BoundaryConditionsContainer.hpp

/*

Copyright (c) 2005-2016, 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 _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_