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Python API with a database of atomic properties for elements in the periodic table

Project Description

Installation | Documentation | Usage | Contributing | License

mendeleev package

This package provides a convenient python API for accessing various properties of elements, ions and isotopes in the periodic table of elements.

Moreover it provides an easy to use interface to pandas and convenient visualization functionality through bokeh that enables you to create customized periodic tables displaying various properties.

The mendeleev package also supplies convenient tools for dealing with electronic configurations, calculating functions of atomic properties, exploring the periodic trends in the periodic tables. If you want to look at some examples there are a few tutorials available as jupyter notebooks.

Interactive web app

If you would like to explore the data available in mendeleev check out the interactive web app at mendeleev.herokuapp.com where you can create your own periodic tables and visualize the relations between various properties of elements.

Data

A comprehensive list of the available data together with appropriate references are available in the documentation. Here the most important entries are listed:

Basic properties

  • atomic number
  • atomic weight
  • block
  • cas
  • electrons
  • electronic configuration
  • group
  • name
  • neutrons
  • period
  • protons
  • series
  • symbol

Standardized colors schemes

  • cpk_color
  • jmol_color
  • molcas_gv_color

Electronegativity scales

  • Allen
  • Allred & Rochow
  • Cottrell & Sutton
  • Ghosh
  • Gordy
  • Li & Xue
  • Nagle
  • Martynov & Batsanov
  • Mulliken
  • Pauling
  • Sanderson

Descriptive properties

  • discoverers
  • discovery location
  • dipole year
  • description
  • name origin
  • sources
  • uses

Physical properties

  • boiling point
  • C<sub>6</sub>
  • density
  • dipole polarizability
  • electron affinity
  • evaporation heat
  • gas basicity
  • ionization energies
  • lattice structure
  • melting point
  • oxidation states
  • proton affinity
  • specific heat
  • thermal conductivity
  • nuclear screening constants (Slater & Clementi)

Isotope properties

  • abundance
  • g_factor
  • half_life
  • radioactivity
  • mass
  • mass number
  • spin
  • quadrupole_moment

Installation

The preferred installation method is with conda and you can install the package from my anaconda channel by

conda install -c lmmentel mendeleev=0.4.1

The package can also be installed using pip

pip install mendeleev

You can also install the most recent version from the repository:

pip install https://bitbucket.org/lukaszmentel/mendeleev/get/tip.tar.gz

Documentation

Documentation is hosted on Read the Docs.

Usage

The simplest way of accessing the element data is by importing elements directly from the mendeleev package by their symbols. For example consider iron (Fe):

>>> from mendeleev import Fe
>>> Fe.name
'Iron'
>>> Fe.atomic_number
26
>>> Fe.thermal_conductivity
80.4

Another, more flexible way is through the element method that returns the Element object:

>>> from mendeleev import element

The element method accepts unique identifiers: atomic number, atomic symbol or element’s name in english. To retrieve the entries on Silicon by symbol type

>>> si = element('Si')
>>> si.name
'Silicon'

Similarly to access the data by atomic number or element names type

>>> al = element(13)
>>> al.name
'Aluminium'
>>> o = element('Oxygen')
>>> o.atomic_number
8

Lists of elements

The element method also accepts list or tuple of identifiers and then returns a list of Element objects

>>> c, h, o = element(['C', 'Hydrogen', 8])
>>> c.name, h.name, o.name
('Carbon', 'Hydrogen', 'Oxygen')
Isotopes

The isotopes attribute returns a list of Isotope objects with the following attributes per isotope

  • atomic_number
  • mass
  • abundance
  • mass_number
>>> fe = element('Fe')
>>> for iso in fe.isotopes:
...     print(iso)
 26   55.93494  91.75%    56
 26   56.93540   2.12%    57
 26   57.93328   0.28%    58
 26   53.93961   5.85%    54

The columns represent the attributes atomic_number, mass, abundance and mass_number respectively.

Tables and the database

mendeleev offers also methods for accessing whole tables of data, e.g. table with the data on all isotopes and methods for interacting directly with the database engine, for more details see the API documentation and this tutorial.

CLI utility

For those who work in the terminal there is a simple command line interface (CLI) for printing the information about a given element. The script name is element.py and it accepts either the symbol or name of the element or it’s atomic number as an argument and prints the data about it. For example, to print the properties of silicon type

$ element.py Si
                            _  _  _  _      _
                          _(_)(_)(_)(_)_   (_)
                         (_)          (_)_  _
                         (_)_  _  _  _  (_)(_)
                           (_)(_)(_)(_)_   (_)
                          _           (_)  (_)
                         (_)_  _  _  _(_)_ (_) _
                           (_)(_)(_)(_) (_)(_)(_)



Description
===========

  Metalloid element belonging to group 14 of the periodic table. It is
  the second most abundant element in the Earth's crust, making up 25.7%
  of it by weight. Chemically less reactive than carbon. First
  identified by Lavoisier in 1787 and first isolated in 1823 by
  Berzelius.

Sources
=======

  Makes up major portion of clay, granite, quartz (SiO2), and sand.
  Commercial production depends on a reaction between sand (SiO2) and
  carbon at a temperature of around 2200 °C.

Uses
====

  Used in glass as silicon dioxide (SiO2). Silicon carbide (SiC) is one
  of the hardest substances known and used in polishing. Also the
  crystalline form is used in semiconductors.

Properties
==========

Abundance crust                                         282000
Abundance sea                                              2.2
Annotation
Atomic number                                               14
Atomic radius                                              132
Atomic radius rahm                                         232
Atomic volume                                             12.1
Atomic weight                                           28.085
Atomic weight uncertainty                                  NaN
Block                                                        p
Boiling point                                             2628
C6                                                         305
C6 gb                                                      308
Cas                                                  7440-21-3
Covalent radius bragg                                      117
Covalent radius cordero                                    111
Covalent radius pyykko                                     116
Covalent radius pyykko double                              107
Covalent radius pyykko triple                              102
Covalent radius slater                                     110
Cpk color                                              #daa520
Density                                                   2.33
Dipole polarizability                                    37.31
Discoverers                                     Jöns Berzelius
Discovery location                                      Sweden
Discovery year                                            1824
Electron affinity                                      1.38952
Electronic configuration                          [Ne] 3s2 3p2
En allen                                                 11.33
En ghosh                                              0.178503
En pauling                                                 1.9
Evaporation heat                                           383
Fusion heat                                               50.6
Gas basicity                                             814.1
Geochemical class                                        major
Goldschmidt class                                    litophile
Group id                                                    14
Heat of formation                                          450
Is monoisotopic                                           None
Is radioactive                                           False
Jmol color                                             #f0c8a0
Lattice constant                                          5.43
Lattice structure                                          DIA
Melting point                                             1683
Metallic radius                                            117
Metallic radius c12                                        138
Molcas gv color                                        #f0c8a0
Name                                                   Silicon
Name origin                    Latin: silex, silicus, (flint).
Period                                                       3
Proton affinity                                            837
Series id                                                    5
Specific heat                                            0.703
Symbol                                                      Si
Thermal conductivity                                       149
Vdw radius                                                 210
Vdw radius alvarez                                         219
Vdw radius batsanov                                        210
Vdw radius bondi                                           210
Vdw radius dreiding                                        427
Vdw radius mm3                                             229
Vdw radius rt                                              NaN
Vdw radius truhlar                                         NaN
Vdw radius uff                                           429.5

Contributing

All contributions are welcome!

Issues

Feel free to submit issues with:

  • data updates and recommendations
  • enhancement requests and new useful features
  • code bugs
  • data or citation inconsistencies

Pull requests

  • fork the repo on bitbucket
  • clone the project to your own machine
  • commit changes to your own branch
  • push your work back up to your fork
  • submit a pull request so that your changes can be reviewed

License

MIT, see LICENSE

Citing

If you use mendeleev in a scientific publication, please consider citing the software as

L. M. Mentel, mendeleev - A Python resource for properties of chemical elements, ions and isotopes. , 2014– . Available at: https://bitbucket.org/lukaszmentel/mendeleev.

Here’s the reference in the BibLaTeX format

 @software{mendeleev2014,
    author = {Mentel, Łukasz},
    title = {{mendeleev} -- A Python resource for properties of chemical elements, ions and isotopes},
    url = {https://bitbucket.org/lukaszmentel/mendeleev},
    version = {0.4.1},
    date = {2014--},
}

or the older BibTeX format

@misc{mendeleev2014,
   auhor = {Mentel, Łukasz},
   title = {mendeleev} -- A Python resource for properties of chemical elements, ions and isotopes, ver. 0.4.1},
   howpublished = {\url{https://bitbucket.org/lukaszmentel/mendeleev}},
   year  = {2014--},
}

Funding

This project is supported by the RCN (The Research Council of Norway) project number 239193.

Release History

Release History

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