SemMeshWriter.cpp

/*

Copyright (c) 2005-2012, University of Oxford.
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 * Redistributions in binary form must reproduce the above copyright notice,
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   software without specific prior written permission.

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IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
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*/

#include "SemMeshWriter.hpp"
#include "Version.hpp"

template<unsigned SPACE_DIM>
struct MeshSemWriterIterators
{
    typename AbstractMesh<SPACE_DIM,SPACE_DIM>::NodeIterator* pNodeIter;
    typename SemMesh<SPACE_DIM>::SemElementIterator* pElemIter;
};

// Implementation

template<unsigned SPACE_DIM>
SemMeshWriter<SPACE_DIM>::SemMeshWriter(const std::string& rDirectory,
                                                           const std::string& rBaseName,
                                                           const bool clearOutputDir)
    : AbstractMeshWriter<SPACE_DIM, SPACE_DIM>(rDirectory, rBaseName, clearOutputDir),
      mpMesh(NULL),
      mpIters(new MeshSemWriterIterators<SPACE_DIM>),
      mpNodeMap(NULL),
      mNodeMapCurrentIndex(0)
{
    mpIters->pNodeIter = NULL;
    mpIters->pElemIter = NULL;
}

template<unsigned SPACE_DIM>
SemMeshWriter<SPACE_DIM>::~SemMeshWriter()
{
    if (mpIters->pNodeIter)
    {
        delete mpIters->pNodeIter;
        delete mpIters->pElemIter;
    }

    delete mpIters;

    if (mpNodeMap)
    {
        delete mpNodeMap;
    }
}

template<unsigned SPACE_DIM>
std::vector<double> SemMeshWriter<SPACE_DIM>::GetNextNode()
{
    if (mpMesh)
    {
        // Sanity check
        assert(this->mNumNodes == mpMesh->GetNumNodes());

        std::vector<double> coordinates(SPACE_DIM+1);

        // Get the node coordinates using the node iterator (thus skipping deleted nodes)
        for (unsigned j=0; j<SPACE_DIM; j++)
        {
            coordinates[j] = (*(mpIters->pNodeIter))->GetPoint()[j];
        }
        coordinates[SPACE_DIM] = (*(mpIters->pNodeIter))->IsBoundaryNode();

        ++(*(mpIters->pNodeIter));

        return coordinates;
    }
    else
    {
        return AbstractMeshWriter<SPACE_DIM,SPACE_DIM>::GetNextNode();
    }
}

template<unsigned SPACE_DIM>
ElementData SemMeshWriter<SPACE_DIM>::GetNextElement()
{
    if (mpMesh)
    {
        assert(this->mNumElements == mpMesh->GetNumElements());

        ElementData elem_data;
        elem_data.NodeIndices.resize((*(mpIters->pElemIter))->GetNumNodes());
        for (unsigned j=0; j<elem_data.NodeIndices.size(); j++)
        {
            unsigned old_index = (*(mpIters->pElemIter))->GetNodeGlobalIndex(j);
            elem_data.NodeIndices[j] = mpMesh->IsMeshChanging() ? mpNodeMap->GetNewIndex(old_index) : old_index;
        }

        // Set attribute
        elem_data.AttributeValue = (*(mpIters->pElemIter))->GetAttribute();
        ++(*(mpIters->pElemIter));

        return elem_data;
    }
    else
    {
        return AbstractMeshWriter<SPACE_DIM, SPACE_DIM>::GetNextElement();
    }
}

template<unsigned SPACE_DIM>
void SemMeshWriter<SPACE_DIM>::WriteFilesUsingMesh(SemMesh<SPACE_DIM>& rMesh)
{
    this->mpMeshReader = NULL;
    mpMesh = &rMesh;

    this->mNumNodes = mpMesh->GetNumNodes();
    this->mNumElements = mpMesh->GetNumElements();

    typedef typename AbstractMesh<SPACE_DIM,SPACE_DIM>::NodeIterator NodeIterType;
    mpIters->pNodeIter = new NodeIterType(mpMesh->GetNodeIteratorBegin());

    typedef typename SemMesh<SPACE_DIM>::SemElementIterator ElemIterType;
    mpIters->pElemIter = new ElemIterType(mpMesh->GetElementIteratorBegin());

    // Set up node map if we might have deleted nodes
    mNodeMapCurrentIndex = 0;
    if (mpMesh->IsMeshChanging())
    {
        mpNodeMap = new NodeMap(mpMesh->GetNumAllNodes());
        for (NodeIterType it = mpMesh->GetNodeIteratorBegin(); it != mpMesh->GetNodeIteratorEnd(); ++it)
        {
            mpNodeMap->SetNewIndex(it->GetIndex(), mNodeMapCurrentIndex++);
        }
    }
    WriteFiles();
}

template<unsigned SPACE_DIM>
void SemMeshWriter<SPACE_DIM>::WriteFiles()
{
    std::string comment = "# " + ChasteBuildInfo::GetProvenanceString();

    // Write node file
    std::string node_file_name = this->mBaseName + ".node";
    out_stream p_node_file = this->mpOutputFileHandler->OpenOutputFile(node_file_name);

    // Write the node header
    unsigned num_attr = 0;
    unsigned max_bdy_marker = 1; // as we include boundary node information in the node file
    unsigned num_nodes = this->GetNumNodes();

    *p_node_file << num_nodes << "\t";
    *p_node_file << SPACE_DIM << "\t";
    *p_node_file << num_attr << "\t";
    *p_node_file << max_bdy_marker << "\n";
    *p_node_file << std::setprecision(6);

    // Write each node's data
    for (unsigned item_num=0; item_num<num_nodes; item_num++)
    {
        std::vector<double> current_item = this->GetNextNode();
        *p_node_file << item_num;
        for (unsigned i=0; i<SPACE_DIM+1; i++)
        {
            *p_node_file << "\t" << current_item[i];
        }
        *p_node_file << "\n";
    }
    *p_node_file << comment << "\n";
    p_node_file->close();

    // Write element file
    std::string element_file_name = this->mBaseName + ".cell";
    out_stream p_element_file = this->mpOutputFileHandler->OpenOutputFile(element_file_name);

    // Write the element header
    unsigned num_elements = this->GetNumElements();

    double first_elem_attribute_value = (*(mpIters->pElemIter))->GetAttribute();
    if (first_elem_attribute_value != 0)
    {
        num_attr = 1;
    }

    *p_element_file << num_elements << "\t";
    *p_element_file << num_attr << "\n";

    // Write each element's data
    for (unsigned item_num=0; item_num<num_elements; item_num++)
    {
        // Get data for this element
        ElementData elem_data = this->GetNextElement();

        // Get the node indices owned by this element
        std::vector<unsigned> node_indices = elem_data.NodeIndices;

        // Write this element's index and the number of nodes owned by it to file
        *p_element_file << item_num <<  "\t" << node_indices.size();

        // Write the node indices owned by this element to file
        for (unsigned i=0; i<node_indices.size(); i++)
        {
            *p_element_file << "\t" << node_indices[i];
        }

        // Write the element attribute if necessary
        if (elem_data.AttributeValue != 0)
        {
            *p_element_file << "\t" << elem_data.AttributeValue;
        }

        // New line
        *p_element_file << "\n";
    }

    *p_element_file << comment << "\n";
    p_element_file->close();
}

// Explicit instantiation

template class SemMeshWriter<1>;
template class SemMeshWriter<2>;
template class SemMeshWriter<3>;