Chaste  Release::2018.1
ElectroMechanicsProblemDefinition.cpp
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35 
36 #include "ElectroMechanicsProblemDefinition.hpp"
37 #include "LabelBasedContractionCellFactory.hpp"
38 
39 template<unsigned DIM>
41  : SolidMechanicsProblemDefinition<DIM>(rMesh),
42  mContractionModelOdeTimeStep(-1.0),
43  mMechanicsSolveTimestep(-1.0),
44  mDeformationAffectsConductivity(false),
45  mDeformationAffectsCellModels(false),
46  mpDefaultMaterialLaw(NULL),
47  mReadFibreSheetInformationFromFile(false),
48  mNumIncrementsForInitialDeformation(1),
49  mApplyCrossFibreTension(false),
50  mSheetTensionFraction(DOUBLE_UNSET),
51  mSheetNormalTensionFraction(DOUBLE_UNSET),
52  mpContractionCellFactory(NULL),
53  mWeMadeCellFactory(false),
54  mSolverType(IMPLICIT) // default solver is implicit
55 {
56 }
57 
58 template<unsigned DIM>
60 {
61  if (mpDefaultMaterialLaw)
62  {
63  delete mpDefaultMaterialLaw;
64  }
65 
66  if (mWeMadeCellFactory)
67  {
68  delete mpContractionCellFactory;
69  }
70 }
71 
72 template<unsigned DIM>
73 void ElectroMechanicsProblemDefinition<DIM>::SetContractionModel(ContractionModelName contractionModel, double timestep)
74 {
75  assert(timestep > 0.0);
76  SetContractionModelOdeTimestep(timestep);
77 
78  if (contractionModel == NASH2004 || contractionModel == CONSTANT)
79  {
80  // These models can use an Explicit solver, default is Implicit.
81  SetSolverType(EXPLICIT);
82  }
83 
84  // Make sure we aren't overwriting a problem that has been set up with a cell factory.
85  assert(mpContractionCellFactory==NULL);
86 
88  mWeMadeCellFactory = true;
89  SetContractionCellFactory(p_factory);
90 }
91 
92 template<unsigned DIM>
94 {
95  if (mpDefaultMaterialLaw)
96  {
97  delete mpDefaultMaterialLaw;
98  }
99 
100  if (compressibilityType == INCOMPRESSIBLE)
101  {
102  mpDefaultMaterialLaw = new NashHunterPoleZeroLaw<DIM>();
103  this->SetMaterialLaw(INCOMPRESSIBLE, mpDefaultMaterialLaw);
104  }
105  else
106  {
107  mpDefaultMaterialLaw = new CompressibleExponentialLaw<DIM>();
108  this->SetMaterialLaw(COMPRESSIBLE, mpDefaultMaterialLaw);
109  }
110 }
111 
112 template<unsigned DIM>
113 void ElectroMechanicsProblemDefinition<DIM>::SetDeformationAffectsElectrophysiology(bool deformationAffectsConductivity, bool deformationAffectsCellModels)
114 {
115  mDeformationAffectsConductivity = deformationAffectsConductivity;
116  mDeformationAffectsCellModels = deformationAffectsCellModels;
117 }
118 
119 template<unsigned DIM>
121 {
122  assert(timestep > 0.0);
123  mMechanicsSolveTimestep = timestep;
124 }
125 
126 template<unsigned DIM>
127 void ElectroMechanicsProblemDefinition<DIM>::SetVariableFibreSheetDirectionsFile(const FileFinder& rFibreSheetDirectionsFile, bool definedPerQuadraturePoint)
128 {
129  mReadFibreSheetInformationFromFile = true;
130  mFibreSheetDirectionsFile = rFibreSheetDirectionsFile;
131  mFibreSheetDirectionsDefinedPerQuadraturePoint = definedPerQuadraturePoint;
132 }
133 
134 template<unsigned DIM>
135 void ElectroMechanicsProblemDefinition<DIM>::SetApplyIsotropicCrossFibreTension(bool applyCrossFibreTension, double crossFibreTensionFraction)
136 {
137  mApplyCrossFibreTension = applyCrossFibreTension;
138  mSheetTensionFraction = crossFibreTensionFraction;
139  mSheetNormalTensionFraction = crossFibreTensionFraction;
140 }
141 
142 template<unsigned DIM>
143 void ElectroMechanicsProblemDefinition<DIM>::SetApplyAnisotropicCrossFibreTension(bool applyCrossFibreTension, double sheetTensionFraction, double sheetNormalTensionFraction)
144 {
145  if (DIM!=3)
146  {
147  EXCEPTION("You can only apply anisotropic cross fibre tensions in a 3D simulation.");
148  }
149  mApplyCrossFibreTension = applyCrossFibreTension;
150  mSheetTensionFraction = sheetTensionFraction;
151  mSheetNormalTensionFraction = sheetNormalTensionFraction;
152 }
153 
154 template<unsigned DIM>
156 {
157  // Make sure we aren't overwriting a problem that has been set up with a cell factory already.
158  assert(mpContractionCellFactory == NULL);
159 
160  mpContractionCellFactory = pCellFactory;
161  mpContractionCellFactory->SetMechanicsMesh(static_cast<QuadraticMesh<DIM>*>(&(this->mrMesh)));
162 }
163 
164 template<unsigned DIM>
166 {
168 
169  if (mMechanicsSolveTimestep < 0.0)
170  {
171  EXCEPTION("Timestep for mechanics solve hasn't been set yet");
172  }
173 
174  if (mContractionModelOdeTimeStep < 0.0)
175  {
176  std::string message = "Contraction model or contraction model ODE timestep have not been set. "
177  "Make sure SetContractionModel(), or SetContractionCellFactory() AND SetContractionModelOdeTimestep "
178  "are called. (Pass in a timestep even if contraction model is algebraic and won't use it). ";
179  EXCEPTION(message);
180  }
181 
182  if (mDeformationAffectsConductivity && this->GetCompressibilityType()==COMPRESSIBLE)
183  {
184  // the conductivity depends on the deformation gradient and also scales in some way with
185  // J=det(F), which is not equal to 1 in the compressible case. The F dependence
186  // is implemented but the J dependence is not yet.
187  EXCEPTION("Deformation affecting the conductivity is currently not implemented fully for compressible problems");
188  }
189 
190  if (mDeformationAffectsCellModels && mReadFibreSheetInformationFromFile && mFibreSheetDirectionsDefinedPerQuadraturePoint)
191  {
192  // This combination is not allowed. For explanation see doxygen for SetDeformationAffectsElectrophysiology()
193  std::stringstream message;
194  message << "Deformation affecting cell models cannot be done when fibres-sheet information is defined for each quadrature point.";
195  message << "Define fibre-sheet information for each element instead.";
196  EXCEPTION(message.str());
197  }
198 }
199 
200 // Explicit instantiation
ElectroMechanicsProblemDefinition(QuadraticMesh< DIM > &rMesh)
void SetContractionCellFactory(AbstractContractionCellFactory< DIM > *pCellFactory)
#define EXCEPTION(message)
Definition: Exception.hpp:143
void SetContractionModel(ContractionModelName contractionModel, double timestep)
void SetMechanicsMesh(QuadraticMesh< DIM > *pMesh)
const double DOUBLE_UNSET
Definition: Exception.hpp:56
void SetVariableFibreSheetDirectionsFile(const FileFinder &rFibreSheetDirectionsFile, bool definedPerQuadPoint)
void SetApplyAnisotropicCrossFibreTension(bool applyCrossFibreTension, double sheetTensionFraction, double sheetNormalTensionFraction)
void SetDeformationAffectsElectrophysiology(bool deformationAffectsConductivity, bool deformationAffectsCellModels)
void SetApplyIsotropicCrossFibreTension(bool applyCrossFibreTension, double crossFibreTensionFraction)
void SetUseDefaultCardiacMaterialLaw(CompressibilityType compressibilityType)