AbstractContinuumMechanicsAssembler.hpp

/*

Copyright (c) 2005-2017, University of Oxford.
All rights reserved.

University of Oxford means the Chancellor, Masters and Scholars of the
University of Oxford, having an administrative office at Wellington
Square, Oxford OX1 2JD, UK.

This file is part of Chaste.

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
 * Redistributions of source code must retain the above copyright notice,
   this list of conditions and the following disclaimer.
 * Redistributions in binary form must reproduce the above copyright notice,
   this list of conditions and the following disclaimer in the documentation
   and/or other materials provided with the distribution.
 * Neither the name of the University of Oxford nor the names of its
   contributors may be used to endorse or promote products derived from this
   software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

*/

#ifndef ABSTRACTCONTINUUMMECHANICSASSEMBLER_HPP_
#define ABSTRACTCONTINUUMMECHANICSASSEMBLER_HPP_

#include "AbstractFeAssemblerInterface.hpp"
#include "AbstractTetrahedralMesh.hpp"
#include "QuadraticMesh.hpp"
#include "DistributedQuadraticMesh.hpp"
#include "LinearBasisFunction.hpp"
#include "QuadraticBasisFunction.hpp"
#include "ReplicatableVector.hpp"
#include "DistributedVector.hpp"
#include "PetscTools.hpp"
#include "PetscVecTools.hpp"
#include "PetscMatTools.hpp"
#include "GaussianQuadratureRule.hpp"


template<unsigned DIM, bool CAN_ASSEMBLE_VECTOR, bool CAN_ASSEMBLE_MATRIX>
class AbstractContinuumMechanicsAssembler : public AbstractFeAssemblerInterface<CAN_ASSEMBLE_VECTOR,CAN_ASSEMBLE_MATRIX>
{
protected:
    static const bool BLOCK_SYMMETRIC_MATRIX = true; //generalise to non-block symmetric matrices later (when needed maybe)

    static const unsigned NUM_VERTICES_PER_ELEMENT = DIM+1;

    static const unsigned NUM_NODES_PER_ELEMENT = (DIM+1)*(DIM+2)/2; // assuming quadratic

    static const unsigned SPATIAL_BLOCK_SIZE_ELEMENTAL = DIM*NUM_NODES_PER_ELEMENT;
    static const unsigned PRESSURE_BLOCK_SIZE_ELEMENTAL = NUM_VERTICES_PER_ELEMENT;

    static const unsigned STENCIL_SIZE = DIM*NUM_NODES_PER_ELEMENT + NUM_VERTICES_PER_ELEMENT;

    AbstractTetrahedralMesh<DIM,DIM>* mpMesh;

    GaussianQuadratureRule<DIM>* mpQuadRule;

    void DoAssemble();


    virtual c_matrix<double,SPATIAL_BLOCK_SIZE_ELEMENTAL,SPATIAL_BLOCK_SIZE_ELEMENTAL> ComputeSpatialSpatialMatrixTerm(
        c_vector<double, NUM_NODES_PER_ELEMENT>& rQuadPhi,
        c_matrix<double, DIM, NUM_NODES_PER_ELEMENT>& rGradQuadPhi,
        c_vector<double,DIM>& rX,
        Element<DIM,DIM>* pElement)
    {
        return zero_matrix<double>(SPATIAL_BLOCK_SIZE_ELEMENTAL,SPATIAL_BLOCK_SIZE_ELEMENTAL);
    }

    virtual c_matrix<double,SPATIAL_BLOCK_SIZE_ELEMENTAL,PRESSURE_BLOCK_SIZE_ELEMENTAL> ComputeSpatialPressureMatrixTerm(
        c_vector<double, NUM_NODES_PER_ELEMENT>& rQuadPhi,
        c_matrix<double, DIM, NUM_NODES_PER_ELEMENT>& rGradQuadPhi,
        c_vector<double, NUM_VERTICES_PER_ELEMENT>& rLinearPhi,
        c_matrix<double, DIM, NUM_VERTICES_PER_ELEMENT>& rGradLinearPhi,
        c_vector<double,DIM>& rX,
        Element<DIM,DIM>* pElement)
    {
        return zero_matrix<double>(SPATIAL_BLOCK_SIZE_ELEMENTAL,PRESSURE_BLOCK_SIZE_ELEMENTAL);
    }


    virtual c_matrix<double,PRESSURE_BLOCK_SIZE_ELEMENTAL,PRESSURE_BLOCK_SIZE_ELEMENTAL> ComputePressurePressureMatrixTerm(
        c_vector<double, NUM_VERTICES_PER_ELEMENT>& rLinearPhi,
        c_matrix<double, DIM, NUM_VERTICES_PER_ELEMENT>& rGradLinearPhi,
        c_vector<double,DIM>& rX,
        Element<DIM,DIM>* pElement)
    {
        return zero_matrix<double>(PRESSURE_BLOCK_SIZE_ELEMENTAL,PRESSURE_BLOCK_SIZE_ELEMENTAL);
    }


    virtual c_vector<double,SPATIAL_BLOCK_SIZE_ELEMENTAL> ComputeSpatialVectorTerm(
        c_vector<double, NUM_NODES_PER_ELEMENT>& rQuadPhi,
        c_matrix<double, DIM, NUM_NODES_PER_ELEMENT>& rGradQuadPhi,
        c_vector<double,DIM>& rX,
        Element<DIM,DIM>* pElement) = 0;


    virtual c_vector<double,PRESSURE_BLOCK_SIZE_ELEMENTAL> ComputePressureVectorTerm(
            c_vector<double, NUM_VERTICES_PER_ELEMENT>& rLinearPhi,
            c_matrix<double, DIM, NUM_VERTICES_PER_ELEMENT>& rGradLinearPhi,
            c_vector<double,DIM>& rX,
            Element<DIM,DIM>* pElement)
    {
        return zero_vector<double>(PRESSURE_BLOCK_SIZE_ELEMENTAL);
    }

    void AssembleOnElement(Element<DIM, DIM>& rElement,
                           c_matrix<double, STENCIL_SIZE, STENCIL_SIZE >& rAElem,
                           c_vector<double, STENCIL_SIZE>& rBElem);

public:
    AbstractContinuumMechanicsAssembler(AbstractTetrahedralMesh<DIM, DIM>* pMesh)
        : AbstractFeAssemblerInterface<CAN_ASSEMBLE_VECTOR,CAN_ASSEMBLE_MATRIX>(),
          mpMesh(pMesh)
    {
        assert(pMesh);

        // Check that the mesh is quadratic
        QuadraticMesh<DIM>* p_quad_mesh = dynamic_cast<QuadraticMesh<DIM>* >(pMesh);
        DistributedQuadraticMesh<DIM>* p_distributed_quad_mesh = dynamic_cast<DistributedQuadraticMesh<DIM>* >(pMesh);

        if ((p_quad_mesh == NULL) && (p_distributed_quad_mesh == NULL))
        {
            EXCEPTION("Continuum mechanics assemblers require a quadratic mesh");
        }

        // In general the Jacobian for a mechanics problem is non-polynomial.
        // We therefore use the highest order integration rule available
        mpQuadRule = new GaussianQuadratureRule<DIM>(3);
    }

//    void SetCurrentSolution(Vec currentSolution);

    virtual ~AbstractContinuumMechanicsAssembler()
    {
        delete mpQuadRule;
    }
};


//template<unsigned DIM, bool CAN_ASSEMBLE_VECTOR, bool CAN_ASSEMBLE_MATRIX>
//void AbstractContinuumMechanicsAssembler<DIM,CAN_ASSEMBLE_VECTOR,CAN_ASSEMBLE_MATRIX>::SetCurrentSolution(Vec currentSolution)
//{
//    assert(currentSolution != NULL);
//
//    // Replicate the current solution and store so can be used in AssembleOnElement
//    HeartEventHandler::BeginEvent(HeartEventHandler::COMMUNICATION);
//    mCurrentSolutionOrGuessReplicated.ReplicatePetscVector(currentSolution);
//    HeartEventHandler::EndEvent(HeartEventHandler::COMMUNICATION);
//
//    // The AssembleOnElement type methods will determine if a current solution or
//    // current guess exists by looking at the size of the replicated vector, so
//    // check the size is zero if there isn't a current solution.
//    assert(mCurrentSolutionOrGuessReplicated.GetSize() > 0);
//}

template<unsigned DIM, bool CAN_ASSEMBLE_VECTOR, bool CAN_ASSEMBLE_MATRIX>
void AbstractContinuumMechanicsAssembler<DIM,CAN_ASSEMBLE_VECTOR,CAN_ASSEMBLE_MATRIX>::DoAssemble()
{
    assert(this->mAssembleMatrix || this->mAssembleVector);
    if (this->mAssembleMatrix)
    {
        if (this->mMatrixToAssemble == NULL)
        {
            EXCEPTION("Matrix to be assembled has not been set");
        }
        if (PetscMatTools::GetSize(this->mMatrixToAssemble) != (DIM+1)*mpMesh->GetNumNodes())
        {
            EXCEPTION("Matrix provided to be assembled has size " << PetscMatTools::GetSize(this->mMatrixToAssemble) << ", not expected size of " << (DIM+1)*mpMesh->GetNumNodes() << " ((dim+1)*num_nodes)");
        }
    }

    if (this->mAssembleVector)
    {
        if (this->mVectorToAssemble == NULL)
        {
            EXCEPTION("Vector to be assembled has not been set");
        }
        if (PetscVecTools::GetSize(this->mVectorToAssemble) != (DIM+1)*mpMesh->GetNumNodes())
        {
            EXCEPTION("Vector provided to be assembled has size " << PetscVecTools::GetSize(this->mVectorToAssemble) << ", not expected size of " << (DIM+1)*mpMesh->GetNumNodes() << " ((dim+1)*num_nodes)");
        }
    }

    // Zero the matrix/vector if it is to be assembled
    if (this->mAssembleVector && this->mZeroVectorBeforeAssembly)
    {
        // Note PetscVecTools::Finalise(this->mVectorToAssemble); on an unused matrix
        // would "compress" data and make any pre-allocated entries redundant.
        PetscVecTools::Zero(this->mVectorToAssemble);
    }
    if (this->mAssembleMatrix && this->mZeroMatrixBeforeAssembly)
    {
        // Note PetscMatTools::Finalise(this->mMatrixToAssemble); on an unused matrix
        // would "compress" data and make any pre-allocated entries redundant.
        PetscMatTools::Zero(this->mMatrixToAssemble);
    }

    c_matrix<double, STENCIL_SIZE, STENCIL_SIZE> a_elem = zero_matrix<double>(STENCIL_SIZE,STENCIL_SIZE);
    c_vector<double, STENCIL_SIZE> b_elem = zero_vector<double>(STENCIL_SIZE);


    // Loop over elements
    for (typename AbstractTetrahedralMesh<DIM, DIM>::ElementIterator iter = mpMesh->GetElementIteratorBegin();
         iter != mpMesh->GetElementIteratorEnd();
         ++iter)
    {
        Element<DIM, DIM>& r_element = *iter;

        // Test for ownership first, since it's pointless to test the criterion on something which we might know nothing about.
        if (r_element.GetOwnership() == true  /*&& ElementAssemblyCriterion(r_element)==true*/)
        {
            // LCOV_EXCL_START
            // note: if assemble matrix only
            if (CommandLineArguments::Instance()->OptionExists("-mech_very_verbose") && this->mAssembleMatrix)
            {
                std::cout << "\r[" << PetscTools::GetMyRank() << "]: Element " << r_element.GetIndex() << " of " << mpMesh->GetNumElements() << std::flush;
            }
            // LCOV_EXCL_STOP

            AssembleOnElement(r_element, a_elem, b_elem);

            // Note that a different ordering is used for the elemental matrix compared to the global matrix.
            // See comments about ordering above.
            unsigned p_indices[STENCIL_SIZE];
            // Work out the mapping for spatial terms
            for (unsigned i=0; i<NUM_NODES_PER_ELEMENT; i++)
            {
                for (unsigned j=0; j<DIM; j++)
                {
                    // DIM+1 on the right-hand side here is the problem dimension
                    p_indices[DIM*i+j] = (DIM+1)*r_element.GetNodeGlobalIndex(i) + j;
                }
            }
            // Work out the mapping for pressure terms
            for (unsigned i=0; i<NUM_VERTICES_PER_ELEMENT; i++)
            {
                p_indices[DIM*NUM_NODES_PER_ELEMENT + i] = (DIM+1)*r_element.GetNodeGlobalIndex(i)+DIM;
            }


            if (this->mAssembleMatrix)
            {
                PetscMatTools::AddMultipleValues<STENCIL_SIZE>(this->mMatrixToAssemble, p_indices, a_elem);
            }

            if (this->mAssembleVector)
            {
                PetscVecTools::AddMultipleValues<STENCIL_SIZE>(this->mVectorToAssemble, p_indices, b_elem);
            }
        }
    }
}

template<unsigned DIM, bool CAN_ASSEMBLE_VECTOR, bool CAN_ASSEMBLE_MATRIX>
void AbstractContinuumMechanicsAssembler<DIM,CAN_ASSEMBLE_VECTOR,CAN_ASSEMBLE_MATRIX>::AssembleOnElement(Element<DIM, DIM>& rElement,
                                                                                                         c_matrix<double, STENCIL_SIZE, STENCIL_SIZE >& rAElem,
                                                                                                         c_vector<double, STENCIL_SIZE>& rBElem)
{
    static c_matrix<double,DIM,DIM> jacobian;
    static c_matrix<double,DIM,DIM> inverse_jacobian;
    double jacobian_determinant;

    mpMesh->GetInverseJacobianForElement(rElement.GetIndex(), jacobian, jacobian_determinant, inverse_jacobian);

    if (this->mAssembleMatrix)
    {
        rAElem.clear();
    }

    if (this->mAssembleVector)
    {
        rBElem.clear();
    }

    // Allocate memory for the basis functions values and derivative values
    static c_vector<double, NUM_VERTICES_PER_ELEMENT> linear_phi;
    static c_vector<double, NUM_NODES_PER_ELEMENT> quad_phi;
    static c_matrix<double, DIM, NUM_NODES_PER_ELEMENT> grad_quad_phi;
    static c_matrix<double, DIM, NUM_VERTICES_PER_ELEMENT> grad_linear_phi;

    c_vector<double,DIM> body_force;

    // Loop over Gauss points
    for (unsigned quadrature_index=0; quadrature_index < mpQuadRule->GetNumQuadPoints(); quadrature_index++)
    {
        double wJ = jacobian_determinant * mpQuadRule->GetWeight(quadrature_index);
        const ChastePoint<DIM>& quadrature_point = mpQuadRule->rGetQuadPoint(quadrature_index);

        // Set up basis function info
        LinearBasisFunction<DIM>::ComputeBasisFunctions(quadrature_point, linear_phi);
        QuadraticBasisFunction<DIM>::ComputeBasisFunctions(quadrature_point, quad_phi);
        QuadraticBasisFunction<DIM>::ComputeTransformedBasisFunctionDerivatives(quadrature_point, inverse_jacobian, grad_quad_phi);
        LinearBasisFunction<DIM>::ComputeTransformedBasisFunctionDerivatives(quadrature_point, inverse_jacobian, grad_linear_phi);

        // interpolate X (ie physical location of this quad point).
        c_vector<double,DIM> X = zero_vector<double>(DIM);
        for (unsigned vertex_index=0; vertex_index<NUM_VERTICES_PER_ELEMENT; vertex_index++)
        {
            for (unsigned j=0; j<DIM; j++)
            {
                X(j) += linear_phi(vertex_index)*rElement.GetNode(vertex_index)->rGetLocation()(j);
            }
        }

        if (this->mAssembleVector)
        {
            c_vector<double,SPATIAL_BLOCK_SIZE_ELEMENTAL> b_spatial
                = ComputeSpatialVectorTerm(quad_phi, grad_quad_phi, X, &rElement);
            c_vector<double,PRESSURE_BLOCK_SIZE_ELEMENTAL> b_pressure = ComputePressureVectorTerm(linear_phi, grad_linear_phi, X, &rElement);

            for (unsigned i=0; i<SPATIAL_BLOCK_SIZE_ELEMENTAL; i++)
            {
                rBElem(i) += b_spatial(i)*wJ;
            }

            for (unsigned i=0; i<PRESSURE_BLOCK_SIZE_ELEMENTAL; i++)
            {
                rBElem(SPATIAL_BLOCK_SIZE_ELEMENTAL + i) += b_pressure(i)*wJ;
            }
        }

        if (this->mAssembleMatrix)
        {
            c_matrix<double,SPATIAL_BLOCK_SIZE_ELEMENTAL,SPATIAL_BLOCK_SIZE_ELEMENTAL> a_spatial_spatial
                = ComputeSpatialSpatialMatrixTerm(quad_phi, grad_quad_phi, X, &rElement);

            c_matrix<double,SPATIAL_BLOCK_SIZE_ELEMENTAL,PRESSURE_BLOCK_SIZE_ELEMENTAL> a_spatial_pressure
                = ComputeSpatialPressureMatrixTerm(quad_phi, grad_quad_phi, linear_phi, grad_linear_phi, X, &rElement);

            c_matrix<double,PRESSURE_BLOCK_SIZE_ELEMENTAL,SPATIAL_BLOCK_SIZE_ELEMENTAL> a_pressure_spatial;
            if (!BLOCK_SYMMETRIC_MATRIX)
            {
                NEVER_REACHED; // to-come: non-mixed problems
                //a_pressure_spatial = ComputeSpatialPressureMatrixTerm(quad_phi, grad_quad_phi, lin_phi, grad_lin_phi, x, &rElement);
            }

            c_matrix<double,PRESSURE_BLOCK_SIZE_ELEMENTAL,PRESSURE_BLOCK_SIZE_ELEMENTAL> a_pressure_pressure
                = ComputePressurePressureMatrixTerm(linear_phi, grad_linear_phi, X, &rElement);

            for (unsigned i=0; i<SPATIAL_BLOCK_SIZE_ELEMENTAL; i++)
            {
                for (unsigned j=0; j<SPATIAL_BLOCK_SIZE_ELEMENTAL; j++)
                {
                    rAElem(i,j) += a_spatial_spatial(i,j)*wJ;
                }

                for (unsigned j=0; j<PRESSURE_BLOCK_SIZE_ELEMENTAL; j++)
                {
                    rAElem(i, SPATIAL_BLOCK_SIZE_ELEMENTAL + j) += a_spatial_pressure(i,j)*wJ;
                }
            }

            for (unsigned i=0; i<PRESSURE_BLOCK_SIZE_ELEMENTAL; i++)
            {
                if (BLOCK_SYMMETRIC_MATRIX)
                {
                    for (unsigned j=0; j<SPATIAL_BLOCK_SIZE_ELEMENTAL; j++)
                    {
                        rAElem(SPATIAL_BLOCK_SIZE_ELEMENTAL + i, j) += a_spatial_pressure(j,i)*wJ;
                    }
                }
                else
                {
                    NEVER_REACHED; // to-come: non-mixed problems
                }

                for (unsigned j=0; j<PRESSURE_BLOCK_SIZE_ELEMENTAL; j++)
                {
                    rAElem(SPATIAL_BLOCK_SIZE_ELEMENTAL + i, SPATIAL_BLOCK_SIZE_ELEMENTAL + j) += a_pressure_pressure(i,j)*wJ;
                }
            }
        }
    }
}

#endif // ABSTRACTCONTINUUMMECHANICSASSEMBLER_HPP_