Merge remote-tracking branch 'origin/main' into finsberg/deploy-pages

Author: finsberg

src/io4dolfinx/checkpointing.py

@@ -6,6 +6,7 @@
 
 from __future__ import annotations
 
+import inspect
 import typing
 from pathlib import Path
 from typing import Any
@@ -383,6 +384,7 @@ def read_mesh(
     read_from_partition: bool = False,
     backend_args: dict[str, Any] | None = None,
     backend: str = "adios2",
+    max_facet_to_cell_links: int = 2,
 ) -> dolfinx.mesh.Mesh:
     """
     Read an ADIOS2 mesh into DOLFINx.
@@ -395,6 +397,8 @@ def read_mesh(
         time: Time stamp associated with mesh
         read_from_partition: Read mesh with partition from file
         backend_args: List of arguments to reader backend
+        max_facet_to_cell_links: Maximum number of cells a facet
+            can be connected to.
     Returns:
         The distributed mesh
     """
@@ -432,9 +436,18 @@ def partitioner(comm: MPI.Intracomm, n, m, topo):
             else:
                 return partition_graph
     else:
-        partitioner = dolfinx.cpp.mesh.create_cell_partitioner(ghost_mode)
+        sig = inspect.signature(dolfinx.mesh.create_cell_partitioner)
+        part_kwargs = {}
+        if "max_facet_to_cell_links" in list(sig.parameters.keys()):
+            part_kwargs["max_facet_to_cell_links"] = max_facet_to_cell_links
+        partitioner = dolfinx.cpp.mesh.create_cell_partitioner(ghost_mode, **part_kwargs)
+
     return dolfinx.mesh.create_mesh(
-        comm, cells=dist_in_data.cells, x=dist_in_data.x, e=domain, partitioner=partitioner
+        comm,
+        cells=dist_in_data.cells,
+        x=dist_in_data.x,
+        e=domain,
+        partitioner=partitioner,
     )
 
 

src/io4dolfinx/readers.py

@@ -6,6 +6,7 @@
 
 from __future__ import annotations
 
+import inspect
 import pathlib
 import typing
 from pathlib import Path
@@ -149,6 +150,7 @@ def read_mesh_from_legacy_h5(
     group: str,
     cell_type: str = "tetrahedron",
     backend: str = "adios2",
+    max_facet_to_cell_links: int = 2,
 ) -> dolfinx.mesh.Mesh:
     """
     Read mesh from `h5`-file generated by legacy DOLFIN `HDF5File.write` or `XDMF.write_checkpoint`.
@@ -158,6 +160,10 @@ def read_mesh_from_legacy_h5(
         filename: Path to `h5` or `xdmf` file
         group: Name of mesh in `h5`-file
         cell_type: What type of cell type, by default tetrahedron.
+        backend: The IO backend to use when reading the mesh (must
+            support legacy mesh reading, e.g., "adios2").
+        max_facet_to_cell_links: Maximum number of cells a facet
+            can be connected to.
     """
     # Make sure we use the HDF5File and check that the file is present
     check_file_exists(filename)
@@ -175,9 +181,18 @@ def read_mesh_from_legacy_h5(
         shape=(mesh_geometry.shape[1],),
     )
     domain = ufl.Mesh(element)
+    sig = inspect.signature(dolfinx.mesh.create_mesh)
+    kwargs: dict[str, int] = {}
+    if "max_facet_to_cell_links" in list(sig.parameters.keys()):
+        kwargs["max_facet_to_cell_links"] = max_facet_to_cell_links
 
     return dolfinx.mesh.create_mesh(
-        comm=MPI.COMM_WORLD, cells=mesh_topology, x=mesh_geometry, e=domain
+        comm=MPI.COMM_WORLD,
+        cells=mesh_topology,
+        x=mesh_geometry,
+        e=domain,
+        partitioner=None,
+        **kwargs,
     )
 
 

tests/conftest.py

@@ -1,7 +1,5 @@
-import sys
 import typing
 from collections import ChainMap
-from unittest.mock import patch
 
 from mpi4py import MPI
 
@@ -36,15 +34,7 @@ def find_backends():
 
 @pytest.fixture(params=find_backends(), scope="function")
 def backend(request):
-    value = request.param
-    if value == "adios2":
-        # Mock h5py to test adios2 only
-        with patch.dict(sys.modules, {"h5py": None}):
-            yield value
-    else:
-        # Mock adios2 to test h5py only
-        with patch.dict(sys.modules, {"adios2": None}):
-            yield value
+    yield request.param
 
 
 @pytest.fixture(scope="module")

tests/test_mesh_writer.py

@@ -89,28 +89,28 @@ def test_mesh_read_writer(backend, encoder, suffix, ghost_mode, tmp_path, store_
     backend_args = None
     if backend == "adios2":
         backend_args = {"engine": encoder}
-
     write_mesh(
         file.with_suffix(suffix),
         mesh,
         store_partition_info=store_partition,
         backend_args=backend_args,
         backend=backend,
     )
+
     mesh.comm.Barrier()
     with dolfinx.io.XDMFFile(mesh.comm, xdmf_file.with_suffix(".xdmf"), "w") as xdmf:
         xdmf.write_mesh(mesh)
     mesh.comm.Barrier()
 
-    mesh_adios = read_mesh(
+    in_mesh = read_mesh(
         file.with_suffix(suffix),
         MPI.COMM_WORLD,
         ghost_mode=ghost_mode,
         read_from_partition=store_partition,
         backend_args=backend_args,
         backend=backend,
     )
-    mesh_adios.comm.Barrier()
+    in_mesh.comm.Barrier()
     if store_partition:
 
         def compute_distance_matrix(points_A, points_B, tol=1e-12):
@@ -120,7 +120,7 @@ def compute_distance_matrix(points_A, points_B, tol=1e-12):
             return distances < tol
 
         cell_map = mesh.topology.index_map(mesh.topology.dim)
-        new_cell_map = mesh_adios.topology.index_map(mesh_adios.topology.dim)
+        new_cell_map = in_mesh.topology.index_map(in_mesh.topology.dim)
         assert cell_map.size_local == new_cell_map.size_local
         assert cell_map.num_ghosts == new_cell_map.num_ghosts
         mesh.topology.create_connectivity(mesh.topology.dim, mesh.topology.dim)
@@ -129,10 +129,10 @@ def compute_distance_matrix(points_A, points_B, tol=1e-12):
             mesh.topology.dim,
             np.arange(cell_map.size_local + cell_map.num_ghosts, dtype=np.int32),
         )
-        mesh_adios.topology.create_connectivity(mesh_adios.topology.dim, mesh_adios.topology.dim)
+        in_mesh.topology.create_connectivity(in_mesh.topology.dim, in_mesh.topology.dim)
         new_midpoints = dolfinx.mesh.compute_midpoints(
-            mesh_adios,
-            mesh_adios.topology.dim,
+            in_mesh,
+            in_mesh.topology.dim,
             np.arange(new_cell_map.size_local + new_cell_map.num_ghosts, dtype=np.int32),
         )
         # Check that all points in owned by initial mesh is owned by the new mesh
@@ -156,27 +156,26 @@ def compute_distance_matrix(points_A, points_B, tol=1e-12):
     for i in range(mesh.topology.dim + 1):
         mesh.topology.create_entities(i)
         mesh_xdmf.topology.create_entities(i)
-        mesh_adios.topology.create_entities(i)
+        in_mesh.topology.create_entities(i)
         assert (
-            mesh_xdmf.topology.index_map(i).size_global
-            == mesh_adios.topology.index_map(i).size_global
+            mesh_xdmf.topology.index_map(i).size_global == in_mesh.topology.index_map(i).size_global
         )
 
     # Check that integration over different entities are consistent
     measures = (
         [ufl.ds, ufl.dx] if ghost_mode is dolfinx.mesh.GhostMode.none else [ufl.ds, ufl.dS, ufl.dx]
     )
     for measure in measures:
-        print(mesh_adios, mesh_adios.ufl_domain().ufl_coordinate_element())
-        c_adios = dolfinx.fem.assemble_scalar(dolfinx.fem.form(1 * measure(domain=mesh_adios)))
+        form = dolfinx.fem.form(1 * measure(domain=in_mesh))
+        c_adios = dolfinx.fem.assemble_scalar(form)
         c_ref = dolfinx.fem.assemble_scalar(dolfinx.fem.form(1 * measure(domain=mesh)))
         c_xdmf = dolfinx.fem.assemble_scalar(dolfinx.fem.form(1 * measure(domain=mesh_xdmf)))
         assert np.isclose(
-            mesh_adios.comm.allreduce(c_adios, MPI.SUM),
+            in_mesh.comm.allreduce(c_adios, MPI.SUM),
             mesh.comm.allreduce(c_xdmf, MPI.SUM),
         )
         assert np.isclose(
-            mesh_adios.comm.allreduce(c_adios, MPI.SUM),
+            in_mesh.comm.allreduce(c_adios, MPI.SUM),
             mesh.comm.allreduce(c_ref, MPI.SUM),
         )