Chaste Commit::ca8ccdedf819b6e02855bc0e8e6f50bdecbc5208
MonodomainPurkinjeCableAssembler.hpp
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35
36#ifndef MONODOMAINPURKINJECABLEASSEMBLER_HPP_
37#define MONODOMAINPURKINJECABLEASSEMBLER_HPP_
38
39#include "AbstractFeCableIntegralAssembler.hpp"
40#include "HeartConfig.hpp"
41#include "PdeSimulationTime.hpp"
42
43
58template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
59class MonodomainPurkinjeCableAssembler : public AbstractFeCableIntegralAssembler<ELEMENT_DIM,SPACE_DIM,2,false,true,NORMAL>
60{
61private:
65 static const unsigned PROBLEM_DIM=2;
66
78 c_matrix<double,PROBLEM_DIM*2,PROBLEM_DIM*2 /*2=number of bases per cable*/> ComputeCableMatrixTerm(
79 c_vector<double, 2>& rPhi,
80 c_matrix<double, ELEMENT_DIM, 2>& rGradPhi,
82 c_vector<double,PROBLEM_DIM>& rU,
83 c_matrix<double,PROBLEM_DIM, SPACE_DIM>& rGradU,
84 Element<1,SPACE_DIM>* pElement)
85 {
86 c_matrix<double,PROBLEM_DIM*2, PROBLEM_DIM*2> ret = zero_matrix<double>(PROBLEM_DIM*2, PROBLEM_DIM*2);
87 double capacitance = HeartConfig::Instance()->GetPurkinjeCapacitance();
89 double conductivity = HeartConfig::Instance()->GetPurkinjeConductivity();
90
91 //We have to scale the assembled matrix by the cross sectional area of the Purkinje
92 //fibre to ensure conservation of current at branch points. See #1899.
93 const double fibre_cross_section_area = M_PI*pElement->GetAttribute()*pElement->GetAttribute();
94
95 for(unsigned i=0; i<2; i++) // 2 = number of basis functions per cable element
96 {
97 for(unsigned j=0; j<2; j++) // 2 = number of basis functions per cable element
98 {
99 ret(2*i, 2*j) = 0; // [V,V] block
100 ret(2*i+1,2*j) = 0; // [Vpurkinje,V] block
101 ret(2*i, 2*j+1) = 0; // [V,Vpurkinje] block
102 ret(2*i+1,2*j+1) = capacitance*chi*PdeSimulationTime::GetPdeTimeStepInverse()*rPhi(i)*rPhi(j);
103
104 for (unsigned dim=0; dim<SPACE_DIM; dim++)
105 {
106 ret(2*i+1,2*j+1) += conductivity*rGradPhi(dim,i)*rGradPhi(dim,j);
107 }
108
109 ret(2*i+1,2*j+1) *= fibre_cross_section_area;
110 }
111 }
112
113 return ret;
114 }
115public:
121 : AbstractFeCableIntegralAssembler<ELEMENT_DIM,SPACE_DIM,2,false,true,NORMAL>(pMesh)
122 {
123 // Check radii have been set on the purkinje elements
125 iter != pMesh->GetCableElementIteratorEnd();
126 ++iter)
127 {
128 double radius = (*iter)->GetAttribute();
129 if (fabs(radius)<=DBL_EPSILON)
130 {
131 EXCEPTION("Radii not provided for all Purkinje elements - should be present in the mesh file or defined in test");
132 }
133 }
134 }
135};
136
137#endif // MONODOMAINPURKINJECABLEASSEMBLER_HPP_
#define EXCEPTION(message)
double GetPurkinjeSurfaceAreaToVolumeRatio()
double GetPurkinjeCapacitance()
double GetPurkinjeConductivity()
static HeartConfig * Instance()
std::vector< Element< 1, SPACE_DIM > * >::const_iterator CableElementIterator
CableElementIterator GetCableElementIteratorEnd() const
CableElementIterator GetCableElementIteratorBegin() const
MonodomainPurkinjeCableAssembler(MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM > *pMesh)
c_matrix< double, PROBLEM_DIM *2, PROBLEM_DIM *2 > ComputeCableMatrixTerm(c_vector< double, 2 > &rPhi, c_matrix< double, ELEMENT_DIM, 2 > &rGradPhi, ChastePoint< SPACE_DIM > &rX, c_vector< double, PROBLEM_DIM > &rU, c_matrix< double, PROBLEM_DIM, SPACE_DIM > &rGradU, Element< 1, SPACE_DIM > *pElement)
static double GetPdeTimeStepInverse()