httk.atomistic.models.sites.sites

The Sites class for httk-atomistic.

Classes

Sites

The sites of a crystal structure: the Nx3 matrix of reduced coordinates, held exactly.

Module Contents

class httk.atomistic.models.sites.sites.Sites(reduced_coords, precision=None)

Bases: httk.atomistic.models.sites.backend.SitesBackend

The sites of a crystal structure: the Nx3 matrix of reduced coordinates, held exactly.

Reduced (fractional) coordinates are the symmetry-native frame: point-group operations are integer matrices and translations are rationals, so no radicals ever appear. They are therefore stored as an exact rational FracVector of shape (N, 3). A Sites object is iterable and indexable over its length-3 coordinate rows (each a FracVector), with len giving the number of sites.

Inputs embed exactly: rationals (and rational-valued floats), rational strings, and numpy arrays all land on their exact rational value. An irrational SurdVector input is rejected; the exact Cartesian frame — where radicals belong — is obtained instead via cartesian_sites().

Parameters:

• reduced_coords (httk.core.VectorLike) – The reduced coordinates, one site per row.

• precision (Any) – The fractional precision carried from the source, if known.

property reduced_coords: httk.core.FracVector

The Nx3 reduced site coordinates as an exact FracVector (one site per row).

property precision: fractions.Fraction | None

How precisely these coordinates were stated, in fractional units, or None.

Fractional and therefore dimensionless: reduced coordinates are fractions of a cell edge, and a Sites carries no cell to convert with. Use cartesian_precision() for the corresponding length, which is the number an interatomic tolerance or an spglib symprec actually wants.

It is the coarsest precision among the coordinates, since a structure is only as precisely stated as its least precisely stated number. None means unknown.

Returns:

The fractional precision, or None when unknown.

Return type:

fractions.Fraction | None

numeric()

Return a plain-numpy presentation of these sites.

Returns:

The numpy-backed presentation.

Raises:

ImportError – If numpy is unavailable.

Return type:

httk.atomistic.models.sites.numeric.NumericSites