Python Composition.items方法代码示例

# 需要导入模块: from pymatgen.core.composition import Composition [as 别名]
# 或者: from pymatgen.core.composition.Composition import items [as 别名]
class Site(collections.Mapping, collections.Hashable, PMGSONable):
    """
    A generalized *non-periodic* site. This is essentially a composition
    at a point in space, with some optional properties associated with it. A
    Composition is used to represent the atoms and occupancy, which allows for
    disordered site representation. Coords are given in standard cartesian
    coordinates.
    """

    position_atol = 1e-5

    def __init__(self, atoms_n_occu, coords, properties=None):
        """
        Create a *non-periodic* site.

        Args:
            atoms_n_occu: Species on the site. Can be:

                i.  A sequence of element / specie specified either as string
                    symbols, e.g. ["Li", "Fe2+", "P", ...] or atomic numbers,
                    e.g., (3, 56, ...) or actual Element or Specie objects.
                ii. List of dict of elements/species and occupancies, e.g.,
                    [{"Fe" : 0.5, "Mn":0.5}, ...]. This allows the setup of
                    disordered structures.
            coords: Cartesian coordinates of site.
            properties: Properties associated with the site as a dict, e.g.
                {"magmom": 5}. Defaults to None.
        """
        if isinstance(atoms_n_occu, collections.Mapping):
            self._species = Composition(atoms_n_occu)
            totaloccu = self._species.num_atoms
            if totaloccu > 1 + Composition.amount_tolerance:
                raise ValueError("Species occupancies sum to more than 1!")
            self._is_ordered = totaloccu == 1 and len(self._species) == 1
        else:
            self._species = Composition({get_el_sp(atoms_n_occu): 1})
            self._is_ordered = True

        self._coords = coords
        self._properties = properties if properties else {}

    @property
    def properties(self):
        """
        Returns a view of properties as a dict.
        """
        return {k: v for k, v in self._properties.items()}

    def __getattr__(self, a):
        #overriding getattr doens't play nice with pickle, so we
        #can't use self._properties
        p = object.__getattribute__(self, '_properties')
        if a in p:
            return p[a]
        raise AttributeError(a)

    def distance(self, other):
        """
        Get distance between two sites.

        Args:
            other: Other site.

        Returns:
            Distance (float)
        """
        return np.linalg.norm(other.coords - self.coords)

    def distance_from_point(self, pt):
        """
        Returns distance between the site and a point in space.

        Args:
            pt: Cartesian coordinates of point.

        Returns:
            Distance (float)
        """
        return np.linalg.norm(np.array(pt) - self._coords)

    @property
    def species_string(self):
        """
        String representation of species on the site.
        """
        if self._is_ordered:
            return list(self._species.keys())[0].__str__()
        else:
            sorted_species = sorted(self._species.keys())
            return ", ".join(["{}:{:.3f}".format(sp, self._species[sp])
                              for sp in sorted_species])

    @property
    def species_and_occu(self):
        """
        The species at the site, i.e., a Composition mapping type of
        element/species to occupancy.
        """
        return self._species

#.........这里部分代码省略.........