C++/Python FEniCS/dolfinx@c1ac475

dolfinx/main/cpp/demos/demo_biharmonic.html

@@ -136,8 +136,8 @@ <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-466a2d45-4d8b-4a73-a47b-c136fba9059c">
-<span class="eqno">(1)<a class="headerlink" href="#equation-466a2d45-4d8b-4a73-a47b-c136fba9059c" title="Permalink to this equation"></a></span>\[\begin{align}
+<div class="amsmath math notranslate nohighlight" id="equation-8c39a9db-e129-470c-8223-87606c0f30b0">
+<span class="eqno">(1)<a class="headerlink" href="#equation-8c39a9db-e129-470c-8223-87606c0f30b0" 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/d0/d1d/MeshTags_8h_source.html

@@ -253,7 +253,7 @@
 <div class="ttc" id="anamespacedolfinx_1_1common_html_a3d4f61eb18edfadf84cdbb81afe141d5"><div class="ttname"><a href="../../d7/de1/namespacedolfinx_1_1common.html#a3d4f61eb18edfadf84cdbb81afe141d5">dolfinx::common::sort_unique</a></div><div class="ttdeci">std::pair&lt; std::vector&lt; typename U::value_type &gt;, std::vector&lt; typename V::value_type &gt; &gt; sort_unique(const U &amp;indices, const V &amp;values)</div><div class="ttdoc">Sort two arrays based on the values in array indices.</div><div class="ttdef"><b>Definition</b> utils.h:30</div></div>
 <div class="ttc" id="anamespacedolfinx_1_1mesh_html"><div class="ttname"><a href="../../dd/d7d/namespacedolfinx_1_1mesh.html">dolfinx::mesh</a></div><div class="ttdoc">Mesh data structures and algorithms on meshes.</div><div class="ttdef"><b>Definition</b> DofMap.h:32</div></div>
 <div class="ttc" id="anamespacedolfinx_1_1mesh_html_a2bdcd9e9469ae3185e6ca6a3ee3fa581"><div class="ttname"><a href="../../dd/d7d/namespacedolfinx_1_1mesh.html#a2bdcd9e9469ae3185e6ca6a3ee3fa581">dolfinx::mesh::create_meshtags</a></div><div class="ttdeci">MeshTags&lt; T &gt; create_meshtags(std::shared_ptr&lt; const Topology &gt; topology, int dim, const graph::AdjacencyList&lt; std::int32_t &gt; &amp;entities, std::span&lt; const T &gt; values)</div><div class="ttdoc">Create MeshTags from arrays.</div><div class="ttdef"><b>Definition</b> MeshTags.h:138</div></div>
-<div class="ttc" id="anamespacedolfinx_1_1mesh_html_af81ae5994989c886b804b3f6b64275fd"><div class="ttname"><a href="../../dd/d7d/namespacedolfinx_1_1mesh.html#af81ae5994989c886b804b3f6b64275fd">dolfinx::mesh::entities_to_index</a></div><div class="ttdeci">std::vector&lt; std::int32_t &gt; entities_to_index(const Topology &amp;topology, int dim, std::span&lt; const std::int32_t &gt; entities)</div><div class="ttdoc">Get entity indices for entities defined by their vertices.</div><div class="ttdef"><b>Definition</b> Topology.cpp:1406</div></div>
+<div class="ttc" id="anamespacedolfinx_1_1mesh_html_af81ae5994989c886b804b3f6b64275fd"><div class="ttname"><a href="../../dd/d7d/namespacedolfinx_1_1mesh.html#af81ae5994989c886b804b3f6b64275fd">dolfinx::mesh::entities_to_index</a></div><div class="ttdeci">std::vector&lt; std::int32_t &gt; entities_to_index(const Topology &amp;topology, int dim, std::span&lt; const std::int32_t &gt; entities)</div><div class="ttdoc">Get entity indices for entities defined by their vertices.</div><div class="ttdef"><b>Definition</b> Topology.cpp:1407</div></div>
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dolfinx/main/cpp/doxygen/d0/d47/mesh_2utils_8h_source.html

@@ -1219,9 +1219,9 @@
 <div class="ttc" id="aclassdolfinx_1_1mesh_1_1Geometry_html_aeec2bf02c10e1b68ca9641158b79c569"><div class="ttname"><a href="../../d8/dfb/classdolfinx_1_1mesh_1_1Geometry.html#aeec2bf02c10e1b68ca9641158b79c569">dolfinx::mesh::Geometry::x</a></div><div class="ttdeci">std::span&lt; const value_type &gt; x() const</div><div class="ttdoc">Access geometry degrees-of-freedom data (const version).</div><div class="ttdef"><b>Definition</b> Geometry.h:169</div></div>
 <div class="ttc" id="aclassdolfinx_1_1mesh_1_1Mesh_html"><div class="ttname"><a href="../../d0/ddf/classdolfinx_1_1mesh_1_1Mesh.html">dolfinx::mesh::Mesh</a></div><div class="ttdoc">A Mesh consists of a set of connected and numbered mesh topological entities, and geometry data.</div><div class="ttdef"><b>Definition</b> Mesh.h:23</div></div>
 <div class="ttc" id="aclassdolfinx_1_1mesh_1_1Topology_html"><div class="ttname"><a href="../../da/d02/classdolfinx_1_1mesh_1_1Topology.html">dolfinx::mesh::Topology</a></div><div class="ttdoc">Topology stores the topology of a mesh, consisting of mesh entities and connectivity (incidence relat...</div><div class="ttdef"><b>Definition</b> Topology.h:45</div></div>
-<div class="ttc" id="aclassdolfinx_1_1mesh_1_1Topology_html_a39db2634618c5273e0f5120e6f4b372e"><div class="ttname"><a href="../../da/d02/classdolfinx_1_1mesh_1_1Topology.html#a39db2634618c5273e0f5120e6f4b372e">dolfinx::mesh::Topology::create_entity_permutations</a></div><div class="ttdeci">void create_entity_permutations()</div><div class="ttdoc">Compute entity permutations and reflections.</div><div class="ttdef"><b>Definition</b> Topology.cpp:916</div></div>
-<div class="ttc" id="aclassdolfinx_1_1mesh_1_1Topology_html_a3f60ad95ea22fbc7aaa71bd6fd6867a3"><div class="ttname"><a href="../../da/d02/classdolfinx_1_1mesh_1_1Topology.html#a3f60ad95ea22fbc7aaa71bd6fd6867a3">dolfinx::mesh::Topology::create_entities</a></div><div class="ttdeci">std::int32_t create_entities(int dim)</div><div class="ttdoc">Create entities of given topological dimension.</div><div class="ttdef"><b>Definition</b> Topology.cpp:836</div></div>
-<div class="ttc" id="aclassdolfinx_1_1mesh_1_1Topology_html_aa1804e93bcd191ae0ad91df7ae775836"><div class="ttname"><a href="../../da/d02/classdolfinx_1_1mesh_1_1Topology.html#aa1804e93bcd191ae0ad91df7ae775836">dolfinx::mesh::Topology::dim</a></div><div class="ttdeci">int dim() const noexcept</div><div class="ttdoc">Return the topological dimension of the mesh.</div><div class="ttdef"><b>Definition</b> Topology.cpp:799</div></div>
+<div class="ttc" id="aclassdolfinx_1_1mesh_1_1Topology_html_a39db2634618c5273e0f5120e6f4b372e"><div class="ttname"><a href="../../da/d02/classdolfinx_1_1mesh_1_1Topology.html#a39db2634618c5273e0f5120e6f4b372e">dolfinx::mesh::Topology::create_entity_permutations</a></div><div class="ttdeci">void create_entity_permutations()</div><div class="ttdoc">Compute entity permutations and reflections.</div><div class="ttdef"><b>Definition</b> Topology.cpp:917</div></div>
+<div class="ttc" id="aclassdolfinx_1_1mesh_1_1Topology_html_a3f60ad95ea22fbc7aaa71bd6fd6867a3"><div class="ttname"><a href="../../da/d02/classdolfinx_1_1mesh_1_1Topology.html#a3f60ad95ea22fbc7aaa71bd6fd6867a3">dolfinx::mesh::Topology::create_entities</a></div><div class="ttdeci">std::int32_t create_entities(int dim)</div><div class="ttdoc">Create entities of given topological dimension.</div><div class="ttdef"><b>Definition</b> Topology.cpp:837</div></div>
+<div class="ttc" id="aclassdolfinx_1_1mesh_1_1Topology_html_aa1804e93bcd191ae0ad91df7ae775836"><div class="ttname"><a href="../../da/d02/classdolfinx_1_1mesh_1_1Topology.html#aa1804e93bcd191ae0ad91df7ae775836">dolfinx::mesh::Topology::dim</a></div><div class="ttdeci">int dim() const noexcept</div><div class="ttdoc">Return the topological dimension of the mesh.</div><div class="ttdef"><b>Definition</b> Topology.cpp:800</div></div>
 <div class="ttc" id="aconceptdolfinx_1_1mesh_1_1MarkerFn_html"><div class="ttname"><a href="../../da/d7b/conceptdolfinx_1_1mesh_1_1MarkerFn.html">dolfinx::mesh::MarkerFn</a></div><div class="ttdoc">Requirements on function for geometry marking.</div><div class="ttdef"><b>Definition</b> utils.h:461</div></div>
 <div class="ttc" id="amesh_2utils_8h_html_a27837f44f6ff45f6809893315743cb38"><div class="ttname"><a href="../../d0/d47/mesh_2utils_8h.html#a27837f44f6ff45f6809893315743cb38">dolfinx::mesh::impl::reorder_list</a></div><div class="ttdeci">void reorder_list(std::span&lt; T &gt; list, std::span&lt; const std::int32_t &gt; nodemap)</div><div class="ttdoc">Re-order an adjacency list of fixed degree.</div><div class="ttdef"><b>Definition</b> utils.h:46</div></div>
 <div class="ttc" id="amesh_2utils_8h_html_a299052cd10f30e851971964dec00d651"><div class="ttname"><a href="../../d0/d47/mesh_2utils_8h.html#a299052cd10f30e851971964dec00d651">dolfinx::mesh::impl::compute_vertex_coords_boundary</a></div><div class="ttdeci">std::tuple&lt; std::vector&lt; std::int32_t &gt;, std::vector&lt; T &gt;, std::vector&lt; std::int32_t &gt; &gt; compute_vertex_coords_boundary(const mesh::Mesh&lt; T &gt; &amp;mesh, int dim, std::span&lt; const std::int32_t &gt; facets)</div><div class="ttdoc">The coordinates of 'vertices' for for entities of a given dimension that are attached to specified fa...</div><div class="ttdef"><b>Definition</b> utils.h:77</div></div>
@@ -1236,13 +1236,13 @@
 <div class="ttc" id="anamespacedolfinx_1_1graph_html_aa2e8bbea5ac3a27249e3155bc455f887"><div class="ttname"><a href="../../d9/d69/namespacedolfinx_1_1graph.html#aa2e8bbea5ac3a27249e3155bc455f887">dolfinx::graph::partition_fn</a></div><div class="ttdeci">std::function&lt; graph::AdjacencyList&lt; std::int32_t &gt;( MPI_Comm, int, const AdjacencyList&lt; std::int64_t &gt; &amp;, bool)&gt; partition_fn</div><div class="ttdoc">Signature of functions for computing the parallel partitioning of a distributed graph.</div><div class="ttdef"><b>Definition</b> partition.h:31</div></div>
 <div class="ttc" id="anamespacedolfinx_1_1graph_html_ab7912ac9b196655f4fc4189efa96d794"><div class="ttname"><a href="../../d9/d69/namespacedolfinx_1_1graph.html#ab7912ac9b196655f4fc4189efa96d794">dolfinx::graph::partition_graph</a></div><div class="ttdeci">AdjacencyList&lt; std::int32_t &gt; partition_graph(MPI_Comm comm, int nparts, const AdjacencyList&lt; std::int64_t &gt; &amp;local_graph, bool ghosting)</div><div class="ttdoc">Partition graph across processes using the default graph partitioner.</div><div class="ttdef"><b>Definition</b> partition.cpp:21</div></div>
 <div class="ttc" id="anamespacedolfinx_1_1mesh_html"><div class="ttname"><a href="../../dd/d7d/namespacedolfinx_1_1mesh.html">dolfinx::mesh</a></div><div class="ttdoc">Mesh data structures and algorithms on meshes.</div><div class="ttdef"><b>Definition</b> DofMap.h:32</div></div>
-<div class="ttc" id="anamespacedolfinx_1_1mesh_html_a332133c6fd59b509e8a60420ba7bc67b"><div class="ttname"><a href="../../dd/d7d/namespacedolfinx_1_1mesh.html#a332133c6fd59b509e8a60420ba7bc67b">dolfinx::mesh::create_topology</a></div><div class="ttdeci">Topology create_topology(MPI_Comm comm, std::span&lt; const std::int64_t &gt; cells, std::span&lt; const std::int64_t &gt; original_cell_index, std::span&lt; const int &gt; ghost_owners, CellType cell_type, std::span&lt; const std::int64_t &gt; boundary_vertices)</div><div class="ttdoc">Create a mesh topology.</div><div class="ttdef"><b>Definition</b> Topology.cpp:1312</div></div>
+<div class="ttc" id="anamespacedolfinx_1_1mesh_html_a332133c6fd59b509e8a60420ba7bc67b"><div class="ttname"><a href="../../dd/d7d/namespacedolfinx_1_1mesh.html#a332133c6fd59b509e8a60420ba7bc67b">dolfinx::mesh::create_topology</a></div><div class="ttdeci">Topology create_topology(MPI_Comm comm, std::span&lt; const std::int64_t &gt; cells, std::span&lt; const std::int64_t &gt; original_cell_index, std::span&lt; const int &gt; ghost_owners, CellType cell_type, std::span&lt; const std::int64_t &gt; boundary_vertices)</div><div class="ttdoc">Create a mesh topology.</div><div class="ttdef"><b>Definition</b> Topology.cpp:1313</div></div>
 <div class="ttc" id="anamespacedolfinx_1_1mesh_html_a38d109d131f3180f43267fcf9fe9c4c4"><div class="ttname"><a href="../../dd/d7d/namespacedolfinx_1_1mesh.html#a38d109d131f3180f43267fcf9fe9c4c4">dolfinx::mesh::GhostMode</a></div><div class="ttdeci">GhostMode</div><div class="ttdoc">Enum for different partitioning ghost modes.</div><div class="ttdef"><b>Definition</b> utils.h:36</div></div>
 <div class="ttc" id="anamespacedolfinx_1_1mesh_html_a4517d9b85ae3658d28f603f29116130a"><div class="ttname"><a href="../../dd/d7d/namespacedolfinx_1_1mesh.html#a4517d9b85ae3658d28f603f29116130a">dolfinx::mesh::create_geometry</a></div><div class="ttdeci">Geometry&lt; typename std::remove_reference_t&lt; typename U::value_type &gt; &gt; create_geometry(const Topology &amp;topology, const std::vector&lt; fem::CoordinateElement&lt; std::remove_reference_t&lt; typename U::value_type &gt; &gt; &gt; &amp;elements, std::span&lt; const std::int64_t &gt; nodes, std::span&lt; const std::int64_t &gt; xdofs, const U &amp;x, int dim, std::function&lt; std::vector&lt; int &gt;(const graph::AdjacencyList&lt; std::int32_t &gt; &amp;)&gt; reorder_fn=nullptr)</div><div class="ttdoc">Build Geometry from input data.</div><div class="ttdef"><b>Definition</b> Geometry.h:264</div></div>
 <div class="ttc" id="anamespacedolfinx_1_1mesh_html_a611ba63b9b9197c08613cccdc41464ee"><div class="ttname"><a href="../../dd/d7d/namespacedolfinx_1_1mesh.html#a611ba63b9b9197c08613cccdc41464ee">dolfinx::mesh::create_mesh</a></div><div class="ttdeci">Mesh&lt; typename std::remove_reference_t&lt; typename U::value_type &gt; &gt; create_mesh(MPI_Comm comm, MPI_Comm commt, std::span&lt; const std::int64_t &gt; cells, const fem::CoordinateElement&lt; typename std::remove_reference_t&lt; typename U::value_type &gt; &gt; &amp;element, MPI_Comm commg, const U &amp;x, std::array&lt; std::size_t, 2 &gt; xshape, const CellPartitionFunction &amp;partitioner)</div><div class="ttdoc">Create a distributed mesh from mesh data using a provided graph partitioning function for determining...</div><div class="ttdef"><b>Definition</b> utils.h:782</div></div>
 <div class="ttc" id="anamespacedolfinx_1_1mesh_html_a67fa456882009e9a0025061837b40e55"><div class="ttname"><a href="../../dd/d7d/namespacedolfinx_1_1mesh.html#a67fa456882009e9a0025061837b40e55">dolfinx::mesh::cell_normals</a></div><div class="ttdeci">std::vector&lt; T &gt; cell_normals(const Mesh&lt; T &gt; &amp;mesh, int dim, std::span&lt; const std::int32_t &gt; entities)</div><div class="ttdoc">Compute normal to given cell (viewed as embedded in 3D)</div><div class="ttdef"><b>Definition</b> utils.h:265</div></div>
 <div class="ttc" id="anamespacedolfinx_1_1mesh_html_a6abcbdca3e3aae2fe00ad6ea7186cb0c"><div class="ttname"><a href="../../dd/d7d/namespacedolfinx_1_1mesh.html#a6abcbdca3e3aae2fe00ad6ea7186cb0c">dolfinx::mesh::cell_entity_type</a></div><div class="ttdeci">CellType cell_entity_type(CellType type, int d, int index)</div><div class="ttdoc">Return type of cell for entity of dimension d at given entity index.</div><div class="ttdef"><b>Definition</b> cell_types.cpp:64</div></div>
-<div class="ttc" id="anamespacedolfinx_1_1mesh_html_a6af09e67e8db0d211e9b00393cf9f5ae"><div class="ttname"><a href="../../dd/d7d/namespacedolfinx_1_1mesh.html#a6af09e67e8db0d211e9b00393cf9f5ae">dolfinx::mesh::create_subtopology</a></div><div class="ttdeci">std::tuple&lt; Topology, std::vector&lt; int32_t &gt;, std::vector&lt; int32_t &gt; &gt; create_subtopology(const Topology &amp;topology, int dim, std::span&lt; const std::int32_t &gt; entities)</div><div class="ttdoc">Create a topology for a subset of entities of a given topological dimension.</div><div class="ttdef"><b>Definition</b> Topology.cpp:1323</div></div>
+<div class="ttc" id="anamespacedolfinx_1_1mesh_html_a6af09e67e8db0d211e9b00393cf9f5ae"><div class="ttname"><a href="../../dd/d7d/namespacedolfinx_1_1mesh.html#a6af09e67e8db0d211e9b00393cf9f5ae">dolfinx::mesh::create_subtopology</a></div><div class="ttdeci">std::tuple&lt; Topology, std::vector&lt; int32_t &gt;, std::vector&lt; int32_t &gt; &gt; create_subtopology(const Topology &amp;topology, int dim, std::span&lt; const std::int32_t &gt; entities)</div><div class="ttdoc">Create a topology for a subset of entities of a given topological dimension.</div><div class="ttdef"><b>Definition</b> Topology.cpp:1324</div></div>
 <div class="ttc" id="anamespacedolfinx_1_1mesh_html_a7f4773c26421814d452b07150df4ece8"><div class="ttname"><a href="../../dd/d7d/namespacedolfinx_1_1mesh.html#a7f4773c26421814d452b07150df4ece8">dolfinx::mesh::locate_entities_boundary</a></div><div class="ttdeci">std::vector&lt; std::int32_t &gt; locate_entities_boundary(const Mesh&lt; T &gt; &amp;mesh, int dim, U marker)</div><div class="ttdoc">Compute indices of all mesh entities that are attached to an owned boundary facet and evaluate to tru...</div><div class="ttdef"><b>Definition</b> utils.h:555</div></div>
 <div class="ttc" id="anamespacedolfinx_1_1mesh_html_a80294da14ab051e9f8eaf72080a7ee17"><div class="ttname"><a href="../../dd/d7d/namespacedolfinx_1_1mesh.html#a80294da14ab051e9f8eaf72080a7ee17">dolfinx::mesh::num_cell_vertices</a></div><div class="ttdeci">int num_cell_vertices(CellType type)</div><div class="ttdef"><b>Definition</b> cell_types.cpp:147</div></div>
 <div class="ttc" id="anamespacedolfinx_1_1mesh_html_a8294c20389ab1f3b4c5b70eaa6f1dc00"><div class="ttname"><a href="../../dd/d7d/namespacedolfinx_1_1mesh.html#a8294c20389ab1f3b4c5b70eaa6f1dc00">dolfinx::mesh::h</a></div><div class="ttdeci">std::vector&lt; T &gt; h(const Mesh&lt; T &gt; &amp;mesh, std::span&lt; const std::int32_t &gt; entities, int dim)</div><div class="ttdoc">Compute greatest distance between any two vertices of the mesh entities (h).</div><div class="ttdef"><b>Definition</b> utils.h:211</div></div>