Chaste Commit::baa90ac2819b962188b7562f2326be23c47859a7
ElectroMechanicsProblemDefinition.cpp
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35
36#include "ElectroMechanicsProblemDefinition.hpp"
37#include "LabelBasedContractionCellFactory.hpp"
38
39template<unsigned DIM>
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
58template<unsigned DIM>
60{
61 if (mpDefaultMaterialLaw)
62 {
63 delete mpDefaultMaterialLaw;
64 }
65
66 if (mWeMadeCellFactory)
67 {
68 delete mpContractionCellFactory;
69 }
70}
71
72template<unsigned DIM>
73void 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
92template<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
112template<unsigned DIM>
113void ElectroMechanicsProblemDefinition<DIM>::SetDeformationAffectsElectrophysiology(bool deformationAffectsConductivity, bool deformationAffectsCellModels)
114{
115 mDeformationAffectsConductivity = deformationAffectsConductivity;
116 mDeformationAffectsCellModels = deformationAffectsCellModels;
117}
118
119template<unsigned DIM>
121{
122 assert(timestep > 0.0);
123 mMechanicsSolveTimestep = timestep;
124}
125
126template<unsigned DIM>
127void ElectroMechanicsProblemDefinition<DIM>::SetVariableFibreSheetDirectionsFile(const FileFinder& rFibreSheetDirectionsFile, bool definedPerQuadraturePoint)
128{
129 mReadFibreSheetInformationFromFile = true;
130 mFibreSheetDirectionsFile = rFibreSheetDirectionsFile;
131 mFibreSheetDirectionsDefinedPerQuadraturePoint = definedPerQuadraturePoint;
132}
133
134template<unsigned DIM>
135void ElectroMechanicsProblemDefinition<DIM>::SetApplyIsotropicCrossFibreTension(bool applyCrossFibreTension, double crossFibreTensionFraction)
136{
137 mApplyCrossFibreTension = applyCrossFibreTension;
138 mSheetTensionFraction = crossFibreTensionFraction;
139 mSheetNormalTensionFraction = crossFibreTensionFraction;
140}
141
142template<unsigned DIM>
143void 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
154template<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
164template<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
const double DOUBLE_UNSET
Definition Exception.hpp:57
#define EXCEPTION(message)
void SetMechanicsMesh(QuadraticMesh< DIM > *pMesh)
void SetContractionModel(ContractionModelName contractionModel, double timestep)
void SetUseDefaultCardiacMaterialLaw(CompressibilityType compressibilityType)
void SetVariableFibreSheetDirectionsFile(const FileFinder &rFibreSheetDirectionsFile, bool definedPerQuadPoint)
ElectroMechanicsProblemDefinition(QuadraticMesh< DIM > &rMesh)
void SetApplyAnisotropicCrossFibreTension(bool applyCrossFibreTension, double sheetTensionFraction, double sheetNormalTensionFraction)
void SetDeformationAffectsElectrophysiology(bool deformationAffectsConductivity, bool deformationAffectsCellModels)
void SetApplyIsotropicCrossFibreTension(bool applyCrossFibreTension, double crossFibreTensionFraction)
void SetContractionCellFactory(AbstractContractionCellFactory< DIM > *pCellFactory)