Chaste Commit::baa90ac2819b962188b7562f2326be23c47859a7
CryptSimulationBoundaryCondition.cpp
1/*
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3Copyright (c) 2005-2024, University of Oxford.
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34*/
35
36#include "CryptSimulationBoundaryCondition.hpp"
37#include "WntConcentration.hpp"
38#include "AbstractCentreBasedCellPopulation.hpp"
39#include "RandomNumberGenerator.hpp"
40#include "StemCellProliferativeType.hpp"
41
42template<unsigned DIM>
48
49template<unsigned DIM>
50void 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 */
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 */
150 }
151 }
152 assert(p_node->rGetLocation()[DIM-1] >= 0.0);
153 }
154 }
155}
156
157template<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
187template<unsigned DIM>
189{
190 mUseJiggledBottomCells = useJiggledBottomCells;
191}
192
193template<unsigned DIM>
195{
196 return mUseJiggledBottomCells;
197}
198
199template<unsigned DIM>
201{
202 *rParamsFile << "\t\t<UseJiggledBottomCells>" << mUseJiggledBottomCells << "</UseJiggledBottomCells>\n";
204 // Call method on direct parent class
206}
207
208// Explicit instantiation
212
213// Serialization for Boost >= 1.36
#define EXPORT_TEMPLATE_CLASS_SAME_DIMS(CLASS)
virtual void OutputCellPopulationBoundaryConditionParameters(out_stream &rParamsFile)=0
CryptSimulationBoundaryCondition(AbstractCellPopulation< DIM > *pCellPopulation)
void SetUseJiggledBottomCells(bool useJiggledBottomCells)
void OutputCellPopulationBoundaryConditionParameters(out_stream &rParamsFile)
void ImposeBoundaryCondition(const std::map< Node< DIM > *, c_vector< double, DIM > > &rOldLocations)
Definition Node.hpp:59
c_vector< double, SPACE_DIM > & rGetModifiableLocation()
Definition Node.cpp:151
const c_vector< double, SPACE_DIM > & rGetLocation() const
Definition Node.cpp:139
static RandomNumberGenerator * Instance()
static WntConcentration * Instance()
static void Destroy()