Chaste  Release::2018.1
VolumeConstraintPottsUpdateRule.cpp
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35 
36 #include "VolumeConstraintPottsUpdateRule.hpp"
37 
38 template<unsigned DIM>
40  : AbstractPottsUpdateRule<DIM>(),
41  mDeformationEnergyParameter(0.5), // Educated guess
42  mMatureCellTargetVolume(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  std::set<unsigned> containing_elements = rCellPopulation.GetNode(currentNodeIndex)->rGetContainingElementIndices();
60  std::set<unsigned> new_location_containing_elements = rCellPopulation.GetNode(targetNodeIndex)->rGetContainingElementIndices();
61 
62  bool current_node_contained = !containing_elements.empty();
63  bool target_node_contained = !new_location_containing_elements.empty();
64 
65  // Every node must each be in at most one element
66  assert(new_location_containing_elements.size() < 2);
67 
68  if (!current_node_contained && !target_node_contained)
69  {
70  EXCEPTION("At least one of the current node or target node must be in an element.");
71  }
72 
73  if (current_node_contained && target_node_contained)
74  {
75  if (*(new_location_containing_elements.begin()) == *(containing_elements.begin()))
76  {
77  EXCEPTION("The current node and target node must not be in the same element.");
78  }
79  }
80 
81  if (current_node_contained) // current node is in an element
82  {
83  unsigned current_element = (*containing_elements.begin());
84  double current_volume = rCellPopulation.rGetMesh().GetVolumeOfElement(current_element);
85  double current_volume_difference = current_volume - mMatureCellTargetVolume;
86 
87  delta_H += mDeformationEnergyParameter*((current_volume_difference + 1.0)*(current_volume_difference + 1.0) - current_volume_difference*current_volume_difference);
88  }
89  if (target_node_contained) // target node is in an element
90  {
91  unsigned target_element = (*new_location_containing_elements.begin());
92  double target_volume = rCellPopulation.rGetMesh().GetVolumeOfElement(target_element);
93  double target_volume_difference = target_volume - mMatureCellTargetVolume;
94 
95  delta_H += mDeformationEnergyParameter*((target_volume_difference - 1.0)*(target_volume_difference - 1.0) - target_volume_difference*target_volume_difference);
96  }
97 
98  return delta_H;
99 }
100 
101 template<unsigned DIM>
103 {
104  return mDeformationEnergyParameter;
105 }
106 
107 template<unsigned DIM>
109 {
110  mDeformationEnergyParameter = deformationEnergyParameter;
111 }
112 
113 template<unsigned DIM>
115 {
116  return mMatureCellTargetVolume;
117 }
118 
119 template<unsigned DIM>
121 {
122  assert(matureCellTargetVolume >= 0.0);
123  mMatureCellTargetVolume = matureCellTargetVolume;
124 }
125 
126 template<unsigned DIM>
128 {
129  *rParamsFile << "\t\t\t<DeformationEnergyParameter>" << mDeformationEnergyParameter << "</DeformationEnergyParameter>\n";
130  *rParamsFile << "\t\t\t<MatureCellTargetVolume>" << mMatureCellTargetVolume << "</MatureCellTargetVolume>\n";
131 
132  // Call method on direct parent class
134 }
135 
136 // Explicit instantiation
140 
141 // Serialization for Boost >= 1.36
virtual void OutputUpdateRuleParameters(out_stream &rParamsFile)
void SetMatureCellTargetVolume(double matureCellTargetVolume)
Node< DIM > * GetNode(unsigned index)
#define EXCEPTION(message)
Definition: Exception.hpp:143
#define EXPORT_TEMPLATE_CLASS_SAME_DIMS(CLASS)
void SetDeformationEnergyParameter(double deformationEnergyParameter)
void OutputUpdateRuleParameters(out_stream &rParamsFile)
double EvaluateHamiltonianContribution(unsigned currentNodeIndex, unsigned targetNodeIndex, PottsBasedCellPopulation< DIM > &rCellPopulation)