Merge branch 'main' into fix_stresses_elasticity

.github/dependabot.yml

@@ -0,0 +1,10 @@
+# Set update schedule for GitHub Actions
+
+version: 2
+updates:
+
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      # Check for updates to GitHub Actions every week
+      interval: "weekly"

.github/workflows/build_tester_base_image.yml

@@ -19,19 +19,19 @@ jobs:
     if: github.repository == 'geodynamics/aspect'
     steps:    
       - name: Checkout code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v2
+        uses: docker/setup-buildx-action@v3
 
       - name: Login to DockerHub
-        uses: docker/login-action@v2
+        uses: docker/login-action@v3
         with:
           username: ${{ secrets.DOCKER_HUB_USERNAME }}
           password: ${{ secrets.DOCKER_HUB_LOGIN }}
 
       - name: Build and push Docker image for main
-        uses: docker/build-push-action@v3
+        uses: docker/build-push-action@v5
         with:
           context: ./contrib/docker/tester/
           cache-from: type=registry,ref=ubuntu:20.04

.github/workflows/docker.yml

@@ -25,30 +25,30 @@ jobs:
     if: github.repository == 'geodynamics/aspect'
     steps:    
       - name: Checkout code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Set up QEMU
-        uses: docker/setup-qemu-action@v2
+        uses: docker/setup-qemu-action@v3
 
       - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v2
+        uses: docker/setup-buildx-action@v3
 
       - name: Log in to the Container registry
-        uses: docker/login-action@v2
+        uses: docker/login-action@v3
         with:
           registry: ghcr.io
           username: ${{ github.actor }}
           password: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Login to DockerHub
-        uses: docker/login-action@v2
+        uses: docker/login-action@v3
         with:
           username: ${{ secrets.DOCKER_HUB_USERNAME }}
           password: ${{ secrets.DOCKER_HUB_LOGIN }}
 
       - name: Build and push Docker image for main
         if: contains(github.event_name, 'push')
-        uses: docker/build-push-action@v4
+        uses: docker/build-push-action@v5
         with:
           context: ./contrib/docker/docker/
           cache-from: type=registry,ref=ubuntu:22.04
@@ -61,7 +61,7 @@ jobs:
 
       - name: Build and push Docker image for release
         if: contains(github.event_name, 'release')
-        uses: docker/build-push-action@v3
+        uses: docker/build-push-action@v5
         with:
           context: ./contrib/docker/docker/
           cache-from: type=registry,ref=ubuntu:22.04
@@ -77,30 +77,30 @@ jobs:
     if: github.repository == 'geodynamics/aspect'
     steps:
       - name: Checkout code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Set up QEMU
-        uses: docker/setup-qemu-action@v2
+        uses: docker/setup-qemu-action@v3
 
       - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v2
+        uses: docker/setup-buildx-action@v3
 
       - name: Login to DockerHub
-        uses: docker/login-action@v2
+        uses: docker/login-action@v3
         with:
           username: ${{ secrets.DOCKER_HUB_USERNAME }}
           password: ${{ secrets.DOCKER_HUB_LOGIN }}
 
       - name: Log in to the Container registry
-        uses: docker/login-action@v2
+        uses: docker/login-action@v3
         with:
           registry: ghcr.io
           username: ${{ github.actor }}
           password: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Build and push Docker image for main
         if: contains(github.event_name, 'push')
-        uses: docker/build-push-action@v4
+        uses: docker/build-push-action@v5
         with:
           context: ./contrib/docker/docker_tacc/
           cache-from: type=registry,ref=ubuntu:22.04
@@ -113,7 +113,7 @@ jobs:
 
       - name: Build and push Docker image for release
         if: contains(github.event_name, 'release')
-        uses: docker/build-push-action@v4
+        uses: docker/build-push-action@v5
         with:
           context: ./contrib/docker/docker_tacc/
           cache-from: type=registry,ref=ubuntu:22.04

.github/workflows/linux.yml

@@ -26,12 +26,12 @@ jobs:
     runs-on: [ubuntu-20.04]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: setup
       run: |
         sudo apt-get update
         sudo apt-get install -y software-properties-common
-        sudo add-apt-repository ppa:ginggs/deal.ii-9.4.0-backports
+        sudo add-apt-repository ppa:ginggs/deal.ii-9.5.1-backports
         sudo apt-get update
         sudo apt-get install -yq --no-install-recommends libdeal.ii-dev
     - name: compile
@@ -48,12 +48,12 @@ jobs:
     runs-on: [ubuntu-20.04]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: setup
       run: |
         sudo apt-get update
         sudo apt-get install -y software-properties-common
-        sudo add-apt-repository ppa:ginggs/deal.ii-9.4.0-backports
+        sudo add-apt-repository ppa:ginggs/deal.ii-9.5.1-backports
         sudo apt-get update
         sudo apt-get install -yq --no-install-recommends texlive-plain-generic texlive-base texlive-latex-recommended texlive-latex-base texlive-fonts-recommended texlive-bibtex-extra lmodern texlive-latex-extra texlive-science graphviz python3-pip python-setuptools libdeal.ii-dev doxygen latexmk biber inkscape
         doxygen --version
@@ -70,7 +70,7 @@ jobs:
         ./contrib/utilities/indent
         git diff > changes-astyle.diff
     - name: archive indent results
-      uses: actions/upload-artifact@v2
+      uses: actions/upload-artifact@v3
       with:
         name: changes-astyle.diff
         path: changes-astyle.diff
@@ -110,6 +110,11 @@ jobs:
             compare-tests: "ON"
             result-file: "changes-test-results-9.4.diff"
             container-options: '--name container'
+          - image: "geodynamics/aspect-tester:focal-dealii-9.5-v1"
+            run-tests: "ON"
+            compare-tests: "OFF"
+            result-file: "changes-test-results-9.5.diff"
+            container-options: '--name container'
           - image: "geodynamics/aspect-tester:focal-dealii-master"
             run-tests: "ON"
             compare-tests: "OFF"
@@ -121,7 +126,7 @@ jobs:
       options: ${{ matrix.container-options }}
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: compile
       run: |
         mkdir build
@@ -158,15 +163,15 @@ jobs:
       run: |
         cd build
         ninja generate_reference_output
-        git diff ../tests > changes-test-results.diff
+        git diff ../tests > ${{ matrix.result-file }}
     - name: archive test results
-      uses: actions/upload-artifact@v2
+      uses: actions/upload-artifact@v3
       with:
         name: ${{ matrix.result-file }}
-        path: build/changes-test-results.diff
+        path: build/${{ matrix.result-file }}}
     - name: check test results
       run: |
-        if [ -f build/test_run_failed ] || [ -s build/changes-test-results.diff ]; then
+        if [ -f build/test_run_failed ] || [ -s build/${{ matrix.result-file}} ]; then
           exit 1
         else
           exit 0

benchmarks/annulus/plugin/annulus.cc

@@ -494,9 +494,9 @@ namespace aspect
           const unsigned int n_components = this->introspection().n_components;
 
           compute_density_error = (material_model.analytical_density() == false);
-          reference_solution.reset (new AnalyticSolutions::FunctionAnnulus<dim>(material_model.get_k(),
-                                                                                n_components,
-                                                                                material_model.use_transient_solution()));
+          reference_solution = std::make_unique<AnalyticSolutions::FunctionAnnulus<dim>>(material_model.get_k(),
+                                                                                          n_components,
+                                                                                          material_model.use_transient_solution());
         }
 
 

benchmarks/burstedde/burstedde.cc

@@ -425,7 +425,7 @@ namespace aspect
         material_model
           = Plugins::get_plugin_as_type<const BursteddeMaterial<dim>>(this->get_material_model());
 
-        ref_func.reset (new AnalyticSolutions::FunctionBurstedde<dim>(material_model.get_beta()));
+        ref_func = std::make_unique<AnalyticSolutions::FunctionBurstedde<dim>>(material_model.get_beta());
       }
 
       const QGauss<dim> quadrature_formula (this->introspection().polynomial_degree.velocities+2);

benchmarks/doneahuerta/doneahuerta.cc

@@ -270,11 +270,8 @@ namespace aspect
     std::pair<std::string,std::string>
     DoneaHuertaPostprocessor<dim>::execute (TableHandler &)
     {
-      std::unique_ptr<Function<dim>> ref_func;
-      {
-
-        ref_func.reset (new AnalyticSolutions::FunctionDoneaHuerta<dim>());
-      }
+      std::unique_ptr<Function<dim>> ref_func =
+        std::make_unique<AnalyticSolutions::FunctionDoneaHuerta<dim>>();
 
       const QGauss<dim> quadrature_formula (this->introspection().polynomial_degree.velocities+2);
 

benchmarks/hollow_sphere/hollow_sphere.cc

@@ -509,7 +509,7 @@ namespace aspect
         material_model
           = Plugins::get_plugin_as_type<const HollowSphereMaterial<dim>>(this->get_material_model());
 
-        ref_func.reset (new AnalyticSolutions::FunctionHollowSphere<dim>(material_model.get_mmm()));
+        ref_func = std::make_unique<AnalyticSolutions::FunctionHollowSphere<dim>>(material_model.get_mmm());
       }
 
       const QGauss<dim> quadrature_formula (this->introspection().polynomial_degree.velocities+2);

benchmarks/inclusion/inclusion.h

@@ -278,18 +278,17 @@ namespace aspect
         std::pair<std::string,std::string>
         execute (TableHandler &/*statistics*/) override
         {
-          std::unique_ptr<Function<dim>> ref_func;
-
           AssertThrow(Plugins::plugin_type_matches<const InclusionMaterial<dim>>(this->get_material_model()),
                       ExcMessage("Postprocessor only works with the inclusion material model."));
 
           const InclusionMaterial<dim> &
           material_model
             = Plugins::get_plugin_as_type<const InclusionMaterial<dim>>(this->get_material_model());
 
-          ref_func.reset (new AnalyticSolutions::FunctionInclusion<dim>(
-                            material_model.get_eta_B(),
-                            this->n_compositional_fields()));
+          std::unique_ptr<Function<dim>> ref_func
+            = std::make_unique<AnalyticSolutions::FunctionInclusion<dim>>(
+                material_model.get_eta_B(),
+                this->n_compositional_fields());
 
           const QGauss<dim> quadrature_formula (this->introspection().polynomial_degree.velocities+2);
 

benchmarks/layeredflow/layeredflow.cc

@@ -335,8 +335,8 @@ namespace aspect
         material_model
           = Plugins::get_plugin_as_type<const LayeredFlowMaterial<dim>>(this->get_material_model());
 
-        ref_func.reset (new AnalyticSolutions::FunctionLayeredFlow<dim>(material_model.get_beta(),
-                                                                        material_model.get_epsilon()));
+        ref_func = std::make_unique<AnalyticSolutions::FunctionLayeredFlow<dim>>(material_model.get_beta(),
+                                                                                  material_model.get_epsilon());
       }
 
       const QGauss<dim> quadrature_formula (this->introspection().polynomial_degree.velocities+2);

benchmarks/shear_bands/shear_bands.cc

@@ -312,7 +312,7 @@ namespace aspect
         double noise_amplitude;
         double background_porosity;
         std::array<unsigned int,dim> grid_intervals;
-        Functions::InterpolatedUniformGridData<dim> *interpolate_noise;
+        std::unique_ptr<Functions::InterpolatedUniformGridData<dim>> interpolate_noise;
     };
 
 
@@ -374,9 +374,10 @@ namespace aspect
             }
         }
 
-      interpolate_noise = new Functions::InterpolatedUniformGridData<dim> (grid_extents,
-                                                                           grid_intervals,
-                                                                           white_noise);
+      interpolate_noise
+        = std::make_unique<Functions::InterpolatedUniformGridData<dim>> (grid_extents,
+                                                                          grid_intervals,
+                                                                          white_noise);
     }
 
 

benchmarks/solcx/solcx.h

@@ -3115,7 +3115,6 @@ namespace aspect
         std::pair<std::string,std::string>
         execute (TableHandler &/*statistics*/) override
         {
-          std::unique_ptr<Function<dim>> ref_func;
 
           AssertThrow(Plugins::plugin_type_matches<const SolCxMaterial<dim>>(this->get_material_model()),
                       ExcMessage("Postprocessor DuretzEtAl only works with the material model SolCx, SolKz, and Inclusion."));
@@ -3124,9 +3123,10 @@ namespace aspect
           material_model
             = Plugins::get_plugin_as_type<const SolCxMaterial<dim>>(this->get_material_model());
 
-          ref_func.reset (new AnalyticSolutions::FunctionSolCx<dim>(material_model.get_eta_B(),
-                                                                    material_model.get_background_density(),
-                                                                    this->n_compositional_fields()));
+          std::unique_ptr<Function<dim>> ref_func
+            = std::make_unique<AnalyticSolutions::FunctionSolCx<dim>>(material_model.get_eta_B(),
+                                                                       material_model.get_background_density(),
+                                                                       this->n_compositional_fields());
 
           const QGauss<dim> quadrature_formula (this->introspection().polynomial_degree.velocities + 2);
 

benchmarks/solitary_wave/solitary_wave.cc

@@ -947,8 +947,8 @@ namespace aspect
       if (this->get_timestep_number()==0)
         {
           store_initial_pressure();
-          ref_func.reset (new AnalyticSolutions::FunctionSolitaryWave<dim>(offset,0.0,initial_pressure,
-                                                                           this->get_geometry_model().maximal_depth(), this->introspection().n_components));
+          ref_func = std::make_unique<AnalyticSolutions::FunctionSolitaryWave<dim>>(offset,0.0,initial_pressure,
+                                                                                     this->get_geometry_model().maximal_depth(), this->introspection().n_components);
         }
 
       double delta=0;

benchmarks/time_dependent_annulus/plugin/time_dependent_annulus.h

@@ -209,7 +209,7 @@ namespace aspect
               {
                 prm.enter_subsection("Function");
                 {
-                  density_function.reset(new Functions::ParsedFunction<dim>(1));
+                  density_function = std::make_unique<Functions::ParsedFunction<dim>>(1);
                   density_function->parse_parameters(prm);
                 }
                 prm.leave_subsection();
@@ -220,7 +220,7 @@ namespace aspect
               {
                 prm.enter_subsection("Function");
                 {
-                  pressure_function.reset(new Functions::ParsedFunction<dim>(1));
+                  pressure_function = std::make_unique<Functions::ParsedFunction<dim>>(1);
                   pressure_function->parse_parameters(prm);
                 }
                 prm.leave_subsection();
@@ -233,7 +233,7 @@ namespace aspect
                 {
                   try
                     {
-                      velocity_function.reset (new Functions::ParsedFunction<dim>(dim));
+                      velocity_function = std::make_unique<Functions::ParsedFunction<dim>>(dim);
                       velocity_function->parse_parameters (prm);
                     }
                   catch (...)
@@ -310,10 +310,10 @@ namespace aspect
           const MaterialModel::TimeDependentAnnulus<dim> &material_model =
             Plugins::get_plugin_as_type<const MaterialModel::TimeDependentAnnulus<dim>>(this->get_material_model());
 
-          ref_func.reset (new AnalyticSolutions::FunctionStreamline<dim>(material_model.get_pressure(),
-                                                                         material_model.get_velocity(),
-                                                                         material_model.get_density(),
-                                                                         1 + dim + 1 + this->n_compositional_fields()));
+          ref_func = std::make_unique<AnalyticSolutions::FunctionStreamline<dim>>(material_model.get_pressure(),
+                                                                                   material_model.get_velocity(),
+                                                                                   material_model.get_density(),
+                                                                                   1 + dim + 1 + this->n_compositional_fields());
         }
 
         std::pair<std::string,std::string>

benchmarks/viscosity_grooves/viscosity_grooves.cc

@@ -383,7 +383,7 @@ namespace aspect
       std::shared_ptr<Function<dim>> ref_func;
       {
 
-        ref_func.reset (new AnalyticSolutions::FunctionViscosityGrooves<dim>(this->get_geometry_model()));
+        ref_func = std::make_unique<AnalyticSolutions::FunctionViscosityGrooves<dim>>(this->get_geometry_model());
       }
 
       const QGauss<dim> quadrature_formula (this->introspection().polynomial_degree.velocities+2);