Chaste Commit::baa90ac2819b962188b7562f2326be23c47859a7
PlaneBoundaryCondition.cpp
1/*
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34*/
35
36#include "PlaneBoundaryCondition.hpp"
37#include "AbstractCentreBasedCellPopulation.hpp"
38#include "VertexBasedCellPopulation.hpp"
39
40template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
42 c_vector<double, SPACE_DIM> point,
43 c_vector<double, SPACE_DIM> normal)
44 : AbstractCellPopulationBoundaryCondition<ELEMENT_DIM,SPACE_DIM>(pCellPopulation),
45 mPointOnPlane(point),
46 mUseJiggledNodesOnPlane(false)
47{
48 assert(norm_2(normal) > 0.0);
49 mNormalToPlane = normal/norm_2(normal);
50}
51
52template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
54{
55 return mPointOnPlane;
56}
57
58template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
60{
61 return mNormalToPlane;
62}
63
64
65template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
67{
68 mUseJiggledNodesOnPlane = useJiggledNodesOnPlane;
69}
70
71template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
73{
74 return mUseJiggledNodesOnPlane;
75}
76
77template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
79 [[maybe_unused]] const std::map<Node<SPACE_DIM>*, c_vector<double, SPACE_DIM> >& rOldLocations)
80{
81 if constexpr ((SPACE_DIM == 2) || (SPACE_DIM == 3))
82 {
84 if (dynamic_cast<AbstractOffLatticeCellPopulation<ELEMENT_DIM,SPACE_DIM>*>(this->mpCellPopulation)==nullptr)
85 {
86 EXCEPTION("PlaneBoundaryCondition requires a subclass of AbstractOffLatticeCellPopulation.");
87 }
88
89 assert((dynamic_cast<AbstractCentreBasedCellPopulation<ELEMENT_DIM,SPACE_DIM>*>(this->mpCellPopulation))
90 || (SPACE_DIM==ELEMENT_DIM && (dynamic_cast<VertexBasedCellPopulation<SPACE_DIM>*>(this->mpCellPopulation))) );
91
92 // This is a magic number
93 double max_jiggle = 1e-4;
94
95 if (dynamic_cast<AbstractCentreBasedCellPopulation<ELEMENT_DIM,SPACE_DIM>*>(this->mpCellPopulation))
96 {
97 for (typename AbstractCellPopulation<ELEMENT_DIM,SPACE_DIM>::Iterator cell_iter = this->mpCellPopulation->Begin();
98 cell_iter != this->mpCellPopulation->End();
99 ++cell_iter)
100 {
101 unsigned node_index = this->mpCellPopulation->GetLocationIndexUsingCell(*cell_iter);
102 Node<SPACE_DIM>* p_node = this->mpCellPopulation->GetNode(node_index);
103
104 c_vector<double, SPACE_DIM> node_location = p_node->rGetLocation();
105
106 double signed_distance = inner_prod(node_location - mPointOnPlane, mNormalToPlane);
107 if (signed_distance > 0.0)
108 {
109 // For the closest point on the plane we travel from node_location the signed_distance in the direction of -mNormalToPlane
110 c_vector<double, SPACE_DIM> nearest_point;
111 if (mUseJiggledNodesOnPlane)
112 {
113 nearest_point = node_location - (signed_distance+max_jiggle*RandomNumberGenerator::Instance()->ranf())*mNormalToPlane;
114 }
115 else
116 {
117 nearest_point = node_location - signed_distance*mNormalToPlane;
118 }
119 p_node->rGetModifiableLocation() = nearest_point;
120 }
121 }
122 }
123 else
124 {
125 assert(SPACE_DIM == ELEMENT_DIM); // LCOV_EXCL_LINE
126 assert(dynamic_cast<VertexBasedCellPopulation<SPACE_DIM>*>(this->mpCellPopulation));
127
128 // Iterate over all nodes and update their positions according to the boundary conditions
129 unsigned num_nodes = this->mpCellPopulation->GetNumNodes();
130 for (unsigned node_index=0; node_index<num_nodes; node_index++)
131 {
132 Node<SPACE_DIM>* p_node = this->mpCellPopulation->GetNode(node_index);
133 c_vector<double, SPACE_DIM> node_location = p_node->rGetLocation();
134
135 double signed_distance = inner_prod(node_location - mPointOnPlane, mNormalToPlane);
136 if (signed_distance > 0.0)
137 {
138 // For the closest point on the plane we travel from node_location the signed_distance in the direction of -mNormalToPlane
139 c_vector<double, SPACE_DIM> nearest_point;
140 if (mUseJiggledNodesOnPlane)
141 {
142 nearest_point = node_location - (signed_distance+max_jiggle*RandomNumberGenerator::Instance()->ranf())*mNormalToPlane;
143 }
144 else
145 {
146 nearest_point = node_location - signed_distance*mNormalToPlane;
147 }
148 p_node->rGetModifiableLocation() = nearest_point;
149 }
150 }
151 }
152 }
153 else
154 {
156 }
157}
158
159template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
161{
162 bool condition_satisfied = true;
163
164 if (SPACE_DIM == 1)
165 {
166 EXCEPTION("PlaneBoundaryCondition is not implemented in 1D");
167 }
168 else
169 {
170 for (typename AbstractCellPopulation<ELEMENT_DIM, SPACE_DIM>::Iterator cell_iter = this->mpCellPopulation->Begin();
171 cell_iter != this->mpCellPopulation->End();
172 ++cell_iter)
173 {
174 c_vector<double, SPACE_DIM> cell_location = this->mpCellPopulation->GetLocationOfCellCentre(*cell_iter);
175
176 if (inner_prod(cell_location - mPointOnPlane, mNormalToPlane) > 0.0)
177 {
178 condition_satisfied = false;
179 break;
180 }
181 }
182 }
183
184 return condition_satisfied;
185}
186
187template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
189{
190 *rParamsFile << "\t\t\t<PointOnPlane>";
191 for (unsigned index=0; index != SPACE_DIM-1U; index++) // Note: inequality avoids testing index < 0U when DIM=1
192 {
193 *rParamsFile << mPointOnPlane[index] << ",";
194 }
195 *rParamsFile << mPointOnPlane[SPACE_DIM-1] << "</PointOnPlane>\n";
196
197 *rParamsFile << "\t\t\t<NormalToPlane>";
198 for (unsigned index=0; index != SPACE_DIM-1U; index++) // Note: inequality avoids testing index < 0U when DIM=1
199 {
200 *rParamsFile << mNormalToPlane[index] << ",";
201 }
202 *rParamsFile << mNormalToPlane[SPACE_DIM-1] << "</NormalToPlane>\n";
203 *rParamsFile << "\t\t\t<UseJiggledNodesOnPlane>" << mUseJiggledNodesOnPlane << "</UseJiggledNodesOnPlane>\n";
204
205 // Call method on direct parent class
207}
208
209// Explicit instantiation
210template class PlaneBoundaryCondition<1,1>;
211template class PlaneBoundaryCondition<1,2>;
212template class PlaneBoundaryCondition<2,2>;
213template class PlaneBoundaryCondition<1,3>;
214template class PlaneBoundaryCondition<2,3>;
215template class PlaneBoundaryCondition<3,3>;
216
217// Serialization for Boost >= 1.36
#define EXCEPTION(message)
#define NEVER_REACHED
#define EXPORT_TEMPLATE_CLASS_ALL_DIMS(CLASS)
virtual void OutputCellPopulationBoundaryConditionParameters(out_stream &rParamsFile)=0
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
const c_vector< double, SPACE_DIM > & rGetNormalToPlane() const
void ImposeBoundaryCondition(const std::map< Node< SPACE_DIM > *, c_vector< double, SPACE_DIM > > &rOldLocations)
void OutputCellPopulationBoundaryConditionParameters(out_stream &rParamsFile)
PlaneBoundaryCondition(AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > *pCellPopulation, c_vector< double, SPACE_DIM > point, c_vector< double, SPACE_DIM > normal)
c_vector< double, SPACE_DIM > mNormalToPlane
const c_vector< double, SPACE_DIM > & rGetPointOnPlane() const
void SetUseJiggledNodesOnPlane(bool useJiggledNodesOnPlane)
static RandomNumberGenerator * Instance()