sisl.geom.AtomIndex

class sisl.geom.AtomIndex

Bases: AtomCategory

Classify atoms based on indices

Parameters:

  • *args (int or list of int) – each value will be equivalent to in=set(args)

  • **kwargs (key, value) – if key is a function it must accept two values value, atom where value is the value on this command. The function should return anything that can be interpreted as a True/False. Multiple key equates to an and statement.

Examples

>>> aidx = AtomIndex(1, 4, 5)
>>> geom.sub(aidx) == geom.sub([1, 4, 5])
>>> aidx = AtomIndex(mod=2) # odd indices
>>> geom.sub(aidx) == geom.sub(range(1, len(geom), 2))
>>> aidx = ~AtomIndex(mod=2) # even indices
>>> geom.sub(aidx) == geom.sub(range(0, len(geom), 2))
>>> aidx = ~AtomIndex(mod=3) # every 3rd atom
>>> geom.sub(aidx) == geom.sub(range(0, len(geom), 3))
>>> aidx = AtomIndex(mod=3) # [1, 2, 4, 5, ...]: range(na) - range(0, na, 3)
>>> geom.sub(aidx) == geom.sub(range(0, len(geom), 3))

Methods

categorize(geometry[, atoms])

Do categorization

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

categorize(geometry, atoms=None)[source]

Do categorization

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