AbstractPerElementWriter.hpp

/*

Copyright (c) 2005-2018, 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 ABSTRACTPERELEMENTWRITER_HPP_
#define ABSTRACTPERELEMENTWRITER_HPP_

#include "AbstractTetrahedralMesh.hpp"
#include "UblasCustomFunctions.hpp"
#include "OutputFileHandler.hpp"
#include "Version.hpp"

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned DATA_SIZE>
class AbstractPerElementWriter
{
private:
    bool mFileIsBinary;  
protected:
    AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>* mpMesh;

    out_stream mpMasterFile;

    virtual void Visit(Element<ELEMENT_DIM, SPACE_DIM>* pElement,
                       unsigned localElementIndex,
                       c_vector<double, DATA_SIZE>& rData)=0;

    virtual void WriteElementOnMaster(const c_vector<double, DATA_SIZE>& rData)
    {
        if (mFileIsBinary)
        {
            //The binary file is row-major
            mpMasterFile->write((char*)&rData[0], DATA_SIZE*sizeof(double));
        }
        else
        {
            for (unsigned i=0; i<DATA_SIZE; i++)
            {
                (*mpMasterFile) << rData[i] << "\t";
            }
            (*mpMasterFile)<<"\n";
        }
    }

    virtual void WriteHeaderOnMaster()
    {
    }

    virtual void PreWriteCalculations(OutputFileHandler& rOutputDirectory)
    {
    }

public:

    AbstractPerElementWriter(AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>* pMesh)
     : mFileIsBinary(false),
       mpMesh(pMesh),
       mpMasterFile(nullptr)
    {

    }

    void WriteData(OutputFileHandler& rHandler, const std::string& rFileName)
    {
        PreWriteCalculations(rHandler);

        c_vector<double, DATA_SIZE> data;
        if (PetscTools::AmMaster())
        {
            mpMasterFile = rHandler.OpenOutputFile(rFileName);
            MPI_Status status;
            status.MPI_ERROR = MPI_SUCCESS; //For MPICH2
            WriteHeaderOnMaster();
            // say whether the fibres are binary in the header line (not ended yet!)
            if (mFileIsBinary)
            {
                *mpMasterFile << "\tBIN\n";
            }
            else
            {
                *mpMasterFile << "\n";
            }
            // The master process needs to keep track of both the global element list
            // (so that all elements are concentrated) and the local element list (so that
            // a local element index can be applied
            unsigned local_element_index=0u; //Data invariant associates iter with local_element_index
            typename AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>::ElementIterator iter = mpMesh->GetElementIteratorBegin();

            for (unsigned global_element_index=0; global_element_index<mpMesh->GetNumElements(); global_element_index++)
            {
                if (mpMesh->CalculateDesignatedOwnershipOfElement(global_element_index))
                {
                    Element<ELEMENT_DIM,SPACE_DIM>* p_elem = mpMesh->GetElement(global_element_index);
                    //Spool forward in the local vector of elements
                    while (&(*iter) != p_elem)
                    {
                        ++iter;
                        local_element_index++;
                        assert(iter != mpMesh->GetElementIteratorEnd());
                    }
                    //Master owns this process and can write it directly
                    Visit(p_elem, local_element_index, data);
                }
                else
                {
                    //Data must come from a remote process
                    MPI_Recv(&data[0], DATA_SIZE, MPI_DOUBLE, MPI_ANY_SOURCE, global_element_index, PETSC_COMM_WORLD, &status);
                }
                WriteElementOnMaster(data);
            }
            *mpMasterFile << "# "<<ChasteBuildInfo::GetProvenanceString();
            mpMasterFile->close();
        }
        else
        {
            //Not master process
            unsigned previous_index = 0u; //Used to check that the indices are monotone
            unsigned local_index = 0u;
            for (typename AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>::ElementIterator iter = mpMesh->GetElementIteratorBegin();
                          iter != mpMesh->GetElementIteratorEnd();
                          ++iter, local_index++)
            {
                unsigned element_index = iter->GetIndex();
                //Check monotonicity
                if (previous_index>0u)
                {
                    assert(element_index > previous_index);
                }
                previous_index = element_index;
                if (mpMesh->CalculateDesignatedOwnershipOfElement(element_index))
                {
                    // The master needs to know about this one.
                    Visit(&(*iter), local_index, data);
                    MPI_Ssend(&data[0], DATA_SIZE, MPI_DOUBLE, 0, element_index, PETSC_COMM_WORLD);//Tag with element_index
                }
            }

        }
    }

     void SetWriteFileAsBinary(bool binary=true)
     {
         mFileIsBinary = binary;
     }

    virtual ~AbstractPerElementWriter()
    {
    }
};


#endif /*ABSTRACTPERELEMENTWRITER_HPP_*/