DistributedTetrahedralMesh.hpp

/*
 
Copyright (c) 2005-2024, 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 DISTRIBUTEDTETRAHEDRALMESH_HPP_
#define DISTRIBUTEDTETRAHEDRALMESH_HPP_
 
#include <map>
#include <vector>
#include <set>
 
#include "ChasteSerialization.hpp"
#include <boost/serialization/base_object.hpp>
 
#include "AbstractTetrahedralMesh.hpp"
#include "Node.hpp"
#include "AbstractMeshReader.hpp"
#include "DistributedTetrahedralMeshPartitionType.hpp"
 
#define UNASSIGNED_NODE UINT_MAX
 
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
class DistributedTetrahedralMesh : public AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM>
{
    friend class TestDistributedTetrahedralMesh;
    friend class TestDistributedQuadraticMesh;
private:
 
    unsigned mTotalNumElements;
 
    unsigned mTotalNumBoundaryElements;
 
    unsigned mTotalNumNodes;
 
    std::vector<Node<SPACE_DIM>* > mHaloNodes;
 
    std::map<unsigned, unsigned> mNodesMapping;
 
    std::map<unsigned, unsigned> mHaloNodesMapping;
 
    std::map<unsigned, unsigned> mElementsMapping;
 
    std::map<unsigned, unsigned> mBoundaryElementsMapping;
 
    ChasteCuboid<SPACE_DIM>* mpSpaceRegion;
 
    DistributedTetrahedralMeshPartitionType::type mPartitioning;
 
    friend class boost::serialization::access;
    template<class Archive>
    void serialize(Archive & archive, const unsigned int version)
    {
        archive & boost::serialization::base_object<AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM> >(*this);
    }
 
 
    void SetElementOwnerships();
 
 
public:
 
    DistributedTetrahedralMesh(DistributedTetrahedralMeshPartitionType::type partitioningMethod=DistributedTetrahedralMeshPartitionType::PARMETIS_LIBRARY);
 
    virtual ~DistributedTetrahedralMesh();
 
    void SetDistributedVectorFactory(DistributedVectorFactory* pFactory);
 
    virtual void ConstructFromMeshReader(AbstractMeshReader<ELEMENT_DIM,SPACE_DIM>& rMeshReader);
 
    unsigned GetNumLocalNodes() const;
 
    unsigned GetNumHaloNodes() const;
 
    unsigned GetNumLocalElements() const;
 
    unsigned GetNumLocalBoundaryElements() const;
 
    unsigned GetNumNodes() const;
 
    unsigned GetNumAllNodes() const;
 
    unsigned GetNumElements() const;
 
    DistributedTetrahedralMeshPartitionType::type GetPartitionType() const;
 
    unsigned GetNumBoundaryElements() const;
 
    void GetHaloNodeIndices(std::vector<unsigned>& rHaloIndices) const;
 
    void SetProcessRegion(ChasteCuboid<SPACE_DIM>* pRegion);
 
    ChasteCuboid<SPACE_DIM>* GetProcessRegion();
 
    bool CalculateDesignatedOwnershipOfElement( unsigned elementIndex );
 
    bool CalculateDesignatedOwnershipOfBoundaryElement( unsigned faceIndex );
 
     void ConstructLinearMesh(unsigned width);
 
    void ConstructRectangularMesh(unsigned width, unsigned height, bool stagger=true);
 
    void ConstructCuboid(unsigned width, unsigned height, unsigned depth);
    virtual void Scale(const double xFactor=1.0, const double yFactor=1.0, const double zFactor=1.0);
 
    Node<SPACE_DIM>* GetNodeOrHaloNode(unsigned index) const;
 
    virtual ChasteCuboid<SPACE_DIM> CalculateBoundingBox() const;
 
    virtual unsigned GetNearestNodeIndex(const ChastePoint<SPACE_DIM>& rTestPoint);
 
    virtual c_vector<double, 2> CalculateMinMaxEdgeLengths();
 
    void Rotate(c_matrix<double , SPACE_DIM, SPACE_DIM> rotationMatrix);
 
    void Translate(const c_vector<double, SPACE_DIM>& rDisplacement);
 
 
protected:
    unsigned SolveNodeMapping(unsigned index) const;
 
    unsigned SolveElementMapping(unsigned index) const;
 
    unsigned SolveBoundaryElementMapping(unsigned index) const;
private:
 
    void RegisterNode(unsigned index);
 
    void RegisterHaloNode(unsigned index);
 
    void RegisterElement(unsigned index);
 
    void RegisterBoundaryElement(unsigned index);
 
 
    void ComputeMeshPartitioning(AbstractMeshReader<ELEMENT_DIM, SPACE_DIM>& rMeshReader,
                                 std::set<unsigned>& rNodesOwned,
                                 std::set<unsigned>& rHaloNodesOwned,
                                 std::set<unsigned>& rElementsOwned,
                                 std::vector<unsigned>& rProcessorsOffset);
 
     void ParMetisLibraryNodeAndElementPartitioning(AbstractMeshReader<ELEMENT_DIM, SPACE_DIM>& rMeshReader,
                                          std::set<unsigned>& rElementsOwned,
                                          std::set<unsigned>& rNodesOwned,
                                          std::set<unsigned>& rHaloNodesOwned,
                                          std::vector<unsigned>& rProcessorsOffset);
 
    void ReorderNodes();
 
    //                            Iterators                             //
 
public:
    // The other iterators aren't (so only need to be dereferenced once). Consistency would be good...
 
    typedef typename std::vector<Node<SPACE_DIM> *>::const_iterator HaloNodeIterator;
 
    HaloNodeIterator GetHaloNodeIteratorBegin() const;
 
    HaloNodeIterator GetHaloNodeIteratorEnd() const;
};
 
#include "SerializationExportWrapper.hpp"
EXPORT_TEMPLATE_CLASS_ALL_DIMS(DistributedTetrahedralMesh)
 
namespace boost
{
namespace serialization
{
template<class Archive, unsigned ELEMENT_DIM, unsigned SPACE_DIM>
inline void save_construct_data(
    Archive & ar, const DistributedTetrahedralMesh<ELEMENT_DIM, SPACE_DIM> * t, const unsigned int file_version)
{
    unsigned num_procs = PetscTools::GetNumProcs();
    const DistributedTetrahedralMeshPartitionType::type partition_type = t->GetPartitionType();
    ar << num_procs;
    ar << partition_type;
}
 
template<class Archive, unsigned ELEMENT_DIM, unsigned SPACE_DIM>
inline void load_construct_data(
    Archive & ar, DistributedTetrahedralMesh<ELEMENT_DIM, SPACE_DIM> * t, const unsigned int file_version)
{
    unsigned num_procs;
    DistributedTetrahedralMeshPartitionType::type partition_type;
 
    ar >> num_procs;
    ar >> partition_type;
 
    // Invoke inplace constructor to initialise instance
    //::new(t)DistributedTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>(partition_type);
    ::new(t)DistributedTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>(DistributedTetrahedralMeshPartitionType::DUMB);
 
    /*
     * The exception needs to be thrown after the call to ::new(t), or Boost will try
     * to free non-allocated memory when the exception is thrown.
     */
    if (DistributedVectorFactory::CheckNumberOfProcessesOnLoad() &&
        num_procs != PetscTools::GetNumProcs())
    {
        EXCEPTION("This archive was written for a different number of processors");
    }
 
}
}
} // namespace ...
 
#endif /*DISTRIBUTEDTETRAHEDRALMESH_HPP_*/