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// ______ ______ _ _ _____ ______ |
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// | ____| ____| | (_)/ ____| | ____| |
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// | |__ | |__ | | _| (___ ___| |__ |
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// | __| | __| | | | |\___ \ / __| __| |
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// | | | |____| |____| |____) | (__| |____ |
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// |_| |______|______|_|_____/ \___|______| |
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// Finite Elements for Life Sciences and Engineering |
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// |
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// License: LGL2.1 License |
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// FELiScE default license: LICENSE in root folder |
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// |
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// Main authors: E. Schenone C. Corrado |
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// |
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// System includes |
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// External includes |
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// Project includes |
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#include "Solver/linearProblemBidomainExtraCell.hpp" |
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#include "Core/felisceTransient.hpp" |
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#include "FiniteElement/elementMatrix.hpp" |
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#include "InputOutput/io.hpp" |
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namespace felisce { |
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LinearProblemBidomainExtraCell::LinearProblemBidomainExtraCell(): |
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LinearProblem("Problem cardiac Bidomain second equation",2), |
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m_fePotExtraCell(nullptr), |
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m_fePotExtraCellCurv(nullptr), |
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m_sortedSol(nullptr), |
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m_fiber(nullptr), |
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m_angleFiber(nullptr), |
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m_endocardiumDistance(nullptr) |
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{} |
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LinearProblemBidomainExtraCell::~LinearProblemBidomainExtraCell() { |
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m_fstransient = nullptr; |
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m_fePotExtraCell = nullptr; |
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m_fePotExtraCellCurv = nullptr; |
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if (m_fiber) |
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delete [] m_fiber; |
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if (m_angleFiber) |
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delete [] m_angleFiber; |
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if (m_endocardiumDistance) |
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delete [] m_endocardiumDistance; |
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delete [] m_sortedSol; |
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} |
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void LinearProblemBidomainExtraCell::initialize(std::vector<GeometricMeshRegion::Pointer>& mesh, FelisceTransient::Pointer fstransient, MPI_Comm& comm, bool doUseSNES) { |
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LinearProblem::initialize(mesh,comm, doUseSNES); |
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m_fstransient = fstransient; |
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std::vector<PhysicalVariable> listVariable(1); |
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std::vector<std::size_t> listNumComp(1); |
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listVariable[0] = potExtraCell; |
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listNumComp[0] = 1; |
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//define unknown of the linear system. |
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m_listUnknown.push_back(potExtraCell); |
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definePhysicalVariable(listVariable,listNumComp); |
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} |
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void LinearProblemBidomainExtraCell::readData(IO& io) { |
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// Read fibers file (*.00000.vct) |
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m_fiber = new double[m_mesh[m_currentMesh]->numPoints()*3]; |
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io.readVariable(0, 0.,m_fiber, m_mesh[m_currentMesh]->numPoints()*3); |
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if (FelisceParam::instance().hasCoupledAtriaVent) { |
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m_angleFiber = new double[m_numDof]; |
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io.readVariable(2, 0.,m_angleFiber, m_numDof); |
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} |
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} |
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void LinearProblemBidomainExtraCell::getFiberDirection(felInt iel, int iUnknown, std::vector<double>& elemFiber) { |
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int numSupport = static_cast<int>(supportDofUnknown(iUnknown).iEle()[iel+1] - supportDofUnknown(iUnknown).iEle()[iel]); |
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elemFiber.resize( numSupport*3,0.); |
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for (int i = 0; i < numSupport; i++) { |
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elemFiber[i*3] = m_fiber[3*(supportDofUnknown(iUnknown).iSupportDof()[supportDofUnknown(iUnknown).iEle()[iel]+i])]; |
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elemFiber[i*3+1] = m_fiber[3*(supportDofUnknown(iUnknown).iSupportDof()[supportDofUnknown(iUnknown).iEle()[iel]+i])+1]; |
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elemFiber[i*3+2] = m_fiber[3*(supportDofUnknown(iUnknown).iSupportDof()[supportDofUnknown(iUnknown).iEle()[iel]+i])+2]; |
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} |
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} |
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void LinearProblemBidomainExtraCell::getAngleFiber(felInt iel, int iUnknown, std::vector<double>& elemAngle) { |
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int numSupport = static_cast<int>(supportDofUnknown(iUnknown).iEle()[iel+1] - supportDofUnknown(iUnknown).iEle()[iel]); |
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elemAngle.resize(numSupport,0.); |
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for (int i = 0; i < numSupport; i++) { |
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elemAngle[i] = m_angleFiber[(supportDofUnknown(iUnknown).iSupportDof()[supportDofUnknown(iUnknown).iEle()[iel]+i])]; |
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} |
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} |
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void LinearProblemBidomainExtraCell::initPerElementType(ElementType eltType, FlagMatrixRHS flagMatrixRHS) { |
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IGNORE_UNUSED_FLAG_MATRIX_RHS; |
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IGNORE_UNUSED_ELT_TYPE; |
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//Init pointer on Finite Element, Variable or idVariable |
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// m_ipotTransMemb = m_listVariable.getVariableIdList(potTransMemb); |
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m_ipotExtraCell = m_listVariable.getVariableIdList(potExtraCell); |
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// m_fePotTransMemb = m_listCurrentFiniteElement[m_ipotTransMemb]; |
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m_fePotExtraCell = m_listCurrentFiniteElement[m_ipotExtraCell]; |
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} |
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void LinearProblemBidomainExtraCell::computeElementArray(const std::vector<Point*>& elemPoint, const std::vector<felInt>& elemIdPoint, felInt& iel, FlagMatrixRHS flagMatrixRHS) { |
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IGNORE_UNUSED_ELEM_ID_POINT; |
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IGNORE_UNUSED_FLAG_MATRIX_RHS; |
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m_fePotExtraCell->updateFirstDeriv(0, elemPoint); |
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std::vector<double> elemFiber; |
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getFiberDirection(iel,m_ipotExtraCell, elemFiber); |
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double eps = 1.0e-6; |
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m_elementMat[0]->phi_i_phi_j(eps,*m_fePotExtraCell,0,0,1); |
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//2nd equation : (\sigma_i^t+\sigma_e^t)) \grad u_e |
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m_elementMat[0]->grad_phi_i_grad_phi_j(FelisceParam::instance().intraTransvTensor+FelisceParam::instance().extraTransvTensor,*m_fePotExtraCell,0,0,1); |
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//2nd equation : ((\sigma_i^l-\sigma_i^t)+(\sigma_e^l-\sigma_e^t)) a vec a \grad u_e |
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m_elementMat[0]->tau_grad_phi_i_tau_grad_phi_j((FelisceParam::instance().intraFiberTensor-FelisceParam::instance().intraTransvTensor)+(FelisceParam::instance().extraFiberTensor-FelisceParam::instance().extraTransvTensor),elemFiber,*m_fePotExtraCell,0,0,1); |
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//2nd equation RHS : -(\sigma_i^t) \grad V_m |
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m_elementMat[1]->grad_phi_i_grad_phi_j(-1.*(FelisceParam::instance().intraTransvTensor),*m_fePotExtraCell,0,0,1); |
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//2nd equation RHS : -(\sigma_i^l-\sigma_i^t) a vec a \grad V_m |
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m_elementMat[1]->tau_grad_phi_i_tau_grad_phi_j(-1.*(FelisceParam::instance().intraFiberTensor-FelisceParam::instance().intraTransvTensor),elemFiber,*m_fePotExtraCell,0,0,1); |
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} |
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void LinearProblemBidomainExtraCell::computeElementArrayBoundaryCondition(const std::vector<Point*>& elemPoint, const std::vector<felInt>& elemIdPoint, felInt& iel, FlagMatrixRHS flagMatrixRHS) { |
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(void) elemIdPoint; |
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(void) flagMatrixRHS; |
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m_ipotExtraCell = m_listVariable.getVariableIdList(potExtraCell); |
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m_fePotExtraCellCurv = m_listCurvilinearFiniteElement[m_ipotExtraCell]; |
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m_fePotExtraCellCurv->updateMeasNormalContra(0, elemPoint); |
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if ((m_currentLabel >= 30) && (m_currentLabel <= 40)) { |
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std::vector<double> elemAngle; |
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getAngleFiber(iel,m_ipotExtraCell,elemAngle); |
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std::vector<double> elemFiber; |
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getFiberDirection(iel,m_ipotExtraCell,elemFiber); |
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// Constant angle |
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//double angle = acos(0.0)/2.0; |
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//2nd equation : (\sigma_i^t+\sigma_e^t) \grad u_e |
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double eps = 1.0e-6; |
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m_elementMatBD[0]->phi_i_phi_j(eps,*m_fePotExtraCellCurv,0,0,1); |
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if (m_currentLabel < 40) { // regular atrial myocardium |
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m_elementMatBD[0]->grad_phi_i_grad_phi_j((FelisceParam::instance().intraTransvTensorAtria+FelisceParam::instance().extraTransvTensorAtria),*m_fePotExtraCellCurv,0,0,1); |
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m_elementMatBD[0]->tau_orthotau_grad_phi_i_grad_phi_j((FelisceParam::instance().intraFiberTensorAtria - FelisceParam::instance().intraTransvTensorAtria + FelisceParam::instance().extraFiberTensorAtria - FelisceParam::instance().extraTransvTensorAtria),elemFiber,elemAngle,*m_fePotExtraCellCurv,0,0,1); |
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} else if (m_currentLabel == 40) { // connexion aera |
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m_elementMatBD[0]->grad_phi_i_grad_phi_j((FelisceParam::instance().intraTransvTensorAtria+FelisceParam::instance().extraTransvTensorAtria)*0.005,*m_fePotExtraCellCurv,0,0,1); |
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} |
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//2nd equation RHS : -(\sigma_i^t) \grad V_m |
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if (m_currentLabel < 40) { // regular atrial myocardium |
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m_elementMatBD[1]->grad_phi_i_grad_phi_j(-1.0*(FelisceParam::instance().intraTransvTensorAtria),*m_fePotExtraCellCurv,0,0,1); |
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m_elementMatBD[1]->tau_orthotau_grad_phi_i_grad_phi_j(-1.0*(FelisceParam::instance().intraFiberTensorAtria - FelisceParam::instance().intraTransvTensorAtria),elemFiber,elemAngle,*m_fePotExtraCellCurv,0,0,1); |
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} else if (m_currentLabel == 40) { // connexion aera |
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m_elementMatBD[1]->grad_phi_i_grad_phi_j(-0.005*(FelisceParam::instance().intraTransvTensorAtria),*m_fePotExtraCellCurv,0,0,1); |
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} |
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} |
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} |
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void LinearProblemBidomainExtraCell::addMatrixRHS() { |
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// _RHS = _Ksigmai * _RHS |
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PetscVector tmpB; |
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tmpB.duplicateFrom(vector()); |
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tmpB.copyFrom(vector()); |
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mult(matrix(1),tmpB,vector()); |
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tmpB.destroy(); |
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} |
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} |
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