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 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

Attributes

`_Z_int`
`_Z_short`
`__dict__`
`__doc__`
`__module__`
`__weakref__`	list of weak references to the object (if defined)
`_atomic_mass`
`_radius_calc`
`_radius_empirical`
`_radius_vdw`

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
`__delattr__`	Implement delattr(self, name).
`__dir__`	Default dir() implementation.
`__eq__`	Return self==value.
`__format__`	Default object formatter.
`__ge__`	Return self>=value.
`__getattribute__`	Return getattr(self, name).
`__gt__`	Return self>value.
`__hash__`	Return hash(self).
`__init__`	Initialize self.
`__init_subclass__`	This method is called when a class is subclassed.
`__le__`	Return self<=value.
`__lt__`	Return self<value.
`__ne__`	Return self!=value.
`__new__`	Create and return a new object.
`__reduce__`	Helper for pickle.
`__reduce_ex__`	Helper for pickle.
`__repr__`	Return repr(self).
`__setattr__`	Implement setattr(self, name, value).
`__sizeof__`	Size of object in memory, in bytes.
`__str__`	Return str(self).
`__subclasshook__`	Abstract classes can override this to customize issubclass().
`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: 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 (array_like 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 (array_like 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 (array_like 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 (array_like 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

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

atomic radius in Ang

Return type

numpy.ndarray or float

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

atomic radius in Ang

Return type

numpy.ndarray or float