BoundaryConditionsContainer.hpp

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*/
 
#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]; 
    std::map< const Node<SPACE_DIM> *, const Node<SPACE_DIM> * >*  mpPeriodicBcMap[PROBLEM_DIM];
 
    NeumannMapIterator mLastNeumannCondition[PROBLEM_DIM];
 
    bool mAnyNonZeroNeumannConditionsForUnknown[PROBLEM_DIM];
 
    ConstBoundaryCondition<SPACE_DIM>* mpZeroBoundaryCondition;
 
    bool mLoadedFromArchive;
 
public:
 
    BoundaryConditionsContainer(bool deleteConditions=true);
 
    ~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 AddPeriodicBoundaryCondition(const Node<SPACE_DIM>* pNode1,
                                      const Node<SPACE_DIM>* pNode2);
 
 
    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 ApplyPeriodicBcsToLinearProblem(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&)
            {
                // 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&)
            {
                // 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_