Metadata-Version: 2.0
Name: mendeleev
Version: 0.3.4
Summary: Python API with a database of atomic properties for elements in the periodic table
Home-page: https://bitbucket.org/lukaszmentel/mendeleev
Author: Lukasz Mentel
Author-email: lmmentel@gmail.com
License: MIT
Download-URL: https://bitbucket.org/lukaszmentel/mendeleev/get/v0.3.4.tar.gz
Keywords: periodic,table,elements,atomic,properties,mendeleev
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 3
Classifier: Topic :: Scientific/Engineering :: Chemistry
Classifier: Topic :: Scientific/Engineering :: Physics
Requires-Dist: numpy
Requires-Dist: pandas
Requires-Dist: sqlalchemy

#################
mendeleev package
#################

.. image:: https://readthedocs.org/projects/mendeleev/badge/
   :target: https://mendeleev.readthedocs.org
   :alt: Documentation Status

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 <http://pandas.pydata.org/>`_
and convenient visualization functionality through `bokeh <http://bokeh.pydata.org/en/latest/>`_
that enables you to create customized periodic tables displaying various properties.

.. image:: docs/source/img/mendeleev_periodic_series.png
    :width: 800px
    :align: center
    :alt: alternate text


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 <http://mendeleev.readthedocs.io/en/stable/tutorials.html>`_
available as `jupyter notebooks <http://jupyter.org/>`_.

*******************
Interactive web app
*******************

If you would like to explore the data available in `mendeleev <http://mendeleev.readthedocs.org/en/latest/>`_
check out the interactive web app at `mendeleev.herokuapp.com <http://mendeleev.herokuapp.com/>`_
where you can create your own periodic tables and visualize the relations between various properties
of elements.


****
Data
****

Following electronegativity scales are available either as stored values or
computed on request from other properties:

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


The following data are currently available:

+-------------------------------+-------+------------------------------------------------------+----------+-------------+
| Name                          | Type  | Comment                                              | Unit     | Data Source |
+===============================+=======+======================================================+==========+=============+
| abundance_crust               | float | Abundance in the Earth's crust                       | mg/kg    | [8]_        |
+-------------------------------+-------+------------------------------------------------------+----------+-------------+
| abundance_sea                 | float | Abundance in the seas                                | mg/L     | [8]_        |
+-------------------------------+-------+------------------------------------------------------+----------+-------------+
| annotation                    | str   | Annotations regarding the data                       |          |             |
+-------------------------------+-------+------------------------------------------------------+----------+-------------+
| atomic_number                 | int   | Atomic number                                        |          |             |
+-------------------------------+-------+------------------------------------------------------+----------+-------------+
| atomic_radius                 | float | Atomic radius                                        | pm       |             |
+-------------------------------+-------+------------------------------------------------------+----------+-------------+
| atomic_radius_rahm            | float | Atomic radius by Rahm et al.                         | pm       | [42]_       |
+-------------------------------+-------+------------------------------------------------------+----------+-------------+
| atomic_volume                 | float | Atomic volume                                        | cm3/mol  |             |
+-------------------------------+-------+------------------------------------------------------+----------+-------------+
| atomic_weight                 | float | Atomic weight                                        |          | [36]_, [37]_|
+-------------------------------+-------+------------------------------------------------------+----------+-------------+
| atomic_weight_uncertainty     | float | Atomic weight uncertainty                            |          | [36]_, [37]_|
+-------------------------------+-------+------------------------------------------------------+----------+-------------+
| block                         | int   | Block in periodic table                              |          |             |
+-------------------------------+-------+------------------------------------------------------+----------+-------------+
| boiling_point                 | float | Boiling temperature                                  | K        |             |
+-------------------------------+-------+------------------------------------------------------+----------+-------------+
| c6                            | float | C_6 dispersion coefficient in a.u.                   | a.u.     | [1]_, [2]_  |
+-------------------------------+-------+------------------------------------------------------+----------+-------------+
| c6_gb                         | float | C_6 dispersion coefficient in a.u. (Gould & Bučko)   | a.u.     | [35]_       |
+-------------------------------+-------+------------------------------------------------------+----------+-------------+
| cas                           | str   | Chemical Abstracts Serice identifier                 |          |             |
+-------------------------------+-------+------------------------------------------------------+----------+-------------+
| covalent_radius_bragg         | float | Covalent radius by Bragg                             | pm       | [3]_        |
+-------------------------------+-------+------------------------------------------------------+----------+-------------+
| covalent_radius_cordero       | float | Covalent radius by Cerdero et al.                    | pm       | [4]_        |
+-------------------------------+-------+------------------------------------------------------+----------+-------------+
| covalent_radius_pyykko        | float | Single bond covalent radius by Pyykko et al.         | pm       | [5]_        |
+-------------------------------+-------+------------------------------------------------------+----------+-------------+
| covalent_radius_pyykko_double | float | Double bond covalent radius by Pyykko et al.         | pm       | [46]_       |
+-------------------------------+-------+------------------------------------------------------+----------+-------------+
| covalent_radius_pyykko_triple | float | Triple bond covalent radius by Pyykko et al.         | pm       | [47]_       |
+-------------------------------+-------+------------------------------------------------------+----------+-------------+
| covalent_radius_slater        | float | Covalent radius by Slater                            | pm       | [6]_        |
+-------------------------------+-------+------------------------------------------------------+----------+-------------+
| cpk_color                     | str   | Element color in CPK convention                      | HEX      | [24]_       |
+-------------------------------+-------+------------------------------------------------------+----------+-------------+
| density                       | float | Density at 295K                                      | g/cm3    |             |
+-------------------------------+-------+------------------------------------------------------+----------+-------------+
| description                   | str   | Short description of the element                     |          |             |
+-------------------------------+-------+------------------------------------------------------+----------+-------------+
| dipole_polarizability         | float | Dipole polarizability                                | a.u.     | [7]_        |
+-------------------------------+-------+------------------------------------------------------+----------+-------------+
| electron_affinity             | float | Electron affinity                                    | eV       | [8]_, [9]_  |
+-------------------------------+-------+------------------------------------------------------+----------+-------------+
| electrons                     | int   | Number of electrons                                  |          |             |
+-------------------------------+-------+------------------------------------------------------+----------+-------------+
| en_allen                      | float | Allen's scale of electronegativity                   | eV       | [10]_, [11]_|
+-------------------------------+-------+------------------------------------------------------+----------+-------------+
| en_ghosh                      | float | Ghosh's scale of electronegativity                   |          | [32]_       |
+-------------------------------+-------+------------------------------------------------------+----------+-------------+
| en_mulliken                   | float | Mulliken's scale of electronegativity                | eV       | [12]_       |
+-------------------------------+-------+------------------------------------------------------+----------+-------------+
| en_pauling                    | float | Pauling's scale of electronegativity                 |          | [8]_        |
+-------------------------------+-------+------------------------------------------------------+----------+-------------+
| econf                         | str   | Ground state electron configuration                  |          |             |
+-------------------------------+-------+------------------------------------------------------+----------+-------------+
| evaporation_heat              | float | Evaporation heat                                     | kJ/mol   |             |
+-------------------------------+-------+------------------------------------------------------+----------+-------------+
| fusion_heat                   | float | Fusion heat                                          | kJ/mol   |             |
+-------------------------------+-------+------------------------------------------------------+----------+-------------+
| gas_basicity                  | float | Gas basicity                                         | kJ/mol   | [8]_        |
+-------------------------------+-------+------------------------------------------------------+----------+-------------+
| geochemical_class             | str   | Geochemical classification                           |          | [43]_       |
+-------------------------------+-------+------------------------------------------------------+----------+-------------+
| goldschmidt_class             | str   | Goldschmidt classification                           |          | [43]_, [44]_|
+-------------------------------+-------+------------------------------------------------------+----------+-------------+
| group                         | int   | Group in periodic table                              |          |             |
+-------------------------------+-------+------------------------------------------------------+----------+-------------+
| heat_of_formation             | float | Heat of formation                                    | kJ/mol   | [8]_        |
+-------------------------------+-------+------------------------------------------------------+----------+-------------+
| ionenergy                     | tuple | Ionization energies                                  | eV       | [13]_       |
+-------------------------------+-------+------------------------------------------------------+----------+-------------+
| ionic_radii                   | list  | Ionic and crystal radii in pm                        | pm       | [14]_       |
+-------------------------------+-------+------------------------------------------------------+----------+-------------+
| is_monoisotopic               | bool  | Is the element monoisotopic                          |          |             |
+-------------------------------+-------+------------------------------------------------------+----------+-------------+
| is_radioactive                | bool  | Is the element radioactive                           |          |             |
+-------------------------------+-------+------------------------------------------------------+----------+-------------+
| isotopes                      | list  | Isotopes                                             |          |             |
+-------------------------------+-------+------------------------------------------------------+----------+-------------+
| jmol_color                    | str   | Element color in Jmol convention                     | HEX      | [25]_       |
+-------------------------------+-------+------------------------------------------------------+----------+-------------+
| lattice_constant              | float | Lattice constant                                     | Angstrom |             |
+-------------------------------+-------+------------------------------------------------------+----------+-------------+
| lattice_structure             | str   | Lattice structure code                               |          |             |
+-------------------------------+-------+------------------------------------------------------+----------+-------------+
| mass_number                   | int   | Mass number (most abundant isotope)                  |          |             |
+-------------------------------+-------+------------------------------------------------------+----------+-------------+
| melting_point                 | float | Melting temperature                                  | K        |             |
+-------------------------------+-------+------------------------------------------------------+----------+-------------+
| metallic_radius               | float | Single-bond metallic radius                          | pm       | [45]_       |
+-------------------------------+-------+------------------------------------------------------+----------+-------------+
| metallic_radius_c12           | float | Metallic radius with 12 nearest neighbors            | pm       | [45]_       |
+-------------------------------+-------+------------------------------------------------------+----------+-------------+
| molcas_gv_color               | str   | Element color in MOCAS GV convention                 | HEX      | [26]_       |
+-------------------------------+-------+------------------------------------------------------+----------+-------------+
| name                          | str   | Name in English                                      |          |             |
+-------------------------------+-------+------------------------------------------------------+----------+-------------+
| neutrons                      | int   | Number of neutrons (most abundant isotope)           |          |             |
+-------------------------------+-------+------------------------------------------------------+----------+-------------+
| oxistates                     | list  | Oxidation states                                     |          |             |
+-------------------------------+-------+------------------------------------------------------+----------+-------------+
| period                        | int   | Period in periodic table                             |          |             |
+-------------------------------+-------+------------------------------------------------------+----------+-------------+
| proton_affinity               | float | Proton affinity                                      | kJ/mol   | [8]_        |
+-------------------------------+-------+------------------------------------------------------+----------+-------------+
| protons                       | int   | Number of protons                                    |          |             |
+-------------------------------+-------+------------------------------------------------------+----------+-------------+
| sconst                        | float | Nuclear charge screening constants                   |          | [15]_, [16]_|
+-------------------------------+-------+------------------------------------------------------+----------+-------------+
| series                        | int   | Index to chemical series                             |          |             |
+-------------------------------+-------+------------------------------------------------------+----------+-------------+
| specific_heat                 | float | Specific heat @ 20 C                                 | J/(g mol)|             |
+-------------------------------+-------+------------------------------------------------------+----------+-------------+
| symbol                        | str   | Chemical symbol                                      |          |             |
+-------------------------------+-------+------------------------------------------------------+----------+-------------+
| thermal_conductivity          | float | Thermal conductivity @25 C                           | W/(m K)  |             |
+-------------------------------+-------+------------------------------------------------------+----------+-------------+
| vdw_radius                    | float | Van der Waals radius                                 | pm       | [8]_        |
+-------------------------------+-------+------------------------------------------------------+----------+-------------+
| vdw_radius_alvarez            | float | Van der Waals radius according to Alvarez            | pm       | [33]_, [34]_|
+-------------------------------+-------+------------------------------------------------------+----------+-------------+
| vdw_radius_batsanov           | float | Van der Waals radius according to Batsanov           | pm       | [17]_       |
+-------------------------------+-------+------------------------------------------------------+----------+-------------+
| vdw_radius_bondi              | float | Van der Waals radius according to Bondi              | pm       | [18]_       |
+-------------------------------+-------+------------------------------------------------------+----------+-------------+
| vdw_radius_dreiding           | float | Van der Waals radius from the DREIDING FF            | pm       | [19]_       |
+-------------------------------+-------+------------------------------------------------------+----------+-------------+
| vdw_radius_mm3                | float | Van der Waals radius from the MM3 FF                 | pm       | [20]_       |
+-------------------------------+-------+------------------------------------------------------+----------+-------------+
| vdw_radius_rt                 | float | Van der Waals radius according to Rowland and Taylor | pm       | [21]_       |
+-------------------------------+-------+------------------------------------------------------+----------+-------------+
| vdw_radius_truhlar            | float | Van der Waals radius according to Truhlar            | pm       | [22]_       |
+-------------------------------+-------+------------------------------------------------------+----------+-------------+
| vdw_radius_uff                | float | Van der Waals radius from the UFF                    | pm       | [23]_       |
+-------------------------------+-------+------------------------------------------------------+----------+-------------+



Isotopes
========

+---------------------------+-------+------------------------------------------------------+--------------+-------------+
| Name                      | Type  | Comment                                              | Unit         | Data Source |
+===========================+=======+======================================================+==============+=============+
| abundance                 | float | Relative Abundance                                   |              | [38]_       |
+---------------------------+-------+------------------------------------------------------+--------------+-------------+
| g_factor                  | float | Nuclear g-factor                                     |              | [40]_       |
+---------------------------+-------+------------------------------------------------------+--------------+-------------+
| half_life                 | float | Half life of the isotope                             |              | [36]_       |
+---------------------------+-------+------------------------------------------------------+--------------+-------------+
| half_life_unit            | str   | Unit in which the half life is given                 |              | [36]_       |
+---------------------------+-------+------------------------------------------------------+--------------+-------------+
| is_radioactive            | bool  | Is the isotope radioactive                           |              | [39]_       |
+---------------------------+-------+------------------------------------------------------+--------------+-------------+
| mass                      | float | Atomic mass                                          | Da           | [39]_       |
+---------------------------+-------+------------------------------------------------------+--------------+-------------+
| mass_number               | int   | Mass number of the isotope                           |              | [39]_       |
+---------------------------+-------+------------------------------------------------------+--------------+-------------+
| mass_uncertainty          | float | Uncertainty of the atomic mass                       |              | [39]_       |
+---------------------------+-------+------------------------------------------------------+--------------+-------------+
| spin                      | float | Nuclear spin quantum number                          |              |             |
+---------------------------+-------+------------------------------------------------------+--------------+-------------+
| quadrupole_moment         | float | Nuclear electric quadrupole moment                   | b [100 fm^2] | [41]_       |
+---------------------------+-------+------------------------------------------------------+--------------+-------------+


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   `doi:10.1002/chem.200901472 <http://doi.org/10.1002/chem.200901472>`_
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   Chemistry - A European Journal, 11(12), 3511–3520.
   `doi:10.1002/chem.200401299 <http://doi.org/10.1002/chem.200401299>`_


************
Installation
************

The package can be installed using `pip <https://pypi.python.org/pypi/pip>`_

.. code-block:: bash

   pip install mendeleev

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

.. code-block:: bash

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

If you use `conda <https://conda.io/docs/intro.html>`_ you can install 
the package from `my anaconda channel <https://anaconda.org/lmmentel/mendeleev>`_ by 

.. code-block:: bash

   conda install -c lmmentel mendeleev=0.3.4


*****
Usage
*****

The simple interface to the data is through the ``element`` method that returns
the ``Element`` objects::

   >>> 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

.. code-block:: python

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

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

.. code-block:: python

   >>> 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

.. code-block:: python

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

Composite Attributes
====================

Currently four of the attributes are more complex object than ``str``, ``int``
or ``float``, those are:

* ``oxistates``, returns a list of oxidation states
* ``ionenergies``, returns a dictionary of ionization energies
* ``isotopes``, returns a list of ``Isotope`` objects
* ``ionic_radii`` returns a list of ``IonicRadius`` objects

Oxidation states
----------------

For examples ``oxistates`` returns a list of oxidation states for
a given element

.. code-block:: python

   >>> fe = element('Fe')
   >>> fe.oxistates
   [6, 3, 2, 0, -2]

Ionization energies
-------------------

The ``ionenergies`` returns a dictionary with ionization energies as values and
degrees of ionization as keys.

.. code-block:: python

   >>> fe = element('Fe')
   >>> fe.ionenergies
   {1: 7.9024678,
    2: 16.1992,
    3: 30.651,
    4: 54.91,
    5: 75.0,
    6: 98.985,
    7: 125.0,
    8: 151.06,
    9: 233.6,
    10: 262.1,
    11: 290.9,
    12: 330.81,
    13: 361.0,
    14: 392.2,
    15: 456.2,
    16: 489.312,
    17: 1262.7,
    18: 1357.8,
    19: 1460.0,
    20: 1575.6,
    21: 1687.0,
    22: 1798.43,
    23: 1950.4,
    24: 2045.759,
    25: 8828.1875,
    26: 9277.681}

Isotopes
--------

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

* ``atomic_number``
* ``mass``
* ``abundance``
* ``mass_number``

.. code-block:: python

   >>> 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.

Ionic radii
-----------

Another composite attribute is ``ionic_radii`` which returns a list of
``IonicRadius`` object with the following attributes

* ``atomic_number``, atomic number of the ion
* ``charge``, charge of the ion
* ``econf``, electronic configuration of the ion
* ``coordination``, coordination type of the ion
* ``spin``, spin state of the ion (*HS* or *LS*)
* ``crystal_radius``
* ``ionic_radius``
* ``origin``, source of the data
* ``most_reliable``, recommended value

.. code-block:: python

   >>> fe = element('Fe')
   >>> for ir in fe.ionic_radii:
   ...     print(ir)
   charge=   2, coordination=IV   , crystal_radius= 0.770, ionic_radius= 0.630
   charge=   2, coordination=IVSQ , crystal_radius= 0.780, ionic_radius= 0.640
   charge=   2, coordination=VI   , crystal_radius= 0.750, ionic_radius= 0.610
   charge=   2, coordination=VI   , crystal_radius= 0.920, ionic_radius= 0.780
   charge=   2, coordination=VIII , crystal_radius= 1.060, ionic_radius= 0.920
   charge=   3, coordination=IV   , crystal_radius= 0.630, ionic_radius= 0.490
   charge=   3, coordination=V    , crystal_radius= 0.720, ionic_radius= 0.580
   charge=   3, coordination=VI   , crystal_radius= 0.690, ionic_radius= 0.550
   charge=   3, coordination=VI   , crystal_radius= 0.785, ionic_radius= 0.645
   charge=   3, coordination=VIII , crystal_radius= 0.920, ionic_radius= 0.780
   charge=   4, coordination=VI   , crystal_radius= 0.725, ionic_radius= 0.585
   charge=   6, coordination=IV   , crystal_radius= 0.390, ionic_radius= 0.250

***********
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 as an
argument and prints the data about it. For example, to print the properties of
silicon type

.. code-block:: bash

   $ 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.

   Properties
   ==========

   Annotation
   Atomic number                       14
   Atomic radius                      132
   Atomic volume                     12.1
   Block                                p
   Boiling point                     2628
   Covalent radius 2008               111
   Covalent radius 2009               116
   Cpk color                      #daa520
   Density                           2.33
   Dipole polarizability            37.31
   Electron affinity              1.38952
   Electronic configuration  [Ne] 3s2 3p2
   En allen                         11.33
   En pauling                         1.9
   Evaporation heat                   383
   Fusion heat                       50.6
   Gas basicity                     814.1
   Group id                            14
   Heat of formation                  450
   Jmol color                     #f0c8a0
   Lattice constant                  5.43
   Lattice structure                  DIA
   Mass                           28.0855
   Melting point                     1683
   Name                           Silicon
   Period                               3
   Proton affinity                    837
   Series id                            5
   Specific heat                    0.703
   Symbol                              Si
   Thermal conductivity               149
   Vdw radius                         210


*************
Documentation
*************


Documentation can be found `here <http://mendeleev.readthedocs.org/en/latest/>`_.

******
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 <https://bitbucket.org/lukaszmentel/mendeleev>`_.



Here's the reference in the `BibLaTeX <https://www.ctan.org/pkg/biblatex?lang=en>`_ format

.. code-block:: latex

   @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 = {0.3.4},
      date = {2014--},
  }

or the older `BibTeX <http://www.bibtex.org/>`_ format

.. code-block:: latex

   @misc{mendeleev2014,
      auhor = {Mentel, Łukasz},
      title = {mendeleev} -- A Python resource for properties of chemical elements, ions and isotopes, ver. 0.3.4},
      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.



