Hdf5ToMeshalyzerConverter.cpp

/*

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#include "Hdf5ToMeshalyzerConverter.hpp"
#include "MeshalyzerMeshWriter.hpp"
#include "GenericMeshReader.hpp"
#include "UblasCustomFunctions.hpp"
#include "PetscTools.hpp"
#include "Exception.hpp"
#include "ReplicatableVector.hpp"
#include "DistributedVector.hpp"
#include "DistributedVectorFactory.hpp"
#include "Version.hpp"

template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void Hdf5ToMeshalyzerConverter<ELEMENT_DIM,SPACE_DIM>::Write(std::string type)
{

    std::string filename = "";
    if (this->mDatasetNames[this->mOpenDatasetIndex] == "Data")
    {
        filename += this->mFileBaseName + "_";
    }
    filename += type + ".dat";

    out_stream p_file = out_stream(nullptr);
    if (PetscTools::AmMaster())
    {
        p_file = this->mpOutputFileHandler->OpenOutputFile(filename);

        // Check how many digits are to be output in the solution (0 goes to default value of digits)
        if (this->mPrecision != 0)
        {
           p_file->precision(this->mPrecision);
        }
    }

    unsigned num_nodes = this->mpReader->GetNumberOfRows();
    unsigned num_timesteps = this->mpReader->GetUnlimitedDimensionValues().size();

    DistributedVectorFactory factory(num_nodes);

    Vec data = factory.CreateVec();
    ReplicatableVector repl_data(num_nodes);
    for (unsigned time_step=0; time_step<num_timesteps; time_step++)
    {
        this->mpReader->GetVariableOverNodes(data, type, time_step);
        repl_data.ReplicatePetscVector(data);

        assert(repl_data.GetSize() == num_nodes);

        if (PetscTools::AmMaster())
        {
            for (unsigned i=0; i<num_nodes; i++)
            {
                *p_file << repl_data[i] << "\n";
            }
        }
    }
    PetscTools::Destroy(data);
    if (PetscTools::AmMaster())
    {
        std::string comment = "# " + ChasteBuildInfo::GetProvenanceString();
        *p_file << comment;
        p_file->close();
    }
}

template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
Hdf5ToMeshalyzerConverter<ELEMENT_DIM,SPACE_DIM>::Hdf5ToMeshalyzerConverter(const FileFinder& rInputDirectory,
                                                                            const std::string& rFileBaseName,
                                                                            AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>* pMesh,
                                                                            bool usingOriginalNodeOrdering,
                                                                            unsigned precision)
    : AbstractHdf5Converter<ELEMENT_DIM,SPACE_DIM>(rInputDirectory, rFileBaseName, pMesh, "output", precision)
{
    do
    {
        std::vector<std::string> variable_names = this->mpReader->GetVariableNames();
        for (unsigned i=0; i<variable_names.size(); i++)
        {
            Write(variable_names[i]);
        }
    }
    while ( this->MoveOntoNextDataset() );

    // Now we might call this class more than once, so we don't always need to write the mesh out.
    // so check to see if it is there already.
    FileFinder test_output("",RelativeTo::ChasteTestOutput);
    std::string output_directory = rInputDirectory.GetRelativePath(test_output) + "/" + this->mRelativeSubdirectory;
    FileFinder mesh_file(output_directory + "/" + rFileBaseName + "_mesh.pts", RelativeTo::ChasteTestOutput);

    if (!mesh_file.IsFile())
    {
        // Write mesh in a suitable form for meshalyzer
        MeshalyzerMeshWriter<ELEMENT_DIM,SPACE_DIM> mesh_writer(output_directory, rFileBaseName + "_mesh", false);

        // Normal case is that the in-memory mesh is converted
        if (!usingOriginalNodeOrdering || !this->mpMesh->IsMeshOnDisk())
        {
            // The second argument tells the writer to not follow original element ordering for performance reasons.
            mesh_writer.WriteFilesUsingMesh(*(this->mpMesh), false);
        }
        else
        {
            // In this case we expect the mesh to have been read in from file
            // Note that the next line will throw if the mesh has not been read from file
            std::string original_file = this->mpMesh->GetMeshFileBaseName();
            std::shared_ptr<AbstractMeshReader<ELEMENT_DIM, SPACE_DIM> > p_original_mesh_reader
                = GenericMeshReader<ELEMENT_DIM, SPACE_DIM>(original_file);
            mesh_writer.WriteFilesUsingMeshReader(*p_original_mesh_reader);
        }
    }
    PetscTools::Barrier("Hdf5ToMeshalyzerConverter");
}

// Explicit instantiation
template class Hdf5ToMeshalyzerConverter<1,1>;
template class Hdf5ToMeshalyzerConverter<1,2>;
template class Hdf5ToMeshalyzerConverter<2,2>;
template class Hdf5ToMeshalyzerConverter<1,3>;
template class Hdf5ToMeshalyzerConverter<2,3>;
template class Hdf5ToMeshalyzerConverter<3,3>;