sisl.geom.AtomNeighbors

class sisl.geom.AtomNeighbors

Bases: AtomCategory

Classify atoms based on number of neighbors

Parameters:

  • min (int, optional) – minimum number of neighbors

  • max (int) – maximum number of neighbors

  • neighbor (Category, optional) – a category the neighbor must be in to be counted

  • R (tuple, float, callable or None, optional) – Value passed to Geometry.close. tuple, directly passed and thus only neigbors within the tuple range are considered float, this will pass (0.01, R) and thus not count the atom itself. callable, the return value of this will be directly passed. If the callable returns a single float it will count the atom itself.

Examples

>>> AtomNeighbors(4) # 4 neighbors within (0.01, Geometry.maxR())
>>> AtomNeighbors(4, R=1.44) # 4 neighbors within (0.01, 1.44)
>>> AtomNeighbors(4, R=(1, 1.44)) # 4 neighbors within (1, Geometry.maxR())
>>> AtomNeighbors(4, R=lambda atom: (0.01, PeriodicTable().radius(atom.Z))) # 4 neighbors within (0.01, <>)

Methods

R(atom)

categorize(geometry[, atoms])

Check if geometry and atoms matches the neighbor criteria

is_class(name[, case])

Query whether name is one of the keywords of this class

kw(**kwargs)

Create categories based on keywords

mask(*args, **kwargs)

Boolean array which is true for the objects in this category

Attributes

name

Name of category
classmethod is_class(name, case=True)

Query whether name is one of the keywords of this class

The keywords are the key and aliases class arguments. Sub-classes may override this method for other matching rules.

Parameters:

  • name (str) – the keyword to match

  • case (bool) – whether the match is case-sensitive

Return type:

bool

classmethod kw(**kwargs)

Create categories based on keywords

This will search through the inherited classes and return and & category object for all keywords.

Since this is a class method one should use this on the base category class in the given section of the code.

Each keyword matches a sub-class through is_class, first case-sensitive, then case-insensitive. The value is passed to the matched class:

  • True creates it without arguments (odd=True),

  • a dict is passed as keyword arguments (odd={}),

  • anything else is passed as the single argument (Z="C").

Raises:

  • TypeError – if no keywords are given

  • ValueError – if a keyword matches no, or more than one, sub-class

R(atom)[source]
categorize(geometry, atoms=None)[source]

Check if geometry and atoms matches the neighbor criteria

Parameters:
mask(*args, **kwargs)

Boolean array which is true for the objects in this category

The arguments are the same as for categorize. The parts of a composite category share their calculations, e.g. the neighbor search of AtomNeighbors.

Returns:

1D boolean array, one value per categorized object.

Return type:

numpy.ndarray

property name

Name of category