NonlinearElasticityAssembler.hpp

/*

Copyright (C) University of Oxford, 2005-2009

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 NONLINEARELASTICITYASSEMBLER_HPP_
#define NONLINEARELASTICITYASSEMBLER_HPP_

/* 
 * NOTE ON COMPILATION ERRORS:
 * 
 * This file won't compile with Intel icpc version 9.1.039, with error message: 
 * "Terminate with:
  (0): internal error: backend signals"
 *
 * Try recompiling with icpc version 10.0.025.
 */
 

//todos:
//factor out Dof handling?

#include "AbstractNonlinearElasticityAssembler.hpp"
//#include "LinearBasisFunction.hpp"
//#include "QuadraticBasisFunction.hpp"
#include "QuadraticMesh.hpp"
#include "GaussianQuadratureRule.hpp"

template<size_t DIM>
class NonlinearElasticityAssembler : public AbstractNonlinearElasticityAssembler<DIM>
{
    friend class TestNonlinearElasticityAssembler;
    
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 STENCIL_SIZE = DIM*NUM_NODES_PER_ELEMENT + NUM_VERTICES_PER_ELEMENT; 
    static const size_t NUM_NODES_PER_BOUNDARY_ELEMENT = DIM*(DIM+1)/2;
    static const size_t BOUNDARY_STENCIL_SIZE = DIM*NUM_NODES_PER_BOUNDARY_ELEMENT + DIM; 

    QuadraticMesh<DIM>* mpQuadMesh;


    std::vector<BoundaryElement<DIM-1,DIM>*> mBoundaryElements;

    GaussianQuadratureRule<DIM>* mpQuadratureRule;
    GaussianQuadratureRule<DIM-1>* mpBoundaryQuadratureRule;
    
    virtual void AssembleOnElement(Element<DIM, DIM>& rElement,
                                   c_matrix<double, STENCIL_SIZE, STENCIL_SIZE >& rAElem,
                                   c_matrix<double, STENCIL_SIZE, STENCIL_SIZE >& rAElemPrecond,
                                   c_vector<double, STENCIL_SIZE>& rBElem,
                                   bool assembleResidual,
                                   bool assembleJacobian);
    
    virtual void AssembleOnBoundaryElement(BoundaryElement<DIM-1,DIM>& rBoundaryElement,
                                           c_matrix<double,BOUNDARY_STENCIL_SIZE,BOUNDARY_STENCIL_SIZE>& rAelem,
                                           c_vector<double,BOUNDARY_STENCIL_SIZE>& rBelem,
                                           c_vector<double,DIM>& rTraction,
                                           bool assembleResidual,
                                           bool assembleJacobian);

    void FormInitialGuess();

    void AssembleSystem(bool assembleResidual, bool assembleJacobian);


    void Initialise(std::vector<c_vector<double,DIM> >* pFixedNodeLocations);

public:
    NonlinearElasticityAssembler(QuadraticMesh<DIM>* pQuadMesh,
                                 AbstractIncompressibleMaterialLaw<DIM>* pMaterialLaw,
                                 c_vector<double,DIM> bodyForce,
                                 double density,
                                 std::string outputDirectory,
                                 std::vector<unsigned>& fixedNodes,
                                 std::vector<c_vector<double,DIM> >* pFixedNodeLocations = NULL);
    
    NonlinearElasticityAssembler(QuadraticMesh<DIM>* pQuadMesh,
                                 std::vector<AbstractIncompressibleMaterialLaw<DIM>*>& rMaterialLaws,
                                 c_vector<double,DIM> bodyForce,
                                 double density,
                                 std::string outputDirectory,
                                 std::vector<unsigned>& fixedNodes,
                                 std::vector<c_vector<double,DIM> >* pFixedNodeLocations = NULL);

    ~NonlinearElasticityAssembler();
    
    void SetSurfaceTractionBoundaryConditions(std::vector<BoundaryElement<DIM-1,DIM>*>& rBoundaryElements,
                                              std::vector<c_vector<double,DIM> >& rSurfaceTractions);

    void SetFunctionalTractionBoundaryCondition(std::vector<BoundaryElement<DIM-1,DIM>*> rBoundaryElements,
                                                c_vector<double,DIM> (*pFunction)(c_vector<double,DIM>&));
    
    std::vector<double>& rGetPressures();
    
    std::vector<c_vector<double,DIM> >& rGetDeformedPosition();
};

#endif /*NONLINEARELASTICITYASSEMBLER_HPP_*/

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