httk.atomistic.structure
========================

.. py:module:: httk.atomistic.structure

.. autoapi-nested-parse::

   The Simple structure representation for httk-atomistic.



Classes
-------

.. autoapisummary::

   httk.atomistic.structure.Structure


Module Contents
---------------

.. py:class:: Structure(cell: httk.atomistic.cell_like.CellLike, sites: httk.atomistic.sites_like.SitesLike, species: collections.abc.Sequence[httk.atomistic.species_like.SpeciesLike], species_at_sites: collections.abc.Sequence[str])

   A crystal structure in the Simple representation.

   A Structure holds a ``cell`` (a ``Cell`` of 3x3 cell vectors), ``sites`` (a ``Sites``
   of Nx3 reduced coordinates), a list of ``species`` (each a ``Species``), and a
   length-N ``species_at_sites`` giving the species name occupying each site. Inputs are
   normalized on construction through the component families: the cell, sites, and each
   species are passed through their ``*Like`` unions, and every ``species_at_sites`` name
   must match one of the (uniquely named) species.

   The numeric model is exact and split by purpose. The fractional frame — reduced coordinates
   and symmetry — is rational and lives in ``sites`` as a :class:`~httk.core.FracVector`. The
   Cartesian frame — where radicals such as the hexagonal ``sqrt(3)`` appear — is exact in the
   squarefree-radical field: ``cell.basis`` is a :class:`~httk.core.SurdVector` and
   :meth:`cartesian_sites` returns the exact Cartesian positions. Pure magnitudes (bond-length
   comparisons) stay rational-exact via ``cell.metric()``. Floats appear only at the presentation
   and JSON boundaries.


   .. py:property:: cell
      :type: httk.atomistic.cell.Cell


      The cell (3x3 cell vectors) as a ``Cell``.


   .. py:property:: sites
      :type: httk.atomistic.sites.Sites


      The site coordinates (Nx3 reduced coordinates) as a ``Sites``.


   .. py:property:: species
      :type: tuple[httk.atomistic.species.Species, Ellipsis]


      The distinct species of this structure.


   .. py:property:: species_at_sites
      :type: tuple[str, Ellipsis]


      The species name occupying each site, in site order.


   .. py:method:: cartesian_sites() -> httk.core.SurdVector

      The exact Cartesian site positions as an ``(N, 3)`` :class:`~httk.core.SurdVector`.

      Under the row-vector convention this is ``reduced_coords * cell.basis`` (each Cartesian
      position is the sum over lattice vectors ``sum_k reduced[k] * basis[k]``). The reduced
      coordinates are rational (a ``FracVector``), the cell basis carries the radicals (a
      ``SurdVector``), so the product is exact in the surd field — the hexagonal ``sqrt(3)``
      survives into the Cartesian positions.



   .. py:method:: numeric() -> httk.atomistic.numeric_structure.NumericStructure

      A plain-numpy presentation of this structure (requires the ``httk-atomistic[numpy]`` extra).