AbstractTetrahedralMeshWriter.hpp

/*

Copyright (c) 2005-2017, 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 _ABSTRACTTETRAHEDRALMESHWRITER_HPP_
#define _ABSTRACTTETRAHEDRALMESHWRITER_HPP_

// Forward declaration prevents circular include chain
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
class AbstractTetrahedralMesh;

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
class DistributedTetrahedralMesh;

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
class MixedDimensionMesh;

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
struct MeshWriterIterators;

#include <fstream>
#include <sstream>
#include <boost/scoped_array.hpp>

#include "AbstractMeshWriter.hpp"
#include "AbstractMesh.hpp"
#include "NodeMap.hpp"

#include "GenericEventHandler.hpp"
class MeshEventHandler : public GenericEventHandler<11, MeshEventHandler>
{
public:
    static const char* EventName[11]; 
    typedef enum
    {
        TRIANGLES=0,
        BINTRI,
        VTK,
        PVTK,
        NODE,
        ELE,
        FACE,
        NCL,
        COMM1,
        COMM2
    } EventType;
};

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
class AbstractTetrahedralMeshWriter : public AbstractMeshWriter<ELEMENT_DIM, SPACE_DIM>
{
private:
    void PostElement(unsigned globalIndex, unsigned indices[], unsigned numIndices, unsigned tag, double attribute)
    {
        MeshEventHandler::BeginEvent(MeshEventHandler::COMM1);
        MPI_Ssend(indices, numIndices, MPI_UNSIGNED, 0,
                  tag, //Elements sent with tags offset
                  PETSC_COMM_WORLD);
        MeshEventHandler::EndEvent(MeshEventHandler::COMM1);
        // Attribute value has the same tag (assume that it doesn't overtake the previous message)
        MeshEventHandler::BeginEvent(MeshEventHandler::COMM2);
        MPI_Ssend(&attribute, 1, MPI_DOUBLE, 0,
                  tag, //Elements sent with tags offset
                  PETSC_COMM_WORLD);
        MeshEventHandler::EndEvent(MeshEventHandler::COMM2);
    }
    void UnpackElement(ElementData& rElementData, unsigned globalIndex, unsigned numIndices, unsigned tag)
    {
        assert( numIndices == rElementData.NodeIndices.size());
        boost::scoped_array<unsigned> raw_indices(new unsigned[numIndices]);
        MPI_Status status;
        // Get it from elsewhere
        MeshEventHandler::BeginEvent(MeshEventHandler::COMM1);
        MPI_Recv(raw_indices.get(), numIndices, MPI_UNSIGNED, MPI_ANY_SOURCE,
                 tag,
                 PETSC_COMM_WORLD, &status);
        MeshEventHandler::EndEvent(MeshEventHandler::COMM1);
        // Convert to std::vector
        for (unsigned j=0; j< rElementData.NodeIndices.size(); j++)
        {
            rElementData.NodeIndices[j] = raw_indices[j];
        }

        // Attribute value has the same tag (assume that it doesn't overtake the previous message)
        double attribute;
        MeshEventHandler::BeginEvent(MeshEventHandler::COMM2);
        MPI_Recv(&attribute, 1U, MPI_DOUBLE, MPI_ANY_SOURCE,
                 tag,
                 PETSC_COMM_WORLD, &status);
        MeshEventHandler::EndEvent(MeshEventHandler::COMM2);

        // Attribute value
        rElementData.AttributeValue = attribute;
    }

    virtual void WriteFilesUsingParallelMesh(bool keepOriginalElementIndexing=true);

    void WriteNclFile(AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>& rMesh,
                      bool invertMeshPermutation=false);

    virtual void CreateFilesWithHeaders();

    virtual void AppendLocalDataToFiles();

    virtual void WriteFilesFooter();

    NodeMap* mpNodeMap; 
protected:

    unsigned mNodesPerElement; 
    unsigned mNodesPerBoundaryElement; 
    AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>* mpMesh; 
    DistributedTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>* mpDistributedMesh; 
    MixedDimensionMesh<ELEMENT_DIM,SPACE_DIM>* mpMixedMesh; 
    MeshWriterIterators<ELEMENT_DIM,SPACE_DIM>* mpIters; 
    bool mIndexFromZero; 
    bool mWriteMetaFile; 
    unsigned mNodeCounterForParallelMesh; 
    unsigned mElementCounterForParallelMesh;
    unsigned mBoundaryElementCounterForParallelMesh;
    unsigned mCableElementCounterForParallelMesh;
    bool mFilesAreBinary;  
public:

    AbstractTetrahedralMeshWriter(const std::string& rDirectory,
                       const std::string& rBaseName,
                       const bool clearOutputDir=true);

    virtual ~AbstractTetrahedralMeshWriter();

    virtual void WriteFilesUsingMesh(AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>& rMesh,
                                     bool keepOriginalElementIndexing=true);

    void WriteFilesUsingMeshReaderAndMesh(AbstractMeshReader<ELEMENT_DIM, SPACE_DIM>& rMeshReader,
                                          AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>& rMesh);

    std::vector<double> GetNextNode();


    ElementData GetNextElement();

    ElementData GetNextBoundaryElement();

    ElementData GetNextCableElement();
};

#endif //_ABSTRACTTETRAHEDRALMESHWRITER_HPP_