httk.atomistic.species
======================

.. py:module:: httk.atomistic.species

.. autoapi-nested-parse::

   Species definition for httk-atomistic, mirroring the OPTIMADE ``species`` entry.



Classes
-------

.. autoapisummary::

   httk.atomistic.species.Species


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

.. py:class:: Species

   A chemical species occupying one or more sites, mirroring the OPTIMADE ``species`` object.

   A species has a ``name`` (unique within a structure; it need not be a chemical
   symbol), a list of ``chemical_symbols`` composing it, and a matching list of
   ``concentration`` values. Each chemical symbol is an element symbol, or one of
   the pseudo-symbols ``"X"`` (unknown) or ``"vacancy"``. The optional ``mass``,
   ``attached``, ``nattached``, and ``original_name`` fields carry the remaining
   OPTIMADE species information; ``attached`` and ``nattached`` must be given
   together and share their length.


   .. py:attribute:: name
      :type:  str


   .. py:attribute:: chemical_symbols
      :type:  tuple[str, Ellipsis]


   .. py:attribute:: concentration
      :type:  tuple[float, Ellipsis]


   .. py:attribute:: mass
      :type:  tuple[float, Ellipsis] | None
      :value: None



   .. py:attribute:: original_name
      :type:  str | None
      :value: None



   .. py:attribute:: attached
      :type:  tuple[str, Ellipsis] | None
      :value: None



   .. py:attribute:: nattached
      :type:  tuple[int, Ellipsis] | None
      :value: None



   .. py:property:: is_single_element
      :type: bool


      Whether this species is a single, unattached, real chemical element.

      True only for a species composed of exactly one element symbol (not ``"X"``
      or ``"vacancy"``) with no attached particles. Such species are the ones that
      can be represented as a bare atomic number in the primitive representation.


   .. py:method:: create(obj: Species | dict[str, Any]) -> Species
      :classmethod:


      Return a Species from either an existing Species (returned unchanged) or an OPTIMADE species dict.