AbstractTetrahedralMesh.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.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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*/

#include "AbstractTetrahedralMesh.hpp"

// Implementation


template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::SetElementOwnerships()
{
    unsigned lo=this->GetDistributedVectorFactory()->GetLow();
    unsigned hi=this->GetDistributedVectorFactory()->GetHigh();
    for (unsigned element_index=0; element_index<mElements.size(); element_index++)
    {
        Element<ELEMENT_DIM, SPACE_DIM>* p_element = mElements[element_index];
        p_element->SetOwnership(false);
        for (unsigned local_node_index=0; local_node_index< p_element->GetNumNodes(); local_node_index++)
        {
            unsigned global_node_index = p_element->GetNodeGlobalIndex(local_node_index);
            if (lo<=global_node_index && global_node_index<hi)
            {
                p_element->SetOwnership(true);
                break;
            }
        }
    }
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::AbstractTetrahedralMesh()
    : mMeshIsLinear(true)
{
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::~AbstractTetrahedralMesh()
{
    // Iterate over elements and free the memory
    for (unsigned i=0; i<mElements.size(); i++)
    {
        delete mElements[i];
    }
    // Iterate over boundary elements and free the memory
    for (unsigned i=0; i<mBoundaryElements.size(); i++)
    {
        delete mBoundaryElements[i];
    }
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::GetNumElements() const
{
    return mElements.size();
}

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::GetNumAllElements() const
{
    return mElements.size();
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::GetNumBoundaryElements() const
{
    return mBoundaryElements.size();
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::GetNumLocalBoundaryElements() const
{
    return GetNumBoundaryElements();
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::GetNumAllBoundaryElements() const
{
    return mBoundaryElements.size();
}


template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::GetNumCableElements() const
{
    return 0u;
}
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::GetNumVertices() const
{
    return this->GetNumNodes();
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
Element<ELEMENT_DIM, SPACE_DIM>* AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::GetElement(unsigned index) const
{
    unsigned local_index = SolveElementMapping(index);
    return mElements[local_index];
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
BoundaryElement<ELEMENT_DIM-1, SPACE_DIM>* AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::GetBoundaryElement(unsigned index) const
{
    unsigned local_index = SolveBoundaryElementMapping(index);
    return mBoundaryElements[local_index];
}

template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
typename AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::BoundaryElementIterator AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::GetBoundaryElementIteratorBegin() const
{
    return mBoundaryElements.begin();
}

template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
typename AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::BoundaryElementIterator AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::GetBoundaryElementIteratorEnd() const
{
    return mBoundaryElements.end();
}

template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::GetInverseJacobianForElement(
        unsigned elementIndex,
        c_matrix<double, SPACE_DIM, ELEMENT_DIM>& rJacobian,
        double& rJacobianDeterminant,
        c_matrix<double, ELEMENT_DIM, SPACE_DIM>& rInverseJacobian) const
{
    mElements[SolveElementMapping(elementIndex)]->CalculateInverseJacobian(rJacobian, rJacobianDeterminant, rInverseJacobian);
}

template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::GetWeightedDirectionForBoundaryElement(
        unsigned elementIndex,
        c_vector<double, SPACE_DIM>& rWeightedDirection,
        double& rJacobianDeterminant) const
{
    mBoundaryElements[SolveBoundaryElementMapping(elementIndex)]->CalculateWeightedDirection(rWeightedDirection, rJacobianDeterminant );
}


template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::CheckOutwardNormals()
{
    if (ELEMENT_DIM <= 1)
    {
        //If the ELEMENT_DIM of the mesh is 1 then the boundary will have ELEMENT_DIM = 0
        EXCEPTION("1-D mesh has no boundary normals");
    }
    for (typename AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::BoundaryElementIterator face_iter = this->GetBoundaryElementIteratorBegin();
         face_iter != this->GetBoundaryElementIteratorEnd();
         ++face_iter)
    {
        //Form a set for the boundary element node indices
        std::set<unsigned> boundary_element_node_indices;
        for (unsigned i=0; i<ELEMENT_DIM; i++)
        {
            boundary_element_node_indices.insert( (*face_iter)->GetNodeGlobalIndex(i) );
        }

        Node<SPACE_DIM>* p_opposite_node = NULL;
        Node<SPACE_DIM>* p_representative_node = (*face_iter)->GetNode(0);
          for (typename Node<SPACE_DIM>::ContainingElementIterator element_iter = p_representative_node->ContainingElementsBegin();
             element_iter != p_representative_node->ContainingElementsEnd();
             ++element_iter)
        {
            Element<ELEMENT_DIM, SPACE_DIM>* p_element = this->GetElement(*element_iter);
            //Form a set for the element node indices
            std::set<unsigned> element_node_indices;
            for (unsigned i=0; i<=ELEMENT_DIM; i++)
            {
                element_node_indices.insert( p_element->GetNodeGlobalIndex(i) );
            }

            std::vector<unsigned> difference(ELEMENT_DIM);

            std::vector<unsigned>::iterator set_iter = std::set_difference(
                    element_node_indices.begin(),element_node_indices.end(),
                    boundary_element_node_indices.begin(), boundary_element_node_indices.end(),
                    difference.begin());
            if (set_iter - difference.begin() == 1)
            {
                p_opposite_node = this -> GetNodeOrHaloNode(difference[0]);
                break;
            }
        }
        assert(p_opposite_node != NULL);

        // Vector from centroid of face to opposite node
        c_vector<double, SPACE_DIM> into_mesh = p_opposite_node->rGetLocation() - (*face_iter)->CalculateCentroid();
        c_vector<double, SPACE_DIM> normal = (*face_iter)->CalculateNormal();

        if (inner_prod(into_mesh, normal) > 0.0)
        {
            EXCEPTION("Inward facing normal in boundary element index "<<(*face_iter)->GetIndex());
        }
    }
}


template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::ConstructLinearMesh(unsigned width)
{
    assert(ELEMENT_DIM == 1);

    for (unsigned node_index=0; node_index<=width; node_index++)
    {
        Node<SPACE_DIM>* p_node = new Node<SPACE_DIM>(node_index, node_index==0 || node_index==width, node_index);
        this->mNodes.push_back(p_node); // create node
        if (node_index==0) // create left boundary node and boundary element
        {
            this->mBoundaryNodes.push_back(p_node);
            this->mBoundaryElements.push_back(new BoundaryElement<ELEMENT_DIM-1,SPACE_DIM>(0, p_node) );
        }
        if (node_index==width) // create right boundary node and boundary element
        {
            this->mBoundaryNodes.push_back(p_node);
            this->mBoundaryElements.push_back(new BoundaryElement<ELEMENT_DIM-1,SPACE_DIM>(1, p_node) );
        }
        if (node_index > 0) // create element
        {
            std::vector<Node<SPACE_DIM>*> nodes;
            nodes.push_back(this->mNodes[node_index-1]);
            nodes.push_back(this->mNodes[node_index]);
            this->mElements.push_back(new Element<ELEMENT_DIM,SPACE_DIM>(node_index-1, nodes) );
        }
    }

    this->RefreshMesh();
}


template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::ConstructRectangularMesh(unsigned width, unsigned height, bool stagger)
{
    assert(SPACE_DIM == 2);
    assert(ELEMENT_DIM == 2);

    //Construct the nodes
    unsigned node_index=0;
    for (unsigned j=0; j<height+1; j++)
    {
        for (unsigned i=0; i<width+1; i++)
        {
            bool is_boundary=false;
            if (i==0 || j==0 || i==width || j==height)
            {
                is_boundary=true;
            }
            //Check in place for parallel
            assert(node_index==(width+1)*(j) + i);
            Node<SPACE_DIM>* p_node = new Node<SPACE_DIM>(node_index++, is_boundary, i, j);
            this->mNodes.push_back(p_node);
            if (is_boundary)
            {
                this->mBoundaryNodes.push_back(p_node);
            }
        }
    }

    //Construct the boundary elements
    unsigned belem_index=0;
    //Top
    for (unsigned i=0; i<width; i++)
    {
        std::vector<Node<SPACE_DIM>*> nodes;
        nodes.push_back(this->mNodes[height*(width+1)+i+1]);
        nodes.push_back(this->mNodes[height*(width+1)+i]);
        assert(belem_index==i);
        this->mBoundaryElements.push_back(new BoundaryElement<ELEMENT_DIM-1,SPACE_DIM>(belem_index++,nodes));
    }
    //Right
    for (unsigned j=1; j<=height; j++)
    {
        std::vector<Node<SPACE_DIM>*> nodes;
        nodes.push_back(this->mNodes[(width+1)*j-1]);
        nodes.push_back(this->mNodes[(width+1)*(j+1)-1]);
        assert(belem_index==width+j-1);
        this->mBoundaryElements.push_back(new BoundaryElement<ELEMENT_DIM-1,SPACE_DIM>(belem_index++,nodes));
    }
    //Bottom
    for (unsigned i=0; i<width; i++)
    {
        std::vector<Node<SPACE_DIM>*> nodes;
        nodes.push_back(this->mNodes[i]);
        nodes.push_back(this->mNodes[i+1]);
        assert(belem_index==width+height+i);
        this->mBoundaryElements.push_back(new BoundaryElement<ELEMENT_DIM-1,SPACE_DIM>(belem_index++,nodes));
    }
    //Left
    for (unsigned j=0; j<height; j++)
    {
        std::vector<Node<SPACE_DIM>*> nodes;
        nodes.push_back(this->mNodes[(width+1)*(j+1)]);
        nodes.push_back(this->mNodes[(width+1)*(j)]);
        assert(belem_index==2*width+height+j);
        this->mBoundaryElements.push_back(new BoundaryElement<ELEMENT_DIM-1,SPACE_DIM>(belem_index++,nodes));
    }

    //Construct the elements
    unsigned elem_index = 0;
    for (unsigned j=0; j<height; j++)
    {
        for (unsigned i=0; i<width; i++)
        {
            unsigned parity=(i+(height-j))%2;//Note that parity is measured from the top-left (not bottom left) for historical reasons
            unsigned nw=(j+1)*(width+1)+i; //ne=nw+1
            unsigned sw=(j)*(width+1)+i;   //se=sw+1
            std::vector<Node<SPACE_DIM>*> upper_nodes;
            upper_nodes.push_back(this->mNodes[nw]);
            upper_nodes.push_back(this->mNodes[nw+1]);
            if (stagger==false  || parity == 1)
            {
                upper_nodes.push_back(this->mNodes[sw+1]);
            }
            else
            {
                upper_nodes.push_back(this->mNodes[sw]);
            }
            assert(elem_index==2*(j*width+i));
            this->mElements.push_back(new Element<ELEMENT_DIM,SPACE_DIM>(elem_index++,upper_nodes));
            std::vector<Node<SPACE_DIM>*> lower_nodes;
            lower_nodes.push_back(this->mNodes[sw+1]);
            lower_nodes.push_back(this->mNodes[sw]);
            if (stagger==false  ||parity == 1)
            {
                lower_nodes.push_back(this->mNodes[nw]);
            }
            else
            {
                lower_nodes.push_back(this->mNodes[nw+1]);
            }
            this->mElements.push_back(new Element<ELEMENT_DIM,SPACE_DIM>(elem_index++,lower_nodes));
        }
    }

    this->RefreshMesh();
}




template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::ConstructCuboid(unsigned width,
        unsigned height,
        unsigned depth)
{
    assert(SPACE_DIM == 3);
    assert(ELEMENT_DIM == 3);
    //Construct the nodes

    unsigned node_index = 0;
    for (unsigned k=0; k<depth+1; k++)
    {
        for (unsigned j=0; j<height+1; j++)
        {
            for (unsigned i=0; i<width+1; i++)
            {
                bool is_boundary = false;
                if (i==0 || j==0 || k==0 || i==width || j==height || k==depth)
                {
                    is_boundary = true;
                }
                assert(node_index == (k*(height+1)+j)*(width+1)+i);
                Node<SPACE_DIM>* p_node = new Node<SPACE_DIM>(node_index++, is_boundary, i, j, k);

                this->mNodes.push_back(p_node);
                if (is_boundary)
                {
                    this->mBoundaryNodes.push_back(p_node);
                }
            }
        }
    }

    // Construct the elements

    unsigned elem_index = 0;
    unsigned belem_index = 0;
    unsigned element_nodes[6][4] = {{0, 1, 5, 7}, {0, 1, 3, 7},
                                        {0, 2, 3, 7}, {0, 2, 6, 7},
                                        {0, 4, 6, 7}, {0, 4, 5, 7}};
/* Alternative tessellation - (gerardus)
 * Note that our method (above) has a bias that all tetrahedra share a
 * common edge (the diagonal 0 - 7).  In the following method the cube is
 * split along the "face diagonal" 1-2-5-6 into two prisms.  This also has a bias.
 *
    unsigned element_nodes[6][4] = {{ 0, 6, 5, 4},
                                    { 0, 2, 6, 1},
                                    { 0, 1, 6, 5},
                                    { 1, 2, 3, 7},
                                    { 1, 2, 6, 7},
                                    { 1, 6, 7, 5 }};
*/
    std::vector<Node<SPACE_DIM>*> tetrahedra_nodes;

    for (unsigned k=0; k<depth; k++)
    {
        if (k!=0)
        {
            // height*width squares on upper face, k layers of 2*height+2*width square aroun
            assert(belem_index ==   2*(height*width+k*2*(height+width)) );
        }
        for (unsigned j=0; j<height; j++)
        {
            for (unsigned i=0; i<width; i++)
            {
                // Compute the nodes' index
                unsigned global_node_indices[8];
                unsigned local_node_index = 0;

                for (unsigned z = 0; z < 2; z++)
                {
                    for (unsigned y = 0; y < 2; y++)
                    {
                        for (unsigned x = 0; x < 2; x++)
                        {
                            global_node_indices[local_node_index] = i+x+(width+1)*(j+y+(height+1)*(k+z));

                            local_node_index++;
                        }
                    }
                }

                for (unsigned m = 0; m < 6; m++)
                {
                    // Tetrahedra #m

                    tetrahedra_nodes.clear();

                    for (unsigned n = 0; n < 4; n++)
                    {
                        tetrahedra_nodes.push_back(this->mNodes[global_node_indices[element_nodes[m][n]]]);
                    }

                    assert(elem_index == 6 * ((k*height+j)*width+i)+m );
                    this->mElements.push_back(new Element<ELEMENT_DIM,SPACE_DIM>(elem_index++, tetrahedra_nodes));
                }

                // Are we at a boundary?
                std::vector<Node<SPACE_DIM>*> triangle_nodes;

                if (i == 0) //low face at x==0
                {
                    triangle_nodes.clear();
                    triangle_nodes.push_back(this->mNodes[global_node_indices[0]]);
                    triangle_nodes.push_back(this->mNodes[global_node_indices[2]]);
                    triangle_nodes.push_back(this->mNodes[global_node_indices[6]]);
                    this->mBoundaryElements.push_back(new BoundaryElement<ELEMENT_DIM-1,SPACE_DIM>(belem_index++,triangle_nodes));
                    triangle_nodes.clear();
                    triangle_nodes.push_back(this->mNodes[global_node_indices[0]]);
                    triangle_nodes.push_back(this->mNodes[global_node_indices[6]]);
                    triangle_nodes.push_back(this->mNodes[global_node_indices[4]]);
                    this->mBoundaryElements.push_back(new BoundaryElement<ELEMENT_DIM-1,SPACE_DIM>(belem_index++,triangle_nodes));
                }
                if (i == width-1) //high face at x=width
                {
                    triangle_nodes.clear();
                    triangle_nodes.push_back(this->mNodes[global_node_indices[1]]);
                    triangle_nodes.push_back(this->mNodes[global_node_indices[5]]);
                    triangle_nodes.push_back(this->mNodes[global_node_indices[7]]);
                    this->mBoundaryElements.push_back(new BoundaryElement<ELEMENT_DIM-1,SPACE_DIM>(belem_index++,triangle_nodes));
                    triangle_nodes.clear();
                    triangle_nodes.push_back(this->mNodes[global_node_indices[1]]);
                    triangle_nodes.push_back(this->mNodes[global_node_indices[7]]);
                    triangle_nodes.push_back(this->mNodes[global_node_indices[3]]);
                    this->mBoundaryElements.push_back(new BoundaryElement<ELEMENT_DIM-1,SPACE_DIM>(belem_index++,triangle_nodes));
                }
                if (j == 0) //low face at y==0
                {
                    triangle_nodes.clear();
                    triangle_nodes.push_back(this->mNodes[global_node_indices[0]]);
                    triangle_nodes.push_back(this->mNodes[global_node_indices[5]]);
                    triangle_nodes.push_back(this->mNodes[global_node_indices[1]]);
                    this->mBoundaryElements.push_back(new BoundaryElement<ELEMENT_DIM-1,SPACE_DIM>(belem_index++,triangle_nodes));
                    triangle_nodes.clear();
                    triangle_nodes.push_back(this->mNodes[global_node_indices[0]]);
                    triangle_nodes.push_back(this->mNodes[global_node_indices[4]]);
                    triangle_nodes.push_back(this->mNodes[global_node_indices[5]]);
                    this->mBoundaryElements.push_back(new BoundaryElement<ELEMENT_DIM-1,SPACE_DIM>(belem_index++,triangle_nodes));
                }
                if (j == height-1) //high face at y=height
                {
                    triangle_nodes.clear();
                    triangle_nodes.push_back(this->mNodes[global_node_indices[2]]);
                    triangle_nodes.push_back(this->mNodes[global_node_indices[3]]);
                    triangle_nodes.push_back(this->mNodes[global_node_indices[7]]);
                    this->mBoundaryElements.push_back(new BoundaryElement<ELEMENT_DIM-1,SPACE_DIM>(belem_index++,triangle_nodes));
                    triangle_nodes.clear();
                    triangle_nodes.push_back(this->mNodes[global_node_indices[2]]);
                    triangle_nodes.push_back(this->mNodes[global_node_indices[7]]);
                    triangle_nodes.push_back(this->mNodes[global_node_indices[6]]);
                    this->mBoundaryElements.push_back(new BoundaryElement<ELEMENT_DIM-1,SPACE_DIM>(belem_index++,triangle_nodes));
                }
                if (k == 0) //low face at z==0
                {
                    triangle_nodes.clear();
                    triangle_nodes.push_back(this->mNodes[global_node_indices[0]]);
                    triangle_nodes.push_back(this->mNodes[global_node_indices[3]]);
                    triangle_nodes.push_back(this->mNodes[global_node_indices[2]]);
                    this->mBoundaryElements.push_back(new BoundaryElement<ELEMENT_DIM-1,SPACE_DIM>(belem_index++,triangle_nodes));
                    triangle_nodes.clear();
                    triangle_nodes.push_back(this->mNodes[global_node_indices[0]]);
                    triangle_nodes.push_back(this->mNodes[global_node_indices[1]]);
                    triangle_nodes.push_back(this->mNodes[global_node_indices[3]]);
                    this->mBoundaryElements.push_back(new BoundaryElement<ELEMENT_DIM-1,SPACE_DIM>(belem_index++,triangle_nodes));
                }
                if (k == depth-1) //high face at z=depth
                {
                    triangle_nodes.clear();
                    triangle_nodes.push_back(this->mNodes[global_node_indices[4]]);
                    triangle_nodes.push_back(this->mNodes[global_node_indices[7]]);
                    triangle_nodes.push_back(this->mNodes[global_node_indices[5]]);
                    this->mBoundaryElements.push_back(new BoundaryElement<ELEMENT_DIM-1,SPACE_DIM>(belem_index++,triangle_nodes));
                    triangle_nodes.clear();
                    triangle_nodes.push_back(this->mNodes[global_node_indices[4]]);
                    triangle_nodes.push_back(this->mNodes[global_node_indices[6]]);
                    triangle_nodes.push_back(this->mNodes[global_node_indices[7]]);
                    this->mBoundaryElements.push_back(new BoundaryElement<ELEMENT_DIM-1,SPACE_DIM>(belem_index++,triangle_nodes));
                }
            }//i
        }//j
    }//k

    this->RefreshMesh();
}

template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::ConstructRegularSlabMesh(double spaceStep, double width, double height, double depth)
{
    assert(spaceStep>0.0);
    assert(width>0.0);
    if (ELEMENT_DIM > 1)
    {
        assert(height>0.0);
    }
    if (ELEMENT_DIM > 2)
    {
        assert(depth>0.0);
    }
    unsigned num_elem_x=(unsigned)((width+0.5*spaceStep)/spaceStep); //0.5*spaceStep is to ensure that rounding down snaps to correct number
    unsigned num_elem_y=(unsigned)((height+0.5*spaceStep)/spaceStep);
    unsigned num_elem_z=(unsigned)((depth+0.5*spaceStep)/spaceStep);

    //Make it obvious that actual_width_x etc. are temporaries used in spotting for exception
    {
        double actual_width_x=num_elem_x*spaceStep;
        double actual_width_y=num_elem_y*spaceStep;
        double actual_width_z=num_elem_z*spaceStep;

        //Note here that in ELEMENT_DIM > 1 cases there may be a zero height or depth - in which case we don't need to use relative comparisons
        // Doing relative comparisons with zero is okay - if we avoid division by zero.
        // However, it's best not to test whether " fabs( 0.0 - 0.0) > DBL_EPSILON*0.0 "
        if (  fabs (actual_width_x - width) > DBL_EPSILON*width
            ||( height!= 0.0 &&  fabs (actual_width_y - height) > DBL_EPSILON*height)
            ||( depth != 0.0 &&  fabs (actual_width_z - depth) > DBL_EPSILON*depth ) )
        {
            EXCEPTION("Space step does not divide the size of the mesh");
        }
    }
    switch (ELEMENT_DIM)
    {
        case 1:
            this->ConstructLinearMesh(num_elem_x);
            break;
        case 2:
            this->ConstructRectangularMesh(num_elem_x, num_elem_y, true); // Stagger=true
            break;
        default:
        case 3:
            this->ConstructCuboid(num_elem_x, num_elem_y, num_elem_z);
    }
    this->Scale(spaceStep, spaceStep, spaceStep);
}

template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
bool AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::CalculateDesignatedOwnershipOfBoundaryElement( unsigned faceIndex )
{
    // This may throw in the distributed parallel case
    unsigned tie_break_index = this->GetBoundaryElement(faceIndex)->GetNodeGlobalIndex(0);

    // if it is in my range
    if (this->GetDistributedVectorFactory()->IsGlobalIndexLocal(tie_break_index))
    {
        return true;
    }
    else
    {
        return false;
    }
}

template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
bool AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::CalculateDesignatedOwnershipOfElement( unsigned elementIndex )
{
    // This may throw in the distributed parallel case
    unsigned tie_break_index = this->GetElement(elementIndex)->GetNodeGlobalIndex(0);

    // if it is in my range
    if (this->GetDistributedVectorFactory()->IsGlobalIndexLocal(tie_break_index))
    {
        return true;
    }
    else
    {
        return false;
    }
}

template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::CalculateMaximumNodeConnectivityPerProcess() const
{
    unsigned max_num = 0u;
    unsigned connected_node_index = 0u;
    for (unsigned local_node_index=0; local_node_index<this->mNodes.size(); local_node_index++)
    {
        unsigned num = this->mNodes[local_node_index]->GetNumContainingElements();
        if (num>max_num)
        {
            max_num = num;
            connected_node_index = local_node_index;
        }
    }
    if (max_num == 0u)
    {
#define COVERAGE_IGNORE
        /*
         * Coverage of this block requires a mesh regular slab mesh with the number of
         * elements in the primary dimension less than (num_procs - 1), e.g. a 1D mesh
         * one element wide with num_procs >=3.
         */

        // This process owns no nodes and thus owns none of the mesh
        assert(this->mNodes.size() == 0u);
        return (1u);

        /*
         * Note that if a process owns no nodes, then it will still need to enter the
         * collective call to MatMPIAIJSetPreallocation. In PetscTools::SetupMat, the
         * rowPreallocation parameter uses the special value zero to indicate no preallocation.
         */
#undef COVERAGE_IGNORE
    }
    // connected_node_index now has the index of a maximally connected node
    std::set<unsigned> forward_star_nodes;
    unsigned nodes_per_element = this->mElements[0]->GetNumNodes(); //Usually ELEMENT_DIM+1, except in Quadratic case
    for (typename Node<SPACE_DIM>::ContainingElementIterator it = this->mNodes[connected_node_index]->ContainingElementsBegin();
        it != this->mNodes[connected_node_index]->ContainingElementsEnd();
        ++it)
    {
        Element<ELEMENT_DIM, SPACE_DIM>* p_elem = this->GetElement(*it);
        for (unsigned i=0; i<nodes_per_element; i++)
        {
            forward_star_nodes.insert(p_elem->GetNodeGlobalIndex(i));
        }
    }
    return forward_star_nodes.size();
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::GetHaloNodeIndices(std::vector<unsigned>& rHaloIndices) const
{
    // Make sure the output vector is empty
    rHaloIndices.clear();
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::ConstructFromMesh(AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>& rOtherMesh)
{
    for (unsigned i=0; i<rOtherMesh.GetNumNodes(); i++)
    {
        Node<SPACE_DIM>* p_node =  rOtherMesh.GetNode(i);
        assert(!p_node->IsDeleted());
        c_vector<double, SPACE_DIM> location=p_node->rGetLocation();
        bool is_boundary=p_node->IsBoundaryNode();

        Node<SPACE_DIM>* p_node_copy = new Node<SPACE_DIM>(i, location, is_boundary);
        this->mNodes.push_back( p_node_copy );
        if (is_boundary)
        {
            this->mBoundaryNodes.push_back( p_node_copy );
        }
    }

    for (unsigned i=0; i<rOtherMesh.GetNumElements(); i++)
    {
        Element<ELEMENT_DIM, SPACE_DIM>* p_elem = rOtherMesh.GetElement(i);
        assert(!p_elem->IsDeleted());
        std::vector<Node<SPACE_DIM>*> nodes_for_element;
        for (unsigned j=0; j<p_elem->GetNumNodes(); j++)
        {
            nodes_for_element.push_back(this->mNodes[ p_elem->GetNodeGlobalIndex(j) ]);
        }
        Element<ELEMENT_DIM, SPACE_DIM>* p_elem_copy = new Element<ELEMENT_DIM, SPACE_DIM>(i, nodes_for_element);
        p_elem_copy->RegisterWithNodes();
        this->mElements.push_back(p_elem_copy);
    }

    for (unsigned i=0; i<rOtherMesh.GetNumBoundaryElements(); i++)
    {
        BoundaryElement<ELEMENT_DIM-1, SPACE_DIM>* p_b_elem =  rOtherMesh.GetBoundaryElement(i);
        assert(!p_b_elem->IsDeleted());
        std::vector<Node<SPACE_DIM>*> nodes_for_element;
        for (unsigned j=0; j<p_b_elem->GetNumNodes(); j++)
        {
            nodes_for_element.push_back(this->mNodes[ p_b_elem->GetNodeGlobalIndex(j) ]);
        }
        BoundaryElement<ELEMENT_DIM-1, SPACE_DIM>* p_b_elem_copy = new BoundaryElement<ELEMENT_DIM-1, SPACE_DIM>(i, nodes_for_element);
        p_b_elem_copy->RegisterWithNodes();
        this->mBoundaryElements.push_back(p_b_elem_copy);
    }
    this->RefreshMesh();

}

template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::CalculateNodeExchange(
                                     std::vector<std::vector<unsigned> >& rNodesToSendPerProcess,
                                     std::vector<std::vector<unsigned> >& rNodesToReceivePerProcess)
{
    assert( rNodesToSendPerProcess.empty() );
    assert( rNodesToReceivePerProcess.empty() );

    //Initialise vectors of sets for the exchange data
    std::vector<std::set<unsigned> > node_sets_to_send_per_process;
    std::vector<std::set<unsigned> > node_sets_to_receive_per_process;

    node_sets_to_send_per_process.resize(PetscTools::GetNumProcs());
    node_sets_to_receive_per_process.resize(PetscTools::GetNumProcs());
    std::vector<unsigned> global_lows = this->GetDistributedVectorFactory()->rGetGlobalLows();

    for (typename AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::ElementIterator iter = this->GetElementIteratorBegin();
         iter != this->GetElementIteratorEnd();
         ++iter)
    {
        std::vector <unsigned> nodes_on_this_process;
        std::vector <unsigned> nodes_not_on_this_process;
        //Calculate local and non-local node indices
        for (unsigned i=0; i<ELEMENT_DIM+1; i++)
        {
            unsigned node_index=iter->GetNodeGlobalIndex(i);
            if (this->GetDistributedVectorFactory()->IsGlobalIndexLocal(node_index))
            {
                nodes_on_this_process.push_back(node_index);
            }
            else
            {
                nodes_not_on_this_process.push_back(node_index);
            }
        }

        /*
         * If this is a TetrahedralMesh (not distributed) then it's possible that we own none
         * of the nodes in this element.  In that case we must skip the element.
         */
        if (nodes_on_this_process.empty())
        {
            continue; //Move on to the next element.
        }
        // If there are any non-local nodes on this element then we need to add to the data exchange
        if (!nodes_not_on_this_process.empty())
        {
            for (unsigned i=0; i<nodes_not_on_this_process.size(); i++)
            {
                // Calculate who owns this remote node
                unsigned remote_process=global_lows.size()-1;
                for (; global_lows[remote_process] > nodes_not_on_this_process[i]; remote_process--)
                {
                }

                // Add this node to the correct receive set
                node_sets_to_receive_per_process[remote_process].insert(nodes_not_on_this_process[i]);

                // Add all local nodes to the send set
                for (unsigned j=0; j<nodes_on_this_process.size(); j++)
                {
                    node_sets_to_send_per_process[remote_process].insert(nodes_on_this_process[j]);
                }
            }
        }
    }

    for (unsigned process_number = 0; process_number < PetscTools::GetNumProcs(); process_number++)
    {
        std::vector<unsigned> process_send_vector( node_sets_to_send_per_process[process_number].begin(),
                                                   node_sets_to_send_per_process[process_number].end()    );
        std::sort(process_send_vector.begin(), process_send_vector.end());

        rNodesToSendPerProcess.push_back(process_send_vector);

        std::vector<unsigned> process_receive_vector( node_sets_to_receive_per_process[process_number].begin(),
                                                      node_sets_to_receive_per_process[process_number].end()    );
        std::sort(process_receive_vector.begin(), process_receive_vector.end());

        rNodesToReceivePerProcess.push_back(process_receive_vector);
    }

}
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
c_vector<double, 2> AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::CalculateMinMaxEdgeLengths()
{

    c_vector<double, 2> min_max;
    min_max[0] = DBL_MAX;
    min_max[1] = 0.0;
    for (typename AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::ElementIterator ele_iter = GetElementIteratorBegin();
            ele_iter != GetElementIteratorEnd();
            ++ele_iter)
    {
        c_vector<double, 2> ele_min_max = ele_iter->CalculateMinMaxEdgeLengths();
        if (ele_min_max[0] < min_max[0])
        {
            min_max[0] = ele_min_max[0];
        }
        if (ele_min_max[1] > min_max[1])
        {
            min_max[1] = ele_min_max[1];
        }
    }
    return min_max;
}



// Explicit instantiation

template class AbstractTetrahedralMesh<1,1>;
template class AbstractTetrahedralMesh<1,2>;
template class AbstractTetrahedralMesh<1,3>;
template class AbstractTetrahedralMesh<2,2>;
template class AbstractTetrahedralMesh<2,3>;
template class AbstractTetrahedralMesh<3,3>;