AbstractTetrahedralMesh.cpp

/*

Copyright (C) University of Oxford, 2005-2011

University of Oxford means the Chancellor, Masters and Scholars of the
University of Oxford, having an administrative office at Wellington
Square, Oxford OX1 2JD, UK.

This file is part of Chaste.

Chaste is free software: you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License as published
by the Free Software Foundation, either version 2.1 of the License, or
(at your option) any later version.

Chaste is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public
License for more details. The offer of Chaste under the terms of the
License is subject to the License being interpreted in accordance with
English Law and subject to any action against the University of Oxford
being under the jurisdiction of the English Courts.

You should have received a copy of the GNU Lesser General Public License
along with Chaste. If not, see <http://www.gnu.org/licenses/>.

*/

#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>::GetNumAllBoundaryElements() const
{
    return mBoundaryElements.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>::GetNumCableElements() const
{
    return 0u;
}

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>::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]);
        nodes.push_back(this->mNodes[height*(width+1)+i+1]);
        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)-1]);
        nodes.push_back(this->mNodes[(width+1)*j-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+1]);
        nodes.push_back(this->mNodes[i]);
        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);
    }
    
}


// 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>;

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