From 9e3aea4c956333c617f4d39be9ac73d09bbc2dd3 Mon Sep 17 00:00:00 2001
From: Weixiong Zheng <weixiong.zheng@berkeley.edu>
Date: Fri, 28 Jul 2017 11:27:08 -0700
Subject: [PATCH] Cleaning continued #10

---
 src/common/bart_driver.cc       |  5 -----
 src/iteration/iteration_base.cc | 29 +++++++++++++----------------
 src/transport/even_parity.cc    |  2 +-
 3 files changed, 14 insertions(+), 22 deletions(-)

diff --git a/src/common/bart_driver.cc b/src/common/bart_driver.cc
index 7e863c0d1..9aecae7c8 100644
--- a/src/common/bart_driver.cc
+++ b/src/common/bart_driver.cc
@@ -246,11 +246,6 @@ void BartDriver<dim>::run ()
 {
   radio ("making grid");
   msh_ptr->make_grid (triangulation);
-  msh_ptr->get_relevant_cell_iterators (dof_handler,
-                                        local_cells,
-                                        ref_bd_cells,
-                                        is_cell_at_bd,
-                                        is_cell_at_ref_bd);
   setup_system ();
   report_system ();
   itr_ptr->do_iterations (msh_ptr, aqd_ptr);
diff --git a/src/iteration/iteration_base.cc b/src/iteration/iteration_base.cc
index bce245419..09994963a 100644
--- a/src/iteration/iteration_base.cc
+++ b/src/iteration/iteration_base.cc
@@ -16,26 +16,29 @@
 using namespace dealii;
 
 template <int dim>
-IterationBase<dim>::IterationBase (ParameterHandler &prm)
+IterationBase<dim>::IterationBase
+(ParameterHandler &prm,
+ const std_cxx11::shared_ptr<MeshGenerator<dim> > msh_ptr,
+ const std_cxx11::shared_ptr<AQBase<dim> > aqd_ptr)
 :
 err_k_tol(1.0e-6),
 err_phi_tol(1.0e-7),
 err_phi_eigen_tol(1.0e-5),
 ho_linear_solver_name(prm.get("HO linear solver name")),
 ho_preconditioner_name(prm.get("HO preconditioner name")),
+is_eigen_problem(prm.get_bool("do eigenvalue calculations")),
+do_nda(prm.get_bool("do NDA")),
 pcout(std::cout,
-      (Utilities::MPI::this_mpi_process(mpi_communicator)
-       == 0))
+      Utilities::MPI::this_mpi_process(MPI_COMM_WORLD)==0)
 {
-  initialize_aq (prm);
   n_total_ho_vars = aqd_ptr->get_n_total_ho_vars ();
-  sol_ptr = std_cxx11::shared_ptr<PreconditionerSolver>
-  (new PreconditionerSolver (prm, n_total_ho_vars, mpi_communicator));
-  def_ptr = std_cxx11::shared_ptr<ProblemDefinition>
-  (new ProblemDefinition(prm));
-  msh_ptr = std_cxx11::shared_ptr<MeshGenerator<dim> >
-  (new MeshGenerator<dim>(prm));
+  sol_ptr = build_solution (prm, n_total_ho_vars);
   mat_ptr = build_material (prm);
+  msh_ptr->get_relevant_cell_iterators (dof_handler,
+                                        local_cells,
+                                        ref_bd_cells,
+                                        is_cell_at_bd,
+                                        is_cell_at_ref_bd);
   this->process_input ();
   sflx_proc.resize (n_group);
   sflx_proc_prev_gen.resize (n_group);
@@ -52,7 +55,6 @@ void IterationBase<dim>::process_input ()
   // basic parameters
   {
     // from basic problem definition
-    transport_model_name = def_ptr->get_transport_model ();
     n_group = def_ptr->get_n_group ();
     n_material = mat_ptr->get_n_material ();
     p_order = def_ptr->get_fe_order ();
@@ -137,11 +139,6 @@ void IterationBase<dim>::scale_fiss_transfer_matrices ()
   }
 }
 
-template <int dim>
-void IterationBase<dim>::generate_ho_fixed_source ()
-{
-}
-
 template <int dim>
 void IterationBase<dim>::initialize_fiss_process ()
 {
diff --git a/src/transport/even_parity.cc b/src/transport/even_parity.cc
index 754cfb4ed..5208d872c 100644
--- a/src/transport/even_parity.cc
+++ b/src/transport/even_parity.cc
@@ -238,7 +238,7 @@ void EvenParity<dim>::generate_ho_rhs ()
 }
 
 template <int dim>
-void EvenParity<dim>::generate_ho_fixed_source ()
+void EvenParity<dim>::generate_ho_fixed_source (std::vector<Vector<double> >)
 {
   for (unsigned int g=0; g<this->n_group; ++g)
     for (unsigned int i_dir=0; i_dir<this->n_dir; ++i_dir)