Chaste Commit::ca8ccdedf819b6e02855bc0e8e6f50bdecbc5208
BuskeElasticForce.cpp
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34*/
35
36#include "BuskeElasticForce.hpp"
37
38template<unsigned DIM>
41 mDeformationEnergyParameter(4.0/(3.0*5.0)) // Denoted by D in Buske et al (2011) (doi:10.1371/journal.pcbi.1001045).
42{
43}
44
45template<unsigned DIM>
47{
48 return mDeformationEnergyParameter;
49}
50
51template<unsigned DIM>
52void BuskeElasticForce<DIM>::SetDeformationEnergyParameter(double deformationEnergyParameter)
53{
54 mDeformationEnergyParameter = deformationEnergyParameter;
55}
56
57template<unsigned DIM>
58c_vector<double, DIM> BuskeElasticForce<DIM>::CalculateForceBetweenNodes(unsigned nodeAGlobalIndex,
59 unsigned nodeBGlobalIndex,
60 AbstractCellPopulation<DIM>& rCellPopulation)
61{
62 // This force class is defined for NodeBasedCellPopulations only
63 assert(dynamic_cast<NodeBasedCellPopulation<DIM>*>(&rCellPopulation) != nullptr);
64
65 // We should only ever calculate the force between two distinct nodes
66 assert(nodeAGlobalIndex != nodeBGlobalIndex);
67
68 Node<DIM>* p_node_a = rCellPopulation.GetNode(nodeAGlobalIndex);
69 Node<DIM>* p_node_b = rCellPopulation.GetNode(nodeBGlobalIndex);
70
71 // Get the node locations
72 const c_vector<double, DIM>& r_node_a_location = p_node_a->rGetLocation();
73 const c_vector<double, DIM>& r_node_b_location = p_node_b->rGetLocation();
74
75 // Get the unit vector parallel to the line joining the two nodes (assuming no periodicities etc.)
76 c_vector<double, DIM> unit_vector = r_node_b_location - r_node_a_location;
77
78 // Calculate the distance between the two nodes
79 double distance_between_nodes = norm_2(unit_vector);
80
81 // Account for any cutoff in the force law
82 if (this->mUseCutOffLength)
83 {
84 if (distance_between_nodes >= this->GetCutOffLength())
85 {
86 return zero_vector<double>(DIM);
87 }
88 }
89
90 // Assert that the nodes are a finite, non-zero distance apart
91 assert(distance_between_nodes > 0);
92 assert(!std::isnan(distance_between_nodes));
93
94 // Normalize the unit vector
95 unit_vector /= distance_between_nodes;
96
97 // Get the cell radii
98 double radius_of_cell_one = p_node_a->GetRadius();
99 double radius_of_cell_two = p_node_b->GetRadius();
100
101 // Compute the force vector
102 c_vector<double, DIM> force_between_nodes = GetMagnitudeOfForce(distance_between_nodes,radius_of_cell_one,radius_of_cell_two) * unit_vector;
103
104 return force_between_nodes;
105}
106
107template<unsigned DIM>
108double BuskeElasticForce<DIM>::GetMagnitudeOfForce(double distanceBetweenNodes, double radiusOfCellOne, double radiusOfCellTwo)
109{
110 // Calculate contribution from deformation interaction energy
111 double dWDdd;
112
113 if (distanceBetweenNodes < radiusOfCellOne + radiusOfCellTwo)
114 {
115 dWDdd = -pow(radiusOfCellOne + radiusOfCellTwo - distanceBetweenNodes,1.5)
116 *pow(radiusOfCellOne*radiusOfCellTwo/(radiusOfCellOne+radiusOfCellTwo),0.5)
117 /mDeformationEnergyParameter;
118 }
119 else // no deformation energy contribution as too far apart
120 {
121 dWDdd = 0.0;
122 }
123
124 return dWDdd; //
125}
126
127template<unsigned DIM>
129{
130 *rParamsFile << "\t\t\t<DeformationEnergyParameter>" << mDeformationEnergyParameter << "</DeformationEnergyParameter>\n";
131
132 // Call method on direct parent class
134}
135
136// Explicit instantiation
137template class BuskeElasticForce<1>;
138template class BuskeElasticForce<2>;
139template class BuskeElasticForce<3>;
140
141// Serialization for Boost >= 1.36
#define EXPORT_TEMPLATE_CLASS_SAME_DIMS(CLASS)
virtual Node< SPACE_DIM > * GetNode(unsigned index)=0
virtual void OutputForceParameters(out_stream &rParamsFile)
double GetMagnitudeOfForce(double distanceBetweenNodes, double radiusOfCellOne, double radiusOfCellTwo)
void SetDeformationEnergyParameter(double deformationEnergyParameter)
virtual void OutputForceParameters(out_stream &rParamsFile)
c_vector< double, DIM > CalculateForceBetweenNodes(unsigned nodeAGlobalIndex, unsigned nodeBGlobalIndex, AbstractCellPopulation< DIM > &rCellPopulation)
double GetDeformationEnergyParameter()
Definition Node.hpp:59
const c_vector< double, SPACE_DIM > & rGetLocation() const
Definition Node.cpp:139
double GetRadius()
Definition Node.cpp:248