From d059d792f579f9e1df15b2b03093e7cb0bb62b0d Mon Sep 17 00:00:00 2001
From: Luca Heltai <luca.heltai@sissa.it>
Date: Fri, 17 Feb 2017 13:34:13 +0100
Subject: [PATCH 1/2] Cleaned up driver.

---
 CMakeLists.txt                  |   2 +-
 docker/debug-release/Dockerfile |  14 -----
 docker/debug/Dockerfile         |  14 -----
 docker/release/Dockerfile       |  14 -----
 include/driver.h                | 102 ++++++++------------------------
 source/driver.cc                |  83 +++-----------------------
 6 files changed, 35 insertions(+), 194 deletions(-)
 delete mode 100644 docker/debug-release/Dockerfile
 delete mode 100644 docker/debug/Dockerfile
 delete mode 100644 docker/release/Dockerfile

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 06e5357..2fdca9f 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -26,7 +26,7 @@ SET(_main source/main.cc)
 # Normally you shouldn't need to change anything below.
 ############################################################
 # Declare all source files the target consists of:
-file(GLOB _files source/*cc)
+file(GLOB _files source/*cc include/*h)
 
 # Don't compile the main file into the library
 IF(NOT "${_main}" STREQUAL "")
diff --git a/docker/debug-release/Dockerfile b/docker/debug-release/Dockerfile
deleted file mode 100644
index 117f910..0000000
--- a/docker/debug-release/Dockerfile
+++ /dev/null
@@ -1,14 +0,0 @@
-FROM heltai/deal2lkit:debug-release
-
-MAINTAINER luca.heltai@gmail.com
-
-# pi-BEM master image
-RUN git clone https://github.com/mathLab/pi-BEM/ &&\
-    mkdir pi-BEM/build && cd pi-BEM/build &&\
-    cmake -DCMAKE_BUILD_TYPE=DebugRelease \
-	  -GNinja \
-          ../ && \
-    ninja -j4 
-
-# Need this for Travis!
-USER root
diff --git a/docker/debug/Dockerfile b/docker/debug/Dockerfile
deleted file mode 100644
index d2a92fc..0000000
--- a/docker/debug/Dockerfile
+++ /dev/null
@@ -1,14 +0,0 @@
-FROM heltai/deal2lkit:debug
-
-MAINTAINER luca.heltai@gmail.com
-
-# pi-BEM master image
-RUN git clone https://github.com/mathLab/pi-BEM/ &&\
-    mkdir pi-BEM/build && cd pi-BEM/build &&\
-    cmake -DCMAKE_BUILD_TYPE=Debug \
-	  -GNinja \
-          ../ && \
-    ninja -j4 
-
-# Need this for Travis!
-USER root
diff --git a/docker/release/Dockerfile b/docker/release/Dockerfile
deleted file mode 100644
index 757f0e5..0000000
--- a/docker/release/Dockerfile
+++ /dev/null
@@ -1,14 +0,0 @@
-FROM heltai/deal2lkit:release
-
-MAINTAINER luca.heltai@gmail.com
-
-# pi-BEM master image
-RUN git clone https://github.com/mathLab/pi-BEM/ &&\
-    mkdir pi-BEM/build && cd pi-BEM/build &&\
-    cmake -DCMAKE_BUILD_TYPE=Release \
-	  -GNinja \
-          ../ && \
-    ninja -j4 
-
-# Need this for Travis!
-USER root
diff --git a/include/driver.h b/include/driver.h
index bab494b..3933161 100644
--- a/include/driver.h
+++ b/include/driver.h
@@ -1,117 +1,65 @@
 #ifndef driver_h
 #define driver_h
 
-#include<deal.II/base/smartpointer.h>
-#include<deal.II/base/convergence_table.h>
-#include<deal.II/base/quadrature_lib.h>
-#include<deal.II/base/quadrature_selector.h>
-#include<deal.II/base/parsed_function.h>
-#include<deal.II/base/utilities.h>
+#include <deal.II/base/utilities.h>
 #include <deal.II/base/conditional_ostream.h>
 
-#include<deal.II/lac/full_matrix.h>
-#include<deal.II/lac/sparse_matrix.h>
-#include<deal.II/lac/matrix_lib.h>
-#include<deal.II/lac/vector.h>
-#include<deal.II/lac/solver_control.h>
-#include<deal.II/lac/solver_gmres.h>
-#include<deal.II/lac/precondition.h>
-//
-//#include <deal.II/lac/trilinos_vector.h>
-//#include <deal.II/lac/trilinos_vector.h>
-//#include <deal.II/lac/trilinos_sparse_matrix.h>
-//#include <deal.II/lac/trilinos_solver.h>
-//#include <deal.II/lac/trilinos_precondition.h>
-//
-//#include <deal.II/lac/petsc_vector.h>
-//#include <deal.II/lac/petsc_parallel_vector.h>
-//#include <deal.II/lac/petsc_parallel_sparse_matrix.h>
-//#include <deal.II/lac/petsc_solver.h>
-//#include <deal.II/lac/petsc_precondition.h>
-
-#include<deal.II/grid/tria.h>
-#include<deal.II/grid/tria_iterator.h>
-#include<deal.II/grid/tria_accessor.h>
-#include<deal.II/grid/grid_generator.h>
-#include<deal.II/grid/grid_in.h>
-#include<deal.II/grid/grid_out.h>
-#include<deal.II/grid/tria_boundary_lib.h>
-
-#include<deal.II/dofs/dof_handler.h>
-#include<deal.II/dofs/dof_accessor.h>
-#include<deal.II/dofs/dof_tools.h>
-#include<deal.II/dofs/dof_renumbering.h>
-#include<deal.II/fe/fe_q.h>
-#include<deal.II/fe/fe_values.h>
-#include<deal.II/fe/fe_system.h>
-#include<deal.II/fe/mapping_q1_eulerian.h>
-#include<deal.II/fe/mapping_q1.h>
-
-#include<deal.II/numerics/data_out.h>
-#include<deal.II/numerics/vector_tools.h>
-#include<deal.II/numerics/solution_transfer.h>
-
-// And here are a few C++ standard header
-// files that we will need:
-#include <cmath>
-#include <iostream>
-#include <fstream>
-#include <string>
-#include <set>
-
 #include "bem_problem.h"
 #include "bem_fma.h"
 #include "boundary_conditions.h"
 #include "computational_domain.h"
+
 #include <deal2lkit/parameter_acceptor.h>
+#include <deal2lkit/utilities.h>
 using namespace dealii;
 
-//using namespace TrilinosWrappers::MPI::Vector;
-//using namespace TrilinosWrappers::MPI::SparseMatrix;
-
 /**
-* This class is in charge of organising the overall BEM simulation. It has interfaces with all the other classes in order to have a complete simulation.
-*/
+ * This class is in charge of organising the overall BEM simulation,
+ * while timing the various phases. It has interfaces with all the
+ * other classes in order to have a complete simulation.
+ */
 template <int dim>
 class Driver : public ParameterAcceptor
 {
 public:
-
+  /**
+   * Initialize variables and setup parameters.
+   */
   Driver();
 
-  ~Driver();
-
-  /// method to declare the parameters
-  /// to be read from the parameters file
-
-  virtual void declare_parameters(ParameterHandler &prm);
-
-  /// method to parse the needed parameters
-  /// from the parameters file
-
-  virtual void parse_parameters(ParameterHandler &prm);
-
-
+  /**
+   * Sets up BEMProblem and ComputationalDomain, then solve BEM.
+   */
   void run();
 
 private:
 
+  /// Monitor output only on first processor.
   ConditionalOStream pcout;
 
+  /// Mpi communicator object.
   MPI_Comm mpi_communicator;
 
+  /// Domain related object.
   ComputationalDomain<dim> computational_domain;
 
+  /// The actual bem solver.
   BEMProblem<dim> bem_problem;
 
+  /// Boundary conditions.
   BoundaryConditions<dim> boundary_conditions;
 
-  ParameterHandler prm;
-
+  /// Flag to use global refinement.
   bool global_refinement;
 
+  /// Total number of processors
   const unsigned int n_mpi_processes;
+
+  /// The id of this processor.
   const unsigned int this_mpi_process;
+
+  /// Time monitor object.
+  TimeMonitor timer;
 };
 
 #endif
diff --git a/source/driver.cc b/source/driver.cc
index 6f353d0..0eddc5f 100644
--- a/source/driver.cc
+++ b/source/driver.cc
@@ -1,17 +1,4 @@
 #include "../include/driver.h"
-#include <sys/time.h>
-
-
-#include "Teuchos_TimeMonitor.hpp"
-
-using Teuchos::Time;
-using Teuchos::TimeMonitor;
-using Teuchos::RCP;
-
-RCP<Time> TotalTime = Teuchos::TimeMonitor::getNewTimer("Total Time");
-RCP<Time> MeshTime = Teuchos::TimeMonitor::getNewTimer("Mesh Time");
-RCP<Time> OutputTime = Teuchos::TimeMonitor::getNewTimer("Output Time");
-RCP<Time> SolveTime = Teuchos::TimeMonitor::getNewTimer("Solve Time");
 
 using namespace std;
 
@@ -22,72 +9,22 @@ Driver<dim>::Driver() :
   computational_domain(mpi_communicator),
   bem_problem(computational_domain,mpi_communicator),
   boundary_conditions(computational_domain, bem_problem),
-  prm(),
+  global_refinement(true),
   n_mpi_processes (Utilities::MPI::n_mpi_processes(mpi_communicator)),
   this_mpi_process (Utilities::MPI::this_mpi_process(mpi_communicator))
 {
   pcout.set_condition(this_mpi_process == 0);
-  //PathSearch search_prm("PARAMETER");
-
-  // Declare the parameter entries..
-  // DeclareParameters();
-  //
-  // deallog.depth_console(this_mpi_process == 0 ? 3 : 0);
-  //
-  // vector<string> args;
-  // for (int i=0; i<argc; ++i)
-  //   args.push_back (argv[i]);
-  //
-  // string default_prm;
-  // // The default parameter file is the name of the application plus prm
-  // default_prm = args[0] + ".prm";
-  //
-  // prm.read_input(default_prm, false, true);
-  //
-  // for (int i=1; i<argc; ++i)
-  //   prm.read_input(args[i], true);
-  //
-  // // Now that we have the final version of the parameters, parse them.
-  // ParseParameters();
-  //
-  // // And write the used ones.
-  // default_prm = args.front() + "_used.prm";
-  // ofstream outprm(default_prm.c_str());
-  // prm.print_parameters(outprm, ParameterHandler::ShortText);
-}
-
-template <int dim>
-Driver<dim>::~Driver()
-{}
-
-
-template <int dim>
-void Driver<dim>::declare_parameters (ParameterHandler &prm)
-{
-  prm.declare_entry("Set Global Refinement", "true",
-                    Patterns::Bool());
-
-
-}
-
-template <int dim>
-void Driver<dim>::parse_parameters (ParameterHandler &prm)
-{
-  global_refinement = prm.get_bool("Set Global Refinement");
-
-
+  add_parameter(global_refinement, "Set Global Refinement");
 }
 
-
 template <int dim>
 void Driver<dim>::run()
 {
   {
-    Teuchos::TimeMonitor LocalTimer(*TotalTime);
+    auto t_ = timer.scoped_timer("Total Time");
     unsigned int local_refinement_cycles = 0;
     {
-      // Teuchos::TimeMonitor LocalTimer(*MeshTime);
-      //computational_domain.create_initial_mesh();
+      auto t_ = timer.scoped_timer("Mesh Time");
       computational_domain.read_domain();
       if (global_refinement)
         {
@@ -95,7 +32,6 @@ void Driver<dim>::run()
         }
       else
         {
-          // computational_domain.conditional_refine_and_resize(1);
           computational_domain.refine_and_resize(1);
           local_refinement_cycles=computational_domain.n_cycles;
         }
@@ -105,7 +41,7 @@ void Driver<dim>::run()
     for (unsigned int i = 0; i<=local_refinement_cycles; ++i)
       {
         {
-          Teuchos::TimeMonitor LocalTimer(*SolveTime);
+          auto t_ = timer.scoped_timer("Solve Time");
           bem_problem.reinit();
           boundary_conditions.solve_problem();
         }
@@ -120,12 +56,11 @@ void Driver<dim>::run()
 
     std::string filename = ( boundary_conditions.output_file_name);
     boundary_conditions.compute_errors();
-    boundary_conditions.output_results(filename);
-    // }
+    {
+      auto t_ = timer.scoped_timer("Output Time");
+      boundary_conditions.output_results(filename);
+    }
   }
-  // Write a summary of all timers
-  Teuchos::TimeMonitor::summarize();
 }
 
-
 template class Driver<3>;

From 70fcf3b6aabb485a4f8ea0bcef433eb5ee87d51c Mon Sep 17 00:00:00 2001
From: Luca Heltai <luca.heltai@sissa.it>
Date: Fri, 17 Feb 2017 13:37:52 +0100
Subject: [PATCH 2/2] Fixed warnings in bem_fma.

---
 source/bem_fma.cc | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/source/bem_fma.cc b/source/bem_fma.cc
index 373b058..09922d7 100644
--- a/source/bem_fma.cc
+++ b/source/bem_fma.cc
@@ -2774,7 +2774,7 @@ void BEMFMA<dim>::compute_geometry_cache()
 
 
   FESystem<dim-1,dim> gradient_fe(*fma_fe, dim);
-  DoFHandler<dim-1, dim> gradient_dh(fma_dh->get_tria());
+  DoFHandler<dim-1, dim> gradient_dh(fma_dh->get_triangulation());
 
   //double tol = 1e-8;
   std::vector<Point<dim> > support_points(fma_dh->n_dofs());
@@ -2827,7 +2827,7 @@ void BEMFMA<dim>::compute_geometry_cache()
 
 
 
-  for (; cell!=endc,gradient_cell!=gradient_endc; ++cell,++gradient_cell)
+  for (; cell!=endc; ++cell,++gradient_cell)
     {
       Assert(cell->index() == gradient_cell->index(), ExcInternalError());
 
@@ -2997,7 +2997,7 @@ void BEMFMA<dim>::generate_octree_blocking()
         delete blocks[ii];
     }
 
-  types::global_dof_index maxNumBlocks = num_octree_levels*fma_dh->get_tria().n_active_cells()*fe_v.n_quadrature_points;
+  types::global_dof_index maxNumBlocks = num_octree_levels*fma_dh->get_triangulation().n_active_cells()*fe_v.n_quadrature_points;
 //unsigned int maxNumBlocks = 0;
 //for (unsigned int ii = 0; ii < num_octree_levels + 1;  ii++)
 //  {