QuadraticMeshHelper.cpp

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*/
 
#include "QuadraticMeshHelper.hpp"
 
#define SEEK_TO_CONTENT(methNameDirect, methNameIncrement, index) \
    if (index > 0u) {                                             \
        if (rMeshReader.IsFileFormatBinary()) {                   \
            rMeshReader.methNameDirect(index - 1u);               \
        } else {                                                  \
            for (unsigned i=0; i<index-1u; ++i) {                 \
                rMeshReader.methNameIncrement();                  \
    } } }
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void SeekToBoundaryElement(AbstractMeshReader<ELEMENT_DIM, SPACE_DIM>& rMeshReader,
                           unsigned boundaryElementIndex)
{
    SEEK_TO_CONTENT(GetFaceData, GetNextFaceData, boundaryElementIndex);
}
 
template<unsigned DIM>
void QuadraticMeshHelper<DIM>::AddInternalNodesToElements(AbstractTetrahedralMesh<DIM, DIM>* pMesh,
                                                          AbstractMeshReader<DIM,DIM>* pMeshReader)
{
    assert(pMesh);
    assert(pMeshReader);
 
    if (pMesh->GetNumLocalElements() > 0u)
    {
        pMeshReader->Reset();
 
        // Create a set of element indices we own
        std::set<unsigned> owned_element_indices;
        for (typename AbstractTetrahedralMesh<DIM,DIM>::ElementIterator iter = pMesh->GetElementIteratorBegin();
             iter != pMesh->GetElementIteratorEnd();
             ++iter)
        {
            owned_element_indices.insert(iter->GetIndex());
        }
 
        const std::vector<unsigned>& r_node_perm = pMesh->rGetNodePermutation();
 
        // Add the extra nodes (1 extra node in 1D, 3 in 2D, 6 in 3D) to the element data
        for (typename AbstractMeshReader<DIM,DIM>::ElementIterator iter = pMeshReader->GetElementIteratorBegin(owned_element_indices);
             iter != pMeshReader->GetElementIteratorEnd();
             ++iter)
        {
            std::vector<unsigned> nodes = iter->NodeIndices;
            assert(nodes.size()==(DIM+1)*(DIM+2)/2);
            Element<DIM,DIM>* p_element = pMesh->GetElement(iter.GetIndex());
            assert(p_element->GetNumNodes()==DIM+1); // Element is initially linear
 
            // Add extra nodes to make it a quad element
            for (unsigned j=DIM+1; j<(DIM+1)*(DIM+2)/2; j++)
            {
                unsigned node_index = nodes[j];
                if (!r_node_perm.empty())
                {
                    node_index = r_node_perm[node_index];
                }
                Node<DIM>* p_node = pMesh->GetNodeOrHaloNode(node_index);
                p_element->AddNode(p_node);
                p_node->AddElement(p_element->GetIndex());
                p_node->MarkAsInternal();
            }
        }
    }
}
 
template<unsigned DIM>
void QuadraticMeshHelper<DIM>::AddInternalNodesToBoundaryElements(AbstractTetrahedralMesh<DIM, DIM>* pMesh,
                                                                  AbstractMeshReader<DIM,DIM>* pMeshReader)
{
    assert(pMesh);
    assert(pMeshReader);
    // We only have boundary elements in 2d or 3d
    if (DIM > 1 && pMesh->GetNumLocalBoundaryElements() > 0u)
    {
        // If the data is on disk our job is easy
        if (pMeshReader->GetOrderOfBoundaryElements() == 2u)
        {
            // The work should have been done in the linear constructor, but let's check
            // that the first face has more than DIM nodes.
            assert((*pMesh->GetBoundaryElementIteratorBegin())->GetNumNodes()==DIM*(DIM+1)/2);
            return;
        }
        else
        {
            AddNodesToBoundaryElements(pMesh, pMeshReader);
        }
    }
}
 
template<unsigned DIM>
void QuadraticMeshHelper<DIM>::AddNodesToBoundaryElements(AbstractTetrahedralMesh<DIM, DIM>* pMesh,
                                                          AbstractMeshReader<DIM,DIM>* pMeshReader)
 {
    // Loop over all boundary elements, find the equivalent face from all
    // the elements, and add the extra nodes to the boundary element
    bool boundary_element_file_has_containing_element_info = false;
 
    if (pMeshReader)
    {
        boundary_element_file_has_containing_element_info = pMeshReader->GetReadContainingElementOfBoundaryElement();
    }
 
    if (DIM > 1)
    {
        if (boundary_element_file_has_containing_element_info)
        {
            pMeshReader->Reset();
        }
 
        // we may need to skip through the boundary element file searching for containing elements hints.
        // This counter keeps track of our position in the file.
        unsigned next_face_on_file = 0u;
 
        for (typename AbstractTetrahedralMesh<DIM,DIM>::BoundaryElementIterator iter
                 = pMesh->GetBoundaryElementIteratorBegin();
             iter != pMesh->GetBoundaryElementIteratorEnd();
             ++iter)
        {
 
            // collect the nodes of this boundary element in a set
            std::set<unsigned> boundary_element_node_indices;
            for (unsigned i=0; i<DIM; i++)
            {
                boundary_element_node_indices.insert( (*iter)->GetNodeGlobalIndex(i) );
            }
 
            bool found_this_boundary_element = false;
 
            // Loop over elements surrounding this face, then loop over each face of that element, and see if it matches
            // this boundary element.
            // Note, if we know what elem it should be in (boundary_element_file_has_containing_element_info==true)
            // we will reset elem_index immediately (below)
            Node<DIM>* p_representative_node = (*iter)->GetNode(0);
            for (typename Node<DIM>::ContainingElementIterator element_iter = p_representative_node->ContainingElementsBegin();
                 element_iter != p_representative_node->ContainingElementsEnd();
                 ++element_iter)
            {
                unsigned elem_index = *element_iter;
 
                // We know what elem it should be in (but we'll still check the node indices match in case)
                if (boundary_element_file_has_containing_element_info)
                {
                    unsigned face_index = (*iter)->GetIndex();
                    do
                    {
                        elem_index = pMeshReader->GetNextFaceData().ContainingElement;
                        next_face_on_file++;
                    }
                    while (face_index >= next_face_on_file);
                }
 
                Element<DIM,DIM>* p_element = pMesh->GetElement(elem_index);
 
                // For each element, loop over faces (the opposites to a node)
                for (unsigned face=0; face<DIM+1; face++)
                {
                    // Collect the node indices for this face
                    std::set<unsigned> node_indices;
                    for (unsigned local_node_index=0; local_node_index<DIM+1; local_node_index++)
                    {
                        if (local_node_index != face)
                        {
                            node_indices.insert( p_element->GetNodeGlobalIndex(local_node_index) );
                        }
                    }
 
                    assert(node_indices.size()==DIM);
 
                    // See if this face matches the boundary element, and add internal nodes if so
                    if (node_indices == boundary_element_node_indices)
                    {
                        QuadraticMeshHelper<DIM>::AddExtraBoundaryNodes(pMesh, *iter, p_element, face);
 
                        found_this_boundary_element = true;
                        break;
                    }
                }
 
                // If the containing element info was given, we must have found the face first time
                if (boundary_element_file_has_containing_element_info && !found_this_boundary_element)
                {
                    // LCOV_EXCL_START
                    //std::cout << (*iter)->GetIndex() << " " <<  pMeshReader->GetNextFaceData().ContainingElement << "\n";
                    EXCEPTION("Boundary element " << (*iter)->GetIndex()
                              << "wasn't found in the containing element given for it "
                              << elem_index);
                    // LCOV_EXCL_STOP
                }
 
                if (found_this_boundary_element)
                {
                    break;
                }
            }
 
            if (!found_this_boundary_element)
            {
                // LCOV_EXCL_START
                EXCEPTION("Unable to find a face of an element which matches one of the boundary elements");
                // LCOV_EXCL_STOP
            }
        }
    }
}
 
template<unsigned DIM>
void QuadraticMeshHelper<DIM>::CheckBoundaryElements(AbstractTetrahedralMesh<DIM, DIM>* pMesh)
{
#ifndef NDEBUG
    unsigned expected_num_nodes = DIM*(DIM+1)/2;
    for (typename AbstractTetrahedralMesh<DIM,DIM>::BoundaryElementIterator iter
             = pMesh->GetBoundaryElementIteratorBegin();
         iter != pMesh->GetBoundaryElementIteratorEnd();
         ++iter)
    {
        assert((*iter)->GetNumNodes() == expected_num_nodes);
    }
#endif
}
 
template<unsigned DIM>
void QuadraticMeshHelper<DIM>::AddNodeToBoundaryElement(AbstractTetrahedralMesh<DIM, DIM>* pMesh,
                                                        BoundaryElement<DIM-1,DIM>* pBoundaryElement,
                                                        Node<DIM>* pNode)
{
    assert(DIM > 1); // LCOV_EXCL_LINE
 
    // Add node to the boundary node list
    if (!pNode->IsBoundaryNode())
    {
        pNode->SetAsBoundaryNode();
        pMesh->mBoundaryNodes.push_back(pNode);
    }
    // Add it to the boundary element
    pBoundaryElement->AddNode(pNode);
}
 
template<unsigned DIM>
void QuadraticMeshHelper<DIM>::AddNodeToBoundaryElement(AbstractTetrahedralMesh<DIM, DIM>* pMesh,
                                                        BoundaryElement<DIM-1,DIM>* pBoundaryElement,
                                                        Element<DIM,DIM>* pElement,
                                                        unsigned internalNode)
{
    assert(DIM > 1); // LCOV_EXCL_LINE
    assert(internalNode >= DIM+1);
    assert(internalNode < (DIM+1)*(DIM+2)/2);
    Node<DIM>* p_internal_node = pElement->GetNode(internalNode);
    AddNodeToBoundaryElement(pMesh, pBoundaryElement, p_internal_node);
}
 
template<unsigned DIM>
void QuadraticMeshHelper<DIM>::AddExtraBoundaryNodes(AbstractTetrahedralMesh<DIM, DIM>* pMesh,
                                                     BoundaryElement<DIM-1,DIM>* pBoundaryElement,
                                                     Element<DIM,DIM>* pElement,
                                                     unsigned nodeIndexOppositeToFace)
{
    assert(DIM!=1); // LCOV_EXCL_LINE
    if (DIM==2)
    {
        assert(nodeIndexOppositeToFace<3);
        // the single internal node of the element's face will be numbered 'face+3'
        AddNodeToBoundaryElement(pMesh, pBoundaryElement, pElement, nodeIndexOppositeToFace+3);
    }
    else
    {
        assert(DIM==3);
 
        unsigned b_elem_n0 = pBoundaryElement->GetNodeGlobalIndex(0);
        unsigned b_elem_n1 = pBoundaryElement->GetNodeGlobalIndex(1);
 
        unsigned offset;
        bool reverse;
 
        if (nodeIndexOppositeToFace==0)
        {
            // face opposite to node 0 = {1,2,3}, with corresponding internals {9,8,5}
            HelperMethod1(b_elem_n0, b_elem_n1, pElement, 1, 2, 3, offset, reverse);
            HelperMethod2(pMesh, pBoundaryElement, pElement, 9, 8, 5, offset, reverse);
        }
        else if (nodeIndexOppositeToFace==1)
        {
            // face opposite to node 1 = {2,0,3}, with corresponding internals {7,9,6}
            HelperMethod1(b_elem_n0, b_elem_n1, pElement, 2, 0, 3, offset, reverse);
            HelperMethod2(pMesh, pBoundaryElement, pElement, 7, 9, 6, offset, reverse);
        }
        else if (nodeIndexOppositeToFace==2)
        {
            // face opposite to node 2 = {0,1,3}, with corresponding internals {8,7,4}
            HelperMethod1(b_elem_n0, b_elem_n1, pElement, 0, 1, 3, offset, reverse);
            HelperMethod2(pMesh, pBoundaryElement, pElement, 8, 7, 4, offset, reverse);
        }
        else
        {
            assert(nodeIndexOppositeToFace==3);
            // face opposite to node 3 = {0,1,2}, with corresponding internals {5,6,4}
            HelperMethod1(b_elem_n0, b_elem_n1, pElement, 0, 1, 2, offset, reverse);
            HelperMethod2(pMesh, pBoundaryElement, pElement, 5, 6, 4, offset, reverse);
        }
    }
}
 
// two unpleasant helper methods for AddExtraBoundaryNodes()
 
// LCOV_EXCL_START /// \todo These helper methods aren't properly covered
template<unsigned DIM>
void QuadraticMeshHelper<DIM>::HelperMethod1(unsigned boundaryElemNode0, unsigned boundaryElemNode1,
                                             Element<DIM,DIM>* pElement,
                                             unsigned node0, unsigned node1, unsigned node2,
                                             unsigned& rOffset,
                                             bool& rReverse)
{
    if (pElement->GetNodeGlobalIndex(node0)==boundaryElemNode0)
    {
        rOffset = 0;
        if (pElement->GetNodeGlobalIndex(node1)==boundaryElemNode1)
        {
            rReverse = false;
        }
        else
        {
            assert(pElement->GetNodeGlobalIndex(node2)==boundaryElemNode1);
            rReverse = true;
        }
    }
    else if (pElement->GetNodeGlobalIndex(node1)==boundaryElemNode0)
    {
        rOffset = 1;
        if (pElement->GetNodeGlobalIndex(node2)==boundaryElemNode1)
        {
            rReverse = false;
        }
        else
        {
            assert(pElement->GetNodeGlobalIndex(node0)==boundaryElemNode1);
            rReverse = true;
        }
    }
    else
    {
        assert(pElement->GetNodeGlobalIndex(node2)==boundaryElemNode0);
        rOffset = 2;
        if (pElement->GetNodeGlobalIndex(node0)==boundaryElemNode1)
        {
            rReverse = false;
        }
        else
        {
            assert(pElement->GetNodeGlobalIndex(node1)==boundaryElemNode1);
            rReverse = true;
        }
    }
}
// LCOV_EXCL_STOP /// \todo These helper methods aren't properly covered
 
 
// LCOV_EXCL_START /// \todo These helper methods aren't properly covered
template<unsigned DIM>
void QuadraticMeshHelper<DIM>::HelperMethod2(AbstractTetrahedralMesh<DIM, DIM>* pMesh,
                                             BoundaryElement<DIM-1,DIM>* pBoundaryElement,
                                             Element<DIM,DIM>* pElement,
                                             unsigned internalNode0, unsigned internalNode1, unsigned internalNode2,
                                             unsigned offset,
                                             bool reverse)
{
    if (offset==1)
    {
        unsigned temp = internalNode0;
        internalNode0 = internalNode1;
        internalNode1 = internalNode2;
        internalNode2 = temp;
    }
    else if (offset == 2)
    {
        unsigned temp = internalNode0;
        internalNode0 = internalNode2;
        internalNode2 = internalNode1;
        internalNode1 = temp;
    }
 
    if (reverse)
    {
        unsigned temp = internalNode1;
        internalNode1 = internalNode2;
        internalNode2 = temp;
    }
 
    AddNodeToBoundaryElement(pMesh, pBoundaryElement, pElement, internalNode0);
    AddNodeToBoundaryElement(pMesh, pBoundaryElement, pElement, internalNode1);
    AddNodeToBoundaryElement(pMesh, pBoundaryElement, pElement, internalNode2);
}
// LCOV_EXCL_STOP /// \todo These helper methods aren't properly covered
 
// Explicit instantiation
template class QuadraticMeshHelper<1>;
template class QuadraticMeshHelper<2>;
template class QuadraticMeshHelper<3>;