| Line |
Branch |
Exec |
Source |
| 1 |
|
|
// ______ ______ _ _ _____ ______ |
| 2 |
|
|
// | ____| ____| | (_)/ ____| | ____| |
| 3 |
|
|
// | |__ | |__ | | _| (___ ___| |__ |
| 4 |
|
|
// | __| | __| | | | |\___ \ / __| __| |
| 5 |
|
|
// | | | |____| |____| |____) | (__| |____ |
| 6 |
|
|
// |_| |______|______|_|_____/ \___|______| |
| 7 |
|
|
// Finite Elements for Life Sciences and Engineering |
| 8 |
|
|
// |
| 9 |
|
|
// License: LGL2.1 License |
| 10 |
|
|
// FELiScE default license: LICENSE in root folder |
| 11 |
|
|
// |
| 12 |
|
|
// Main authors: E. Schenone C. Corrado |
| 13 |
|
|
// |
| 14 |
|
|
|
| 15 |
|
|
// System includes |
| 16 |
|
|
|
| 17 |
|
|
// External includes |
| 18 |
|
|
|
| 19 |
|
|
// Project includes |
| 20 |
|
|
#include "Solver/linearProblemBidomainTransMemb.hpp" |
| 21 |
|
|
#include "InputOutput/io.hpp" |
| 22 |
|
|
#include "FiniteElement/elementMatrix.hpp" |
| 23 |
|
|
|
| 24 |
|
|
namespace felisce { |
| 25 |
|
✗ |
LinearProblemBidomainTransMemb::LinearProblemBidomainTransMemb(): |
| 26 |
|
|
LinearProblem("Problem cardiac Bidomain first equation",3), |
| 27 |
|
✗ |
m_fePotTransMemb(nullptr), |
| 28 |
|
✗ |
m_fePotTransMembCurv(nullptr), |
| 29 |
|
✗ |
m_bdf(nullptr), |
| 30 |
|
✗ |
m_fiber(nullptr), |
| 31 |
|
✗ |
m_angleFiber(nullptr), |
| 32 |
|
✗ |
m_endocardiumDistance(nullptr) { |
| 33 |
|
✗ |
if(FelisceParam::instance().monodomain) |
| 34 |
|
✗ |
this->setNumberOfMatrix(2); |
| 35 |
|
|
|
| 36 |
|
|
} |
| 37 |
|
|
|
| 38 |
|
✗ |
LinearProblemBidomainTransMemb::~LinearProblemBidomainTransMemb() { |
| 39 |
|
✗ |
m_fstransient = nullptr; |
| 40 |
|
✗ |
m_fePotTransMemb = nullptr; |
| 41 |
|
✗ |
m_fePotTransMembCurv = nullptr; |
| 42 |
|
✗ |
m_bdf = nullptr; |
| 43 |
|
✗ |
if (m_fiber) |
| 44 |
|
✗ |
delete [] m_fiber; |
| 45 |
|
✗ |
if (m_angleFiber) |
| 46 |
|
✗ |
delete [] m_angleFiber; |
| 47 |
|
✗ |
if (m_endocardiumDistance) |
| 48 |
|
✗ |
delete [] m_endocardiumDistance; |
| 49 |
|
|
} |
| 50 |
|
|
|
| 51 |
|
✗ |
void LinearProblemBidomainTransMemb::initialize(std::vector<GeometricMeshRegion::Pointer>& mesh, FelisceTransient::Pointer fstransient, MPI_Comm& comm, bool doUseSNES) { |
| 52 |
|
✗ |
LinearProblem::initialize(mesh,comm, doUseSNES); |
| 53 |
|
✗ |
m_fstransient = fstransient; |
| 54 |
|
✗ |
std::vector<PhysicalVariable> listVariable(1); |
| 55 |
|
✗ |
std::vector<std::size_t> listNumComp(1); |
| 56 |
|
|
|
| 57 |
|
✗ |
listVariable[0] = potTransMemb; |
| 58 |
|
✗ |
listNumComp[0] = 1; |
| 59 |
|
|
|
| 60 |
|
|
//define unknown of the linear system. |
| 61 |
|
✗ |
m_listUnknown.push_back(potTransMemb); |
| 62 |
|
|
|
| 63 |
|
✗ |
definePhysicalVariable(listVariable,listNumComp); |
| 64 |
|
|
} |
| 65 |
|
|
|
| 66 |
|
✗ |
void LinearProblemBidomainTransMemb::readData(IO& io) { |
| 67 |
|
|
// Read fibers file (*.00000.vct) |
| 68 |
|
✗ |
m_fiber = new double[m_mesh[m_currentMesh]->numPoints()*3]; |
| 69 |
|
✗ |
io.readVariable(0, 0.,m_fiber, m_mesh[m_currentMesh]->numPoints()*3); |
| 70 |
|
✗ |
if (FelisceParam::instance().hasCoupledAtriaVent) { |
| 71 |
|
✗ |
m_angleFiber = new double[m_numDof]; |
| 72 |
|
✗ |
io.readVariable(2, 0.,m_angleFiber, m_numDof); |
| 73 |
|
|
} |
| 74 |
|
|
// Read distance from endocardium file for Zygote geometry (*.00000.scl) |
| 75 |
|
✗ |
if ( (FelisceParam::instance().typeOfAppliedCurrent == "zygote") || (FelisceParam::instance().typeOfAppliedCurrent == "zygoteImproved") || (FelisceParam::instance().typeOfAppliedCurrent == "heart") || (FelisceParam::instance().typeOfAppliedCurrent == "ellipseheart") ) { |
| 76 |
|
✗ |
m_endocardiumDistance = new double[m_numDof]; |
| 77 |
|
✗ |
io.readVariable(1, 0.,m_endocardiumDistance, m_numDof); |
| 78 |
|
|
} |
| 79 |
|
|
} |
| 80 |
|
✗ |
void LinearProblemBidomainTransMemb::getFiberDirection(felInt iel, int iUnknown, std::vector<double>& elemFiber) { |
| 81 |
|
✗ |
int numSupport = static_cast<int>(supportDofUnknown(iUnknown).iEle()[iel+1] - supportDofUnknown(iUnknown).iEle()[iel]); |
| 82 |
|
✗ |
elemFiber.resize( numSupport*3,0.); |
| 83 |
|
✗ |
for (int i = 0; i < numSupport; i++) { |
| 84 |
|
✗ |
elemFiber[i*3] = m_fiber[3*(supportDofUnknown(iUnknown).iSupportDof()[supportDofUnknown(iUnknown).iEle()[iel]+i])]; |
| 85 |
|
✗ |
elemFiber[i*3+1] = m_fiber[3*(supportDofUnknown(iUnknown).iSupportDof()[supportDofUnknown(iUnknown).iEle()[iel]+i])+1]; |
| 86 |
|
✗ |
elemFiber[i*3+2] = m_fiber[3*(supportDofUnknown(iUnknown).iSupportDof()[supportDofUnknown(iUnknown).iEle()[iel]+i])+2]; |
| 87 |
|
|
} |
| 88 |
|
|
} |
| 89 |
|
|
|
| 90 |
|
✗ |
void LinearProblemBidomainTransMemb::getAngleFiber(felInt iel, int iUnknown, std::vector<double>& elemAngle) { |
| 91 |
|
✗ |
int numSupport = static_cast<int>(supportDofUnknown(iUnknown).iEle()[iel+1] - supportDofUnknown(iUnknown).iEle()[iel]); |
| 92 |
|
✗ |
elemAngle.resize(numSupport,0.); |
| 93 |
|
✗ |
for (int i = 0; i < numSupport; i++) { |
| 94 |
|
✗ |
elemAngle[i] = m_angleFiber[(supportDofUnknown(iUnknown).iSupportDof()[supportDofUnknown(iUnknown).iEle()[iel]+i])]; |
| 95 |
|
|
} |
| 96 |
|
|
} |
| 97 |
|
|
|
| 98 |
|
✗ |
void LinearProblemBidomainTransMemb::initPerElementType(ElementType eltType, FlagMatrixRHS flagMatrixRHS) { |
| 99 |
|
|
IGNORE_UNUSED_ELT_TYPE; |
| 100 |
|
|
IGNORE_UNUSED_FLAG_MATRIX_RHS; |
| 101 |
|
|
//Init pointer on Finite Element, Variable or idVariable |
| 102 |
|
✗ |
m_ipotTransMemb = m_listVariable.getVariableIdList(potTransMemb); |
| 103 |
|
✗ |
m_fePotTransMemb = m_listCurrentFiniteElement[m_ipotTransMemb]; |
| 104 |
|
|
} |
| 105 |
|
|
|
| 106 |
|
✗ |
void LinearProblemBidomainTransMemb::computeElementArray(const std::vector<Point*>& elemPoint, const std::vector<felInt>& elemIdPoint, felInt& iel, FlagMatrixRHS flagMatrixRHS) { |
| 107 |
|
|
IGNORE_UNUSED_FLAG_MATRIX_RHS; |
| 108 |
|
|
IGNORE_UNUSED_ELEM_ID_POINT; |
| 109 |
|
✗ |
m_fePotTransMemb->updateMeasQuadPt(0, elemPoint); |
| 110 |
|
✗ |
m_fePotTransMemb->updateFirstDeriv(0, elemPoint); |
| 111 |
|
✗ |
std::vector<double> elemFiber; |
| 112 |
|
✗ |
getFiberDirection(iel,m_ipotTransMemb, elemFiber); |
| 113 |
|
|
|
| 114 |
|
|
//Bdf coeff not initialized at iteration 0, so need to be added to matrix(at)first iteration. |
| 115 |
|
✗ |
double coefTime = 1./m_fstransient->timeStep; |
| 116 |
|
✗ |
double coefAm = FelisceParam::instance().Am; |
| 117 |
|
✗ |
double coefCm = FelisceParam::instance().Cm; |
| 118 |
|
✗ |
double coef = m_bdf->coeffDeriv0()*coefTime*coefAm*coefCm; |
| 119 |
|
|
//1st equation : Am*C*/dT V_m |
| 120 |
|
✗ |
m_elementMat[0]->phi_i_phi_j(coef,*m_fePotTransMemb,0,0,1); |
| 121 |
|
|
|
| 122 |
|
|
//1st equation : \sigma_i^t \grad V_m |
| 123 |
|
✗ |
m_elementMat[0]->grad_phi_i_grad_phi_j(FelisceParam::instance().intraTransvTensor,*m_fePotTransMemb,0,0,1); |
| 124 |
|
|
|
| 125 |
|
|
//1st equation : (\sigma_i^l-\sigma_i^t) a vec a \grad V_m |
| 126 |
|
✗ |
m_elementMat[0]->tau_grad_phi_i_tau_grad_phi_j(FelisceParam::instance().intraFiberTensor-FelisceParam::instance().intraTransvTensor,elemFiber,*m_fePotTransMemb,0,0,1); |
| 127 |
|
|
|
| 128 |
|
|
//1st equation RHS1 : mass RHS |
| 129 |
|
✗ |
m_elementMat[1]->phi_i_phi_j(1.,*m_fePotTransMemb,0,0,1); |
| 130 |
|
|
|
| 131 |
|
✗ |
if(!FelisceParam::instance().monodomain) { |
| 132 |
|
|
//1st equation RHS2 : - \sigma_i^t \grad u_e |
| 133 |
|
✗ |
m_elementMat[2]->grad_phi_i_grad_phi_j(-1.*(FelisceParam::instance().intraTransvTensor),*m_fePotTransMemb,0,0,1); |
| 134 |
|
|
|
| 135 |
|
|
//1st equation RHS2 : - (\sigma_i^l-\sigma_i^t) a vec a \grad u_e |
| 136 |
|
✗ |
m_elementMat[2]->tau_grad_phi_i_tau_grad_phi_j(-1.*(FelisceParam::instance().intraFiberTensor-FelisceParam::instance().intraTransvTensor),elemFiber,*m_fePotTransMemb,0,0,1); |
| 137 |
|
|
} |
| 138 |
|
|
|
| 139 |
|
|
} |
| 140 |
|
|
|
| 141 |
|
|
|
| 142 |
|
✗ |
void LinearProblemBidomainTransMemb::computeElementArrayBoundaryCondition(const std::vector<Point*>& elemPoint, const std::vector<felInt>& elemIdPoint, felInt& iel, FlagMatrixRHS flagMatrixRHS) { |
| 143 |
|
|
IGNORE_UNUSED_FLAG_MATRIX_RHS; |
| 144 |
|
|
IGNORE_UNUSED_ELEM_ID_POINT;; |
| 145 |
|
✗ |
m_ipotTransMemb = m_listVariable.getVariableIdList(potTransMemb); |
| 146 |
|
✗ |
m_fePotTransMembCurv = m_listCurvilinearFiniteElement[m_ipotTransMemb]; |
| 147 |
|
|
|
| 148 |
|
✗ |
m_fePotTransMembCurv->updateMeasNormalContra(0, elemPoint); |
| 149 |
|
|
|
| 150 |
|
|
|
| 151 |
|
✗ |
if ((m_currentLabel >= 30) && (m_currentLabel <= 40)) { |
| 152 |
|
✗ |
std::vector<double> elemAngle; |
| 153 |
|
✗ |
getAngleFiber(iel,m_ipotTransMemb,elemAngle); |
| 154 |
|
|
|
| 155 |
|
✗ |
std::vector<double> elemFiber; |
| 156 |
|
✗ |
getFiberDirection(iel,m_ipotTransMemb,elemFiber); |
| 157 |
|
|
|
| 158 |
|
|
// Constant angle |
| 159 |
|
|
//double angle = acos(0.0)/2.0; |
| 160 |
|
|
|
| 161 |
|
|
// Assembling matrix(0) |
| 162 |
|
✗ |
double coefTime = 1./m_fstransient->timeStep; |
| 163 |
|
✗ |
double coefAm = FelisceParam::instance().Am; |
| 164 |
|
✗ |
double coefCm = FelisceParam::instance().Cm; |
| 165 |
|
✗ |
double coef = m_bdf->coeffDeriv0()*coefTime*coefAm*coefCm; |
| 166 |
|
|
|
| 167 |
|
|
//1st equation : Am*Cm/dt V_m |
| 168 |
|
✗ |
m_elementMatBD[0]->phi_i_phi_j(coef,*m_fePotTransMembCurv,0,0,1); |
| 169 |
|
|
|
| 170 |
|
|
//1st equation : \sigma_i^t \grad V_m |
| 171 |
|
✗ |
if (m_currentLabel < 40) { // regular atrial myocardium |
| 172 |
|
✗ |
m_elementMatBD[0]->grad_phi_i_grad_phi_j(FelisceParam::instance().intraTransvTensorAtria,*m_fePotTransMembCurv,0,0,1); |
| 173 |
|
✗ |
m_elementMatBD[0]->tau_orthotau_grad_phi_i_grad_phi_j((FelisceParam::instance().intraFiberTensorAtria - FelisceParam::instance().intraTransvTensorAtria),elemFiber,elemAngle,*m_fePotTransMembCurv,0,0,1); |
| 174 |
|
|
} |
| 175 |
|
|
|
| 176 |
|
|
|
| 177 |
|
|
//Assembling matrix(1) = mass (only first quadrant if hasAppliedExteriorCurrent = false) |
| 178 |
|
|
//1st equation RHS1 : mass RHS |
| 179 |
|
✗ |
m_elementMatBD[1]->phi_i_phi_j(1.,*m_fePotTransMembCurv,0,0,1); |
| 180 |
|
|
|
| 181 |
|
✗ |
if(!FelisceParam::instance().monodomain) { |
| 182 |
|
|
//1st equation RHS2 : - \sigma_i^t \grad u_e |
| 183 |
|
✗ |
if (m_currentLabel < 40) { // regular atrial myocardium |
| 184 |
|
✗ |
m_elementMatBD[2]->grad_phi_i_grad_phi_j(-1.0*(FelisceParam::instance().intraTransvTensorAtria),*m_fePotTransMembCurv,0,0,1); |
| 185 |
|
✗ |
m_elementMatBD[2]->tau_orthotau_grad_phi_i_grad_phi_j(-1.0*(FelisceParam::instance().intraFiberTensorAtria - FelisceParam::instance().intraTransvTensorAtria),elemFiber,elemAngle,*m_fePotTransMembCurv,0,0,1); |
| 186 |
|
|
} |
| 187 |
|
|
} |
| 188 |
|
|
} |
| 189 |
|
|
} |
| 190 |
|
|
|
| 191 |
|
✗ |
void LinearProblemBidomainTransMemb::addMatrixRHS() { |
| 192 |
|
|
// _RHS = m_mass * m_massRHS |
| 193 |
|
✗ |
mult(matrix(1),m_massRHS,vector()); |
| 194 |
|
|
|
| 195 |
|
✗ |
if(!FelisceParam::instance().monodomain) { |
| 196 |
|
|
// _RHS = _RHS + _Ksigmai * _KsigmaiRHS |
| 197 |
|
✗ |
multAdd(matrix(2),_KsigmaiRHS,vector(),vector()); |
| 198 |
|
|
} |
| 199 |
|
|
|
| 200 |
|
✗ |
m_massRHS.zeroEntries(); |
| 201 |
|
✗ |
_KsigmaiRHS.zeroEntries(); |
| 202 |
|
|
} |
| 203 |
|
|
|
| 204 |
|
|
} |
| 205 |
|
|
|