VoltageInterpolaterOntoMechanicsMesh.cpp

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#include "VoltageInterpolaterOntoMechanicsMesh.hpp"
#include "Hdf5ToCmguiConverter.hpp"
#include "FineCoarseMeshPair.hpp"
#include "ReplicatableVector.hpp"
#include "HeartConfig.hpp"
#include "Hdf5DataReader.hpp"
#include "PetscTools.hpp"
#include "Hdf5DataWriter.hpp"
 
template<unsigned DIM>
VoltageInterpolaterOntoMechanicsMesh<DIM>::VoltageInterpolaterOntoMechanicsMesh(
                                     TetrahedralMesh<DIM,DIM>& rElectricsMesh,
                                     QuadraticMesh<DIM>& rMechanicsMesh,
                                     std::vector<std::string>& rVariableNames,
                                     std::string directory,
                                     std::string inputFileNamePrefix)
{
    // Read the data from the HDF5 file
    Hdf5DataReader reader(directory,inputFileNamePrefix);
 
    unsigned num_timesteps = reader.GetUnlimitedDimensionValues().size();
 
    // set up the elements and weights for the coarse nodes in the fine mesh
    FineCoarseMeshPair<DIM> mesh_pair(rElectricsMesh, rMechanicsMesh);
    mesh_pair.SetUpBoxesOnFineMesh();
    mesh_pair.ComputeFineElementsAndWeightsForCoarseNodes(true);
    assert(mesh_pair.rGetElementsAndWeights().size()==rMechanicsMesh.GetNumNodes());
 
    // create and setup a writer
    Hdf5DataWriter* p_writer = new Hdf5DataWriter(*rMechanicsMesh.GetDistributedVectorFactory(),
                                                  directory,
                                                  "voltage_mechanics_mesh",
                                                  false, //don't clean
                                                  false);
 
    std::vector<int> columns_id;
    for (unsigned var_index = 0; var_index < rVariableNames.size(); var_index++)
    {
        std::string var_name = rVariableNames[var_index];
        columns_id.push_back( p_writer->DefineVariable(var_name,"mV") );
    }
 
    p_writer->DefineUnlimitedDimension("Time","msecs", num_timesteps);
    p_writer->DefineFixedDimension( rMechanicsMesh.GetNumNodes() );
    p_writer->EndDefineMode();
 
    assert(columns_id.size() == rVariableNames.size());
 
    // set up a vector to read into
    DistributedVectorFactory factory(rElectricsMesh.GetNumNodes());
    Vec voltage = factory.CreateVec();
    std::vector<double> interpolated_voltages(rMechanicsMesh.GetNumNodes());
    Vec voltage_coarse = NULL;
 
    for (unsigned time_step=0; time_step<num_timesteps; time_step++)
    {
        for (unsigned var_index = 0; var_index < rVariableNames.size(); var_index++)
        {
            std::string var_name = rVariableNames[var_index];
            // read
            reader.GetVariableOverNodes(voltage, var_name, time_step);
            ReplicatableVector voltage_repl(voltage);
 
            // interpolate
            for (unsigned i=0; i<mesh_pair.rGetElementsAndWeights().size(); i++)
            {
                double interpolated_voltage = 0;
 
                Element<DIM,DIM>& element = *(rElectricsMesh.GetElement(mesh_pair.rGetElementsAndWeights()[i].ElementNum));
                for (unsigned node_index = 0; node_index<element.GetNumNodes(); node_index++)
                {
                    unsigned global_node_index = element.GetNodeGlobalIndex(node_index);
                    interpolated_voltage += voltage_repl[global_node_index]*mesh_pair.rGetElementsAndWeights()[i].Weights(node_index);
                }
 
                interpolated_voltages[i] = interpolated_voltage;
            }
 
            if (voltage_coarse != NULL)
            {
                PetscTools::Destroy(voltage_coarse);
            }
            voltage_coarse = PetscTools::CreateVec(interpolated_voltages);
            // write
            p_writer->PutVector(columns_id[var_index], voltage_coarse);
        }
        p_writer->PutUnlimitedVariable(time_step);
        p_writer->AdvanceAlongUnlimitedDimension();
    }
 
    if (voltage_coarse != NULL)
    {
        PetscTools::Destroy(voltage);
        PetscTools::Destroy(voltage_coarse);
    }
 
    // delete to flush
    delete p_writer;
 
    // Convert the new data to CMGUI format.
    // alter the directory in HeartConfig as that is where Hdf5ToCmguiConverter decides
    // where to output
    std::string config_directory = HeartConfig::Instance()->GetOutputDirectory();
    HeartConfig::Instance()->SetOutputDirectory(directory);
    Hdf5ToCmguiConverter<DIM,DIM> converter(FileFinder(directory, RelativeTo::ChasteTestOutput),
                                            "voltage_mechanics_mesh",
                                            &rMechanicsMesh,
                                            false);
    HeartConfig::Instance()->SetOutputDirectory(config_directory);
}
 
// Explicit instantiation
template class VoltageInterpolaterOntoMechanicsMesh<1>;
template class VoltageInterpolaterOntoMechanicsMesh<2>;
template class VoltageInterpolaterOntoMechanicsMesh<3>;