mendeleev 0.2.5

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

=================
mendeleev package
=================

This package provides an API for accessing various properties of elements from
the periodic table of elements.

Electronegativity scales
------------------------

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

Data
====

The followig 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_volume | float | Atomic volume | cm3/mol | |
+-------------------------+-------+------------------------------------------------------+----------+-------------+
| 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]_ |
+-------------------------+-------+------------------------------------------------------+----------+-------------+
| 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 | Covalent radius by Pyykko et al. | pm | [5]_ |
+-------------------------+-------+------------------------------------------------------+----------+-------------+
| 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_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]_ |
+-------------------------+-------+------------------------------------------------------+----------+-------------+
| 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]_ |
+-------------------------+-------+------------------------------------------------------+----------+-------------+
| 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 | float | Relative atomic mass | | |
+-------------------------+-------+------------------------------------------------------+----------+-------------+
| mass_number | int | Mass number (most abundant isotope) | | |
+-------------------------+-------+------------------------------------------------------+----------+-------------+
| melting_point | float | Melting temperature | K | |
+-------------------------+-------+------------------------------------------------------+----------+-------------+
| 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_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]_ |
+-------------------------+-------+------------------------------------------------------+----------+-------------+

.. [1] Chu, X., & Dalgarno, A. (2004). Linear response time-dependent density
functional theory for van der Waals coefficients. The Journal of Chemical
Physics, 121(9), 4083. `doi:10.1063/1.1779576 <http://dx.doi.org/10.1063/1.1779576>`_
.. [2] Tang, K. T., Norbeck, J. M., & Certain, P. R. (1976). Upper and lower bounds of
two- and three-body dipole, quadrupole, and octupole van der Waals coefficients
for hydrogen, noble gas, and alkali atom interactions. The Journal of Chemical
Physics, 64(7), 3063. `doi:10.1063/1.432569 <http://dx.doi.org/10.1063/1.432569>`_
.. [3] Bragg, W. L. (1920). The arrangement of atoms in crystals. Philosophical
Magazine, 40(236), 169-189.
`doi:10.1080/14786440808636111 <http://dx.doi.org/10.1080/14786440808636111>`_
.. [4] Cordero, B., Gomez, V., Platero-Prats, A. E., Reves, M., Echeverria, J.,
Cremades, E., ... Alvarez, S. (2008). Covalent radii revisited. Dalton
Transactions, (21), 2832. `doi:10.1039/b801115j <http://www.dx.doi.org/10.1039/b801115j>`_
.. [5] Pyykko, P., & Atsumi, M. (2009). Molecular Single-Bond Covalent Radii
for Elements 1-118. Chemistry - A European Journal, 15(1), 186-197.
`doi:10.1002/chem.200800987 <http://www.dx.doi.org/10.1002/chem.200800987>`_
.. [6] Slater, J. C. (1964). Atomic Radii in Crystals. The Journal of Chemical
Physics, 41(10), 3199. `doi:10.1063/1.1725697 <http://dx.doi.org/10.1063/1.1725697>`_
.. [7] P. Schwerdtfeger "Table of experimental and calculated static dipole
polarizabilities for the electronic ground states of the neutral elements
(in atomic units)", February 11, 2014 `source <http://ctcp.massey.ac.nz/Tablepol2014.pdf>`_
.. [8] W. M. Haynes, Handbook of Chemistry and Physics 95th Edition, CRC Press,
New York, 2014, ISBN-10: 1482208679, ISBN-13: 978-1482208672.
.. [9] Andersen, T. (2004). Atomic negative ions: structure, dynamics and collisions.
Physics Reports, 394(4-5), 157-313.
`doi:10.1016/j.physrep.2004.01.001 <http://www.dx.doi.org/10.1016/j.physrep.2004.01.001>`_
.. [10] Mann, J. B., Meek, T. L., & Allen, L. C. (2000). Configuration Energies of the
Main Group Elements. Journal of the American Chemical Society, 122(12),
2780-2783. `doi:10.1021/ja992866e <http://dx.doi.org/10.1021/ja992866e>`_
.. [11] Mann, J. B., Meek, T. L., Knight, E. T., Capitani, J. F., & Allen, L. C.
(2000). Configuration Energies of the d-Block Elements. Journal of the American
Chemical Society, 122(21), 5132-5137.
`doi:10.1021/ja9928677 <http://dx.doi.org/10.1021/ja9928677>`_
.. [12] Mulliken, R. S. (1934). A New Electroaffinity Scale; Together with Data on
Valence States and on Valence Ionization Potentials and Electron Affinities.
The Journal of Chemical Physics, 2(11), 782.
`doi:10.1063/1.1749394 <http://dx.doi.org/10.1063/1.1749394>`_
.. [13] `NIST Atomic Database <http://physics.nist.gov/cgi-bin/ASD/ie.pl>`_
accessed on April 13, 2015
.. [14] Shannon, R. D. (1976). Revised effective ionic radii and systematic
studies of interatomic distances in halides and chalcogenides.
Acta Crystallographica Section A.
`doi:10.1107/S0567739476001551 <http://www.dx.doi.org/10.1107/S0567739476001551>`_
.. [15] Clementi, E., & Raimondi, D. L. (1963). Atomic Screening Constants from
SCF Functions. The Journal of Chemical Physics, 38(11), 2686.
`doi:10.1063/1.1733573 <http://www.dx.doi.org/10.1063/1.1733573>`_
.. [16] Clementi, E. (1967). Atomic Screening Constants from SCF Functions. II.
Atoms with 37 to 86 Electrons. The Journal of Chemical Physics, 47(4), 1300.
`doi:10.1063/1.1712084 <http://www.dx.doi.org/10.1063/1.1712084>`_
.. [17] Batsanov, S. S. (2001). Van der Waals radii of elements. Inorganic Materials,
37(9), 871-885.
`doi:10.1023/A:1011625728803 <http://www.dx.doi.org/10.1023/A:1011625728803>`_
.. [18] Bondi, A. (1964). van der Waals Volumes and Radii. The Journal of Physical
Chemistry, 68(3), 441-451.
`doi:10.1021/j100785a001 <http://www.dx.doi.org/10.1021/j100785a001>`_
.. [19] Mayo, S. L., Olafson, B. D., & Goddard, W. A. (1990). DREIDING: a generic force
field for molecular simulations. The Journal of Physical Chemistry, 94(26), 8897-8909.
`doi:10.1021/j100389a010 <http://www.dx.doi.org/10.1021/j100389a010>`_
.. [20] Allinger, N. L., Zhou, X., & Bergsma, J. (1994). Molecular mechanics
parameters. Journal of Molecular Structure: THEOCHEM, 312(1), 69-83.
`doi:10.1016/S0166-1280(09)80008-0 <http://www.dx.doi.org/10.1016/S0166-1280(09)80008-0>`_
.. [21] Rowland, R. S., & Taylor, R. (1996). Intermolecular Nonbonded Contact Distances
in Organic Crystal Structures: Comparison with Distances Expected from van der
Waals Radii. The Journal of Physical Chemistry, 100(18), 7384-7391.
`doi:10.1021/jp953141+ <http://www.dx.doi.org/10.1021/jp953141+>`_
.. [22] Mantina, M., Chamberlin, A. C., Valero, R., Cramer, C. J., & Truhlar, D. G.
(2009). Consistent van der Waals Radii for the Whole Main Group. The Journal of
Physical Chemistry A, 113(19), 5806-5812.
`doi:10.1021/jp8111556 <http://dx.doi.org/10.1021/jp8111556>`_
.. [23] Rappe, A. K., Casewit, C. J., Colwell, K. S., Goddard, W. A., & Skiff, W. M.
(1992). UFF, a full periodic table force field for molecular mechanics and
molecular dynamics simulations. Journal of the American Chemical Society,
114(25), 10024-10035.
`doi:10.1021/ja00051a040 <http://www.dx.doi.org/10.1021/ja00051a040>`_
.. [24] `CPK colors <https://en.wikipedia.org/wiki/CPK_coloring>`_
.. [25] `Jmol colors <http://jmol.sourceforge.net/jscolors/#color_U>`_
.. [26] `MOLCAS GV colors <http://www.molcas.org/GV/>`_
.. [27] R. T. Sanderson, Chemical Bonds and Bond Energy, Academic Press, New York,
1976, ISBN: 0-12-618060-1
.. [28] Allen, L. C., & Huheey, J. E. (1980). The definition of electronegativity and
the chemistry of the noble gases. Journal of Inorganic and Nuclear Chemistry,
42(10), 1523-1524. doi:10.1016/0022-1902(80)80132-1
.. [29] Luo, Z., Chen, X., Li, J., & Ning, C. (2016). Precision measurement of
the electron affinity of niobium. Physical Review A, 93(2), 020501.
`doi:10.1103/PhysRevA.93.020501 <http://dx.doi.org/10.1103/PhysRevA.93.020501>`_

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

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
Element(
annotation=u'',
atomic_number=14,
atomic_radius=132.0,
atomic_volume=12.1,
block=u'p',
boiling_point=2628.0,
covalent_radius_2008=111.00000000000001,
covalent_radius_2009=115.99999999999999,
density=2.33,
description=u"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.",
dipole_polarizability=37.31,
ec=1s2 2s2 2p6 3s2 3p2,
econf=u'[Ne] 3s2 3p2',
electron_affinity=1.3895211,
en_allen=11.33,
en_pauling=1.9,
evaporation_heat=383.0,
fusion_heat=50.6,
group_id=14,
lattice_constant=5.43,
lattice_structure=u'DIA',
mass=28.0855,
melting_point=u'1683',
name=u'Silicon',
period=3,
specific_heat=0.703,
symbol=u'Si',
thermal_conductivity=149.0,
vdw_radius=210.0,
)

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
=============

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

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

Citing
======

If you use *mendeleev* in a scientific publication, please cite the software as

| L. M. Mentel, *mendeleev*, 2014. Available at: `https://bitbucket.org/lukaszmentel/mendeleev <https://bitbucket.org/lukaszmentel/mendeleev>`_.


Funding
=======

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


.. include:: LICENSE.rst

.. include:: CHANGES.rst