Merge branch 'main' into release

.github/actions/install-dependencies/action.yml

@@ -3,8 +3,7 @@ name: Install dependencies
 runs:
   using: composite
   steps:
-      - name: Install apt dependencies and upgrade pip
-        shell: bash -el {0}
-        run: |
-          apt-get update && apt-get install -y libgl1-mesa-glx libxrender1 xvfb
-          python3 -m pip install -U pip
+    - name: Install apt dependencies and upgrade pip
+      shell: bash -el {0}
+      run: |
+        apt-get update && apt-get install -y libxrender1 xvfb

.github/workflows/publish_docker.yml

@@ -54,12 +54,10 @@ jobs:
           platforms: linux/amd64
           tags: ${{ steps.meta.outputs.tags }}
           labels: ${{ steps.meta.outputs.labels }}
-
-
 
       - name: Build (arm) and push (amd/arm) Docker image
         uses: docker/build-push-action@v5
-        if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
+        if: github.event_name == 'push'
         with:
           context: .
           push: true

.github/workflows/test_nightly.yml

@@ -32,7 +32,12 @@ jobs:
         uses: ./.github/actions/install-dependencies
 
       - name: Install requirements
-        run: python3 -m pip install --no-cache-dir --no-binary=h5py . --upgrade
+        run: |
+          python3 -m pip install --break-system-packages -U pip setuptools pkgconfig
+          python3 -m pip install --no-build-isolation --break-system-packages --no-cache-dir --no-binary=h5py . --upgrade
+
+      - name: Test building the book
+        run: PYVISTA_OFF_SCREEN=false jupyter-book build  -W .
 
       - name: Test building the book
         run: PYVISTA_OFF_SCREEN=false jupyter-book build  -W .
@@ -42,30 +47,29 @@ jobs:
         run: |
           export PKG_CONFIG_PATH=/usr/local/dolfinx-complex/lib/pkgconfig:$PKG_CONFIG_PATH
           export PETSC_ARCH=linux-gnu-complex128-32
-          export PYTHONPATH=/usr/local/dolfinx-complex/lib/python3.10/dist-packages:$PYTHONPATH
+          export PYTHONPATH=/usr/local/dolfinx-complex/lib/python3.12/dist-packages:$PYTHONPATH
           export LD_LIBRARY_PATH=/usr/local/dolfinx-complex/lib:$LD_LIBRARY_PATH
           python3 complex_mode.py
           mpirun -n 2 python3 complex_mode.py
 
       - name: Test chapter 1
         working-directory: chapter1
         run: |
-            python3 -c "from pyvista import start_xvfb; start_xvfb(0.1)"
-            mpirun -n 2 python3 fundamentals_code.py
-            mpirun -n 2 python3 nitsche.py
-            mpirun -n 2 python3 membrane_code.py
+          python3 -c "from pyvista import start_xvfb; start_xvfb(0.1)"
+          mpirun -n 2 python3 fundamentals_code.py
+          mpirun -n 2 python3 nitsche.py
+          mpirun -n 2 python3 membrane_code.py
 
       - name: Test chapter 2
         working-directory: chapter2
-        run: |    
+        run: |
           mpirun -n 2 python3 diffusion_code.py
           mpirun -n 2 python3 heat_code.py
           mpirun -n 2 python3 linearelasticity_code.py
           mpirun -n 2 python3 hyperelasticity.py
           mpirun -n 2 python3 nonlinpoisson_code.py
           mpirun -n 2 python3 ns_code1.py
           mpirun -n 2 python3 ns_code2.py
-       
       - name: Test chapter 3
         working-directory: chapter3
         run: |
@@ -75,7 +79,6 @@ jobs:
           mpirun -n 2 python3 robin_neumann_dirichlet.py
           mpirun -n 2 python3 component_bc.py
           mpirun -n 2 python3 em.py
-  
       - name: Test chapter 4
         working-directory: chapter4
         run: |

Changelog.md

@@ -1,5 +1,10 @@
 # Changelog
 
+## v0.9.0
+
+- `scale` in `apply_lifting` has been renamed to `alpha`
+- Use `dolfinx.fem.Function.x.petsc_vec` as opposed to `dolfinx.fem.Function.vector`
+
 ## v0.8.0
 
 - Replace all `ufl.FiniteElement` and `ufl.VectorElement` with the appropriate `basix.ufl.element`

Dockerfile

@@ -1,4 +1,4 @@
-FROM ghcr.io/jorgensd/dolfinx-tutorial:v0.7.2
+FROM ghcr.io/jorgensd/dolfinx-tutorial:release
 
 # create user with a home directory
 ARG NB_USER=jovyan

chapter1/complex_mode.ipynb

@@ -39,19 +39,10 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "id": "b52b39d9-260d-4c54-b62a-7440c3b92e5a",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "float64\n",
-      "complex128\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "from mpi4py import MPI\n",
     "import dolfinx\n",
@@ -80,18 +71,10 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "id": "4d5b03e3-4d7f-45b7-95eb-9130a5141f34",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "<class 'numpy.complex128'>\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "from petsc4py import PETSc\n",
     "from dolfinx.fem.petsc import assemble_vector\n",
@@ -110,7 +93,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": null,
    "id": "be8461a0-a089-4ff3-8bc8-61b016407e70",
    "metadata": {},
    "outputs": [],
@@ -137,19 +120,10 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": null,
    "id": "779ab267-4609-4628-9577-a280b9c18b6d",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "{ c_0 * (conj((v_0))) } * dx(<Mesh #0>[everywhere], {})\n",
-      "{ c_0 * (conj((v_0))) } * dx(<Mesh #0>[everywhere], {})\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "L2 = f * ufl.conj(v) * ufl.dx\n",
     "print(L)\n",
@@ -166,78 +140,10 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": null,
    "id": "d61c477a-d364-4a81-9362-42f1eb4cd8ee",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "[4.21666667e-03+3.33333333e-05j 1.58750000e-03+8.33333333e-06j\n",
-      " 4.68333333e-03+1.00000000e-04j 8.13333333e-03+2.66666667e-04j\n",
-      " 3.35000000e-03+3.33333333e-05j 4.68333333e-03+3.66666667e-04j\n",
-      " 6.43333333e-03+2.66666667e-04j 8.13333333e-03+8.66666667e-04j\n",
-      " 2.58333333e-03+3.33333333e-05j 4.68333333e-03+8.33333333e-04j\n",
-      " 4.93333333e-03+2.66666667e-04j 6.43333333e-03+8.66666667e-04j\n",
-      " 8.13333333e-03+1.86666667e-03j 1.91666667e-03+3.33333333e-05j\n",
-      " 4.68333333e-03+1.50000000e-03j 3.63333333e-03+2.66666667e-04j\n",
-      " 4.93333333e-03+8.66666667e-04j 6.43333333e-03+1.86666667e-03j\n",
-      " 8.13333333e-03+3.26666667e-03j 1.35000000e-03+3.33333333e-05j\n",
-      " 4.68333333e-03+2.36666667e-03j 2.53333333e-03+2.66666667e-04j\n",
-      " 3.63333333e-03+8.66666667e-04j 4.93333333e-03+1.86666667e-03j\n",
-      " 6.43333333e-03+3.26666667e-03j 8.13333333e-03+5.06666667e-03j\n",
-      " 8.83333333e-04+3.33333333e-05j 4.68333333e-03+3.43333333e-03j\n",
-      " 1.63333333e-03+2.66666667e-04j 2.53333333e-03+8.66666667e-04j\n",
-      " 3.63333333e-03+1.86666667e-03j 4.93333333e-03+3.26666667e-03j\n",
-      " 6.43333333e-03+5.06666667e-03j 8.13333333e-03+7.26666667e-03j\n",
-      " 5.16666667e-04+3.33333333e-05j 4.68333333e-03+4.70000000e-03j\n",
-      " 9.33333333e-04+2.66666667e-04j 1.63333333e-03+8.66666667e-04j\n",
-      " 2.53333333e-03+1.86666667e-03j 3.63333333e-03+3.26666667e-03j\n",
-      " 4.93333333e-03+5.06666667e-03j 6.43333333e-03+7.26666667e-03j\n",
-      " 8.13333333e-03+9.86666667e-03j 2.50000000e-04+3.33333333e-05j\n",
-      " 4.68333333e-03+6.16666667e-03j 4.33333333e-04+2.66666667e-04j\n",
-      " 9.33333333e-04+8.66666667e-04j 1.63333333e-03+1.86666667e-03j\n",
-      " 2.53333333e-03+3.26666667e-03j 3.63333333e-03+5.06666667e-03j\n",
-      " 4.93333333e-03+7.26666667e-03j 6.43333333e-03+9.86666667e-03j\n",
-      " 8.13333333e-03+1.28666667e-02j 8.33333333e-05+3.33333333e-05j\n",
-      " 4.68333333e-03+7.83333333e-03j 1.33333333e-04+2.66666667e-04j\n",
-      " 4.33333333e-04+8.66666667e-04j 9.33333333e-04+1.86666667e-03j\n",
-      " 1.63333333e-03+3.26666667e-03j 2.53333333e-03+5.06666667e-03j\n",
-      " 3.63333333e-03+7.26666667e-03j 4.93333333e-03+9.86666667e-03j\n",
-      " 6.43333333e-03+1.28666667e-02j 8.13333333e-03+1.62666667e-02j\n",
-      " 1.25000000e-05+2.50000000e-05j 3.09583333e-03+6.19166667e-03j\n",
-      " 1.66666667e-05+1.66666667e-04j 1.33333333e-04+8.66666667e-04j\n",
-      " 4.33333333e-04+1.86666667e-03j 9.33333333e-04+3.26666667e-03j\n",
-      " 1.63333333e-03+5.06666667e-03j 2.53333333e-03+7.26666667e-03j\n",
-      " 3.63333333e-03+9.86666667e-03j 4.93333333e-03+1.28666667e-02j\n",
-      " 6.43333333e-03+1.62666667e-02j 3.91666667e-03+9.36666667e-03j\n",
-      " 1.66666667e-05+5.00000000e-04j 1.33333333e-04+1.86666667e-03j\n",
-      " 4.33333333e-04+3.26666667e-03j 9.33333333e-04+5.06666667e-03j\n",
-      " 1.63333333e-03+7.26666667e-03j 2.53333333e-03+9.86666667e-03j\n",
-      " 3.63333333e-03+1.28666667e-02j 4.93333333e-03+1.62666667e-02j\n",
-      " 3.08333333e-03+9.36666667e-03j 1.66666667e-05+1.03333333e-03j\n",
-      " 1.33333333e-04+3.26666667e-03j 4.33333333e-04+5.06666667e-03j\n",
-      " 9.33333333e-04+7.26666667e-03j 1.63333333e-03+9.86666667e-03j\n",
-      " 2.53333333e-03+1.28666667e-02j 3.63333333e-03+1.62666667e-02j\n",
-      " 2.35000000e-03+9.36666667e-03j 1.66666667e-05+1.76666667e-03j\n",
-      " 1.33333333e-04+5.06666667e-03j 4.33333333e-04+7.26666667e-03j\n",
-      " 9.33333333e-04+9.86666667e-03j 1.63333333e-03+1.28666667e-02j\n",
-      " 2.53333333e-03+1.62666667e-02j 1.71666667e-03+9.36666667e-03j\n",
-      " 1.66666667e-05+2.70000000e-03j 1.33333333e-04+7.26666667e-03j\n",
-      " 4.33333333e-04+9.86666667e-03j 9.33333333e-04+1.28666667e-02j\n",
-      " 1.63333333e-03+1.62666667e-02j 1.18333333e-03+9.36666667e-03j\n",
-      " 1.66666667e-05+3.83333333e-03j 1.33333333e-04+9.86666667e-03j\n",
-      " 4.33333333e-04+1.28666667e-02j 9.33333333e-04+1.62666667e-02j\n",
-      " 7.50000000e-04+9.36666667e-03j 1.66666667e-05+5.16666667e-03j\n",
-      " 1.33333333e-04+1.28666667e-02j 4.33333333e-04+1.62666667e-02j\n",
-      " 4.16666667e-04+9.36666667e-03j 1.66666667e-05+6.70000000e-03j\n",
-      " 1.33333333e-04+1.62666667e-02j 1.83333333e-04+9.36666667e-03j\n",
-      " 1.66666667e-05+8.43333333e-03j 5.00000000e-05+9.36666667e-03j\n",
-      " 4.16666667e-06+3.17500000e-03j]\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "J = u_c**2 * ufl.dx\n",
     "F = ufl.derivative(J, u_c, ufl.conj(v))\n",
@@ -256,7 +162,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": null,
    "id": "eb2357ae-ac71-4407-bf37-432f1b1e31d0",
    "metadata": {},
    "outputs": [],
@@ -281,18 +187,10 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": null,
    "id": "f51d9a7a-2cde-4d0f-8606-91f91c372c4b",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "(0.0007865435216227239+0.0017660156338113711j) 3.553078358632328e-06\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "x = ufl.SpatialCoordinate(mesh)\n",
     "u_ex = 0.5 * x[0]**2 + 1j*x[1]**2\n",
@@ -322,6 +220,7 @@
    "source": [
     "import pyvista\n",
     "pyvista.start_xvfb()\n",
+    "mesh.topology.create_connectivity(mesh.topology.dim, mesh.topology.dim)\n",
     "p_mesh = pyvista.UnstructuredGrid(*dolfinx.plot.vtk_mesh(mesh, mesh.topology.dim))\n",
     "pyvista_cells, cell_types, geometry = dolfinx.plot.vtk_mesh(V)\n",
     "grid = pyvista.UnstructuredGrid(pyvista_cells, cell_types, geometry)\n",

chapter1/complex_mode.py

@@ -126,6 +126,7 @@
 
 import pyvista
 pyvista.start_xvfb()
+mesh.topology.create_connectivity(mesh.topology.dim, mesh.topology.dim)
 p_mesh = pyvista.UnstructuredGrid(*dolfinx.plot.vtk_mesh(mesh, mesh.topology.dim))
 pyvista_cells, cell_types, geometry = dolfinx.plot.vtk_mesh(V)
 grid = pyvista.UnstructuredGrid(pyvista_cells, cell_types, geometry)

chapter1/fundamentals_code.ipynb

@@ -453,6 +453,7 @@
    "source": [
     "from dolfinx import plot\n",
     "pyvista.start_xvfb()\n",
+    "domain.topology.create_connectivity(tdim, tdim)\n",
     "topology, cell_types, geometry = plot.vtk_mesh(domain, tdim)\n",
     "grid = pyvista.UnstructuredGrid(topology, cell_types, geometry)"
    ]

chapter1/fundamentals_code.py

@@ -232,6 +232,7 @@
 # + vscode={"languageId": "python"}
 from dolfinx import plot
 pyvista.start_xvfb()
+domain.topology.create_connectivity(tdim, tdim)
 topology, cell_types, geometry = plot.vtk_mesh(domain, tdim)
 grid = pyvista.UnstructuredGrid(topology, cell_types, geometry)
 # -

chapter1/membrane_code.ipynb

@@ -338,7 +338,7 @@
    "metadata": {},
    "source": [
     "Now we can compute which cells the bounding box tree collides with using `dolfinx.geometry.compute_collisions_points`. This function returns a list of cells whose bounding box collide for each input point. As different points might have different number of cells, the data is stored in `dolfinx.cpp.graph.AdjacencyList_int32`, where one can access the cells for the `i`th point by calling `links(i)`.\n",
-    "However, as the bounding box of a cell spans more of $\\mathbb{R}^n$ than the actual cell, we check that the actual cell collides with cell\n",
+    "However, as the bounding box of a cell spans more of $\\mathbb{R}^n$ than the actual cell, we check that the actual cell collides with the input point\n",
     "using `dolfinx.geometry.select_colliding_cells`, which measures the exact distance between the point and the cell (approximated as a convex hull for higher order geometries).\n",
     "This function also returns an adjacency-list, as the point might align with a facet, edge or vertex that is shared between multiple cells in the mesh.\n",
     "\n",

chapter1/membrane_code.py

@@ -171,7 +171,7 @@ def on_boundary(x):
 bb_tree = geometry.bb_tree(domain, domain.topology.dim)
 
 # Now we can compute which cells the bounding box tree collides with using `dolfinx.geometry.compute_collisions_points`. This function returns a list of cells whose bounding box collide for each input point. As different points might have different number of cells, the data is stored in `dolfinx.cpp.graph.AdjacencyList_int32`, where one can access the cells for the `i`th point by calling `links(i)`.
-# However, as the bounding box of a cell spans more of $\mathbb{R}^n$ than the actual cell, we check that the actual cell collides with cell
+# However, as the bounding box of a cell spans more of $\mathbb{R}^n$ than the actual cell, we check that the actual cell collides with the input point
 # using `dolfinx.geometry.select_colliding_cells`, which measures the exact distance between the point and the cell (approximated as a convex hull for higher order geometries).
 # This function also returns an adjacency-list, as the point might align with a facet, edge or vertex that is shared between multiple cells in the mesh.
 #

chapter2/diffusion_code.ipynb

@@ -24,7 +24,6 @@
    "outputs": [],
    "source": [
     "import matplotlib as mpl\n",
-    "import matplotlib.pyplot as plt\n",
     "import pyvista\n",
     "import ufl\n",
     "import numpy as np\n",

chapter2/diffusion_code.py

@@ -27,7 +27,6 @@
 
 # +
 import matplotlib as mpl
-import matplotlib.pyplot as plt
 import pyvista
 import ufl
 import numpy as np

chapter2/ns_code1.ipynb

@@ -579,6 +579,7 @@
     "glyphs = function_grid.glyph(orient=\"u\", factor=0.2)\n",
     "\n",
     "# Create a pyvista-grid for the mesh\n",
+    "mesh.topology.create_connectivity(mesh.topology.dim, mesh.topology.dim)\n",
     "grid = pyvista.UnstructuredGrid(*vtk_mesh(mesh, mesh.topology.dim))\n",
     "\n",
     "# Create plotter\n",

chapter2/ns_code1.py

@@ -345,6 +345,7 @@ def u_exact(x):
 glyphs = function_grid.glyph(orient="u", factor=0.2)
 
 # Create a pyvista-grid for the mesh
+mesh.topology.create_connectivity(mesh.topology.dim, mesh.topology.dim)
 grid = pyvista.UnstructuredGrid(*vtk_mesh(mesh, mesh.topology.dim))
 
 # Create plotter

chapter3/em.ipynb

@@ -1077,8 +1077,10 @@
    "source": [
     "pyvista.start_xvfb()\n",
     "plotter = pyvista.Plotter()\n",
-    "grid = pyvista.UnstructuredGrid(*vtk_mesh(mesh, mesh.topology.dim))\n",
-    "num_local_cells = mesh.topology.index_map(mesh.topology.dim).size_local\n",
+    "tdim = mesh.topology.dim\n",
+    "mesh.topology.create_connectivity(tdim, tdim)\n",
+    "grid = pyvista.UnstructuredGrid(*vtk_mesh(mesh, tdim))\n",
+    "num_local_cells = mesh.topology.index_map(tdim).size_local\n",
     "grid.cell_data[\"Marker\"] = ct.values[ct.indices < num_local_cells]\n",
     "grid.set_active_scalars(\"Marker\")\n",
     "actor = plotter.add_mesh(grid, show_edges=True)\n",
@@ -1288,6 +1290,7 @@
     "# We include ghosts cells as we access all degrees of freedom (including ghosts) on each process\n",
     "top_imap = mesh.topology.index_map(mesh.topology.dim)\n",
     "num_cells = top_imap.size_local + top_imap.num_ghosts\n",
+    "mesh.topology.create_connectivity(mesh.topology.dim, mesh.topology.dim)\n",
     "midpoints = compute_midpoints(mesh, mesh.topology.dim, np.arange(num_cells, dtype=np.int32))\n",
     "\n",
     "num_dofs = W.dofmap.index_map.size_local + W.dofmap.index_map.num_ghosts\n",