Chaste Commit::baa90ac2819b962188b7562f2326be23c47859a7
BuskeElasticForce.cpp
1/*
2
3Copyright (c) 2005-2024, University of Oxford.
4All rights reserved.
5
6University of Oxford means the Chancellor, Masters and Scholars of the
7University of Oxford, having an administrative office at Wellington
8Square, Oxford OX1 2JD, UK.
9
10This file is part of Chaste.
11
12Redistribution and use in source and binary forms, with or without
13modification, are permitted provided that the following conditions are met:
14 * Redistributions of source code must retain the above copyright notice,
15 this list of conditions and the following disclaimer.
16 * Redistributions in binary form must reproduce the above copyright notice,
17 this list of conditions and the following disclaimer in the documentation
18 and/or other materials provided with the distribution.
19 * Neither the name of the University of Oxford nor the names of its
20 contributors may be used to endorse or promote products derived from this
21 software without specific prior written permission.
22
23THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
24AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
25IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
26ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
27LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
28CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
29GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
30HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
31LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
32OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
33
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