1. create list of Vertex which are referred by blocks only.
        2. sort vertex according to (x, y, z)
        3. assign sequence number for each Vertex
        4. sorted list is saved as self.valid_vertices

def assign_vertexid(self):
        """1. create list of Vertex which are referred by blocks only.
        2. sort vertex according to (x, y, z)
        3. assign sequence number for each Vertex
        4. sorted list is saved as self.valid_vertices
        """

        # gather 'uniq' names which are refferred by blocks
        validvnames = set()
        self.valid_vertices = []
        for b in self.blocks.values():
            for n in b.vnames:
                v = self.vertices[n]
                if v.name not in validvnames:
                    validvnames.update([v.name])
                    self.valid_vertices.append(v)

        self.valid_vertices = sorted(self.valid_vertices)
        for i, v in enumerate(self.valid_vertices):
            v.index = i