Chaste  Release::2018.1
CardiacElectroMechanicsProblem.hpp
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36 
37 #ifndef CARDIACELECTROMECHANICSPROBLEM_HPP_
38 #define CARDIACELECTROMECHANICSPROBLEM_HPP_
39 
40 #include <vector>
41 #include <string>
42 #include "UblasIncludes.hpp"
43 
44 #include "AbstractCardiacCellFactory.hpp"
45 #include "MonodomainProblem.hpp"
46 #include "TetrahedralMesh.hpp"
47 #include "QuadraticMesh.hpp"
48 #include "AbstractOdeBasedContractionModel.hpp"
49 #include "AbstractCardiacMechanicsSolver.hpp"
50 #include "AbstractCardiacMechanicsSolverInterface.hpp"
51 #include "FineCoarseMeshPair.hpp"
52 #include "AbstractConductivityModifier.hpp"
53 #include "ElectroMechanicsProblemDefinition.hpp"
54 
59 typedef enum ElectricsProblemType_
60 {
61  MONODOMAIN,
62  BIDOMAIN,
63  BIDOMAIN_WITH_BATH
64  //EXTENDED_BIDOMAIN
65 } ElectricsProblemType;
66 
93 template<unsigned DIM, unsigned ELEC_PROB_DIM=1>
95  : public AbstractConductivityModifier<DIM,DIM> // this only inherits from this class so it can be passed to the tissue to
96  // allow deformation-based altering of the conductivity
97 {
98 friend class TestAbstractContractionCellFactory;
99 friend class TestCardiacElectroMechanicsProblem;
100 friend class TestCardiacElectroMechanicsFurtherFunctionality;
101 friend class TestElectroMechanicsExactSolution;
102 
103 protected :
105  CompressibilityType mCompressibilityType;
106 
109 
116 
119 
124  std::vector<double> mInterpolatedCalciumConcs;
125 
130  std::vector<double> mInterpolatedVoltages;
131 
136 
139 
141  bool mHasBath;
142 
145 
147  std::string mOutputDirectory;
154 
156  static const int WRITE_EVERY_NTH_TIME = 1; //hardcoded for the time being ///\todo, allow user to set this
157 
161  c_vector<double,DIM> mWatchedLocation;
168 
171 
175  std::vector<c_matrix<double,DIM,DIM> > mDeformationGradientsForEachMechanicsElement;
176 
178  c_matrix<double,DIM,DIM> mModifiedConductivityTensor;
179 
183  void DetermineWatchedNodes();
184 
185 
192  void WriteWatchedLocationData(double time, Vec voltage);
193 
194 
195 public :
196 
207  CardiacElectroMechanicsProblem(CompressibilityType compressibilityType,
208  ElectricsProblemType electricsProblemType,
209  TetrahedralMesh<DIM,DIM>* pElectricsMesh,
210  QuadraticMesh<DIM>* pMechanicsMesh,
211  AbstractCardiacCellFactory<DIM>* pCellFactory,
212  ElectroMechanicsProblemDefinition<DIM>* pProblemDefinition,
213  std::string outputDirectory);
214 
224 
229  void Initialise();
230 
234  void Solve();
235 
241  double Max(std::vector<double>& vec);
242 
244  void SetNoElectricsOutput();
245 
256  void SetWatchedPosition(c_vector<double,DIM> watchedLocation);
257 
265  void SetOutputDeformationGradientsAndStress(double timestep);
266 
268  std::vector<c_vector<double,DIM> >& rGetDeformedPosition();
269 
270 
279  c_matrix<double,DIM,DIM>& rCalculateModifiedConductivityTensor(unsigned elementIndex, const c_matrix<double,DIM,DIM>& rOriginalConductivity, unsigned domainIndex);
280 
281 
285  virtual void PrepareForSolve(){}
286 
291  virtual void OnEndOfTimeStep(unsigned counter)
292  {
293  }
294 
301  {
302  assert(mpMechanicsSolver);
303  return mpMechanicsSolver;
304  }
305 };
306 
307 #endif /*CARDIACELECTROMECHANICSPROBLEM_HPP_*/
AbstractCardiacMechanicsSolverInterface< DIM > * mpCardiacMechSolver
virtual void OnEndOfTimeStep(unsigned counter)
void WriteWatchedLocationData(double time, Vec voltage)
double Max(std::vector< double > &vec)
std::vector< c_vector< double, DIM > > & rGetDeformedPosition()
CardiacElectroMechanicsProblem(CompressibilityType compressibilityType, ElectricsProblemType electricsProblemType, TetrahedralMesh< DIM, DIM > *pElectricsMesh, QuadraticMesh< DIM > *pMechanicsMesh, AbstractCardiacCellFactory< DIM > *pCellFactory, ElectroMechanicsProblemDefinition< DIM > *pProblemDefinition, std::string outputDirectory)
ElectroMechanicsProblemDefinition< DIM > * mpProblemDefinition
AbstractNonlinearElasticitySolver< DIM > * GetMechanicsSolver()
void SetOutputDeformationGradientsAndStress(double timestep)
std::vector< c_matrix< double, DIM, DIM > > mDeformationGradientsForEachMechanicsElement
c_matrix< double, DIM, DIM > & rCalculateModifiedConductivityTensor(unsigned elementIndex, const c_matrix< double, DIM, DIM > &rOriginalConductivity, unsigned domainIndex)
AbstractNonlinearElasticitySolver< DIM > * mpMechanicsSolver
AbstractCardiacProblem< DIM, DIM, ELEC_PROB_DIM > * mpElectricsProblem
c_matrix< double, DIM, DIM > mModifiedConductivityTensor
TetrahedralMesh< DIM, DIM > * mpElectricsMesh
void SetWatchedPosition(c_vector< double, DIM > watchedLocation)