CmguiDeformedSolutionsWriter.cpp

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#include "CmguiDeformedSolutionsWriter.hpp"
#include "Exception.hpp"

template<unsigned DIM>
CmguiDeformedSolutionsWriter<DIM>::CmguiDeformedSolutionsWriter(std::string outputDirectory,
                                                                std::string baseName,
                                                                AbstractTetrahedralMesh<DIM,DIM>& rQuadraticMesh,
                                                                CmguiMeshWriteType writeType)
    : CmguiMeshWriter<DIM, DIM>(outputDirectory, baseName),
      mpQuadraticMesh(&rQuadraticMesh),
      mFinalCounter(0)
{

    QuadraticMesh<DIM>* p_quad_mesh = dynamic_cast<QuadraticMesh<DIM>* >(&rQuadraticMesh);

    if(p_quad_mesh == NULL)
    {
        EXCEPTION("CmguiDeformedSolutionsWriter only supports use of a QuadraticMesh");
    }

    mNumNodesToUse = mpQuadraticMesh->GetNumVertices();

    if (writeType==WRITE_QUADRATIC_MESH)
    {
        mNumNodesToUse = mpQuadraticMesh->GetNumNodes();

        switch (DIM)
        {
            //WriteCmguiScript Commented as CmguiDeformedSolutionsWriter is meant to correspond to
            // output of nonlinear elasticity problems - 2d or 3d only, and there is
            // no explicit instantiation of this class in 1d.
            //case 1:
            //{
            //   this->mElementFileHeader = CmguiElementFileHeader1DQuadratic;
            //    this->mCoordinatesFileHeader = CmguiCoordinatesFileHeader1DQuadratic;
            //    this->mAdditionalFieldHeader = CmguiAdditionalFieldHeader1DQuadratic;
            //    this->mNumNodesPerElement = 3;
            //    this->mReordering.resize(this->mNumNodesPerElement);
            //    unsigned reordering[6] = {0,2,1};
            //    for (unsigned i=0; i<3; i++)
            //    {
            //        this->mReordering[i] = reordering[i];
            //    }
            //    break;
            //};

            case 2:
            {
                this->mElementFileHeader = CmguiElementFileHeader2DQuadratic;
                this->mCoordinatesFileHeader = CmguiCoordinatesFileHeader2DQuadratic;
                this->mAdditionalFieldHeader = CmguiAdditionalFieldHeader2DQuadratic;
                this->mNumNodesPerElement = 6;
                this->mReordering.resize(this->mNumNodesPerElement);

                // Go from Chaste(tetgen ordering) (see example comments in
                // QuadraticBasisFunction::ComputeBasisFunction() to CMGUI ordering
                // ("psi1 increasing, then psi1 increasing")
                unsigned reordering[6] = {0,5,1,4,3,2};
                for (unsigned i=0; i<6; i++)
                {
                    this->mReordering[i] = reordering[i];
                }
                break;
            }
            case 3:
            {
                this->mElementFileHeader = CmguiElementFileHeader3DQuadratic;
                this->mCoordinatesFileHeader = CmguiCoordinatesFileHeader3DQuadratic;
                this->mAdditionalFieldHeader = CmguiAdditionalFieldHeader3DQuadratic;
                this->mNumNodesPerElement = 10;
                this->mReordering.resize(this->mNumNodesPerElement);

                // Go from Chaste(tetgen ordering) (see example comments in
                // QuadraticBasisFunction::ComputeBasisFunction() to CMGUI ordering
                // ("psi1 increasing, then psi2 increasing, then psi3 increasing")
                unsigned reordering[10] = {0,4,1,6,5,2,7,8,9,3};
                for (unsigned i=0; i<10; i++)
                {
                    this->mReordering[i] = reordering[i];
                }
                break;
            }
            default:
            {
                NEVER_REACHED;
            }
        }
    }
}

template<unsigned DIM>
void CmguiDeformedSolutionsWriter<DIM>::WriteInitialMesh(std::string fileName)
{
    std::string saved_base_name = this->mBaseName;
    if(fileName == "")
    {
        this->mBaseName = this->mBaseName + "_0";
    }
    else
    {
        this->mBaseName = fileName;
    }
    this->WriteFilesUsingMesh(*mpQuadraticMesh);
    this->mBaseName = saved_base_name;
}

template<unsigned DIM>
void CmguiDeformedSolutionsWriter<DIM>::WriteDeformationPositions(std::vector<c_vector<double,DIM> >& rDeformedPositions,
                                                                  unsigned counter)
{
    if (mpQuadraticMesh->GetNumNodes() != rDeformedPositions.size() )
    {
        EXCEPTION("The size of rDeformedPositions does not match the number of nodes in the mesh");
    }

    mFinalCounter = counter;
    std::stringstream node_file_name_stringstream;
    node_file_name_stringstream <<  this->mBaseName << "_" << counter << ".exnode";

    out_stream p_node_file = this->mpOutputFileHandler->OpenOutputFile(node_file_name_stringstream.str());

    this->WriteNodeFileHeader(p_node_file);

    // Write each node's data
    for (unsigned index=0; index<this->GetNumNodes(); index++)
    {
        *p_node_file << "Node:\t" << index+1 << "\t";

        for (unsigned i=0; i<DIM; i++)
        {
            *p_node_file << rDeformedPositions[index](i) << "\t";
        }
        *p_node_file << "\n";
    }
    p_node_file->close();
}

template<unsigned DIM>
void CmguiDeformedSolutionsWriter<DIM>::WriteCmguiScript(std::string fieldBaseName, std::string undeformedBaseName)
{
    std::string field_string = "";
    if (fieldBaseName != "")
    {
        field_string = " gfx read node " + fieldBaseName + "_$i time $i\n";
    }

    out_stream p_script_file = this->mpOutputFileHandler->OpenOutputFile("LoadSolutions.com");
    *p_script_file << "#\n# Cmgui script automatically generated by Chaste\n#\n";

    if(undeformedBaseName != "")
    {
        *p_script_file << "gfx read node " << undeformedBaseName << " time -1\n";
    }

    *p_script_file << "for ($i=0; $i<=" << mFinalCounter << "; $i++) { \n"
                   << "  gfx read node " << this->mBaseName << "_$i time $i\n"
                   << field_string
                   << "}\n";

    if(undeformedBaseName != "")
    {
        for (unsigned region_index=0; region_index<this->mRegionNames.size(); region_index++)
        {
            *p_script_file << "gfx read ele " << this->mRegionNames[region_index] << "\n";
        }
    }
    else
    {
        *p_script_file << "gfx read ele " << this->mBaseName << "_0\n";
    }
    *p_script_file << "gfx define faces egroup "<<this->mBaseName<<"\n";
    *p_script_file << "gfx modify g_element "<<this->mBaseName<<" lines select_on material default spectrum default selected_material default_selected;\n";
    *p_script_file << "gfx cr win\n\n";
    p_script_file->close();
}

template<unsigned DIM>
void CmguiDeformedSolutionsWriter<DIM>::ConvertOutput(std::string inputDirectory,
                                                      std::string inputFileBaseName,
                                                      unsigned finalCounter)
{
    // write the mesh to <inputFileBaseName>_0.exnode and <inputFileBaseName>_0.exelem
    WriteInitialMesh();

    std::vector<c_vector<double,DIM> > deformed_position(mpQuadraticMesh->GetNumNodes(), zero_vector<double>(DIM));

    for (unsigned i=1; i<=finalCounter; i++) //not i=0
    {
        std::stringstream in_file_stream;
        in_file_stream << inputDirectory << "/" << inputFileBaseName << "_" << i << ".nodes";

        std::ifstream ifs(in_file_stream.str().c_str());
        if (!ifs.is_open())
        {
            EXCEPTION("Could not open file: " + in_file_stream.str());
        }

        // the file into deformed_position
        double data;
        for (unsigned index=0; index<mpQuadraticMesh->GetNumNodes(); index++)
        {
            for (unsigned j=0; j<DIM; j++)
            {
                ifs >> data;
                if (ifs.fail())
                {
                    EXCEPTION("Error occurred when reading file " << in_file_stream.str()
                                  << ". Expected " << mpQuadraticMesh->GetNumNodes() << " rows and "
                                  << DIM << " columns");
                }
                deformed_position[index](j) = data;
            }
        }

        ifs.close();

        // convert
        WriteDeformationPositions(deformed_position, i);
    }

    WriteCmguiScript();
}


template class CmguiDeformedSolutionsWriter<2>;
template class CmguiDeformedSolutionsWriter<3>;