AbstractContinuumMechanicsAssembler.hpp

/*

Copyright (C) University of Oxford, 2005-2011

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.

Chaste is free software: you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License as published
by the Free Software Foundation, either version 2.1 of the License, or
(at your option) any later version.

Chaste is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public
License for more details. The offer of Chaste under the terms of the
License is subject to the License being interpreted in accordance with
English Law and subject to any action against the University of Oxford
being under the jurisdiction of the English Courts.

You should have received a copy of the GNU Lesser General Public License
along with Chaste. If not, see <http://www.gnu.org/licenses/>.

*/

#ifndef ABSTRACTCONTINUUMMECHANICSASSEMBLER_HPP_
#define ABSTRACTCONTINUUMMECHANICSASSEMBLER_HPP_

#include "AbstractFeAssemblerInterface.hpp"
#include "QuadraticMesh.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>
{
    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;

protected:
    QuadraticMesh<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)
    {
        return zero_vector<double>(SPATIAL_BLOCK_SIZE_ELEMENTAL);
    }


    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(QuadraticMesh<DIM>* pMesh, unsigned numQuadPoints = 3)
        : AbstractFeAssemblerInterface<CAN_ASSEMBLE_VECTOR,CAN_ASSEMBLE_MATRIX>(),
          mpMesh(pMesh)
    {
        assert(pMesh);
        mpQuadRule = new GaussianQuadratureRule<DIM>(numQuadPoints);
    }


//    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*mpMesh->GetNumNodes()+mpMesh->GetNumVertices() )
        {
            EXCEPTION("Matrix provided to be assembled has size " << PetscMatTools::GetSize(this->mMatrixToAssemble) << ", not expected size of " << DIM*mpMesh->GetNumNodes()+mpMesh->GetNumVertices() << " (dim*num_nodes+num_vertices)");
        }
    }

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

    // Zero the matrix/vector if it is to be assembled
    if (this->mAssembleVector && this->mZeroVectorBeforeAssembly)
    {
        PetscVecTools::Zero(this->mVectorToAssemble);
    }
    if (this->mAssembleMatrix && this->mZeroMatrixBeforeAssembly)
    {
        PetscMatTools::Zero(this->mMatrixToAssemble);
    }

//todo!
//mpPreconditionMatrixLinearSystem->ZeroLhsMatrix();

    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*/ )
        {
            AssembleOnElement(r_element, a_elem, b_elem);

            unsigned p_indices[STENCIL_SIZE];
            for (unsigned i=0; i<NUM_NODES_PER_ELEMENT; i++)
            {
                for (unsigned j=0; j<DIM; j++)
                {
                    p_indices[DIM*i+j] = DIM*r_element.GetNodeGlobalIndex(i) + j;
                }
            }

            for (unsigned i=0; i<NUM_VERTICES_PER_ELEMENT; i++)
            {
                p_indices[DIM*NUM_NODES_PER_ELEMENT + i] = DIM*mpMesh->GetNumNodes() + r_element.GetNodeGlobalIndex(i);
            }

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

//mpPreconditionMatrixLinearSystem->AddLhsMultipleValues(p_indices, a_elem_precond);

            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_