Exemplo n.º 1
0
int main(int argc, char *argv[])
{
#ifdef HAVE_MPI
  Teuchos::GlobalMPISession mpiSession(&argc, &argv,0);
#endif

  {
    // 1D tests
    CellTopoPtr line_2 = Teuchos::rcp( new shards::CellTopology(shards::getCellTopologyData<shards::Line<2> >() ) );

    // let's draw a line
    vector<double> v0 = makeVertex(0);
    vector<double> v1 = makeVertex(1);
    vector<double> v2 = makeVertex(2);

    vector< vector<double> > vertices;
    vertices.push_back(v0);
    vertices.push_back(v1);
    vertices.push_back(v2);

    vector<unsigned> line1VertexList;
    vector<unsigned> line2VertexList;
    line1VertexList.push_back(0);
    line1VertexList.push_back(1);
    line2VertexList.push_back(1);
    line2VertexList.push_back(2);

    vector< vector<unsigned> > elementVertices;
    elementVertices.push_back(line1VertexList);
    elementVertices.push_back(line2VertexList);

    vector< CellTopoPtr > cellTopos;
    cellTopos.push_back(line_2);
    cellTopos.push_back(line_2);
    MeshGeometryPtr meshGeometry = Teuchos::rcp( new MeshGeometry(vertices, elementVertices, cellTopos) );

    MeshTopologyPtr meshTopology = Teuchos::rcp( new MeshTopology(meshGeometry) );

    FunctionPtr x = Function::xn(1);
    FunctionPtr function = x;
    FunctionPtr fbdr = Function::restrictToCellBoundary(function);
    vector<FunctionPtr> functions;
    functions.push_back(function);
    functions.push_back(function);
    vector<string> functionNames;
    functionNames.push_back("function1");
    functionNames.push_back("function2");

    {
      XDMFExporter exporter(meshTopology, "function1", false);
      exporter.exportFunction(function, "function1");
    }
    {
      XDMFExporter exporter(meshTopology, "boundary1", false);
      exporter.exportFunction(fbdr, "boundary1");
    }
    {
      XDMFExporter exporter(meshTopology, "functions1", false);
      exporter.exportFunction(functions, functionNames);
    }
  }
  {
    // 2D tests
    CellTopoPtr quad_4 = Teuchos::rcp( new shards::CellTopology(shards::getCellTopologyData<shards::Quadrilateral<4> >() ) );
    CellTopoPtr tri_3 = Teuchos::rcp( new shards::CellTopology(shards::getCellTopologyData<shards::Triangle<3> >() ) );

    // let's draw a little house
    vector<double> v0 = makeVertex(-1,0);
    vector<double> v1 = makeVertex(1,0);
    vector<double> v2 = makeVertex(1,2);
    vector<double> v3 = makeVertex(-1,2);
    vector<double> v4 = makeVertex(0.0,3);

    vector< vector<double> > vertices;
    vertices.push_back(v0);
    vertices.push_back(v1);
    vertices.push_back(v2);
    vertices.push_back(v3);
    vertices.push_back(v4);

    vector<unsigned> quadVertexList;
    quadVertexList.push_back(0);
    quadVertexList.push_back(1);
    quadVertexList.push_back(2);
    quadVertexList.push_back(3);

    vector<unsigned> triVertexList;
    triVertexList.push_back(3);
    triVertexList.push_back(2);
    triVertexList.push_back(4);

    vector< vector<unsigned> > elementVertices;
    elementVertices.push_back(quadVertexList);
    elementVertices.push_back(triVertexList);

    vector< CellTopoPtr > cellTopos;
    cellTopos.push_back(quad_4);
    cellTopos.push_back(tri_3);
    MeshGeometryPtr meshGeometry = Teuchos::rcp( new MeshGeometry(vertices, elementVertices, cellTopos) );

    MeshTopologyPtr meshTopology = Teuchos::rcp( new MeshTopology(meshGeometry) );

    FunctionPtr x2 = Function::xn(2);
    FunctionPtr y2 = Function::yn(2);
    FunctionPtr function = x2 + y2;
    FunctionPtr vect = Function::vectorize(x2, y2);
    FunctionPtr fbdr = Function::restrictToCellBoundary(function);
    vector<FunctionPtr> functions;
    functions.push_back(function);
    functions.push_back(vect);
    vector<string> functionNames;
    functionNames.push_back("function");
    functionNames.push_back("vect");
    vector<FunctionPtr> bdrfunctions;
    bdrfunctions.push_back(fbdr);
    bdrfunctions.push_back(fbdr);
    vector<string> bdrfunctionNames;
    bdrfunctionNames.push_back("bdr1");
    bdrfunctionNames.push_back("bdr2");

    map<int, int> cellIDToNum1DPts;
    cellIDToNum1DPts[1] = 4;

    {
      XDMFExporter exporter(meshTopology, "Grid2D", false);
      // exporter.exportFunction(function, "function2", 0, 10);
      // exporter.exportFunction(vect, "vect2", 1, 10, cellIDToNum1DPts);
      // exporter.exportFunction(fbdr, "boundary2", 0);
      exporter.exportFunction(functions, functionNames, 1, 10);
    }
    {
      XDMFExporter exporter(meshTopology, "BdrGrid2D", false);
      // exporter.exportFunction(function, "function2", 0, 10);
      // exporter.exportFunction(vect, "vect2", 1, 10, cellIDToNum1DPts);
      // exporter.exportFunction(fbdr, "boundary2", 0);
      exporter.exportFunction(bdrfunctions, bdrfunctionNames, 1, 10);
    }

    ////////////////////   DECLARE VARIABLES   ///////////////////////
    // define test variables
    VarFactory varFactory;
    VarPtr tau = varFactory.testVar("tau", HDIV);
    VarPtr v = varFactory.testVar("v", HGRAD);

    // define trial variables
    VarPtr uhat = varFactory.traceVar("uhat");
    VarPtr fhat = varFactory.fluxVar("fhat");
    VarPtr u = varFactory.fieldVar("u");
    VarPtr sigma = varFactory.fieldVar("sigma", VECTOR_L2);

    ////////////////////   DEFINE BILINEAR FORM   ///////////////////////
    BFPtr bf = Teuchos::rcp( new BF(varFactory) );
    // tau terms:
    bf->addTerm(sigma, tau);
    bf->addTerm(u, tau->div());
    bf->addTerm(-uhat, tau->dot_normal());

    // v terms:
    bf->addTerm( sigma, v->grad() );
    bf->addTerm( fhat, v);

    ////////////////////   BUILD MESH   ///////////////////////
    int H1Order = 4, pToAdd = 2;
    Teuchos::RCP<Mesh> mesh = Teuchos::rcp( new Mesh (meshTopology, bf, H1Order, pToAdd) );

    ////////////////////   DEFINE INNER PRODUCT(S)   ///////////////////////
    IPPtr ip = bf->graphNorm();

    ////////////////////   SPECIFY RHS   ///////////////////////
    RHSPtr rhs = RHS::rhs();
    // Teuchos::RCP<RHS> rhs = Teuchos::rcp( new RHS );
    FunctionPtr one = Function::constant(1.0);
    rhs->addTerm( one * v );

    ////////////////////   CREATE BCs   ///////////////////////
    // Teuchos::RCP<BC> bc = Teuchos::rcp( new BCEasy );
    BCPtr bc = BC::bc();
    FunctionPtr zero = Function::zero();
    SpatialFilterPtr entireBoundary = Teuchos::rcp( new EntireBoundary );
    bc->addDirichlet(uhat, entireBoundary, zero);

    ////////////////////   SOLVE & REFINE   ///////////////////////
    Teuchos::RCP<Solution> solution = Teuchos::rcp( new Solution(mesh, bc, rhs, ip) );
    solution->solve(false);
    RefinementStrategy refinementStrategy( solution, 0.2);

    // Output solution
    FunctionPtr uSoln = Function::solution(u, solution);
    FunctionPtr sigmaSoln = Function::solution(sigma, solution);
    FunctionPtr uhatSoln = Function::solution(uhat, solution);
    FunctionPtr fhatSoln = Function::solution(fhat, solution);
    {
      XDMFExporter exporter(meshTopology, "Poisson", false);
      exporter.exportFunction(uSoln, "u", 0, 4);
      exporter.exportFunction(uSoln, "u", 1, 5);
      exporter.exportFunction(uhatSoln, "uhat", 0, 4);
      exporter.exportFunction(uhatSoln, "uhat", 1, 5);
      // exporter.exportFunction(fhatSoln, "fhat", 0, 4);
      // exporter.exportFunction(fhatSoln, "fhat", 1, 5);
    }
    {
      XDMFExporter exporter(meshTopology, "PoissonSolution", false);
      exporter.exportSolution(solution, mesh, varFactory, 0, 2, cellIDToSubdivision(mesh, 10));
      refinementStrategy.refine(true);
      solution->solve(false);
      exporter.exportSolution(solution, mesh, varFactory, 1, 2, cellIDToSubdivision(mesh, 10));
    }
    // exporter.exportFunction(sigmaSoln, "Poisson-s", "sigma", 0, 5);
    // exporter.exportFunction(uhatSoln, "Poisson-uhat", "uhat", 1, 6);
  }

  {
    // 3D tests
    CellTopoPtr hex = Teuchos::rcp(new shards::CellTopology(shards::getCellTopologyData<shards::Hexahedron<8> >() ));

    // let's draw a little box
    vector<double> v0 = makeVertex(0,0,0);
    vector<double> v1 = makeVertex(1,0,0);
    vector<double> v2 = makeVertex(1,1,0);
    vector<double> v3 = makeVertex(0,1,0);
    vector<double> v4 = makeVertex(0,0,1);
    vector<double> v5 = makeVertex(1,0,1);
    vector<double> v6 = makeVertex(1,1,1);
    vector<double> v7 = makeVertex(0,1,1);

    vector< vector<double> > vertices;
    vertices.push_back(v0);
    vertices.push_back(v1);
    vertices.push_back(v2);
    vertices.push_back(v3);
    vertices.push_back(v4);
    vertices.push_back(v5);
    vertices.push_back(v6);
    vertices.push_back(v7);

    vector<unsigned> hexVertexList;
    hexVertexList.push_back(0);
    hexVertexList.push_back(1);
    hexVertexList.push_back(2);
    hexVertexList.push_back(3);
    hexVertexList.push_back(4);
    hexVertexList.push_back(5);
    hexVertexList.push_back(6);
    hexVertexList.push_back(7);

    // vector<unsigned> triVertexList;
    // triVertexList.push_back(2);
    // triVertexList.push_back(3);
    // triVertexList.push_back(4);

    vector< vector<unsigned> > elementVertices;
    elementVertices.push_back(hexVertexList);
    // elementVertices.push_back(triVertexList);

    vector< CellTopoPtr > cellTopos;
    cellTopos.push_back(hex);
    // cellTopos.push_back(tri_3);
    MeshGeometryPtr meshGeometry = Teuchos::rcp( new MeshGeometry(vertices, elementVertices, cellTopos) );

    MeshTopologyPtr meshTopology = Teuchos::rcp( new MeshTopology(meshGeometry) );

    FunctionPtr x = Function::xn(1);
    FunctionPtr y = Function::yn(1);
    FunctionPtr z = Function::zn(1);
    FunctionPtr function = x + y + z;
    FunctionPtr fbdr = Function::restrictToCellBoundary(function);
    FunctionPtr vect = Function::vectorize(x, y, z);
    vector<FunctionPtr> functions;
    functions.push_back(function);
    functions.push_back(vect);
    vector<string> functionNames;
    functionNames.push_back("function");
    functionNames.push_back("vect");

    {
      XDMFExporter exporter(meshTopology, "function3", false);
      exporter.exportFunction(function, "function3");
    }
    {
      XDMFExporter exporter(meshTopology, "boundary3", false);
      exporter.exportFunction(fbdr, "boundary3");
    }
    {
      XDMFExporter exporter(meshTopology, "vect3", false);
      exporter.exportFunction(vect, "vect3");
    }
    {
      XDMFExporter exporter(meshTopology, "functions3", false);
      exporter.exportFunction(functions, functionNames);
    }
  }
}
Exemplo n.º 2
0
int main(int argc, char *argv[]) {
#ifdef HAVE_MPI
  Teuchos::GlobalMPISession mpiSession(&argc, &argv,0);
  choice::MpiArgs args( argc, argv );
#else
  choice::Args args( argc, argv );
#endif
  int commRank = Teuchos::GlobalMPISession::getRank();
  int numProcs = Teuchos::GlobalMPISession::getNProc();

  // Required arguments
  int numRefs = args.Input<int>("--numRefs", "number of refinement steps");
  int norm = args.Input<int>("--norm", "0 = graph\n    1 = robust\n    2 = coupled robust");

  // Optional arguments (have defaults)
  bool enforceLocalConservation = args.Input<bool>("--conserve", "enforce local conservation", false);
  double Re = args.Input("--Re", "Reynolds number", 40);
  double nu = 1./Re;
  double lambda = Re/2.-sqrt(Re*Re/4+4*pi*pi);
  int maxNewtonIterations = args.Input("--maxIterations", "maximum number of Newton iterations", 20);
  int polyOrder = args.Input("--polyOrder", "polynomial order for field variables", 2);
  int deltaP = args.Input("--deltaP", "how much to enrich test space", 2);
  // string saveFile = args.Input<string>("--meshSaveFile", "file to which to save refinement history", "");
  // string replayFile = args.Input<string>("--meshLoadFile", "file with refinement history to replay", "");
  args.Process();

  // if (commRank==0)
  // {
  //   cout << "saveFile is " << saveFile << endl;
  //   cout << "loadFile is " << replayFile << endl;
  // }

  ////////////////////   PROBLEM DEFINITIONS   ///////////////////////
  int H1Order = polyOrder+1;

  ////////////////////   DECLARE VARIABLES   ///////////////////////
  // define test variables
  VarFactory varFactory;
  VarPtr tau11 = varFactory.testVar("tau11", HGRAD);
  VarPtr tau12 = varFactory.testVar("tau12", HGRAD);
  VarPtr tau22 = varFactory.testVar("tau22", HGRAD);
  VarPtr v1 = varFactory.testVar("v1", HGRAD);
  VarPtr v2 = varFactory.testVar("v2", HGRAD);

  // define trial variables
  VarPtr u1 = varFactory.fieldVar("u1");
  VarPtr u2 = varFactory.fieldVar("u2");
  VarPtr sigma11 = varFactory.fieldVar("sigma11");
  VarPtr sigma12 = varFactory.fieldVar("sigma12");
  VarPtr sigma22 = varFactory.fieldVar("sigma22");
  VarPtr u1hat = varFactory.traceVar("u1hat");
  VarPtr u2hat = varFactory.traceVar("u2hat");
  VarPtr t1hat = varFactory.fluxVar("t1hat");
  VarPtr t2hat = varFactory.fluxVar("t2hat");

  ////////////////////   BUILD MESH   ///////////////////////
  BFPtr bf = Teuchos::rcp( new BF(varFactory) );

  // define nodes for mesh
  FieldContainer<double> meshBoundary(4,2);
  double xmin = -0.5;
  double xmax =  1.0;
  double ymin = -0.5;
  double ymax =  1.5;

  meshBoundary(0,0) =  xmin; // x1
  meshBoundary(0,1) =  ymin; // y1
  meshBoundary(1,0) =  xmax;
  meshBoundary(1,1) =  ymin;
  meshBoundary(2,0) =  xmax;
  meshBoundary(2,1) =  ymax;
  meshBoundary(3,0) =  xmin;
  meshBoundary(3,1) =  ymax;

  int horizontalCells = 6, verticalCells = 8;

  // create a pointer to a new mesh:
  Teuchos::RCP<Mesh> mesh = MeshFactory::buildQuadMesh(meshBoundary, horizontalCells, verticalCells,
                                                bf, H1Order, H1Order+deltaP);

  ////////////////////////////////////////////////////////////////////
  // INITIALIZE BACKGROUND FLOW FUNCTIONS
  ////////////////////////////////////////////////////////////////////

  BCPtr nullBC = Teuchos::rcp((BC*)NULL);
  RHSPtr nullRHS = Teuchos::rcp((RHS*)NULL);
  IPPtr nullIP = Teuchos::rcp((IP*)NULL);
  SolutionPtr backgroundFlow = Teuchos::rcp(new Solution(mesh, nullBC, nullRHS, nullIP) );

  vector<double> e1(2); // (1,0)
  e1[0] = 1;
  vector<double> e2(2); // (0,1)
  e2[1] = 1;

  FunctionPtr u1_prev = Function::solution(u1, backgroundFlow);
  FunctionPtr u2_prev = Function::solution(u2, backgroundFlow);
  // FunctionPtr sigma11_prev = Function::solution(sigma11, backgroundFlow);
  // FunctionPtr sigma12_prev = Function::solution(sigma12, backgroundFlow);
  // FunctionPtr sigma22_prev = Function::solution(sigma22, backgroundFlow);

  FunctionPtr zero = Teuchos::rcp( new ConstantScalarFunction(0.0) );
  FunctionPtr one = Teuchos::rcp( new ConstantScalarFunction(1.0) );
  FunctionPtr u1Exact     = Teuchos::rcp( new ExactU1(lambda) );
  FunctionPtr u2Exact     = Teuchos::rcp( new ExactU2(lambda) );

  // ==================== SET INITIAL GUESS ==========================
  map<int, Teuchos::RCP<Function> > functionMap;
  // functionMap[u1->ID()] = u1Exact;
  // functionMap[u2->ID()] = u2Exact;
  functionMap[u1->ID()] = zero;
  functionMap[u2->ID()] = zero;

  backgroundFlow->projectOntoMesh(functionMap);

  ////////////////////   DEFINE BILINEAR FORM   ///////////////////////

  // stress equation
  bf->addTerm( 1./nu*sigma11, tau11 );
  bf->addTerm( 1./nu*sigma12, tau12 );
  bf->addTerm( 1./nu*sigma12, tau12 );
  bf->addTerm( 1./nu*sigma22, tau22 );
  bf->addTerm( -0.5/nu*sigma11, tau11 );
  bf->addTerm( -0.5/nu*sigma22, tau11 );
  bf->addTerm( -0.5/nu*sigma11, tau22 );
  bf->addTerm( -0.5/nu*sigma22, tau22 );
  bf->addTerm( 2*u1, tau11->dx() );
  bf->addTerm( 2*u1, tau12->dy() );
  bf->addTerm( 2*u2, tau12->dx() );
  bf->addTerm( 2*u2, tau22->dy() );
  bf->addTerm( -2*u1hat, tau11->times_normal_x() );
  bf->addTerm( -2*u1hat, tau12->times_normal_y() );
  bf->addTerm( -2*u2hat, tau12->times_normal_x() );
  bf->addTerm( -2*u2hat, tau22->times_normal_y() );

  // momentum equation
  bf->addTerm( -2.*u1_prev*u1, v1->dx() );
  bf->addTerm( -u2_prev*u1, v1->dy() );
  bf->addTerm( -u1_prev*u2, v1->dy() );
  bf->addTerm( -u2_prev*u1, v2->dx() );
  bf->addTerm( -u1_prev*u2, v2->dx() );
  bf->addTerm( -2.*u2_prev*u2, v2->dy() );
  bf->addTerm( sigma11, v1->dx() );
  bf->addTerm( sigma12, v1->dy() );
  bf->addTerm( sigma12, v2->dx() );
  bf->addTerm( sigma22, v2->dy() );
  bf->addTerm( t1hat, v1);
  bf->addTerm( t2hat, v2);

  ////////////////////   SPECIFY RHS   ///////////////////////
  RHSPtr rhs = RHS::rhs();

  // stress equation
  rhs->addTerm( -2*u1_prev * tau11->dx() );
  rhs->addTerm( -2*u1_prev * tau12->dy() );
  rhs->addTerm( -2*u2_prev * tau12->dx() );
  rhs->addTerm( -2*u2_prev * tau22->dy() );

  // momentum equation
  rhs->addTerm( u1_prev*u1_prev * v1->dx() );
  rhs->addTerm( u2_prev*u1_prev * v1->dy() );
  rhs->addTerm( u2_prev*u1_prev * v2->dx() );
  rhs->addTerm( u2_prev*u2_prev * v2->dy() );

  ////////////////////   DEFINE INNER PRODUCT(S)   ///////////////////////
  IPPtr ip = Teuchos::rcp(new IP);
  if (norm == 0)
  {
    ip = bf->graphNorm();
  }
  else if (norm == 1)
  {
    ip->addTerm( 0.5/nu*tau11-0.5/nu*tau22 + v1->dx() );
    ip->addTerm( 1./nu*tau12 + v1->dy() );
    ip->addTerm( 1./nu*tau12 + v2->dx() );
    ip->addTerm( 0.5/nu*tau22-0.5/nu*tau11 + v2->dy() );

    ip->addTerm( 2*tau11->dx() + 2*tau12->dy() - 2*u1_prev*v1->dx() - u2_prev*v1->dy() - u2_prev*v2->dx() );
    ip->addTerm( 2*tau12->dx() + 2*tau22->dy() - 2*u2_prev*v2->dy() - u1_prev*v1->dy() - u1_prev*v2->dx() );

    ip->addTerm( v1 );
    ip->addTerm( v2 );
    ip->addTerm( tau11 );
    ip->addTerm( tau12 );
    ip->addTerm( tau12 );
    ip->addTerm( tau22 );
  }
  else if (norm == 2)
  {
    // ip->addTerm( 0.5/sqrt(nu)*tau11-0.5/nu*tau22 );
    // ip->addTerm( 1./sqrt(nu)*tau12 );
    // ip->addTerm( 1./sqrt(nu)*tau12 );
    // ip->addTerm( 0.5/sqrt(nu)*tau22-0.5/nu*tau11 );
    ip->addTerm( tau11 );
    ip->addTerm( tau12 );
    ip->addTerm( tau12 );
    ip->addTerm( tau22 );

    ip->addTerm( 2*tau11->dx() + 2*tau12->dy() - 2*u1_prev*v1->dx() - u2_prev*v1->dy() - u2_prev*v2->dx() );
    ip->addTerm( 2*tau12->dx() + 2*tau22->dy() - 2*u2_prev*v2->dy() - u1_prev*v1->dy() - u1_prev*v2->dx() );

    ip->addTerm( 2*u1_prev*v1->dx() + u2_prev*v1->dy() + u2_prev*v2->dx() );
    ip->addTerm( 2*u2_prev*v2->dy() + u1_prev*v1->dy() + u1_prev*v2->dx() );

    ip->addTerm( sqrt(nu)*v1->grad() );
    ip->addTerm( sqrt(nu)*v2->grad() );

    ip->addTerm( v1 );
    ip->addTerm( v2 );
  }

  ////////////////////   CREATE BCs   ///////////////////////
  BCPtr bc = BC::bc();
  // Teuchos::RCP<PenaltyConstraints> pc = Teuchos::rcp( new PenaltyConstraints );
  SpatialFilterPtr left = Teuchos::rcp( new ConstantXBoundary(-0.5) );
  SpatialFilterPtr right = Teuchos::rcp( new ConstantXBoundary(1) );
  SpatialFilterPtr top = Teuchos::rcp( new ConstantYBoundary(-0.5) );
  SpatialFilterPtr bottom = Teuchos::rcp( new ConstantYBoundary(1.5) );
  bc->addDirichlet(u1hat, left, u1Exact);
  bc->addDirichlet(u2hat, left, u2Exact);
  bc->addDirichlet(u1hat, right, u1Exact);
  bc->addDirichlet(u2hat, right, u2Exact);
  bc->addDirichlet(u1hat, top, u1Exact);
  bc->addDirichlet(u2hat, top, u2Exact);
  bc->addDirichlet(u1hat, bottom, u1Exact);
  bc->addDirichlet(u2hat, bottom, u2Exact);
  // bc->addDirichlet(u1hat, left, zero);
  // bc->addDirichlet(u2hat, left, zero);
  // bc->addDirichlet(u1hat, right, zero);
  // bc->addDirichlet(u2hat, right, zero);
  // bc->addDirichlet(u1hat, top, zero);
  // bc->addDirichlet(u2hat, top, zero);
  // bc->addDirichlet(u1hat, bottom, zero);
  // bc->addDirichlet(u2hat, bottom, zero);

  // pc->addConstraint(u1hat*u2hat-t1hat == zero, top);
  // pc->addConstraint(u2hat*u2hat-t2hat == zero, top);

  Teuchos::RCP<Solution> solution = Teuchos::rcp( new Solution(mesh, bc, rhs, ip) );
  // solution->setFilter(pc);

  // if (enforceLocalConservation) {
  //   solution->lagrangeConstraints()->addConstraint(u1hat->times_normal_x() + u2hat->times_normal_y() == zero);
  // }

  // ==================== Register Solutions ==========================
  mesh->registerSolution(solution);
  mesh->registerSolution(backgroundFlow);

  // Teuchos::RCP< RefinementHistory > refHistory = Teuchos::rcp( new RefinementHistory );
  // mesh->registerObserver(refHistory);

  ////////////////////   SOLVE & REFINE   ///////////////////////
  double energyThreshold = 0.2; // for mesh refinements
  RefinementStrategy refinementStrategy( solution, energyThreshold );
  HDF5Exporter exporter(mesh, "Kovasznay_np");

  ofstream convOut;
  stringstream convOutFile;
  convOutFile << "Kovasznay_conv_" << Re <<".txt";
  if (commRank == 0)
    convOut.open(convOutFile.str().c_str());

  set<int> nonlinearVars;
  nonlinearVars.insert(u1->ID());
  nonlinearVars.insert(u2->ID());

  double nonlinearRelativeEnergyTolerance = 1e-5; // used to determine convergence of the nonlinear solution
  for (int refIndex=0; refIndex<=numRefs; refIndex++)
  {
    double L2Update = 1e10;
    int iterCount = 0;
    while (L2Update > nonlinearRelativeEnergyTolerance && iterCount < maxNewtonIterations)
    {
      solution->solve(false);
      double u1L2Update = solution->L2NormOfSolutionGlobal(u1->ID());
      double u2L2Update = solution->L2NormOfSolutionGlobal(u2->ID());
      L2Update = sqrt(u1L2Update*u1L2Update + u2L2Update*u2L2Update);

      // Check local conservation
      if (commRank == 0)
      {
        cout << "L2 Norm of Update = " << L2Update << endl;

        // if (saveFile.length() > 0) {
        //   std::ostringstream oss;
        //   oss << string(saveFile) << refIndex ;
        //   cout << "on refinement " << refIndex << " saving mesh file to " << oss.str() << endl;
        //   refHistory->saveToFile(oss.str());
        // }
      }

      // line search algorithm
      double alpha = 1.0;
      backgroundFlow->addSolution(solution, alpha, nonlinearVars);
      iterCount++;
    }

    exporter.exportSolution(backgroundFlow, varFactory, refIndex, 2, cellIDToSubdivision(mesh, 4));

    FunctionPtr u1Soln = Function::solution(u1, backgroundFlow);
    FunctionPtr u2Soln = Function::solution(u2, backgroundFlow);
    FunctionPtr u1Sqr = (u1Soln-u1Exact)*(u1Soln-u1Exact);
    FunctionPtr u2Sqr = (u2Soln-u2Exact)*(u2Soln-u2Exact);
    double u1L2Error = u1Sqr->integrate(mesh, 1e-5);
    double u2L2Error = u2Sqr->integrate(mesh, 1e-5);
    double l2Error = sqrt(u1L2Error+u2L2Error);
    double energyError = solution->energyErrorTotal();
    cout << "L2 Error: " << l2Error << " Energy Error: " << energyError << endl;

    if (refIndex < numRefs)
      refinementStrategy.refine(commRank==0); // print to console on commRank 0
  }

  return 0;
}