Chaste  Release::3.4
CryptSimulationBoundaryCondition.cpp
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35 
36 #include "CryptSimulationBoundaryCondition.hpp"
37 #include "WntConcentration.hpp"
38 #include "AbstractCentreBasedCellPopulation.hpp"
39 #include "RandomNumberGenerator.hpp"
40 #include "StemCellProliferativeType.hpp"
41 
42 template<unsigned DIM>
44  : AbstractCellPopulationBoundaryCondition<DIM>(pCellPopulation),
45  mUseJiggledBottomCells(false)
46 {
47 }
48 
49 template<unsigned DIM>
50 void CryptSimulationBoundaryCondition<DIM>::ImposeBoundaryCondition(const std::map<Node<DIM>*, c_vector<double, DIM> >& rOldLocations)
51 {
52  // We only allow jiggling of bottom cells in 2D
53  if (DIM == 1)
54  {
55  mUseJiggledBottomCells = false;
56  }
57 
58  // Check whether a WntConcentration singleton has been set up
59  bool is_wnt_included = WntConcentration<DIM>::Instance()->IsWntSetUp();
60  if (!is_wnt_included)
61  {
63  }
64 
65  // We iterate differently depending on whether we are using a centre- or vertex-based model
66  if (dynamic_cast<AbstractCentreBasedCellPopulation<DIM>*>(this->mpCellPopulation))
67  {
68  // Iterate over all nodes associated with real cells to update their positions
69  for (typename AbstractCellPopulation<DIM>::Iterator cell_iter = this->mpCellPopulation->Begin();
70  cell_iter != this->mpCellPopulation->End();
71  ++cell_iter)
72  {
73  // Get index of node associated with cell
74  unsigned node_index = this->mpCellPopulation->GetLocationIndexUsingCell(*cell_iter);
75 
76  // Get pointer to this node
77  Node<DIM>* p_node = this->mpCellPopulation->GetNode(node_index);
78 
79  if (!is_wnt_included)
80  {
81  /*
82  * If WntConcentration is not set up then stem cells must be pinned,
83  * so we reset the location of each stem cell.
84  */
85  if (cell_iter->GetCellProliferativeType()->template IsType<StemCellProliferativeType>())
86  {
87  // Get old node location
88  c_vector<double, DIM> old_node_location = rOldLocations.find(p_node)->second;
89 
90  // Return node to old location
91  p_node->rGetModifiableLocation() = old_node_location;
92  }
93  }
94 
95  // Any cell that has moved below the bottom of the crypt must be moved back up
96  if (p_node->rGetLocation()[DIM-1] < 0.0)
97  {
98  p_node->rGetModifiableLocation()[DIM-1] = 0.0;
99 
100  if (mUseJiggledBottomCells)
101  {
102  /*
103  * Here we give the cell a push upwards so that it doesn't
104  * get stuck on the bottom of the crypt (as per #422).
105  *
106  * Note that all stem cells may get moved to the same height, so
107  * we use a random perturbation to help ensure we are not simply
108  * faced with the same problem at a different height!
109  */
110  p_node->rGetModifiableLocation()[DIM-1] = 0.05*RandomNumberGenerator::Instance()->ranf();
111  }
112  }
113  assert(p_node->rGetLocation()[DIM-1] >= 0.0);
114  }
115  }
116  else
117  {
118  // Iterate over all nodes to update their positions
119  for (unsigned node_index=0; node_index<this->mpCellPopulation->GetNumNodes(); node_index++)
120  {
121  // Get pointer to this node
122  Node<DIM>* p_node = this->mpCellPopulation->GetNode(node_index);
123 
124  if (!is_wnt_included)
125  {
126  /*
127  * If WntConcentration is not set up then stem cells must be pinned,
128  * so we reset the location of each node whose height was close to zero.
129  */
130  double node_height = rOldLocations.find(p_node)->second[DIM-1];
131  if (node_height < DBL_EPSILON)
132  {
133  // Return node to its old height, but allow it to slide left or right
134  p_node->rGetModifiableLocation()[DIM-1] = node_height;
135  }
136  }
137 
138  // Any node that has moved below the bottom of the crypt must be moved back up
139  if (p_node->rGetLocation()[DIM-1] < 0.0)
140  {
141  p_node->rGetModifiableLocation()[DIM-1] = 0.0;
142 
143  if (mUseJiggledBottomCells)
144  {
145  /*
146  * Here we give the node a push upwards so that it doesn't
147  * get stuck on the bottom of the crypt.
148  */
149  p_node->rGetModifiableLocation()[DIM-1] = 0.05*RandomNumberGenerator::Instance()->ranf();
150  }
151  }
152  assert(p_node->rGetLocation()[DIM-1] >= 0.0);
153  }
154  }
155 }
156 
157 template<unsigned DIM>
159 {
160  bool boundary_condition_satisfied = true;
161 
162  /*
163  * Here we verify that the boundary condition is still satisfied by simply
164  * checking that no cells lies below the y=0 boundary.
165  */
166  for (typename AbstractCellPopulation<DIM>::Iterator cell_iter = this->mpCellPopulation->Begin();
167  cell_iter != this->mpCellPopulation->End();
168  ++cell_iter)
169  {
170  // Get index of node associated with cell
171  unsigned node_index = this->mpCellPopulation->GetLocationIndexUsingCell(*cell_iter);
172 
173  // Get pointer to this node
174  Node<DIM>* p_node = this->mpCellPopulation->GetNode(node_index);
175 
176  // If this node lies below the y=0 boundary, break and return false
177  if (p_node->rGetLocation()[DIM-1] < 0.0)
178  {
179  boundary_condition_satisfied = false;
180  break;
181  }
182  }
183 
184  return boundary_condition_satisfied;
185 }
186 
187 template<unsigned DIM>
189 {
190  mUseJiggledBottomCells = useJiggledBottomCells;
191 }
192 
193 template<unsigned DIM>
195 {
196  return mUseJiggledBottomCells;
197 }
198 
199 template<unsigned DIM>
201 {
202  *rParamsFile << "\t\t<UseJiggledBottomCells>" << mUseJiggledBottomCells << "</UseJiggledBottomCells>\n";
204  // Call method on direct parent class
206 }
207 
212 
213 // Serialization for Boost >= 1.36
Definition: Node.hpp:58
static void Destroy()
void ImposeBoundaryCondition(const std::map< Node< DIM > *, c_vector< double, DIM > > &rOldLocations)
#define EXPORT_TEMPLATE_CLASS_SAME_DIMS(CLASS)
static WntConcentration * Instance()
CryptSimulationBoundaryCondition(AbstractCellPopulation< DIM > *pCellPopulation)
static RandomNumberGenerator * Instance()
const c_vector< double, SPACE_DIM > & rGetLocation() const
Definition: Node.cpp:140
void SetUseJiggledBottomCells(bool useJiggledBottomCells)
void OutputCellPopulationBoundaryConditionParameters(out_stream &rParamsFile)
c_vector< double, SPACE_DIM > & rGetModifiableLocation()
Definition: Node.cpp:152
virtual void OutputCellPopulationBoundaryConditionParameters(out_stream &rParamsFile)=0