Node.cpp

/*
 
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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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LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
*/
 
#include <cassert>
 
#include "Node.hpp"
#include "Exception.hpp"
 
// Constructors
 
template<unsigned SPACE_DIM>
void Node<SPACE_DIM>::CommonConstructor(unsigned index, bool isBoundaryNode)
{
    mIndex = index;
    mIsBoundaryNode = isBoundaryNode;
    mIsInternal = false;
    mIsDeleted = false;
    mpNodeAttributes = nullptr;
}
 
template<unsigned SPACE_DIM>
Node<SPACE_DIM>::Node(unsigned index, ChastePoint<SPACE_DIM> point, bool isBoundaryNode)
{
    mLocation = point.rGetLocation();
    CommonConstructor(index, isBoundaryNode);
}
 
template<unsigned SPACE_DIM>
Node<SPACE_DIM>::Node(unsigned index, std::vector<double> coords, bool isBoundaryNode)
{
    for (unsigned i=0; i<SPACE_DIM; i++)
    {
        mLocation(i) = coords.at(i);
    }
    CommonConstructor(index, isBoundaryNode);
}
 
template<unsigned SPACE_DIM>
Node<SPACE_DIM>::Node(unsigned index, c_vector<double, SPACE_DIM> location, bool isBoundaryNode)
{
    mLocation = location;
    CommonConstructor(index, isBoundaryNode);
}
 
template<unsigned SPACE_DIM>
Node<SPACE_DIM>::Node(unsigned index, bool isBoundaryNode, double v1, double v2, double v3)
{
    mLocation[0] = v1;
    if (SPACE_DIM > 1)
    {
        mLocation[1] = v2;
        if (SPACE_DIM > 2)
        {
            mLocation[2] = v3;
        }
    }
    CommonConstructor(index, isBoundaryNode);
}
 
template<unsigned SPACE_DIM>
Node<SPACE_DIM>::Node(unsigned index, double *location, bool isBoundaryNode)
{
    for (unsigned i=0; i<SPACE_DIM; i++)
    {
        mLocation(i) = location[i];
    }
    CommonConstructor(index, isBoundaryNode);
}
 
template<unsigned SPACE_DIM>
Node<SPACE_DIM>::~Node()
{
    delete mpNodeAttributes;
}
 
// Methods dealing with node location
 
template<unsigned SPACE_DIM>
void Node<SPACE_DIM>::SetPoint(ChastePoint<SPACE_DIM> point)
{
    mLocation = point.rGetLocation();
}
 
template<unsigned SPACE_DIM>
void Node<SPACE_DIM>::SetIndex(unsigned index)
{
    mIndex = index;
}
 
template<unsigned SPACE_DIM>
void Node<SPACE_DIM>::SetAsBoundaryNode(bool value)
{
    mIsBoundaryNode = value;
}
 
template<unsigned SPACE_DIM>
ChastePoint<SPACE_DIM> Node<SPACE_DIM>::GetPoint() const
{
    return ChastePoint<SPACE_DIM>(mLocation);
}
 
template<unsigned SPACE_DIM>
const c_vector<double, SPACE_DIM>& Node<SPACE_DIM>::rGetLocation() const
{
    // This assert statement is a useful warning: when new nodes are created we overwrite previously deleted nodes if there are any.
    // This means that we can not use this method to interrogate deleted nodes about their position before deletion because we can't
    // guarantee that the node has not been overwritten already. Hence, when implementing new functionality we need to make sure
    // that this functionality does not rely on being able to interrogate deleted nodes for their location.
    // \todo #2401: make this an exception.
    assert(!mIsDeleted);
    return mLocation;
}
 
template<unsigned SPACE_DIM>
c_vector<double, SPACE_DIM>& Node<SPACE_DIM>::rGetModifiableLocation()
{
    assert(!mIsDeleted);
    return mLocation;
}
 
template<unsigned SPACE_DIM>
unsigned Node<SPACE_DIM>::GetIndex() const
{
    return mIndex;
}
 
template<unsigned SPACE_DIM>
bool Node<SPACE_DIM>::IsBoundaryNode() const
{
    return mIsBoundaryNode;
}
 
template<unsigned SPACE_DIM>
void Node<SPACE_DIM>::AddNodeAttribute(double attribute)
{
    ConstructNodeAttributes();
 
    mpNodeAttributes->AddAttribute(attribute);
}
 
template<unsigned SPACE_DIM>
std::vector<double>& Node<SPACE_DIM>::rGetNodeAttributes()
{
    CheckForNodeAttributes();
 
    return mpNodeAttributes->rGetAttributes();
}
 
template<unsigned SPACE_DIM>
unsigned Node<SPACE_DIM>::GetNumNodeAttributes()
{
    unsigned num_attributes;
    if (!mpNodeAttributes)
    {
        num_attributes = 0u;
    }
    else
    {
        num_attributes = mpNodeAttributes->rGetAttributes().size();
    }
 
    return num_attributes;
}
 
template<unsigned SPACE_DIM>
bool Node<SPACE_DIM>::HasNodeAttributes()
{
    return (mpNodeAttributes != nullptr);
}
 
template<unsigned SPACE_DIM>
c_vector<double, SPACE_DIM>& Node<SPACE_DIM>::rGetAppliedForce()
{
    CheckForNodeAttributes();
 
    return mpNodeAttributes->rGetAppliedForce();
}
 
template<unsigned SPACE_DIM>
void Node<SPACE_DIM>::ClearAppliedForce()
{
    ConstructNodeAttributes();
 
    mpNodeAttributes->ClearAppliedForce();
}
 
template<unsigned SPACE_DIM>
void Node<SPACE_DIM>::AddAppliedForceContribution(const c_vector<double, SPACE_DIM>& rForceContribution)
{
    ConstructNodeAttributes();
 
    mpNodeAttributes->AddAppliedForceContribution(rForceContribution);
}
 
template<unsigned SPACE_DIM>
bool Node<SPACE_DIM>::IsParticle()
{
    CheckForNodeAttributes();
 
    return mpNodeAttributes->IsParticle();
}
 
template<unsigned SPACE_DIM>
void Node<SPACE_DIM>::SetIsParticle(bool isParticle)
{
    ConstructNodeAttributes();
 
    mpNodeAttributes->SetIsParticle(isParticle);
}
 
template<unsigned SPACE_DIM>
double Node<SPACE_DIM>::GetRadius()
{
    CheckForNodeAttributes();
 
    return mpNodeAttributes->GetRadius();
}
 
template<unsigned SPACE_DIM>
void Node<SPACE_DIM>::SetRadius(double radius)
{
    ConstructNodeAttributes();
 
    mpNodeAttributes->SetRadius(radius);
}
 
// Tracking (boundary) elements which contain this node as a vertex
 
template<unsigned SPACE_DIM>
void Node<SPACE_DIM>::AddElement(unsigned index)
{
    mElementIndices.insert(index);
}
 
template<unsigned SPACE_DIM>
void Node<SPACE_DIM>::RemoveElement(unsigned index)
{
    unsigned count = mElementIndices.erase(index);
    if (count == 0)
    {
        EXCEPTION("Tried to remove an index which was not in the set");
    }
}
 
template<unsigned SPACE_DIM>
void Node<SPACE_DIM>::RemoveBoundaryElement(unsigned index)
{
    unsigned count = mBoundaryElementIndices.erase(index);
    if (count == 0)
    {
        EXCEPTION("Tried to remove an index which was not in the set");
    }
}
 
template<unsigned SPACE_DIM>
void Node<SPACE_DIM>::AddBoundaryElement(unsigned index)
{
    mBoundaryElementIndices.insert(index);
}
 
template<unsigned SPACE_DIM>
std::set<unsigned>& Node<SPACE_DIM>::rGetContainingElementIndices()
{
    return mElementIndices;
}
 
template<unsigned SPACE_DIM>
std::set<unsigned>& Node<SPACE_DIM>::rGetContainingBoundaryElementIndices()
{
    return mBoundaryElementIndices;
}
 
template<unsigned SPACE_DIM>
unsigned Node<SPACE_DIM>::GetNumContainingElements() const
{
    return mElementIndices.size();
}
 
template<unsigned SPACE_DIM>
unsigned Node<SPACE_DIM>::GetNumBoundaryElements() const
{
    return mBoundaryElementIndices.size();
}
 
// Tracking neighbours of the node
 
template<unsigned SPACE_DIM>
void Node<SPACE_DIM>::AddNeighbour(unsigned index)
{
    ConstructNodeAttributes();
 
    return mpNodeAttributes->AddNeighbour(index);
}
 
template<unsigned SPACE_DIM>
void Node<SPACE_DIM>::ClearNeighbours()
{
    ConstructNodeAttributes();
 
    mpNodeAttributes->ClearNeighbours();
}
 
template<unsigned SPACE_DIM>
void Node<SPACE_DIM>::RemoveDuplicateNeighbours()
{
    CheckForNodeAttributes();
 
    mpNodeAttributes->RemoveDuplicateNeighbours();
}
 
template<unsigned SPACE_DIM>
bool Node<SPACE_DIM>::NeighboursIsEmpty()
{
    CheckForNodeAttributes();
 
    return mpNodeAttributes->NeighboursIsEmpty();
}
 
template<unsigned SPACE_DIM>
void Node<SPACE_DIM>::SetNeighboursSetUp(bool flag)
{
    ConstructNodeAttributes();
 
    mpNodeAttributes->SetNeighboursSetUp(flag);
};
 
template<unsigned SPACE_DIM>
bool Node<SPACE_DIM>::GetNeighboursSetUp()
{
    CheckForNodeAttributes();
 
    return mpNodeAttributes->GetNeighboursSetUp();
};
 
template<unsigned SPACE_DIM>
std::vector<unsigned>& Node<SPACE_DIM>::rGetNeighbours()
{
    CheckForNodeAttributes();
 
    return mpNodeAttributes->rGetNeighbours();
};
 
// Methods dealing with some node flags (deleted, region)
 
template<unsigned SPACE_DIM>
void Node<SPACE_DIM>::CheckForNodeAttributes() const
{
    if (mpNodeAttributes == nullptr)
    {
        EXCEPTION("Node has no attributes associated with it. Construct attributes first");
    }
}
 
template<unsigned SPACE_DIM>
void Node<SPACE_DIM>::ConstructNodeAttributes()
{
    if (mpNodeAttributes == nullptr)
    {
        mpNodeAttributes = new NodeAttributes<SPACE_DIM>();
    }
}
 
template<unsigned SPACE_DIM>
void Node<SPACE_DIM>::MarkAsDeleted()
{
    mIsDeleted = true;
}
 
template<unsigned SPACE_DIM>
bool Node<SPACE_DIM>::IsDeleted() const
{
    return mIsDeleted;
}
 
template<unsigned SPACE_DIM>
void Node<SPACE_DIM>::MarkAsInternal()
{
    mIsInternal = true;
}
 
template<unsigned SPACE_DIM>
bool Node<SPACE_DIM>::IsInternal() const
{
    return mIsInternal;
}
 
template<unsigned SPACE_DIM>
void Node<SPACE_DIM>::SetRegion(unsigned region)
{
    ConstructNodeAttributes();
    mpNodeAttributes->SetRegion(region);
}
 
template<unsigned SPACE_DIM>
unsigned Node<SPACE_DIM>::GetRegion() const
{
    unsigned region = 0;
 
    if (mpNodeAttributes)
    {
        region = mpNodeAttributes->GetRegion();
    }
 
    return region;
}
 
 
 
// Explicit instantiation
template class Node<1>;
template class Node<2>;
template class Node<3>;