AbstractNonlinearElasticitySolver.hpp

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#ifndef ABSTRACTNONLINEARELASTICITYSOLVER_HPP_
#define ABSTRACTNONLINEARELASTICITYSOLVER_HPP_
 
#include <vector>
#include <cmath>
#include "AbstractContinuumMechanicsSolver.hpp"
#include "LinearSystem.hpp"
#include "LogFile.hpp"
#include "MechanicsEventHandler.hpp"
#include "ReplicatableVector.hpp"
#include "FourthOrderTensor.hpp"
#include "CmguiDeformedSolutionsWriter.hpp"
#include "AbstractMaterialLaw.hpp"
#include "QuadraticBasisFunction.hpp"
#include "SolidMechanicsProblemDefinition.hpp"
#include "Timer.hpp"
#include "AbstractPerElementWriter.hpp"
#include "petscsnes.h"
 
//#define MECH_USE_HYPRE    // uses HYPRE to solve linear systems, requires PETSc to be installed with HYPRE
 
typedef enum StrainType_
{
    DEFORMATION_GRADIENT_F = 0,
    DEFORMATION_TENSOR_C,
    LAGRANGE_STRAIN_E
} StrainType;
 
// Bizarrely PETSc 2.2 has this, but doesn't put it in the petscksp.h header...
#if (PETSC_VERSION_MAJOR == 2 && PETSC_VERSION_MINOR == 2) //PETSc 2.2
extern PetscErrorCode KSPInitialResidual(KSP,Vec,Vec,Vec,Vec,Vec);
#endif
 
//  Globals functions used by the SNES solver
 
template<unsigned DIM>
PetscErrorCode AbstractNonlinearElasticitySolver_ComputeResidual(SNES snes,
                                                                 Vec currentGuess,
                                                                 Vec residualVector,
                                                                 void* pContext);
 
#if ((PETSC_VERSION_MAJOR==3) && (PETSC_VERSION_MINOR>=5))
    template<unsigned DIM>
    PetscErrorCode AbstractNonlinearElasticitySolver_ComputeJacobian(SNES snes,
                                                                     Vec currentGuess,
                                                                     Mat globalJacobian,
                                                                     Mat preconditioner,
                                                                     void* pContext);
#else
template<unsigned DIM>
PetscErrorCode AbstractNonlinearElasticitySolver_ComputeJacobian(SNES snes,
                                                                 Vec currentGuess,
                                                                 Mat* pGlobalJacobian,
                                                                 Mat* pPreconditioner,
                                                                 MatStructure* pMatStructure,
                                                                 void* pContext);
#endif
 
template <unsigned DIM>
class  AbstractNonlinearElasticitySolver; //Forward declaration
 
template<unsigned DIM>
class StressPerElementWriter : public AbstractPerElementWriter<DIM, DIM, DIM*DIM>
{
private:
    AbstractNonlinearElasticitySolver<DIM>* mpSolver; 
public:
 
    StressPerElementWriter(AbstractTetrahedralMesh<DIM, DIM>* pMesh,
                           AbstractNonlinearElasticitySolver<DIM>* pSolver)
     : AbstractPerElementWriter<DIM, DIM, DIM*DIM>(pMesh),
       mpSolver(pSolver)
    {
    }
 
    void Visit(Element<DIM, DIM>* pElement, unsigned localIndex, c_vector<double, DIM*DIM>& rData)
    {
        assert(localIndex == pElement->GetIndex()); //Will fail when we move to DistributedQuadraticMesh
        //Flatten the matrix
        c_matrix<double, DIM, DIM> data = mpSolver->GetAverageStressPerElement(localIndex);
        for (unsigned i=0; i<DIM; i++)
        {
            for (unsigned j=0; j<DIM; j++)
            {
                rData[i*DIM+j] = data(i,j);
            }
        }
    }
};
 
template<unsigned DIM>
class AbstractNonlinearElasticitySolver : public AbstractContinuumMechanicsSolver<DIM>
{
    friend class StressRecoveror<DIM>;
    friend class VtkNonlinearElasticitySolutionWriter<DIM>;
 
 
protected:
 
    static const size_t NUM_VERTICES_PER_ELEMENT = DIM+1;
 
    static const size_t NUM_NODES_PER_ELEMENT = (DIM+1)*(DIM+2)/2;      // assuming quadratic
 
    static const size_t NUM_NODES_PER_BOUNDARY_ELEMENT = DIM*(DIM+1)/2; // assuming quadratic
 
    static const size_t BOUNDARY_STENCIL_SIZE = DIM*NUM_NODES_PER_BOUNDARY_ELEMENT;
 
    static double MAX_NEWTON_ABS_TOL;
 
    static double MIN_NEWTON_ABS_TOL;
 
    static double NEWTON_REL_TOL;
 
    SolidMechanicsProblemDefinition<DIM>& mrProblemDefinition;
 
    Mat& mrJacobianMatrix;
 
    c_matrix<double,DIM,DIM> mChangeOfBasisMatrix;
 
    double mKspAbsoluteTol;
 
    bool mWriteOutputEachNewtonIteration;
 
    FourthOrderTensor<DIM,DIM,DIM,DIM> dTdE;
 
    unsigned mNumNewtonIterations;
 
    double mCurrentTime;
 
 
    bool mCheckedOutwardNormals;
 
    bool mUseSnesSolver;
 
    double mLastDampingValue;
 
    bool mFirstStep;
 
    bool mTakeFullFirstNewtonStep;
 
    bool mPetscDirectSolve;
 
    bool mIncludeActiveTension;
 
    bool mSetComputeAverageStressPerElement;
 
    std::vector<c_vector<double,DIM*(DIM+1)/2> > mAverageStressesPerElement;
 
    void AddStressToAverageStressPerElement(c_matrix<double,DIM,DIM>& rT, unsigned elementIndex);
 
    virtual void SetKspSolverAndPcType(KSP solver);
 
 
    virtual void AssembleSystem(bool assembleResidual, bool assembleLinearSystem)=0;
 
    virtual void FinishAssembleSystem(bool assembleResidual, bool assembleLinearSystem);
 
    //
    // Element level methods
    //
 
    void GetElementCentroidStrain(StrainType strainType,
                                  Element<DIM,DIM>& rElement,
                                  c_matrix<double,DIM,DIM>& rDeformationGradient);
 
    virtual void AddActiveStressAndStressDerivative(c_matrix<double,DIM,DIM>& rC,
                                                    unsigned elementIndex,
                                                    unsigned currentQuadPointGlobalIndex,
                                                    c_matrix<double,DIM,DIM>& rT,
                                                    FourthOrderTensor<DIM,DIM,DIM,DIM>& rDTdE,
                                                    bool addToDTdE)
    {
        // does nothing - subclass needs to overload this if there are active stresses
    }
 
    virtual void SetupChangeOfBasisMatrix(unsigned elementIndex, unsigned currentQuadPointGlobalIndex)
    {
    }
 
    void AssembleOnBoundaryElement(BoundaryElement<DIM-1, DIM>& rBoundaryElement,
                                   c_matrix<double, BOUNDARY_STENCIL_SIZE, BOUNDARY_STENCIL_SIZE>& rAelem,
                                   c_vector<double, BOUNDARY_STENCIL_SIZE>& rBelem,
                                   bool assembleResidual,
                                   bool assembleJacobian,
                                   unsigned boundaryConditionIndex);
 
 
    bool ShouldAssembleMatrixTermForPressureOnDeformedBc();
 
    void AssembleOnBoundaryElementForPressureOnDeformedBc(BoundaryElement<DIM-1,DIM>& rBoundaryElement,
                                                          c_matrix<double,BOUNDARY_STENCIL_SIZE,BOUNDARY_STENCIL_SIZE>& rAelem,
                                                          c_vector<double,BOUNDARY_STENCIL_SIZE>& rBelem,
                                                          bool assembleResidual,
                                                          bool assembleJacobian,
                                                          unsigned boundaryConditionIndex);
 
    //
    //    These methods form the non-SNES nonlinear solver
    //
 
    double ComputeResidualAndGetNorm(bool allowException);
 
    double CalculateResidualNorm();
 
    void VectorSum(std::vector<double>& rX, ReplicatableVector& rY, double a, std::vector<double>& rZ);
 
    void PrintLineSearchResult(double s, double residNorm);
 
    double TakeNewtonStep();
 
    double UpdateSolutionUsingLineSearch(Vec solution);
 
    virtual void PostNewtonStep(unsigned counter, double normResidual);
 
    void SolveNonSnes(double tol=-1.0);
 
 
    //
    //    These methods form the SNES nonlinear solver
    //
public: // need to be public as are called by global functions
    void ComputeResidual(Vec currentGuess, Vec residualVector);
 
    void ComputeJacobian(Vec currentGuess, Mat* pJacobian, Mat* pPreconditioner);
 
private:
    void SolveSnes();
 
public:
 
    AbstractNonlinearElasticitySolver(AbstractTetrahedralMesh<DIM,DIM>& rQuadMesh,
                                      SolidMechanicsProblemDefinition<DIM>& rProblemDefinition,
                                      std::string outputDirectory,
                                      CompressibilityType compressibilityType);
 
    virtual ~AbstractNonlinearElasticitySolver();
 
    void Solve(double tol=-1.0);
 
    void SetIncludeActiveTension(bool includeActiveTension = true)
    {
        mIncludeActiveTension = includeActiveTension;
    }
 
    unsigned GetNumNewtonIterations();
 
 
    void SetWriteOutputEachNewtonIteration(bool writeOutputEachNewtonIteration=true)
    {
        mWriteOutputEachNewtonIteration = writeOutputEachNewtonIteration;
    }
 
    void SetKspAbsoluteTolerance(double kspAbsoluteTolerance)
    {
        assert(kspAbsoluteTolerance > 0);
        mKspAbsoluteTol = kspAbsoluteTolerance;
    }
 
    void SetTakeFullFirstNewtonStep(bool takeFullFirstStep = true)
    {
        mTakeFullFirstNewtonStep = takeFullFirstStep;
    }
 
    void SetUsePetscDirectSolve(bool usePetscDirectSolve = true)
    {
        mPetscDirectSolve = usePetscDirectSolve;
    }
 
 
    void SetCurrentTime(double time)
    {
        mCurrentTime = time;
    }
 
    void CreateCmguiOutput();
 
 
    void WriteCurrentStrains(StrainType strainType, std::string fileName, int counterToAppend = -1);
 
    void SetComputeAverageStressPerElementDuringSolve(bool setComputeAverageStressPerElement = true);
 
    void WriteCurrentAverageElementStresses(std::string fileName, int counterToAppend = -1);
 
    std::vector<c_vector<double,DIM> >& rGetSpatialSolution();
 
    std::vector<c_vector<double,DIM> >& rGetDeformedPosition();
 
    c_matrix<double,DIM,DIM> GetAverageStressPerElement(unsigned elementIndex);
};
 
// Implementation: first, the non-nonlinear-solve methods
 
template<unsigned DIM>
AbstractNonlinearElasticitySolver<DIM>::AbstractNonlinearElasticitySolver(AbstractTetrahedralMesh<DIM,DIM>& rQuadMesh,
                                                                          SolidMechanicsProblemDefinition<DIM>& rProblemDefinition,
                                                                          std::string outputDirectory,
                                                                          CompressibilityType compressibilityType)
    : AbstractContinuumMechanicsSolver<DIM>(rQuadMesh, rProblemDefinition, outputDirectory, compressibilityType),
      mrProblemDefinition(rProblemDefinition),
      mrJacobianMatrix(this->mSystemLhsMatrix),
      mKspAbsoluteTol(-1),
      mWriteOutputEachNewtonIteration(false),
      mNumNewtonIterations(0),
      mCurrentTime(0.0),
      mCheckedOutwardNormals(false),
      mLastDampingValue(0.0),
      mIncludeActiveTension(true),
      mSetComputeAverageStressPerElement(false)
{
    mUseSnesSolver = (mrProblemDefinition.GetSolveUsingSnes() ||
                      CommandLineArguments::Instance()->OptionExists("-mech_use_snes") );
 
    mChangeOfBasisMatrix = identity_matrix<double>(DIM,DIM);
 
    mTakeFullFirstNewtonStep = CommandLineArguments::Instance()->OptionExists("-mech_full_first_newton_step");
    mPetscDirectSolve = CommandLineArguments::Instance()->OptionExists("-mech_petsc_direct_solve");
}
 
template<unsigned DIM>
AbstractNonlinearElasticitySolver<DIM>::~AbstractNonlinearElasticitySolver()
{
}
 
template<unsigned DIM>
void AbstractNonlinearElasticitySolver<DIM>::FinishAssembleSystem(bool assembleResidual, bool assembleJacobian)
{
    PetscVecTools::Finalise(this->mResidualVector);
 
    if (assembleJacobian)
    {
        PetscMatTools::SwitchWriteMode(mrJacobianMatrix);
        PetscMatTools::SwitchWriteMode(this->mPreconditionMatrix);
 
        VecCopy(this->mResidualVector, this->mLinearSystemRhsVector);
    }
 
    // Apply Dirichlet boundary conditions
    if (assembleJacobian)
    {
        this->ApplyDirichletBoundaryConditions(NONLINEAR_PROBLEM_APPLY_TO_EVERYTHING, this->mCompressibilityType==COMPRESSIBLE);
    }
    else if (assembleResidual)
    {
        this->ApplyDirichletBoundaryConditions(NONLINEAR_PROBLEM_APPLY_TO_RESIDUAL_ONLY, this->mCompressibilityType==COMPRESSIBLE);
    }
 
    if (assembleResidual)
    {
        PetscVecTools::Finalise(this->mResidualVector);
    }
    if (assembleJacobian)
    {
        PetscMatTools::Finalise(mrJacobianMatrix);
        PetscMatTools::Finalise(this->mPreconditionMatrix);
        PetscVecTools::Finalise(this->mLinearSystemRhsVector);
    }
}
 
template<unsigned DIM>
std::vector<c_vector<double,DIM> >& AbstractNonlinearElasticitySolver<DIM>::rGetSpatialSolution()
{
    this->mSpatialSolution.clear();
    this->mSpatialSolution.resize(this->mrQuadMesh.GetNumNodes(), zero_vector<double>(DIM));
    for (unsigned i=0; i<this->mrQuadMesh.GetNumNodes(); i++)
    {
        for (unsigned j=0; j<DIM; j++)
        {
            this->mSpatialSolution[i](j) = this->mrQuadMesh.GetNode(i)->rGetLocation()[j] + this->mCurrentSolution[this->mProblemDimension*i+j];
        }
    }
    return this->mSpatialSolution;
}
 
template<unsigned DIM>
std::vector<c_vector<double,DIM> >& AbstractNonlinearElasticitySolver<DIM>::rGetDeformedPosition()
{
    return rGetSpatialSolution();
}
 
template<unsigned DIM>
void AbstractNonlinearElasticitySolver<DIM>::WriteCurrentStrains(StrainType strainType, std::string fileName, int counterToAppend)
{
    if (!this->mWriteOutput)
    {
        return;
    }
 
    std::stringstream file_name;
    file_name << fileName;
    if (counterToAppend >= 0)
    {
        file_name << "_" << counterToAppend;
    }
    file_name << ".strain";
 
    out_stream p_file = this->mpOutputFileHandler->OpenOutputFile(file_name.str());
 
    c_matrix<double,DIM,DIM> strain;
 
    for (typename AbstractTetrahedralMesh<DIM,DIM>::ElementIterator iter = this->mrQuadMesh.GetElementIteratorBegin();
         iter != this->mrQuadMesh.GetElementIteratorEnd();
         ++iter)
    {
        GetElementCentroidStrain(strainType, *iter, strain);
        for (unsigned i=0; i<DIM; i++)
        {
            for (unsigned j=0; j<DIM; j++)
            {
                *p_file << strain(i,j) << " ";
            }
        }
        *p_file << "\n";
    }
    p_file->close();
}
 
template<unsigned DIM>
void AbstractNonlinearElasticitySolver<DIM>::WriteCurrentAverageElementStresses(std::string fileName, int counterToAppend)
{
    if (!this->mWriteOutput)
    {
        return;
    }
 
    if (!mSetComputeAverageStressPerElement)
    {
        EXCEPTION("Call SetComputeAverageStressPerElementDuringSolve() before solve if calling WriteCurrentAverageElementStresses()");
    }
 
    std::stringstream file_name;
    file_name << fileName;
    if (counterToAppend >= 0)
    {
        file_name << "_" << counterToAppend;
    }
    file_name << ".stress";
    assert(mAverageStressesPerElement.size()==this->mrQuadMesh.GetNumElements());
 
    StressPerElementWriter<DIM> stress_writer(&(this->mrQuadMesh),this);
    stress_writer.WriteData(*(this->mpOutputFileHandler), file_name.str());
}
 
template<unsigned DIM>
void AbstractNonlinearElasticitySolver<DIM>::CreateCmguiOutput()
{
    if (this->mOutputDirectory == "")
    {
        EXCEPTION("No output directory was given so no output was written, cannot convert to cmgui format");
    }
 
    CmguiDeformedSolutionsWriter<DIM> writer(this->mOutputDirectory + "/cmgui",
                                             "solution",
                                             this->mrQuadMesh,
                                             WRITE_QUADRATIC_MESH);
 
    std::vector<c_vector<double,DIM> >& r_deformed_positions = this->rGetDeformedPosition();
    writer.WriteInitialMesh(); // this writes solution_0.exnode and .exelem
    writer.WriteDeformationPositions(r_deformed_positions, 1); // this writes the final solution as solution_1.exnode
    writer.WriteCmguiScript(); // writes LoadSolutions.com
}
 
template<unsigned DIM>
void AbstractNonlinearElasticitySolver<DIM>::SetComputeAverageStressPerElementDuringSolve(bool setComputeAverageStressPerElement)
{
    mSetComputeAverageStressPerElement = setComputeAverageStressPerElement;
    if (setComputeAverageStressPerElement && mAverageStressesPerElement.size()==0)
    {
        mAverageStressesPerElement.resize(this->mrQuadMesh.GetNumElements(), zero_vector<double>(DIM*(DIM+1)/2));
    }
}
 
template<unsigned DIM>
void AbstractNonlinearElasticitySolver<DIM>::AddStressToAverageStressPerElement(c_matrix<double,DIM,DIM>& rT, unsigned elemIndex)
{
    assert(mSetComputeAverageStressPerElement);
    assert(elemIndex<this->mrQuadMesh.GetNumElements());
 
    // In 2d the matrix is
    // [T00 T01]
    // [T10 T11]
    // where T01 = T10. We store this as a vector
    // [T00 T01 T11]
    //
    // Similarly, for 3d we store
    // [T00 T01 T02 T11 T12 T22]
    for (unsigned i=0; i<DIM*(DIM+1)/2; i++)
    {
        unsigned row;
        unsigned col;
        if (DIM == 2)
        {
            row = i<=1 ? 0 : 1;
            col = i==0 ? 0 : 1;
        }
        else // DIM == 3
        {
            row = i<=2 ? 0 : (i<=4? 1 : 2);
            col = i==0 ? 0 : (i==1 || i==3? 1 : 2);
        }
 
        this->mAverageStressesPerElement[elemIndex](i) += rT(row,col);
    }
}
 
template<unsigned DIM>
c_matrix<double,DIM,DIM> AbstractNonlinearElasticitySolver<DIM>::GetAverageStressPerElement(unsigned elementIndex)
{
    if (!mSetComputeAverageStressPerElement)
    {
        EXCEPTION("Call SetComputeAverageStressPerElementDuringSolve() before solve if calling GetAverageStressesPerElement()");
    }
    assert(elementIndex<this->mrQuadMesh.GetNumElements());
 
    c_matrix<double,DIM,DIM> stress;
 
    // In 2d the matrix is
    // [T00 T01]
    // [T10 T11]
    // where T01 = T10, and was stored as
    // [T00 T01 T11]
    //
    // Similarly, for 3d the matrix was stored as
    // [T00 T01 T02 T11 T12 T22]
    if (DIM == 2)
    {
        stress(0,0) = mAverageStressesPerElement[elementIndex](0);
        stress(1,0) = stress(0,1) = mAverageStressesPerElement[elementIndex](1);
        stress(1,1) = mAverageStressesPerElement[elementIndex](2);
    }
    else
    {
        stress(0,0) = mAverageStressesPerElement[elementIndex](0);
        stress(1,0) = stress(0,1) = mAverageStressesPerElement[elementIndex](1);
        stress(2,0) = stress(0,2) = mAverageStressesPerElement[elementIndex](2);
        stress(1,1) = mAverageStressesPerElement[elementIndex](3);
        stress(2,1) = stress(1,2) = mAverageStressesPerElement[elementIndex](4);
        stress(2,2) = mAverageStressesPerElement[elementIndex](5);
    }
 
    return stress;
}
 
// Methods at the 'element level'.
 
template<unsigned DIM>
void AbstractNonlinearElasticitySolver<DIM>::GetElementCentroidStrain(StrainType strainType,
                                                                      Element<DIM,DIM>& rElement,
                                                                      c_matrix<double,DIM,DIM>& rStrain)
{
    static c_matrix<double,DIM,DIM> jacobian;
    static c_matrix<double,DIM,DIM> inverse_jacobian;
    double jacobian_determinant;
 
    this->mrQuadMesh.GetInverseJacobianForElement(rElement.GetIndex(), jacobian, jacobian_determinant, inverse_jacobian);
 
    // Get the current displacement at the nodes
    static c_matrix<double,DIM,NUM_NODES_PER_ELEMENT> element_current_displacements;
    for (unsigned II=0; II<NUM_NODES_PER_ELEMENT; II++)
    {
        for (unsigned JJ=0; JJ<DIM; JJ++)
        {
            element_current_displacements(JJ,II) = this->mCurrentSolution[this->mProblemDimension*rElement.GetNodeGlobalIndex(II) + JJ];
        }
    }
 
    // Allocate memory for the basis functions values and derivative values
    static c_matrix<double, DIM, NUM_NODES_PER_ELEMENT> grad_quad_phi;
    static c_matrix<double,DIM,DIM> grad_u; // grad_u = (du_i/dX_M)
 
    // we need the point in the canonical element which corresponds to the centroid of the
    // version of the element in physical space. This point can be shown to be (1/3,1/3).
    ChastePoint<DIM> quadrature_point;
    if (DIM == 2)
    {
        quadrature_point.rGetLocation()(0) = 1.0/3.0;
        quadrature_point.rGetLocation()(1) = 1.0/3.0;
    }
    else
    {
        assert(DIM==3);
        quadrature_point.rGetLocation()(0) = 1.0/4.0;
        quadrature_point.rGetLocation()(1) = 1.0/4.0;
        quadrature_point.rGetLocation()(2) = 1.0/4.0;
    }
 
    QuadraticBasisFunction<DIM>::ComputeTransformedBasisFunctionDerivatives(quadrature_point, inverse_jacobian, grad_quad_phi);
 
    // Interpolate grad_u
    grad_u = zero_matrix<double>(DIM,DIM);
    for (unsigned node_index=0; node_index<NUM_NODES_PER_ELEMENT; node_index++)
    {
        for (unsigned i=0; i<DIM; i++)
        {
            for (unsigned M=0; M<DIM; M++)
            {
                grad_u(i,M) += grad_quad_phi(M,node_index)*element_current_displacements(i,node_index);
            }
        }
    }
 
    c_matrix<double,DIM,DIM> deformation_gradient;
 
    for (unsigned i=0; i<DIM; i++)
    {
        for (unsigned M=0; M<DIM; M++)
        {
            deformation_gradient(i,M) = (i==M?1:0) + grad_u(i,M);
        }
    }
 
    switch(strainType)
    {
        case DEFORMATION_GRADIENT_F:
        {
            rStrain = deformation_gradient;
            break;
        }
        case DEFORMATION_TENSOR_C:
        {
            rStrain = prod(trans(deformation_gradient),deformation_gradient);
            break;
        }
        case LAGRANGE_STRAIN_E:
        {
            c_matrix<double,DIM,DIM> C = prod(trans(deformation_gradient),deformation_gradient);
            for (unsigned M=0; M<DIM; M++)
            {
                for (unsigned N=0; N<DIM; N++)
                {
                    rStrain(M,N) = 0.5* ( C(M,N)-(M==N?1:0) );
                }
            }
            break;
        }
        default:
        {
            NEVER_REACHED;
            break;
        }
    }
}
 
template<unsigned DIM>
void AbstractNonlinearElasticitySolver<DIM>::AssembleOnBoundaryElement(
            BoundaryElement<DIM-1,DIM>& rBoundaryElement,
            c_matrix<double,BOUNDARY_STENCIL_SIZE,BOUNDARY_STENCIL_SIZE>& rAelem,
            c_vector<double,BOUNDARY_STENCIL_SIZE>& rBelem,
            bool assembleResidual,
            bool assembleJacobian,
            unsigned boundaryConditionIndex)
{
    if (this->mrProblemDefinition.GetTractionBoundaryConditionType() == PRESSURE_ON_DEFORMED
        || this->mrProblemDefinition.GetTractionBoundaryConditionType() == FUNCTIONAL_PRESSURE_ON_DEFORMED)
    {
        AssembleOnBoundaryElementForPressureOnDeformedBc(rBoundaryElement, rAelem, rBelem,
                                                         assembleResidual, assembleJacobian, boundaryConditionIndex);
        return;
    }
 
    rAelem.clear();
    rBelem.clear();
 
    if (assembleJacobian && !assembleResidual)
    {
        // Nothing to do
        return;
    }
 
    c_vector<double, DIM> weighted_direction;
    double jacobian_determinant;
    this->mrQuadMesh.GetWeightedDirectionForBoundaryElement(rBoundaryElement.GetIndex(), weighted_direction, jacobian_determinant);
 
    c_vector<double,NUM_NODES_PER_BOUNDARY_ELEMENT> phi;
 
    for (unsigned quad_index=0; quad_index<this->mpBoundaryQuadratureRule->GetNumQuadPoints(); quad_index++)
    {
        double wJ = jacobian_determinant * this->mpBoundaryQuadratureRule->GetWeight(quad_index);
 
        const ChastePoint<DIM-1>& quad_point = this->mpBoundaryQuadratureRule->rGetQuadPoint(quad_index);
 
        QuadraticBasisFunction<DIM-1>::ComputeBasisFunctions(quad_point, phi);
 
        // Get the required traction, interpolating X (slightly inefficiently,
        // as interpolating using quad bases) if necessary
        c_vector<double,DIM> traction = zero_vector<double>(DIM);
        switch (this->mrProblemDefinition.GetTractionBoundaryConditionType())
        {
            case FUNCTIONAL_TRACTION:
            {
                c_vector<double,DIM> X = zero_vector<double>(DIM);
                for (unsigned node_index=0; node_index<NUM_NODES_PER_BOUNDARY_ELEMENT; node_index++)
                {
                    X += phi(node_index)*this->mrQuadMesh.GetNode( rBoundaryElement.GetNodeGlobalIndex(node_index) )->rGetLocation();
                }
                traction = this->mrProblemDefinition.EvaluateTractionFunction(X, this->mCurrentTime);
                break;
            }
            case ELEMENTWISE_TRACTION:
            {
                traction = this->mrProblemDefinition.rGetElementwiseTractions()[boundaryConditionIndex];
                break;
            }
            default:
                NEVER_REACHED;
        }
 
 
        for (unsigned index=0; index<NUM_NODES_PER_BOUNDARY_ELEMENT*DIM; index++)
        {
            unsigned spatial_dim = index%DIM;
            unsigned node_index = (index-spatial_dim)/DIM;
 
            assert(node_index < NUM_NODES_PER_BOUNDARY_ELEMENT);
 
            rBelem(index) -=   traction(spatial_dim)
                             * phi(node_index)
                             * wJ;
        }
    }
}
 
template<unsigned DIM>
bool AbstractNonlinearElasticitySolver<DIM>::ShouldAssembleMatrixTermForPressureOnDeformedBc()
{
    if (mUseSnesSolver)
    {
        // although not using this in the first few steps might be useful when the deformation
        // is large, the snes solver is more robust, so we have this on all the time. (Also because
        // for cardiac problems and in timesteps after the initial large deformation, we want this on
        // in the first step
        return true;
 
        // could do something like this, if make the snes a member variable
        //PetscInt iteration_number;
        //SNESGetIterationNumber(mSnes,&iteration_number);
        //return (iteration_number >= 3);
    }
    else
    {
        return (mLastDampingValue >= 0.5);
    }
}
 
template<unsigned DIM>
void AbstractNonlinearElasticitySolver<DIM>::AssembleOnBoundaryElementForPressureOnDeformedBc(
            BoundaryElement<DIM-1,DIM>& rBoundaryElement,
            c_matrix<double,BOUNDARY_STENCIL_SIZE,BOUNDARY_STENCIL_SIZE>& rAelem,
            c_vector<double,BOUNDARY_STENCIL_SIZE>& rBelem,
            bool assembleResidual,
            bool assembleJacobian,
            unsigned boundaryConditionIndex)
{
    assert(   this->mrProblemDefinition.GetTractionBoundaryConditionType()==PRESSURE_ON_DEFORMED
           || this->mrProblemDefinition.GetTractionBoundaryConditionType()==FUNCTIONAL_PRESSURE_ON_DEFORMED);
 
    rAelem.clear();
    rBelem.clear();
 
    c_vector<double, DIM> weighted_direction;
    double jacobian_determinant;
    // note: jacobian determinant may be over-written below
    this->mrQuadMesh.GetWeightedDirectionForBoundaryElement(rBoundaryElement.GetIndex(), weighted_direction, jacobian_determinant);
 
    // Find the volume element of the mesh which
    // contains this boundary element
 
    Element<DIM,DIM>* p_containing_vol_element = nullptr;
 
    std::set<unsigned> potential_elements = rBoundaryElement.GetNode(0)->rGetContainingElementIndices();
    for (std::set<unsigned>::iterator iter = potential_elements.begin();
        iter != potential_elements.end();
        iter++)
    {
        p_containing_vol_element = this->mrQuadMesh.GetElement(*iter);
 
        bool this_vol_ele_contains_surf_ele = true;
        // loop over the nodes of boundary element and see if they are in the volume element
        for (unsigned i=1; i<NUM_NODES_PER_BOUNDARY_ELEMENT; i++) // don't need to start at 0, given looping over contain elems of node 0
        {
            unsigned surf_element_node_index = rBoundaryElement.GetNodeGlobalIndex(i);
            bool found_this_node = false;
            for (unsigned j=0; j<p_containing_vol_element->GetNumNodes(); j++)
            {
                unsigned vol_element_node_index = p_containing_vol_element->GetNodeGlobalIndex(j);
                if (surf_element_node_index == vol_element_node_index)
                {
                    found_this_node = true;
                    break;
                }
            }
            if (!found_this_node)
            {
                this_vol_ele_contains_surf_ele = false;
                break;
            }
        }
        if (this_vol_ele_contains_surf_ele)
        {
            break;
        }
    }
 
    // Find the local node index in the volume element for each node in the boundary element
    std::vector<unsigned> surf_to_vol_map(NUM_NODES_PER_BOUNDARY_ELEMENT);
    for (unsigned i=0; i<NUM_NODES_PER_BOUNDARY_ELEMENT; i++)
    {
        unsigned index = rBoundaryElement.GetNodeGlobalIndex(i);
        for (unsigned j=0; j<NUM_NODES_PER_ELEMENT; j++)
        {
            if (p_containing_vol_element->GetNodeGlobalIndex(j)==index)
            {
                surf_to_vol_map[i] = j;
                break;
            }
        }
    }
 
 
    // We require the volume element to compute F, which requires grad_phi on the volume element. For this we will
    // need the inverse jacobian for the volume element
    static c_matrix<double,DIM,DIM> jacobian_vol_element;
    static c_matrix<double,DIM,DIM> inverse_jacobian_vol_element;
    double jacobian_determinant_vol_element;
    this->mrQuadMesh.GetInverseJacobianForElement(p_containing_vol_element->GetIndex(), jacobian_vol_element, jacobian_determinant_vol_element, inverse_jacobian_vol_element);
 
    // Get the current displacements at each node of the volume element, to be used in computing F
    static c_matrix<double,DIM,NUM_NODES_PER_ELEMENT> element_current_displacements;
    for (unsigned II=0; II<NUM_NODES_PER_ELEMENT; II++)
    {
        for (unsigned JJ=0; JJ<DIM; JJ++)
        {
            element_current_displacements(JJ,II) = this->mCurrentSolution[this->mProblemDimension*p_containing_vol_element->GetNodeGlobalIndex(II) + JJ];
        }
    }
 
 
    // We will need both {grad phi_i} for the quadratic bases of the volume element, for computing F..
    static c_matrix<double, DIM, NUM_NODES_PER_ELEMENT> grad_quad_phi_vol_element;
    // ..the phi_i for each of the quadratic bases of the surface element, for the standard FE assembly part.
    c_vector<double,NUM_NODES_PER_BOUNDARY_ELEMENT> quad_phi_surf_element;
    // We need this too, which is obtained by taking a subset of grad_quad_phi_vol_element
    static c_matrix<double, DIM, NUM_NODES_PER_BOUNDARY_ELEMENT> grad_quad_phi_surf_element;
 
    c_matrix<double,DIM,DIM> F;
    c_matrix<double,DIM,DIM> invF;
 
    c_vector<double,DIM> normal = rBoundaryElement.CalculateNormal();
    c_matrix<double,1,DIM> normal_as_mat;
    for (unsigned i=0; i<DIM; i++)
    {
        normal_as_mat(0,i) = normal(i);
    }
 
    double normal_pressure;
    switch (this->mrProblemDefinition.GetTractionBoundaryConditionType())
    {
        case PRESSURE_ON_DEFORMED:
            normal_pressure = this->mrProblemDefinition.GetNormalPressure();
            break;
        case FUNCTIONAL_PRESSURE_ON_DEFORMED:
            normal_pressure = this->mrProblemDefinition.EvaluateNormalPressureFunction(this->mCurrentTime);
            break;
        default:
            NEVER_REACHED;
    }
 
    for (unsigned quad_index=0; quad_index<this->mpBoundaryQuadratureRule->GetNumQuadPoints(); quad_index++)
    {
        double wJ = jacobian_determinant * this->mpBoundaryQuadratureRule->GetWeight(quad_index);
 
        // Get the quadrature point on this surface element (in canonical space) - so eg, for a 2D problem,
        // the quad point is in 1D space
        const ChastePoint<DIM-1>& quadrature_point = this->mpBoundaryQuadratureRule->rGetQuadPoint(quad_index);
        QuadraticBasisFunction<DIM-1>::ComputeBasisFunctions(quadrature_point, quad_phi_surf_element);
 
        // We will need the xi coordinates of this quad point in the volume element. We could do this by figuring
        // out how the nodes of the surface element are ordered in the list of nodes in the volume element,
        // however it is less fiddly to compute directly. Firstly, compute the corresponding physical location
        // of the quad point, by interpolating
        c_vector<double,DIM> X = zero_vector<double>(DIM);
        for (unsigned node_index=0; node_index<NUM_NODES_PER_BOUNDARY_ELEMENT; node_index++)
        {
            X += quad_phi_surf_element(node_index)*rBoundaryElement.GetNode(node_index)->rGetLocation();
        }
 
 
        // Now compute the xi coordinates of the quad point in the volume element
        c_vector<double,DIM+1> weight = p_containing_vol_element->CalculateInterpolationWeights(X);
        c_vector<double,DIM> xi;
        for (unsigned i=0; i<DIM; i++)
        {
            xi(i) = weight(i+1); // Note, in 2d say, weights = [1-xi(0)-xi(1), xi(0), xi(1)]
        }
 
        // Check one of the weights was zero, as the quad point is on the boundary of the volume element
        if (DIM == 2)
        {
            assert( DIM!=2 || (fabs(weight(0))<1e-6) || (fabs(weight(1))<1e-6) || (fabs(weight(2))<1e-6) );
        }
        else
        {
            assert( DIM!=3 || (fabs(weight(0))<1e-6) || (fabs(weight(1))<1e-6) || (fabs(weight(2))<1e-6)  || (fabs(weight(3))<1e-6) ); // LCOV_EXCL_LINE
        }
 
        // Now we can compute the grad_phi and then interpolate F
        QuadraticBasisFunction<DIM>::ComputeTransformedBasisFunctionDerivatives(xi, inverse_jacobian_vol_element, grad_quad_phi_vol_element);
 
        F = identity_matrix<double>(DIM,DIM);
        for (unsigned node_index=0; node_index<NUM_NODES_PER_ELEMENT; node_index++)
        {
            for (unsigned i=0; i<DIM; i++)
            {
                for (unsigned M=0; M<DIM; M++)
                {
                    F(i,M) += grad_quad_phi_vol_element(M,node_index)*element_current_displacements(i,node_index);
                }
            }
        }
 
        double detF = Determinant(F);
        invF = Inverse(F);
 
        if (assembleResidual)
        {
            c_vector<double,DIM> traction = detF*normal_pressure*prod(trans(invF),normal);
 
            // assemble
            for (unsigned index=0; index<NUM_NODES_PER_BOUNDARY_ELEMENT*DIM; index++)
            {
                unsigned spatial_dim = index%DIM;
                unsigned node_index = (index-spatial_dim)/DIM;
 
                assert(node_index < NUM_NODES_PER_BOUNDARY_ELEMENT);
 
                rBelem(index) -=   traction(spatial_dim)
                                 * quad_phi_surf_element(node_index)
                                 * wJ;
            }
        }
 
        // Sometimes we don't include the analytic jacobian for this integral
        // in the jacobian that is assembled - the ShouldAssembleMatrixTermForPressureOnDeformedBc()
        // bit below - see the documentation for this method to see why.
        if (assembleJacobian && ShouldAssembleMatrixTermForPressureOnDeformedBc())
        {
            for (unsigned II=0; II<NUM_NODES_PER_BOUNDARY_ELEMENT; II++)
            {
                for (unsigned N=0; N<DIM; N++)
                {
                    grad_quad_phi_surf_element(N,II) = grad_quad_phi_vol_element(N,surf_to_vol_map[II]);
                }
            }
 
            static FourthOrderTensor<DIM,DIM,DIM,DIM> tensor1;
            for (unsigned N=0; N<DIM; N++)
            {
                for (unsigned e=0; e<DIM; e++)
                {
                    for (unsigned M=0; M<DIM; M++)
                    {
                        for (unsigned d=0; d<DIM; d++)
                        {
                            tensor1(N,e,M,d) = invF(N,e)*invF(M,d) - invF(M,e)*invF(N,d);
                        }
                    }
                }
            }
 
            // tensor2(II,e,M,d) = tensor1(N,e,M,d)*grad_quad_phi_surf_element(N,II)
            static FourthOrderTensor<NUM_NODES_PER_BOUNDARY_ELEMENT,DIM,DIM,DIM> tensor2;
            tensor2.template SetAsContractionOnFirstDimension<DIM>( trans(grad_quad_phi_surf_element), tensor1);
 
            // tensor3 is really a third-order tensor
            // tensor3(II,e,0,d) = tensor2(II,e,M,d)*normal(M)
            static FourthOrderTensor<NUM_NODES_PER_BOUNDARY_ELEMENT,DIM,1,DIM> tensor3;
            tensor3.template SetAsContractionOnThirdDimension<DIM>( normal_as_mat, tensor2);
 
            for (unsigned index1=0; index1<NUM_NODES_PER_BOUNDARY_ELEMENT*DIM; index1++)
            {
                unsigned spatial_dim1 = index1%DIM;
                unsigned node_index1 = (index1-spatial_dim1)/DIM;
 
                for (unsigned index2=0; index2<NUM_NODES_PER_BOUNDARY_ELEMENT*DIM; index2++)
                {
                    unsigned spatial_dim2 = index2%DIM;
                    unsigned node_index2 = (index2-spatial_dim2)/DIM;
 
                    rAelem(index1,index2) -=    normal_pressure
                                              * detF
                                              * tensor3(node_index2,spatial_dim2,0,spatial_dim1)
                                              * quad_phi_surf_element(node_index1)
                                              * wJ;
                }
            }
        }
    }
}
 
template<unsigned DIM>
void AbstractNonlinearElasticitySolver<DIM>::Solve(double tol)
{
    // Check the problem definition is set up correctly (and fully).
    mrProblemDefinition.Validate();
 
    // If the problem includes specified pressures on deformed surfaces (as opposed
    // to specified tractions), the code needs to compute normals, and they need
    // to be consistently all facing outward (or all facing inward). Check the undeformed
    // mesh boundary elements has nodes that are ordered so that all normals are
    // outward-facing
    if (mrProblemDefinition.GetTractionBoundaryConditionType()==PRESSURE_ON_DEFORMED && mCheckedOutwardNormals==false)
    {
        this->mrQuadMesh.CheckOutwardNormals();
        mCheckedOutwardNormals = true;
    }
 
    // Write the initial solution
    this->WriteCurrentSpatialSolution("initial", "nodes");
 
    if (mUseSnesSolver)
    {
        SolveSnes();
    }
    else
    {
        SolveNonSnes(tol);
    }
 
    // Remove pressure dummy values (P=0 at internal nodes, which should have been
    // been the result of the solve above), by linear interpolating from vertices of
    // edges to the internal node of the edge
    if (this->mCompressibilityType==INCOMPRESSIBLE)
    {
        this->RemovePressureDummyValuesThroughLinearInterpolation();
    }
 
    // Write the final solution
    this->WriteCurrentSpatialSolution("solution", "nodes");
}
 
template<unsigned DIM>
void AbstractNonlinearElasticitySolver<DIM>::SetKspSolverAndPcType(KSP solver)
{
    // Four alternatives
    //   (a) Petsc direct solve
    //   Otherwise iterative solve with:
    //   (b) Incompressible: GMRES with ILU preconditioner (or bjacobi=ILU on each process) [default]. Very poor on large problems.
    //   (c) Incompressible: GMRES with AMG preconditioner. Uncomment #define MECH_USE_HYPRE above. Requires Petsc3 with HYPRE installed.
    //   (d) Compressible: CG with ICC
 
    PC pc;
    KSPGetPC(solver, &pc);
 
    if (mPetscDirectSolve)
    {
        if (this->mCompressibilityType==COMPRESSIBLE)
        {
            KSPSetType(solver,KSPPREONLY);
 
        }
        PCSetType(pc, PCLU);
 
        // See #2057
        // PCFactorSetMatSolverPackage(pc,"mumps");
    }
    else
    {
        if (this->mCompressibilityType==COMPRESSIBLE)
        {
            KSPSetType(solver,KSPCG);
            if (PetscTools::IsSequential())
            {
                PCSetType(pc, PCICC);
                //Note that PetscOptionsSetValue is dangerous because we can't easily do
                //regression testing.  If a name changes, then the behaviour of the code changes
                //because it won't recognise the old name.  However, it won't fail to compile/run.
                #if (PETSC_VERSION_MAJOR == 3 && PETSC_VERSION_MINOR >= 1) //PETSc 3.1 or later
                    PetscTools::SetOption("-pc_factor_shift_type", "positive_definite");
                #else
                    PetscTools::SetOption("-pc_factor_shift_positive_definite", "");
                #endif
            }
            else
            {
                PCSetType(pc, PCBJACOBI);
            }
        }
        else
        {
            unsigned num_restarts = 100;
            KSPSetType(solver,KSPGMRES);
            KSPGMRESSetRestart(solver,num_restarts);
 
            #ifndef MECH_USE_HYPRE
                PCSetType(pc, PCBJACOBI); // BJACOBI = ILU on each block (block = part of matrix on each process)
            #else
                // Speed up linear solve time massively for larger simulations (in fact GMRES may stagnate without
                // this for larger problems), by using a AMG preconditioner -- needs HYPRE installed
                PetscTools::SetOption("-pc_hypre_type", "boomeramg");
                // PetscTools::SetOption("-pc_hypre_boomeramg_max_iter", "1");
                // PetscTools::SetOption("-pc_hypre_boomeramg_strong_threshold", "0.0");
 
                PCSetType(pc, PCHYPRE);
                #if (PETSC_VERSION_MAJOR == 3 && PETSC_VERSION_MINOR >=2) //PETSc 3.2 or later
                    KSPSetPCSide(solver, PC_RIGHT);
                #else
                    KSPSetPreconditionerSide(solver, PC_RIGHT);
                #endif
 
                // other possible preconditioners..
                //PCBlockDiagonalMechanics* p_custom_pc = new PCBlockDiagonalMechanics(solver, this->mPreconditionMatrix, mBlock1Size, mBlock2Size);
                //PCLDUFactorisationMechanics* p_custom_pc = new PCLDUFactorisationMechanics(solver, this->mPreconditionMatrix, mBlock1Size, mBlock2Size);
                //remember to delete memory..
                //KSPSetPreconditionerSide(solver, PC_RIGHT);
            #endif
        }
    }
}
 
//  The code for the non-SNES solver - maybe remove all this
//  as SNES solver appears better
 
template<unsigned DIM>
double AbstractNonlinearElasticitySolver<DIM>::ComputeResidualAndGetNorm(bool allowException)
{
    if (!allowException)
    {
        // Assemble the residual
        AssembleSystem(true, false);
    }
    else
    {
        try
        {
            // Try to assemble the residual using this current solution
            AssembleSystem(true, false);
        }
        catch(Exception&)
        {
            // If fail (because e.g. ODEs fail to solve, or strains are too large for material law), return infinity
            return DBL_MAX;
        }
    }
 
    // Return the scaled norm of the residual
    return CalculateResidualNorm();
}
 
template<unsigned DIM>
double AbstractNonlinearElasticitySolver<DIM>::CalculateResidualNorm()
{
    double norm;
 
    //\todo Change to NORM_1 and remove the division by mNumDofs...
    VecNorm(this->mResidualVector, NORM_2, &norm);
    return norm/this->mNumDofs;
}
 
template<unsigned DIM>
void AbstractNonlinearElasticitySolver<DIM>::VectorSum(std::vector<double>& rX,
                                                       ReplicatableVector& rY,
                                                       double a,
                                                       std::vector<double>& rZ)
{
    assert(rX.size()==rY.GetSize());
    assert(rY.GetSize()==rZ.size());
    for (unsigned i=0; i<rX.size(); i++)
    {
        rZ[i] = rX[i] + a*rY[i];
    }
}
 
template<unsigned DIM>
double AbstractNonlinearElasticitySolver<DIM>::TakeNewtonStep()
{
    if (this->mVerbose)
    {
        Timer::Reset();
    }
 
    // Assemble Jacobian (and preconditioner)
    MechanicsEventHandler::BeginEvent(MechanicsEventHandler::ASSEMBLE);
    AssembleSystem(true, true);
    MechanicsEventHandler::EndEvent(MechanicsEventHandler::ASSEMBLE);
    if (this->mVerbose)
    {
        Timer::PrintAndReset("AssembleSystem");
    }
 
    // Solve the linear system.
    MechanicsEventHandler::BeginEvent(MechanicsEventHandler::SOLVE);
 
    Vec solution;
    VecDuplicate(this->mResidualVector,&solution);
 
    KSP solver;
    KSPCreate(PETSC_COMM_WORLD,&solver);
 
#if ((PETSC_VERSION_MAJOR==3) && (PETSC_VERSION_MINOR>=5))
    KSPSetOperators(solver, mrJacobianMatrix, this->mPreconditionMatrix);
#else
    KSPSetOperators(solver, mrJacobianMatrix, this->mPreconditionMatrix, DIFFERENT_NONZERO_PATTERN /*in precond between successive solves*/);
#endif
 
    // Set the type of KSP solver (CG, GMRES etc) and preconditioner (ILU, HYPRE, etc)
    SetKspSolverAndPcType(solver);
 
    //PetscTools::SetOption("-ksp_monitor","");
    //PetscTools::SetOption("-ksp_norm_type","natural");
 
    KSPSetFromOptions(solver);
    KSPSetUp(solver);
 
 
    // Set the linear system absolute tolerance.
    // This is either the user provided value, or set to
    // max {1e-6 * initial_residual, 1e-12}
    if (mKspAbsoluteTol < 0)
    {
        Vec temp;
        VecDuplicate(this->mResidualVector, &temp);
        Vec temp2;
        VecDuplicate(this->mResidualVector, &temp2);
        Vec linsys_residual;
        VecDuplicate(this->mResidualVector, &linsys_residual);
 
        KSPInitialResidual(solver, solution, temp, temp2, linsys_residual, this->mLinearSystemRhsVector);
        double initial_resid_norm;
        VecNorm(linsys_residual, NORM_2, &initial_resid_norm);
 
        PetscTools::Destroy(temp);
        PetscTools::Destroy(temp2);
        PetscTools::Destroy(linsys_residual);
 
        double ksp_rel_tol = 1e-6;
        double absolute_tol = ksp_rel_tol * initial_resid_norm;
        if (absolute_tol < 1e-12)
        {
            absolute_tol = 1e-12;
        }
        KSPSetTolerances(solver, 1e-16, absolute_tol, PETSC_DEFAULT, 1000 /* max iters */); // Note: some machines - max iters seems to be 1000 whatever we give here
    }
    else
    {
        KSPSetTolerances(solver, 1e-16, mKspAbsoluteTol, PETSC_DEFAULT, 1000 /* max iters */); // Note: some machines - max iters seems to be 1000 whatever we give here
    }
 
    if (this->mVerbose)
    {
        Timer::PrintAndReset("KSP Setup");
    }
 
    KSPSolve(solver,this->mLinearSystemRhsVector,solution);
 
//    ///// For printing matrix when debugging
//    OutputFileHandler handler("TEMP",false);
//    std::stringstream ss;
//    static unsigned counter = 0;
//    ss << "all_" << counter++ << ".txt";
//    out_stream p_file = handler.OpenOutputFile(ss.str());
//    *p_file << std::setprecision(10);
//    for (unsigned i=0; i<this->mNumDofs; i++)
//    {
//        for (unsigned j=0; j<this->mNumDofs; j++)
//        {
//            *p_file << PetscMatTools::GetElement(mrJacobianMatrix, i, j) << " ";
//        }
//        *p_file << PetscVecTools::GetElement(this->mLinearSystemRhsVector, i) << " ";
//        *p_file << PetscVecTools::GetElement(solution, i) << "\n";
//    }
//    p_file->close();
 
 
    // Error checking for linear solve
 
    // warn if ksp reports failure
    KSPConvergedReason reason;
    KSPGetConvergedReason(solver,&reason);
    if (reason == KSP_DIVERGED_ITS || reason == KSP_DIVERGED_BREAKDOWN)
    {
        // DIVERGED_ITS or DIVERGED_BREAKDOWN just means it didn't converge in the given maximum number of iterations,
        // or similar, which is potentially not a problem, as the nonlinear solver may (and often will) still converge.
        // Just warn once.
        // (Very difficult to cover in normal tests, requires relative and absolute ksp tols to be very small, there
        // is no interface for setting both of these. Could be covered by setting up a problem the solver
        // finds difficult to solve, but this would be overkill.)
        // LCOV_EXCL_START
        WARN_ONCE_ONLY("Linear solve (within a mechanics solve) didn't converge, but this may not stop nonlinear solve converging")
        // LCOV_EXCL_STOP
    }
    else
    {
        // Throw an exception if the solver failed for any reason other than DIVERGED_ITS.
        // This is not covered as would be difficult to cover - requires a bad matrix to
        // assembled, for example.
        // LCOV_EXCL_START
        KSPEXCEPT(reason);
        // LCOV_EXCL_STOP
    }
 
    // quit if no ksp iterations were done
    int num_iters;
    KSPGetIterationNumber(solver, &num_iters);
    if (num_iters==0)
    {
        PetscTools::Destroy(solution);
        KSPDestroy(PETSC_DESTROY_PARAM(solver));
        EXCEPTION("KSP Absolute tolerance was too high, linear system wasn't solved - there will be no decrease in Newton residual. Decrease KspAbsoluteTolerance");
    }
 
 
    if (this->mVerbose)
    {
        Timer::PrintAndReset("KSP Solve");
        std::cout << "[" << PetscTools::GetMyRank() << "]: Num iterations = " << num_iters << "\n" << std::flush;
    }
 
    MechanicsEventHandler::EndEvent(MechanicsEventHandler::SOLVE);
 
    // Update the solution
    //  Newton method:       sol = sol - update, where update=Jac^{-1}*residual
    //  Newton with damping: sol = sol - s*update, where s is chosen
    //   such that |residual(sol)| is minimised. Damping is important to
    //   avoid initial divergence.
    //
    // Normally, finding the best s from say 0.05,0.1,0.2,..,1.0 is cheap,
    // but this is not the case in cardiac electromechanics calculations.
    // Therefore, we initially check s=1 (expected to be the best most of the
    // time, then s=0.9. If the norm of the residual increases, we assume
    // s=1 is the best. Otherwise, check s=0.8 to see if s=0.9 is a local min.
    MechanicsEventHandler::BeginEvent(MechanicsEventHandler::UPDATE);
    double new_norm_resid = UpdateSolutionUsingLineSearch(solution);
    MechanicsEventHandler::EndEvent(MechanicsEventHandler::UPDATE);
 
    PetscTools::Destroy(solution);
    KSPDestroy(PETSC_DESTROY_PARAM(solver));
 
    return new_norm_resid;
}
 
template<unsigned DIM>
void AbstractNonlinearElasticitySolver<DIM>::PrintLineSearchResult(double s, double residNorm)
{
    if (this->mVerbose)
    {
        std::cout << "\tTesting s = " << s << ", |f| = " << residNorm << "\n" << std::flush;
    }
}
 
template<unsigned DIM>
double AbstractNonlinearElasticitySolver<DIM>::UpdateSolutionUsingLineSearch(Vec solution)
{
    double initial_norm_resid = CalculateResidualNorm();
    if (this->mVerbose)
    {
        std::cout << "\tInitial |f| [corresponding to s=0] is " << initial_norm_resid << "\n"  << std::flush;
    }
 
    ReplicatableVector update(solution);
 
    std::vector<double> old_solution = this->mCurrentSolution;
 
    std::vector<double> damping_values; // = {1.0, 0.9, .., 0.2, 0.1, 0.05} ie size 11
    for (unsigned i=10; i>=1; i--)
    {
        damping_values.push_back((double)i/10.0);
    }
    damping_values.push_back(0.05);
    assert(damping_values.size()==11);
 
    // let mCurrentSolution = old_solution - damping_val[0]*update; and compute residual
    unsigned index = 0;
    VectorSum(old_solution, update, -damping_values[index], this->mCurrentSolution);
    double current_resid_norm = ComputeResidualAndGetNorm(true);
    PrintLineSearchResult(damping_values[index], current_resid_norm);
 
    // let mCurrentSolution = old_solution - damping_val[1]*update; and compute residual
    index = 1;
    VectorSum(old_solution, update, -damping_values[index], this->mCurrentSolution);
    double next_resid_norm = ComputeResidualAndGetNorm(true);
    PrintLineSearchResult(damping_values[index], next_resid_norm);
 
    index = 2;
    // While f(s_next) < f(s_current), [f = residnorm], keep trying new damping values,
    // ie exit thus loop when next norm of the residual first increases
    while (    (next_resid_norm==DBL_MAX) // the residual is returned as infinity if the deformation is so large to cause exceptions in the material law/EM contraction model
            || ( (next_resid_norm < current_resid_norm) && (index<damping_values.size()) ) )
    {
        current_resid_norm = next_resid_norm;
 
        // let mCurrentSolution = old_solution - damping_val*update; and compute residual
        VectorSum(old_solution, update, -damping_values[index], this->mCurrentSolution);
        next_resid_norm = ComputeResidualAndGetNorm(true);
        PrintLineSearchResult(damping_values[index], next_resid_norm);
 
        index++;
    }
 
    unsigned best_index;
 
    if (index==damping_values.size() && (next_resid_norm < current_resid_norm))
    {
        // Difficult to come up with large forces/tractions such that it had to
        // test right down to s=0.05, but overall doesn't fail.
        // The possible damping values have been manually temporarily altered to
        // get this code to be called, it appears to work correctly. Even if it
        // didn't tests wouldn't fail, they would just be v. slightly less efficient.
        // LCOV_EXCL_START
        // if we exited because we got to the end of the possible damping values, the
        // best one was the last one (excl the final index++ at the end)
        current_resid_norm = next_resid_norm;
        best_index = index-1;
        // LCOV_EXCL_STOP
    }
    else
    {
        // else the best one must have been the second last one (excl the final index++ at the end)
        // (as we would have exited when the resid norm first increased)
        best_index = index-2;
    }
 
    // See documentation for SetTakeFullFirstNewtonStep()
    bool full_first_step = mTakeFullFirstNewtonStep && mFirstStep;
 
 
    // Check out best was better than the original residual-norm
    if (initial_norm_resid < current_resid_norm && !full_first_step)
    {
        // LCOV_EXCL_START
        EXCEPTION("Residual does not appear to decrease in newton direction, quitting");
        // LCOV_EXCL_STOP
    }
 
    // See documentation for SetTakeFullFirstNewtonStep()
    if (full_first_step)
    {
        if (this->mVerbose)
        {
            std::cout << "\tTaking full first Newton step...\n";
        }
        best_index = 0;
    }
 
    if (this->mVerbose)
    {
        std::cout << "\tChoosing s = " << damping_values[best_index] << "\n"  << std::flush;
    }
 
 
//
//    double l_inf_disp = 0.0;
//    double l_inf_pressure = 0.0;
//
//    if (this->mCompressibilityType==INCOMPRESSIBLE)
//    {
//        for (unsigned i=0; i<this->mrQuadMesh.GetNumNodes(); i++)
//        {
//            for (unsigned j=0; j<DIM; j++)
//            {
//                double value = update[(DIM+1)*i + j]*damping_values[best_index];
//                l_inf_disp = std::max(l_inf_disp, fabs(value));
//            }
//            l_inf_pressure = std::max(l_inf_pressure, fabs(update[(DIM+1)*i + DIM]*damping_values[best_index]));
//        }
//        std::cout << "l_inf_disp, l_inf_pressure = " << l_inf_disp << " " << l_inf_pressure << "\n";
//    }
//    else
//    {
//        for (unsigned i=0; i<this->mrQuadMesh.GetNumNodes(); i++)
//        {
//            for (unsigned j=0; j<DIM; j++)
//            {
//                double value = update[DIM*i + j]*damping_values[best_index];
//                l_inf_disp = std::max(l_inf_disp, fabs(value));
//            }
//        }
//        std::cout << "l_inf_disp = " << l_inf_disp << "\n";
//    }
 
    VectorSum(old_solution, update, -damping_values[best_index], this->mCurrentSolution);
 
    mLastDampingValue = damping_values[best_index];
    return current_resid_norm;
}
 
template<unsigned DIM>
void AbstractNonlinearElasticitySolver<DIM>::PostNewtonStep(unsigned counter, double normResidual)
{
}
 
template<unsigned DIM>
void AbstractNonlinearElasticitySolver<DIM>::SolveNonSnes(double tol)
{
    mLastDampingValue = 0;
 
    if (mWriteOutputEachNewtonIteration)
    {
        this->WriteCurrentSpatialSolution("newton_iteration", "nodes", 0);
    }
 
    // Compute residual
    double norm_resid = ComputeResidualAndGetNorm(false);
    if (this->mVerbose)
    {
        std::cout << "\nNorm of residual is " << norm_resid << "\n";
    }
 
    mNumNewtonIterations = 0;
    unsigned iteration_number = 1;
 
    if (tol < 0) // i.e. if wasn't passed in as a parameter
    {
        tol = NEWTON_REL_TOL*norm_resid;
 
        // LCOV_EXCL_START // not going to have tests in cts for everything
        if (tol > MAX_NEWTON_ABS_TOL)
        {
            tol = MAX_NEWTON_ABS_TOL;
        }
        if (tol < MIN_NEWTON_ABS_TOL)
        {
            tol = MIN_NEWTON_ABS_TOL;
        }
        // LCOV_EXCL_STOP
    }
 
    if (this->mVerbose)
    {
        std::cout << "Solving with tolerance " << tol << "\n";
    }
 
    while (norm_resid > tol)
    {
        if (this->mVerbose)
        {
            std::cout <<  "\n-------------------\n"
                      <<   "Newton iteration " << iteration_number
                      << ":\n-------------------\n";
        }
 
        // take newton step (and get returned residual)
        mFirstStep = (iteration_number==1);
        norm_resid = TakeNewtonStep();
 
        if (this->mVerbose)
        {
            std::cout << "Norm of residual is " << norm_resid << "\n";
        }
 
        if (mWriteOutputEachNewtonIteration)
        {
            this->WriteCurrentSpatialSolution("newton_iteration", "nodes", iteration_number);
        }
 
        mNumNewtonIterations = iteration_number;
 
        PostNewtonStep(iteration_number,norm_resid);
 
        iteration_number++;
        if (iteration_number==20)
        {
            // LCOV_EXCL_START
            EXCEPTION("Not converged after 20 newton iterations, quitting");
            // LCOV_EXCL_STOP
        }
    }
 
    if (norm_resid > tol)
    {
        // LCOV_EXCL_START
        EXCEPTION("Failed to converge");
        // LCOV_EXCL_STOP
    }
}
 
template<unsigned DIM>
unsigned AbstractNonlinearElasticitySolver<DIM>::GetNumNewtonIterations()
{
    return mNumNewtonIterations;
}
 
//  SNES version of the nonlinear solver
 
template<unsigned DIM>
void AbstractNonlinearElasticitySolver<DIM>::SolveSnes()
{
    // Set up solution guess for residuals
    Vec initial_guess;
    VecDuplicate(this->mResidualVector, &initial_guess);
    double* p_initial_guess;
    VecGetArray(initial_guess, &p_initial_guess);
    int lo, hi;
    VecGetOwnershipRange(initial_guess, &lo, &hi);
    for (int global_index=lo; global_index<hi; global_index++)
    {
        int local_index = global_index - lo;
        p_initial_guess[local_index] = this->mCurrentSolution[global_index];
    }
    VecRestoreArray(initial_guess, &p_initial_guess);
    PetscVecTools::Finalise(initial_guess);
 
    Vec snes_residual_vec;
    VecDuplicate(this->mResidualVector, &snes_residual_vec);
 
    SNES snes;
 
    SNESCreate(PETSC_COMM_WORLD, &snes);
    SNESSetFunction(snes, snes_residual_vec, &AbstractNonlinearElasticitySolver_ComputeResidual<DIM>, this);
    SNESSetJacobian(snes, mrJacobianMatrix, this->mPreconditionMatrix, &AbstractNonlinearElasticitySolver_ComputeJacobian<DIM>, this);
#if (PETSC_VERSION_MAJOR == 3 && PETSC_VERSION_MINOR >= 4) //PETSc 3.4 or later
    SNESSetType(snes, SNESNEWTONLS);
#else
    SNESSetType(snes, SNESLS);
#endif
    SNESSetTolerances(snes, 1e-5, 1e-5, PETSC_DEFAULT, PETSC_DEFAULT, PETSC_DEFAULT);
 
#if (PETSC_VERSION_MAJOR == 3 && PETSC_VERSION_MINOR == 3) //PETSc 3.3
    SNESLineSearch linesearch;
    SNESGetSNESLineSearch(snes, &linesearch);
    // Use 'critical point' line search algorithm.  This was changed from 'backtracking'; see #2916
    SNESLineSearchSetType(linesearch, "cp");
#elif (PETSC_VERSION_MAJOR == 3 && PETSC_VERSION_MINOR >= 4) //PETSc 3.4 or later
    SNESLineSearch linesearch;
    SNESGetLineSearch(snes, &linesearch);
    // Use 'critical point' line search algorithm.  This was changed from 'backtracking'; see #2916
    SNESLineSearchSetType(linesearch, "cp");
#endif
 
    SNESSetMaxLinearSolveFailures(snes,100);
 
    KSP ksp;
    SNESGetKSP(snes, &ksp);
 
    KSPSetTolerances(ksp, PETSC_DEFAULT, PETSC_DEFAULT, PETSC_DEFAULT, 1000 /* max iters */); // Note: some machines - max iters seems to be 1000 whatever we give here
 
    // Set the type of KSP solver (CG, GMRES etc) and preconditioner (ILU, HYPRE, etc)
    SetKspSolverAndPcType(ksp);
 
    if (this->mVerbose)
    {
        PetscTools::SetOption("-snes_monitor","");
    }
    SNESSetFromOptions(snes);
 
#if (PETSC_VERSION_MAJOR == 2 && PETSC_VERSION_MINOR == 2) //PETSc 2.2
    PetscErrorCode err = SNESSolve(snes, initial_guess);
#else
    PetscErrorCode err = SNESSolve(snes, CHASTE_PETSC_NULLPTR, initial_guess);
#endif
 
    SNESConvergedReason reason;
    SNESGetConvergedReason(snes,&reason);
 
// LCOV_EXCL_START
    if (err != 0)
    {
        std::stringstream err_stream;
        err_stream << err;
        PetscTools::Destroy(initial_guess);
        PetscTools::Destroy(snes_residual_vec);
        SNESDestroy(PETSC_DESTROY_PARAM(snes));
        EXCEPTION("Nonlinear Solver failed. PETSc error code: "+err_stream.str()+" .");
    }
 
    if (reason < 0)
    {
        std::stringstream reason_stream;
        reason_stream << reason;
        PetscTools::Destroy(initial_guess);
        PetscTools::Destroy(snes_residual_vec);
        SNESDestroy(PETSC_DESTROY_PARAM(snes));
        EXCEPTION("Nonlinear Solver did not converge. PETSc reason code: "+reason_stream.str()+" .");
    }
// LCOV_EXCL_STOP
 
    PetscInt num_iters;
    SNESGetIterationNumber(snes,&num_iters);
    mNumNewtonIterations = num_iters;
 
    PetscTools::Destroy(initial_guess);
    PetscTools::Destroy(snes_residual_vec);
    SNESDestroy(PETSC_DESTROY_PARAM(snes));
}
 
template<unsigned DIM>
void AbstractNonlinearElasticitySolver<DIM>::ComputeResidual(Vec currentGuess, Vec residualVector)
{
    // Note: AssembleSystem() assumes the current solution is in this->mCurrentSolution and assembles
    // this->mResiduaVector and/or this->mrJacobianMatrix. Since PETSc wants us to use the input
    // currentGuess, and write the output to residualVector, we have to copy do some copies below.
 
    ReplicatableVector guess_repl(currentGuess);
    for (unsigned i=0; i<guess_repl.GetSize(); i++)
    {
        this->mCurrentSolution[i] = guess_repl[i];
    }
    AssembleSystem(true,false);
    VecCopy(this->mResidualVector, residualVector);
}
 
template<unsigned DIM>
void AbstractNonlinearElasticitySolver<DIM>::ComputeJacobian(Vec currentGuess, Mat* pJacobian, Mat* pPreconditioner)
{
    // Note: AssembleSystem() assumes the current solution is in this->mCurrentSolution and assembles
    // this->mResiduaVector and/or this->mrJacobianMatrix.
    // We need to copy the input currentGuess into the local mCurrentGuess.
    // We don't have to copy mrJacobianMatrix to pJacobian, which would be expensive, as they will
    // point to the same memory.
 
    // check Petsc data corresponds to internal Mats
    assert(mrJacobianMatrix==*pJacobian);
    assert(this->mPreconditionMatrix==*pPreconditioner);
 
    MechanicsEventHandler::BeginEvent(MechanicsEventHandler::ASSEMBLE);
    ReplicatableVector guess_repl(currentGuess);
    for (unsigned i=0; i<guess_repl.GetSize(); i++)
    {
        this->mCurrentSolution[i] = guess_repl[i];
    }
 
    AssembleSystem(false,true);
    MechanicsEventHandler::EndEvent(MechanicsEventHandler::ASSEMBLE);
}
 
template<unsigned DIM>
PetscErrorCode AbstractNonlinearElasticitySolver_ComputeResidual(SNES snes,
                                                                 Vec currentGuess,
                                                                 Vec residualVector,
                                                                 void* pContext)
{
    // Extract the solver from the void*
    AbstractNonlinearElasticitySolver<DIM>* p_solver = (AbstractNonlinearElasticitySolver<DIM>*)pContext;
    p_solver->ComputeResidual(currentGuess, residualVector);
    return 0;
}
 
template<unsigned DIM>
#if ((PETSC_VERSION_MAJOR==3) && (PETSC_VERSION_MINOR>=5))
    PetscErrorCode AbstractNonlinearElasticitySolver_ComputeJacobian(SNES snes,
                                                                     Vec currentGuess,
                                                                     Mat globalJacobian,
                                                                     Mat preconditioner,
                                                                     void* pContext)
    {
        // Extract the solver from the void*
        AbstractNonlinearElasticitySolver<DIM>* p_solver = (AbstractNonlinearElasticitySolver<DIM>*) pContext;
        p_solver->ComputeJacobian(currentGuess, &globalJacobian, &preconditioner);
        return 0;
    }
#else
    PetscErrorCode AbstractNonlinearElasticitySolver_ComputeJacobian(SNES snes,
                                                                     Vec currentGuess,
                                                                     Mat* pGlobalJacobian,
                                                                     Mat* pPreconditioner,
                                                                     MatStructure* pMatStructure,
                                                                     void* pContext)
    {
        // Extract the solver from the void*
        AbstractNonlinearElasticitySolver<DIM>* p_solver = (AbstractNonlinearElasticitySolver<DIM>*) pContext;
        p_solver->ComputeJacobian(currentGuess, pGlobalJacobian, pPreconditioner);
        return 0;
    }
#endif
 
 
// Constant setting definitions
 
template<unsigned DIM>
double AbstractNonlinearElasticitySolver<DIM>::MAX_NEWTON_ABS_TOL = 1e-7;
 
template<unsigned DIM>
double AbstractNonlinearElasticitySolver<DIM>::MIN_NEWTON_ABS_TOL = 1e-10;
 
template<unsigned DIM>
double AbstractNonlinearElasticitySolver<DIM>::NEWTON_REL_TOL = 1e-4;
 
#endif /*ABSTRACTNONLINEARELASTICITYSOLVER_HPP_*/