BoundaryConditionsContainer.hpp

/*

Copyright (C) University of Oxford, 2005-2010

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 _BOUNDARYCONDITIONSCONTAINER_HPP_
#define _BOUNDARYCONDITIONSCONTAINER_HPP_

#include <map>
#include "ChasteSerialization.hpp"
#include <boost/serialization/split_member.hpp>
#include <boost/serialization/map.hpp>

#include "AbstractBoundaryConditionsContainer.hpp"
#include "AbstractBoundaryCondition.hpp"
#include "AbstractTetrahedralMesh.hpp"
#include "BoundaryElement.hpp"
#include "Node.hpp"
#include "LinearSystem.hpp"
#include "PetscException.hpp"
#include "ChastePoint.hpp"
#include "ConstBoundaryCondition.hpp"
#include "DistributedVectorFactory.hpp"


template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
class BoundaryConditionsContainer : public AbstractBoundaryConditionsContainer<ELEMENT_DIM,SPACE_DIM,PROBLEM_DIM>
{
public:

    typedef typename std::map< const BoundaryElement<ELEMENT_DIM-1, SPACE_DIM>*, const AbstractBoundaryCondition<SPACE_DIM>* >::const_iterator
        NeumannMapIterator;

    typedef AbstractBoundaryConditionsContainer<ELEMENT_DIM,SPACE_DIM,PROBLEM_DIM> BaseClassType;

private:

    std::map< const BoundaryElement<ELEMENT_DIM-1, SPACE_DIM> *, const AbstractBoundaryCondition<SPACE_DIM>* >*
        mpNeumannMap[PROBLEM_DIM]; 
    NeumannMapIterator mLastNeumannCondition[PROBLEM_DIM];

    bool mAnyNonZeroNeumannConditionsForUnknown[PROBLEM_DIM];

    ConstBoundaryCondition<SPACE_DIM>* mpZeroBoundaryCondition;

    bool mLoadedFromArchive;

public:

    BoundaryConditionsContainer();

    ~BoundaryConditionsContainer();

    void AddDirichletBoundaryCondition(const Node<SPACE_DIM>* pBoundaryNode,
                                       const AbstractBoundaryCondition<SPACE_DIM>* pBoundaryCondition,
                                       unsigned indexOfUnknown = 0,
                                       bool checkIfBoundaryNode = true);

    void AddNeumannBoundaryCondition(const BoundaryElement<ELEMENT_DIM-1, SPACE_DIM>* pBoundaryElement,
                                     const AbstractBoundaryCondition<SPACE_DIM>* pBoundaryCondition,
                                     unsigned indexOfUnknown = 0);

    void DefineZeroDirichletOnMeshBoundary(AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>* pMesh,
                                           unsigned indexOfUnknown = 0);

    void DefineConstantDirichletOnMeshBoundary(AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>* pMesh,
                                               double value,
                                               unsigned indexOfUnknown = 0);

    void DefineZeroNeumannOnMeshBoundary(AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>* pMesh,
                                         unsigned indexOfUnknown = 0);

    void ApplyDirichletToLinearProblem(LinearSystem& rLinearSystem,
                                       bool applyToMatrix = true,
                                       bool applyToRhsVector = true);

    void ApplyDirichletToNonlinearResidual(const Vec currentSolution, Vec residual,
                                           DistributedVectorFactory& rFactory);

    void ApplyDirichletToNonlinearJacobian(Mat jacobian);

    bool Validate(AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>* pMesh);

    double GetNeumannBCValue(const BoundaryElement<ELEMENT_DIM-1,SPACE_DIM>* pSurfaceElement,
                             const ChastePoint<SPACE_DIM>& rX,
                             unsigned indexOfUnknown = 0);

    bool HasNeumannBoundaryCondition(const BoundaryElement<ELEMENT_DIM-1,SPACE_DIM>* pSurfaceElement,
                                     unsigned indexOfUnknown = 0);

    bool AnyNonZeroNeumannConditions();

    NeumannMapIterator BeginNeumann();

    NeumannMapIterator EndNeumann();

    template <class Archive>
    void LoadFromArchive(Archive & archive, AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>* pMesh)
    {
        if (mLoadedFromArchive)
        {
            return;
        }

        MergeFromArchive(archive, pMesh);
    }

    template <class Archive>
    void MergeFromArchive(Archive & archive, AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>* pMesh);

private:
    friend class boost::serialization::access;

    template<class Archive>
    void save(Archive & archive, const unsigned int version) const;

    template<class Archive>
    void load(Archive & archive, const unsigned int version)
    {
    }

    BOOST_SERIALIZATION_SPLIT_MEMBER()

};


template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
template<class Archive>
void BoundaryConditionsContainer<ELEMENT_DIM,SPACE_DIM,PROBLEM_DIM>::save(
        Archive & archive, const unsigned int version) const
{
    typedef typename std::map<unsigned, const AbstractBoundaryCondition<SPACE_DIM> *> archive_map_type;
    // Save Dirichlet conditions
    for (unsigned index_of_unknown=0; index_of_unknown<PROBLEM_DIM; index_of_unknown++)
    {
        archive_map_type bc_map;
        typename BaseClassType::DirichletIteratorType it = this->mpDirichletMap[index_of_unknown]->begin();
        while (it != this->mpDirichletMap[index_of_unknown]->end() )
        {
            unsigned node_index = it->first->GetIndex();
            const AbstractBoundaryCondition<SPACE_DIM> * p_cond = it->second;
            bc_map[node_index] = p_cond;

            it++;
        }
        archive & bc_map;
    }

    // Save Neumann conditions
    for (unsigned index_of_unknown=0; index_of_unknown<PROBLEM_DIM; index_of_unknown++)
    {
        archive_map_type bc_map;
        for (NeumannMapIterator it = mpNeumannMap[index_of_unknown]->begin();
             it != mpNeumannMap[index_of_unknown]->end();
             ++it)
        {
            unsigned elem_index = it->first->GetIndex();
            const AbstractBoundaryCondition<SPACE_DIM>* p_cond = it->second;
            bc_map[elem_index] = p_cond;
        }
        archive & bc_map;
    }
}


template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
template<class Archive>
void BoundaryConditionsContainer<ELEMENT_DIM,SPACE_DIM,PROBLEM_DIM>::MergeFromArchive(
        Archive & archive, AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>* pMesh)
{
    mLoadedFromArchive = true;

    typedef typename std::map<unsigned, AbstractBoundaryCondition<SPACE_DIM>*> archive_map_type;
    // Keep track of conditions that might need deleting
    std::set<const AbstractBoundaryCondition<SPACE_DIM>*> maybe_unused_bcs;
    std::set<const AbstractBoundaryCondition<SPACE_DIM>*> used_bcs;
    
    // Load Dirichlet conditions
    for (unsigned index_of_unknown=0; index_of_unknown<PROBLEM_DIM; index_of_unknown++)
    {
        archive_map_type bc_map;
        archive & bc_map;
        for (typename archive_map_type::iterator it = bc_map.begin();
             it != bc_map.end();
             ++it)
        {
            unsigned node_index = it->first;
            this->mHasDirichletBCs=true;  //We know that a Dirichlet is being added, even if not by this process
            Node<SPACE_DIM>* p_node;
            try
            {
                p_node = pMesh->GetNodeFromPrePermutationIndex(node_index);
            }
            catch (Exception& e)
            {
                // It's a distributed mesh and we don't own this node - skip to the next BC
                maybe_unused_bcs.insert(it->second);
                continue;
            }
            AddDirichletBoundaryCondition(p_node, it->second, index_of_unknown, false);
            used_bcs.insert(it->second);
        }
    }
    this->mCheckedAndCommunicatedIfDirichletBcs=true; // Whether the Dirichlet BCC was empty or not, all processes know the status.

    // Load Neumann conditions
    for (unsigned index_of_unknown=0; index_of_unknown<PROBLEM_DIM; index_of_unknown++)
    {
        archive_map_type bc_map;
        archive & bc_map;
        for (typename archive_map_type::iterator it = bc_map.begin();
             it != bc_map.end();
             ++it)
        {
            unsigned boundary_element_index = it->first;
            BoundaryElement<ELEMENT_DIM-1, SPACE_DIM>* p_boundary_element;
            try
            {
                p_boundary_element = pMesh->GetBoundaryElement(boundary_element_index);
            }
            catch (Exception& e)
            {
                // It's a distributed mesh and we don't own this element - skip to the next BC
                maybe_unused_bcs.insert(it->second);
                continue;
            }
            AddNeumannBoundaryCondition(p_boundary_element, it->second, index_of_unknown);
            used_bcs.insert(it->second);
        }
    }
    
    // Free any unused BCs
    for (typename std::set<const AbstractBoundaryCondition<SPACE_DIM>*>::iterator it=maybe_unused_bcs.begin();
         it != maybe_unused_bcs.end();
         ++it)
    {
        typename std::set<const AbstractBoundaryCondition<SPACE_DIM>*>::iterator used = used_bcs.find(*it);
        if (used == used_bcs.end())
        {
            delete (*it);
        }
    }
}

#endif //_BOUNDARYCONDITIONSCONTAINER_HPP_

---