C++/Python FEniCS/dolfinx@e842cb3

Author: FEniCS GitHub Actions

dolfinx/main/cpp/demos/demo_biharmonic.html

@@ -135,8 +135,8 @@ <h3>Weak formulation<a class="headerlink" href="#weak-formulation" title="Link t
 \forall \ K \in \mathcal{T} \right\}
 \]</div>
 <p>and considering the boundary conditions</p>
-<div class="amsmath math notranslate nohighlight" id="equation-c71e9064-751d-4c26-95b8-26620dd67d00">
-<span class="eqno">(1)<a class="headerlink" href="#equation-c71e9064-751d-4c26-95b8-26620dd67d00" title="Permalink to this equation"></a></span>\[\begin{align}
+<div class="amsmath math notranslate nohighlight" id="equation-79c699de-77cf-4844-9553-75a79d1abdd0">
+<span class="eqno">(1)<a class="headerlink" href="#equation-79c699de-77cf-4844-9553-75a79d1abdd0" title="Permalink to this equation"></a></span>\[\begin{align}
 u &amp;= 0 \quad {\rm on} \ \partial\Omega, \\
 \nabla^{2} u &amp;= 0 \quad {\rm on} \ \partial\Omega,
 \end{align}\]</div>

dolfinx/main/cpp/doxygen/d2/d8a/interval_8h_source.html

@@ -222,7 +222,7 @@
 <div class="line"><a id="l00129" name="l00129"></a><span class="lineno">  129</span>      = <a class="code hl_function" href="../../d9/dd6/namespacedolfinx_1_1refinement.html#aaa134a721f1c98625a950d8da05a29f4">adjust_indices</a>(*mesh.topology()-&gt;index_map(0), number_of_refined_cells);</div>
 <div class="line"><a id="l00130" name="l00130"></a><span class="lineno">  130</span> </div>
 <div class="line"><a id="l00131" name="l00131"></a><span class="lineno">  131</span>  <span class="comment">// Build the topology on the new vertices</span></div>
-<div class="line"><a id="l00132" name="l00132"></a><span class="lineno">  132</span>  <span class="keyword">const</span> std::int32_t refined_cell_count</div>
+<div class="line"><a id="l00132" name="l00132"></a><span class="lineno">  132</span>  std::size_t refined_cell_count</div>
 <div class="line"><a id="l00133" name="l00133"></a><span class="lineno">  133</span>      = mesh.topology()-&gt;index_map(1)-&gt;size_local() + number_of_refined_cells;</div>
 <div class="line"><a id="l00134" name="l00134"></a><span class="lineno">  134</span> </div>
 <div class="line"><a id="l00135" name="l00135"></a><span class="lineno">  135</span>  std::vector&lt;std::int64_t&gt; cell_topology;</div>

dolfinx/main/cpp/doxygen/d3/d12/discreteoperators_8h_source.html

@@ -279,9 +279,9 @@
 <div class="line"><a id="l00214" name="l00214"></a><span class="lineno">  214</span>  <span class="comment">// 3**rank to ensure that we can visualize them correctly in Paraview</span></div>
 <div class="line"><a id="l00215" name="l00215"></a><span class="lineno">  215</span>  std::span&lt;const std::size_t&gt; value_shape</div>
 <div class="line"><a id="l00216" name="l00216"></a><span class="lineno">  216</span>      = u.function_space()-&gt;element()-&gt;value_shape();</div>
-<div class="line"><a id="l00217" name="l00217"></a><span class="lineno">  217</span>  <span class="keywordtype">int</span> <a class="code hl_function" href="../../da/dfe/namespacedolfinx_1_1MPI.html#ab6a01b5be2487cb6674b70ce6a89bad0">rank</a> = value_shape.size();</div>
-<div class="line"><a id="l00218" name="l00218"></a><span class="lineno">  218</span>  <span class="keywordtype">int</span> num_comp = std::reduce(value_shape.begin(), value_shape.end(), 1,</div>
-<div class="line"><a id="l00219" name="l00219"></a><span class="lineno">  219</span>                             std::multiplies{});</div>
+<div class="line"><a id="l00217" name="l00217"></a><span class="lineno">  217</span>  std::size_t <a class="code hl_function" href="../../da/dfe/namespacedolfinx_1_1MPI.html#ab6a01b5be2487cb6674b70ce6a89bad0">rank</a> = value_shape.size();</div>
+<div class="line"><a id="l00218" name="l00218"></a><span class="lineno">  218</span>  std::size_t num_comp = std::reduce(value_shape.begin(), value_shape.end(), 1,</div>
+<div class="line"><a id="l00219" name="l00219"></a><span class="lineno">  219</span>                                     std::multiplies{});</div>
 <div class="line"><a id="l00220" name="l00220"></a><span class="lineno">  220</span>  <span class="keywordflow">if</span> (num_comp &lt; std::pow(3, rank))</div>
 <div class="line"><a id="l00221" name="l00221"></a><span class="lineno">  221</span>    num_comp = std::pow(3, rank);</div>
 <div class="line"><a id="l00222" name="l00222"></a><span class="lineno">  222</span> </div>
@@ -483,8 +483,8 @@
 <div class="line"><a id="l00462" name="l00462"></a><span class="lineno">  462</span>            <span class="keyword">const</span> <span class="keyword">typename</span> adios2_writer::U&lt;T&gt;&amp; u, std::string engine,</div>
 <div class="line"><a id="l00463" name="l00463"></a><span class="lineno">  463</span>            VTXMeshPolicy mesh_policy = VTXMeshPolicy::update)</div>
 <div class="line"><a id="l00464" name="l00464"></a><span class="lineno">  464</span>      : ADIOS2Writer(comm, filename, <span class="stringliteral">&quot;VTX function writer&quot;</span>, engine),</div>
-<div class="line"><a id="l00465" name="l00465"></a><span class="lineno">  465</span>        _mesh(impl_adios2::extract_common_mesh&lt;T&gt;(u)),</div>
-<div class="line"><a id="l00466" name="l00466"></a><span class="lineno">  466</span>        _mesh_reuse_policy(mesh_policy), _u(u), _is_piecewise_constant(false)</div>
+<div class="line"><a id="l00465" name="l00465"></a><span class="lineno">  465</span>        _mesh(impl_adios2::extract_common_mesh&lt;T&gt;(u)), _u(u),</div>
+<div class="line"><a id="l00466" name="l00466"></a><span class="lineno">  466</span>        _mesh_reuse_policy(mesh_policy), _is_piecewise_constant(false)</div>
 <div class="line"><a id="l00467" name="l00467"></a><span class="lineno">  467</span>  {</div>
 <div class="line"><a id="l00468" name="l00468"></a><span class="lineno">  468</span>    <span class="keywordflow">if</span> (u.empty())</div>
 <div class="line"><a id="l00469" name="l00469"></a><span class="lineno">  469</span>      <span class="keywordflow">throw</span> std::runtime_error(<span class="stringliteral">&quot;VTXWriter fem::Function list is empty.&quot;</span>);</div>

dolfinx/main/cpp/doxygen/d6/d6e/Expression_8h_source.html

@@ -770,10 +770,10 @@
 <div class="ttc" id="aclassdolfinx_1_1fem_1_1CoordinateElement_html_ac6b1bbe66ff8d6c90fc0ab516405b7fb"><div class="ttname"><a href="../../d9/d35/classdolfinx_1_1fem_1_1CoordinateElement.html#ac6b1bbe66ff8d6c90fc0ab516405b7fb">dolfinx::fem::CoordinateElement::is_affine</a></div><div class="ttdeci">bool is_affine() const noexcept</div><div class="ttdef"><b>Definition</b> CoordinateElement.h:266</div></div>
 <div class="ttc" id="aclassdolfinx_1_1fem_1_1CoordinateElement_html_ad1ee76129425323769389247a42971c8"><div class="ttname"><a href="../../d9/d35/classdolfinx_1_1fem_1_1CoordinateElement.html#ad1ee76129425323769389247a42971c8">dolfinx::fem::CoordinateElement::compute_jacobian_determinant</a></div><div class="ttdeci">static double compute_jacobian_determinant(const U &amp;J, std::span&lt; typename U::value_type &gt; w)</div><div class="ttdoc">Compute the determinant of the Jacobian.</div><div class="ttdef"><b>Definition</b> CoordinateElement.h:159</div></div>
 <div class="ttc" id="aclassdolfinx_1_1fem_1_1Expression_html"><div class="ttname"><a href="../../d2/db9/classdolfinx_1_1fem_1_1Expression.html">dolfinx::fem::Expression</a></div><div class="ttdoc">An Expression represents a mathematical expression evaluated at a pre-defined points on a reference c...</div><div class="ttdef"><b>Definition</b> Expression.h:41</div></div>
-<div class="ttc" id="aclassdolfinx_1_1fem_1_1Expression_html_a076c44ef333ff656ae7b28587f524aea"><div class="ttname"><a href="../../d2/db9/classdolfinx_1_1fem_1_1Expression.html#a076c44ef333ff656ae7b28587f524aea">dolfinx::fem::Expression::X</a></div><div class="ttdeci">std::pair&lt; std::vector&lt; geometry_type &gt;, std::array&lt; std::size_t, 2 &gt; &gt; X() const</div><div class="ttdoc">Evaluation point coordinates on the reference cell.</div><div class="ttdef"><b>Definition</b> Expression.h:165</div></div>
-<div class="ttc" id="aclassdolfinx_1_1fem_1_1Expression_html_a11e930f85bec72f7e366d5f47fd65688"><div class="ttname"><a href="../../d2/db9/classdolfinx_1_1fem_1_1Expression.html#a11e930f85bec72f7e366d5f47fd65688">dolfinx::fem::Expression::coefficients</a></div><div class="ttdeci">const std::vector&lt; std::shared_ptr&lt; const Function&lt; scalar_type, geometry_type &gt; &gt; &gt; &amp; coefficients() const</div><div class="ttdoc">Expression coefficients.</div><div class="ttdef"><b>Definition</b> Expression.h:114</div></div>
-<div class="ttc" id="aclassdolfinx_1_1fem_1_1Expression_html_a31c80a8331ab87d3b2c7cd89b1d50c99"><div class="ttname"><a href="../../d2/db9/classdolfinx_1_1fem_1_1Expression.html#a31c80a8331ab87d3b2c7cd89b1d50c99">dolfinx::fem::Expression::argument_space</a></div><div class="ttdeci">std::shared_ptr&lt; const FunctionSpace&lt; geometry_type &gt; &gt; argument_space() const</div><div class="ttdoc">Argument function space.</div><div class="ttdef"><b>Definition</b> Expression.h:105</div></div>
-<div class="ttc" id="aclassdolfinx_1_1fem_1_1Expression_html_a7d326295a6362a9b6f112e0efa5a7de7"><div class="ttname"><a href="../../d2/db9/classdolfinx_1_1fem_1_1Expression.html#a7d326295a6362a9b6f112e0efa5a7de7">dolfinx::fem::Expression::value_size</a></div><div class="ttdeci">int value_size() const</div><div class="ttdoc">Value size of the Expression result.</div><div class="ttdef"><b>Definition</b> Expression.h:155</div></div>
+<div class="ttc" id="aclassdolfinx_1_1fem_1_1Expression_html_a076c44ef333ff656ae7b28587f524aea"><div class="ttname"><a href="../../d2/db9/classdolfinx_1_1fem_1_1Expression.html#a076c44ef333ff656ae7b28587f524aea">dolfinx::fem::Expression::X</a></div><div class="ttdeci">std::pair&lt; std::vector&lt; geometry_type &gt;, std::array&lt; std::size_t, 2 &gt; &gt; X() const</div><div class="ttdoc">Evaluation point coordinates on the reference cell.</div><div class="ttdef"><b>Definition</b> Expression.h:166</div></div>
+<div class="ttc" id="aclassdolfinx_1_1fem_1_1Expression_html_a11e930f85bec72f7e366d5f47fd65688"><div class="ttname"><a href="../../d2/db9/classdolfinx_1_1fem_1_1Expression.html#a11e930f85bec72f7e366d5f47fd65688">dolfinx::fem::Expression::coefficients</a></div><div class="ttdeci">const std::vector&lt; std::shared_ptr&lt; const Function&lt; scalar_type, geometry_type &gt; &gt; &gt; &amp; coefficients() const</div><div class="ttdoc">Expression coefficients.</div><div class="ttdef"><b>Definition</b> Expression.h:115</div></div>
+<div class="ttc" id="aclassdolfinx_1_1fem_1_1Expression_html_a31c80a8331ab87d3b2c7cd89b1d50c99"><div class="ttname"><a href="../../d2/db9/classdolfinx_1_1fem_1_1Expression.html#a31c80a8331ab87d3b2c7cd89b1d50c99">dolfinx::fem::Expression::argument_space</a></div><div class="ttdeci">std::shared_ptr&lt; const FunctionSpace&lt; geometry_type &gt; &gt; argument_space() const</div><div class="ttdoc">Argument function space.</div><div class="ttdef"><b>Definition</b> Expression.h:106</div></div>
+<div class="ttc" id="aclassdolfinx_1_1fem_1_1Expression_html_a7d326295a6362a9b6f112e0efa5a7de7"><div class="ttname"><a href="../../d2/db9/classdolfinx_1_1fem_1_1Expression.html#a7d326295a6362a9b6f112e0efa5a7de7">dolfinx::fem::Expression::value_size</a></div><div class="ttdeci">int value_size() const</div><div class="ttdoc">Value size of the Expression result.</div><div class="ttdef"><b>Definition</b> Expression.h:156</div></div>
 <div class="ttc" id="aclassdolfinx_1_1fem_1_1FunctionSpace_html"><div class="ttname"><a href="../../d9/d69/classdolfinx_1_1fem_1_1FunctionSpace.html">dolfinx::fem::FunctionSpace</a></div><div class="ttdoc">This class represents a finite element function space defined by a mesh, a finite element,...</div><div class="ttdef"><b>Definition</b> FunctionSpace.h:34</div></div>
 <div class="ttc" id="aclassdolfinx_1_1fem_1_1Function_html"><div class="ttname"><a href="../../d7/d76/classdolfinx_1_1fem_1_1Function.html">dolfinx::fem::Function</a></div><div class="ttdef"><b>Definition</b> Function.h:47</div></div>
 <div class="ttc" id="aclassdolfinx_1_1fem_1_1Function_html_a04ce55eb3c49b869437e81d8c4c14ffc"><div class="ttname"><a href="../../d7/d76/classdolfinx_1_1fem_1_1Function.html#a04ce55eb3c49b869437e81d8c4c14ffc">dolfinx::fem::Function::geometry_type</a></div><div class="ttdeci">U geometry_type</div><div class="ttdoc">Geometry type of the Mesh that the Function is defined on.</div><div class="ttdef"><b>Definition</b> Function.h:53</div></div>

dolfinx/main/cpp/doxygen/df/d34/ADIOS2Writers_8h_source.html

@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "markdown",
-   "id": "4486d074",
+   "id": "685ae755",
    "metadata": {},
    "source": [
     "# Matrix-free conjugate gradient solver for the Poisson equation\n",
@@ -73,7 +73,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "bca0779c",
+   "id": "ddc66fd9",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -83,7 +83,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "c9947055",
+   "id": "6964d0d1",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -93,7 +93,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "1d2e4902",
+   "id": "44255e51",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -104,7 +104,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "46b2652a",
+   "id": "59c3e9e9",
    "metadata": {},
    "source": [
     "We begin by using {py:func}`create_rectangle\n",
@@ -117,7 +117,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "0421b6f3",
+   "id": "6b6f83fb",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -130,7 +130,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "1ad4cabc",
+   "id": "3a8a67e4",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -141,7 +141,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "3d4bf154",
+   "id": "6365aa84",
    "metadata": {},
    "source": [
     "The second argument to {py:class}`functionspace\n",
@@ -160,7 +160,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "d1915452",
+   "id": "876114dd",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -171,7 +171,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "ad6a49c7",
+   "id": "167fdd03",
    "metadata": {},
    "source": [
     "We now find the degrees of freedom that are associated with the boundary\n",
@@ -182,7 +182,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "31b1c299",
+   "id": "198bd848",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -191,7 +191,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "734df530",
+   "id": "0cd1423c",
    "metadata": {},
    "source": [
     "and use {py:func}`dirichletbc <dolfinx.fem.dirichletbc>` to define the\n",
@@ -204,7 +204,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "89d4ec67",
+   "id": "bf29a7d3",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -215,7 +215,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "a687b3f1",
+   "id": "c5e4c95f",
    "metadata": {},
    "source": [
     "Next, we express the variational problem using UFL."
@@ -224,7 +224,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "9457e35d",
+   "id": "2c9126c7",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -239,7 +239,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "e56777dc",
+   "id": "2a3ee408",
    "metadata": {},
    "source": [
     "For the matrix-free solvers we also define a second linear form `M` as\n",
@@ -255,7 +255,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "92e2df3d",
+   "id": "5cec9588",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -266,7 +266,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "8c4e304f",
+   "id": "779cb6a8",
    "metadata": {},
    "source": [
     "### Matrix-free conjugate gradient solver\n",
@@ -280,7 +280,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "116d0266",
+   "id": "a22a065b",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -295,7 +295,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "3302e107",
+   "id": "a8d3f546",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -306,7 +306,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "8654e846",
+   "id": "331102cb",
    "metadata": {
     "lines_to_next_cell": 2
    },
@@ -319,7 +319,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "d6b8ac8e",
+   "id": "15242a9f",
    "metadata": {
     "lines_to_next_cell": 2
    },
@@ -342,7 +342,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "65d78966",
+   "id": "8e07715b",
    "metadata": {
     "lines_to_next_cell": 2
    },
@@ -358,7 +358,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "b385c10f",
+   "id": "17cc1fbe",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -404,7 +404,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "6e45da1a",
+   "id": "1af84b00",
    "metadata": {},
    "source": [
     "This matrix-free solver is now used to compute the finite element\n",
@@ -415,7 +415,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "1968ac88",
+   "id": "d59e612d",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -427,7 +427,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4dafa784",
+   "id": "d9a56f9b",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -438,7 +438,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "291f1b7e",
+   "id": "f7edce05",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -450,7 +450,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "fe7733e9",
+   "id": "6a6913df",
    "metadata": {},
    "outputs": [],
    "source": [