Chaste Release::3.1
BuskeElasticForce.cpp
00001 /*
00002 
00003 Copyright (c) 2005-2012, University of Oxford.
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00034 */
00035 
00036 #include "BuskeElasticForce.hpp"
00037 
00038 template<unsigned DIM>
00039 BuskeElasticForce<DIM>::BuskeElasticForce()
00040    : AbstractTwoBodyInteractionForce<DIM>(),
00041      mDeformationEnergyParameter(4.0/(3.0*5.0)) // Denoted by D in Buske et al (2011) (doi:10.1371/journal.pcbi.1001045).
00042 {
00043 }
00044 
00045 template<unsigned DIM>
00046 double BuskeElasticForce<DIM>::GetDeformationEnergyParameter()
00047 {
00048     return mDeformationEnergyParameter;
00049 }
00050 
00051 template<unsigned DIM>
00052 void BuskeElasticForce<DIM>::SetDeformationEnergyParameter(double deformationEnergyParameter)
00053 {
00054     mDeformationEnergyParameter = deformationEnergyParameter;
00055 }
00056 
00057 template<unsigned DIM>
00058 c_vector<double, DIM> BuskeElasticForce<DIM>::CalculateForceBetweenNodes(unsigned nodeAGlobalIndex,
00059                                                                              unsigned nodeBGlobalIndex,
00060                                                                              AbstractCellPopulation<DIM>& rCellPopulation)
00061 {
00062     // This force class is defined for NodeBasedCellPopulations only
00063     assert(dynamic_cast<NodeBasedCellPopulation<DIM>*>(&rCellPopulation) != NULL);
00064 
00065     // We should only ever calculate the force between two distinct nodes
00066     assert(nodeAGlobalIndex != nodeBGlobalIndex);
00067 
00068     // Get the node locations
00069     c_vector<double, DIM> node_a_location = rCellPopulation.GetNode(nodeAGlobalIndex)->rGetLocation();
00070     c_vector<double, DIM> node_b_location = rCellPopulation.GetNode(nodeBGlobalIndex)->rGetLocation();
00071 
00072     // Get the unit vector parallel to the line joining the two nodes (assuming no periodicities etc.)
00073     c_vector<double, DIM> unit_vector = node_b_location - node_a_location;
00074 
00075     // Calculate the distance between the two nodes
00076     double distance_between_nodes = norm_2(unit_vector);
00077 
00078     // Account for any cutoff in the force law
00079     if (this->mUseCutOffLength)
00080     {
00081         if (distance_between_nodes >= this->GetCutOffLength())
00082         {
00083             return zero_vector<double>(DIM);
00084         }
00085     }
00086 
00087     // Assert that the nodes are a finite, non-zero distance apart
00088     assert(distance_between_nodes > 0);
00089     assert(!std::isnan(distance_between_nodes));
00090 
00091     // Normalize the unit vector
00092     unit_vector /= distance_between_nodes;
00093 
00094     // Get the cell radii
00095     NodesOnlyMesh<DIM>& r_mesh = static_cast<NodeBasedCellPopulation<DIM>*>(&rCellPopulation)->rGetMesh();
00096     double radius_of_cell_one = r_mesh.GetCellRadius(nodeAGlobalIndex);
00097     double radius_of_cell_two = r_mesh.GetCellRadius(nodeBGlobalIndex);
00098 
00099     // Compute the force vector
00100     c_vector<double, DIM> force_between_nodes = GetMagnitudeOfForce(distance_between_nodes,radius_of_cell_one,radius_of_cell_two) * unit_vector;
00101 
00102     return force_between_nodes;
00103 }
00104 
00105 template<unsigned DIM>
00106 double BuskeElasticForce<DIM>::GetMagnitudeOfForce(double distanceBetweenNodes, double radiusOfCellOne, double radiusOfCellTwo)
00107 {
00108     // Calculate contribution from deformation interaction energy
00109     double dWDdd;
00110 
00111     if (distanceBetweenNodes < radiusOfCellOne + radiusOfCellTwo)
00112     {
00113         dWDdd = -pow(radiusOfCellOne + radiusOfCellTwo - distanceBetweenNodes,1.5)
00114                 *pow(radiusOfCellOne*radiusOfCellTwo/(radiusOfCellOne+radiusOfCellTwo),0.5)
00115                 /mDeformationEnergyParameter;
00116     }
00117     else  // no deformation energy contribution as too far apart
00118     {
00119         dWDdd = 0.0;
00120     }
00121 
00122     return dWDdd; //
00123 }
00124 
00125 template<unsigned DIM>
00126 void BuskeElasticForce<DIM>::OutputForceParameters(out_stream& rParamsFile)
00127 {
00128     *rParamsFile << "\t\t\t<DeformationEnergyParameter>" << mDeformationEnergyParameter << "</DeformationEnergyParameter>\n";
00129 
00130     // Call method on direct parent class
00131     AbstractTwoBodyInteractionForce<DIM>::OutputForceParameters(rParamsFile);
00132 }
00133 
00135 // Explicit instantiation
00137 
00138 template class BuskeElasticForce<1>;
00139 template class BuskeElasticForce<2>;
00140 template class BuskeElasticForce<3>;
00141 
00142 // Serialization for Boost >= 1.36
00143 #include "SerializationExportWrapperForCpp.hpp"
00144 EXPORT_TEMPLATE_CLASS_SAME_DIMS(BuskeElasticForce)