Merge pull request #257 from Rombur/update_dealii

Clean up

cpp/source/deal.II/electrochemical_physics.h

@@ -1,4 +1,4 @@
-/* Copyright (c) 2016, the Cap authors.
+/* Copyright (c) 2016 - 2017, the Cap authors.
  *
  * This file is subject to the Modified BSD License and may not be distributed
  * without copyright and license information. Please refer to the file LICENSE
@@ -61,8 +61,8 @@ class ElectrochemicalPhysics : public Physics<dim>
   void assemble_system(std::shared_ptr<PhysicsParameters<dim> const> parameters,
                        bool const inhomogeneous_bc);
 
-  unsigned int solid_potential_component;
-  unsigned int liquid_potential_component;
+  unsigned int _solid_potential_component;
+  unsigned int _liquid_potential_component;
   Timer _assembly_timer;
   Timer _setup_timer;
 };

cpp/source/deal.II/electrochemical_physics.templates.h

@@ -1,4 +1,4 @@
-/* Copyright (c) 2016, the Cap authors.
+/* Copyright (c) 2016 - 2017, the Cap authors.
  *
  * This file is subject to the Modified BSD License and may not be distributed
  * without copyright and license information. Please refer to the file LICENSE
@@ -22,17 +22,17 @@ template <int dim>
 ElectrochemicalPhysics<dim>::ElectrochemicalPhysics(
     std::shared_ptr<PhysicsParameters<dim> const> parameters,
     boost::mpi::communicator mpi_communicator)
-    : Physics<dim>(parameters, mpi_communicator), solid_potential_component(-1),
-      liquid_potential_component(-1),
+    : Physics<dim>(parameters, mpi_communicator),
+      _solid_potential_component(-1), _liquid_potential_component(-1),
       _assembly_timer(mpi_communicator, "ElectrochemicalPhysics assembly"),
       _setup_timer(mpi_communicator, "ElectrochemicalPhysics setup")
 {
   _setup_timer.start();
   boost::property_tree::ptree const &database = parameters->database;
 
   // clang-format off
-  this->solid_potential_component  = database.get<unsigned int>("solid_potential_component");
-  this->liquid_potential_component = database.get<unsigned int>("liquid_potential_component");
+  this->_solid_potential_component  = database.get<unsigned int>("solid_potential_component");
+  this->_liquid_potential_component = database.get<unsigned int>("liquid_potential_component");
   // clang-format on
 
   auto const &anode_boundary_ids = (*this->geometry->get_boundaries())["anode"];
@@ -63,7 +63,7 @@ ElectrochemicalPhysics<dim>::ElectrochemicalPhysics(
   unsigned int const n_components =
       dealii::DoFTools::n_components(*(this->dof_handler));
   std::vector<bool> mask(n_components, false);
-  mask[this->solid_potential_component] = true;
+  mask[this->_solid_potential_component] = true;
   dealii::ComponentMask component_mask(mask);
   typename dealii::FunctionMap<dim>::type dirichlet_boundary_condition;
   dealii::ZeroFunction<dim> homogeneous_bc(n_components);
@@ -133,9 +133,9 @@ void ElectrochemicalPhysics<dim>::assemble_system(
   dealii::FiniteElement<dim> const &fe = dof_handler.get_fe();
 
   dealii::FEValuesExtractors::Scalar const solid_potential(
-      this->solid_potential_component);
+      this->_solid_potential_component);
   dealii::FEValuesExtractors::Scalar const liquid_potential(
-      this->liquid_potential_component);
+      this->_liquid_potential_component);
   dealii::QGauss<dim> quadrature_rule(fe.degree + 1);
   dealii::FEValues<dim> fe_values(
       fe, quadrature_rule, dealii::update_values | dealii::update_gradients |

cpp/source/deal.II/post_processor.h

@@ -1,4 +1,4 @@
-/* Copyright (c) 2016, the Cap authors.
+/* Copyright (c) 2016 - 2017, the Cap authors.
  *
  * This file is subject to the Modified BSD License and may not be distributed
  * without copyright and license information. Please refer to the file LICENSE
@@ -94,11 +94,11 @@ class SuperCapacitorPostprocessor : public Postprocessor<dim>
       std::shared_ptr<PostprocessorParameters<dim> const> parameters) override;
 
 private:
-  bool debug_material_ids;
-  bool debug_boundary_ids;
-  std::vector<std::string> debug_material_properties;
-  std::vector<std::string> debug_solution_fields;
-  std::vector<std::string> debug_solution_fluxes;
+  bool _debug_material_ids;
+  bool _debug_boundary_ids;
+  std::vector<std::string> _debug_material_properties;
+  std::vector<std::string> _debug_solution_fields;
+  std::vector<std::string> _debug_solution_fluxes;
   std::shared_ptr<Geometry<dim> const> _geometry;
 };
 

cpp/source/deal.II/post_processor.templates.h

@@ -1,4 +1,4 @@
-/* Copyright (c) 2016, the Cap authors.
+/* Copyright (c) 2016 - 2017, the Cap authors.
  *
  * This file is subject to the Modified BSD License and may not be distributed
  * without copyright and license information. Please refer to the file LICENSE
@@ -82,9 +82,9 @@ SuperCapacitorPostprocessor<dim>::SuperCapacitorPostprocessor(
     std::shared_ptr<Geometry<dim> const> geometry,
     boost::mpi::communicator mpi_communicator)
     : Postprocessor<dim>(parameters, mpi_communicator),
-      debug_material_ids(false), debug_boundary_ids(false),
-      debug_material_properties(), debug_solution_fields(),
-      debug_solution_fluxes(), _geometry(geometry)
+      _debug_material_ids(false), _debug_boundary_ids(false),
+      _debug_material_properties(), _debug_solution_fields(),
+      _debug_solution_fluxes(), _geometry(geometry)
 {
   dealii::DoFHandler<dim> const &dof_handler = *(this->dof_handler);
   this->values["voltage"] = 0.0;
@@ -102,34 +102,34 @@ SuperCapacitorPostprocessor<dim>::SuperCapacitorPostprocessor(
   std::shared_ptr<boost::property_tree::ptree const> database =
       parameters->database;
 
-  this->debug_material_properties = cap::to_vector<std::string>(
+  this->_debug_material_properties = cap::to_vector<std::string>(
       database->get("debug.material_properties", ""));
-  this->debug_solution_fields =
+  this->_debug_solution_fields =
       cap::to_vector<std::string>(database->get("debug.solution_fields", ""));
-  this->debug_solution_fluxes =
+  this->_debug_solution_fluxes =
       cap::to_vector<std::string>(database->get("debug.solution_fluxes", ""));
-  this->debug_boundary_ids = database->get("debug.boundary_ids", false);
-  this->debug_material_ids = database->get("debug.material_ids", false);
+  this->_debug_boundary_ids = database->get("debug.boundary_ids", false);
+  this->_debug_material_ids = database->get("debug.material_ids", false);
 
   // n_active_cells is the total number of locally owned cells. This includes
   // the ghost cells and the artificial cells. They are filtered out by DataOut.
   unsigned int const n_active_cells =
       dof_handler.get_triangulation().n_active_cells();
-  if (this->debug_material_ids)
+  if (this->_debug_material_ids)
     this->vectors["material_id"] = dealii::Vector<double>(n_active_cells);
-  if (this->debug_boundary_ids)
+  if (this->_debug_boundary_ids)
     throw dealii::StandardExceptions::ExcMessage("not implemented yet");
   for (std::vector<std::string>::const_iterator it =
-           this->debug_material_properties.begin();
-       it != this->debug_material_properties.end(); ++it)
+           this->_debug_material_properties.begin();
+       it != this->_debug_material_properties.end(); ++it)
     this->vectors[*it] = dealii::Vector<double>(n_active_cells);
   for (std::vector<std::string>::const_iterator it =
-           this->debug_solution_fields.begin();
-       it != this->debug_solution_fields.end(); ++it)
+           this->_debug_solution_fields.begin();
+       it != this->_debug_solution_fields.end(); ++it)
     this->vectors[*it] = dealii::Vector<double>(n_active_cells);
   for (std::vector<std::string>::const_iterator it =
-           this->debug_solution_fluxes.begin();
-       it != this->debug_solution_fluxes.end(); ++it)
+           this->_debug_solution_fluxes.begin();
+       it != this->_debug_solution_fluxes.end(); ++it)
     for (int d = 0; d < dim; ++d)
       this->vectors[(*it) + "_" + std::to_string(d)] =
           dealii::Vector<double>(n_active_cells);
@@ -289,12 +289,12 @@ void SuperCapacitorPostprocessor<dim>::reset(
           // do nothing
         }
       } // end for quadrature point
-      if (this->debug_material_ids)
+      if (this->_debug_material_ids)
         this->vectors["material_id"][cell->active_cell_index()] =
             static_cast<double>(cell->material_id());
       for (std::vector<std::string>::const_iterator it =
-               this->debug_material_properties.begin();
-           it != this->debug_material_properties.end(); ++it)
+               this->_debug_material_properties.begin();
+           it != this->_debug_material_properties.end(); ++it)
       {
         std::vector<double> values(n_q_points);
         this->mp_values->get_values(*it, fe_values, values);
@@ -307,8 +307,8 @@ void SuperCapacitorPostprocessor<dim>::reset(
         this->vectors[*it][cell->active_cell_index()] = cell_averaged_value;
       }
       for (std::vector<std::string>::const_iterator it =
-               this->debug_solution_fields.begin();
-           it != this->debug_solution_fields.end(); ++it)
+               this->_debug_solution_fields.begin();
+           it != this->_debug_solution_fields.end(); ++it)
       {
         std::vector<double> values(n_q_points);
         if (it->compare("solid_potential") == 0)
@@ -351,8 +351,8 @@ void SuperCapacitorPostprocessor<dim>::reset(
         this->vectors[*it][cell->active_cell_index()] = cell_averaged_value;
       }
       for (std::vector<std::string>::const_iterator it =
-               this->debug_solution_fluxes.begin();
-           it != this->debug_solution_fluxes.end(); ++it)
+               this->_debug_solution_fluxes.begin();
+           it != this->_debug_solution_fluxes.end(); ++it)
       {
         std::vector<dealii::Tensor<1, dim>> values(n_q_points);
         if (it->compare("solid_current_density") == 0)

cpp/source/deal.II/supercapacitor.h

@@ -1,4 +1,4 @@
-/* Copyright (c) 2016, the Cap authors.
+/* Copyright (c) 2016 - 2017, the Cap authors.
  *
  * This file is subject to the Modified BSD License and may not be distributed
  * without copyright and license information. Please refer to the file LICENSE
@@ -28,7 +28,7 @@ class SuperCapacitorInspector : public EnergyStorageDeviceInspector
   SuperCapacitorInspector() = default;
 
   /**
-   * Output the mesh with the suddomain IDs associated to each cells. It can
+   * Output the mesh with the subdomain IDs associated to each cells. It can
    * also be used to output some quantities of interest.
    */
   void inspect(EnergyStorageDevice *device) override;
@@ -146,40 +146,40 @@ class SuperCapacitor : public EnergyStorageDevice
    * Maximum number of iterations of the Krylov solver in
    * evolve_one_time_step().
    */
-  unsigned int max_iter;
+  unsigned int _max_iter;
   /**
    * Verbosity level of the Krylov solver in evolve_one_time_step().
    */
-  unsigned int verbose_lvl;
+  unsigned int _verbose_lvl;
   /**
    * Absolute tolerance of the Krylov solver in evolve_one_time_step(). The
    * tolerance used by the Krylov solver is the maximum of the relative and the
    * absolute tolerance.
    */
-  double abs_tolerance;
+  double _abs_tolerance;
   /**
    * Relative tolerance of the Krylov solver in evolve_one_time_step(), i.e. the
-   * tolerance is @p rel_toleracne \f$ \times ||b||_{2}\f$. The tolerance used
+   * tolerance is @p rel_tolerance \f$ \times ||b||_{2}\f$. The tolerance used
    * by the Krylov solver is the maximum of the relative and the absolute
    * tolerance.
    */
-  double rel_tolerance;
+  double _rel_tolerance;
   /**
    * Area of the cathode.
    */
-  double surface_area;
+  double _surface_area;
 
   std::shared_ptr<Geometry<dim>> _geometry;
   std::shared_ptr<dealii::FESystem<dim>> _fe;
-  std::shared_ptr<dealii::DoFHandler<dim>> dof_handler;
-  std::shared_ptr<dealii::Trilinos::MPI::BlockVector> solution;
+  std::shared_ptr<dealii::DoFHandler<dim>> _dof_handler;
+  std::shared_ptr<dealii::Trilinos::MPI::BlockVector> _solution;
 
   std::shared_ptr<ElectrochemicalPhysicsParameters<dim>>
-      electrochemical_physics_params;
-  std::shared_ptr<ElectrochemicalPhysics<dim>> electrochemical_physics;
+      _electrochemical_physics_params;
+  std::shared_ptr<ElectrochemicalPhysics<dim>> _electrochemical_physics;
   std::shared_ptr<SuperCapacitorPostprocessorParameters<dim>>
-      post_processor_params;
-  std::shared_ptr<SuperCapacitorPostprocessor<dim>> post_processor;
+      _post_processor_params;
+  std::shared_ptr<SuperCapacitorPostprocessor<dim>> _post_processor;
   boost::property_tree::ptree const _ptree;
   Timer _setup_timer;
   Timer _solver_timer;