Chaste Commit::baa90ac2819b962188b7562f2326be23c47859a7
MonodomainPurkinjeProblem.cpp
1/*
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34*/
35
36#include "MonodomainPurkinjeProblem.hpp"
37#include "MonodomainPurkinjeSolver.hpp"
38#include "Exception.hpp"
39#include "ReplicatableVector.hpp"
40
41
42template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
47
48
49template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
51{
52 assert(!HeartConfig::Instance()->GetUseReactionDiffusionOperatorSplitting());
54 EXCEPT_IF_NOT(p_mesh);
55 MonodomainTissue<ELEMENT_DIM,SPACE_DIM>* p_tissue = dynamic_cast<MonodomainTissue<ELEMENT_DIM,SPACE_DIM>*>(this->GetTissue());
56 assert(p_tissue);
58 p_tissue,
59 this->mpBoundaryConditionsContainer.get());
60}
61
62template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
67
68
69template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
71{
73
74 // Get the Purkinje voltage stripe
75 DistributedVector ic = this->mpMesh->GetDistributedVectorFactory()->CreateDistributedVector(init_cond);
76 DistributedVector::Stripe purkinje_voltage_stripe = DistributedVector::Stripe(ic, 1);
77
78 for (DistributedVector::Iterator index = ic.Begin();
79 index != ic.End();
80 ++index)
81 {
82 purkinje_voltage_stripe[index] = this->GetTissue()->GetPurkinjeCell(index.Global)->GetVoltage();
83 // Note that it doesn't matter if the cell is fake, as this will give a zero voltage for nodes not in the
84 // Purkinje network.
85 }
86 ic.Restore();
87
88 return init_cond;
89}
90
91
92template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
98
99
100// LCOV_EXCL_START
101template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
103 : AbstractCardiacProblem<ELEMENT_DIM, SPACE_DIM, 2>(),
104 mPurkinjeVoltageColumnId(UNSIGNED_UNSET)
105{
106}
107// LCOV_EXCL_STOP
108
109template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
113
114
115template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
117{
119 {
120 std::cout << "Solved to time " << time << "\n" << std::flush;
121 }
122
123 double v_max, v_min, v_purk_max, v_purk_min;
124
125 VecStrideMax( this->mSolution, 0, CHASTE_PETSC_NULLPTR, &v_max );
126 VecStrideMin( this->mSolution, 0, CHASTE_PETSC_NULLPTR, &v_min );
127
128 VecStrideMax( this->mSolution, 1, CHASTE_PETSC_NULLPTR, &v_purk_max );
129 VecStrideMin( this->mSolution, 1, CHASTE_PETSC_NULLPTR, &v_purk_min );
130
131 // avoid printing 1e-320 etc
132 if(fabs(v_purk_min)<1e-20)
133 {
134 // It's very hard to hit this, as you'd need the whole Purkinje system to be activated
135 v_purk_min = 0.0; // LCOV_EXCL_LINE
136 }
137
138 if(fabs(v_purk_max)<1e-20)
139 {
140 v_purk_max = 0.0;
141 }
142
144 {
145 std::cout << " V_myo; V_purk = " << "[" <<v_min << ", " << v_max << "]" << ";\t"
146 << "[" << v_purk_min << ", " << v_purk_max << "]" << "\n"
147 << std::flush;
148 }
149}
150
151
152template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
154{
156 if (extending)
157 {
158 mPurkinjeVoltageColumnId = this->mpWriter->GetVariableByName("V_purk");
159 }
160 else
161 {
162 mPurkinjeVoltageColumnId = this->mpWriter->DefineVariable("V_purk","mV");
163 }
165}
166
167
168template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
170{
171 this->mpWriter->PutUnlimitedVariable(time);
172 std::vector<int> variable_ids;
173 variable_ids.push_back(this->mVoltageColumnId);
174 variable_ids.push_back(mPurkinjeVoltageColumnId);
175 this->mpWriter->PutStripedVector(variable_ids, voltageVec);
177}
178
179
181// Explicit instantiation
183
184template class MonodomainPurkinjeProblem<2,2>;
185template class MonodomainPurkinjeProblem<3,3>;
186
187
188
189// Serialization for Boost >= 1.36
#define EXCEPT_IF_NOT(test)
const unsigned UNSIGNED_UNSET
Definition Exception.hpp:53
#define CHASTE_PETSC_NULLPTR
A macro to define PETSc null pointer based on the PETSc version.
#define EXPORT_TEMPLATE_CLASS2(CLASS, E, S)
void DefineExtraVariablesWriterColumns(bool extending)
virtual void DefineWriterColumns(bool extending)
static HeartConfig * Instance()
AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, 2 > * CreateSolver()
virtual void WriteOneStep(double time, Vec voltageVec)
AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM > * CreateCardiacTissue()
virtual void DefineWriterColumns(bool extending)
static bool AmMaster()