Python Lattice.get_cartesian_coords方法代码示例

# 需要导入模块: from pymatgen.core import Lattice [as 别名]
# 或者: from pymatgen.core.Lattice import get_cartesian_coords [as 别名]
    def __mul__(self, scaling_matrix):
        """
        Replicates the graph, creating a supercell,
        intelligently joining together
        edges that lie on periodic boundaries.
        In principle, any operations on the expanded
        graph could also be done on the original
        graph, but a larger graph can be easier to
        visualize and reason about.
        :param scaling_matrix: same as Structure.__mul__
        :return:
        """

        # Developer note: a different approach was also trialed, using
        # a simple Graph (instead of MultiDiGraph), with node indices
        # representing both site index and periodic image. Here, the
        # number of nodes != number of sites in the Structure. This
        # approach has many benefits, but made it more difficult to
        # keep the graph in sync with its corresponding Structure.

        # Broadly, it would be easier to multiply the Structure
        # *before* generating the StructureGraph, but this isn't
        # possible when generating the graph using critic2 from
        # charge density.

        # Multiplication works by looking for the expected position
        # of an image node, and seeing if that node exists in the
        # supercell. If it does, the edge is updated. This is more
        # computationally expensive than just keeping track of the
        # which new lattice images present, but should hopefully be
        # easier to extend to a general 3x3 scaling matrix.

        # code adapted from Structure.__mul__
        scale_matrix = np.array(scaling_matrix, np.int16)
        if scale_matrix.shape != (3, 3):
            scale_matrix = np.array(scale_matrix * np.eye(3), np.int16)
        else:
            # TODO: test __mul__ with full 3x3 scaling matrices
            raise NotImplementedError('Not tested with 3x3 scaling matrices yet.')
        new_lattice = Lattice(np.dot(scale_matrix, self.structure.lattice.matrix))

        f_lat = lattice_points_in_supercell(scale_matrix)
        c_lat = new_lattice.get_cartesian_coords(f_lat)

        new_sites = []
        new_graphs = []

        for v in c_lat:

            # create a map of nodes from original graph to its image
            mapping = {n: n + len(new_sites) for n in range(len(self.structure))}

            for idx, site in enumerate(self.structure):

                s = PeriodicSite(site.species_and_occu, site.coords + v,
                                 new_lattice, properties=site.properties,
                                 coords_are_cartesian=True, to_unit_cell=False)

                new_sites.append(s)

            new_graphs.append(nx.relabel_nodes(self.graph, mapping, copy=True))

        new_structure = Structure.from_sites(new_sites)

        # merge all graphs into one big graph
        new_g = nx.MultiDiGraph()
        for new_graph in new_graphs:
            new_g = nx.union(new_g, new_graph)

        edges_to_remove = []  # tuple of (u, v, k)
        edges_to_add = []  # tuple of (u, v, attr_dict)

        # list of new edges inside supercell
        # for duplicate checking
        edges_inside_supercell = [{u, v} for u, v, d in new_g.edges(data=True)
                                  if d['to_jimage'] == (0, 0, 0)]
        new_periodic_images = []

        orig_lattice = self.structure.lattice

        # use k-d tree to match given position to an
        # existing Site in Structure
        kd_tree = KDTree(new_structure.cart_coords)

        # tolerance in Å for sites to be considered equal
        # this could probably be a lot smaller
        tol = 0.05

        for u, v, k, d in new_g.edges(keys=True, data=True):

            to_jimage = d['to_jimage']  # for node v

            # reduce unnecessary checking
            if to_jimage != (0, 0, 0):

                # get index in original site
                n_u = u % len(self.structure)
                n_v = v % len(self.structure)

                # get fractional co-ordinates of where atoms defined
#.........这里部分代码省略.........