sisl.PeriodicTable

class sisl.PeriodicTable

Bases: object

Periodic table for creating an Atom, or retrieval of atomic information via atomic numbers

Enables lookup of atomic numbers/names/labels to get the atomic number.

Several quantities available to the atomic species are available from <https://en.wikipedia.org/wiki/Atomic_radii_of_the_elements_(data_page)>.

The following values are accessible:

atomic mass (in atomic units)
empirical atomic radius (in Ang)
calculated atomic radius (in Ang)
van der Waals atomic radius (in Ang)

For certain species the above quantities are not available and a negative number is returned.

Examples

>>> 79 == PeriodicTable().Z('Au')
True
>>> 79 == PeriodicTable().Z_int('Au')
True
>>> 'Au' == PeriodicTable().Z_short(79)
True
>>> 'Au' == PeriodicTable().Z_label(79)
True
>>> 'Au' == PeriodicTable().Z_label('Gold')
True
>>> 12.0107 == PeriodicTable().atomic_mass('C')
True
>>> 12.0107 == PeriodicTable().atomic_mass(6)
True
>>> 12.0107 == PeriodicTable().atomic_mass('Carbon')
True
>>> .67 == PeriodicTable().radius('Carbon')
True
>>> .67 == PeriodicTable().radius(6,'calc')
True
>>> .7  == PeriodicTable().radius(6,'empirical')
True
>>> 1.7 == PeriodicTable().radius(6,'vdw')
True

Methods

`Z`(key)	Atomic number based on general input
`Z_int`(key)	Atomic number based on general input
`Z_label`(key)	Atomic label of the corresponding atom
`Z_short`(key)	Atomic label of the corresponding atom
`atomic_mass`(key)	Atomic mass of the corresponding atom
`radius`(key[, method])	Atomic radius using different methods

Z(key)[source]

Atomic number based on general input

Return the atomic number corresponding to the key lookup.

Parameters:: key (ndarray or str or int) – Uses value to lookup the atomic number in the PeriodicTable object.
Returns:: atomic number corresponding to key, if key is array_like, so will the returned value be.
Return type:: numpy.ndarray or int

Examples

>>> 79 == PeriodicTable().Z_int('Au')
True
>>> 79 == PeriodicTable().Z('Au')
True
>>> 6 == PeriodicTable().Z('Carbon')
True

Z_int(key)

Atomic number based on general input

Return the atomic number corresponding to the key lookup.

Parameters:: key (ndarray or str or int) – Uses value to lookup the atomic number in the PeriodicTable object.
Returns:: atomic number corresponding to key, if key is array_like, so will the returned value be.
Return type:: numpy.ndarray or int

Examples

>>> 79 == PeriodicTable().Z_int('Au')
True
>>> 79 == PeriodicTable().Z('Au')
True
>>> 6 == PeriodicTable().Z('Carbon')
True

Z_label(key)[source]

Atomic label of the corresponding atom

Return the atomic short name corresponding to the key lookup.

Parameters:: key (ndarray or str or int) – Uses value to lookup the atomic short name in the PeriodicTable object.
Returns:: atomic short name corresponding to key, if key is array_like, so will the returned value be.
Return type:: numpy.ndarray or str

Z_short(key)

Atomic label of the corresponding atom

Return the atomic short name corresponding to the key lookup.

Parameters:: key (ndarray or str or int) – Uses value to lookup the atomic short name in the PeriodicTable object.
Returns:: atomic short name corresponding to key, if key is array_like, so will the returned value be.
Return type:: numpy.ndarray or str

atomic_mass(key)[source]

Atomic mass of the corresponding atom

Return the atomic mass corresponding to the key lookup.

Parameters:: key (ndarray or str or int) – Uses value to lookup the atomic mass in the PeriodicTable object.
Returns:: atomic mass in atomic units corresponding to key, if key is array_like, so will the returned value be.
Return type:: numpy.ndarray or float

radius(key, method='calc')[source]

Atomic radius using different methods

Return the atomic radius.

Parameters:

key (ndarray or str or int) – Uses value to lookup the atomic mass in the PeriodicTable object.
method ({'calc', 'empirical', 'vdw'}) –
There are 3 different radii stored:
1. calc, the calculated atomic radius
2. empirical, the empirically found values
3. vdw, the van-der-Waals found values

Returns:

atomic radius in Ang

Return type:

numpy.ndarray or float