ObsoleteBoxCollection.cpp

/*

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 * Redistributions of source code must retain the above copyright notice,
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 * Redistributions in binary form must reproduce the above copyright notice,
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   software without specific prior written permission.

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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 "ObsoleteBoxCollection.hpp"
#include "Exception.hpp"

// ObsoleteBoxCollection methods

// Static member for "fudge factor" is instantiated here
template<unsigned DIM>
const double ObsoleteBoxCollection<DIM>::msFudge = 5e-14;

template<unsigned DIM>
ObsoleteBoxCollection<DIM>::ObsoleteBoxCollection(double boxWidth, c_vector<double, 2 * DIM> domainSize, bool isPeriodicInX,
                                                  bool isPeriodicInY, bool isPeriodicInZ)
                                                  : mDomainSize(domainSize),
                                                    mBoxWidth(boxWidth)
{
    // Populate mIsDomainPeriodic
    switch (DIM)
    {
        case 1:
        {
            mIsDomainPeriodic[0] = isPeriodicInX;
            break;
        }
        case 2:
        {
            mIsDomainPeriodic[0] = isPeriodicInX;
            mIsDomainPeriodic[1] = isPeriodicInY;
            break;
        }
        case 3:
        {
            mIsDomainPeriodic[0] = isPeriodicInX;
            mIsDomainPeriodic[1] = isPeriodicInY;
            mIsDomainPeriodic[2] = isPeriodicInZ;
            break;
        }
        default:
        {
            NEVER_REACHED;
        }
    }

    // Calculating the number of boxes in each direction and total number of boxes.
    unsigned num_boxes = 1;

    for (unsigned i = 0; i < DIM; i++)
    {
        mNumBoxesEachDirection(i) = (unsigned) floor((domainSize(2 * i + 1) - domainSize(2 * i)) / boxWidth + msFudge) + 1;
        num_boxes *= mNumBoxesEachDirection(i);
    }

    // Create the correct number of boxes
    mBoxes.resize(num_boxes);
}

template<unsigned DIM>
void ObsoleteBoxCollection<DIM>::EmptyBoxes()
{
    for (unsigned i = 0; i < mBoxes.size(); i++)
    {
        mBoxes[i].ClearNodes();
    }
}

template<unsigned DIM>
unsigned ObsoleteBoxCollection<DIM>::CalculateContainingBox(Node<DIM>* pNode)
{
    // Get the location of the node
    c_vector<double, DIM> location = pNode->rGetLocation();
    return CalculateContainingBox(location);
}

template<unsigned DIM>
unsigned ObsoleteBoxCollection<DIM>::CalculateContainingBox(c_vector<double, DIM>& rLocation)
{
    // Confirm that the location is in the domain
    for (unsigned i = 0; i < DIM; i++)
    {
        if (!(rLocation[i] >= mDomainSize[2*i] && rLocation[i] <= mDomainSize[2*i + 1]))
        {
            std::stringstream location_error;
            location_error << "Location in dimension " << i << " is " << rLocation[i] << " which is not in the domain ["
            << mDomainSize[2*i] << ", " << mDomainSize[2*i + 1] << "].";

            EXCEPTION(location_error.str());
        }
    }

    // Compute the containing box index in each dimension
    c_vector<int, DIM> containing_box_indices;
    for (unsigned i = 0; i < DIM; i++)
    {
        containing_box_indices[i] = (int) floor((rLocation[i] - mDomainSize(2 * i) + msFudge) / mBoxWidth);
    }

    return GetLinearIndex(containing_box_indices);
}

template<unsigned DIM>
Box<DIM>& ObsoleteBoxCollection<DIM>::rGetBox(unsigned boxIndex)
{
    assert(boxIndex < mBoxes.size());
    return mBoxes[boxIndex];
}

template<unsigned DIM>
unsigned ObsoleteBoxCollection<DIM>::GetNumBoxes()
{
    return mBoxes.size();
}

template<unsigned DIM>
unsigned ObsoleteBoxCollection<DIM>::GetLinearIndex(c_vector<int, DIM> gridIndices)
{
    /*
     * This function may be passed values outside the range in one or more
     * dimensions in the case of a periodic domain.  We therefore assume that
     * these values represent a situation with periodicity and adjust them
     * accordingly before calculating the linear index.
     */

    // Adjust for periodicity if necessary
    for (unsigned dim = 0; dim < DIM; dim++)
    {
        // Check for values too large
        if (gridIndices(dim) >= (int)mNumBoxesEachDirection(dim))
        {
            assert(mIsDomainPeriodic(dim));
            gridIndices(dim) -= (int)mNumBoxesEachDirection(dim);
        }

        // Check for negative values
        else if (gridIndices(dim) < 0)
        {
            assert(mIsDomainPeriodic(dim));
            gridIndices(dim) += (int)mNumBoxesEachDirection(dim);
        }
    }

    // Calculate linear index
    unsigned linear_index;

    switch (DIM)
    {
        case 1:
        {
            linear_index = gridIndices(0);
            break;
        }
        case 2:
        {
            linear_index = gridIndices(0) +
                           gridIndices(1) * mNumBoxesEachDirection(0);
            break;
        }
        case 3:
        {
            linear_index = gridIndices(0) +
                           gridIndices(1) * mNumBoxesEachDirection(0) +
                           gridIndices(2) * mNumBoxesEachDirection(0) * mNumBoxesEachDirection(1);
            break;
        }
        default:
        {
            NEVER_REACHED;
        }
    }

    return linear_index;
}

template<unsigned DIM>
c_vector<unsigned, DIM> ObsoleteBoxCollection<DIM>::GetGridIndices(unsigned linearIndex)
{
    c_vector<unsigned, DIM> grid_indices;

    switch (DIM)
    {
        case 1:
        {
            grid_indices(0) = linearIndex;
            break;
        }
        case 2:
        {
            unsigned num_x = mNumBoxesEachDirection(0);
            grid_indices(0) = linearIndex % num_x;
            grid_indices(1) = (linearIndex - grid_indices(0)) / num_x;
            break;
        }
        case 3:
        {
            unsigned num_x = mNumBoxesEachDirection(0);
            unsigned num_xy = mNumBoxesEachDirection(0)*mNumBoxesEachDirection(1);
            grid_indices(0) = linearIndex % num_x;
            grid_indices(1) = (linearIndex % num_xy - grid_indices(0)) / num_x;
            grid_indices(2) = linearIndex / num_xy;
            break;
        }
        default:
        {
            NEVER_REACHED;
        }
    }

    return grid_indices;
}

template<unsigned DIM>
bool ObsoleteBoxCollection<DIM>::IsBoxInDomain(c_vector<unsigned, DIM> gridIndices)
{
    /*
     * We assume that, for a given dimension, any location is in the domain
     * if the domain is periodic in that dimension.
     *
     * This method can only return false in the case of one or more
     * dimensions being aperiodic and a location in one of those dimensions
     * being outside the range.
     */

    bool is_in_domain = true;

    for (unsigned dim = 0; dim < DIM; dim++)
    {
        if (!mIsDomainPeriodic(dim))
        {
            if (gridIndices(dim) >= mNumBoxesEachDirection(dim))
            {
                is_in_domain = false;
            }
        }
    }

    return is_in_domain;
}

template<unsigned DIM>
c_vector<bool,DIM> ObsoleteBoxCollection<DIM>::IsIndexPenultimate(c_vector<unsigned, DIM> gridIndices)
{
    c_vector<bool,DIM> is_penultimate;

    for (unsigned dim = 0 ; dim < DIM ; dim++)
    {
        is_penultimate(dim) = (gridIndices(dim) == mNumBoxesEachDirection(dim) - 2);
    }

    return is_penultimate;
}

template<unsigned DIM>
void ObsoleteBoxCollection<DIM>::SetupLocalBoxesHalfOnly()
{
    // Populate a list of half the neighbours in this number of dimensions
    std::vector<c_vector<int,DIM> > neighbours;

    switch (DIM)
    {
        case 1:
        {
            // Just one neighbour, plus the current box (zero vector)
            neighbours = std::vector<c_vector<int,DIM> >(2);

            neighbours[0](0) = 0; // current box
            neighbours[1](0) = 1; // right

            break;
        }
        case 2:
        {
            // Four neighbours, plus the current box (zero vector)
            neighbours = std::vector<c_vector<int,DIM> >(5);

            neighbours[0](0) = 0; neighbours[0](1) = 1; // up
            neighbours[1](0) = 1; neighbours[1](1) = 1; // up right
            neighbours[2](0) = 1; neighbours[2](1) = 0; // right
            neighbours[3](0) = 1; neighbours[3](1) =-1; // down right
            neighbours[4](0) = 0; neighbours[4](1) = 0; // current box

            break;
        }
        case 3:
        {
            /*
             * We need to pick 13 neighbours in such a way as to ensure all interactions are captured,
             * in addition to the current box.
             *
             * The 26 cubes on the outside of a 3x3 arrangement either adjacent to a whole face of
             * the central cube, only an edge of the central cube, or only a vertex of the central
             * cube:
             *
             *    6 contact faces, and come in the following 3 pairs:
             *        +x        -x                  (1, 0, 0)
             *        +y        -y                  (0, 1, 0)
             *        +z        -z                  (0, 0, 1)
             *
             *    12 contact edges, and come in the following 6 pairs:
             *        +x+y      -x-y                (1, 1, 0)
             *        +x+z      -x-z                (1, 0, 1)
             *        +x-y      -x+y                (1,-1, 0)
             *        +x-z      -x+z                (1, 0,-1)
             *        +y+z      -y-z                (0, 1, 1)
             *        +y-z      -y+z                (0, 1,-1)
             *
             *    8 contact vertices, and come in the following 4 pairs:
             *        +x+y+z    -x-y-z              (1, 1, 1)
             *        +x+y-z    -x-y+z              (1, 1,-1)
             *        +x-y+z    -x+y-z              (1,-1, 1)
             *        +x-y-z    -x+y+z              (1,-1,-1)
             *
             * We will simply pick the 13 from the left-hand column above, which can be represented
             * as an integer offset in three dimensions from the middle cube, as shown in the third
             * column above.
             */

            neighbours = std::vector<c_vector<int,DIM> >(14);

            neighbours[0](0)  = 1; neighbours[0](1)  = 0; neighbours[0](2)  = 0;
            neighbours[1](0)  = 0; neighbours[1](1)  = 1; neighbours[1](2)  = 0;
            neighbours[2](0)  = 0; neighbours[2](1)  = 0; neighbours[2](2)  = 1;
            neighbours[3](0)  = 1; neighbours[3](1)  = 1; neighbours[3](2)  = 0;
            neighbours[4](0)  = 1; neighbours[4](1)  = 0; neighbours[4](2)  = 1;
            neighbours[5](0)  = 1; neighbours[5](1)  =-1; neighbours[5](2)  = 0;
            neighbours[6](0)  = 1; neighbours[6](1)  = 0; neighbours[6](2)  =-1;
            neighbours[7](0)  = 0; neighbours[7](1)  = 1; neighbours[7](2)  = 1;
            neighbours[8](0)  = 0; neighbours[8](1)  = 1; neighbours[8](2)  =-1;
            neighbours[9](0)  = 1; neighbours[9](1)  = 1; neighbours[9](2)  = 1;
            neighbours[10](0) = 1; neighbours[10](1) = 1; neighbours[10](2) =-1;
            neighbours[11](0) = 1; neighbours[11](1) =-1; neighbours[11](2) = 1;
            neighbours[12](0) = 1; neighbours[12](1) =-1; neighbours[12](2) =-1;

            neighbours[13](0) = 0; neighbours[13](1) = 0; neighbours[13](2) = 0; // current box

            break;
        }
        default:
        {
            NEVER_REACHED;
        }
    }

    // Pass the list of possible neighbours to SetupLocalBoxes()
    SetupLocalBoxes(neighbours);
}

template<unsigned DIM>
void ObsoleteBoxCollection<DIM>::SetupAllLocalBoxes()
{
    // Populate a list of all neighbours in this number of dimensions
    std::vector<c_vector<int, DIM> > neighbours;

    switch (DIM)
    {
        case 1:
        {
            // 3 neighbours
            neighbours.clear();

            for (int x_dim = -1 ; x_dim < 2 ; x_dim++)
            {
                c_vector<int, DIM> neighbour;
                neighbour(0) = x_dim;

                neighbours.push_back(neighbour);
            }

            break;
        }
        case 2:
        {
            // 3x3 neighbours
            neighbours.clear();

            for (int x_dim = -1 ; x_dim < 2 ; x_dim++)
            {
                for (int y_dim = -1 ; y_dim < 2 ; y_dim++)
                {
                    c_vector<int, DIM> neighbour;
                    neighbour(0) = x_dim;
                    neighbour(1) = y_dim;

                    neighbours.push_back(neighbour);
                }
            }

            break;
        }
        case 3:
        {
            // 3x3x3 neighbours
            neighbours.clear();

            for (int x_dim = -1 ; x_dim < 2 ; x_dim++)
            {
                for (int y_dim = -1 ; y_dim < 2 ; y_dim++)
                {
                    for (int z_dim = -1 ; z_dim < 2 ; z_dim++)
                    {
                        c_vector<int, DIM> neighbour;
                        neighbour(0) = x_dim;
                        neighbour(1) = y_dim;
                        neighbour(2) = z_dim;

                        neighbours.push_back(neighbour);
                    }
                }
            }

            break;
        }
        default:
        {
            NEVER_REACHED;
        }
    }

    // Pass the list of possible neighbours to SetupLocalBoxes()
    SetupLocalBoxes(neighbours);
}

template<unsigned DIM>
void ObsoleteBoxCollection<DIM>::SetupLocalBoxes(const std::vector<c_vector<int, DIM> >& rNeighbours)
{
    mLocalBoxes.clear();

    // Loop over all boxes and add all necessary local boxes
    for (unsigned box_idx = 0 ; box_idx < mBoxes.size() ; box_idx++)
    {
        std::set<unsigned> local_boxes;

        // The grid indices (i), (i,j) or (i,j,k) depending on DIM, corresponding to box_idx
        c_vector<unsigned, DIM> grid_indices = GetGridIndices(box_idx);

        // Check all neighbours (1 or 2 in 1D, 4 or 8 in 2D, 13 or 26 in 3D) and add them as local
        // boxes if they are in the domain
        for (unsigned neighbour = 0 ; neighbour < rNeighbours.size() ; neighbour++)
        {
            if (IsBoxInDomain(grid_indices + rNeighbours[neighbour]))
            {
                local_boxes.insert(GetLinearIndex(grid_indices + rNeighbours[neighbour]));
            }
        }

        /*
         * If we are in a periodic domain, we need to add additional boxes if the
         * current box is in the penultimate position of any dimension.
         *
         * The additional boxes we need to add are just all the neighbours of the box
         * in the final position in that dimension.  Because we use set::insert, it
         * doesn't matter if we try and add the same box multiple times (only one
         * copy of the index will be included).
         */

        // Find if the current indices are penultimate in any dimension in which collection is periodic
        c_vector<bool, DIM> is_penultimate_periodic = IsIndexPenultimate(grid_indices);
        unsigned num_penultimate_periodic_dimensions = 0;

        for (unsigned dim = 0 ; dim < DIM ; dim++)
        {
            is_penultimate_periodic(dim) = is_penultimate_periodic(dim) && mIsDomainPeriodic(dim);
            if (is_penultimate_periodic(dim))
            {
                num_penultimate_periodic_dimensions++;
            }
        }

        // First, deal with at least one penultimate dimension
        if (num_penultimate_periodic_dimensions > 0)
        {
            // Loop over each dimension.  If penultimate in dimension DIM move one box and add all neighbours
            for (unsigned dim = 0 ; dim < DIM ; dim++)
            {
                if (is_penultimate_periodic(dim))
                {
                    // If we're penultimate in dimension dim, move to the final location and add each neighbour as before.
                    // The call to IsBoxInDomain() will handle periodicity.
                    // Note that we define this vector before setting it as otherwise the profiling build will break (see #2367)
                    c_vector<unsigned, DIM> ultimate_indices; // Initialisation on next line for profile compiler
                    ultimate_indices = grid_indices;
                    ultimate_indices(dim) ++;

                    for (unsigned neighbour = 0 ; neighbour < rNeighbours.size() ; neighbour++)
                    {
                        if (IsBoxInDomain(ultimate_indices + rNeighbours[neighbour]))
                        {
                            local_boxes.insert(GetLinearIndex(ultimate_indices + rNeighbours[neighbour]));
                        }
                    }
                }
            }
        }

        // The final consideration is cases of multiple dimensions of periodicity.
        if (num_penultimate_periodic_dimensions > 1)
        {
            switch (DIM)
            {
                case 2:
                {
                    // Must have x and y periodicity - just have to add one extra box
                    assert(mIsDomainPeriodic(0) && mIsDomainPeriodic(1));

                    local_boxes.insert(0);

                    break;
                }
                case 3:
                {
                    // Could have X and Y, X and Z, Y and Z, or X, Y and Z periodicity

                    // X and Y
                    if (is_penultimate_periodic(0) && is_penultimate_periodic(1))
                    {
                        c_vector<unsigned, DIM> ultimate_indices;
                        ultimate_indices = grid_indices;
                        ultimate_indices(0) ++;
                        ultimate_indices(1) ++;

                        for (unsigned neighbour = 0 ; neighbour < rNeighbours.size() ; neighbour++)
                        {
                            if (IsBoxInDomain(ultimate_indices + rNeighbours[neighbour]))
                            {
                                local_boxes.insert(GetLinearIndex(ultimate_indices + rNeighbours[neighbour]));
                            }
                        }
                    }

                    // X and Z
                    if (is_penultimate_periodic(0) && is_penultimate_periodic(2))
                    {
                        c_vector<unsigned, DIM> ultimate_indices;
                        ultimate_indices = grid_indices;
                        ultimate_indices(0) ++;
                        ultimate_indices(2) ++;

                        for (unsigned neighbour = 0 ; neighbour < rNeighbours.size() ; neighbour++)
                        {
                            if (IsBoxInDomain(ultimate_indices + rNeighbours[neighbour]))
                            {
                                local_boxes.insert(GetLinearIndex(ultimate_indices + rNeighbours[neighbour]));
                            }
                        }
                    }

                    // Y and Z
                    if (is_penultimate_periodic(1) && is_penultimate_periodic(2))
                    {
                        c_vector<unsigned, DIM> ultimate_indices;
                        ultimate_indices = grid_indices;
                        ultimate_indices(1) ++;
                        ultimate_indices(2) ++;

                        for (unsigned neighbour = 0 ; neighbour < rNeighbours.size() ; neighbour++)
                        {
                            if (IsBoxInDomain(ultimate_indices + rNeighbours[neighbour]))
                            {
                                local_boxes.insert(GetLinearIndex(ultimate_indices + rNeighbours[neighbour]));
                            }
                        }
                    }

                    // X Y and Z
                    if (num_penultimate_periodic_dimensions == 3)
                    {
                        assert(mIsDomainPeriodic(0) && mIsDomainPeriodic(1) && mIsDomainPeriodic(1));
                        local_boxes.insert(0);
                    }

                    break;
                }
                default:
                {
                    NEVER_REACHED;
                }
            }
        }

        // Add the local boxes to the member vector
        mLocalBoxes.push_back(local_boxes);
    }
}

template<unsigned DIM>
std::set<unsigned>& ObsoleteBoxCollection<DIM>::rGetLocalBoxes(unsigned boxIndex)
{
    assert(boxIndex < mLocalBoxes.size());
    return mLocalBoxes[boxIndex];
}

template<unsigned DIM>
const c_vector<double, 2 * DIM>& ObsoleteBoxCollection<DIM>::rGetDomainSize() const
{
    return mDomainSize;
}

template<unsigned DIM>
void ObsoleteBoxCollection<DIM>::CalculateNodePairs(std::vector<Node<DIM>*>& rNodes,
                                            std::vector<std::pair<Node<DIM>*, Node<DIM>*> >& rNodePairs)
{
    rNodePairs.clear();

    // Ensure all boxes are empty
    EmptyBoxes();

    // Create an empty set of neighbours for each node, and add each node to its correct box
    for (unsigned node_index = 0; node_index < rNodes.size(); node_index++)
    {
        rNodes[node_index]->ClearNeighbours();

        unsigned box_index = CalculateContainingBox(rNodes[node_index]);
        mBoxes[box_index].AddNode(rNodes[node_index]);
    }

    for (unsigned i = 0; i < rNodes.size(); i++)
    {
        Node<DIM>* this_node = rNodes[i];
        unsigned node_index = this_node->GetIndex();

        // Get the box containing this node
        unsigned this_node_box_index = CalculateContainingBox(this_node);

        // Get the local boxes to this node
        std::set<unsigned> local_boxes_indices = rGetLocalBoxes(this_node_box_index);

        // Loop over all the local boxes
        for (std::set<unsigned>::iterator box_iter = local_boxes_indices.begin(); box_iter != local_boxes_indices.end();
                box_iter++)
        {
            // Get the set of nodes contained in this box
            std::set<Node<DIM>*>& r_contained_nodes = mBoxes[*box_iter].rGetNodesContained();

            // Loop over these nodes
            for (typename std::set<Node<DIM>*>::iterator node_iter = r_contained_nodes.begin();
                    node_iter != r_contained_nodes.end(); ++node_iter)
            {
                // Get the index of the other node
                unsigned other_node_index = (*node_iter)->GetIndex();

                // If we're in the same box, then take care not to store the node pair twice
                if (*box_iter == this_node_box_index)
                {
                    if (other_node_index > this_node->GetIndex())
                    {
                        rNodePairs.push_back(std::pair<Node<DIM>*, Node<DIM>*>(this_node, (*node_iter)));
                        this_node->AddNeighbour(other_node_index);
                        (*node_iter)->AddNeighbour(node_index);
                    }
                }
                else
                {
                    rNodePairs.push_back(std::pair<Node<DIM>*, Node<DIM>*>(this_node, (*node_iter)));
                    this_node->AddNeighbour(other_node_index);
                    (*node_iter)->AddNeighbour(node_index);
                }
            }
        }
    }

    for (unsigned i = 0; i < rNodes.size(); i++)
    {
        rNodes[i]->RemoveDuplicateNeighbours();
    }
}


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