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    #include <config.h>
    
    #include <dune/grid/onedgrid.hh>
    #include <dune/grid/uggrid.hh>
    
    #include <dune/disc/elasticity/linearelasticityassembler.hh>
    #include <dune/disc/operators/p1operator.hh>
    #include <dune/istl/io.hh>
    #include <dune/grid/io/file/amirameshreader.hh>
    #include <dune/grid/io/file/amirameshwriter.hh>
    
    
    #include <dune/common/bitfield.hh>
    #include <dune/common/configparser.hh>
    
    
    #include "../common/multigridstep.hh"
    
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    #include "../solver/iterativesolver.hh"
    #include "../common/projectedblockgsstep.hh"
    #include "../common/readbitfield.hh"
    #include "../common/energynorm.hh"
    #include "../common/boundarypatch.hh"
    #include "../common/prolongboundarypatch.hh"
    
    #include "../common/neumannassembler.hh"
    
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    #include "src/quaternion.hh"
    
    #include "src/rodassembler.hh"
    
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    #include "src/configuration.hh"
    #include "src/averageinterface.hh"
    #include "src/rodsolver.hh"
    #include "src/rodwriter.hh"
    
    // Space dimension
    const int dim = 3;
    
    using namespace Dune;
    using std::string;
    
    int main (int argc, char *argv[]) try
    {
        // Some types that I need
    
        typedef BCRSMatrix<FieldMatrix<double, dim, dim> >   MatrixType;
        typedef BlockVector<FieldVector<double, dim> >       VectorType;
        typedef std::vector<Configuration>                   RodSolutionType;
    
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        // parse data file
        ConfigParser parameterSet;
        parameterSet.parseFile("dirneucoupling.parset");
    
        // read solver settings
        const int minLevel            = parameterSet.get("minLevel", int(0));
        const int maxLevel            = parameterSet.get("maxLevel", int(0));
        const int maxDirichletNeumannSteps = parameterSet.get("maxDirichletNeumannSteps", int(0));
        const int maxTrustRegionSteps = parameterSet.get("maxTrustRegionSteps", int(0));
    
        const int multigridIterations = parameterSet.get("numIt", int(0));
    
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        const int nu1              = parameterSet.get("nu1", int(0));
        const int nu2              = parameterSet.get("nu2", int(0));
        const int mu               = parameterSet.get("mu", int(0));
    
        const int baseIterations   = parameterSet.get("baseIt", int(0));
        const double mgTolerance     = parameterSet.get("tolerance", double(0));
    
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        const double baseTolerance = parameterSet.get("baseTolerance", double(0));
    
        const int initialTrustRegionRadius = parameterSet.get("initialTrustRegionRadius", int(0));
        const double damping       = parameterSet.get("damping", double(1));
    
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        // Problem settings
        std::string path = parameterSet.get("path", "xyz");
        std::string objectName = parameterSet.get("gridFile", "xyz");
        std::string dirichletNodesFile  = parameterSet.get("dirichletNodes", "xyz");
        std::string dirichletValuesFile = parameterSet.get("dirichletValues", "xyz");
        std::string interfaceNodesFile  = parameterSet.get("interfaceNodes", "xyz");
        const int numRodBaseElements = parameterSet.get("numRodBaseElements", int(0));
        
        
        // ///////////////////////////////////////
        //    Create the rod grid
        // ///////////////////////////////////////
        typedef OneDGrid<1,1> RodGridType;
        RodGridType rodGrid(numRodBaseElements, 0, 5);
    
        // ///////////////////////////////////////
        //    Create the grid for the 3d object
        // ///////////////////////////////////////
        typedef UGGrid<dim,dim> GridType;
        GridType grid;
        grid.setRefinementType(GridType::COPY);
        
        AmiraMeshReader<GridType>::read(grid, path + objectName);
    
    
        std::vector<BitField> dirichletNodes(1);
    
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        RodSolutionType rodX(rodGrid.size(0,1));
    
        // //////////////////////////
        //   Initial solution
        // //////////////////////////
    
        for (int i=0; i<rodX.size(); i++) {
            rodX[i].r = 0.5;
            rodX[i].r[2] = i+5;
            rodX[i].q = Quaternion<double>::identity();
        }
    
        rodX[rodX.size()-1].r[0] = 0.5;
        rodX[rodX.size()-1].r[1] = 0.5;
        rodX[rodX.size()-1].r[2] = 11;
    //     rodX[rodX.size()-1].q[0] = 0;
    //     rodX[rodX.size()-1].q[1] = 0;
    //     rodX[rodX.size()-1].q[2] = 1/sqrt(2);
    //     rodX[rodX.size()-1].q[3] = 1/sqrt(2);
    
    //     std::cout << "Left boundary orientation:" << std::endl;
    //     std::cout << "director 0:  " << rodX[0].q.director(0) << std::endl;
    //     std::cout << "director 1:  " << rodX[0].q.director(1) << std::endl;
    //     std::cout << "director 2:  " << rodX[0].q.director(2) << std::endl;
    //     std::cout << std::endl;
        std::cout << "Right boundary orientation:" << std::endl;
        std::cout << "director 0:  " << rodX[rodX.size()-1].q.director(0) << std::endl;
        std::cout << "director 1:  " << rodX[rodX.size()-1].q.director(1) << std::endl;
        std::cout << "director 2:  " << rodX[rodX.size()-1].q.director(2) << std::endl;
    //     exit(0);
    
        int toplevel = rodGrid.maxLevel();
    
        // /////////////////////////////////////////////////////
        //   Determine the Dirichlet nodes
        // /////////////////////////////////////////////////////
        Array<VectorType> dirichletValues;
        dirichletValues.resize(toplevel+1);
        dirichletValues[0].resize(grid.size(0, dim));
        AmiraMeshReader<int>::readFunction(dirichletValues[0], path + dirichletValuesFile);
    
    
        std::vector<BoundaryPatch<GridType> > dirichletBoundary;
    
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        dirichletBoundary.resize(maxLevel+1);
        dirichletBoundary[0].setup(grid, 0);
        readBoundaryPatch(dirichletBoundary[0], path + dirichletNodesFile);
        PatchProlongator<GridType>::prolong(dirichletBoundary);
    
        dirichletNodes.resize(toplevel+1);
        for (int i=0; i<=toplevel; i++) {
            
    
            dirichletNodes[i].resize( dim*grid.size(i,dim));
    
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            for (int j=0; j<grid.size(i,dim); j++)
                for (int k=0; k<dim; k++)
                    dirichletNodes[i][j*dim+k] = dirichletBoundary[i].containsVertex(j);
            
        }
        
    
        // /////////////////////////////////////////////////////
        //   Determine the interface boundary
        // /////////////////////////////////////////////////////
        std::vector<BoundaryPatch<GridType> > interfaceBoundary;
        interfaceBoundary.resize(maxLevel+1);
        interfaceBoundary[0].setup(grid, 0);
        readBoundaryPatch(interfaceBoundary[0], path + interfaceNodesFile);
        PatchProlongator<GridType>::prolong(interfaceBoundary);
    
    
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        // //////////////////////////////////////////
        //   Assemble 3d linear elasticity problem
        // //////////////////////////////////////////
        LeafP1Function<GridType,double,dim> u(grid),f(grid);
        LinearElasticityLocalStiffness<GridType,double> lstiff(2.5e5, 0.3);
        LeafP1OperatorAssembler<GridType,double,dim> hessian3d(grid);
        hessian3d.assemble(lstiff,u,f);
    
    
        // ////////////////////////////////////////////////////////////
        //    Create solution and rhs vectors
        // ////////////////////////////////////////////////////////////
        
    
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        VectorType x3d(grid.size(toplevel,dim));
        VectorType rhs3d(grid.size(toplevel,dim));
    
        // No external forces
        rhs3d = 0;
    
        // Set initial solution
        x3d = 0;
        for (int i=0; i<x3d.size(); i++) 
            for (int j=0; j<dim; j++)
                if (dirichletNodes[toplevel][i*dim+j])
                    x3d[i][j] = dirichletValues[toplevel][i][j];
    
    
        // ///////////////////////////////////////////
        //   Create a solver for the rod problem
        // ///////////////////////////////////////////
        RodAssembler<RodGridType> rodAssembler(rodGrid);
        rodAssembler.setShapeAndMaterial(1, 1, 1, 2.5e5, 0.3);
    
        RodSolver<RodGridType> rodSolver;
        rodSolver.setup(rodGrid, 
                        &rodAssembler,
                        rodX,
                        maxTrustRegionSteps,
                        initialTrustRegionRadius,
                        multigridIterations,
                        mgTolerance,
                        mu, nu1, nu2,
                        baseIterations,
                        baseTolerance);
    
    
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        // ////////////////////////////////
        //   Create a multigrid solver
        // ////////////////////////////////
    
        // First create a gauss-seidel base solver
    
        BlockGSStep<MatrixType, VectorType> baseSolverStep;
    
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        EnergyNorm<MatrixType, VectorType> baseEnergyNorm(baseSolverStep);
    
    
        IterativeSolver<MatrixType, VectorType> baseSolver(&baseSolverStep,
                                                           baseIterations,
                                                           baseTolerance,
                                                           &baseEnergyNorm,
                                                           Solver::QUIET);
    
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        // Make pre and postsmoothers
    
        BlockGSStep<MatrixType, VectorType> presmoother, postsmoother;
    
        MultigridStep<MatrixType, VectorType> multigridStep(*hessian3d, x3d, rhs3d, 1);
    
        multigridStep.setMGType(mu, nu1, nu2);
        multigridStep.dirichletNodes_    = &dirichletNodes;
        multigridStep.basesolver_        = &baseSolver;
        multigridStep.presmoother_       = &presmoother;
        multigridStep.postsmoother_      = &postsmoother;    
        multigridStep.verbosity_         = Solver::REDUCED;
    
        EnergyNorm<MatrixType, VectorType> energyNorm(multigridStep);
    
        IterativeSolver<MatrixType, VectorType> solver(&multigridStep,
                                                       multigridIterations,
                                                       mgTolerance,
                                                       &energyNorm,
                                                       Solver::FULL);
    
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        // ////////////////////////////////////
        //   Create the transfer operators
        // ////////////////////////////////////
    
        for (int k=0; k<multigridStep.mgTransfer_.size(); k++)
            delete(multigridStep.mgTransfer_[k]);
    
        multigridStep.mgTransfer_.resize(toplevel);
    
        for (int i=0; i<multigridStep.mgTransfer_.size(); i++){
    
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            TruncatedMGTransfer<VectorType>* newTransferOp = new TruncatedMGTransfer<VectorType>;
            newTransferOp->setup(grid,i,i+1);
    
            multigridStep.mgTransfer_[i] = newTransferOp;
    
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        }
    
        // /////////////////////////////////////////////////////
        //   Dirichlet-Neumann Solver
        // /////////////////////////////////////////////////////
    
        // Init interface value
    
        Configuration referenceInterface = rodX[0];
        Configuration lambda = referenceInterface;
    
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        for (int i=0; i<maxDirichletNeumannSteps; i++) {
            
            std::cout << "----------------------------------------------------" << std::endl;
            std::cout << "      Dirichlet-Neumann Step Number: " << i << std::endl;
            std::cout << "----------------------------------------------------" << std::endl;
            
            // //////////////////////////////////////////////////
            //   Dirichlet step for the rod
            // //////////////////////////////////////////////////
    
            rodX[0] = lambda;
    
            rodSolver.setInitialSolution(rodX);
    
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            rodSolver.solve();
    
    
            rodX = rodSolver.getSol();
    
    
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            // ///////////////////////////////////////////////////////////
            //   Extract Neumann values and transfer it to the 3d object
            // ///////////////////////////////////////////////////////////
    
            FieldVector<double,dim> resultantForce  = rodAssembler.getResultantForce(rodX);
            std::cout << "resultant force: " << resultantForce << std::endl;
    #if 0
            FieldVector<double,dim> resultantTorque = rodAssembler.getResultantTorque(grid, rodX);
    #endif
            VectorType neumannValues(grid.size(dim));
            neumannValues = 0;
            for (int j=0; j<neumannValues.size(); j++)
                if (interfaceBoundary[grid.maxLevel()].containsVertex(j))
                    neumannValues[j] = resultantForce;
    
            rhs3d = 0;
            assembleAndAddNeumannTerm<GridType, VectorType>(interfaceBoundary[grid.maxLevel()],
                                                            neumannValues,
                                                            rhs3d);
    
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            // ///////////////////////////////////////////////////////////
            //   Solve the Neumann problem for the 3d body
            // ///////////////////////////////////////////////////////////
    
            multigridStep.setProblem(*hessian3d, x3d, rhs3d, grid.maxLevel()+1);
            
            solver.preprocess();
            multigridStep.preprocess();
            
            solver.solve();
            
            x3d = multigridStep.getSol();
    
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            // ///////////////////////////////////////////////////////////
            //   Extract new interface position and orientation
            // ///////////////////////////////////////////////////////////
    
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            Configuration averageInterface;
    
    //         x3d = 0;
    //         for (int i=0; i<x3d.size(); i++)
    //             x3d[i][2] = 1;
    
            computeAverageInterface(interfaceBoundary[toplevel], x3d, averageInterface);
    
            std::cout << "average interface: " << averageInterface << std::endl;
    
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            // ///////////////////////////////////////////////////////////
            //   Compute new damped interface value
            // ///////////////////////////////////////////////////////////
    
    
            for (int j=0; j<dim; j++)
                lambda.r[j] = (1-damping) * lambda.r[j] + damping * (referenceInterface.r[j] + averageInterface.r[j]);
            lambda.q = averageInterface.q.mult(referenceInterface.q);
    
    
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        }
    
        // //////////////////////////////
        //   Output result
        // //////////////////////////////
        AmiraMeshWriter<GridType>::writeGrid(grid, "grid.result");
        AmiraMeshWriter<GridType>::writeBlockVector(grid, x3d, "grid.sol");
        writeRod(rodX, "rod3d.result");
    
    
        for (int i=0; i<rodX.size(); i++)
            std::cout << rodX[i] << std::endl;
    
    
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     } catch (Exception e) {
    
        std::cout << e << std::endl;
    
     }