diff --git a/.github/workflows/book_stable.yml b/.github/workflows/book_stable.yml index 77e83091..9f71ce1f 100644 --- a/.github/workflows/book_stable.yml +++ b/.github/workflows/book_stable.yml @@ -15,7 +15,7 @@ env: jobs: build-book: runs-on: ubuntu-latest - container: ghcr.io/fenics/dolfinx/lab:v0.7.2 + container: ghcr.io/fenics/dolfinx/lab:v0.7.3 env: PYVISTA_TRAME_SERVER_PROXY_PREFIX: "/proxy/" @@ -35,7 +35,8 @@ jobs: - name: Build the book run: jupyter-book build . -W - - uses: actions/upload-artifact@v3 + - uses: actions/upload-artifact@v4 + if : always() with: name: webpage path: ./_build/html diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml index ade2d945..85d8a006 100644 --- a/.github/workflows/deploy.yml +++ b/.github/workflows/deploy.yml @@ -47,16 +47,16 @@ jobs: uses: actions/configure-pages@v4 - name: Download docs artifact - uses: actions/download-artifact@v3 + uses: actions/download-artifact@v4 with: name: webpage path: "./public" - name: Upload page artifact - uses: actions/upload-pages-artifact@v2 + uses: actions/upload-pages-artifact@v3 with: path: "./public" - name: Deploy coverage report to GH Pages id: deployment - uses: actions/deploy-pages@v3 + uses: actions/deploy-pages@v4 diff --git a/.github/workflows/publish_docker.yml b/.github/workflows/publish_docker.yml index fd2bdc84..9407a66f 100644 --- a/.github/workflows/publish_docker.yml +++ b/.github/workflows/publish_docker.yml @@ -23,13 +23,13 @@ jobs: 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: ${{ env.REGISTRY }} username: ${{ github.actor }} @@ -37,12 +37,12 @@ jobs: - name: Extract metadata (tags, labels) for Docker id: meta - uses: docker/metadata-action@v4 + uses: docker/metadata-action@v5 with: images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }} - name: Build and push Docker image - uses: docker/build-push-action@v3 + uses: docker/build-push-action@v5 with: context: . push: true diff --git a/.github/workflows/test_nightly.yml b/.github/workflows/test_nightly.yml index ccb882b5..c61f0e66 100644 --- a/.github/workflows/test_nightly.yml +++ b/.github/workflows/test_nightly.yml @@ -85,7 +85,8 @@ jobs: - name: Test building the book run: PYVISTA_OFF_SCREEN=false jupyter-book build -W . - - uses: actions/upload-artifact@v3 + - uses: actions/upload-artifact@v4 + if: always() with: name: webpage path: ./_build/html diff --git a/.github/workflows/test_stable.yml b/.github/workflows/test_stable.yml index 86e2fd8d..7e525c67 100644 --- a/.github/workflows/test_stable.yml +++ b/.github/workflows/test_stable.yml @@ -72,7 +72,7 @@ jobs: mpirun -n 2 python3 compiler_parameters.py - name: Upload Navier-Stokes DFG 2D 3 plots - uses: actions/upload-artifact@v3 + uses: actions/upload-artifact@v4 with: name: DFG2D-3 path: chapter2/figures diff --git a/chapter1/nitsche.ipynb b/chapter1/nitsche.ipynb index 4ba3df42..247afaf0 100644 --- a/chapter1/nitsche.ipynb +++ b/chapter1/nitsche.ipynb @@ -6,12 +6,13 @@ "metadata": {}, "source": [ "# Weak imposition of Dirichlet conditions for the Poisson problem\n", + "\n", "Author: Jørgen S. Dokken\n", "\n", - "In this section, we will go through how to solve the Poisson problem from the [Fundamentals](fundamentals.ipynb) tutorial using Nitsche's method {cite}`Nitsche1971`.\n", + "In this section, we will go through how to solve the Poisson problem from the [Fundamentals](fundamentals_code.ipynb) tutorial using Nitsche's method {cite}`Nitsche1971`.\n", "The idea of weak imposition is that we add additional terms to the variational formulation to impose the boundary condition, instead of modifying the matrix system using strong imposition (lifting).\n", "\n", - "We start by importing the required modules and creating the mesh and function space for our solution" + "We start by importing the required modules and creating the mesh and function space for our solution\n" ] }, { @@ -38,7 +39,7 @@ "id": "surrounded-carrier", "metadata": {}, "source": [ - "Next, we create a function containing the exact solution (which will also be used in the Dirichlet boundary condition) and the corresponding source function for the right hand side. Note that we use `ufl.SpatialCoordinate` to define the exact solution, which in turn is interpolated into `uD` and used to create the source function `f`." + "Next, we create a function containing the exact solution (which will also be used in the Dirichlet boundary condition) and the corresponding source function for the right hand side. Note that we use `ufl.SpatialCoordinate` to define the exact solution, which in turn is interpolated into `uD` and used to create the source function `f`.\n" ] }, { @@ -63,20 +64,20 @@ "As opposed to the first tutorial, we now have to have another look at the variational form.\n", "We start by integrating the problem by parts, to obtain\n", "\\begin{align}\n", - " \\int_{\\Omega} \\nabla u \\cdot \\nabla v~\\mathrm{d}x - \\int_{\\partial\\Omega}\\nabla u \\cdot n v~\\mathrm{d}s = \\int_{\\Omega} f v~\\mathrm{d}x.\n", + "\\int*{\\Omega} \\nabla u \\cdot \\nabla v~\\mathrm{d}x - \\int*{\\partial\\Omega}\\nabla u \\cdot n v~\\mathrm{d}s = \\int*{\\Omega} f v~\\mathrm{d}x.\n", "\\end{align}\n", "As we are not using strong enforcement, we do not set the trace of the test function to $0$ on the outer boundary.\n", "Instead, we add the following two terms to the variational formulation\n", "\\begin{align}\n", - " -\\int_{\\partial\\Omega} \\nabla v \\cdot n (u-u_D)~\\mathrm{d}s + \\frac{\\alpha}{h} \\int_{\\partial\\Omega} (u-u_D)v~\\mathrm{d}s.\n", + "-\\int*{\\partial\\Omega} \\nabla v \\cdot n (u-u*D)~\\mathrm{d}s + \\frac{\\alpha}{h} \\int*{\\partial\\Omega} (u-u*D)v~\\mathrm{d}s.\n", "\\end{align}\n", "where the first term enforces symmetry to the bilinear form, while the latter term enforces coercivity.\n", "$u_D$ is the known Dirichlet condition, and $h$ is the diameter of the circumscribed sphere of the mesh element.\n", "We create bilinear and linear form, $a$ and $L$\n", "\\begin{align}\n", - " a(u, v) &= \\int_{\\Omega} \\nabla u \\cdot \\nabla v~\\mathrm{d}x + \\int_{\\partial\\Omega}-(n \\cdot\\nabla u) v - (n \\cdot \\nabla v) u + \\frac{\\alpha}{h} uv~\\mathrm{d}s,\\\\\n", - " L(v) &= \\int_{\\Omega} fv~\\mathrm{d}x + \\int_{\\partial\\Omega} -(n \\cdot \\nabla v) u_D + \\frac{\\alpha}{h} u_Dv~\\mathrm{d}s\n", - "\\end{align}" + "a(u, v) &= \\int*{\\Omega} \\nabla u \\cdot \\nabla v~\\mathrm{d}x + \\int*{\\partial\\Omega}-(n \\cdot\\nabla u) v - (n \\cdot \\nabla v) u + \\frac{\\alpha}{h} uv~\\mathrm{d}s,\\\\\n", + "L(v) &= \\int*{\\Omega} fv~\\mathrm{d}x + \\int\\_{\\partial\\Omega} -(n \\cdot \\nabla v) u_D + \\frac{\\alpha}{h} u_Dv~\\mathrm{d}s\n", + "\\end{align}\n" ] }, { @@ -102,7 +103,7 @@ "id": "971dc391", "metadata": {}, "source": [ - "As we now have the variational form, we can solve the linear problem" + "As we now have the variational form, we can solve the linear problem\n" ] }, { @@ -121,7 +122,7 @@ "id": "fac3387f", "metadata": {}, "source": [ - "We compute the error of the computation by comparing it to the analytical solution" + "We compute the error of the computation by comparing it to the analytical solution\n" ] }, { @@ -152,7 +153,7 @@ "metadata": {}, "source": [ "We observe that the $L^2$-error is of the same magnitude as in the first tutorial.\n", - "As in the previous tutorial, we also compute the maximal error for all the degrees of freedom." + "As in the previous tutorial, we also compute the maximal error for all the degrees of freedom.\n" ] }, { @@ -180,7 +181,7 @@ "id": "f5ba8c79", "metadata": {}, "source": [ - "We observe that as we weakly impose the boundary condition, we no longer fullfill the equation to machine precision at the mesh vertices. We also plot the solution using `pyvista`" + "We observe that as we weakly impose the boundary condition, we no longer fullfill the equation to machine precision at the mesh vertices. We also plot the solution using `pyvista`\n" ] }, { @@ -191,540 +192,16 @@ "outputs": [ { "data": { - "application/javascript": [ - "(function(root) {\n", - " function now() {\n", - " return new Date();\n", - " }\n", - "\n", - " var force = true;\n", - " var py_version = '3.2.1'.replace('rc', '-rc.').replace('.dev', '-dev.');\n", - " var is_dev = py_version.indexOf(\"+\") !== -1 || py_version.indexOf(\"-\") !== -1;\n", - " var reloading = false;\n", - " var Bokeh = root.Bokeh;\n", - " var bokeh_loaded = Bokeh != null && (Bokeh.version === py_version || (Bokeh.versions !== undefined && Bokeh.versions.has(py_version)));\n", - "\n", - " if (typeof (root._bokeh_timeout) === \"undefined\" || force) {\n", - " root._bokeh_timeout = Date.now() + 5000;\n", - " root._bokeh_failed_load = false;\n", - " }\n", - "\n", - " function run_callbacks() {\n", - " try {\n", - " root._bokeh_onload_callbacks.forEach(function(callback) {\n", - " if (callback != null)\n", - " callback();\n", - " });\n", - " } 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root._bokeh_failed_load = false;\n }\n\n function run_callbacks() {\n try {\n root._bokeh_onload_callbacks.forEach(function(callback) {\n if (callback != null)\n callback();\n });\n } finally {\n delete root._bokeh_onload_callbacks;\n }\n console.debug(\"Bokeh: all callbacks have finished\");\n }\n\n function load_libs(css_urls, js_urls, js_modules, js_exports, callback) {\n if (css_urls == null) css_urls = [];\n if (js_urls == null) js_urls = [];\n if (js_modules == null) js_modules = [];\n if (js_exports == null) js_exports = {};\n\n root._bokeh_onload_callbacks.push(callback);\n\n if (root._bokeh_is_loading > 0) {\n console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n return null;\n }\n if (js_urls.length === 0 && js_modules.length === 0 && Object.keys(js_exports).length === 0) {\n run_callbacks();\n return null;\n }\n if (!reloading) {\n console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n }\n\n function on_load() {\n root._bokeh_is_loading--;\n if (root._bokeh_is_loading === 0) {\n console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n run_callbacks()\n }\n }\n window._bokeh_on_load = on_load\n\n function on_error() {\n console.error(\"failed to load \" + url);\n }\n\n var skip = [];\n if (window.requirejs) {\n window.requirejs.config({'packages': {}, 'paths': {'vtk': 'https://cdn.jsdelivr.net/npm/vtk.js@20.0.1/vtk', 'jspanel': 'https://cdn.jsdelivr.net/npm/jspanel4@4.12.0/dist/jspanel', 'jspanel-modal': 'https://cdn.jsdelivr.net/npm/jspanel4@4.12.0/dist/extensions/modal/jspanel.modal', 'jspanel-tooltip': 'https://cdn.jsdelivr.net/npm/jspanel4@4.12.0/dist/extensions/tooltip/jspanel.tooltip', 'jspanel-hint': 'https://cdn.jsdelivr.net/npm/jspanel4@4.12.0/dist/extensions/hint/jspanel.hint', 'jspanel-layout': 'https://cdn.jsdelivr.net/npm/jspanel4@4.12.0/dist/extensions/layout/jspanel.layout', 'jspanel-contextmenu': 'https://cdn.jsdelivr.net/npm/jspanel4@4.12.0/dist/extensions/contextmenu/jspanel.contextmenu', 'jspanel-dock': 'https://cdn.jsdelivr.net/npm/jspanel4@4.12.0/dist/extensions/dock/jspanel.dock', 'gridstack': 'https://cdn.jsdelivr.net/npm/gridstack@7.2.3/dist/gridstack-all', 'notyf': 'https://cdn.jsdelivr.net/npm/notyf@3/notyf.min'}, 'shim': {'vtk': {'exports': 'vtk'}, 'jspanel': {'exports': 'jsPanel'}, 'gridstack': {'exports': 'GridStack'}}});\n require([\"vtk\"], function() {\n\ton_load()\n })\n require([\"jspanel\"], function(jsPanel) {\n\twindow.jsPanel = jsPanel\n\ton_load()\n })\n require([\"jspanel-modal\"], function() {\n\ton_load()\n })\n require([\"jspanel-tooltip\"], function() {\n\ton_load()\n })\n require([\"jspanel-hint\"], function() {\n\ton_load()\n })\n require([\"jspanel-layout\"], function() {\n\ton_load()\n })\n require([\"jspanel-contextmenu\"], function() {\n\ton_load()\n })\n require([\"jspanel-dock\"], function() {\n\ton_load()\n })\n require([\"gridstack\"], function(GridStack) {\n\twindow.GridStack = GridStack\n\ton_load()\n })\n require([\"notyf\"], function() {\n\ton_load()\n })\n root._bokeh_is_loading = css_urls.length + 10;\n } else {\n root._bokeh_is_loading = css_urls.length + js_urls.length + js_modules.length + Object.keys(js_exports).length;\n }\n\n var existing_stylesheets = []\n var links = document.getElementsByTagName('link')\n for (var i = 0; i < links.length; i++) {\n var link = links[i]\n if (link.href != null) {\n\texisting_stylesheets.push(link.href)\n }\n }\n for (var i = 0; i < css_urls.length; i++) {\n var url = css_urls[i];\n if (existing_stylesheets.indexOf(url) !== -1) {\n\ton_load()\n\tcontinue;\n }\n const element = document.createElement(\"link\");\n element.onload = on_load;\n element.onerror = on_error;\n element.rel = \"stylesheet\";\n element.type = \"text/css\";\n element.href = url;\n console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n document.body.appendChild(element);\n } if (((window['vtk'] !== undefined) && (!(window['vtk'] instanceof HTMLElement))) || window.requirejs) {\n var urls = ['https://cdn.holoviz.org/panel/1.2.1/dist/bundled/abstractvtkplot/vtk.js@20.0.1/vtk.js'];\n for (var i = 0; i < urls.length; i++) {\n skip.push(urls[i])\n }\n } if (((window['jsPanel'] !== undefined) && (!(window['jsPanel'] instanceof HTMLElement))) || window.requirejs) {\n var urls = ['https://cdn.holoviz.org/panel/1.2.1/dist/bundled/floatpanel/jspanel4@4.12.0/dist/jspanel.js', 'https://cdn.holoviz.org/panel/1.2.1/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/modal/jspanel.modal.js', 'https://cdn.holoviz.org/panel/1.2.1/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/tooltip/jspanel.tooltip.js', 'https://cdn.holoviz.org/panel/1.2.1/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/hint/jspanel.hint.js', 'https://cdn.holoviz.org/panel/1.2.1/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/layout/jspanel.layout.js', 'https://cdn.holoviz.org/panel/1.2.1/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/contextmenu/jspanel.contextmenu.js', 'https://cdn.holoviz.org/panel/1.2.1/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/dock/jspanel.dock.js'];\n for (var i = 0; i < urls.length; i++) {\n skip.push(urls[i])\n }\n } if (((window['GridStack'] !== undefined) && (!(window['GridStack'] instanceof HTMLElement))) || window.requirejs) {\n var urls = ['https://cdn.holoviz.org/panel/1.2.1/dist/bundled/gridstack/gridstack@7.2.3/dist/gridstack-all.js'];\n for (var i = 0; i < urls.length; i++) {\n skip.push(urls[i])\n }\n } if (((window['Notyf'] !== undefined) && (!(window['Notyf'] instanceof HTMLElement))) || window.requirejs) {\n var urls = ['https://cdn.holoviz.org/panel/1.2.1/dist/bundled/notificationarea/notyf@3/notyf.min.js'];\n for (var i = 0; i < urls.length; i++) {\n skip.push(urls[i])\n }\n } var existing_scripts = []\n var scripts = document.getElementsByTagName('script')\n for (var i = 0; i < scripts.length; i++) {\n var script = scripts[i]\n if (script.src != null) {\n\texisting_scripts.push(script.src)\n }\n }\n for (var i = 0; i < js_urls.length; i++) {\n var url = js_urls[i];\n if (skip.indexOf(url) !== -1 || existing_scripts.indexOf(url) !== -1) {\n\tif (!window.requirejs) {\n\t on_load();\n\t}\n\tcontinue;\n }\n var element = document.createElement('script');\n element.onload = on_load;\n element.onerror = on_error;\n element.async = false;\n element.src = url;\n console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n document.head.appendChild(element);\n }\n for (var i = 0; i < js_modules.length; i++) {\n var url = js_modules[i];\n if (skip.indexOf(url) !== -1 || existing_scripts.indexOf(url) !== -1) {\n\tif (!window.requirejs) {\n\t on_load();\n\t}\n\tcontinue;\n }\n var element = document.createElement('script');\n element.onload = on_load;\n element.onerror = on_error;\n element.async = false;\n element.src = url;\n element.type = \"module\";\n console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n document.head.appendChild(element);\n }\n for (const name in js_exports) {\n var url = js_exports[name];\n if (skip.indexOf(url) >= 0 || root[name] != null) {\n\tif (!window.requirejs) {\n\t on_load();\n\t}\n\tcontinue;\n }\n var element = document.createElement('script');\n element.onerror = on_error;\n element.async = false;\n element.type = \"module\";\n console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n element.textContent = `\n import ${name} from \"${url}\"\n window.${name} = ${name}\n window._bokeh_on_load()\n `\n document.head.appendChild(element);\n }\n if (!js_urls.length && !js_modules.length) {\n on_load()\n }\n };\n\n function inject_raw_css(css) {\n const element = document.createElement(\"style\");\n element.appendChild(document.createTextNode(css));\n document.body.appendChild(element);\n }\n\n var js_urls = [\"https://cdn.holoviz.org/panel/1.2.1/dist/bundled/abstractvtkplot/vtk.js@20.0.1/vtk.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-3.2.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.2.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.2.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.2.1.min.js\", \"https://cdn.holoviz.org/panel/1.2.1/dist/panel.min.js\"];\n var js_modules = [];\n var js_exports = {};\n var css_urls = [];\n var inline_js = [ function(Bokeh) {\n Bokeh.set_log_level(\"info\");\n },\nfunction(Bokeh) {} // ensure no trailing comma for IE\n ];\n\n function run_inline_js() {\n if ((root.Bokeh !== undefined) || (force === true)) {\n for (var i = 0; i < inline_js.length; i++) {\n inline_js[i].call(root, root.Bokeh);\n }\n // Cache old bokeh versions\n if (Bokeh != undefined && !reloading) {\n\tvar NewBokeh = root.Bokeh;\n\tif (Bokeh.versions === undefined) {\n\t Bokeh.versions = new Map();\n\t}\n\tif (NewBokeh.version !== Bokeh.version) {\n\t Bokeh.versions.set(NewBokeh.version, NewBokeh)\n\t}\n\troot.Bokeh = Bokeh;\n }} else if (Date.now() < root._bokeh_timeout) {\n setTimeout(run_inline_js, 100);\n } else if (!root._bokeh_failed_load) {\n console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n root._bokeh_failed_load = true;\n }\n root._bokeh_is_initializing = false\n }\n\n function load_or_wait() {\n // Implement a backoff loop that tries to ensure we do not load multiple\n // versions of Bokeh and its dependencies at the same time.\n // In recent versions we use the root._bokeh_is_initializing flag\n // to determine whether there is an ongoing attempt to initialize\n // bokeh, however for backward compatibility we also try to ensure\n // that we do not start loading a newer (Panel>=1.0 and Bokeh>3) version\n // before older versions are fully initialized.\n if (root._bokeh_is_initializing && Date.now() > root._bokeh_timeout) {\n root._bokeh_is_initializing = false;\n root._bokeh_onload_callbacks = undefined;\n console.log(\"Bokeh: BokehJS was loaded multiple times but one version failed to initialize.\");\n load_or_wait();\n } else if (root._bokeh_is_initializing || (typeof root._bokeh_is_initializing === \"undefined\" && root._bokeh_onload_callbacks !== undefined)) {\n setTimeout(load_or_wait, 100);\n } else {\n Bokeh = root.Bokeh;\n bokeh_loaded = Bokeh != null && (Bokeh.version === py_version || (Bokeh.versions !== undefined && Bokeh.versions.has(py_version)));\n root._bokeh_is_initializing = true\n root._bokeh_onload_callbacks = []\n if (!reloading && (!bokeh_loaded || is_dev)) {\n\troot.Bokeh = undefined;\n }\n load_libs(css_urls, js_urls, js_modules, js_exports, function() {\n\tconsole.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n\trun_inline_js();\n });\n }\n }\n // Give older versions of the autoload script a head-start to ensure\n // they initialize before we start loading newer version.\n setTimeout(load_or_wait, 100)\n}(window));" + "application/javascript": "(function(root) {\n function now() {\n return new Date();\n }\n\n var force = true;\n var py_version = '3.2.1'.replace('rc', '-rc.').replace('.dev', '-dev.');\n var is_dev = py_version.indexOf(\"+\") !== -1 || py_version.indexOf(\"-\") !== -1;\n var reloading = false;\n var Bokeh = root.Bokeh;\n var bokeh_loaded = Bokeh != null && (Bokeh.version === py_version || (Bokeh.versions !== undefined && Bokeh.versions.has(py_version)));\n\n if (typeof (root._bokeh_timeout) === \"undefined\" || force) {\n root._bokeh_timeout = Date.now() + 5000;\n root._bokeh_failed_load = false;\n }\n\n function run_callbacks() {\n try {\n root._bokeh_onload_callbacks.forEach(function(callback) {\n if (callback != null)\n callback();\n });\n } finally {\n delete root._bokeh_onload_callbacks;\n }\n console.debug(\"Bokeh: all callbacks have finished\");\n }\n\n function load_libs(css_urls, js_urls, js_modules, js_exports, callback) {\n if (css_urls == null) css_urls = [];\n if (js_urls == null) js_urls = [];\n if (js_modules == null) js_modules = [];\n if (js_exports == null) js_exports = {};\n\n root._bokeh_onload_callbacks.push(callback);\n\n if (root._bokeh_is_loading > 0) {\n console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n return null;\n }\n if (js_urls.length === 0 && js_modules.length === 0 && Object.keys(js_exports).length === 0) {\n run_callbacks();\n return null;\n }\n if (!reloading) {\n console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n }\n\n function on_load() {\n root._bokeh_is_loading--;\n if (root._bokeh_is_loading === 0) {\n console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n run_callbacks()\n }\n }\n window._bokeh_on_load = on_load\n\n function on_error() {\n console.error(\"failed to load \" + url);\n }\n\n var skip = [];\n if (window.requirejs) {\n window.requirejs.config({'packages': {}, 'paths': {'vtk': 'https://cdn.jsdelivr.net/npm/vtk.js@20.0.1/vtk', 'jspanel': 'https://cdn.jsdelivr.net/npm/jspanel4@4.12.0/dist/jspanel', 'jspanel-modal': 'https://cdn.jsdelivr.net/npm/jspanel4@4.12.0/dist/extensions/modal/jspanel.modal', 'jspanel-tooltip': 'https://cdn.jsdelivr.net/npm/jspanel4@4.12.0/dist/extensions/tooltip/jspanel.tooltip', 'jspanel-hint': 'https://cdn.jsdelivr.net/npm/jspanel4@4.12.0/dist/extensions/hint/jspanel.hint', 'jspanel-layout': 'https://cdn.jsdelivr.net/npm/jspanel4@4.12.0/dist/extensions/layout/jspanel.layout', 'jspanel-contextmenu': 'https://cdn.jsdelivr.net/npm/jspanel4@4.12.0/dist/extensions/contextmenu/jspanel.contextmenu', 'jspanel-dock': 'https://cdn.jsdelivr.net/npm/jspanel4@4.12.0/dist/extensions/dock/jspanel.dock', 'gridstack': 'https://cdn.jsdelivr.net/npm/gridstack@7.2.3/dist/gridstack-all', 'notyf': 'https://cdn.jsdelivr.net/npm/notyf@3/notyf.min'}, 'shim': {'vtk': {'exports': 'vtk'}, 'jspanel': {'exports': 'jsPanel'}, 'gridstack': {'exports': 'GridStack'}}});\n require([\"vtk\"], function() {\n\ton_load()\n })\n require([\"jspanel\"], function(jsPanel) {\n\twindow.jsPanel = jsPanel\n\ton_load()\n })\n require([\"jspanel-modal\"], function() {\n\ton_load()\n })\n require([\"jspanel-tooltip\"], function() {\n\ton_load()\n })\n require([\"jspanel-hint\"], function() {\n\ton_load()\n })\n require([\"jspanel-layout\"], function() {\n\ton_load()\n })\n require([\"jspanel-contextmenu\"], function() {\n\ton_load()\n })\n require([\"jspanel-dock\"], function() {\n\ton_load()\n })\n require([\"gridstack\"], function(GridStack) {\n\twindow.GridStack = GridStack\n\ton_load()\n })\n require([\"notyf\"], function() {\n\ton_load()\n })\n root._bokeh_is_loading = css_urls.length + 10;\n } else {\n root._bokeh_is_loading = css_urls.length + js_urls.length + js_modules.length + Object.keys(js_exports).length;\n }\n\n var existing_stylesheets = []\n var links = document.getElementsByTagName('link')\n for (var i = 0; i < links.length; i++) {\n var link = links[i]\n if (link.href != null) {\n\texisting_stylesheets.push(link.href)\n }\n }\n for (var i = 0; i < css_urls.length; i++) {\n var url = css_urls[i];\n if (existing_stylesheets.indexOf(url) !== -1) {\n\ton_load()\n\tcontinue;\n }\n const element = document.createElement(\"link\");\n element.onload = on_load;\n element.onerror = on_error;\n element.rel = \"stylesheet\";\n element.type = \"text/css\";\n element.href = url;\n console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n document.body.appendChild(element);\n } if (((window['vtk'] !== undefined) && (!(window['vtk'] instanceof HTMLElement))) || window.requirejs) {\n var urls = ['https://cdn.holoviz.org/panel/1.2.1/dist/bundled/abstractvtkplot/vtk.js@20.0.1/vtk.js'];\n for (var i = 0; i < urls.length; i++) {\n skip.push(urls[i])\n }\n } if (((window['jsPanel'] !== undefined) && (!(window['jsPanel'] instanceof HTMLElement))) || window.requirejs) {\n var urls = ['https://cdn.holoviz.org/panel/1.2.1/dist/bundled/floatpanel/jspanel4@4.12.0/dist/jspanel.js', 'https://cdn.holoviz.org/panel/1.2.1/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/modal/jspanel.modal.js', 'https://cdn.holoviz.org/panel/1.2.1/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/tooltip/jspanel.tooltip.js', 'https://cdn.holoviz.org/panel/1.2.1/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/hint/jspanel.hint.js', 'https://cdn.holoviz.org/panel/1.2.1/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/layout/jspanel.layout.js', 'https://cdn.holoviz.org/panel/1.2.1/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/contextmenu/jspanel.contextmenu.js', 'https://cdn.holoviz.org/panel/1.2.1/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/dock/jspanel.dock.js'];\n for (var i = 0; i < urls.length; i++) {\n skip.push(urls[i])\n }\n } if (((window['GridStack'] !== undefined) && (!(window['GridStack'] instanceof HTMLElement))) || window.requirejs) {\n var urls = ['https://cdn.holoviz.org/panel/1.2.1/dist/bundled/gridstack/gridstack@7.2.3/dist/gridstack-all.js'];\n for (var i = 0; i < urls.length; i++) {\n skip.push(urls[i])\n }\n } if (((window['Notyf'] !== undefined) && (!(window['Notyf'] instanceof HTMLElement))) || window.requirejs) {\n var urls = ['https://cdn.holoviz.org/panel/1.2.1/dist/bundled/notificationarea/notyf@3/notyf.min.js'];\n for (var i = 0; i < urls.length; i++) {\n skip.push(urls[i])\n }\n } var existing_scripts = []\n var scripts = document.getElementsByTagName('script')\n for (var i = 0; i < scripts.length; i++) {\n var script = scripts[i]\n if (script.src != null) {\n\texisting_scripts.push(script.src)\n }\n }\n for (var i = 0; i < js_urls.length; i++) {\n var url = js_urls[i];\n if (skip.indexOf(url) !== -1 || existing_scripts.indexOf(url) !== -1) {\n\tif (!window.requirejs) {\n\t on_load();\n\t}\n\tcontinue;\n }\n var element = document.createElement('script');\n element.onload = on_load;\n element.onerror = on_error;\n element.async = false;\n element.src = url;\n console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n document.head.appendChild(element);\n }\n for (var i = 0; i < js_modules.length; i++) {\n var url = js_modules[i];\n if (skip.indexOf(url) !== -1 || existing_scripts.indexOf(url) !== -1) {\n\tif (!window.requirejs) {\n\t on_load();\n\t}\n\tcontinue;\n }\n var element = document.createElement('script');\n element.onload = on_load;\n element.onerror = on_error;\n element.async = false;\n element.src = url;\n element.type = \"module\";\n console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n document.head.appendChild(element);\n }\n for (const name in js_exports) {\n var url = js_exports[name];\n if (skip.indexOf(url) >= 0 || root[name] != null) {\n\tif (!window.requirejs) {\n\t on_load();\n\t}\n\tcontinue;\n }\n var element = document.createElement('script');\n element.onerror = on_error;\n element.async 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append_mime, {\n safe: true,\n index: 0\n });\n}\n\nif (window.Jupyter !== undefined) {\n try {\n var events = require('base/js/events');\n var OutputArea = require('notebook/js/outputarea').OutputArea;\n if (OutputArea.prototype.mime_types().indexOf(EXEC_MIME_TYPE) == -1) {\n register_renderer(events, OutputArea);\n }\n } catch(err) {\n }\n}\n", + "application/vnd.holoviews_load.v0+json": "" }, "metadata": {}, "output_type": "display_data" @@ -943,7 +420,7 @@ "source": [ "```{bibliography}\n", " :filter: cited and ({\"chapter1/nitsche\"} >= docnames)\n", - "```" + "```\n" ] }, { diff --git a/chapter1/nitsche.py b/chapter1/nitsche.py index 001a092e..1beea3e0 100644 --- a/chapter1/nitsche.py +++ b/chapter1/nitsche.py @@ -16,7 +16,7 @@ # # Weak imposition of Dirichlet conditions for the Poisson problem # Author: Jørgen S. Dokken # -# In this section, we will go through how to solve the Poisson problem from the [Fundamentals](fundamentals.ipynb) tutorial using Nitsche's method {cite}`Nitsche1971`. +# In this section, we will go through how to solve the Poisson problem from the [Fundamentals](fundamentals_code.ipynb) tutorial using Nitsche's method {cite}`Nitsche1971`. # The idea of weak imposition is that we add additional terms to the variational formulation to impose the boundary condition, instead of modifying the matrix system using strong imposition (lifting). # # We start by importing the required modules and creating the mesh and function space for our solution diff --git a/docker/Dockerfile b/docker/Dockerfile index 2aafeb5a..a858ed35 100644 --- a/docker/Dockerfile +++ b/docker/Dockerfile @@ -1,6 +1,6 @@ # Execute from root of repo as: docker buildx build --platform=linux/arm64,linux/amd64 -f docker/Dockerfile ./docker/ --progress=plain -FROM ghcr.io/fenics/dolfinx/lab:v0.7.2 +FROM ghcr.io/fenics/dolfinx/lab:v0.7.3 ARG TARGETPLATFORM @@ -30,7 +30,7 @@ RUN if [ "$TARGETPLATFORM" = "linux/arm64" ]; then python3 -m pip install "https RUN if [ "$TARGETPLATFORM" = "linux/amd64" ]; then python3 -m pip install vtk; fi ADD pyproject.toml /tmp/pyproject.toml -RUN python3 -m pip install --no-cache-dir --no-binary=h5py -v pyproject.toml +RUN python3 -m pip install --no-cache-dir --no-binary=h5py -v . RUN python3 -m pip cache purge RUN jupyter lab build ENTRYPOINT ["jupyter", "lab", "--ip", "0.0.0.0", "--no-browser", "--allow-root"] diff --git a/pyproject.toml b/pyproject.toml index d9ecf8bc..a63b9500 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -7,8 +7,6 @@ name = "DOLFINx_Tutorial" version = "0.7.2" dependencies = [ "jupyter-book", - # Pin docutils due to https://github.com/executablebooks/jupyter-book/issues/1970#issuecomment-1466051277 - "docutils==0.17.1", "meshio", "h5py", "seaborn",