Chaste  Release::3.4
ExtendedBidomainProblem.hpp
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36 
37 #ifndef EXTENDEDBIDOMAINPROBLEM_HPP_
38 #define EXTENDEDBIDOMAINPROBLEM_HPP_
39 
40 #include "ChasteSerialization.hpp"
41 #include <boost/serialization/base_object.hpp>
42 
43 #include <vector>
44 #include <boost/shared_ptr.hpp>
45 #include <boost/serialization/shared_ptr.hpp>
46 
47 #include "AbstractCardiacProblem.hpp"
48 #include "AbstractCardiacTissue.hpp"
49 #include "AbstractExtendedBidomainSolver.hpp"
50 #include "AbstractCardiacCellFactory.hpp"
51 #include "Electrodes.hpp"
52 #include "ExtendedBidomainTissue.hpp"
53 
54 #include "HeartRegionCodes.hpp"
55 #include "DistributedTetrahedralMesh.hpp"
56 #include "AbstractStimulusFactory.hpp"
57 #include "ElectrodesStimulusFactory.hpp"
58 
84 template<unsigned DIM>
86 {
89 
90  friend class TestArchivingExtendedBidomain;//for testing
91 
98  template<class Archive>
99  void save(Archive & archive, const unsigned int version) const
100  {
101  archive & boost::serialization::base_object<AbstractCardiacProblem<DIM, DIM, 3> >(*this);
102  archive & mpExtendedBidomainTissue;
104  //archive & mIntracellularConductivitiesSecondCell; not allowed in some versions of boost
105  archive & mVariablesIDs;
108  archive & mAmFirstCell;
109  archive & mAmSecondCell;
110  archive & mAmGap;
111  archive & mCmFirstCell;
112  archive & mCmSecondCell;
113  archive & mGGap;
114  archive & mGgapHeterogeneityRegions;
115  archive & mGgapHeterogenousValues;
116  archive & mRowForAverageOfPhiZeroed;
119  archive & mHasBath;
120  //archive & mpSolver;
121 
122  //archive the values for the conductivies of the second cell
123  for (unsigned i = 0; i < DIM; i++)
124  {
125  double conductivity = mIntracellularConductivitiesSecondCell(i);
126  archive & conductivity;
127  }
128 
129  bool has_solution = (this->mSolution != NULL);
130  archive & has_solution;
131  if (has_solution)
132  {
133  // Please see the todo tag (#1317) in AbstractCardiacProblem
134  Hdf5DataWriter writer(*this->mpMesh->GetDistributedVectorFactory(), ArchiveLocationInfo::GetArchiveRelativePath(), "AbstractCardiacProblem_mSolution", false);
135  writer.DefineFixedDimension(this->mpMesh->GetDistributedVectorFactory()->GetProblemSize());
136  writer.DefineUnlimitedDimension("Time", "msec", 1);
137 
138  int V = writer.DefineVariable("V","mV");
139  int V_2 = writer.DefineVariable("V_2","mV");
140  int phie = writer.DefineVariable("Phi_e","mV");
141  std::vector<int> variable_ids;
142  variable_ids.push_back(V);
143  variable_ids.push_back(V_2);
144  variable_ids.push_back(phie);
145  writer.EndDefineMode();
146  writer.PutUnlimitedVariable(0.0);
147 
148 
149  writer.PutStripedVector(variable_ids, this->mSolution);
150  }
151  }
152 
159  template<class Archive>
160  void load(Archive & archive, const unsigned int version)
161  {
162  archive & boost::serialization::base_object<AbstractCardiacProblem<DIM, DIM, 3> >(*this);
163  archive & mpExtendedBidomainTissue;
165  //archive & mIntracellularConductivitiesSecondCell; not allowed in some versions of boost
166  archive & mVariablesIDs;
169  archive & mAmFirstCell;
170  archive & mAmSecondCell;
171  archive & mAmGap;
172  archive & mCmFirstCell;
173  archive & mCmSecondCell;
174  archive & mGGap;
175  archive & mGgapHeterogeneityRegions;
176  archive & mGgapHeterogenousValues;
177  archive & mRowForAverageOfPhiZeroed;
180  archive & mHasBath;
181  //archive & mpSolver;
182 
183  //load the values for the conductivies of the second cell
184  for (unsigned i = 0; i < DIM; i++)
185  {
186  double conductivity;
187  archive & conductivity;
188  mIntracellularConductivitiesSecondCell(i) = conductivity;
189  }
190 
191  bool has_solution;
192  archive & has_solution;
193 
194  if (has_solution)
195  {
196  this->mSolution = this->mpMesh->GetDistributedVectorFactory()->CreateVec(3);
197  DistributedVector mSolution_distri = this->mpMesh->GetDistributedVectorFactory()->CreateDistributedVector(this->mSolution);
198 
199  std::string archive_dir = ArchiveLocationInfo::GetArchiveRelativePath();
200  Hdf5DataReader reader(archive_dir, "AbstractCardiacProblem_mSolution", !FileFinder::IsAbsolutePath(archive_dir));
201 
202  Vec V = this->mpMesh->GetDistributedVectorFactory()->CreateVec();
203  Vec V_2 = this->mpMesh->GetDistributedVectorFactory()->CreateVec();
204  Vec phie = this->mpMesh->GetDistributedVectorFactory()->CreateVec();
205 
206  reader.GetVariableOverNodes(V, "V", 0);
207  reader.GetVariableOverNodes(V_2, "V_2", 0);
208  reader.GetVariableOverNodes(phie, "Phi_e", 0);
209 
210  //from transmembrane voltages back to phi_i now...
211  DistributedVector vm_first_cell_distri = this->mpMesh->GetDistributedVectorFactory()->CreateDistributedVector(V);
212  DistributedVector vm_second_cell_distri = this->mpMesh->GetDistributedVectorFactory()->CreateDistributedVector(V_2);
213  DistributedVector phie_distri = this->mpMesh->GetDistributedVectorFactory()->CreateDistributedVector(phie);
214 
215  DistributedVector::Stripe mSolution_V_1(mSolution_distri,0);
216  DistributedVector::Stripe mSolution_V_2(mSolution_distri,1);
217  DistributedVector::Stripe mSolution_phie(mSolution_distri,2);
218 
219  for (DistributedVector::Iterator index = mSolution_distri.Begin();
220  index != mSolution_distri.End();
221  ++index)
222  {
223  mSolution_V_1[index] = vm_first_cell_distri[index];
224  mSolution_V_2[index] = vm_second_cell_distri[index];
225  mSolution_phie[index] = phie_distri[index];
226  }
228  PetscTools::Destroy(V_2);
229  PetscTools::Destroy(phie);
230 
231  mSolution_distri.Restore();
232  }
233  }
234  BOOST_SERIALIZATION_SPLIT_MEMBER()
235 
236 
237 protected:
238 
241 
244 
246  std::vector<unsigned> mFixedExtracellularPotentialNodes;
247 
250 
258  std::vector<signed int> mVariablesIDs;
259 
263 
266 
268  double mAmFirstCell;
272  double mAmGap;
274  double mCmFirstCell;
279  double mGGap;
280 
286  std::vector<boost::shared_ptr<AbstractChasteRegion<DIM> > > mGgapHeterogeneityRegions;
287 
289  std::vector<double> mGgapHeterogenousValues;
290 
291 
294 
300 
309 
312 
314  bool mHasBath;
315 
322 
327  void AnalyseMeshForBath();
328 
339 
346 
349 
351  virtual AbstractDynamicLinearPdeSolver<DIM,DIM,3>* CreateSolver();
352 
353 public:
364  ExtendedBidomainProblem(AbstractCardiacCellFactory<DIM>* pCellFactory, AbstractCardiacCellFactory<DIM>* pSecondCellFactory, bool hasBath = false);
365 
370 
374  virtual ~ExtendedBidomainProblem();
375 
386  void SetFixedExtracellularPotentialNodes(std::vector<unsigned> nodes);
387 
393  void SetIntracellularConductivitiesForSecondCell(c_vector<double, DIM> conductivities);
394 
407  void SetExtendedBidomainParameters(double Am1, double Am2, double AmGap, double Cm1, double Cm2, double Ggap);
408 
417  void SetGgapHeterogeneities ( std::vector<boost::shared_ptr<AbstractChasteRegion<DIM> > >& rGgapHeterogeneityRegions, std::vector<double>& rGgapValues);
418 
425 
426 
434  void SetNodeForAverageOfPhiZeroed(unsigned node);
435 
436 
441 
447  void WriteInfo(double time);
448 
457  virtual void DefineWriterColumns(bool extending);
458 
474  virtual void WriteOneStep(double time, Vec voltageVec);
475 
480  void PreSolveChecks();
481 
482 
486  bool GetHasBath();
487 
494  void SetHasBath(bool hasBath);
495 
496 };
497 
498 #include "SerializationExportWrapper.hpp" // Must be last
499 EXPORT_TEMPLATE_CLASS_SAME_DIMS(ExtendedBidomainProblem)
500 
501 #endif /*EXTENDEDBIDOMAINPROBLEM_HPP_*/
void SetExtendedBidomainParameters(double Am1, double Am2, double AmGap, double Cm1, double Cm2, double Ggap)
virtual AbstractDynamicLinearPdeSolver< DIM, DIM, 3 > * CreateSolver()
virtual AbstractCardiacTissue< DIM > * CreateCardiacTissue()
AbstractStimulusFactory< DIM > * mpExtracellularStimulusFactory
ExtendedBidomainTissue< DIM > * GetExtendedBidomainTissue()
void SetExtracellularStimulusFactory(AbstractStimulusFactory< DIM > *pFactory)
static bool IsAbsolutePath(const std::string &rPath)
Definition: FileFinder.cpp:528
virtual void WriteOneStep(double time, Vec voltageVec)
void SetIntracellularConductivitiesForSecondCell(c_vector< double, DIM > conductivities)
void SetGgapHeterogeneities(std::vector< boost::shared_ptr< AbstractChasteRegion< DIM > > > &rGgapHeterogeneityRegions, std::vector< double > &rGgapValues)
void SetNodeForAverageOfPhiZeroed(unsigned node)
void GetVariableOverNodes(Vec data, const std::string &rVariableName, unsigned timestep=0)
friend class boost::serialization::access
virtual void DefineWriterColumns(bool extending)
AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > * mpMesh
AbstractExtendedBidomainSolver< DIM, DIM > * mpSolver
#define EXPORT_TEMPLATE_CLASS_SAME_DIMS(CLASS)
void SetFixedExtracellularPotentialNodes(std::vector< unsigned > nodes)
void load(Archive &archive, const unsigned int version)
std::vector< boost::shared_ptr< AbstractChasteRegion< DIM > > > mGgapHeterogeneityRegions
static void Destroy(Vec &rVec)
Definition: PetscTools.hpp:351
void DefineFixedDimension(long dimensionSize)
std::vector< signed int > mVariablesIDs
ExtendedBidomainTissue< DIM > * mpExtendedBidomainTissue
AbstractCardiacCellFactory< DIM, DIM > * mpSecondCellFactory
void save(Archive &archive, const unsigned int version) const
static std::string GetArchiveRelativePath()
std::vector< double > mGgapHeterogenousValues
c_vector< double, DIM > mIntracellularConductivitiesSecondCell
std::vector< unsigned > mFixedExtracellularPotentialNodes