Node.cpp

/*

Copyright (c) 2005-2014, University of Oxford.
All rights reserved.

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This file is part of Chaste.

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modification, are permitted provided that the following conditions are met:
 * Redistributions of source code must retain the above copyright notice,
   this list of conditions and the following disclaimer.
 * Redistributions in binary form must reproduce the above copyright notice,
   this list of conditions and the following disclaimer in the documentation
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 * Neither the name of the University of Oxford nor the names of its
   contributors may be used to endorse or promote products derived from this
   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
ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
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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 = NULL;
}

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
{
    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 != NULL);
}

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(c_vector<double, SPACE_DIM>& forceContribution)
{
    ConstructNodeAttributes();

    mpNodeAttributes->AddAppliedForceContribution(forceContribution);
}

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();
}

// Methods dealing with some node flags (deleted, region)

template<unsigned SPACE_DIM>
void Node<SPACE_DIM>::CheckForNodeAttributes() const
{
    if (mpNodeAttributes == NULL)
    {
        EXCEPTION("Node has no attributes associated with it. Construct attributes first");
    }
}

template<unsigned SPACE_DIM>
void Node<SPACE_DIM>::ConstructNodeAttributes()
{
    if (mpNodeAttributes == NULL)
    {
        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>;