sisl.geom.AtomXYZ

class sisl.geom.AtomXYZ

Bases: AtomCategory

Classify atoms based on coordinates

Parameters:

  • *args (Shape) – any shape that implements Shape.within

  • **kwargs –

    keys are operator specifications and values are used in those specifications. The keys are split into 3 sections <options>_<direction>_<operator>

    • options are made of combinations of ['a', 'f'] i.e. "af", "f" or "a" are all valid. An a takes the absolute value, f means a fractional coordinate. This part is optional.

    • direction is anything that gets parsed in sisl.utils.misc.direction either one of {0, "X", "x", "a", 1, "Y", "y", "b", 2, "Z", "z", "c"}.

    • operator is a name for an operator defined in the operator module.

    For instance a_z_lt=3. will be equivalent to the boolean operation np.fabs(geometry.xyz[:, 2]) < 3..

    Optionally one need not specify the operator in which case one should provide an argument of two values.

    For instance c=(3., 6.) will be equivalent to the boolean operation 3. <= geometry.xyz[:, 2]) <= 6..

x, y, z, fx, fy, fz, ax, ay, az

Shortcuts for creating an AtomXYZ category.

AtomXYZ.x(-2, 3) == AtomXYZ(x=(-2, 3))
AtomXYZ.fx < 3 == AtomXYZ.fx(None, 3) == AtomXYZ(f_x=(None, 3)) == AtomXYZ(f_x_lt=3)
Type:

AtomCategory

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
ax

alias of Atomax

ay

alias of Atomay

az

alias of Atomaz

fx

alias of Atomfx

fy

alias of Atomfy

fz

alias of Atomfz

x

alias of Atomx

y

alias of Atomy

z

alias of Atomz

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