# Mesh refinement in dolfinx **URL:** \ **Category:** dolfinx\ **Created:** [July 14, 2023, 7:19am UTC](https://fenicsproject.discourse.group/t/mesh-refinement-in-dolfinx/11733 "2023-07-14T07:19:29Z")\ **Posts on this page:** 5\ **Page:** 1
**Author:** ![SvenH](https://avatars.discourse-cdn.com/v4/letter/s/eb8c5e/32.png) [@SvenH](https://fenicsproject.discourse.group/u/SvenH)\ **Post date:** [July 14, 2023, 7:19am UTC](https://fenicsproject.discourse.group/t/mesh-refinement-in-dolfinx/11733/1 "2023-07-14T07:19:29Z")
Hi everyone, I need help translating some legacy dolfin code to dolfinx (0.6.0). The code is about marking cells depending on the value of the cell midpoint of function cn1\_ and then refine all cells that are marked. This was my approach in legacy dolfin: ```auto cell_markers = MeshFunction("bool", mesh_initial, mesh_initial.topology().dim()) cell_markers.set_all(False) for cell in cells(mesh_initial): if cn1_(cell.midpoint()) > 0.01 and cn1_(cell.midpoint()) < 0.99: cell_markers[cell] = True mesh = refine(mesh_initial, cell_markers) ``` any help is greatly appreciated. Best regards, Sven ---
**Author:** ![dokken](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/dokken/32/1560_2.png) [@dokken](https://fenicsproject.discourse.group/u/dokken)\ **Post date:** [July 14, 2023, 7:39am UTC](https://fenicsproject.discourse.group/t/mesh-refinement-in-dolfinx/11733/2 "2023-07-14T07:39:38Z")
Consider the following code, that avoids loops in Python by using vectorized numpy operations and DOLFINx functions (written in C++) ```python import dolfinx from mpi4py import MPI import numpy as np def cell_criterion(x): """Given mesh coordinates, return if each point satisfies x[0]<0.3 or x[1]>0.4 :param x: Input coordinates, shape (num_points, 3) :returns: Boolean array of shape (num_points, ) """ return (x[0] < 0.3) | (x[1] > 0.4) mesh = dolfinx.mesh.create_unit_square(MPI.COMM_WORLD, 10, 10) # Compute midpoints for all cells on process cells_local = np.arange(mesh.topology.index_map( mesh.topology.dim).size_local, dtype=np.int32) midpoints = dolfinx.mesh.compute_midpoints( mesh, mesh.topology.dim, cells_local).T # Check midpoint criterion and find edges connected to cells should_refine = np.flatnonzero(cell_criterion(midpoints)).astype(np.int32) mesh.topology.create_entities(1) local_edges = dolfinx.mesh.compute_incident_entities( mesh, should_refine, mesh.topology.dim, 1) refined_mesh = dolfinx.mesh.refine(mesh, local_edges) with dolfinx.io.XDMFFile(refined_mesh.comm, "refined_mesh.xdmf", "w") as xdmf: xdmf.write_mesh(refined_mesh) ``` giving the mesh ![image](https://global.discourse-cdn.com/free1/uploads/fenicsproject1/original/2X/c/c288eb674de94b4b34d734aa414db97ab7336be1.png) ---
**Author:** ![SvenH](https://avatars.discourse-cdn.com/v4/letter/s/eb8c5e/32.png) [@SvenH](https://fenicsproject.discourse.group/u/SvenH)\ **Post date:** [July 11, 2024, 9:27am UTC](https://fenicsproject.discourse.group/t/mesh-refinement-in-dolfinx/11733/3 "2024-07-11T09:27:49Z")
This approach gives the following error in version v.0.8.0: ```python Traceback (most recent call last): File "/root/shared/refinement_dolfinx_test.py", line 27, in local_edges = dolfinx.mesh.compute_incident_entities( File "/usr/local/dolfinx-real/lib/python3.10/dist-packages/dolfinx/mesh.py", line 216, in compute_incident_entities return _cpp.mesh.compute_incident_entities(topology, entities, d0, d1) TypeError: compute_incident_entities(): incompatible function arguments. The following argument types are supported: 1. compute_incident_entities(mesh: dolfinx.cpp.mesh.Topology, entities: ndarray[dtype=int32, writable=False, shape=(*), order='C'], d0: int, d1: int) -> numpy.ndarray[dtype=int32,] Invoked with types: dolfinx.mesh.Mesh, ndarray, int, int ``` ---
**Author:** ![francesco-ballarin](https://avatars.discourse-cdn.com/v4/letter/f/f05b48/32.png) [@francesco-ballarin](https://fenicsproject.discourse.group/u/francesco-ballarin)\ **Post date:** [July 11, 2024, 1:02pm UTC](https://fenicsproject.discourse.group/t/mesh-refinement-in-dolfinx/11733/4 "2024-07-11T13:02:29Z")
Please read the error message carefully, as it was surely giving an hint on how to proceed: the first input argument is a mesh, while it was supposed to be a `Topology` object. `mesh.topology` is used all over the place in the code, so a simple guess would have been to replace `mesh` with `mesh.topology`. The updated code is (changes highlighted with my initials FB) ```auto import dolfinx from mpi4py import MPI import numpy as np def cell_criterion(x): """Given mesh coordinates, return if each point satisfies x[0]<0.3 or x[1]>0.4 :param x: Input coordinates, shape (num_points, 3) :returns: Boolean array of shape (num_points, ) """ return (x[0] < 0.3) | (x[1] > 0.4) mesh = dolfinx.mesh.create_unit_square(MPI.COMM_WORLD, 10, 10) # Compute midpoints for all cells on process cells_local = np.arange(mesh.topology.index_map( mesh.topology.dim).size_local, dtype=np.int32) mesh.topology.create_connectivity(mesh.topology.dim, mesh.topology.dim) # FB: ADDED HERE midpoints = dolfinx.mesh.compute_midpoints( mesh, mesh.topology.dim, cells_local).T # Check midpoint criterion and find edges connected to cells should_refine = np.flatnonzero(cell_criterion(midpoints)).astype(np.int32) mesh.topology.create_entities(1) local_edges = dolfinx.mesh.compute_incident_entities( mesh.topology, should_refine, mesh.topology.dim, 1) # FB: CHANGED HERE refined_mesh = dolfinx.mesh.refine(mesh, local_edges) with dolfinx.io.XDMFFile(refined_mesh.comm, "refined_mesh.xdmf", "w") as xdmf: xdmf.write_mesh(refined_mesh) ``` ---
**Author:** ![SvenH](https://avatars.discourse-cdn.com/v4/letter/s/eb8c5e/32.png) [@SvenH](https://fenicsproject.discourse.group/u/SvenH)\ **Post date:** [July 11, 2024, 1:31pm UTC](https://fenicsproject.discourse.group/t/mesh-refinement-in-dolfinx/11733/5 "2024-07-11T13:31:05Z")
I appreciate the help, thank you!