Chaste Commit::1fd4e48e3990e67db148bc1bc4cf6991a0049d0c
OffLatticeSimulation.cpp
1/*
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34*/
35
36#include "OffLatticeSimulation.hpp"
37
38#include <boost/make_shared.hpp>
39
40#include "CellBasedEventHandler.hpp"
41#include "ForwardEulerNumericalMethod.hpp"
42#include "StepSizeException.hpp"
43
44template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
46 bool deleteCellPopulationInDestructor,
47 bool initialiseCells)
48 : AbstractCellBasedSimulation<ELEMENT_DIM,SPACE_DIM>(rCellPopulation, deleteCellPopulationInDestructor, initialiseCells)
49{
50 if (!dynamic_cast<AbstractOffLatticeCellPopulation<ELEMENT_DIM,SPACE_DIM>*>(&rCellPopulation))
51 {
52 EXCEPTION("OffLatticeSimulations require a subclass of AbstractOffLatticeCellPopulation.");
53 }
54}
55
56template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
58{
59 mForceCollection.push_back(pForce);
60}
61
62template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
64{
65 mForceCollection.clear();
66}
67
68template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
70{
71 mBoundaryConditions.push_back(pBoundaryCondition);
72}
73
74template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
79
80template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
82{
83 mpNumericalMethod = pNumericalMethod;
84}
85
86template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
87const boost::shared_ptr<AbstractNumericalMethod<ELEMENT_DIM, SPACE_DIM> > OffLatticeSimulation<ELEMENT_DIM,SPACE_DIM>::GetNumericalMethod() const
88{
89 return mpNumericalMethod;
90}
91
92template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
93const std::vector<boost::shared_ptr<AbstractForce<ELEMENT_DIM, SPACE_DIM> > >& OffLatticeSimulation<ELEMENT_DIM,SPACE_DIM>::rGetForceCollection() const
94{
95 return mForceCollection;
96}
97
98template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
100{
101 CellBasedEventHandler::BeginEvent(CellBasedEventHandler::POSITION);
102
103 double time_advanced_so_far = 0;
104 double target_time_step = this->mDt;
105 double present_time_step = this->mDt;
106
107 while (time_advanced_so_far < target_time_step)
108 {
109 // Store the initial node positions (these may be needed when applying boundary conditions)
110 std::map<Node<SPACE_DIM>*, c_vector<double, SPACE_DIM> > old_node_locations;
112 for (typename AbstractMesh<ELEMENT_DIM, SPACE_DIM>::NodeIterator node_iter = this->mrCellPopulation.rGetMesh().GetNodeIteratorBegin();
113 node_iter != this->mrCellPopulation.rGetMesh().GetNodeIteratorEnd();
114 ++node_iter)
115 {
116 old_node_locations[&(*node_iter)] = (node_iter)->rGetLocation();
117 }
118
119 // Try to update node positions according to the numerical method
120 try
121 {
122 mpNumericalMethod->UpdateAllNodePositions(present_time_step);
123 ApplyBoundaries(old_node_locations);
124
125 // Successful time step! Update time_advanced_so_far
126 time_advanced_so_far += present_time_step;
127
128 // If using adaptive timestep, then increase the present_time_step (by 1% for now)
129 if (mpNumericalMethod->HasAdaptiveTimestep())
130 {
132 double timestep_increase = 0.01;
133 present_time_step = std::min((1+timestep_increase)*present_time_step, target_time_step - time_advanced_so_far);
134 }
135
137 catch (StepSizeException& e)
138 {
139 // Detects if a node has travelled too far in a single time step
140 if (mpNumericalMethod->HasAdaptiveTimestep())
141 {
142 // If adaptivity is switched on, revert node locations and choose a suitably smaller time step
143 RevertToOldLocations(old_node_locations);
144 present_time_step = std::min(e.GetSuggestedNewStep(), target_time_step - time_advanced_so_far);
145 }
146 else
147 {
148 // If adaptivity is switched off, terminate with an error
149 EXCEPTION(e.what());
150 }
151 }
152 }
153
154 CellBasedEventHandler::EndEvent(CellBasedEventHandler::POSITION);
155}
156
157template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
158void OffLatticeSimulation<ELEMENT_DIM,SPACE_DIM>::RevertToOldLocations(std::map<Node<SPACE_DIM>*, c_vector<double, SPACE_DIM> > oldNodeLoctions)
159{
160 for (typename AbstractMesh<ELEMENT_DIM, SPACE_DIM>::NodeIterator node_iter = this->mrCellPopulation.rGetMesh().GetNodeIteratorBegin();
161 node_iter != this->mrCellPopulation.rGetMesh().GetNodeIteratorEnd();
162 ++node_iter)
164 (node_iter)->rGetModifiableLocation() = oldNodeLoctions[&(*node_iter)];
165 }
166}
167
168template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
169void OffLatticeSimulation<ELEMENT_DIM,SPACE_DIM>::ApplyBoundaries(std::map<Node<SPACE_DIM>*,c_vector<double, SPACE_DIM> > oldNodeLoctions)
171 // Apply any boundary conditions
172 for (typename std::vector<boost::shared_ptr<AbstractCellPopulationBoundaryCondition<ELEMENT_DIM,SPACE_DIM> > >::iterator bcs_iter = mBoundaryConditions.begin();
173 bcs_iter != mBoundaryConditions.end();
174 ++bcs_iter)
176 (*bcs_iter)->ImposeBoundaryCondition(oldNodeLoctions);
177 }
178
179 // Verify that each boundary condition is now satisfied
180 for (typename std::vector<boost::shared_ptr<AbstractCellPopulationBoundaryCondition<ELEMENT_DIM,SPACE_DIM> > >::iterator bcs_iter = mBoundaryConditions.begin();
181 bcs_iter != mBoundaryConditions.end();
182 ++bcs_iter)
183 {
184 if (!((*bcs_iter)->VerifyBoundaryCondition()))
185 {
186 EXCEPTION("The cell population boundary conditions are incompatible.");
188 }
189}
190
191template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
193{
195 {
196 for (unsigned i=0; i<this->mForceCollection.size(); i++)
197 {
198 this->mForceCollection[i]->WriteDataToVisualizerSetupFile(this->mpVizSetupFile);
199 }
200
201 this->mrCellPopulation.WriteDataToVisualizerSetupFile(this->mpVizSetupFile);
202 }
204
205template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
207{
208 // Clear all forces
209 for (typename AbstractMesh<ELEMENT_DIM, SPACE_DIM>::NodeIterator node_iter = this->mrCellPopulation.rGetMesh().GetNodeIteratorBegin();
210 node_iter != this->mrCellPopulation.rGetMesh().GetNodeIteratorEnd();
211 ++node_iter)
212 {
213 node_iter->ClearAppliedForce();
214 }
215
216 // Use a forward Euler method by default, unless a numerical method has been specified already
217 if (mpNumericalMethod == nullptr)
218 {
219 mpNumericalMethod = boost::make_shared<ForwardEulerNumericalMethod<ELEMENT_DIM, SPACE_DIM> >();
220 }
221 mpNumericalMethod->SetCellPopulation(dynamic_cast<AbstractOffLatticeCellPopulation<ELEMENT_DIM,SPACE_DIM>*>(&(this->mrCellPopulation)));
222 mpNumericalMethod->SetForceCollection(&mForceCollection);
223 mpNumericalMethod->SetBoundaryConditions(&mBoundaryConditions);
224}
225
226template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
228{
229 // Loop over forces
230 *rParamsFile << "\n\t<Forces>\n";
231 for (typename std::vector<boost::shared_ptr<AbstractForce<ELEMENT_DIM,SPACE_DIM> > >::iterator iter = mForceCollection.begin();
232 iter != mForceCollection.end();
233 ++iter)
234 {
235 // Output force details
236 (*iter)->OutputForceInfo(rParamsFile);
237 }
238 *rParamsFile << "\t</Forces>\n";
239
240 // Loop over cell population boundary conditions
241 *rParamsFile << "\n\t<CellPopulationBoundaryConditions>\n";
242 for (typename std::vector<boost::shared_ptr<AbstractCellPopulationBoundaryCondition<ELEMENT_DIM,SPACE_DIM> > >::iterator iter = mBoundaryConditions.begin();
243 iter != mBoundaryConditions.end();
244 ++iter)
245 {
246 // Output cell boundary condition details
247 (*iter)->OutputCellPopulationBoundaryConditionInfo(rParamsFile);
248 }
249 *rParamsFile << "\t</CellPopulationBoundaryConditions>\n";
250
251 // Output numerical method details
252 *rParamsFile << "\n\t<NumericalMethod>\n";
253 mpNumericalMethod->OutputNumericalMethodInfo(rParamsFile);
254 *rParamsFile << "\t</NumericalMethod>\n";
255}
256
257template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
259{
260 // No new parameters to output, so just call method on direct parent class
262}
263
264// Explicit instantiation
265template class OffLatticeSimulation<1,1>;
266template class OffLatticeSimulation<1,2>;
267template class OffLatticeSimulation<2,2>;
268template class OffLatticeSimulation<1,3>;
269template class OffLatticeSimulation<2,3>;
270template class OffLatticeSimulation<3,3>;
271
272// Serialization for Boost >= 1.36
#define EXCEPTION(message)
#define EXPORT_TEMPLATE_CLASS_ALL_DIMS(CLASS)
virtual void OutputSimulationParameters(out_stream &rParamsFile)=0
Definition Node.hpp:59
const boost::shared_ptr< AbstractNumericalMethod< ELEMENT_DIM, SPACE_DIM > > GetNumericalMethod() const
virtual void UpdateCellLocationsAndTopology()
void OutputAdditionalSimulationSetup(out_stream &rParamsFile)
void AddCellPopulationBoundaryCondition(boost::shared_ptr< AbstractCellPopulationBoundaryCondition< ELEMENT_DIM, SPACE_DIM > > pBoundaryCondition)
const std::vector< boost::shared_ptr< AbstractForce< ELEMENT_DIM, SPACE_DIM > > > & rGetForceCollection() const
void SetNumericalMethod(boost::shared_ptr< AbstractNumericalMethod< ELEMENT_DIM, SPACE_DIM > > pNumericalMethod)
void ApplyBoundaries(std::map< Node< SPACE_DIM > *, c_vector< double, SPACE_DIM > > oldNodeLoctions)
virtual void WriteVisualizerSetupFile()
virtual void OutputSimulationParameters(out_stream &rParamsFile)
void RevertToOldLocations(std::map< Node< SPACE_DIM > *, c_vector< double, SPACE_DIM > > oldNodeLoctions)
void AddForce(boost::shared_ptr< AbstractForce< ELEMENT_DIM, SPACE_DIM > > pForce)
OffLatticeSimulation(AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > &rCellPopulation, bool deleteCellPopulationInDestructor=false, bool initialiseCells=true)
static bool AmMaster()