PeriodicTable

class sisl.PeriodicTable[source]

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(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
radii(key[, method]) Atomic radii using different methods
radius(key[, method]) Atomic radii using different methods
Z(key)[source]

Atomic number based on general input

Return the atomic number corresponding to the key lookup.

Parameters:
key : array_like or str or int

Uses value to lookup the atomic number in the PeriodicTable object.
Returns:
Z : ndarray or int

The 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(key)

Atomic number based on general input

Return the atomic number corresponding to the key lookup.

Parameters:
key : array_like or str or int

Uses value to lookup the atomic number in the PeriodicTable object.
Returns:
Z : ndarray or int

The 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(key)[source]

Atomic label of the corresponding atom

Return the atomic short name corresponding to the key lookup.

Parameters:
key : array_like or str or int

Uses value to lookup the atomic short name in the PeriodicTable object.
Returns:
name : ndarray or str

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

Atomic label of the corresponding atom

Return the atomic short name corresponding to the key lookup.

Parameters:
key : array_like or str or int

Uses value to lookup the atomic short name in the PeriodicTable object.
Returns:
name : ndarray or str

The atomic short name corresponding to key, if key is array_like, so will the returned value be.
atomic_mass(key)[source]

Atomic mass of the corresponding atom

Return the atomic mass corresponding to the key lookup.

Parameters:
key : array_like or str or int

Uses value to lookup the atomic mass in the PeriodicTable object.
Returns:
name : ndarray or float

The atomic mass in atomic units corresponding to key, if key is array_like, so will the returned value be.
radii(key, method='calc')

Atomic radii using different methods

Return the atomic radii.

Parameters:
key : array_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:
radius : ndarray or float

The atomic radius in Ang
radius(key, method='calc')[source]

Atomic radii using different methods

Return the atomic radii.

Parameters:
key : array_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:
radius : ndarray or float

The atomic radius in Ang