Merge pull request #15386 from drwells/codespell-9.5

Release preparation: Run codespell.
dealii · Jun 20, 2023 · 971eabf · 971eabf
2 parents a8a5855 + 642f32c
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diff --git a/contrib/python-bindings/source/export_mapping.cc b/contrib/python-bindings/source/export_mapping.cc
@@ -37,7 +37,7 @@ namespace python
     " face with the given face number face_no. Ideally the point is     \n"
     " near the face face_no, but any point in the cell can technically  \n"
     " be projected. The returned point is of dimension dim with         \n"
-    " dim-1 coodinate value explicitly set to zero.                     \n";
+    " dim-1 coordinate value explicitly set to zero.                    \n";
 
 
   void

diff --git a/contrib/python-bindings/source/export_triangulation.cc b/contrib/python-bindings/source/export_triangulation.cc
@@ -229,8 +229,8 @@ namespace python
     "with respect to the origin. Additional points are sums of these dim    \n"
     "vectors. Colorizing is done according to hyper_rectangle().            \n"
     "Note: This function silently reorders the vertices on the cells to     \n"
-    "lexicographic ordering (see GridReordering::reoder_grid()). In other   \n"
-    "words, if reordering of the vertices does occur, the ordering of       \n"
+    "lexicographic ordering (see GridTools::consistently_order_cells()). In \n"
+    "other words, if reordering of the vertices does occur, the ordering of \n"
     "vertices in the array of corners will no longer refer to the same      \n"
     "triangulation.                                                         \n";
 

diff --git a/contrib/python-bindings/source/triangulation_wrapper.cc b/contrib/python-bindings/source/triangulation_wrapper.cc
@@ -1191,7 +1191,7 @@ namespace python
     AssertThrow(
       spacedim == dim,
       ExcMessage(
-        "This function is only implementd for dim equal to spacedim."));
+        "This function is only implemented for dim equal to spacedim."));
     // Extract the PointWrapper object from the python list
     const int size = boost::python::len(vertices);
     AssertThrow(size > 0, ExcMessage("The vertices list is empty."));
@@ -1718,7 +1718,7 @@ namespace python
     else
       AssertThrow(false,
                   ExcMessage(
-                    "Thie combination of dim-spacedim is not supported."));
+                    "This combination of dim-spacedim is not supported."));
   }
 
 

diff --git a/contrib/utilities/indent.py b/contrib/utilities/indent.py
@@ -276,7 +276,7 @@ def process(arguments):
     # Blocks (some) threads until all the threads finished their tasks.
     # Works similar to MPI_Barrier().
     # In other words, threads wait until all the tasks in task_queue
-    # have finshed.
+    # have finished.
     #
     task_queue.join()
 

diff --git a/doc/doxygen/CMakeLists.txt b/doc/doxygen/CMakeLists.txt
@@ -126,7 +126,7 @@ file(GLOB _source_files
 foreach (_source ${_source_files})
   file(READ "${_source}" contents)
   string(REGEX MATCH "Copyright .C. +([0-9]+ - )?([0-9]+)" _copyright "${contents}")
-  if (NOT _copright STREQUAL "")
+  if (NOT "${_copyright}" STREQUAL "")
     string(REGEX MATCH "[0-9]+\$" _year "${_copyright}")
 
     if (NOT _year STREQUAL ""   AND   _year GREATER _last_year)

diff --git a/doc/news/changes/incompatibilities/20221211Munch b/doc/news/changes/incompatibilities/20221211Munch
@@ -1,9 +1,9 @@
-Fixed: The function ParamerHandler::add_parameter() used to
+Fixed: The function ParameterHandler::add_parameter() used to
 call the internal action. Within that step, the action
 converts the default value to a string and back afterwards.
 This can lead to round-off errors so that the default
 values might change in the case of floating-point numbers.
-The action is not called any more during ParamerHandler::add_parameter(),
+The action is not called any more during ParameterHandler::add_parameter(),
 fixing the problem.
 <br>
 (Peter Munch, Magdalena Schreter, 2022/12/11)
diff --git a/doc/news/changes/incompatibilities/20230511Turcksin b/doc/news/changes/incompatibilities/20230511Turcksin
@@ -1,3 +1,3 @@
-Extensive rework of CUDAWrappers::MatrixFree and CUDAWrappers::FEEvalution.
+Extensive rework of CUDAWrappers::MatrixFree and CUDAWrappers::FEEvaluation.
 <br>
 (Bruno Turcksin, 2023/05/11)
diff --git a/doc/news/changes/minor/20230118Heinz b/doc/news/changes/minor/20230118Heinz
@@ -1,4 +1,4 @@
 Improved: Introduce a function that only checks if Bounding Boxes are overlapping.
-Fixed: If a 1D BBox is completely contained in another one, it was not recognized as mergable neighbor.
+Fixed: If a 1D BBox is completely contained in another one, it was not recognized as mergeable neighbor.
 <br>
 (Johannes Heinz, 2022/07/07)
diff --git a/examples/step-27/doc/results.dox b/examples/step-27/doc/results.dox
@@ -296,6 +296,6 @@ it, we recommend reading step-18 for the former and step-40 for the
 latter case first for further background information on the topic, and
 then come back to this tutorial to try out your newly acquired skills.
 
-We go one step further in step-75: Here, we combine hp-adapative and
+We go one step further in step-75: Here, we combine hp-adaptive and
 MatrixFree methods in combination with
 parallel::distributed::Triangulation objects.
diff --git a/examples/step-44/step-44.cc b/examples/step-44/step-44.cc
@@ -73,7 +73,7 @@
 
 // Defined in these two headers are some operations that are pertinent to
 // finite strain elasticity. The first will help us compute some kinematic
-// quantities, and the second provides some stanard tensor definitions.
+// quantities, and the second provides some standard tensor definitions.
 #include <deal.II/physics/elasticity/kinematics.h>
 #include <deal.II/physics/elasticity/standard_tensors.h>
 

diff --git a/examples/step-50/doc/results.dox b/examples/step-50/doc/results.dox
@@ -293,7 +293,7 @@ matrix in 2d, and a $27\times 27$ matrix in 3d; for the coarse mesh we
 use on the $L$-shaped domain of the current program, these sizes are
 $21\times 21$ in 2d and $117\times 117$ in 3d. But if the coarse mesh
 consists of hundreds or thousands of cells, this approach will no
-longer work and might start to dominate the overall run-time of each V-cyle.
+longer work and might start to dominate the overall run-time of each V-cycle.
 A common approach is then to solve the coarse mesh problem using an
 algebraic multigrid preconditioner; this would then, however, require
 assembling the coarse matrix (even for the matrix-free version) as

diff --git a/examples/step-50/step-50.cc b/examples/step-50/step-50.cc
@@ -909,7 +909,7 @@ void LaplaceProblem<dim, degree>::assemble_multigrid()
 // This function has two parts in the integration loop: applying the negative
 // of matrix $A$ to $u_0$ by submitting the negative of the gradient, and adding
 // the right-hand side contribution by submitting the value $f$. We must be sure
-// to use `read_dof_values_plain()` for evaluating $u_0$ as `read_dof_vaues()`
+// to use `read_dof_values_plain()` for evaluating $u_0$ as `read_dof_values()`
 // would set all Dirichlet values to zero.
 //
 // Finally, the system_rhs vector is of type LA::MPI::Vector, but the

diff --git a/examples/step-69/doc/results.dox b/examples/step-69/doc/results.dox
@@ -199,7 +199,7 @@ One can also with relative ease further extend this to the 3d case:
 Solving this becomes expensive, however: The simulation was done with
 1,817 million degrees of freedom (continuous $Q_1$ finite elements)
 per component (for a total of 9.09 billion spatial degrees of freedom)
-and ran on 30,720 MPI ranks. The code achieved an average througput of
+and ran on 30,720 MPI ranks. The code achieved an average throughput of
 969M grid points per second (0.04M gridpoints per second per CPU). The
 front and back wall show a "Schlieren plot": the magnitude of the
 gradient of the density on an exponential scale from white (low) to

diff --git a/examples/step-82/step-82.cc b/examples/step-82/step-82.cc
@@ -1351,7 +1351,7 @@ namespace Step82
     // neighboring <code>neighbor_cell</code> of <code>cell</code>, namely we
     // fill-in the variable <code>discrete_hessians_neigh[face_no][i][q]</code>.
     // For the lifting terms, we only need to add the contribution of the
-    // face adjecent to <code>cell</code> and <code>neighbor_cell</code>.
+    // face adjacent to <code>cell</code> and <code>neighbor_cell</code>.
     for (unsigned int face_no = 0; face_no < cell->n_faces(); ++face_no)
       {
         const typename DoFHandler<dim>::face_iterator face =

diff --git a/include/deal.II/base/config.h.in b/include/deal.II/base/config.h.in
@@ -121,7 +121,7 @@
 /*
  * This sets the largest number of vectorization bits detected for the given
  * compiler flags and hardware (e.g. 256 for AVX on x86-64 architectures) for
- * use in deal.II's instrinsics-based VectorizedArray class.
+ * use in deal.II's intrinsics-based VectorizedArray class.
  */
 #define DEAL_II_VECTORIZATION_WIDTH_IN_BITS @DEAL_II_VECTORIZATION_WIDTH_IN_BITS@
 

diff --git a/include/deal.II/base/hdf5.h b/include/deal.II/base/hdf5.h
@@ -399,7 +399,7 @@ namespace HDF5
 
   protected:
     /**
-     * Name of the HDF5Oject. In the case of File, @p name corresponds to the
+     * Name of the HDF5Object. In the case of File, @p name corresponds to the
      * file name. In the case of Group and DataSet @p name corresponds to the
      * name of the object in the HDF5 file.
      */

diff --git a/include/deal.II/base/index_set.h b/include/deal.II/base/index_set.h
@@ -195,7 +195,7 @@ class IndexSet
    * @pre The condition <code>begin@<=end</code> needs to be satisfied. They
    * also obviously have to point into the same container.
    *
-   * @note The operations of this function are substantially more efficient if
+   * @note The operations of this function are substantially more efficient
    *   if the indices pointed to by the range of iterators are already sorted.
    *   As a consequence, it is often worth sorting the range of indices
    *   before calling this function.

diff --git a/include/deal.II/base/memory_space.h b/include/deal.II/base/memory_space.h
@@ -38,7 +38,7 @@ namespace MemorySpace
   /**
    * Structure describing the default memory space. If Kokkos was configured
    * with a GPU backend, the default memory space is the one corresponding to
-   * that backend. Otherwise, the default memory space is the the same as the
+   * that backend. Otherwise, the default memory space is the same as the
    * Host memory space.
    */
   struct Default

diff --git a/include/deal.II/base/memory_space_data.h b/include/deal.II/base/memory_space_data.h
@@ -76,7 +76,7 @@ namespace MemorySpace
      * @p values when using shared memory and the memory space is
      * MemorySpace::Host. Otherwise it is not set.
      */
-    // This a shared pointer pointer so that MemorySpaceData can be copied and
+    // This a shared pointer so that MemorySpaceData can be copied and
     // MemorySpaceData::values can be used in Kokkos::parallel_for. This
     // pointer owns the data when using shared memory with MPI. In this case,
     // the Kokkos::View @p values is non-owning. When shared memory with MPI is

diff --git a/include/deal.II/base/mpi.h b/include/deal.II/base/mpi.h
@@ -451,7 +451,7 @@ namespace Utilities
      *
      * This class models these two steps by taking two constructor
      * arguments that correspond to these two operations. It ensures
-     * that that upon destruction of the current object, both the
+     * that upon destruction of the current object, both the
      * wait and clean-up functions are called. Because the clean-up
      * function can only be called once, objects of the current
      * class can not be copied, but they can be moved.
@@ -1029,7 +1029,7 @@ namespace Utilities
      * @note This function performs a single reduction sweep.
      *
      * @pre Size of the input ArrayView has to be the same on all processes
-     *   and the input and output ArrayVew have to have the same size.
+     *   and the input and output ArrayView have to have the same size.
      */
     void
     min_max_avg(const ArrayView<const double> &my_values,

diff --git a/include/deal.II/base/mpi_remote_point_evaluation.h b/include/deal.II/base/mpi_remote_point_evaluation.h
@@ -100,7 +100,7 @@ namespace Utilities
        * GridTools::internal::DistributedComputePointLocationsInternal.
        *
        * This function is called internally by the reinit() function above.
-       * Having it as a seperate function makes it possible to setup the class
+       * Having it as a separate function makes it possible to setup the class
        * if it is known in which cells corresponding reference points are
        * located (e.g. if intersections of cells are known).
        */

diff --git a/include/deal.II/base/parameter_handler.h b/include/deal.II/base/parameter_handler.h
@@ -212,7 +212,7 @@ class MultipleParameterLoop;
  *     }
  *   @endcode
  * The advantage of using json-files is that this format is natively supported
- * by Python, simplifying the running of paramter studies tremendously.
+ * by Python, simplifying the running of parameter studies tremendously.
  *
  * <h3>Including other input files</h3>
  *

diff --git a/include/deal.II/base/parsed_convergence_table.h b/include/deal.II/base/parsed_convergence_table.h
@@ -106,7 +106,7 @@ class ParameterHandler;
  * By calling the method add_parameters() passing a ParameterHandler object,
  * the following options will be defined in the given ParameterHandler object
  * (in the current level of the ParameterHandler object, i.e., whatever level
- * you have entered with the ParamterHandler::enter_subsection() method),
+ * you have entered with the ParameterHandler::enter_subsection() method),
  * and can be modified at run time through a parameter file:
  * @code
  * set Enable computation of the errors = true

diff --git a/include/deal.II/base/polynomials_wedge.h b/include/deal.II/base/polynomials_wedge.h
@@ -30,15 +30,15 @@ namespace internal
 {
   /**
    * Decompose the shape-function index of a linear wedge into an index
-   * to access the right shape function within the triangle and and within
+   * to access the right shape function within the triangle and within
    * the line.
    */
   static const constexpr dealii::ndarray<unsigned int, 6, 2> wedge_table_1{
     {{{0, 0}}, {{1, 0}}, {{2, 0}}, {{0, 1}}, {{1, 1}}, {{2, 1}}}};
 
   /**
    * Decompose the shape-function index of a quadratic wedge into an index
-   * to access the right shape function within the triangle and and within
+   * to access the right shape function within the triangle and within
    * the line.
    */
   static const constexpr dealii::ndarray<unsigned int, 18, 2> wedge_table_2{

diff --git a/include/deal.II/base/tensor.h b/include/deal.II/base/tensor.h
@@ -579,7 +579,6 @@ class Tensor
    *
    * This constructor obviously requires that the @p ElementType type is
    * either equal to @p Number, or is convertible to @p Number.
-   * Number.
    *
    * @note This function can also be used in @ref GlossDevice "device" code.
    */

diff --git a/include/deal.II/base/time_stepping.templates.h b/include/deal.II/base/time_stepping.templates.h
@@ -50,11 +50,11 @@ namespace TimeStepping
     AssertThrow(
       F.size() == 0,
       ExcMessage(
-        "RungeKutta methods cannot handle more that one function to integate."));
+        "RungeKutta methods cannot handle more that one function to integrate."));
     AssertThrow(
       J_inverse.size() == 0,
       ExcMessage(
-        "RungeKutta methods cannot handle more that one function to integate."));
+        "RungeKutta methods cannot handle more that one function to integrate."));
 
     return evolve_one_time_step(F[0], J_inverse[0], t, delta_t, y);
   }

diff --git a/include/deal.II/base/vectorization.h b/include/deal.II/base/vectorization.h
@@ -4138,7 +4138,7 @@ vectorized_load_and_transpose(const unsigned int          n_entries,
   const unsigned int n_chunks = n_entries / 4;
 
   // To avoid warnings about uninitialized variables, need to initialize one
-  // variable to a pre-exisiting value in out, which will never get used in
+  // variable to a pre-existing value in out, which will never get used in
   // the end. Keep the initialization outside the loop because of a bug in
   // gcc-9.1 which generates a "vmovapd" instruction instead of "vmovupd" in
   // case t3 is initialized to zero (inside/outside of loop), see

diff --git a/include/deal.II/distributed/repartitioning_policy_tools.h b/include/deal.II/distributed/repartitioning_policy_tools.h
@@ -23,7 +23,7 @@
 DEAL_II_NAMESPACE_OPEN
 
 /**
- * A namespace with repartitioning policies. These classes return vectors of
+ * A namespace with repartitioning policies. These classes return vectors
  * of the new owners of the active locally owned and ghost cells of a
  * Triangulation object. The returned vectors can be used, e.g., in
  * TriangulationDescription::Utilities::create_description_from_triangulation()

diff --git a/include/deal.II/fe/fe_interface_values.h b/include/deal.II/fe/fe_interface_values.h
@@ -2155,7 +2155,7 @@ class FEInterfaceValues
 
   /**
    * Return the jump in the third derivatives of the
-   * the finite element function characterized by <tt>fe_function</tt> at
+   * finite element function characterized by <tt>fe_function</tt> at
    * the quadrature points of the cell interface selected the last time
    * the <tt>reinit</tt> function of the FEInterfaceValues object was called.
    *
@@ -2191,7 +2191,7 @@ class FEInterfaceValues
 
   /**
    * Return the average of the gradients of the
-   * the finite element function characterized by <tt>fe_function</tt> at the
+   * finite element function characterized by <tt>fe_function</tt> at the
    * quadrature points of the cell interface selected the last time
    * the <tt>reinit</tt> function of the FEInterfaceValues object was called.
    * @dealiiRequiresUpdateFlags{update_gradients}
@@ -2205,7 +2205,7 @@ class FEInterfaceValues
 
   /**
    * Return the average of the Hessians of the
-   * the finite element function characterized by <tt>fe_function</tt> at the
+   * finite element function characterized by <tt>fe_function</tt> at the
    * quadrature points of the cell interface selected the last time
    * the <tt>reinit</tt> function of the FEInterfaceValues object was called.
    * @dealiiRequiresUpdateFlags{update_hessians}

diff --git a/include/deal.II/fe/fe_series.h b/include/deal.II/fe/fe_series.h
@@ -543,7 +543,7 @@ FESeries::process_coefficients(
   std::vector<double>       norm_values;
 
   // first, parse all table elements into a map of predicate values and
-  // coefficients. We could have stored (predicate values ->TableIndicies) map,
+  // coefficients. We could have stored (predicate values ->TableIndices) map,
   // but its processing would have been much harder later on.
   std::map<unsigned int, std::vector<CoefficientType>> pred_to_values;
   internal::FESeriesImplementation::fill_map(coefficients,

diff --git a/include/deal.II/fe/fe_tools.h b/include/deal.II/fe/fe_tools.h
@@ -495,7 +495,7 @@ namespace FETools
    * with M>N unknowns is well-defined, but often yields funny and non-
    * intuitive results. Secondly, one would think that if the quadrature point
    * data is defined in the support points of the finite element, i.e. the
-   * quadrature points of <tt>ths_quadrature</tt> equal
+   * quadrature points of <tt>rhs_quadrature</tt> equal
    * <tt>fe.get_unit_support_points()</tt>, then the projection should be the
    * identity, i.e. each degree of freedom of the finite element equals the
    * value of the given data in the support point of the corresponding shape

diff --git a/include/deal.II/lac/generic_linear_algebra.h b/include/deal.II/lac/generic_linear_algebra.h
@@ -183,7 +183,7 @@ namespace LinearAlgebraTrilinos
   using SolverCG = TrilinosWrappers::SolverCG;
 
   /**
-   * Typdef for the GMRES solver type used.
+   * Typedef for the GMRES solver type used.
    */
   using SolverGMRES = TrilinosWrappers::SolverGMRES;
 

diff --git a/include/deal.II/lac/la_parallel_vector.h b/include/deal.II/lac/la_parallel_vector.h
@@ -221,7 +221,7 @@ namespace LinearAlgebra
      *
      * @note By default, the GPU @ref GlossDevice "device" id is chosen in a round-robin fashion
      * according to the local MPI rank id. To choose a different @ref GlossDevice "device", Kokkos
-     * has to be initialized explicitly providing the respective devide id
+     * has to be initialized explicitly providing the respective device id
      * explicitly.
      *
      * <h4>MPI-3 shared-memory support</h4>

diff --git a/include/deal.II/lac/lapack_full_matrix.h b/include/deal.II/lac/lapack_full_matrix.h
@@ -793,7 +793,7 @@ class LAPACKFullMatrix : public TransposeTable<number>
    * values of A. V is a NxN orthonal matrix containing the right singular
    * vectors corresponding the singular values of A.
    *
-   * Note that the variable #svd_vt contains the tranpose of V and can be
+   * Note that the variable #svd_vt contains the transpose of V and can be
    * accessed by get_svd_vt(), while U is accessed with get_svd_u().
    */
   void

diff --git a/include/deal.II/lac/petsc_communication_pattern.h b/include/deal.II/lac/petsc_communication_pattern.h
@@ -75,7 +75,7 @@ namespace PETScWrappers
      * associated to the @p indices_want only.
      *
      * This emulates the corresponding constructor in
-     * Utilies::MPI::NoncontiguousPartitioner.
+     * Utilities::MPI::NoncontiguousPartitioner.
      */
     void
     reinit(const std::vector<types::global_dof_index> &indices_locally_owned,

diff --git a/include/deal.II/lac/petsc_precondition.h b/include/deal.II/lac/petsc_precondition.h
@@ -96,7 +96,7 @@ namespace PETScWrappers
     Tvmult(VectorBase &dst, const VectorBase &src) const;
 
     /**
-     * Explictly call setup. This is usually not needed since PETSc will
+     * Explicitly call setup. This is usually not needed since PETSc will
      * automatically call the setup function when needed.
      */
     void

diff --git a/include/deal.II/lac/petsc_snes.h b/include/deal.II/lac/petsc_snes.h
@@ -66,7 +66,7 @@ namespace PETScWrappers
      * @param maximum_non_linear_iterations Maximum number of iterations allowed.
      * @param max_n_function_evaluations Maximum number of function evaluations allowed.
      *
-     * @note All parameters values specified here can be overriden by
+     * @note All parameters values specified here can be overridden by
      * command line choices.
      *
      * @ingroup PETScWrappers

diff --git a/include/deal.II/lac/petsc_snes.templates.h b/include/deal.II/lac/petsc_snes.templates.h
@@ -571,7 +571,7 @@ namespace PETScWrappers
           // case is to use FD and thus assemble a dense operator by finite
           // differencing the residual callbacks. Here instead we decide to
           // use a full matrix-free approach by default. This choice can always
-          // be overriden from command line.
+          // be overridden from command line.
           {
             set_use_matrix_free(snes, false, true);
           }
@@ -580,7 +580,7 @@ namespace PETScWrappers
     // In case solve_with_jacobian is provided, create a shell
     // preconditioner wrapping the user call. The internal Krylov
     // solver will apply the preconditioner only once. This choice
-    // can be overriden by command line and users can use any other
+    // can be overridden by command line and users can use any other
     // Krylov method if their solve is not accurate enough.
     // Using solve_with_jacobian as a preconditioner allows users
     // to provide approximate solvers and possibly iterate on a matrix-free