Add support for Serendipity (order 2) coordinate elements

[jorgensd]

Adds the missing pieces for being able to use S2 (serendipity 2) elements as coordinate elements, and read the meshes to and from XDMF.
MWE

from mpi4py import MPI
import dolfinx
import numpy as np
import basix.ufl

filename = "serendipity.xdmf"

if MPI.COMM_WORLD.rank == 0:
    mesh = dolfinx.mesh.create_unit_square(MPI.COMM_SELF, 10, 12, cell_type=dolfinx.cpp.mesh.CellType.quadrilateral)
    #mesh = dolfinx.mesh.create_unit_cube(MPI.COMM_SELF, 3, 4,5  , cell_type=dolfinx.cpp.mesh.CellType.hexahedron)
    num_cells = mesh.topology.index_map(mesh.topology.dim).size_local
    mesh.topology.create_connectivity(1, mesh.topology.dim)

    edge_map = mesh.topology.index_map(1)
    num_edges_local = edge_map.size_local

    midpoints = dolfinx.mesh.compute_midpoints(mesh, 1, np.arange(num_edges_local, dtype=np.int32))

    org_nodes = mesh.geometry.x

    connectivity = mesh.geometry.dofmap
    num_edges_per_cell = dolfinx.cpp.mesh.cell_num_entities(mesh.topology.cell_type,1)
    new_connectivity = np.zeros((num_cells, connectivity.shape[1] + num_edges_per_cell ), dtype=np.int64)
    new_connectivity[:,:connectivity.shape[1]] = connectivity

    mesh.topology.create_connectivity(mesh.topology.dim, 1)
    c_to_e = mesh.topology.connectivity(mesh.topology.dim,1).array.copy().reshape(-1, num_edges_per_cell)
    node_offset = org_nodes.shape[0]
    c_to_e += node_offset
    new_connectivity[:,connectivity.shape[1]:] = c_to_e
    new_nodes = np.vstack([org_nodes, midpoints])[:,:mesh.geometry.dim]

    coord_el = basix.ufl.element(
    basix.ElementFamily.serendipity,
    mesh.basix_cell(),
    2,
    lagrange_variant=basix.LagrangeVariant.equispaced,
    dpc_variant=basix.DPCVariant.simplex_equispaced,
    shape=(mesh.geometry.dim,),
)

    new_mesh = dolfinx.mesh.create_mesh(MPI.COMM_SELF, new_connectivity, new_nodes, coord_el)


    new_coords = new_mesh.geometry.x
    new_coords[:, 0] += 0.2*np.sin(new_coords[:,1])
    new_coords[:, 1] += 0.1*np.cos(new_coords[:,0])
    import ufl
    print(dolfinx.fem.assemble_scalar(dolfinx.fem.form(1*ufl.dx(domain=new_mesh))))
    with dolfinx.io.XDMFFile(MPI.COMM_SELF, filename, "w") as xdmf:
        xdmf.write_mesh(new_mesh)

MPI.COMM_WORLD.Barrier()
with dolfinx.io.XDMFFile(MPI.COMM_WORLD, filename, "r") as xdmf:
    mesh2 = xdmf.read_mesh()

with dolfinx.io.XDMFFile(MPI.COMM_WORLD, "output.xdmf", "w") as xdmf:
    xdmf.write_mesh(mesh2)

2D:

3D: