sisl.geom.AtomFracSite

class sisl.geom.AtomFracSite

Bases: AtomCategory

Classify atoms based on fractional sites for a given supercell

Match atomic coordinates based on the fractional positions.

Parameters:

  • lattice – an object that defines the lattice vectors.

  • atol – the absolute tolerance (in Ang) to check whether the site is an integer site.

  • offset – an offset made to the geometry coordinates before calculating the fractional coordinates according to lattice

  • foffset – fractional offset of the fractional coordinates, this allows to select sub-regions in the lattice lattice vectors.

Examples

>>> gr = graphene() * (4, 5, 1)
>>> A_site = AtomFracSite(graphene())
>>> B_site = AtomFracSite(graphene(), foffset=(-1/3, -1/3, 0))
>>> cat = (A_site | B_site).categorize(gr)
>>> for ia, c in enumerate(cat):
...    if ia % 2 == 0:
...        assert c == A_site
...    else:
...        assert c == B_site

Methods

categorize(geometry[, atoms])

Do categorization

is_class(name[, case])

Query whether name matches the class name by removing a prefix kw

kw(**kwargs)

Create categories based on keywords

Attributes

name

Name of category
categorize(geometry, atoms=None)[source]

Do categorization

Parameters:
classmethod is_class(name, case=True)

Query whether name matches the class name by removing a prefix kw

This is important to ensure that users match the full class name by omitting the prefix returned from this method.

This is an abstract method to ensure sub-classes of Category implements it.

For instance:

class MyCategory(Category):

    @classmethod
    def is_class(cls, name):
         # strip "My" and do comparison
         return cl.__name__.lower()[2:] == name.lower()

would enable one to compare against the base category scheme.

This has the option to search case-sensitivity or not.

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.

property name

Name of category