NodesOnlyMesh.cpp

/*

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*/

#include <map>
#include "NodesOnlyMesh.hpp"
#include "ChasteCuboid.hpp"

template<unsigned SPACE_DIM>
NodesOnlyMesh<SPACE_DIM>::NodesOnlyMesh()
        : MutableMesh<SPACE_DIM, SPACE_DIM>(),
          mMaximumInteractionDistance(1.0),
          mIndexCounter(0u),
          mMinimumNodeDomainBoundarySeparation(1.0),
          mMaxAddedNodeIndex(0u),
          mpBoxCollection(NULL),
          mCalculateNodeNeighbours(true)
{
}

template<unsigned SPACE_DIM>
NodesOnlyMesh<SPACE_DIM>::~NodesOnlyMesh()
{
    Clear();
    ClearBoxCollection();
}

template<unsigned SPACE_DIM>
void NodesOnlyMesh<SPACE_DIM>::ConstructNodesWithoutMesh(const std::vector<Node<SPACE_DIM>*>& rNodes, double maxInteractionDistance)
{
    assert(maxInteractionDistance > 0.0 && maxInteractionDistance < DBL_MAX);
    mMaximumInteractionDistance = maxInteractionDistance;

    mMinimumNodeDomainBoundarySeparation = mMaximumInteractionDistance;

    Clear();

    SetUpBoxCollection(rNodes);

    mLocalInitialNodes.resize(rNodes.size(), false);

    for (unsigned i=0; i<rNodes.size(); i++)
    {
        if (mpBoxCollection->IsOwned(rNodes[i]))
        {
            mLocalInitialNodes[i] = true;

            assert(!rNodes[i]->IsDeleted());
            c_vector<double, SPACE_DIM> location = rNodes[i]->rGetLocation();

            Node<SPACE_DIM>* p_node_copy = new Node<SPACE_DIM>(GetNextAvailableIndex(), location);
            p_node_copy->SetRadius(0.5);    // Default value.

            this->mNodes.push_back(p_node_copy);

            // Update the node map
            mNodesMapping[p_node_copy->GetIndex()] = this->mNodes.size()-1;
        }
    }
}

template<unsigned SPACE_DIM>
void NodesOnlyMesh<SPACE_DIM>::ConstructNodesWithoutMesh(const AbstractMesh<SPACE_DIM,SPACE_DIM>& rGeneratingMesh, double maxInteractionDistance)
{
    ConstructNodesWithoutMesh(rGeneratingMesh.mNodes, maxInteractionDistance);
}

template<unsigned SPACE_DIM>
std::vector<bool>& NodesOnlyMesh<SPACE_DIM>::rGetInitiallyOwnedNodes()
{
    return mLocalInitialNodes;
}

template<unsigned SPACE_DIM>
unsigned NodesOnlyMesh<SPACE_DIM>::SolveNodeMapping(unsigned index) const
{
    std::map<unsigned, unsigned>::const_iterator node_position = mNodesMapping.find(index);

    if (node_position == mNodesMapping.end())
    {
        EXCEPTION("Requested node " << index << " does not belong to process " << PetscTools::GetMyRank());
    }

    return node_position->second;
}

template<unsigned SPACE_DIM>
void NodesOnlyMesh<SPACE_DIM>::Clear()
{
    // Call Clear() on the parent class
    MutableMesh<SPACE_DIM,SPACE_DIM>::Clear();

    // Clear the nodes mapping
    mNodesMapping.clear();

    mIndexCounter = 0;
}

template<unsigned SPACE_DIM>
DistributedBoxCollection<SPACE_DIM>* NodesOnlyMesh<SPACE_DIM>::GetBoxCollection()
{
    return mpBoxCollection;
}

template <unsigned SPACE_DIM>
Node<SPACE_DIM>* NodesOnlyMesh<SPACE_DIM>::GetNodeOrHaloNode(unsigned index) const
{
    Node<SPACE_DIM>* p_node;

    std::map<unsigned, unsigned>::const_iterator node_position = mHaloNodesMapping.find(index);

    if (node_position != mHaloNodesMapping.end())
    {
        p_node = mHaloNodes[node_position->second].get();
    }
    else
    {
        p_node = this->GetNode(index);
    }

    assert(p_node != NULL);

    return p_node;
}

template<unsigned SPACE_DIM>
bool NodesOnlyMesh<SPACE_DIM>::IsOwned(c_vector<double, SPACE_DIM>& location)
{
    return mpBoxCollection->IsOwned(location);
}

template<unsigned SPACE_DIM>
unsigned NodesOnlyMesh<SPACE_DIM>::GetNumNodes() const
{
    return this->mNodes.size() - this->mDeletedNodeIndices.size();
}

template<unsigned SPACE_DIM>
unsigned NodesOnlyMesh<SPACE_DIM>::GetMaximumNodeIndex()
{
    return std::max(mIndexCounter* PetscTools::GetNumProcs() + PetscTools::GetMyRank(), mMaxAddedNodeIndex);
}

template<unsigned SPACE_DIM>
void NodesOnlyMesh<SPACE_DIM>::SetMaximumInteractionDistance(double maxDistance)
{
    mMaximumInteractionDistance = maxDistance;
}

template<unsigned SPACE_DIM>
double NodesOnlyMesh<SPACE_DIM>::GetMaximumInteractionDistance()
{
    return mMaximumInteractionDistance;
}

template<unsigned SPACE_DIM>
double NodesOnlyMesh<SPACE_DIM>::GetWidth(const unsigned& rDimension) const
{
    double local_width = AbstractMesh<SPACE_DIM, SPACE_DIM>::GetWidth(rDimension);
    double global_width;

    MPI_Allreduce(&local_width, &global_width, 1, MPI_DOUBLE, MPI_MAX, PetscTools::GetWorld());

    return global_width;
}

template<unsigned SPACE_DIM>
void NodesOnlyMesh<SPACE_DIM>::SetCalculateNodeNeighbours(bool calculateNodeNeighbours)
{
    mCalculateNodeNeighbours = calculateNodeNeighbours;
}

template<unsigned SPACE_DIM>
void NodesOnlyMesh<SPACE_DIM>::CalculateInteriorNodePairs(std::vector<std::pair<Node<SPACE_DIM>*, Node<SPACE_DIM>*> >& rNodePairs, std::map<unsigned, std::set<unsigned> >& rNodeNeighbours)
{
    assert(mpBoxCollection);

    mpBoxCollection->CalculateInteriorNodePairs(this->mNodes, rNodePairs, rNodeNeighbours);
}

template<unsigned SPACE_DIM>
void NodesOnlyMesh<SPACE_DIM>::CalculateBoundaryNodePairs(std::vector<std::pair<Node<SPACE_DIM>*, Node<SPACE_DIM>*> >& rNodePairs, std::map<unsigned, std::set<unsigned> >& rNodeNeighbours)
{
    assert(mpBoxCollection);

    mpBoxCollection->CalculateBoundaryNodePairs(this->mNodes, rNodePairs, rNodeNeighbours);
}

template<unsigned SPACE_DIM>
void NodesOnlyMesh<SPACE_DIM>::ReMesh(NodeMap& map)
{
    map.ResetToIdentity();

    RemoveDeletedNodes(map);

    this->mDeletedNodeIndices.clear();
    this->mAddedNodes = false;

    UpdateNodeIndices();

    this->SetMeshHasChangedSinceLoading();
}

template<unsigned SPACE_DIM>
void NodesOnlyMesh<SPACE_DIM>::RemoveDeletedNodes(NodeMap& map)
{
    typename std::vector<Node<SPACE_DIM>* >::iterator node_iter = this->mNodes.begin();
    while (node_iter != this->mNodes.end())
    {
        if ((*node_iter)->IsDeleted())
        {
            map.SetDeleted((*node_iter)->GetIndex());

            mNodesMapping.erase((*node_iter)->GetIndex());

            // Free memory before erasing the pointer from the list of nodes.
            delete (*node_iter);
            node_iter = this->mNodes.erase(node_iter);
        }
        else
        {
            ++node_iter;
        }
    }
}

template<unsigned SPACE_DIM>
void NodesOnlyMesh<SPACE_DIM>::UpdateNodeIndices()
{
    mNodesMapping.clear();
    for (unsigned location_in_vector=0; location_in_vector < this->mNodes.size(); location_in_vector++)
    {
        unsigned global_index = this->mNodes[location_in_vector]->GetIndex();
        mNodesMapping[global_index] = location_in_vector;
    }
}

template<unsigned SPACE_DIM>
void NodesOnlyMesh<SPACE_DIM>::CalculateNodesOutsideLocalDomain()
{
    mNodesToSendRight.clear();
    mNodesToSendLeft.clear();

    for (typename AbstractMesh<SPACE_DIM, SPACE_DIM>::NodeIterator node_iter = this->GetNodeIteratorBegin();
            node_iter != this->GetNodeIteratorEnd();
            ++node_iter)
    {
        unsigned owning_process = mpBoxCollection->GetProcessOwningNode(&(*node_iter));
        if (owning_process == PetscTools::GetMyRank())
        {
            // Do nothing.
        }
        else if (owning_process == PetscTools::GetMyRank() + 1)
        {
            mNodesToSendRight.push_back(node_iter->GetIndex());
        }
        else if (owning_process == PetscTools::GetMyRank() - 1)
        {
            mNodesToSendLeft.push_back(node_iter->GetIndex());
        }
    }
}

template<unsigned SPACE_DIM>
std::vector<unsigned>& NodesOnlyMesh<SPACE_DIM>::rGetNodesToSendLeft()
{
    return mNodesToSendLeft;
}

template<unsigned SPACE_DIM>
std::vector<unsigned>& NodesOnlyMesh<SPACE_DIM>::rGetNodesToSendRight()
{
    return mNodesToSendRight;
}

template<unsigned SPACE_DIM>
std::vector<unsigned>& NodesOnlyMesh<SPACE_DIM>::rGetHaloNodesToSendRight()
{
    return mpBoxCollection->rGetHaloNodesRight();
}

template<unsigned SPACE_DIM>
std::vector<unsigned>& NodesOnlyMesh<SPACE_DIM>::rGetHaloNodesToSendLeft()
{
    return mpBoxCollection->rGetHaloNodesLeft();
}

template<unsigned SPACE_DIM>
void NodesOnlyMesh<SPACE_DIM>::AddNodeWithFixedIndex(Node<SPACE_DIM>* pNewNode)
{
    unsigned location_in_nodes_vector = 0;

    if (this->mDeletedNodeIndices.empty())
    {
        this->mNodes.push_back(pNewNode);
        location_in_nodes_vector = this->mNodes.size() - 1;
    }
    else
    {
        location_in_nodes_vector = this->mDeletedNodeIndices.back();
        this->mDeletedNodeIndices.pop_back();
        delete this->mNodes[location_in_nodes_vector];
        this->mNodes[location_in_nodes_vector] = pNewNode;
    }

    this->mAddedNodes = true;

    mMaxAddedNodeIndex = (pNewNode->GetIndex() > mMaxAddedNodeIndex) ? pNewNode->GetIndex() : mMaxAddedNodeIndex;

    // Update mNodesMapping
    mNodesMapping[pNewNode->GetIndex()] = location_in_nodes_vector;

    // Then update cell radius to default.
    pNewNode->SetRadius(0.5);
}

template<unsigned SPACE_DIM>
void NodesOnlyMesh<SPACE_DIM>::AddHaloNode(boost::shared_ptr<Node<SPACE_DIM> > pNewNode)
{
    mHaloNodes.push_back(pNewNode);
    mHaloNodesMapping[pNewNode->GetIndex()] = mHaloNodes.size() - 1;
}

template<unsigned SPACE_DIM>
void NodesOnlyMesh<SPACE_DIM>::ClearHaloNodes()
{
    mHaloNodes.clear();

    mHaloNodesMapping.clear();
}

template<unsigned SPACE_DIM>
unsigned NodesOnlyMesh<SPACE_DIM>::AddNode(Node<SPACE_DIM>* pNewNode)
{
    unsigned fresh_global_index = GetNextAvailableIndex();
    pNewNode->SetIndex(fresh_global_index);

    AddNodeWithFixedIndex(pNewNode);

    return fresh_global_index;
}

template<unsigned SPACE_DIM>
void NodesOnlyMesh<SPACE_DIM>::SetNode(unsigned nodeIndex, ChastePoint<SPACE_DIM> point, bool concreteMove)
{
    // concreteMove should always be false for a NodesOnlyMesh as there are no elements to check
    assert(!concreteMove);

    // Update the node's location
    this->GetNode(nodeIndex)->SetPoint(point);
}

template<unsigned SPACE_DIM>
void NodesOnlyMesh<SPACE_DIM>::AddMovedNode(boost::shared_ptr<Node<SPACE_DIM> > pMovedNode)
{
    // Make a deep copy of this node pointer so that it isn't accidentally deleted.
    unsigned index = pMovedNode->GetIndex();
    c_vector<double, SPACE_DIM> location = pMovedNode->rGetLocation();

    Node<SPACE_DIM>* p_node = new Node<SPACE_DIM>(index, location);

    if (pMovedNode->HasNodeAttributes())
    {
        double radius = pMovedNode->GetRadius();
        p_node->SetRadius(radius);

        unsigned region = pMovedNode->GetRegion();
        p_node->SetRegion(region);

        bool is_particle = pMovedNode->IsParticle();
        p_node->SetIsParticle(is_particle);

        for (unsigned i=0; i<pMovedNode->GetNumNodeAttributes(); i++)
        {
            double attribute = pMovedNode->rGetNodeAttributes()[i];
            p_node->AddNodeAttribute(attribute);
        }
    }

    AddNodeWithFixedIndex(p_node);
}

template<unsigned SPACE_DIM>
void NodesOnlyMesh<SPACE_DIM>::DeleteNode(unsigned index)
{
    if (this->GetNode(index)->IsDeleted())
    {
        EXCEPTION("Trying to delete a deleted node");
    }

    unsigned local_index = SolveNodeMapping(index);

    this->mNodes[local_index]->MarkAsDeleted();
    this->mDeletedNodeIndices.push_back(local_index);
    mDeletedGlobalNodeIndices.push_back(index);
}

template<unsigned SPACE_DIM>
void NodesOnlyMesh<SPACE_DIM>::DeleteMovedNode(unsigned index)
{
    DeleteNode(index);

    // Remove index from deleted indices, as moved indices must not be re-used.
    mDeletedGlobalNodeIndices.pop_back();
}

template<unsigned SPACE_DIM>
void NodesOnlyMesh<SPACE_DIM>::SetMinimumNodeDomainBoundarySeparation(double separation)
{
    assert(!(separation < 0.0));

    mMinimumNodeDomainBoundarySeparation = separation;
}

template<unsigned SPACE_DIM>
unsigned NodesOnlyMesh<SPACE_DIM>::GetNextAvailableIndex()
{
    unsigned index;

    if (!this->mDeletedGlobalNodeIndices.empty())
    {
        index = this->mDeletedGlobalNodeIndices.back();
        this->mDeletedGlobalNodeIndices.pop_back();
    }
    else
    {
        unsigned counter = mIndexCounter;
        mIndexCounter++;
        index = counter * PetscTools::GetNumProcs() + PetscTools::GetMyRank();
    }

    return index;
}

template<unsigned SPACE_DIM>
void NodesOnlyMesh<SPACE_DIM>::EnlargeBoxCollection()
{
    assert(mpBoxCollection);

    int num_local_rows = mpBoxCollection->GetNumLocalRows();
    int new_local_rows = num_local_rows + (int)(PetscTools::AmTopMost()) + (int)(PetscTools::AmMaster());

    c_vector<double, 2*SPACE_DIM> current_domain_size = mpBoxCollection->rGetDomainSize();
    c_vector<double, 2*SPACE_DIM> new_domain_size;

    double fudge = 1e-14;
    for (unsigned d=0; d < SPACE_DIM; d++)
    {
        new_domain_size[2*d] = current_domain_size[2*d] - (mMaximumInteractionDistance - fudge);
        new_domain_size[2*d+1] = current_domain_size[2*d+1] + (mMaximumInteractionDistance - fudge);
    }

    SetUpBoxCollection(mMaximumInteractionDistance, new_domain_size, new_local_rows);
}

template<unsigned SPACE_DIM>
bool NodesOnlyMesh<SPACE_DIM>::IsANodeCloseToDomainBoundary()
{
    assert(mpBoxCollection);

    int is_local_node_close = 0;
    c_vector<double, 2*SPACE_DIM> domain_boundary = mpBoxCollection->rGetDomainSize();

    for (typename AbstractMesh<SPACE_DIM, SPACE_DIM>::NodeIterator node_iter = this->GetNodeIteratorBegin();
         node_iter != this->GetNodeIteratorEnd();
         ++node_iter)
    {
        // Note that we define this vector before setting it as otherwise the profiling build will break (see #2367)
        c_vector<double, SPACE_DIM> location;
        location = node_iter->rGetLocation();

        for (unsigned d=0; d<SPACE_DIM; d++)
        {
            if (location[d] < (domain_boundary[2*d] + mMinimumNodeDomainBoundarySeparation) ||  location[d] > (domain_boundary[2*d+1] - mMinimumNodeDomainBoundarySeparation))
            {
                is_local_node_close = 1;
                break;
            }
        }
        if (is_local_node_close)
        {
            break;  // Saves checking every node if we find one close to the boundary
        }
    }

    // Synchronise between processes
    int is_any_node_close = 0;
    MPI_Allreduce(&is_local_node_close, &is_any_node_close, 1, MPI_INT, MPI_SUM, PetscTools::GetWorld());

    return (is_any_node_close > 0);
}

template<unsigned SPACE_DIM>
void NodesOnlyMesh<SPACE_DIM>::ClearBoxCollection()
{
    if (mpBoxCollection)
    {
        delete mpBoxCollection;
    }
    mpBoxCollection = NULL;
}

template<unsigned SPACE_DIM>
void NodesOnlyMesh<SPACE_DIM>::SetInitialBoxCollection(const c_vector<double, 2*SPACE_DIM> domainSize, double maxInteractionDistance)
{
    this->SetUpBoxCollection(maxInteractionDistance, domainSize);
}

template<unsigned SPACE_DIM>
void NodesOnlyMesh<SPACE_DIM>::SetUpBoxCollection(const std::vector<Node<SPACE_DIM>* >& rNodes)
{
    ClearBoxCollection();

    ChasteCuboid<SPACE_DIM> bounding_box = this->CalculateBoundingBox(rNodes);

    c_vector<double, 2*SPACE_DIM> domain_size;
    for (unsigned i=0; i < SPACE_DIM; i++)
    {
        domain_size[2*i] = bounding_box.rGetLowerCorner()[i] - 1e-14;
        domain_size[2*i+1] = bounding_box.rGetUpperCorner()[i] + 1e-14;
    }

    SetUpBoxCollection(mMaximumInteractionDistance, domain_size);
}

template<unsigned SPACE_DIM>
void NodesOnlyMesh<SPACE_DIM>::SetUpBoxCollection(double cutOffLength, c_vector<double, 2*SPACE_DIM> domainSize, int numLocalRows, bool isPeriodic)
{
     ClearBoxCollection();

     mpBoxCollection = new DistributedBoxCollection<SPACE_DIM>(cutOffLength, domainSize, isPeriodic, numLocalRows);
     mpBoxCollection->SetupLocalBoxesHalfOnly();
     mpBoxCollection->SetupHaloBoxes();
     mpBoxCollection->SetCalculateNodeNeighbours(mCalculateNodeNeighbours);
}

template<unsigned SPACE_DIM>
void NodesOnlyMesh<SPACE_DIM>::AddNodesToBoxes()
{
     // Put the nodes in the boxes.
     for (typename AbstractMesh<SPACE_DIM, SPACE_DIM>::NodeIterator node_iter = this->GetNodeIteratorBegin();
               node_iter != this->GetNodeIteratorEnd();
               ++node_iter)
     {
          unsigned box_index = mpBoxCollection->CalculateContainingBox(&(*node_iter));
          mpBoxCollection->rGetBox(box_index).AddNode(&(*node_iter));
     }
}

template<unsigned SPACE_DIM>
void NodesOnlyMesh<SPACE_DIM>::AddHaloNodesToBoxes()
{
    // Add halo nodes
    for (typename std::vector<boost::shared_ptr<Node<SPACE_DIM> > >::iterator halo_node_iter = mHaloNodes.begin();
            halo_node_iter != mHaloNodes.end();
            ++halo_node_iter)
    {
        unsigned box_index = mpBoxCollection->CalculateContainingBox((*halo_node_iter).get());
        mpBoxCollection->rGetHaloBox(box_index).AddNode((*halo_node_iter).get());
    }
}

template<unsigned SPACE_DIM>
void NodesOnlyMesh<SPACE_DIM>::UpdateBoxCollection()
{
    assert(mpBoxCollection);

    // Remove node pointers from boxes in BoxCollection.
    mpBoxCollection->EmptyBoxes();

    AddNodesToBoxes();

    mpBoxCollection->UpdateHaloBoxes();
}

template<unsigned SPACE_DIM>
void NodesOnlyMesh<SPACE_DIM>::ResizeBoxCollection()
{
    if (!mpBoxCollection)
    {
        SetUpBoxCollection(this->mNodes);
    }

    while (IsANodeCloseToDomainBoundary())
    {
        EnlargeBoxCollection();
    }
}

template<unsigned SPACE_DIM>
void NodesOnlyMesh<SPACE_DIM>::LoadBalanceMesh()
{
    std::vector<int> local_node_distribution = mpBoxCollection->CalculateNumberOfNodesInEachStrip();

    unsigned new_rows = mpBoxCollection->LoadBalance(local_node_distribution);

    c_vector<double, 2*SPACE_DIM> current_domain_size = mpBoxCollection->rGetDomainSize();

    // This ensures the domain will stay the same size.
    double fudge = 1e-14;
    for (unsigned d=0; d < SPACE_DIM; d++)
    {
        current_domain_size[2*d] = current_domain_size[2*d] + fudge;
        current_domain_size[2*d+1] = current_domain_size[2*d+1] - fudge;
    }
    SetUpBoxCollection(mMaximumInteractionDistance, current_domain_size, new_rows);
}

template<unsigned SPACE_DIM>
void NodesOnlyMesh<SPACE_DIM>::ConstructFromMeshReader(AbstractMeshReader<SPACE_DIM, SPACE_DIM>& rMeshReader)
{
    TetrahedralMesh<SPACE_DIM, SPACE_DIM>::ConstructFromMeshReader(rMeshReader);

    // Set the correct global node indices
    for (unsigned i=0; i<this->mNodes.size(); i++)
    {
        this->mNodes[i]->SetIndex(GetNextAvailableIndex());
    }
}

// Explicit instantiation

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

// Serialization for Boost >= 1.36
#include "SerializationExportWrapperForCpp.hpp"
EXPORT_TEMPLATE_CLASS_SAME_DIMS(NodesOnlyMesh)