Merge branch 'main' into inclusion_map

ChangeLog.rst

@@ -28,7 +28,7 @@ solver <https://bitbucket.org/fenics-project/dolfin/>`_.
 - Remove ``Mesh::size``. Use ``Mesh::num_entities`` instead.
 - Improved mesh topology computation performance.
 - Remove excessive calls to MPI init. It may now be necessary in some
-  cases to explicitly intialise MPI.
+  cases to explicitly initialise MPI.
 - Improvements to sparsity pattern computation.
 - Addition of some interfaces using ``Eigen::Map/ref`` in addition to
   ``dolfin::Array(View)``.  ``dolfin::Array(View)``interfaces will be
@@ -146,7 +146,7 @@ solver <https://bitbucket.org/fenics-project/dolfin/>`_.
 - Require polynomial degree or finite element for Expressions in the
   Python interface (fixes Issue #355,
   https://bitbucket.org/fenics-project/dolfin/issues/355)
-- Switch to Google Test framwork for C++ unit tests
+- Switch to Google Test framework for C++ unit tests
 - Fix bug when reading domain data from mesh file for a ghosted mesh
 - Add interface for manipulating mesh geometry using (higher-order) FE
   functions: free functions set_coordinates, get_coordinates,
@@ -223,7 +223,7 @@ solver <https://bitbucket.org/fenics-project/dolfin/>`_.
   #443)
 - Add quadrature rules for multimesh/cut-cell integration up to order
   6
-- Implement MPI reductions and XML ouput of Table class
+- Implement MPI reductions and XML output of Table class
 - list_timings() is now collective and returns MPI average across
   processes
 - Add dump_timings_to_xml()
@@ -324,7 +324,7 @@ solver <https://bitbucket.org/fenics-project/dolfin/>`_.
   module
 - Add function Form::set_some_coefficients()
 - Remove Boost.MPI dependency
-- Change GenericMatrix::compresss to return a new matrix (7be3a29)
+- Change GenericMatrix::compress to return a new matrix (7be3a29)
 - Add function GenericTensor::empty()
 - Deprecate resizing of linear algebra via the GenericFoo interfaces
   (fixes #213)
@@ -387,7 +387,7 @@ solver <https://bitbucket.org/fenics-project/dolfin/>`_.
 - Fixes bug where child/parent hierarchy in Python were destroyed
 - Add utility script dolfin-get-demos
 - MeshFunctions in python now support iterable protocol
-- Add timed VTK output for Mesh and MeshFunction in addtion to
+- Add timed VTK output for Mesh and MeshFunction in addition to
   Functions
 - Expose ufc::dofmap::tabulate_entity_dofs to GenericDofMap interface
 - Expose ufc::dofmap::num_entity_dofs to GenericDofMap interface
@@ -477,7 +477,7 @@ solver <https://bitbucket.org/fenics-project/dolfin/>`_.
 - Add sparray method in the Python interface of GenericMatrix,
   requires scipy.sparse
 - Make methods that return a view of contiguous c-arrays, via a NumPy
-  array, keep a reference from the object so it wont get out of scope
+  array, keep a reference from the object so it won't get out of scope
 - Add parameter: "use_petsc_signal_handler", which enables/disable
   PETSc system signals
 - Avoid unnecessary resize of result vector for A*b
@@ -684,7 +684,7 @@ solver <https://bitbucket.org/fenics-project/dolfin/>`_.
 - Thread-safe fixed in Function class
 - Make GenericFunction::eval thread-safe (Data class removed)
 - Optimize and speedup topology computation (mesh.init())
-- Add function Mesh::clean() for cleaning out auxilliary topology data
+- Add function Mesh::clean() for cleaning out auxiliary topology data
 - Improve speed and accuracy of timers
 - Fix bug in 3D uniform mesh refinement
 - Add built-in meshes UnitTriangle and UnitTetrahedron
@@ -761,7 +761,7 @@ solver <https://bitbucket.org/fenics-project/dolfin/>`_.
   refinement
 - Add functionality for smoothing the boundary of a mesh
 - Speedup assembly over exterior facets by not using BoundaryMesh
-- Mesh refinement improvements, remove unecessary copying in Python
+- Mesh refinement improvements, remove unnecessary copying in Python
   interface
 - Clean PETSc and Epetra Krylov solvers
 - Add separate preconditioner classes for PETSc and Epetra solvers
@@ -935,7 +935,7 @@ solver <https://bitbucket.org/fenics-project/dolfin/>`_.
   check range
 - Add unit tests to the memorycheck
 - Add call to clean up libxml2 parser at exit
-- Remove unecessary arguments in DofMap member functions
+- Remove unnecessary arguments in DofMap member functions
 - Remove reference constructors from DofMap, FiniteElement and
   FunctionSpace
 - Use a shared_ptr to store the mesh in DofMap objects
@@ -1215,7 +1215,7 @@ solver <https://bitbucket.org/fenics-project/dolfin/>`_.
 - Disable PETSc by default, use --enable-petsc to enable
 - Modify ODE solver interface for u0() and f()
 - Add class ConvectionMatrix
-- Readd classes LoadVector, MassMatrix, StiffnessMatrix
+- Read classes LoadVector, MassMatrix, StiffnessMatrix
 - Add matrix factory for simple creation of standard finite element
   matrices
 - Collect static solvers in LU and GMRES
@@ -1500,7 +1500,7 @@ solver <https://bitbucket.org/fenics-project/dolfin/>`_.
 - Update PETSc wrappers NewVector, NewMatrix, and NewGMRES
 - Fix initialization of PETSc
 - Add mono-adaptive cG(q) and dG(q) solvers (experimental)
-- Implementation of new assebly: NewFEM, using output from FFC
+- Implementation of new assembly: NewFEM, using output from FFC
 - Add access to mesh for nodes, cells, faces and edges
 - Add Tecplot I/O interface; contributed by Garth N. Wells
 
@@ -1623,7 +1623,7 @@ solver <https://bitbucket.org/fenics-project/dolfin/>`_.
 - Optimize Lagrange polynomials
 - Optimize sparsity: use stl containers
 - Optimize choice of discrete residual for multi-adaptive solver
-- Don't save solution in benchmark proble
+- Don't save solution in benchmark problem
 - Improve computation of divergence factor for underdamped systems
 - Don't check residual on first slab for fixed time step
 - Decrease largest (default) time step to 0.1

cpp/CMakeLists.txt

@@ -382,7 +382,7 @@ if(NOT DOLFINX_UFCX_PYTHON)
   # Check in CONFIG mode, i.e. look for installed ufcxConfig.cmake
   find_package(ufcx 0.10 REQUIRED CONFIG)
 else()
-  # Check in MODULE mode (using FindUFCX.cmake) using Python intepreter.
+  # Check in MODULE mode (using FindUFCX.cmake) using Python interpreter.
   find_package(
     Python3
     COMPONENTS Interpreter

cpp/doc/Doxyfile

@@ -86,7 +86,7 @@ CREATE_SUBDIRS         = YES
 # level increment doubles the number of directories, resulting in 4096
 # directories at level 8 which is the default and also the maximum value. The
 # sub-directories are organized in 2 levels, the first level always has a fixed
-# numer of 16 directories.
+# number of 16 directories.
 # Minimum value: 0, maximum value: 8, default value: 8.
 # This tag requires that the tag CREATE_SUBDIRS is set to YES.
 
@@ -1007,7 +1007,7 @@ RECURSIVE              = YES
 # Note that relative paths are relative to the directory from which doxygen is
 # run.
 
-# EXCLUDE                = 
+# EXCLUDE                =
 
 # The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
 # directories that are symbolic links (a Unix file system feature) are excluded

cpp/doc/source/jupytext_process.py

@@ -54,7 +54,7 @@ def process():
             with open(myst_file, "w") as fw:
                 fw.write(cpp_myst_text)
 
-            # There is a posibility to use jupyter-notebooks with C++/C kernels
+            # There is a possibility to use jupyter-notebooks with C++/C kernels
             # ipynb_file = (demo_doc_dir / fname.name).with_suffix(".ipynb")
             # jupytext.write(cpp_demo, ipynb_file, fmt="ipynb")
 

cpp/dolfinx/common/IndexMap.cpp

@@ -416,7 +416,7 @@ compute_submap_indices(const IndexMap& imap,
   // If required, preserve the order of the ghost indices
   if (order == IndexMapOrder::preserve)
   {
-    // Build (old postion, new position) list for ghosts and sort
+    // Build (old position, new position) list for ghosts and sort
     std::vector<std::pair<std::int32_t, std::int32_t>> pos;
     pos.reserve(submap_ghost.size());
     for (std::int32_t idx : submap_ghost)

cpp/dolfinx/common/sort.h

@@ -32,7 +32,7 @@ struct __radix_sort
   /// dolfixn::radix_sort(a); // a = {1, 2, 3}
   /// @endcode
   /// Additionally the projection based approach of the STL library is
-  /// adpated, which allows for versatile usage, for example the easy
+  /// adapted, which allows for versatile usage, for example the easy
   /// realization of an argsort
   /// @code
   /// std::array<std::int16_t, 3> a{2, 3, 1};

cpp/dolfinx/fem/DirichletBC.h

@@ -338,7 +338,7 @@ class DirichletBC
     if (g->shape.size() != V->element()->value_shape().size())
     {
       throw std::runtime_error(
-          "Rank mis-match between Constant and function space in DirichletBC");
+          "Rank mismatch between Constant and function space in DirichletBC");
     }
 
     if (g->value.size() != _function_space->dofmap()->bs())

cpp/dolfinx/fem/FiniteElement.h

@@ -39,7 +39,7 @@ struct BasixElementData
       element; ///< Finite element.
   std::optional<std::vector<std::size_t>> value_shape
       = std::nullopt;    ///< Value shape. Can only be set for scalar `element`.
-  bool symmetry = false; ///< Symmetry. Should ony set set for 2nd-order tensor
+  bool symmetry = false; ///< Symmetry. Should only set set for 2nd-order tensor
                          ///< blocked elements.
 };
 
@@ -65,8 +65,8 @@ class FiniteElement
   /// for a vector in 3D or `{2, 2}` for a rank-2 tensor in 2D. Can only
   /// be set for blocked scalar `element`. For other elements and scalar
   /// elements it should be `std::nullopt`.
-  /// @param[in] symmetric Is the element a symmetric tensor? Should ony
-  /// set for 2nd-order tensor blocked elements.
+  /// @param[in] symmetric Is the element a symmetric tensor? Should
+  /// only set for 2nd-order tensor blocked elements.
   FiniteElement(const basix::FiniteElement<geometry_type>& element,
                 std::optional<std::vector<std::size_t>> value_shape
                 = std::nullopt,
@@ -792,7 +792,7 @@ class FiniteElement
   /// consistent physical element degree-of-freedom ordering. The
   /// permutation is computed in-place.
   ///
-  /// @param[in,out] doflist Indicies associated with the
+  /// @param[in,out] doflist Indices associated with the
   /// degrees-of-freedom. Size=`num_dofs`.
   /// @param[in] cell_permutation Permutation data for the cell.
   void permute(std::span<std::int32_t> doflist,
@@ -811,7 +811,7 @@ class FiniteElement
   /// element degree-of-freedom ordering. The permutation is computed
   /// in-place.
   ///
-  /// @param[in,out] doflist Indicies associated with the
+  /// @param[in,out] doflist Indices associated with the
   /// degrees-of-freedom. Size=`num_dofs`.
   /// @param[in] cell_permutation Permutation data for the cell.
   void permute_inv(std::span<std::int32_t> doflist,

cpp/dolfinx/fem/Form.h

@@ -48,8 +48,8 @@ struct integral_data
   /// @param[in] id Domain ID.
   /// @param[in] kernel Integration kernel.
   /// @param[in] entities Indices of entities to integrate over.
-  /// @param[in] coeffs Indicies of the coefficients are present
-  /// (active) in `kernel`.
+  /// @param[in] coeffs Indices of the coefficients are present (active)
+  /// in `kernel`.
   template <typename K, typename V, typename W>
     requires std::is_convertible_v<
                  std::remove_cvref_t<K>,
@@ -70,11 +70,11 @@ struct integral_data
   /// @param[in] id Domain ID.
   /// @param[in] kernel Integration kernel.
   /// @param[in] entities Indices of entities to integrate over.
-  /// @param[in] coeffs Indicies of the coefficients that are active in
+  /// @param[in] coeffs Indices of the coefficients that are active in
   /// the `kernel`.
   ///
-  /// @note This version allows `entities` to be passed as a std::span,
-  /// which is then copied.
+  /// @note This version allows `entities` to be passed as a
+  /// `std::span`, which is then copied.
   template <typename K, typename W>
     requires std::is_convertible_v<
                  std::remove_cvref_t<K>,

cpp/dolfinx/fem/interpolate.h

@@ -128,7 +128,7 @@ void interpolate(Function<T, U>& u, std::span<const T> f,
 
 namespace impl
 {
-/// @brief Convenience typdef
+/// @brief Convenience typedef
 template <typename T, std::size_t D>
 using mdspan_t = MDSPAN_IMPL_STANDARD_NAMESPACE::mdspan<
     T, MDSPAN_IMPL_STANDARD_NAMESPACE::dextents<std::size_t, D>>;

cpp/dolfinx/graph/partitioners.cpp

@@ -634,7 +634,7 @@ graph::partition_fn graph::kahip::partitioner(int mode, int seed,
     // KaHIP internally relies on an unsigned long long int type, which is not
     // easily convertible to a general mpi type due to platform specific
     // differences. So we can not rely on the general mpi_t<> mapping and do it
-    // by hand in this sole occurence.
+    // by hand in this sole occurrence.
     MPI_Allgather(&num_local_nodes, 1, MPI_UNSIGNED_LONG_LONG,
                   node_disp.data() + 1, 1, MPI_UNSIGNED_LONG_LONG, comm);
     std::partial_sum(node_disp.begin(), node_disp.end(), node_disp.begin());

cpp/dolfinx/io/XDMFFile.cpp

@@ -422,7 +422,7 @@ std::pair<mesh::CellType, int> XDMFFile::read_cell_type(std::string grid_name,
   const std::pair<std::string, int> cell_type_str
       = xdmf_utils::get_cell_type(topology_node);
 
-  // Get toplogical dimensions
+  // Get topological dimensions
   mesh::CellType cell_type = mesh::to_type(cell_type_str.first);
 
   return {cell_type, cell_type_str.second};

cpp/dolfinx/io/xdmf_function.cpp

@@ -128,7 +128,7 @@ void xdmf_function::add_function(MPI_Comm comm, const fem::Function<T, U>& u,
     if (cmap.degree() > 2
         and element->basix_element().lagrange_variant() != cmap.variant())
     {
-      throw std::runtime_error("Mis-match in Lagrange family. Maybe the "
+      throw std::runtime_error("Mismatch in Lagrange family. Maybe the "
                                "Function needs to be interpolated?");
     }
 

cpp/dolfinx/io/xdmf_mesh.cpp

@@ -302,7 +302,7 @@ xdmf_mesh::read_topology_data(MPI_Comm comm, hid_t h5_id,
   const std::pair<std::string, int> cell_type_str
       = xdmf_utils::get_cell_type(topology_node);
 
-  // Get toplogical dimensions
+  // Get topological dimensions
   mesh::CellType cell_type = mesh::to_type(cell_type_str.first);
 
   // Get topology dataset node

cpp/dolfinx/la/Vector.h

@@ -344,7 +344,7 @@ void orthonormalize(std::vector<std::reference_wrapper<V>> basis)
 
 /// @brief Test if basis is orthonormal.
 ///
-/// Returns true if ||x_i - x_j|| - delta_{ij} < eps fro all i, j, and
+/// Returns true if ||x_i - x_j|| - delta_{ij} < eps for all i, j, and
 /// otherwise false.
 ///
 /// @param[in] basis Set of vectors to check.
@@ -361,7 +361,7 @@ bool is_orthonormal(
   for (std::size_t i = 0; i < basis.size(); i++)
   {
     for (std::size_t j = i; j < basis.size(); j++)
-    {
+  {
       T delta_ij = (i == j) ? T(1) : T(0);
       auto dot_ij = inner_product(basis[i].get(), basis[j].get());
       if (std::norm(delta_ij - dot_ij) > eps)

cpp/dolfinx/mesh/Geometry.h

@@ -77,7 +77,7 @@ class Geometry
   {
     assert(_x.size() % 3 == 0);
     if (_x.size() / 3 != _input_global_indices.size())
-      throw std::runtime_error("Geometry size mis-match");
+      throw std::runtime_error("Geometry size mismatch.");
 
     if (_dofmaps.size() != _cmaps.size())
     {

cpp/dolfinx/mesh/utils.h

@@ -975,7 +975,7 @@ Mesh<typename std::remove_reference_t<typename U::value_type>> create_mesh(
       auto [unique_end, range_end] = std::ranges::unique(vertices);
       vertices.erase(unique_end, range_end);
 
-      // Remove -1 if it appears as first entity. This can happend in
+      // Remove -1 if it appears as first entity. This can happen in
       // mixed topology meshes where '-1' is used to pad facet data when
       // cells facets have differing numbers of vertices.
       if (!vertices.empty() and vertices.front() == -1)
@@ -1003,7 +1003,7 @@ Mesh<typename std::remove_reference_t<typename U::value_type>> create_mesh(
         }
       }
 
-      // Compute row permutaion
+      // Compute row permutation
       const std::vector<std::int32_t> perm = dolfinx::sort_by_perm(
           std::span<const std::int64_t>(facets0), max_v);
 
@@ -1132,7 +1132,7 @@ Mesh<typename std::remove_reference_t<typename U::value_type>> create_mesh(
 /// rank for each cell. If not callable, cells are not redistributed.
 /// @return A mesh distributed on the communicator `comm`.
 ///
-/// This constructor provdes a simplified interface to the more general
+/// This constructor provides a simplified interface to the more general
 /// ::create_mesh constructor, which supports meshes with more than one
 /// cell type.
 template <typename U>

cpp/dolfinx/refinement/interval.h

@@ -176,7 +176,7 @@ compute_refinement_data(const mesh::Mesh<T>& mesh,
   }
 
   assert(cell_topology.size() == 2 * refined_cell_count);
-  assert((!compute_parent_cell) || (parent_cell->size() == refined_cell_count));
+  assert(!compute_parent_cell or parent_cell->size() == refined_cell_count);
 
   std::vector<std::int32_t> offsets(refined_cell_count + 1);
   std::ranges::generate(offsets, [i = 0]() mutable { return 2 * i++; });

cpp/test/mesh/generation.cpp

@@ -112,7 +112,7 @@ TEMPLATE_TEST_CASE("Interval mesh (parallel)", "[mesh][interval]", float,
               {2}, {2}, {2, 0}, {0, 2}, {0},    {0},    {0}};
     }
     else
-      FAIL("Test only supports <= 3 processes");
+      SKIP("Test only supports <= 3 processes");
 
     return graph::AdjacencyList<std::int32_t>(std::move(data));
   };

cpp/test/mesh/refinement/interval.cpp

@@ -243,9 +243,9 @@ TEMPLATE_TEST_CASE("Interval Refinement (parallel)",
 TEMPLATE_TEST_CASE("Interval uniform refinement", "[refinement][interva]",
                    double, float)
 {
-  auto interval
-      = dolfinx::mesh::create_interval<TestType>(MPI_COMM_WORLD, 2, {0.0, 1.0});
+  auto interval = dolfinx::mesh::create_interval<TestType>(MPI_COMM_WORLD, 20,
+                                                           {0.0, 1.0});
   auto [refined, parent_edge, parent_facet]
       = dolfinx::refinement::refine(interval, std::nullopt);
-  CHECK(refined.topology()->index_map(0)->size_global() == 5);
+  CHECK(refined.topology()->index_map(0)->size_global() == 41);
 }

python/demo/demo_half_loaded_waveguide.py

@@ -94,7 +94,6 @@
 # $\mathrm{TM}_x$ modes, and the possible $k_z$ can be found by solving
 # a set of transcendental equations, which is shown here below:
 #
-#
 # $$
 # \textrm{For TE}_x \textrm{ modes}:
 # \begin{cases}
@@ -234,7 +233,7 @@ def Omega_v(x):
 # wavelength, which we consider fixed at $\lambda = h/0.2$. If we focus
 # on non-magnetic material only, we can also use $\mu_r=1$.
 #
-# Now we can assume a known dependance on $z$:
+# Now we can assume a known dependence on $z$:
 #
 # $$
 # \mathbf{E}(x, y, z)=\left[\mathbf{E}_{t}(x, y)+\hat{z} E_{z}(x, y)\right]

python/demo/demo_hdg.py

@@ -166,11 +166,13 @@ def u_e(x):
 # Apply Dirichlet boundary conditions
 # We begin by locating the boundary facets of msh
 msh_boundary_facets = mesh.exterior_facet_indices(msh.topology)
+
 # Since the boundary condition is enforced in the facet space, we must
 # use the mesh_to_facet_mesh map to get the corresponding facets in
 # facet_mesh
 facet_mesh_boundary_facets = mesh_to_facet_mesh[msh_boundary_facets]
-# Get the dofs and apply the bondary condition
+
+# Get the dofs and apply the boundary condition
 facet_mesh.topology.create_connectivity(fdim, fdim)
 dofs = fem.locate_dofs_topological(Vbar, fdim, facet_mesh_boundary_facets)
 bc = fem.dirichletbc(dtype(0.0), dofs, Vbar)