GmshMeshReader.cpp

/*

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 * Redistributions of source code must retain 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
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*/
#include <cassert>
#include <sstream>
#include <iostream>

#include "GmshMeshReader.hpp"
#include "Exception.hpp"

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
GmshMeshReader<ELEMENT_DIM, SPACE_DIM>::GmshMeshReader(std::string pathBaseName,
                                                       unsigned orderOfElements,
                                                       unsigned orderOfBoundaryElements) :
       mFileName(pathBaseName),
       mOrderOfElements(orderOfElements),
       mOrderOfBoundaryElements(orderOfBoundaryElements)
{
    // Only linear and quadratic elements
    assert(mOrderOfElements==1 || mOrderOfElements==2);

    if (mOrderOfElements==1)
    {
        mNodesPerElement = ELEMENT_DIM+1;
    }
    else
    {
        mNodesPerElement = (ELEMENT_DIM+1)*(ELEMENT_DIM+2)/2;
    }

    if (mOrderOfBoundaryElements==1)
    {
        mNodesPerBoundaryElement = ELEMENT_DIM;
    }
    else
    {
        mNodesPerBoundaryElement = ELEMENT_DIM*(ELEMENT_DIM+1)/2;
    }

    OpenFiles();
    ReadHeaders();
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
GmshMeshReader<ELEMENT_DIM, SPACE_DIM>::~GmshMeshReader()
{
    CloseFiles();
}

template<unsigned  ELEMENT_DIM, unsigned  SPACE_DIM>
void GmshMeshReader<ELEMENT_DIM, SPACE_DIM>::OpenFiles()
{
    // Open mesh file
    mNodeFile.open(mFileName.c_str());
    mElementFile.open(mFileName.c_str());
    mFaceFile.open(mFileName.c_str());
    if (!mNodeFile.is_open() || !mElementFile.is_open() || !mFaceFile.is_open() )
    {
        EXCEPTION("Could not open data file: " + mFileName);
    }
}

template<unsigned  ELEMENT_DIM, unsigned  SPACE_DIM>
void GmshMeshReader<ELEMENT_DIM, SPACE_DIM>::CloseFiles()
{
    mNodeFile.close();
    mElementFile.close();
    mFaceFile.close();
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void GmshMeshReader<ELEMENT_DIM, SPACE_DIM>::ReadHeaders()
{
    /*
     * Read mesh format information from the file header
     */
    std::string this_line;
    getline(mNodeFile, this_line);

    assert(this_line == "$MeshFormat");

    //Read the version no.
    getline(mNodeFile, this_line);
    std::stringstream line(this_line);

    line >> mVersionNumber >> mFileType >> mDataSize;

    if (mVersionNumber != 2.2)
    {
        EXCEPTION("Only .msh version 2.2 files are supported.");
    }
    assert(mFileType == 0);

    //Check mesh format close string
    getline(mNodeFile, this_line);
    assert(this_line == "$EndMeshFormat");

    ReadNodeHeader();
    ReadElementHeader(); // This reads the total number of elements in the file into mTotalNumElementsAndFaces
    ReadFaceHeader();

    if (mTotalNumElementsAndFaces != mNumElements + mNumFaces)
    {
        EXCEPTION("Unrecognised element types present in the .msh file: check mesh generation settings in gmsh.");
        // If you hit this, then the .msh file lists elements that are not simply
        // in 2D:
        //   linear/quadratic lines for faces, triangles for elements
        // in 3D:
        //   linear/quadratic traingles for faces, tets for elements.
        // which probably means something funny happened in the mesh generation.
    }
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void GmshMeshReader<ELEMENT_DIM, SPACE_DIM>::ReadNodeHeader()
{
    // Search for the start of the node section
    std::string this_line;
    std::stringstream line(this_line);

    while (this_line != "$Nodes")
    {
        getline(mNodeFile, this_line);
    }
    getline(mNodeFile, this_line);

    line.clear();
    line.str(this_line);
    line >> mNumNodes; // mNodesFile should now be pointing at the start of the node lines in the file.
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void GmshMeshReader<ELEMENT_DIM, SPACE_DIM>::ReadElementHeader()
{
    // Search for the start of the elements section
    std::string this_line;
    std::stringstream line(this_line);

    getline(mElementFile, this_line);
    while (this_line != "$Elements")
    {
        getline(mElementFile, this_line);
    }
    getline(mElementFile, this_line); //Throw away the line that says the number of elements specified in the file
    line.clear();
    line.str(this_line);
    line >> mTotalNumElementsAndFaces;
    int ele_start = mElementFile.tellg(); //Pointer to the start of the element block.

    mNumElements = 0u;
    getline(mElementFile, this_line);

    while (this_line != "$EndElements")
    {
        line.clear();
        line.str(this_line);

        unsigned ele_index;
        unsigned ele_type;
        line >> ele_index >> ele_type;

        if (ELEMENT_DIM == 2 && (ele_type == GmshTypes::TRIANGLE || ele_type == GmshTypes::QUADRATIC_TRIANGLE))
        {
            mNumElements++;
        }
        else if (ELEMENT_DIM == 3 && (ele_type == GmshTypes::TETRAHEDRON || ele_type == GmshTypes::QUADRATIC_TETRAHEDRON))
        {
            mNumElements++;
        }

        getline(mElementFile, this_line);
    }

    mElementFile.seekg(ele_start); //mElementFile should now be pointing at the start of the node lines in the file.
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void GmshMeshReader<ELEMENT_DIM, SPACE_DIM>::ReadFaceHeader()
{
    // Search for the start of the elements section
    std::string this_line;
    std::stringstream line(this_line);

    getline(mFaceFile, this_line);
    while (this_line != "$Elements")
    {
        getline(mFaceFile, this_line);
    }
    getline(mFaceFile, this_line); // Throw away the line that says the number of elements specified in the file
    int face_start = mFaceFile.tellg(); // Pointer to the start of the element block.

    mNumFaces = 0u;
    getline(mFaceFile, this_line);

    while (this_line != "$EndElements")
    {
        line.clear();
        line.str(this_line);

        unsigned ele_index;
        unsigned ele_type;
        line >> ele_index >> ele_type;

        if (ELEMENT_DIM == 2 && (ele_type == GmshTypes::LINE || ele_type == GmshTypes::QUADRATIC_LINE))
        {
            mNumFaces++;
        }
        else if (ELEMENT_DIM == 3 && (ele_type == GmshTypes::TRIANGLE || ele_type == GmshTypes::QUADRATIC_TRIANGLE))
        {
            mNumFaces++;
        }

        getline(mFaceFile, this_line);
    }

    mFaceFile.seekg(face_start); //mFacesFile should now be pointing at the start of the node lines in the file.
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned GmshMeshReader<ELEMENT_DIM, SPACE_DIM>::GetNumElements() const
{
    return mNumElements;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned GmshMeshReader<ELEMENT_DIM, SPACE_DIM>::GetNumNodes() const
{
    return mNumNodes;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned GmshMeshReader<ELEMENT_DIM, SPACE_DIM>::GetNumFaces() const
{
    return mNumFaces;
}

// LCOV_EXCL_START
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned GmshMeshReader<ELEMENT_DIM, SPACE_DIM>::GetNumCableElements() const
{
    NEVER_REACHED;
    //return mNumCableElements;
}
// LCOV_EXCL_STOP

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned GmshMeshReader<ELEMENT_DIM, SPACE_DIM>::GetOrderOfElements()
{
    return mOrderOfElements;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned GmshMeshReader<ELEMENT_DIM, SPACE_DIM>::GetOrderOfBoundaryElements()
{
    return mOrderOfBoundaryElements;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned GmshMeshReader<ELEMENT_DIM, SPACE_DIM>::GetNumElementAttributes() const
{
    return mNumElementAttributes;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned GmshMeshReader<ELEMENT_DIM, SPACE_DIM>::GetNumFaceAttributes() const
{
    return mNumFaceAttributes;
}

// LCOV_EXCL_START
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned GmshMeshReader<ELEMENT_DIM, SPACE_DIM>::GetNumCableElementAttributes() const
{
    NEVER_REACHED;
    //return mNumCableElementAttributes;
}
// LCOV_EXCL_STOP

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void GmshMeshReader<ELEMENT_DIM, SPACE_DIM>::Reset()
{
    CloseFiles();

    OpenFiles();
    ReadHeaders();
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
std::vector<double> GmshMeshReader<ELEMENT_DIM, SPACE_DIM>::GetNextNode()
{
    std::vector<double> ret_coords(SPACE_DIM);

    std::string this_line;
    getline(mNodeFile, this_line);

    std::stringstream line(this_line);

    unsigned node_index;
    line >> node_index >> ret_coords[0] >> ret_coords[1];

    if (SPACE_DIM == 3)
    {
        line >> ret_coords[2];
    }

    return ret_coords;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
std::vector<double> GmshMeshReader<ELEMENT_DIM, SPACE_DIM>::GetNodeAttributes()
{
    return std::vector<double>(0);
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
ElementData GmshMeshReader<ELEMENT_DIM, SPACE_DIM>::GetNextElementData()
{
    ElementData element_data;
    element_data.NodeIndices.resize(mNodesPerElement);
    element_data.AttributeValue = 0.0; // If an attribute is not read this stays as zero, otherwise overwritten.

    std::string this_line;
    std::stringstream line(this_line);

    unsigned ele_index;
    unsigned ele_type;
    unsigned ele_attributes = 0;
    bool volume_element_found = false;

    while (!volume_element_found)
    {
        getline(mElementFile, this_line);
        line.clear();
        line.str(this_line);

        line >> ele_index >> ele_type >> ele_attributes;

        if ((ELEMENT_DIM == 2 && (ele_type == GmshTypes::TRIANGLE || ele_type == GmshTypes::QUADRATIC_TRIANGLE) ) ||
           (ELEMENT_DIM == 3 && (ele_type == GmshTypes::TETRAHEDRON || ele_type == GmshTypes::QUADRATIC_TETRAHEDRON)))
        {
            volume_element_found = true;
        }
    }

    //Gmsh can have arbitrary numbers of element attributes, but Chaste only handles one. We pick the first attribute and throw
    //away the remainder.
    if (ele_attributes > 0)
    {
        mNumElementAttributes = 1u;
        line >> element_data.AttributeValue;
    }
    unsigned unused_attr;
    for (unsigned attr_index = 0; attr_index < (ele_attributes-1); ++attr_index)
    {
        line >> unused_attr;
    }

    //Read the node indices
    for (unsigned node_index = 0; node_index < mNodesPerElement; ++node_index)
    {
        line >> element_data.NodeIndices[node_index];

        element_data.NodeIndices[node_index]--; //Gmsh *always* indexes from 1, we index from 0
    }

    return element_data;
}

// LCOV_EXCL_START
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
ElementData GmshMeshReader<ELEMENT_DIM, SPACE_DIM>::GetNextCableElementData()
{
    NEVER_REACHED;
}
// LCOV_EXCL_STOP

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
ElementData GmshMeshReader<ELEMENT_DIM, SPACE_DIM>::GetNextFaceData()
{
    ElementData face_data;
    face_data.NodeIndices.resize(mNodesPerBoundaryElement);
    face_data.AttributeValue = 0.0; // If an attribute is not read this stays as zero, otherwise overwritten.

    std::string this_line;
    std::stringstream line(this_line);

    unsigned face_index;
    unsigned face_type;
    unsigned face_attributes=0;
    bool surface_element_found = false;

    while (!surface_element_found)
    {
        getline(mFaceFile, this_line);
        line.clear();
        line.str(this_line);

        line >> face_index >> face_type >> face_attributes;

        if ((ELEMENT_DIM == 2 && (face_type == GmshTypes::LINE || face_type == GmshTypes::QUADRATIC_LINE) ) ||
           (ELEMENT_DIM == 3 && (face_type == GmshTypes::TRIANGLE || face_type == GmshTypes::QUADRATIC_TRIANGLE)))
        {
            surface_element_found = true;
        }
    }

    //Gmsh can have arbitrary numbers of element attributes, but Chaste only handles one. We pick the first attribute and throw
    //away the remainder.
    if (face_attributes > 0)
    {
        mNumFaceAttributes = 1u;
        line >> face_data.AttributeValue;
    }
    unsigned unused_attr;
    for (unsigned attr_index = 0; attr_index < (face_attributes-1); ++attr_index)
    {
        line >> unused_attr;
    }

    //Read the node indices
    for (unsigned node_index = 0; node_index < mNodesPerBoundaryElement; ++node_index)
    {
        line >> face_data.NodeIndices[node_index];

        face_data.NodeIndices[node_index]--; //Gmsh *always* indexes from 1, we index from 0
    }

    return face_data;
}

// LCOV_EXCL_START
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
std::vector<double> GmshMeshReader<ELEMENT_DIM, SPACE_DIM>::GetNode(unsigned index)
{
    NEVER_REACHED;
}
// LCOV_EXCL_STOP

// LCOV_EXCL_START
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
ElementData GmshMeshReader<ELEMENT_DIM, SPACE_DIM>::GetElementData(unsigned index)
{
    NEVER_REACHED;
}
// LCOV_EXCL_STOP

// LCOV_EXCL_START
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
ElementData GmshMeshReader<ELEMENT_DIM, SPACE_DIM>::GetFaceData(unsigned index)
{
    NEVER_REACHED;
}
// LCOV_EXCL_STOP

// Explicit instantiation
template class GmshMeshReader<0,1>;
template class GmshMeshReader<1,1>;
template class GmshMeshReader<1,2>;
template class GmshMeshReader<1,3>;
template class GmshMeshReader<2,2>;
template class GmshMeshReader<2,3>;
template class GmshMeshReader<3,3>;