chemical elements data. It's code was initially based on PeriodicTable Julia package, whereas the data come mainly from the Python mendeleev package. It can be used as a replacement for PeriodicTable.
Installation
As usual
] add MendeleevIntentions
The aim was to have a package compatible with PeriodicTable, but with much more comprehensive data from possibly reliable and traceable sources. The package should still be possibly lightweight like PeriodicTable.
Like it's predessor, Mendeleev has only minimal direct dependencies, keeps data in static form, and takes about the same time to load (about half a second on a medium-range medium-aged notebook), most of the load time due to Unitful in both cases. For compatibility details, see below.
Another aim was to make it easier to update data. Most data are read out from the (Python) mendeleev database by a separate external skript and converted to static Julia code, which further can be relatively straightforwardly edited, should that be necessary.
Usage
Mendeleev.jl provides a Julia interface to a database of element properties for all of the elements in the periodic table. In particular Mendeleev exports a global variable called chem_elements, which is a collection of ChemElem data structures.
julia> using Mendeleev
julia> chem_elements
Elements(…118 elements…):
H He
Li Be B C N O F Ne
Na Mg Al Si P S Cl Ar
K Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Kr
Rb Sr Y Zr Nb Mo Tc Ru Rh Pd Ag Cd In Sn Sb Te I Xe
Cs Ba Hf Ta W Re Os Ir Pt Au Hg Tl Pb Bi Po At Rn
Fr Ra Rf Db Sg Bh Hs Mt Ds Rg Cn Nh Fl Mc Lv Ts Og
Uue
La Ce Pr Nd Pm Sm Eu Gd Tb Dy Ho Er Tm Yb Lu
Ac Th Pa U Np Pu Am Cm Bk Cf Es Fm Md No LrYou can look up elements by name (case-insensitive) via chem_elements["oxygen"], by symbol via chem_elements[:O], by number via chem_elements[8], or via the field chem_elements.O for example.
All physical quantities are unitful.
The data is pretty-printed when you look up an element in the Julia REPL. For example:
julia> chem_elements["oxygen"]
Oxygen (O), number 8:
category: diatomic nonmetal
atomic mass: 15.999 u
natural isotopes: ((99.738% ¹⁶O m=15.99491462 u ), (0.04% ¹⁷O m=16.999131757 u ), (0.222% ¹⁸O m=17.999159613 u ))
density: 0.001308 g/cm³
molar heat cap.: 29.378 J/mol⋅K
melting point: 54.8 K
boiling point: 90.19 K
phase: Gas
shells: [2, 6]
e⁻-configuration: 1s² 2s² 2p⁴
summary: Oxygen is a chemical element with symbol O and atomic number 8. It is a member of the chalcogen group on the periodic table and is a highly reactive nonmetal and oxidizing agent that readily forms compounds (notably oxides) with most elements. By mass, oxygen is the third-most abundant element in the universe, after hydrogen and helium.
CAS identifier: 7782-44-7
discovered by: 1774 by Joseph Priestly, Carl Wilhelm Scheele in England/Sweden
NIST webbook: https://webbook.nist.gov/cgi/inchi/InChI%3D1S/O2/c1-2
wikipedia URL: https://en.wikipedia.org/wiki/Oxygen
spectral image: https://en.wikipedia.org/wiki/File:Oxygen_spectre.jpg
Data access, indexing and filtering by example
Access to elements and element properties
julia> using Mendeleev
julia> using Mendeleev: elements # for PeriodicTable compatibility
julia> using Mendeleev: els # for lazy typists
julia> @assert chem_elements === elements === els
julia> @assert chem_elements[26] === chem_elements[:Fe] === chem_elements["iron"] === chem_elements.Fe # four ways to get an element
julia> chem_elements[1:4] # list of elements
4-element Vector{ChemElem}:
Element(Hydrogen)
Element(Helium)
Element(Lithium)
Element(Beryllium)
julia> els.Fe.boiling_point # get a property - see Elements Data Fields
3023.0 KAccess to ionic radii
julia> feir = els.Fe.ionic_radii # I'm not a good typist, thus ´els´ and not ´chem_elements´ here
ionic radii for Iron
(Fe2+, coordination=IV, econf=3d6, spin=HS, crystal_radius=77.0 pm, ionic_radius=63.0 pm, ionic_potential=0.03175 e pm⁻¹, most_reliable=false)
(Fe2+, coordination=IVSQ, econf=3d6, spin=HS, crystal_radius=78.0 pm, ionic_radius=64.0 pm, ionic_potential=0.03125 e pm⁻¹, most_reliable=false)
...
(Fe4+, coordination=VI, econf=3d4, crystal_radius=72.5 pm, ionic_radius=58.5 pm, ionic_potential=0.06838 e pm⁻¹, origin=from r^3 vs V plots, , most_reliable=false)
(Fe6+, coordination=IV, econf=3d2, crystal_radius=39.0 pm, ionic_radius=25.0 pm, ionic_potential=0.24 e pm⁻¹, origin=from r^3 vs V plots, , most_reliable=false)
julia> feir[1] # indexing
(Fe2+, coordination=IV, econf=3d6, spin=HS, crystal_radius=77.0 pm, ionic_radius=63.0 pm, ionic_potential=0.03175 e pm⁻¹, most_reliable=false)
julia> feir[1:2] # indexing
2-element Vector{Mendeleev.IonicRadius}:
(Fe2+, coordination=IV, econf=3d6, spin=HS, crystal_radius=77.0 pm, ionic_radius=63.0 pm, ionic_potential=0.03175 e pm⁻¹, most_reliable=false)
(Fe2+, coordination=IVSQ, econf=3d6, spin=HS, crystal_radius=78.0 pm, ionic_radius=64.0 pm, ionic_potential=0.03125 e pm⁻¹, most_reliable=false)
julia> feir(;most_reliable=true) # filtering
3-element Vector{Mendeleev.IonicRadius}:
(Fe2+, coordination=VI, econf=3d6, spin=HS, crystal_radius=92.0 pm, ionic_radius=78.0 pm, ionic_potential=0.02564 e pm⁻¹, origin=from r^3 vs V plots, , most_reliable=true)
(Fe3+, coordination=IV, econf=3d5, spin=HS, crystal_radius=63.0 pm, ionic_radius=49.0 pm, ionic_potential=0.06122 e pm⁻¹, most_reliable=true)
(Fe3+, coordination=VI, econf=3d5, spin=HS, crystal_radius=78.5 pm, ionic_radius=64.5 pm, ionic_potential=0.04651 e pm⁻¹, origin=from r^3 vs V plots, , most_reliable=true)
julia> feir(;charge=2, coordination=:VI, econf="3d6", spin=:HS, most_reliable=true) #filtering
1-element Vector{Mendeleev.IonicRadius}:
(Fe2+, coordination=VI, econf=3d6, spin=HS, crystal_radius=92.0 pm, ionic_radius=78.0 pm, ionic_potential=0.02564 e pm⁻¹, origin=from r^3 vs V plots, , most_reliable=true)
Access to electronegativities according to Li and Xue scale
julia> felx = chem_elements.Fe.eneg.Li
Li-Xue Electronegativities for Fe
(Fe2+, coordination=IV, spin=HS, value=4.889 pm⁻¹)
(Fe2+, coordination=IVSQ, spin=HS, value=4.826 pm⁻¹)
...
(Fe4+, coordination=VI, value=9.56 pm⁻¹)
(Fe6+, coordination=IV, value=23.86 pm⁻¹)
julia> felx[2] # indexing
(Fe2+, coordination=IVSQ, spin=HS, value=4.826 pm⁻¹)
julia> felx(;charge=2, spin=:HS, coordination=:VI) # filtering
1-element Vector{Mendeleev.LiXueDSet}:
(Fe2+, coordination=VI, spin=HS, value=4.092 pm⁻¹)Data by
The data used for this package has been pulled up mainly from the Python package mendeleev by Lukasz Mentel. See mendeleev documentation for the data sources. Some information (but no physical quantities) taken over from PeriodicTable.jl, which was in turn taken mostly from here. Some data cross-checked between mendeleev, PeriodicTable.jl, and IsotopeTable.jl, and discrepancy cases re-checked by other sources by the autor of this package.
List of ChemElement properties:
Types
Compatibility Issues
PeriodicTable.jl exports global variable called elements, which is a collection of Element data structures. In Mendeleev.jl these called correspondingly chem_elements and ChemElem, the word "element" having too much meanings IMO. For legacy application you however still may use the old names:
julia> using Mendeleev: elements, ElementOne property (color) was omitted completely, one (named_by) is omitted, but there exists a similar property. The PeriodicTable.jl property source contained link to Wikipedia article, and is re-named to wikipedia in this package. For details, see Elements Data section.
Missing data were encoded in the PeriodicTable.jl resp. by empty strings and by NaN, as the package predated introduction of Missing. Here, we are using Missing.
Developed by
Credits
Developers of PeriodicTable.jl
Some data originally from
Most data from mendeleev by Lukasz Mentel
Wikipedia and CRC Handbook of Chemistry and Physics (ISBN 9781482208689) were the most used primary data sources for words, words, words and for numbers, respectively.