pymatgen_diffusion/neb/full_path_mapper.py
def _get_pos_and_migration_path(self, u, v, w):
        """
        insert a single MigrationPath object on a graph edge
        Args:
          u (int): index of initial node
          v (int): index of final node
          w (int): index for multiple edges that share the same two nodes

        """
        edge = self.s_graph.graph[u][v][w]
        i_site = self.only_sites.sites[u]
        f_site = PeriodicSite(
            self.only_sites.sites[v].species,
            self.only_sites.sites[v].frac_coords + np.array(edge["to_jimage"]),
            lattice=self.only_sites.lattice,
        )
        # Positions might be useful for plotting
        edge["ipos"] = i_site.frac_coords
        edge["epos"] = f_site.frac_coords
        edge["ipos_cart"] = np.dot(i_site.frac_coords, self.only_sites.lattice.matrix)
        edge["epos_cart"] = np.dot(f_site.frac_coords, self.only_sites.lattice.matrix)

        edge["hop"] = MigrationPath(i_site, f_site, self.symm_structure)

        insert a single MigrationPath object on a graph edge
        Args:
          u (int): index of initial node
          v (int): index of final node
          w (int): index for multiple edges that share the same two nodes

        
insert a single MigrationPath object on a graph edge
insert a single MigrationPath object on a graph edge
def _get_pos_and_migration_path(self, u, v, w):
        edge = self.s_graph.graph[u][v][w]
        i_site = self.only_sites.sites[u]
        f_site = PeriodicSite(
            self.only_sites.sites[v].species,
            self.only_sites.sites[v].frac_coords + np.array(edge["to_jimage"]),
            lattice=self.only_sites.lattice,
        )
        edge["ipos"] = i_site.frac_coords
        edge["epos"] = f_site.frac_coords
        edge["ipos_cart"] = np.dot(i_site.frac_coords, self.only_sites.lattice.matrix)
        edge["epos_cart"] = np.dot(f_site.frac_coords, self.only_sites.lattice.matrix)
        edge["hop"] = MigrationPath(i_site, f_site, self.symm_structure)
def _get_pos_and_migration_path ( self , u , v , w ) : edge = self . s_graph . graph [ u ] [ v ] [ w ] i_site = self . only_sites . sites [ u ] f_site = PeriodicSite ( self . only_sites . sites [ v ] . species , self . only_sites . sites [ v ] . frac_coords + np . array ( edge [ "to_jimage" ] ) , lattice = self . only_sites . lattice , ) edge [ "ipos" ] = i_site . frac_coords edge [ "epos" ] = f_site . frac_coords edge [ "ipos_cart" ] = np . dot ( i_site . frac_coords , self . only_sites . lattice . matrix ) edge [ "epos_cart" ] = np . dot ( f_site . frac_coords , self . only_sites . lattice . matrix ) edge [ "hop" ] = MigrationPath ( i_site , f_site , self . symm_structure )
insert a single MigrationPath object on a graph edge
insert a single MigrationPath object on a graph edge
"""
        insert a single MigrationPath object on a graph edge
        Args:
          u (int): index of initial node
          v (int): index of final node
          w (int): index for multiple edges that share the same two nodes

        """ # Positions might be useful for plotting
self
u
index of initial node
index of initial node
v
index of final node
index of final node
w
index for multiple edges that share the same two nodes
index for multiple edges that share the same two nodes