Update elasticity_scaling.md

.github/workflows/book_stable.yml

@@ -12,11 +12,12 @@ env:
   HDF5_DIR: "/usr/local/"
   DISPLAY: ":99.0"
   DEB_PYTHON_INSTALL_LAYOUT: deb_system
+  LIBGL_ALWAYS_SOFTWARE: 1
 
 jobs:
   build-book:
     runs-on: ubuntu-latest
-    container: ghcr.io/fenics/dolfinx/lab:v0.8.0
+    container: ghcr.io/fenics/dolfinx/lab:stable
 
     env:
       PYVISTA_TRAME_SERVER_PROXY_PREFIX: "/proxy/"
@@ -37,7 +38,7 @@ jobs:
         run: jupyter-book build . -W
 
       - uses: actions/upload-artifact@v4
-        if : always()
+        if: always()
         with:
           name: webpage
           path: ./_build/html

.github/workflows/deploy.yml

@@ -38,7 +38,7 @@ jobs:
         uses: actions/checkout@v4
 
       - name: Setup Pages
-        uses: actions/configure-pages@v4
+        uses: actions/configure-pages@v5
 
       - name: Download docs artifact
         uses: actions/download-artifact@v4

.github/workflows/publish_docker.yml

@@ -45,7 +45,7 @@ jobs:
           images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
 
       - name: Build Docker image
-        uses: docker/build-push-action@v5
+        uses: docker/build-push-action@v6
         with:
           context: .
           load: true
@@ -56,7 +56,7 @@ jobs:
           labels: ${{ steps.meta.outputs.labels }}
 
       - name: Build (arm) and push (amd/arm) Docker image
-        uses: docker/build-push-action@v5
+        uses: docker/build-push-action@v6
         if: github.event_name == 'push'
         with:
           context: .

.github/workflows/test_nightly.yml

@@ -24,6 +24,7 @@ jobs:
       PYVISTA_OFF_SCREEN: true
       DISPLAY: ":99.0"
       PYVISTA_JUPYTER_BACKEND: html
+      LIBGL_ALWAYS_SOFTWARE: 1
 
     steps:
       - uses: actions/checkout@v4
@@ -39,6 +40,9 @@ jobs:
       - 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 .
+
       - name: Test complex notebooks in parallel
         working-directory: chapter1
         run: |
@@ -67,7 +71,6 @@ jobs:
           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: |
@@ -77,7 +80,6 @@ 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: |

.github/workflows/test_stable.yml

@@ -10,17 +10,20 @@ env:
   HDF5_DIR: "/usr/local/"
   DISPLAY: ":99.0"
   DEB_PYTHON_INSTALL_LAYOUT: deb_system
+  LIBGL_ALWAYS_SOFTWARE: 1
 
 jobs:
   test:
     runs-on: ubuntu-latest
-    container: ghcr.io/fenics/dolfinx/lab:v0.8.0
+    container: ghcr.io/fenics/dolfinx/lab:stable
     env:
       PYVISTA_OFF_SCREEN: true
 
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
       - uses: actions/checkout@v4
+        with:
+          ref: release
 
       - uses: ./.github/actions/install-dependencies
 
@@ -33,30 +36,30 @@ 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: |
@@ -66,7 +69,7 @@ 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`

chapter2/elasticity_scaling.md

@@ -18,6 +18,6 @@ where $\beta = 1+\frac{\lambda}{\mu}$ is a dimensionless elasticity parameter an
 ```
 is a dimensionless variable reflecting the ratio of the load $\rho g$ and the shear stress term $\mu \nabla^2u \sim \mu \frac{U}{L^2}$ in the PDE.
 
-One option for the scaling is to chose $U$ such that $\gamma$ is of unit size ($U=\frac{\rho g L^2}{\mu}$). However, in elasticity, this leads to displacements of the size of the geometry. This can be achieved by choosing $U$ equal to the maximum deflection of a clamped beam, for which there actually exists a formula: $U=\frac{3}{2} \rho g L^2\frac{\delta^2}{E}$ where $\delta=\frac{L}{W}$ is a parameter reflecting how slender the beam is, and $E$ is the modulus of elasticity. Thus the dimensionless parameter $\delta$ is very important in the problem (as expected $\delta\gg 1$ is what gives beam theory!). Taking $E$ to be of the same order as $\mu$, which in this case and for many materials, we realize that $\gamma \sim \delta^{-2}$ is an appropriate choice. Experimenting with the code to find a displacement that "looks right" in the plots of the deformed geometry, points to $\gamma=0.4\delta^{-2}$ as our final choice of $\gamma$.
+One option for the scaling is to choose $U$ such that $\gamma$ is of unit size ($U=\frac{\rho g L^2}{\mu}$). However, in elasticity, this leads to displacements of the size of the geometry. This can be achieved by choosing $U$ equal to the maximum deflection of a clamped beam, for which there actually exists a formula: $U=\frac{3}{2} \rho g L^2\frac{\delta^2}{E}$ where $\delta=\frac{L}{W}$ is a parameter reflecting how slender the beam is, and $E$ is the modulus of elasticity. Thus the dimensionless parameter $\delta$ is very important in the problem (as expected $\delta\gg 1$ is what gives beam theory!). Taking $E$ to be of the same order as $\mu$, which in this case and for many materials, we realize that $\gamma \sim \delta^{-2}$ is an appropriate choice. Experimenting with the code to find a displacement that "looks right" in the plots of the deformed geometry, points to $\gamma=0.4\delta^{-2}$ as our final choice of $\gamma$.
 
-The simulation code implements the problem with dimensions and physical parameters $\lambda, \mu, \rho, g, L$ and $W$. However, we can easily reuse this code for a scaled problem: Just set $\mu=\rho=L=1$, $W$ as $W/L(\delta^{-1})$, $g=\gamma$ and $\lambda=\beta$.
+The simulation code implements the problem with dimensions and physical parameters $\lambda, \mu, \rho, g, L$ and $W$. However, we can easily reuse this code for a scaled problem: Just set $\mu=\rho=L=1$, $W$ as $W/L(\delta^{-1})$, $g=\gamma$ and $\lambda=\beta$.

chapter2/ns_code2.ipynb

@@ -651,6 +651,7 @@
     "            if pressure is not None:\n",
     "                p_diff[i] -= pressure[0]\n",
     "                break\n",
+    "progress.close()\n",
     "vtx_u.close()\n",
     "vtx_p.close()"
    ]

chapter2/ns_code2.py

@@ -478,6 +478,7 @@ def __call__(self, x):
             if pressure is not None:
                 p_diff[i] -= pressure[0]
                 break
+progress.close()
 vtx_u.close()
 vtx_p.close()
 

chapter4/compiler_parameters.ipynb

@@ -50,7 +50,7 @@
    "id": "2",
    "metadata": {},
    "source": [
-    "Next we generate a general function to assemble the mass matrix for a unit cube. Note that we use `dolfinx.fem.Form` to compile the variational form. For codes using `dolfinx.LinearProblem`, you can supply `jit_options` as a keyword argument."
+    "Next we generate a general function to assemble the mass matrix for a unit cube. Note that we use `dolfinx.fem.form` to compile the variational form. For codes using `dolfinx.fem.petsc.LinearProblem`, you can supply `jit_options` as a keyword argument."
    ]
   },
   {

chapter4/compiler_parameters.py

@@ -46,7 +46,7 @@
 print(f"Directory to put C files in: {cache_dir}")
 # -
 
-# Next we generate a general function to assemble the mass matrix for a unit cube. Note that we use `dolfinx.fem.Form` to compile the variational form. For codes using `dolfinx.LinearProblem`, you can supply `jit_options` as a keyword argument.
+# Next we generate a general function to assemble the mass matrix for a unit cube. Note that we use `dolfinx.fem.form` to compile the variational form. For codes using `dolfinx.fem.petsc.LinearProblem`, you can supply `jit_options` as a keyword argument.
 
 # +
 

fem.md

@@ -40,13 +40,13 @@ The tutorial uses several dependencies for meshing, plotting and timings. A comp
 To use the notebooks in this tutorial with DOLFINx on your own computer, you should use the docker image obtained using the following command:
 
 ```bash
-  docker run --init -p 8888:8888 -v "$(pwd)":/root/shared ghcr.io/jorgensd/dolfinx-tutorial:v0.7.2
+  docker run --init -p 8888:8888 -v "$(pwd)":/root/shared ghcr.io/jorgensd/dolfinx-tutorial:release
 ```
 
 This image can also be used as a normal docker container by adding:
 
 ```bash
-  docker run --ti -v "$(pwd)":/root/shared  --entrypoint="/bin/bash" ghcr.io/jorgensd/dolfinx-tutorial:v0.7.2
+  docker run --ti -v "$(pwd)":/root/shared  --entrypoint="/bin/bash" ghcr.io/jorgensd/dolfinx-tutorial:release
 ```
 
 The tutorials can also be exported as an IPython notebook or PDF by clicking the ![Download](save.png)-symbol in the top right corner of the relevant tutorial. The notebook can in turn be used with a Python kernel which has DOLFINx.
@@ -58,7 +58,7 @@ The [Dockerfile](https://github.com/FEniCS/dolfinx/blob/main/docker/Dockerfile)
 provides a definitive build recipe. As the DOLFINx docker images are hosted at Docker-hub, one can directly access the image using:
 
 ```bash
-docker run dolfinx/dolfinx:v0.8.0
+docker run dolfinx/dolfinx:stable
 ```
 
 There are several ways of customizing a docker container, such as mounting volumes/sharing folder, setting a working directory, sharing graphical interfaces etc. See `docker run --help` for an extensive list.