Chaste Commit::ca8ccdedf819b6e02855bc0e8e6f50bdecbc5208
SurfaceAreaConstraintPottsUpdateRule.cpp
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34*/
35
36#include "SurfaceAreaConstraintPottsUpdateRule.hpp"
37
38template<unsigned DIM>
41 mDeformationEnergyParameter(0.5), // Educated guess
42 mMatureCellTargetSurfaceArea(16.0) // Defaults to a 4*4 cell size
43{
45}
46
47template<unsigned DIM>
51
52template<unsigned DIM>
54 unsigned targetNodeIndex,
55 PottsBasedCellPopulation<DIM>& rCellPopulation)
56{
57 double delta_H = 0.0;
58
59 // This method only works in 2D and 3D at present
60 assert(DIM == 2 || DIM == 3); // LCOV_EXCL_LINE
61
62 std::set<unsigned> containing_elements = rCellPopulation.GetNode(currentNodeIndex)->rGetContainingElementIndices();
63 std::set<unsigned> new_location_containing_elements = rCellPopulation.GetNode(targetNodeIndex)->rGetContainingElementIndices();
64
65 bool current_node_contained = !containing_elements.empty();
66 bool target_node_contained = !new_location_containing_elements.empty();
67
68 // Every node must each be in at most one element
69 assert(new_location_containing_elements.size() < 2);
70
71 if (!current_node_contained && !target_node_contained)
72 {
73 EXCEPTION("At least one of the current node or target node must be in an element.");
74 }
75
76 if (current_node_contained && target_node_contained)
77 {
78 if (*(new_location_containing_elements.begin()) == *(containing_elements.begin()))
79 {
80 EXCEPTION("The current node and target node must not be in the same element.");
81 }
82 }
83
84 // Iterate over nodes neighbouring the target node to work out the change in surface area
85 unsigned neighbours_in_same_element_as_current_node = 0;
86 unsigned neighbours_in_same_element_as_target_node = 0;
87 std::set<unsigned> target_neighbouring_node_indices = rCellPopulation.rGetMesh().GetVonNeumannNeighbouringNodeIndices(targetNodeIndex);
88 for (std::set<unsigned>::iterator iter = target_neighbouring_node_indices.begin();
89 iter != target_neighbouring_node_indices.end();
90 ++iter)
91 {
92 std::set<unsigned> neighbouring_node_containing_elements = rCellPopulation.rGetMesh().GetNode(*iter)->rGetContainingElementIndices();
93
94 // Every node must each be in at most one element
95 assert(neighbouring_node_containing_elements.size() < 2);
96
97 bool neighbouring_node_contained = !neighbouring_node_containing_elements.empty();
98
99 if (neighbouring_node_contained && target_node_contained)
100 {
101 unsigned neighbour_element = (*neighbouring_node_containing_elements.begin());
102 unsigned target_element = (*new_location_containing_elements.begin());
103 if (target_element == neighbour_element)
104 {
105 neighbours_in_same_element_as_target_node++;
106 }
107 }
108 if (neighbouring_node_contained && current_node_contained)
109 {
110 unsigned neighbour_element = (*neighbouring_node_containing_elements.begin());
111 unsigned current_element = (*containing_elements.begin());
112 if (current_element == neighbour_element)
113 {
114 neighbours_in_same_element_as_current_node++;
115 }
116 }
117 }
118
119 if (DIM == 2)
120 {
121 assert(neighbours_in_same_element_as_current_node<5);
122 assert(neighbours_in_same_element_as_target_node<5);
123
124 double change_in_surface_area[5] = {4,2,0,-2,-4};
125
126 if (current_node_contained) // current node is in an element
127 {
128 unsigned current_element = (*containing_elements.begin());
129 double current_surface_area = rCellPopulation.rGetMesh().GetSurfaceAreaOfElement(current_element);
130 double current_surface_area_difference = current_surface_area - mMatureCellTargetSurfaceArea;
131 double current_surface_area_difference_after_switch = current_surface_area_difference + change_in_surface_area[neighbours_in_same_element_as_current_node];
132
133 delta_H += mDeformationEnergyParameter*(current_surface_area_difference_after_switch*current_surface_area_difference_after_switch - current_surface_area_difference*current_surface_area_difference);
134 }
135 if (target_node_contained) // target node is in an element
136 {
137 unsigned target_element = (*new_location_containing_elements.begin());
138 double target_surface_area = rCellPopulation.rGetMesh().GetSurfaceAreaOfElement(target_element);
139 double target_surface_area_difference = target_surface_area - mMatureCellTargetSurfaceArea;
140 double target_surface_area_difference_after_switch = target_surface_area_difference - change_in_surface_area[neighbours_in_same_element_as_target_node];
141
142 delta_H += mDeformationEnergyParameter*(target_surface_area_difference_after_switch*target_surface_area_difference_after_switch - target_surface_area_difference*target_surface_area_difference);
143 }
144 }
145 else if (DIM==3)
146 {
147 assert(neighbours_in_same_element_as_current_node < 7);
148 assert(neighbours_in_same_element_as_target_node < 7);
149
150 double change_in_surface_area[7] = {6,4,2,0,-2,-4,-6};
151
152 if (current_node_contained) // current node is in an element
153 {
154 unsigned current_element = (*containing_elements.begin());
155 double current_surface_area = rCellPopulation.rGetMesh().GetSurfaceAreaOfElement(current_element);
156 double current_surface_area_difference = current_surface_area - mMatureCellTargetSurfaceArea;
157 double current_surface_area_difference_after_switch = current_surface_area_difference + change_in_surface_area[neighbours_in_same_element_as_current_node];
158
159 delta_H += mDeformationEnergyParameter*(current_surface_area_difference_after_switch*current_surface_area_difference_after_switch - current_surface_area_difference*current_surface_area_difference);
160 }
161 if (target_node_contained) // target node is in an element
162 {
163 unsigned target_element = (*new_location_containing_elements.begin());
164 double target_surface_area = rCellPopulation.rGetMesh().GetSurfaceAreaOfElement(target_element);
165 double target_surface_area_difference = target_surface_area - mMatureCellTargetSurfaceArea;
166 double target_surface_area_difference_after_switch = target_surface_area_difference - change_in_surface_area[neighbours_in_same_element_as_target_node];
167
168 delta_H += mDeformationEnergyParameter*(target_surface_area_difference_after_switch*target_surface_area_difference_after_switch - target_surface_area_difference*target_surface_area_difference);
169 }
170 }
171
172 return delta_H;
173}
174
175template<unsigned DIM>
177{
178 return mDeformationEnergyParameter;
179}
180
181template<unsigned DIM>
183{
184 mDeformationEnergyParameter = deformationEnergyParameter;
185}
186
187template<unsigned DIM>
189{
190 return mMatureCellTargetSurfaceArea;
191}
192
193template<unsigned DIM>
195{
196 assert(matureCellTargetSurfaceArea >= 0.0);
197 mMatureCellTargetSurfaceArea = matureCellTargetSurfaceArea;
198}
199
200template<unsigned DIM>
202{
203 *rParamsFile << "\t\t\t<DeformationEnergyParameter>" << mDeformationEnergyParameter << "</DeformationEnergyParameter>\n";
204 *rParamsFile << "\t\t\t<MatureCellTargetSurfaceArea>" << mMatureCellTargetSurfaceArea << "</MatureCellTargetSurfaceArea>\n";
205
206 // Call method on direct parent class
208}
209
210// Explicit instantiation
214
215// Serialization for Boost >= 1.36
#define EXCEPTION(message)
#define EXPORT_TEMPLATE_CLASS_SAME_DIMS(CLASS)
virtual void OutputUpdateRuleParameters(out_stream &rParamsFile)
std::set< unsigned > & rGetContainingElementIndices()
Definition Node.cpp:300
Node< DIM > * GetNode(unsigned index)
void SetDeformationEnergyParameter(double deformationEnergyParameter)
void SetMatureCellTargetSurfaceArea(double matureCellTargetSurfaceArea)
double EvaluateHamiltonianContribution(unsigned currentNodeIndex, unsigned targetNodeIndex, PottsBasedCellPopulation< DIM > &rCellPopulation)