Chaste  Release::3.4
AdhesionPottsUpdateRule.cpp
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35 
36 #include "AdhesionPottsUpdateRule.hpp"
37 
38 template<unsigned DIM>
40  : AbstractPottsUpdateRule<DIM>(),
41  mCellCellAdhesionEnergyParameter(0.1), // Educated guess
42  mCellBoundaryAdhesionEnergyParameter(0.2) // Educated guess
43 {
44 }
45 
46 template<unsigned DIM>
48 {
49 }
50 
51 template<unsigned DIM>
53  unsigned targetNodeIndex,
54  PottsBasedCellPopulation<DIM>& rCellPopulation)
55 {
56  std::set<unsigned> containing_elements = rCellPopulation.GetNode(currentNodeIndex)->rGetContainingElementIndices();
57  std::set<unsigned> new_location_containing_elements = rCellPopulation.GetNode(targetNodeIndex)->rGetContainingElementIndices();
58 
59  bool current_node_contained = !containing_elements.empty();
60  bool target_node_contained = !new_location_containing_elements.empty();
61 
62  // Every node must each be in at most one element
63  assert(new_location_containing_elements.size() < 2);
64 
65  if (!current_node_contained && !target_node_contained)
66  {
67  EXCEPTION("At least one of the current node or target node must be in an element.");
68  }
69 
70  if (current_node_contained && target_node_contained)
71  {
72  if (*(new_location_containing_elements.begin()) == *(containing_elements.begin()))
73  {
74  EXCEPTION("The current node and target node must not be in the same element.");
75  }
76  }
77 
78  // Iterate over nodes neighbouring the target node to work out the contact energy contribution
79  double delta_H = 0.0;
80  std::set<unsigned> target_neighbouring_node_indices = rCellPopulation.rGetMesh().GetVonNeumannNeighbouringNodeIndices(targetNodeIndex);
81  for (std::set<unsigned>::iterator iter = target_neighbouring_node_indices.begin();
82  iter != target_neighbouring_node_indices.end();
83  ++iter)
84  {
85  std::set<unsigned> neighbouring_node_containing_elements = rCellPopulation.rGetMesh().GetNode(*iter)->rGetContainingElementIndices();
86 
87  // Every node must each be in at most one element
88  assert(neighbouring_node_containing_elements.size() < 2);
89 
90  bool neighbouring_node_contained = !neighbouring_node_containing_elements.empty();
91 
98  if (neighbouring_node_contained && target_node_contained)
99  {
100  unsigned neighbour_element = (*neighbouring_node_containing_elements.begin());
101  unsigned target_element = (*new_location_containing_elements.begin());
102  if (target_element != neighbour_element)
103  {
104  // The nodes are currently contained in different elements
105  delta_H -= GetCellCellAdhesionEnergy(rCellPopulation.GetCellUsingLocationIndex(target_element), rCellPopulation.GetCellUsingLocationIndex(neighbour_element));
106  }
107  }
108  else if (neighbouring_node_contained && !target_node_contained)
109  {
110  // The neighbouring node is contained in a Potts element, but the target node is not
111  unsigned neighbour_element = (*neighbouring_node_containing_elements.begin());
112  delta_H -= GetCellBoundaryAdhesionEnergy(rCellPopulation.GetCellUsingLocationIndex(neighbour_element));
113  }
114  else if (!neighbouring_node_contained && target_node_contained)
115  {
116  // The target node is contained in a Potts element, but the neighbouring node is not
117  unsigned target_element = (*new_location_containing_elements.begin());
118  delta_H -= GetCellBoundaryAdhesionEnergy(rCellPopulation.GetCellUsingLocationIndex(target_element));
119  }
120 
127  if (neighbouring_node_contained && current_node_contained)
128  {
129  unsigned neighbour_element = (*neighbouring_node_containing_elements.begin());
130  unsigned current_element = (*containing_elements.begin());
131  if (current_element != neighbour_element)
132  {
133  // The nodes are currently contained in different elements
134  delta_H += GetCellCellAdhesionEnergy(rCellPopulation.GetCellUsingLocationIndex(current_element),rCellPopulation.GetCellUsingLocationIndex(neighbour_element));
135  }
136  }
137  else if (neighbouring_node_contained && !current_node_contained)
138  {
139  // The neighbouring node is contained in a Potts element, but the current node is not
140  unsigned neighbour_element = (*neighbouring_node_containing_elements.begin());
141  delta_H += GetCellBoundaryAdhesionEnergy(rCellPopulation.GetCellUsingLocationIndex(neighbour_element));
142  }
143  else if (!neighbouring_node_contained && current_node_contained)
144  {
145  // The current node is contained in a Potts element, but the neighbouring node is not
146  unsigned current_element = (*containing_elements.begin());
147  delta_H += GetCellBoundaryAdhesionEnergy(rCellPopulation.GetCellUsingLocationIndex(current_element));
148  }
149  }
150 
151  return delta_H;
152 }
153 
154 template<unsigned DIM>
155 double AdhesionPottsUpdateRule<DIM>::GetCellCellAdhesionEnergy(CellPtr pCellA, CellPtr pCellB)
156 {
157  return GetCellCellAdhesionEnergyParameter();
158 }
159 
160 template<unsigned DIM>
162 {
163  return GetCellBoundaryAdhesionEnergyParameter();
164 }
165 
166 template<unsigned DIM>
168 {
169  return mCellCellAdhesionEnergyParameter;
170 }
171 
172 template<unsigned DIM>
174 {
175  return mCellBoundaryAdhesionEnergyParameter;
176 }
177 
178 template<unsigned DIM>
179 void AdhesionPottsUpdateRule<DIM>::SetCellCellAdhesionEnergyParameter(double cellCellAdhesionEnergyParameter)
180 {
181  mCellCellAdhesionEnergyParameter = cellCellAdhesionEnergyParameter;
182 }
183 
184 template<unsigned DIM>
185 void AdhesionPottsUpdateRule<DIM>::SetCellBoundaryAdhesionEnergyParameter(double cellBoundaryAdhesionEnergyParameter)
186 {
187  mCellBoundaryAdhesionEnergyParameter = cellBoundaryAdhesionEnergyParameter;
188 }
189 
190 template<unsigned DIM>
192 {
193  *rParamsFile << "\t\t\t<CellCellAdhesionEnergyParameter>" << mCellCellAdhesionEnergyParameter << "</CellCellAdhesionEnergyParameter>\n";
194  *rParamsFile << "\t\t\t<CellBoundaryAdhesionEnergyParameter>" << mCellBoundaryAdhesionEnergyParameter << "</CellBoundaryAdhesionEnergyParameter>\n";
195 
196  // Call method on direct parent class
198 }
199 
201 template class AdhesionPottsUpdateRule<1>;
202 template class AdhesionPottsUpdateRule<2>;
203 template class AdhesionPottsUpdateRule<3>;
204 
205 // Serialization for Boost >= 1.36
virtual CellPtr GetCellUsingLocationIndex(unsigned index)
Node< DIM > * GetNode(unsigned index)
virtual double GetCellCellAdhesionEnergy(CellPtr pCellA, CellPtr pCellB)
#define EXCEPTION(message)
Definition: Exception.hpp:143
void OutputUpdateRuleParameters(out_stream &rParamsFile)
virtual double GetCellBoundaryAdhesionEnergy(CellPtr pCell)
double EvaluateHamiltonianContribution(unsigned currentNodeIndex, unsigned targetNodeIndex, PottsBasedCellPopulation< DIM > &rCellPopulation)
#define EXPORT_TEMPLATE_CLASS_SAME_DIMS(CLASS)
virtual void OutputUpdateRuleParameters(out_stream &rParamsFile)=0
void SetCellBoundaryAdhesionEnergyParameter(double cellBoundaryAdhesionEnergyParameter)
void SetCellCellAdhesionEnergyParameter(double cellCellAdhesionEnergyEnergyParameter)