PeriodicTable

class sisl.PeriodicTable

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 accesible:

• atomic mass (in atomic units)

• empirical atomic radii (in Ang)

• calculated atomic radii (in Ang)

• van der Waals atomic radii (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().radii('Carbon')
True
>>> .67 == PeriodicTable().radii(6,'calc')
True
>>> .7  == PeriodicTable().radii(6,'empirical')
True
>>> 1.7 == PeriodicTable().radii(6,'vdw')
True

Methods

Z(self, key)	Atomic number based on general input
Z_int(self, key)	Atomic number based on general input
Z_label(self, key)	Atomic label of the corresponding atom
Z_short(self, key)	Atomic label of the corresponding atom
__init__(self, /, \*args, \*\*kwargs)	Initialize self.
atomic_mass(self, key)	Atomic mass of the corresponding atom
radii(self, key[, method])	Atomic radii using different methods
radius(self, key[, method])	Atomic radii using different methods

Z(self, key)

Atomic number based on general input

Return the atomic number corresponding to the key lookup.

Parameters

keyarray_like or str or int

Uses value to lookup the atomic number in the PeriodicTable object.

Returns

numpy.ndarray or int

atomic number corresponding to key, if key is array_like, so will the returned value be.

Examples

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

Z_int(self, key)

Atomic number based on general input

Return the atomic number corresponding to the key lookup.

Parameters

keyarray_like or str or int

Uses value to lookup the atomic number in the PeriodicTable object.

Returns

numpy.ndarray or int

atomic number corresponding to key, if key is array_like, so will the returned value be.

Examples

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

Z_label(self, key)

Atomic label of the corresponding atom

Return the atomic short name corresponding to the key lookup.

Parameters

keyarray_like or str or int

Uses value to lookup the atomic short name in the PeriodicTable object.

Returns

numpy.ndarray or str

atomic short name corresponding to key, if key is array_like, so will the returned value be.

Z_short(self, key)

Atomic label of the corresponding atom

Return the atomic short name corresponding to the key lookup.

Parameters

keyarray_like or str or int

Uses value to lookup the atomic short name in the PeriodicTable object.

Returns

numpy.ndarray or str

atomic short name corresponding to key, if key is array_like, so will the returned value be.

atomic_mass(self, key)

Atomic mass of the corresponding atom

Return the atomic mass corresponding to the key lookup.

Parameters

keyarray_like or str or int

Uses value to lookup the atomic mass in the PeriodicTable object.

Returns

numpy.ndarray or float

atomic mass in atomic units corresponding to key, if key is array_like, so will the returned value be.

radii(self, key, method='calc')

Atomic radii using different methods

Return the atomic radii.

Parameters

keyarray_like 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 radii

2. empirical, the empirically found values

3. vdw, the van-der-Waals found values

Returns

numpy.ndarray or float

atomic radius in Ang

radius(self, key, method='calc')

Atomic radii using different methods

Return the atomic radii.

Parameters

keyarray_like 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 radii

2. empirical, the empirically found values

3. vdw, the van-der-Waals found values

Returns

numpy.ndarray or float

atomic radius in Ang