Hdf5ToTxtConverter.cpp

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#include "UblasCustomFunctions.hpp"
#include "Hdf5ToTxtConverter.hpp"
#include "PetscTools.hpp"
#include "Exception.hpp"
#include "ReplicatableVector.hpp"
#include "DistributedVector.hpp"
#include "DistributedVectorFactory.hpp"
#include "DistributedTetrahedralMesh.hpp"
#include "Warnings.hpp"

template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
Hdf5ToTxtConverter<ELEMENT_DIM, SPACE_DIM>::Hdf5ToTxtConverter(const FileFinder& rInputDirectory,
                                                               const std::string& rFileBaseName,
                                                               AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>* pMesh)
    : AbstractHdf5Converter<ELEMENT_DIM,SPACE_DIM>(rInputDirectory, rFileBaseName, pMesh, "txt_output", 0u)
{
    // Make sure that we are never trying to write from an incomplete data HDF5 file
    assert(this->mpReader->GetNumberOfRows() == pMesh->GetNumNodes());

    FileFinder output_directory(this->mRelativeSubdirectory,rInputDirectory);
    OutputFileHandler handler(output_directory);

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

    DistributedVectorFactory* p_factory = pMesh->GetDistributedVectorFactory();
    Vec data = p_factory->CreateVec();
    ReplicatableVector repl_data(num_nodes);

    // Loop over time steps
    for (unsigned time_step=0; time_step<num_timesteps; time_step++)
    {
        // Loop over variables
        for (unsigned var_index=0; var_index<this->mNumVariables; var_index++)
        {
            std::string variable_name = this->mpReader->GetVariableNames()[var_index];

            // Create a .txt file for this time step and this variable
            std::stringstream file_name;
            file_name << rFileBaseName << "_" << variable_name << "_" << time_step << ".txt";
            out_stream p_file = handler.OpenOutputFile(file_name.str());

            this->mpReader->GetVariableOverNodes(data, variable_name, 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";
                }
            }
            p_file->close();
        }
    }

    // Tidy up
    PetscTools::Destroy(data);
}

// Explicit instantiation

template class Hdf5ToTxtConverter<1,1>;
template class Hdf5ToTxtConverter<1,2>;
template class Hdf5ToTxtConverter<2,2>;
template class Hdf5ToTxtConverter<1,3>;
template class Hdf5ToTxtConverter<2,3>;
template class Hdf5ToTxtConverter<3,3>;