PeriodicNodesOnlyMesh.cpp

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*/
 
#include <map>
#include "PeriodicNodesOnlyMesh.hpp"
 
template<unsigned SPACE_DIM>
PeriodicNodesOnlyMesh<SPACE_DIM>::PeriodicNodesOnlyMesh(c_vector<double,SPACE_DIM> width)
        : NodesOnlyMesh<SPACE_DIM>(),
          mWidth(width)
{
    // Convert periodic widths into a boolean vector
    mIsDimPeriodic = zero_vector<bool>(SPACE_DIM);
 
    for (unsigned i = 0; i < SPACE_DIM; i++)
    {
        if (width[i]>0.0)
        {
            mIsDimPeriodic[i] = true;
        }
    }
}
 
template<unsigned SPACE_DIM>
void PeriodicNodesOnlyMesh<SPACE_DIM>::SetUpBoxCollection(double cutOffLength, c_vector<double, 2*SPACE_DIM> domainSize, int numLocalRows, c_vector<bool,SPACE_DIM> isDimPeriodic)
{
 
    // Check that we haven't got too many processors; the maximum number of processors is width/cutOffLength in the y (2D)/z (3D) direction
    if ( mIsDimPeriodic[SPACE_DIM-1] && ((mWidth[SPACE_DIM-1]+1e-14)/cutOffLength) < PetscTools::GetNumProcs() )
    {
        EXCEPTION("Too many processors for the periodic domain width and cut off length. NumProcs should be less than or equal to Y (in 2D) or Z (in 3D) width / Cut off length.\n");
    }
    // Container for converting the periodic dims vector to a true/false input into box collection setup
    // For each periodic dimension:
 
    for (unsigned i=0; i < SPACE_DIM; i++)
    {
        if (mIsDimPeriodic[i])
        {
            // Ensure that the width is a multiple of cut-off length
            if ( fmod(mWidth[i]+1e-14,cutOffLength ) > 2e-14 )
            {
                EXCEPTION("The periodic width must be a multiple of cut off length.");
            }
            // A width of two boxes gives different simulation results as some connections are considered twice.
            else if ( mWidth[i]/cutOffLength <= (2.0+1e-14) )
            {
                EXCEPTION( "The periodic domain width cannot be less than 2*CutOffLength." );
            }
 
            // We force the domain to the periodic widths
            domainSize[ i*2 ] = 0;
            domainSize[ i*2+1 ] = mWidth[i];
        }
    }
    NodesOnlyMesh<SPACE_DIM>::SetUpBoxCollection(cutOffLength, domainSize, PETSC_DECIDE, mIsDimPeriodic);
 
    this->AddNodesToBoxes();
}
 
template<unsigned SPACE_DIM>
c_vector<double, SPACE_DIM> PeriodicNodesOnlyMesh<SPACE_DIM>::GetPeriodicWidths() const
{
    return mWidth;
}
 
template<unsigned SPACE_DIM>
double PeriodicNodesOnlyMesh<SPACE_DIM>::GetWidth(const unsigned& rDimension) const
{
    double width = 0.0;
    assert(rDimension < SPACE_DIM);
 
    if ( !mIsDimPeriodic[rDimension] )
    {
        // If we are not a periodic dimension, we just return the width
        width = MutableMesh<SPACE_DIM,SPACE_DIM>::GetWidth(rDimension);
    }
    else
    {
        width = mWidth[rDimension];
    }
    return width;
}
 
template<unsigned SPACE_DIM>
void PeriodicNodesOnlyMesh<SPACE_DIM>::SetNode(unsigned nodeIndex, ChastePoint<SPACE_DIM> point, bool concreteMove)
{
    // concreteMove should always be false for NodesOnlyMesh as no elements to check
    assert(!concreteMove);
 
    c_vector<double, SPACE_DIM>& point_coord = point.rGetLocation();
 
    // Loop over the periodic dimensions and perform a periodic movement if necessary
    for ( unsigned i = 0; i < SPACE_DIM; i++ )
    {
        if ( mIsDimPeriodic[i] )
        {
            double local_point_coord = point_coord(i);
            double local_width = mWidth[i];
            // We need to make sure that the fudge factor is greater than the one used to calculate the containing
            // box in distributed box collection. Otherwise the forced domain width causes issues at the right domain edge.
            double fudge_factor = 1.0e-13;
            if ( local_point_coord >= local_width )
            {
                double new_coord = local_point_coord - local_width;
 
                point.SetCoordinate(i,new_coord);
            }
            else if ( local_point_coord > (local_width-fudge_factor))
            {
                // This is to ensure that the position is never equal to mWidth, which would be outside the box domain.
                // This is due to the fact that mWidth-1e-16=mWidth
                point.SetCoordinate(i,local_width-fudge_factor);
            }
            else if ( local_point_coord < 0.0 )
            {
                double new_coord = local_point_coord + local_width;
 
                // This is to ensure that the position is never equal to mWidth, which would be outside the box domain.
                // This is due to the fact that mWidth-1e-16=mWidth
                if ( new_coord > local_width-fudge_factor )
                {
                    new_coord = local_width-fudge_factor;
                }
                point.SetCoordinate(i, new_coord);
            }
        }
    }
 
    // Update the node's location
    this->GetNode(nodeIndex)->SetPoint(point);
}
 
template<unsigned SPACE_DIM>
unsigned PeriodicNodesOnlyMesh<SPACE_DIM>::AddNode(Node<SPACE_DIM>* pNewNode)
{
    // Call method on parent class
    unsigned node_index = NodesOnlyMesh<SPACE_DIM>::AddNode(pNewNode);
 
    // If necessary move it to be back on the cylinder
    ChastePoint<SPACE_DIM> new_node_point = pNewNode->GetPoint();
    SetNode(node_index, new_node_point);
 
    return node_index;
 
}
 
template<unsigned SPACE_DIM>
c_vector<double, SPACE_DIM> PeriodicNodesOnlyMesh<SPACE_DIM>::GetVectorFromAtoB(const c_vector<double, SPACE_DIM>& rLocation1, const c_vector<double, SPACE_DIM>& rLocation2)
{
    c_vector<double, SPACE_DIM> vector = rLocation2 - rLocation1;
 
    // Loop over the periodic dimensions and measure across boundaries
    // if points are more than halfway across the width apart
    for ( unsigned i = 0; i < SPACE_DIM; i++ )
    {
        if ( mIsDimPeriodic[i] )
        {
            vector(i) = fmod(vector(i),mWidth[i]);
            if ( vector(i) > 0.5*mWidth[i] )
            {
                vector(i) -= mWidth[i];
            }
            else if (vector(i) < -0.5*mWidth[i] )
            {
                vector(i) += mWidth[i];
            }
        }
    }
 
    return vector;
}
 
// Refresh mesh -> Check and then move if outside box
template<unsigned SPACE_DIM>
void PeriodicNodesOnlyMesh<SPACE_DIM>::RefreshMesh()
{
    // Loop over the periodic dimensions and if they are
    // outside the domain, get the fmod and relocate
    for ( typename std::vector<Node<SPACE_DIM> *>::iterator it_node = this->mNodes.begin();
            it_node != this->mNodes.end(); ++it_node )
    {
        c_vector<double,SPACE_DIM> & location = (*it_node)->rGetModifiableLocation();
 
        for ( unsigned i = 0; i < SPACE_DIM; i++ )
        {
            if ( mIsDimPeriodic[i] )
            {
                if ( location(i) < 0.0 )
                {
                    location(i) = fmod( location(i), mWidth[i] ) + mWidth[i];
                }
                else if ( location(i) >= mWidth[i] )
                {
                    location(i) = fmod( location(i), mWidth[i] );
                }
            }
        }
    }
 
    // Now run the base class method
    NodesOnlyMesh<SPACE_DIM>::RefreshMesh();
}
 
// Explicit instantiation
 
template class PeriodicNodesOnlyMesh<1>;
template class PeriodicNodesOnlyMesh<2>;
template class PeriodicNodesOnlyMesh<3>;
 
// Serialization for Boost >= 1.36
#include "SerializationExportWrapperForCpp.hpp"
EXPORT_TEMPLATE_CLASS_SAME_DIMS(PeriodicNodesOnlyMesh)