Merge pull request #44 from luca-heltai/dim-spacedim

Change the way dim and spacedim work.
luca-heltai · Jun 24, 2024 · 4ddff07 · 4ddff07
2 parents 6d00429 + 731b345
commit 4ddff07
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diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml
@@ -2,31 +2,44 @@ name: github-docker
 
 on: 
   push: 
-    branches: [main]
+    branches: [main, 'docker*']
 
 jobs:
   build-master-docker:
     runs-on: ubuntu-latest
     steps:          
       - name: Checkout code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
+
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v3
 
       - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v1
+        uses: docker/setup-buildx-action@v3
 
       - name: Login to DockerHub
         uses: docker/login-action@v1
         with:
           username: ${{ secrets.DOCKER_USERNAME }}
           password: ${{ secrets.DOCKER_PASSWORD }}
 
+      - name: Log in to the Container registry
+        uses: docker/login-action@v3
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
       - name: Build and push Docker image of master 
-        uses: docker/build-push-action@v3
+        uses: docker/build-push-action@v6
         with:
           context: ./docker/
           file: ./docker/Dockerfile.fsi-suite
           cache-from: type=registry,ref=heltai/dealii:vscode
           cache-to: type=inline
+          platforms: linux/arm64,linux/amd64
           push: true
-          tags: heltai/fsi-suite:latest
+          tags: |
+            heltai/fsi-suite:latest
+            ghr.io/${{ github.repository }}:latest
 
diff --git a/.vscode/settings.json b/.vscode/settings.json
@@ -86,27 +86,46 @@
         "random": "cpp",
         "codecvt": "cpp",
         "filesystem": "cpp",
-        "*.ipp": "cpp"
+        "*.ipp": "cpp",
+        "__bit_reference": "cpp",
+        "__config": "cpp",
+        "__hash_table": "cpp",
+        "__locale": "cpp",
+        "__node_handle": "cpp",
+        "__split_buffer": "cpp",
+        "__threading_support": "cpp",
+        "__tree": "cpp",
+        "__verbose_abort": "cpp",
+        "any": "cpp",
+        "charconv": "cpp",
+        "execution": "cpp",
+        "ios": "cpp",
+        "locale": "cpp",
+        "queue": "cpp",
+        "regex": "cpp",
+        "source_location": "cpp",
+        "span": "cpp",
+        "stack": "cpp"
     },
     "peacock.remoteColor": "#dd0531",
     "peacock.color": "#215732",
     "workbench.colorCustomizations": {
-        "activityBar.activeBackground": "#fa1b49",
+        "activityBar.activeBackground": "#2f7c47",
         "activityBar.activeBorder": "#155e02",
-        "activityBar.background": "#fa1b49",
+        "activityBar.background": "#2f7c47",
         "activityBar.foreground": "#e7e7e7",
         "activityBar.inactiveForeground": "#e7e7e799",
-        "activityBarBadge.background": "#155e02",
+        "activityBarBadge.background": "#422c74",
         "activityBarBadge.foreground": "#e7e7e7",
-        "sash.hoverBorder": "#fa1b49",
-        "statusBar.background": "#dd0531",
+        "sash.hoverBorder": "#2f7c47",
+        "statusBar.background": "#215732",
         "statusBar.foreground": "#e7e7e7",
-        "statusBarItem.hoverBackground": "#fa1b49",
-        "statusBarItem.remoteBackground": "#dd0531",
+        "statusBarItem.hoverBackground": "#2f7c47",
+        "statusBarItem.remoteBackground": "#215732",
         "statusBarItem.remoteForeground": "#e7e7e7",
-        "titleBar.activeBackground": "#dd0531",
+        "titleBar.activeBackground": "#215732",
         "titleBar.activeForeground": "#e7e7e7",
-        "titleBar.inactiveBackground": "#dd053199",
+        "titleBar.inactiveBackground": "#21573299",
         "titleBar.inactiveForeground": "#e7e7e799",
         "commandCenter.border": "#e7e7e799"
     },

diff --git a/README.md b/README.md
@@ -6,22 +6,23 @@ interaction problems: mathematical modeling and numerical approximation"**
 |  <!-- --> | <!-- --> |
 | -- | -- |
 | **Author** | Luca Heltai <luca.heltai@sissa.it> |
-| **GitHub Repository:** | https://github.com/luca-heltai/fsi-suite |
-| **GitHub Pages:** | https://luca-heltai.github.io/fsi-suite/ |
+| **GitHub Repository:** | <https://github.com/luca-heltai/fsi-suite> |
+| **GitHub Pages:** | <https://luca-heltai.github.io/fsi-suite/> |
 | **Licence:** | see the file [LICENCE.md](./LICENCE.md) |
+
 ## Course Introduction
 
 Fluid-structure interaction (FSI) refers to the multiphysics coupling between
-the laws that describe fluid dynamics and structural mechanics. 
+the laws that describe fluid dynamics and structural mechanics.
 
 This page collects the material that I have used for a course given at Kaust
-(https://www.kaust.edu.sa/en) during the spring semester of 2022. 
+(<https://www.kaust.edu.sa/en>) during the spring semester of 2022.
 
 The course covers three main topics: i) basics of continuum mechanics, ii)
 mathematical modeling of FSI problems, and iii) numerical implementations based
 on the finite element method. Theoretical lectures are backed up by applied
 laboratories based on the C++ language, using example codes developed with the
-open source finite element library deal.II (www.dealii.org). I cover basic
+open source finite element library deal.II (<www.dealii.org>). I cover basic
 principles of continuum mechanics, discuss Lagrangian, Eulerian, and Arbitrary
 Lagrangian-Eulerian formulations, and cover different coupling strategies, both
 from the theoretical point of view, and with the aid of computational
@@ -32,8 +33,8 @@ finite element approximations for the solution of continuum mechanics problems,
 including non-linear mechanics, computational fluid dynamics, and
 fluid-structure-interaction problems.
 
-A glimpse of the PDEs that are discussed in the course is given by the following 
-graph 
+A glimpse of the PDEs that are discussed in the course is given by the following
+graph
 
 @dotfile serial.dot width=100%
 
@@ -42,7 +43,7 @@ graph
 The laboratory part should enable a PhD student working on numerical analysis
 of PDEs to implement state-of-the-art adaptive finite element codes for FSI
 problems, that run in parallel, using modern C++ libraries. The implementation
-are based on the `deal.II` library (www.dealii.org).
+are based on the `deal.II` library (<www.dealii.org>).
 
 Main topics covered by these lectures:
 
@@ -57,27 +58,27 @@ Main topics covered by these lectures:
 Continuous Integration Status
 -----------------------------
 
-Up to date online documentation for the codes used in the laboratories is here: 
+Up to date online documentation for the codes used in the laboratories is here:
 
-https://luca-heltai.github.io/fsi-suite/
+<https://luca-heltai.github.io/fsi-suite/>
 
 | System |  Status |
-| ------ | ------- | 
+| ------ | ------- |
 | **Continous Integration**  | [![GitHub CI](https://github.com/luca-heltai/fsi-suite/actions/workflows/tests.yml/badge.svg)](https://github.com/luca-heltai/fsi-suite/actions/workflows/tests.yml)   |
 | **Docker** |  [![github-docker](https://github.com/luca-heltai/fsi-suite/actions/workflows/docker.yml/badge.svg)](https://github.com/luca-heltai/fsi-suite/actions/workflows/docker.yml) |
 | **Doxygen**  | [![Doxygen](https://github.com/luca-heltai/fsi-suite/actions/workflows/doxygen.yml/badge.svg)](https://github.com/luca-heltai/fsi-suite/actions/workflows/doxygen.yml) |
 | **Indent** | [![Indent](https://github.com/luca-heltai/fsi-suite/actions/workflows/indentation.yml/badge.svg)](https://github.com/luca-heltai/fsi-suite/actions/workflows/indentation.yml) |
 
-
 ## Useful links
 
 One of my courses on theory and practice of finite elements:
-- https://www.math.sissa.it/course/phd-course/theory-and-practice-finite-element-methods
+
+- <https://www.math.sissa.it/course/phd-course/theory-and-practice-finite-element-methods>
 
 Exceptional video lectures by Prof. Wolfgang Bangerth, that cover all the
 things you will ever need for finite element programming.
 
-- https://www.math.colostate.edu/~bangerth/videos.html
+- <https://www.math.colostate.edu/~bangerth/videos.html>
 
 ## Quick start
 
@@ -94,23 +95,23 @@ you should see the following output:
 
     Will run program-name with program-options, possibly via mpirun, passing -np N to mpirun.
     Here is a list of programs you can run:
-    linear_elasticity.g	 mpi_stokes.g
-    distributed_lagrange	mesh_handler		 poisson
-    distributed_lagrange.g	mesh_handler.g		 poisson.g
-    dof_plotter		mpi_linear_elasticity	 reduced_lagrange
-    dof_plotter.g		mpi_linear_elasticity.g  reduced_lagrange.g
-    fsi_test		mpi_poisson		 stokes
-    fsi_test.g		mpi_poisson.g		 stokes.g
-    linear_elasticity	mpi_stokes
+    linear_elasticity.g  mpi_stokes.g
+    distributed_lagrange mesh_handler   poisson
+    distributed_lagrange.g mesh_handler.g   poisson.g
+    dof_plotter  mpi_linear_elasticity  reduced_lagrange
+    dof_plotter.g  mpi_linear_elasticity.g  reduced_lagrange.g
+    fsi_test  mpi_poisson   stokes
+    fsi_test.g  mpi_poisson.g   stokes.g
+    linear_elasticity mpi_stokes
 
     Programs ending with .g are compiled with debug symbols. To see help on how to run
     any of the programs, add a -h flag at the end.
 
 The above command will download the latest docker image from the `main` branch
 of this repository (which is built and uploaded to
-https://hub.docker.com/r/heltai/fsi-suite at every commit to master), mount the
+<https://hub.docker.com/r/heltai/fsi-suite> at every commit to master), mount the
 current directory, in a directory with the same path inside the container, and
-the program you selected. For example, 
+the program you selected. For example,
 
     ./fsi-suite.sh -np 4 mpi_poisson.g
 
@@ -119,10 +120,10 @@ problem in parallel, using 4 processors. You can change grid, boundary
 conditions, forcing terms, finite element spaces, etc. by editing the
 configuration file which is created the first time you run the program, and then
 passing it as an argument to the program itself, i.e., in the example above, the
-parameter file that would be generated is `used_mpi_poisson.g_2d.prm`, which you
+parameter file that would be generated is `used_mpi_poisson.g.prm`, which you
 can edit and then pass as input to the program itself:
 
-    ./fsi-suite.sh -np 4 mpi_poisson.g used_mpi_poisson.g_2d.prm
+    ./fsi-suite.sh -np 4 mpi_poisson.g used_mpi_poisson.g.prm
 
 If you want to read some documentation of what each parameter does and how it
 works, you can call the program passing a non-existing parameter file:
@@ -143,7 +144,7 @@ works, you can call the program passing a non-existing parameter file:
 
 The created parameter file will also contain documentation for each parameter.
 Running again the same command will now use the parameter file that was just
-created: 
+created:
 
     ./fsi-suite.sh -np 4 mpi_poisson.g my_test.prm
 
@@ -170,28 +171,29 @@ created:
     | setup_system                    |         1 |    0.0124s |        18% |
     | solve                           |         1 |   0.00547s |       7.8% |
     +---------------------------------+-----------+------------+------------+
+
 ## Course program
 
-A tentative detailed program is shown below 
+A tentative detailed program is shown below
 (this will be updated during the course to reflect the actual course content)
 
-1. Course introduction. 
+1. Course introduction.
     - Motivating examples
     - Basic principles and background knowledge.
 
 2. Recap on Finite Element Methods
     - Introduction to deal.II.
 
-3. Basic principles of continuum mechanics 
-    - conservation equations 
+3. Basic principles of continuum mechanics
+    - conservation equations
     - constitutive equations
     - kinematics
     - transport theorems
 
 3. Lagrangian formulation of continuum mechanics (solids).
     - Static and compressible linear elasticity
 
-4. Recap on mixed problems 
+4. Recap on mixed problems
     - Static incompressible linear elasticity
 
 5. Eulerian formulation of continuum mechanics
@@ -200,13 +202,13 @@ A tentative detailed program is shown below
 6. Recap on time discretization schemes
     - Time dependent Stokes problem
     - Time dependent linear elasticity (wave equations)
-    
-7. Treating non-linearities 
+
+7. Treating non-linearities
     - IMEX
     - predictor corrector
     - fixed point
     - Newton
-    
+
 8. Navier-Stokes equations
 
 9. Segregated coupling