fix for initing / seting up preconditioners with adaptivity

examples/adaptivity/adaptivity_ex2/adaptivity_ex2.C

@@ -440,9 +440,6 @@ int main (int argc, char** argv)
   if(!read_solution)
     {
       // Print out the H1 norm of the saved solution, for verification purposes:
-      TransientLinearImplicitSystem& system =
-	equation_systems.get_system<TransientLinearImplicitSystem>
-          ("Convection-Diffusion");
       Real H1norm = system.calculate_norm(*system.solution, SystemNorm(H1));
 
       std::cout << "Final H1 norm = " << H1norm << std::endl << std::endl;

examples/adaptivity/adaptivity_ex3/adaptivity_ex3.C

@@ -578,7 +578,7 @@ void assemble_laplace(EquationSystems& es,
   const MeshBase& mesh = es.get_mesh();
 
   // The dimension that we are running
-  const unsigned int dim = mesh.mesh_dimension();
+  const unsigned int mesh_dim = mesh.mesh_dimension();
 
   // Get a reference to the LinearImplicitSystem we are solving
   LinearImplicitSystem& system = es.get_system<LinearImplicitSystem>("Laplace");
@@ -597,12 +597,12 @@ void assemble_laplace(EquationSystems& es,
   // \p FEBase::build() member dynamically creates memory we will
   // store the object as an \p AutoPtr<FEBase>.  This can be thought
   // of as a pointer that will clean up after itself.
-  AutoPtr<FEBase> fe      (FEBase::build(dim, fe_type));
-  AutoPtr<FEBase> fe_face (FEBase::build(dim, fe_type));
+  AutoPtr<FEBase> fe      (FEBase::build(mesh_dim, fe_type));
+  AutoPtr<FEBase> fe_face (FEBase::build(mesh_dim, fe_type));
 
   // Quadrature rules for numerical integration.
-  AutoPtr<QBase> qrule(fe_type.default_quadrature_rule(dim));
-  AutoPtr<QBase> qface(fe_type.default_quadrature_rule(dim-1));
+  AutoPtr<QBase> qrule(fe_type.default_quadrature_rule(mesh_dim));
+  AutoPtr<QBase> qface(fe_type.default_quadrature_rule(mesh_dim-1));
 
   // Tell the finite element object to use our quadrature rule.
   fe->attach_quadrature_rule      (qrule.get());
@@ -709,7 +709,7 @@ void assemble_laplace(EquationSystems& es,
             Ke(i,j) += JxW[qp]*(dphi[i][qp]*dphi[j][qp]);
 
       // We need a forcing function to make the 1D case interesting
-      if (dim == 1)
+      if (mesh_dim == 1)
         for (unsigned int qp=0; qp<qrule->n_points(); qp++)
           {
             Real x = q_point[qp](0);

examples/adaptivity/adaptivity_ex5/adaptivity_ex5.C

@@ -415,9 +415,6 @@ int main (int argc, char** argv)
       // vector assignment.  Since only \p TransientLinearImplicitSystems
       // (and systems derived from them) contain old solutions
       // we need to specify the system type when we ask for it.
-      TransientLinearImplicitSystem &  system =
-        equation_systems.get_system<TransientLinearImplicitSystem>("Convection-Diffusion");
-
       *system.old_local_solution = *system.current_local_solution;
 
       // The number of refinement steps per time step.
@@ -432,8 +429,7 @@ int main (int argc, char** argv)
           system.solve();
 
           // Print out the H1 norm, for verification purposes:
-          Real H1norm = system.calculate_norm(*system.solution, SystemNorm(H1));
-
+          H1norm = system.calculate_norm(*system.solution, SystemNorm(H1));
           std::cout << "H1 norm = " << H1norm << std::endl;
 
           // Possibly refine the mesh
@@ -515,10 +511,7 @@ int main (int argc, char** argv)
   if(!read_solution)
     {
       // Print out the H1 norm of the saved solution, for verification purposes:
-      TransientLinearImplicitSystem& system =
-	equation_systems.get_system<TransientLinearImplicitSystem>
-          ("Convection-Diffusion");
-      Real H1norm = system.calculate_norm(*system.solution, SystemNorm(H1));
+      H1norm = system.calculate_norm(*system.solution, SystemNorm(H1));
 
       std::cout << "Final H1 norm = " << H1norm << std::endl << std::endl;
 

examples/adjoints/adjoints_ex1/L-shaped.h

@@ -13,9 +13,9 @@ class LaplaceSystem : public FEMSystem
 public:
   // Constructor
   LaplaceSystem(EquationSystems& es,
-               const std::string& name,
-               const unsigned int number)
-  : FEMSystem(es, name, number),
+               const std::string& name_in,
+               const unsigned int number_in)
+  : FEMSystem(es, name_in, number_in),
     _fe_family("LAGRANGE"), _fe_order(1),
     _analytic_jacobians(true) { qoi.resize(2); }
 

examples/adjoints/adjoints_ex2/L-shaped.h

@@ -14,9 +14,9 @@ class LaplaceSystem : public FEMSystem
 public:
   // Constructor
   LaplaceSystem(EquationSystems& es,
-               const std::string& name,
-               const unsigned int number)
-  : FEMSystem(es, name, number),
+               const std::string& name_in,
+               const unsigned int number_in)
+  : FEMSystem(es, name_in, number_in),
     _fe_family("LAGRANGE"), _fe_order(1),
     _analytic_jacobians(true) { }
 

examples/adjoints/adjoints_ex2/adjoints_ex2.C

@@ -263,7 +263,6 @@ int main (int argc, char** argv)
       }
   }
   GetPot infile("general.in");
-  GetPot infile_l_shaped("l-shaped.in");
 
   // Read in parameters from the input file
   FEMParameters param;
@@ -364,12 +363,12 @@ int main (int argc, char** argv)
 	// Now that we have solved the adjoint, set the adjoint_already_solved boolean to true, so we dont solve unneccesarily in the error estimator
 	system.set_adjoint_already_solved(true);
 
-	GetPot infile("l-shaped.in");
+	GetPot infile_l_shaped("l-shaped.in");
 
 	Number sensitivity_QoI_0_0_computed = sensitivities[0][0];
-	Number sensitivity_QoI_0_0_exact = infile("sensitivity_0_0", 0.0);
+	Number sensitivity_QoI_0_0_exact = infile_l_shaped("sensitivity_0_0", 0.0);
 	Number sensitivity_QoI_0_1_computed = sensitivities[0][1];
-	Number sensitivity_QoI_0_1_exact = infile("sensitivity_0_1", 0.0);
+	Number sensitivity_QoI_0_1_exact = infile_l_shaped("sensitivity_0_1", 0.0);
 
 	std::cout << "Adaptive step " << a_step << ", we have " << mesh.n_active_elem()
                       << " active elements and "
@@ -482,12 +481,12 @@ int main (int argc, char** argv)
 	// Now that we have solved the adjoint, set the adjoint_already_solved boolean to true, so we dont solve unneccesarily in the error estimator
 	system.set_adjoint_already_solved(true);
 
-	GetPot infile("l-shaped.in");
+	GetPot infile_l_shaped("l-shaped.in");
 
 	Number sensitivity_QoI_0_0_computed = sensitivities[0][0];
-	Number sensitivity_QoI_0_0_exact = infile("sensitivity_0_0", 0.0);
+	Number sensitivity_QoI_0_0_exact = infile_l_shaped("sensitivity_0_0", 0.0);
 	Number sensitivity_QoI_0_1_computed = sensitivities[0][1];
-	Number sensitivity_QoI_0_1_exact = infile("sensitivity_0_1", 0.0);
+	Number sensitivity_QoI_0_1_exact = infile_l_shaped("sensitivity_0_1", 0.0);
 
 	std::cout << "Adaptive step " << a_step << ", we have " << mesh.n_active_elem()
 		  << " active elements and "

examples/adjoints/adjoints_ex3/coupled_system.h

@@ -34,9 +34,9 @@ class CoupledSystem : public FEMSystem
 public:
   // Constructor
   CoupledSystem(EquationSystems& es,
-               const std::string& name,
-               const unsigned int number)
-    : FEMSystem(es, name, number), Peclet(1.) {qoi.resize(1);}
+               const std::string& name_in,
+               const unsigned int number_in)
+    : FEMSystem(es, name_in, number_in), Peclet(1.) {qoi.resize(1);}
 
   // Function to get computed QoI values
 

examples/adjoints/adjoints_ex4/L-shaped.h

@@ -13,9 +13,9 @@ class LaplaceSystem : public FEMSystem
 public:
   // Constructor
   LaplaceSystem(EquationSystems& es,
-               const std::string& name,
-               const unsigned int number)
-  : FEMSystem(es, name, number),
+               const std::string& name_in,
+               const unsigned int number_in)
+  : FEMSystem(es, name_in, number_in),
     _fe_family("LAGRANGE"), _fe_order(1),
     _analytic_jacobians(true) { qoi.resize(2); }
 

examples/adjoints/adjoints_ex5/adjoints_ex5.C

@@ -96,13 +96,10 @@
 #include "libmesh/solution_history.h"
 #include "libmesh/memory_solution_history.h"
 
-// Some (older) compilers do not offer full stream
-// functionality, OStringStream works around this.
-#include "libmesh/o_string_stream.h"
-
 // C++ includes
 #include <iostream>
 #include <sys/time.h>
+#include <iomanip>
 
 void write_output(EquationSystems &es,		                   
 		  unsigned int a_step,       // The adaptive step count

examples/adjoints/adjoints_ex5/factoryfunction.C

@@ -28,14 +28,14 @@ using namespace libMesh;
 
 class ExampleOneFunction : public FunctionBase<Number>
 {
-  virtual Number operator() (const Point& p,
-                             const Real time = 0)
+  virtual Number operator() (const Point&  /*p*/,
+                             const Real /*time*/)
     {
       return 1;
     }
 
-  virtual void operator() (const Point& p,
-                           const Real time,
+  virtual void operator() (const Point&  /*p*/,
+                           const Real /*time*/,
                            DenseVector<Number>& output)
     {
       for (unsigned int i=0; i != output.size(); ++i)

examples/adjoints/adjoints_ex5/femparameters.C

@@ -282,17 +282,17 @@ void FEMParameters::read(GetPot &input)
           {
             unsigned int myboundary =
               input("periodic_boundaries", -1, i);
-            unsigned int pairedboundary = 0;
+            // unsigned int pairedboundary = 0;
             RealVectorValue translation_vector;
             if (dimension == 2)
               switch (myboundary)
               {
               case 0:
-                pairedboundary = 2;
+                // pairedboundary = 2;
                 translation_vector = RealVectorValue(0., domain_edge_length);
                 break;
               case 1:
-                pairedboundary = 3;
+                // pairedboundary = 3;
                 translation_vector = RealVectorValue(-domain_edge_width, 0);
                 break;
               default:
@@ -304,15 +304,15 @@ void FEMParameters::read(GetPot &input)
               switch (myboundary)
               {
               case 0:
-                pairedboundary = 5;
+                // pairedboundary = 5;
                 translation_vector = RealVectorValue(0., 0., domain_edge_height);
                 break;
               case 1:
-                pairedboundary = 3;
+                // pairedboundary = 3;
                 translation_vector = RealVectorValue(0., domain_edge_length, 0.);
                 break;
               case 2:
-                pairedboundary = 4;
+                // pairedboundary = 4;
                 translation_vector = RealVectorValue(-domain_edge_width, 0., 0.);
                 break;
               default:
@@ -389,11 +389,11 @@ void FEMParameters::read(GetPot &input)
         const std::string variable_set =
           input("dirichlet_condition_variables", empty_string, i);
 
-        for (unsigned int i=0; i != variable_set.size(); ++i)
+        for (unsigned int j=0; j != variable_set.size(); ++j)
           {
-            if (variable_set[i] == '1')
-              dirichlet_condition_variables[func_boundary].push_back(i);
-            else if (variable_set[i] != '0')
+            if (variable_set[j] == '1')
+              dirichlet_condition_variables[func_boundary].push_back(j);
+            else if (variable_set[j] != '0')
               {
                 libMesh::out << "Unable to understand Dirichlet variable set" 
                              << variable_set << std::endl;
@@ -460,11 +460,11 @@ void FEMParameters::read(GetPot &input)
         const std::string variable_set =
           input("neumann_condition_variables", empty_string, i);
 
-        for (unsigned int i=0; i != variable_set.size(); ++i)
+        for (unsigned int j=0; j != variable_set.size(); ++j)
           {
-            if (variable_set[i] == '1')
-              neumann_condition_variables[func_boundary].push_back(i);
-            else if (variable_set[i] != '0')
+            if (variable_set[j] == '1')
+              neumann_condition_variables[func_boundary].push_back(j);
+            else if (variable_set[j] != '0')
               {
                 libMesh::out << "Unable to understand Neumann variable set" 
                              << variable_set << std::endl;

examples/adjoints/adjoints_ex5/heatsystem.C

@@ -157,15 +157,15 @@ bool HeatSystem::element_time_derivative (bool request_jacobian,
 }
 
 // Perturb and accumulate dual weighted residuals
-void HeatSystem::perturb_accumulate_residuals(const ParameterVector& parameters)
+void HeatSystem::perturb_accumulate_residuals(const ParameterVector& parameters_in)
 {
-  const unsigned int Np = parameters.size();
+  const unsigned int Np = parameters_in.size();
 
   for (unsigned int j=0; j != Np; ++j)
     {
-      Number old_parameter = *parameters[j];
+      Number old_parameter = *parameters_in[j];
 
-      *parameters[j] = old_parameter - dp;
+      *parameters_in[j] = old_parameter - dp;
 
       this->assembly(true, false);
 
@@ -177,7 +177,7 @@ void HeatSystem::perturb_accumulate_residuals(const ParameterVector& parameters)
       // But since we compute the residual already scaled by dt, there is no need for the * dt 
       R_minus_dp += -R_minus->dot(this->get_adjoint_solution(0));
 
-      *parameters[j] = old_parameter + dp;
+      *parameters_in[j] = old_parameter + dp;
 
       this->assembly(true, false);
 
@@ -187,7 +187,7 @@ void HeatSystem::perturb_accumulate_residuals(const ParameterVector& parameters)
 
       R_plus_dp += -R_plus->dot(this->get_adjoint_solution(0));
 
-      *parameters[j] = old_parameter;
+      *parameters_in[j] = old_parameter;
 
     }
 }

examples/adjoints/adjoints_ex5/heatsystem.h

@@ -28,9 +28,9 @@ class HeatSystem : public FEMSystem
 public:
   // Constructor
   HeatSystem(EquationSystems& es,
-               const std::string& name,
-               const unsigned int number)
-  : FEMSystem(es, name, number),
+               const std::string& name_in,
+               const unsigned int number_in)
+  : FEMSystem(es, name_in, number_in),
     _k(1.0),
     _fe_family("LAGRANGE"), _fe_order(1),
     _analytic_jacobians(true), R_plus_dp(0.0), R_minus_dp(0.0), dp(1.e-6) { qoi.resize(1); }

examples/fem_system/fem_system_ex1/naviersystem.h

@@ -28,9 +28,9 @@ class NavierSystem : public FEMSystem
 public:
   // Constructor
   NavierSystem(EquationSystems& es,
-               const std::string& name,
-               const unsigned int number)
-    : FEMSystem(es, name, number), Reynolds(1.), application(0) {}
+               const std::string& name_in,
+               const unsigned int number_in)
+    : FEMSystem(es, name_in, number_in), Reynolds(1.), application(0) {}
 
   // System initialization
   virtual void init_data ();

examples/fem_system/fem_system_ex2/nonlinear_neohooke_cc.h

@@ -37,8 +37,8 @@ using namespace libMesh;
 class NonlinearNeoHookeCurrentConfig {
 public:
   NonlinearNeoHookeCurrentConfig(
-      const std::vector<std::vector<RealGradient> >& dphi, GetPot& args) :
-      dphi(dphi) {
+      const std::vector<std::vector<RealGradient> >& dphi_in, GetPot& args) :
+      dphi(dphi_in) {
     E = args("material/neohooke/e_modulus", 10000.0);
     nu = args("material/neohooke/nu", 0.3);
   }

examples/fem_system/fem_system_ex2/solid_system.C

@@ -43,9 +43,9 @@
 // Bring in everything from the libMesh namespace
 using namespace libMesh;
 
-SolidSystem::SolidSystem(EquationSystems& es, const std::string& name,
-    const unsigned int number) :
-    FEMSystem(es, name, number) {
+SolidSystem::SolidSystem(EquationSystems& es, const std::string& name_in,
+    const unsigned int number_in) :
+    FEMSystem(es, name_in, number_in) {
 
   // Add a time solver. We are just looking at a steady state problem here.
   this->time_solver = AutoPtr<TimeSolver>(new SteadySolver(*this));

examples/miscellaneous/miscellaneous_ex3/miscellaneous_ex3.C

@@ -83,7 +83,7 @@ const Real sigma = 0.2;
 // This function computes the Jacobian K(x)
 void compute_jacobian (const NumericVector<Number>& soln,
                        SparseMatrix<Number>&  jacobian,
-                       NonlinearImplicitSystem& sys)
+                       NonlinearImplicitSystem& /*sys*/)
 {
   // Get a reference to the equation system.
   EquationSystems &es = *_equation_system;
@@ -213,7 +213,7 @@ void compute_jacobian (const NumericVector<Number>& soln,
 // x is passed in the soln vector
 void compute_residual (const NumericVector<Number>& soln,
                        NumericVector<Number>& residual,
-                       NonlinearImplicitSystem& sys)
+                       NonlinearImplicitSystem& /*sys*/)
 {
   EquationSystems &es = *_equation_system;
 

examples/miscellaneous/miscellaneous_ex4/miscellaneous_ex4.C

@@ -110,7 +110,6 @@ int main (int argc, char** argv)
 
   // Create an equation systems object.
   EquationSystems equation_systems (mesh);
-  MeshRefinement mesh_refinement (mesh);
 
   MeshTools::Generation::build_square (mesh,
 				       16,