Chaste  Release::3.4
SurfaceAreaConstraintPottsUpdateRule.cpp
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35 
36 #include "SurfaceAreaConstraintPottsUpdateRule.hpp"
37 
38 template<unsigned DIM>
40  : AbstractPottsUpdateRule<DIM>(),
41  mDeformationEnergyParameter(0.5), // Educated guess
42  mMatureCellTargetSurfaceArea(16.0) // Defaults to a 4*4 cell size
43 {
45 }
46 
47 template<unsigned DIM>
49 {
50 }
51 
52 template<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);
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 
175 template<unsigned DIM>
177 {
178  return mDeformationEnergyParameter;
179 }
180 
181 template<unsigned DIM>
183 {
184  mDeformationEnergyParameter = deformationEnergyParameter;
185 }
186 
187 template<unsigned DIM>
189 {
190  return mMatureCellTargetSurfaceArea;
191 }
192 
193 template<unsigned DIM>
195 {
196  assert(matureCellTargetSurfaceArea >= 0.0);
197  mMatureCellTargetSurfaceArea = matureCellTargetSurfaceArea;
198 }
199 
200 template<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 
214 
215 // Serialization for Boost >= 1.36
Node< DIM > * GetNode(unsigned index)
#define EXCEPTION(message)
Definition: Exception.hpp:143
double EvaluateHamiltonianContribution(unsigned currentNodeIndex, unsigned targetNodeIndex, PottsBasedCellPopulation< DIM > &rCellPopulation)
void SetMatureCellTargetSurfaceArea(double matureCellTargetSurfaceArea)
void SetDeformationEnergyParameter(double deformationEnergyParameter)
#define EXPORT_TEMPLATE_CLASS_SAME_DIMS(CLASS)
virtual void OutputUpdateRuleParameters(out_stream &rParamsFile)=0