Remove unused files.

These are present in the serial versions of the solver (to which I link)
but are not used in the parallel version (which is the only solver
included in the gallery).

diff --git a/cdr/common/include/deal.II-cdr/assemble_system.h b/cdr/common/include/deal.II-cdr/assemble_system.h
deleted file mode 100644 (file)
index 9eb4026..0000000
--- a/cdr/common/include/deal.II-cdr/assemble_system.h
+++ /dev/null
@@ -1,33 +0,0 @@
-#ifndef dealii__cdr_assemble_system_h
-#define dealii__cdr_assemble_system_h
-#include <deal.II/base/quadrature_lib.h>
-#include <deal.II/base/function_parser.h>
-
-#include <deal.II/dofs/dof_handler.h>
-
-#include <deal.II/fe/fe_q.h>
-
-#include <deal.II/lac/constraint_matrix.h>
-
-#include <functional>
-
-#include <deal.II-cdr/parameters.h>
-
-namespace CDR
-{
-  using namespace dealii;
-
-  template<int dim, typename MatrixType, typename VectorType>
-  void assemble_system
-  (const DoFHandler<dim>                                 &dof_handler,
-   const QGauss<dim>                                     &quad,
-   const std::function<Tensor<1, dim>(const Point<dim>)> convection_function,
-   const std::function<double(double, const Point<dim>)> forcing_function,
-   const CDR::Parameters                                 &parameters,
-   const VectorType                                      &current_solution,
-   const ConstraintMatrix                                &constraints,
-   const double                                          current_time,
-   MatrixType                                            &system_matrix,
-   VectorType                                            &system_rhs);
-}
-#endif

diff --git a/cdr/common/include/deal.II-cdr/assemble_system.templates.h b/cdr/common/include/deal.II-cdr/assemble_system.templates.h
deleted file mode 100644 (file)
index f76dc94..0000000
--- a/cdr/common/include/deal.II-cdr/assemble_system.templates.h
+++ /dev/null
@@ -1,98 +0,0 @@
-#ifndef dealii__cdr_assemble_system_templates_h
-#define dealii__cdr_assemble_system_templates_h
-#include <deal.II/fe/fe_values.h>
-
-#include <deal.II/lac/vector.h>
-
-#include <vector>
-
-#include <deal.II-cdr/assemble_system.h>
-
-namespace CDR
-{
-  using namespace dealii;
-
-  template<int dim, typename MatrixType, typename VectorType>
-  void assemble_system
-  (const DoFHandler<dim>                                 &dof_handler,
-   const QGauss<dim>                                     &quad,
-   const std::function<Tensor<1, dim>(const Point<dim>)> convection_function,
-   const std::function<double(double, const Point<dim>)> forcing_function,
-   const CDR::Parameters                                 &parameters,
-   const VectorType                                      &current_solution,
-   const ConstraintMatrix                                &constraints,
-   const double                                          current_time,
-   MatrixType                                            &system_matrix,
-   VectorType                                            &system_rhs)
-  {
-    auto &fe = dof_handler.get_fe();
-    const auto dofs_per_cell = fe.dofs_per_cell;
-    const double time_step = (parameters.stop_time - parameters.start_time)
-      /parameters.n_time_steps;
-    FEValues<dim> fe_values(fe, quad, update_values | update_gradients |
-                            update_quadrature_points | update_JxW_values);
-
-    Vector<double> cell_rhs(dofs_per_cell);
-    FullMatrix<double> cell_matrix(dofs_per_cell, dofs_per_cell);
-
-    Vector<double> current_fe_coefficients(dofs_per_cell);
-    std::vector<types::global_dof_index> local_indices(dofs_per_cell);
-
-    auto previous_time = current_time - time_step;
-
-    for (const auto &cell : dof_handler.active_cell_iterators())
-      {
-        if (cell->is_locally_owned())
-          {
-            fe_values.reinit(cell);
-            cell_rhs = 0.0;
-            cell_matrix = 0.0;
-            cell->get_dof_indices(local_indices);
-            for (unsigned int i = 0; i < dofs_per_cell; ++i)
-              {
-                current_fe_coefficients[i] = current_solution[local_indices[i]];
-              }
-
-            for (unsigned int q = 0; q < quad.size(); ++q)
-              {
-                const auto current_convection =
-                  convection_function(fe_values.quadrature_point(q));
-                const auto current_forcing =
-                  forcing_function(current_time, fe_values.quadrature_point(q));
-                const auto previous_forcing =
-                  forcing_function(previous_time, fe_values.quadrature_point(q));
-
-                for (unsigned int i = 0; i < dofs_per_cell; ++i)
-                  {
-                    for (unsigned int j = 0; j < dofs_per_cell; ++j)
-                      {
-                        const auto convection_contribution = current_convection
-                          *fe_values.shape_grad(j, q);
-
-                        const double mass_part
-                          {fe_values.shape_value(i, q)*fe_values.shape_value(j, q)};
-                        const double system_part
-                          {time_step/2.0*
-                            // convection part
-                             (fe_values.shape_value(i, q)*convection_contribution
-                              // diffusion part
-                              + parameters.diffusion_coefficient
-                              *fe_values.shape_grad(i, q)*fe_values.shape_grad(j, q)
-                              // reaction part
-                              + parameters.reaction_coefficient*mass_part)};
-                        cell_rhs(i) += fe_values.JxW(q)
-                          *((mass_part - system_part)*current_fe_coefficients[j]
-                          + time_step/2.0*fe_values.shape_value(i, q)
-                          *(current_forcing + previous_forcing));
-                        cell_matrix(i, j) +=
-                          fe_values.JxW(q)*(mass_part + system_part);
-                      }
-                  }
-              }
-            constraints.distribute_local_to_global
-              (cell_matrix, cell_rhs, local_indices, system_matrix, system_rhs, true);
-          }
-      }
-  }
-}
-#endif

diff --git a/cdr/common/include/deal.II-cdr/write_xdmf_output.h b/cdr/common/include/deal.II-cdr/write_xdmf_output.h
deleted file mode 100644 (file)
index 6a1a696..0000000
--- a/cdr/common/include/deal.II-cdr/write_xdmf_output.h
+++ /dev/null
@@ -1,40 +0,0 @@
-#ifndef dealii__cdr_write_xmdf_output_h
-#define dealii__cdr_write_xmdf_output_h
-#include <deal.II/base/data_out_base.h>
-
-#include <deal.II/dofs/dof_handler.h>
-
-#include <deal.II/lac/vector.h>
-
-#include <deal.II/numerics/data_component_interpretation.h>
-
-#include <string>
-#include <vector>
-
-
-namespace CDR
-{
-  using namespace dealii;
-
-  class WriteXDMFOutput
-  {
-  public:
-    WriteXDMFOutput(const unsigned int patch_level,
-                    const bool update_mesh_at_each_step = true);
-
-    template<int dim, typename VectorType>
-    void write_output(const DoFHandler<dim> &dof_handler,
-                      const VectorType      &solution,
-                      const unsigned int    time_step_n,
-                      const double          current_time);
-  private:
-    const unsigned int patch_level;
-    const bool update_mesh_at_each_step;
-    const std::string xdmf_file_name;
-    const std::vector<DataComponentInterpretation::DataComponentInterpretation>
-    data_component_interpretation;
-    std::vector<XDMFEntry> xdmf_entries;
-    bool write_mesh;
-  };
-}
-#endif

diff --git a/cdr/common/include/deal.II-cdr/write_xdmf_output.templates.h b/cdr/common/include/deal.II-cdr/write_xdmf_output.templates.h
deleted file mode 100644 (file)
index e944d92..0000000
--- a/cdr/common/include/deal.II-cdr/write_xdmf_output.templates.h
+++ /dev/null
@@ -1,52 +0,0 @@
-#ifndef dealii__cdr_write_xmdf_output_templates_h
-#define dealii__cdr_write_xmdf_output_templates_h
-#include <deal.II/base/utilities.h>
-
-#include <deal.II/numerics/data_out.h>
-
-#include <deal.II-cdr/write_xdmf_output.h>
-
-namespace CDR
-{
-  template<int dim, typename VectorType>
-  void WriteXDMFOutput::write_output(const DoFHandler<dim> &dof_handler,
-                                     const VectorType      &solution,
-                                     const unsigned int    time_step_n,
-                                     const double          current_time)
-  {
-    DataOut<dim> data_out;
-    data_out.attach_dof_handler(dof_handler);
-    data_out.add_data_vector(solution, "u", DataOut<dim>::type_dof_data,
-                             data_component_interpretation);
-    data_out.build_patches(patch_level);
-
-    auto solution_file_name = "solution-"
-      + Utilities::int_to_string(time_step_n, 9) + ".h5";
-    std::string mesh_file_name;
-    if (update_mesh_at_each_step)
-      {
-        mesh_file_name = "mesh-"
-          + Utilities::int_to_string(time_step_n, 9) + ".h5";
-      }
-    else
-      {
-        mesh_file_name = "mesh.h5";
-      }
-
-    DataOutBase::DataOutFilter data_filter
-      (DataOutBase::DataOutFilterFlags(true, true));
-    data_out.write_filtered_data(data_filter);
-    data_out.write_hdf5_parallel(data_filter, write_mesh, mesh_file_name,
-                                 solution_file_name, MPI_COMM_WORLD);
-    if (!update_mesh_at_each_step)
-      {
-        write_mesh = false;
-      }
-
-    xdmf_entries.push_back(data_out.create_xdmf_entry
-                           (data_filter, mesh_file_name, solution_file_name,
-                            current_time, MPI_COMM_WORLD));
-    data_out.write_xdmf_file(xdmf_entries, xdmf_file_name, MPI_COMM_WORLD);
-  }
-}
-#endif

diff --git a/cdr/common/source/assemble_system.cc b/cdr/common/source/assemble_system.cc
deleted file mode 100644 (file)
index 73c5bba..0000000
--- a/cdr/common/source/assemble_system.cc
+++ /dev/null
@@ -1,65 +0,0 @@
-#include <deal.II/lac/trilinos_sparse_matrix.h>
-#include <deal.II/lac/trilinos_vector.h>
-
-#include <deal.II/lac/sparse_matrix.h>
-
-#include <deal.II-cdr/assemble_system.templates.h>
-
-namespace CDR
-{
-  using namespace dealii;
-
-  template
-  void assemble_system<2, SparseMatrix<double>, Vector<double>>
-  (const DoFHandler<2>                                 &dof_handler,
-   const QGauss<2>                                     &quad,
-   const std::function<Tensor<1, 2>(const Point<2>)>   convection_function,
-   const std::function<double(double, const Point<2>)> forcing_function,
-   const CDR::Parameters                               &parameters,
-   const Vector<double>                                &current_solution,
-   const ConstraintMatrix                              &constraints,
-   const double                                        current_time,
-   SparseMatrix<double>                                &system_matrix,
-   Vector<double>                                      &system_rhs);
-
-  template
-  void assemble_system<3, SparseMatrix<double>, Vector<double>>
-  (const DoFHandler<3>                                 &dof_handler,
-   const QGauss<3>                                     &quad,
-   const std::function<Tensor<1, 3>(const Point<3>)>   convection_function,
-   const std::function<double(double, const Point<3>)> forcing_function,
-   const CDR::Parameters                               &parameters,
-   const Vector<double>                                &current_solution,
-   const ConstraintMatrix                              &constraints,
-   const double                                        current_time,
-   SparseMatrix<double>                                &system_matrix,
-   Vector<double>                                      &system_rhs);
-
-  template
-  void assemble_system<2, TrilinosWrappers::SparseMatrix,
-                       TrilinosWrappers::MPI::Vector>
-  (const DoFHandler<2>                                 &dof_handler,
-   const QGauss<2>                                     &quad,
-   const std::function<Tensor<1, 2>(const Point<2>)>   convection_function,
-   const std::function<double(double, const Point<2>)> forcing_function,
-   const CDR::Parameters                               &parameters,
-   const TrilinosWrappers::MPI::Vector                 &current_solution,
-   const ConstraintMatrix                              &constraints,
-   const double                                        current_time,
-   TrilinosWrappers::SparseMatrix                      &system_matrix,
-   TrilinosWrappers::MPI::Vector                       &system_rhs);
-
-  template
-  void assemble_system<3, TrilinosWrappers::SparseMatrix,
-                       TrilinosWrappers::MPI::Vector>
-  (const DoFHandler<3>                                 &dof_handler,
-   const QGauss<3>                                     &quad,
-   const std::function<Tensor<1, 3>(const Point<3>)>   convection_function,
-   const std::function<double(double, const Point<3>)> forcing_function,
-   const CDR::Parameters                               &parameters,
-   const TrilinosWrappers::MPI::Vector                 &current_solution,
-   const ConstraintMatrix                              &constraints,
-   const double                                        current_time,
-   TrilinosWrappers::SparseMatrix                      &system_matrix,
-   TrilinosWrappers::MPI::Vector                       &system_rhs);
-}

diff --git a/cdr/common/source/write_xdmf_output.cc b/cdr/common/source/write_xdmf_output.cc
deleted file mode 100644 (file)
index 4a6b3a7..0000000
--- a/cdr/common/source/write_xdmf_output.cc
+++ /dev/null
@@ -1,42 +0,0 @@
-#include <deal.II/lac/trilinos_vector.h>
-
-#include <deal.II-cdr/write_xdmf_output.templates.h>
-
-namespace CDR
-{
-  using namespace dealii;
-
-  WriteXDMFOutput::WriteXDMFOutput(const unsigned int patch_level,
-                                   const bool update_mesh_at_each_step)
-    : patch_level {patch_level},
-      update_mesh_at_each_step {update_mesh_at_each_step},
-      xdmf_file_name {"solution.xdmf"},
-      data_component_interpretation
-  {DataComponentInterpretation::component_is_scalar},
-  write_mesh {true}
-  {}
-
-  template
-  void WriteXDMFOutput::write_output(const DoFHandler<2>  &dof_handler,
-                                     const Vector<double> &solution,
-                                     const unsigned int   time_step_n,
-                                     const double         current_time);
-
-  template
-  void WriteXDMFOutput::write_output(const DoFHandler<2>                 &dof_handler,
-                                     const TrilinosWrappers::MPI::Vector &solution,
-                                     const unsigned int                  time_step_n,
-                                     const double                        current_time);
-
-  template
-  void WriteXDMFOutput::write_output(const DoFHandler<3>  &dof_handler,
-                                     const Vector<double> &solution,
-                                     const unsigned int   time_step_n,
-                                     const double         current_time);
-
-  template
-  void WriteXDMFOutput::write_output(const DoFHandler<3>                 &dof_handler,
-                                     const TrilinosWrappers::MPI::Vector &solution,
-                                     const unsigned int                  time_step_n,
-                                     const double                        current_time);
-}