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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: A. Collin |
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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/linearProblemBidomainCurv.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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{ |
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LinearProblemBidomainCurv::LinearProblemBidomainCurv(): |
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LinearProblem("Problem cardiac Bidomain",2), |
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m_sortedSol(nullptr), |
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allocateSeqVec(false), |
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allocateLevelSet(false), |
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allocateSol_n_1(false), |
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m_avHeavU0(0.), |
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m_avHeavMinusU0(0.) { |
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if (allocateSeqVec) { |
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m_seqIon.destroy(); |
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m_seqBdfRHS.destroy(); |
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} |
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if (allocateLevelSet) { |
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m_levelSet.destroy(); |
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m_levelSetSeq.destroy(); |
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} |
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if (allocateSol_n_1) { |
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m_sol_n_1.destroy(); |
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} |
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} |
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LinearProblemBidomainCurv::~LinearProblemBidomainCurv() { |
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delete [] m_sortedSol; |
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} |
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void LinearProblemBidomainCurv::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(2); |
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std::vector<std::size_t> listNumComp(2); |
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listVariable[0] = potTransMemb; |
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listNumComp[0] = 1; |
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listVariable[1] = potExtraCell; |
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listNumComp[1] = 1; |
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//define unknown of the linear system. |
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m_listUnknown.push_back(potTransMemb); |
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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 LinearProblemBidomainCurv::readData(IO& io) { |
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m_vectorFiber.resize(m_mesh[m_currentMesh]->numPoints()*3); |
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io.readVariable(0, 0.,&m_vectorFiber[0], m_vectorFiber.size()); |
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m_vectorAngle.resize(m_mesh[m_currentMesh]->numPoints()); |
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io.readVariable(1, 0.,&m_vectorAngle[0],m_vectorAngle.size()); |
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if (!FelisceParam::instance().hasHeteroCondAtria) { |
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m_vectorRef.resize(m_mesh[m_currentMesh]->numPoints()); //m_numDof; |
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io.readVariable(2, 0.,&m_vectorRef[0],m_vectorRef.size()); |
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} |
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} |
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void LinearProblemBidomainCurv::readDataForDA(IO& io, double iteration) { |
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m_data.resize(m_mesh[m_currentMesh]->numPoints()); |
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if (FelisceParam::instance().typeOfAppliedCurrent != "atria") |
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io.readVariable(2, iteration*m_fstransient->timeStep, &m_data[0],m_data.size()); |
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else |
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io.readVariable(3, iteration*m_fstransient->timeStep, &m_data[0],m_data.size()); |
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} |
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void LinearProblemBidomainCurv::getFiberDirection(felInt iel, int iUnknown, std::vector<double>& elemFiber) { |
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//Warning: the fibers must be normalized. |
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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_vectorFiber[3*(supportDofUnknown(iUnknown).iSupportDof()[supportDofUnknown(iUnknown).iEle()[iel]+i])]; |
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elemFiber[i*3+1] = m_vectorFiber[3*(supportDofUnknown(iUnknown).iSupportDof()[supportDofUnknown(iUnknown).iEle()[iel]+i])+1]; |
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elemFiber[i*3+2] = m_vectorFiber[3*(supportDofUnknown(iUnknown).iSupportDof()[supportDofUnknown(iUnknown).iEle()[iel]+i])+2]; |
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} |
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} |
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void LinearProblemBidomainCurv::getAngle(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_vectorAngle[(supportDofUnknown(iUnknown).iSupportDof()[supportDofUnknown(iUnknown).iEle()[iel]+i])]; |
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} |
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} |
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void LinearProblemBidomainCurv::getData(felInt iel, int iUnknown, std::vector<double>& elemData) { |
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//double& vGate = FelisceParam::instance().vGate; |
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double vGate = -67.; |
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int numSupport = static_cast<int>(supportDofUnknown(iUnknown).iEle()[iel+1] - supportDofUnknown(iUnknown).iEle()[iel]); |
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elemData.clear(); |
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elemData.resize(numSupport,0.); |
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for (int i = 0; i < numSupport; i++) { |
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if (m_data[(supportDofUnknown(iUnknown).iSupportDof()[supportDofUnknown(iUnknown).iEle()[iel]+i])] > vGate) { |
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elemData[i] = 1.0; |
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} else |
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elemData[i] = -1.0; |
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} |
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} |
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void LinearProblemBidomainCurv::initPerElementTypeBD(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_listCurvilinearFiniteElement[m_ipotTransMemb]; |
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m_fePotExtraCell = m_fePotTransMemb; |
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if (FelisceParam::instance().dataAssimilation) { |
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m_elemFieldVm.initialize(DOF_FIELD,*m_fePotTransMemb,1); |
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m_elemFieldLSVm.initialize(DOF_FIELD,*m_fePotTransMemb,1); |
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m_avHeavU0 = averageLS(m_fePotTransMemb,m_ipotTransMemb,0); |
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m_avHeavMinusU0 = averageLS(m_fePotTransMemb,m_ipotTransMemb,1); |
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} |
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} |
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double LinearProblemBidomainCurv::conductivityHom(int currentLabel) { |
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double conductivity = 1.0; |
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if (FelisceParam::instance().hasHeteroCondAtria) { |
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if (std::fabs(currentLabel - 31.0) < 1.0e-12) { //SN |
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conductivity = 0.3; |
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} else if (std::fabs(currentLabel - 32.0) < 1.0e-12) { //CT |
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conductivity = 3.0; |
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} else if (std::fabs(currentLabel - 33.0) < 1.0e-12) { //BB |
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conductivity = 4.75; |
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} else if (std::fabs(currentLabel - 34.0) < 1.0e-12) { //RAI |
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conductivity = 0.375; |
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} else if (std::fabs(currentLabel - 35.0) < 1.0e-12) { //PM |
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conductivity = 1.5; |
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} else { //regular atria and F0 |
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conductivity = 1.0; |
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} |
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} |
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return conductivity; |
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} |
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double LinearProblemBidomainCurv::conductivityHet(int currentLabel) { |
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double conductivity = 1.0; |
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if (FelisceParam::instance().hasHeteroCondAtria) { |
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if (std::fabs(currentLabel - 31.0) < 1.0e-12) { //SN |
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conductivity = 0.36; |
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} else if (std::fabs(currentLabel - 32.0) < 1.0e-12) { //CT |
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conductivity = 4.5; |
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} else if (std::fabs(currentLabel - 33.0) < 1.0e-12) { //BB |
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conductivity = 7.75; |
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} else if (std::fabs(currentLabel - 34.0) < 1.0e-12) { //RAI |
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conductivity = 0.45; |
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} else if (std::fabs(currentLabel - 35.0) < 1.0e-12) { //PM |
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conductivity = 1.8; |
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} else if (std::fabs(currentLabel - 36.0) < 1.0e-12) { //F0 |
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conductivity = 0.9; |
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} else { //regular atria |
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conductivity = 1.0; |
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} |
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} |
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return conductivity; |
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} |
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void LinearProblemBidomainCurv::initLevelSet() { |
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m_levelSet.duplicateFrom(solution()); |
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m_levelSet.zeroEntries(); |
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m_levelSet.assembly(); |
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m_levelSetSeq.createSeq(PETSC_COMM_SELF,m_numDof); |
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m_levelSetSeq.set(0.0); |
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allocateLevelSet = true; |
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} |
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void LinearProblemBidomainCurv::levelSet(double min, double max) { |
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//double& vGate = FelisceParam::instance().vGate; |
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double vGate = -67.; |
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felInt pos; |
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double value_sol; |
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double value_levelSet; |
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for (felInt i = 0; i < numDofLocalPerUnknown(potTransMemb) ; i++) { |
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ISLocalToGlobalMappingApply(mappingDofLocalToDofGlobal(potTransMemb),1,&i,&pos); |
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solution().getValues(1,&pos,&value_sol); |
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if( value_sol > vGate) { |
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value_levelSet = max; |
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} else if( value_sol < vGate) { |
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value_levelSet = min; |
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} else |
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value_levelSet = 0.0; |
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m_levelSet.setValue(pos,value_levelSet, INSERT_VALUES); |
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} |
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m_levelSet.assembly(); |
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gatherVector(m_levelSet, m_levelSetSeq); |
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} |
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void LinearProblemBidomainCurv::initSolutionTimeBef() { |
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m_sol_n_1.duplicateFrom(solution()); |
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m_sol_n_1.copyFrom(solution()); |
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allocateSol_n_1 = true; |
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} |
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void LinearProblemBidomainCurv::solutionTimeBef() { |
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m_sol_n_1.copyFrom(solution()); |
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} |
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double LinearProblemBidomainCurv::averageLS(CurvilinearFiniteElement* fePtr, int idfe, int minus) { |
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FEL_ASSERT(fePtr) |
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CurvilinearFiniteElement& fe = *fePtr; |
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Variable variablePotTransMemb = m_listVariable[idfe]; |
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int numComp = variablePotTransMemb.numComponent(); |
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// dofValue contains : values in dof by element. |
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double dofValueSeqSol[fe.numDof()*numComp]; |
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// idGlobalDof contains: global number od dof by element. |
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felInt idGlobalDof[fe.numDof()*numComp]; |
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//geometric element type in the mesh. |
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ElementType eltType; |
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//number of points per geometric element. |
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int numPointPerElt = 0; |
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//number of element for one label and one eltType. |
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felInt numEltPerLabel = 0; |
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//Points of the current element. |
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std::vector<Point*> elemPoint; |
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//Id of points of the element. |
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std::vector<felInt> elemIdPoint; |
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// use to identify global id of dof. |
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felInt idDof; |
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felInt cpt = 0; |
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double integralValue = 0.; |
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double heavisideMeasure = 0.; |
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double elementValueHeav = 0.; |
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double elementValueHeavU0 = 0.; |
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//Id link element to its supportDof. |
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felInt ielSupportDof; |
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double vGate = -67.; |
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// initialize global numbering from mesh. |
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felInt numElement[ GeometricMeshRegion::m_numTypesOfElement ]; |
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for (int ityp=0; ityp<GeometricMeshRegion::m_numTypesOfElement; ityp++ ) { |
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eltType = (ElementType)ityp; |
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numElement[eltType] = 0; |
| 272 |
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} |
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// Loop on elementType. |
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const std::vector<ElementType>& bagElementTypeDomain = m_meshLocal[m_currentMesh]->bagElementTypeDomain(); |
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for (std::size_t i = 0; i < bagElementTypeDomain.size(); ++i) { |
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eltType = bagElementTypeDomain[i]; |
| 278 |
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numPointPerElt = GeometricMeshRegion::m_numPointsPerElt[eltType]; |
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elemPoint.resize(numPointPerElt, nullptr); |
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elemIdPoint.resize(numPointPerElt,0); |
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// Loop on region define in the mesh. |
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for(auto itRef = m_meshLocal[m_currentMesh]->intRefToBegEndMaps[eltType].begin(); |
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itRef != m_meshLocal[m_currentMesh]->intRefToBegEndMaps[eltType].end(); itRef++) { |
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numEltPerLabel = itRef->second.second; |
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// Loop on elements. |
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for ( felInt iel = 0; iel < numEltPerLabel; iel++) { |
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// get points of element. |
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setElemPoint(eltType, numElement[eltType], elemPoint, elemIdPoint, &ielSupportDof); |
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// compute measure of the current element. |
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fe.updateMeas(0, elemPoint); |
| 293 |
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cpt = 0; |
| 295 |
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// identify global id of Dof for the current element. |
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for(int iComp = 0; iComp<numComp; iComp++) { |
| 297 |
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for(int iDof=0; iDof<fe.numDof(); iDof++) { |
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dof().loc2glob(ielSupportDof,iDof,m_ipotTransMemb,iComp,idDof); |
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idGlobalDof[cpt] = idDof; |
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cpt++; |
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} |
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} |
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✗ |
std::vector<double> dofValueData; |
| 305 |
|
✗ |
getData(ielSupportDof, m_ipotTransMemb, dofValueData); |
| 306 |
|
|
|
| 307 |
|
|
//mapping to obtain new global numbering. (I/O array: idGlobalDof). |
| 308 |
|
✗ |
AOApplicationToPetsc(m_ao,fe.numDof()*numComp,idGlobalDof); |
| 309 |
|
|
//gets values of associate dofs. |
| 310 |
|
|
|
| 311 |
|
✗ |
this->sequentialSolution().getValues(fe.numDof()*numComp,idGlobalDof,dofValueSeqSol); |
| 312 |
|
|
|
| 313 |
|
|
//Interpolation |
| 314 |
|
✗ |
for(int ig=0; ig<fe.numQuadraturePoint(); ig++) { |
| 315 |
|
✗ |
elementValueHeavU0 = 0.; |
| 316 |
|
✗ |
elementValueHeav = 0.; |
| 317 |
|
✗ |
cpt = 0; |
| 318 |
|
✗ |
for(int icomp=0; icomp<numComp; icomp++) { |
| 319 |
|
✗ |
for(int j=0; j<fe.numDof(); j++) { |
| 320 |
|
✗ |
if (minus == 1) { |
| 321 |
|
✗ |
if (dofValueSeqSol[cpt] < vGate) { |
| 322 |
|
✗ |
elementValueHeavU0 += fe.phi[ig](j) * 2. * dofValueData[cpt]; |
| 323 |
|
✗ |
elementValueHeav += fe.phi[ig](j) * 2.; |
| 324 |
|
|
} |
| 325 |
|
|
} else { |
| 326 |
|
✗ |
if (dofValueSeqSol[cpt] > vGate) { |
| 327 |
|
✗ |
elementValueHeavU0 += fe.phi[ig](j) * 2. * dofValueData[cpt]; |
| 328 |
|
✗ |
elementValueHeav += fe.phi[ig](j) * 2.; |
| 329 |
|
|
} |
| 330 |
|
|
} |
| 331 |
|
|
|
| 332 |
|
✗ |
cpt++; |
| 333 |
|
|
} |
| 334 |
|
✗ |
integralValue += elementValueHeavU0 * fe.weightMeas(ig); |
| 335 |
|
✗ |
heavisideMeasure += elementValueHeav * fe.weightMeas(ig); |
| 336 |
|
|
} |
| 337 |
|
|
} |
| 338 |
|
✗ |
numElement[eltType]++; |
| 339 |
|
|
} |
| 340 |
|
|
} |
| 341 |
|
|
} |
| 342 |
|
|
|
| 343 |
|
✗ |
double valueReceive = 0.; |
| 344 |
|
✗ |
MPI_Allreduce(&integralValue,&valueReceive, 1,MPI_DOUBLE,MPI_SUM,MpiInfo::petscComm()); |
| 345 |
|
✗ |
integralValue = valueReceive; |
| 346 |
|
✗ |
valueReceive = 0.; |
| 347 |
|
✗ |
MPI_Allreduce(&heavisideMeasure,&valueReceive, 1,MPI_DOUBLE,MPI_SUM,MpiInfo::petscComm()); |
| 348 |
|
✗ |
heavisideMeasure = valueReceive; |
| 349 |
|
|
|
| 350 |
|
✗ |
return integralValue/(heavisideMeasure+0.000000001); |
| 351 |
|
|
} |
| 352 |
|
|
|
| 353 |
|
|
|
| 354 |
|
✗ |
void LinearProblemBidomainCurv::computeElementArrayBD(const std::vector<Point*>& elemPoint, const std::vector<felInt>& elemIdPoint, felInt& iel, FlagMatrixRHS flagMatrixRHS) { |
| 355 |
|
|
IGNORE_UNUSED_ELEM_ID_POINT; |
| 356 |
|
|
|
| 357 |
|
✗ |
m_fePotTransMemb->updateMeasNormalContra(0, elemPoint); |
| 358 |
|
|
|
| 359 |
|
✗ |
if (flagMatrixRHS == FlagMatrixRHS::only_rhs) { |
| 360 |
|
✗ |
if (FelisceParam::instance().dataAssimilation) { |
| 361 |
|
✗ |
std::vector<double> elemData; |
| 362 |
|
✗ |
getData(iel,m_ipotTransMemb,elemData); |
| 363 |
|
|
|
| 364 |
|
✗ |
m_elemFieldVm.setValue(this->sequentialSolution(), *m_fePotTransMemb, iel, m_ipotTransMemb, m_ao, dof()); |
| 365 |
|
|
|
| 366 |
|
✗ |
m_elemFieldLSVm.setValue(m_levelSetSeq, *m_fePotTransMemb, iel, m_ipotTransMemb, m_ao, dof()); |
| 367 |
|
|
|
| 368 |
|
✗ |
m_elementVectorBD[0]->grad_u_dot_grad_LSu_v(1.0, m_elemFieldVm, m_elemFieldLSVm, elemData, m_avHeavU0, m_avHeavMinusU0, FelisceParam::instance().insidePar, FelisceParam::instance().outsidePar, *m_fePotTransMemb,0); |
| 369 |
|
|
} |
| 370 |
|
|
} else { |
| 371 |
|
|
// Assembling matrix(0) |
| 372 |
|
✗ |
const double coefTime = 1./m_fstransient->timeStep; |
| 373 |
|
✗ |
const double coefAm = FelisceParam::instance().Am; |
| 374 |
|
✗ |
const double coefCm = FelisceParam::instance().Cm; |
| 375 |
|
✗ |
const double coef = m_bdf->coeffDeriv0()*coefTime*coefAm*coefCm; |
| 376 |
|
|
|
| 377 |
|
|
//1st equation : Am*Cm/dt V_m |
| 378 |
|
|
|
| 379 |
|
✗ |
m_elementMatBD[0]->phi_i_phi_j(coef,*m_fePotTransMemb,0,0,1); |
| 380 |
|
|
|
| 381 |
|
✗ |
if (FelisceParam::instance().testCase == 1) { |
| 382 |
|
✗ |
std::vector<double> elemFiber; |
| 383 |
|
✗ |
getFiberDirection(iel,m_ipotTransMemb,elemFiber); |
| 384 |
|
|
|
| 385 |
|
✗ |
std::vector<double> elemAngle; |
| 386 |
|
✗ |
getAngle(iel,m_ipotTransMemb,elemAngle); |
| 387 |
|
|
|
| 388 |
|
|
//1st equation : \sigma_i^t \grad V_m |
| 389 |
|
✗ |
m_elementMatBD[0]->grad_phi_i_grad_phi_j(FelisceParam::instance().intraTransvTensor*conductivityHom(m_currentLabel),*m_fePotTransMemb,0,0,1); |
| 390 |
|
✗ |
m_elementMatBD[0]->tau_orthotau_grad_phi_i_grad_phi_j((FelisceParam::instance().intraFiberTensor - FelisceParam::instance().intraTransvTensor)*conductivityHet(m_currentLabel),elemFiber,elemAngle,*m_fePotTransMemb,0,0,1); |
| 391 |
|
|
//m_elementMatBD[0]->tau_grad_phi_i_tau_grad_phi_j((FelisceParam::instance().intraFiberTensor - FelisceParam::instance().intraTransvTensor),elemFiber,*m_fePotTransMemb,0,0,1); |
| 392 |
|
|
|
| 393 |
|
|
//1st equation : \sigma_i^t \grad u_e |
| 394 |
|
✗ |
m_elementMatBD[0]->grad_phi_i_grad_phi_j(FelisceParam::instance().intraTransvTensor*conductivityHom(m_currentLabel),*m_fePotExtraCell,0,1,1); |
| 395 |
|
✗ |
m_elementMatBD[0]->tau_orthotau_grad_phi_i_grad_phi_j((FelisceParam::instance().intraFiberTensor - FelisceParam::instance().intraTransvTensor)*conductivityHet(m_currentLabel),elemFiber,elemAngle,*m_fePotExtraCell,0,1,1); |
| 396 |
|
|
//m_elementMatBD[0]->tau_grad_phi_i_tau_grad_phi_j((FelisceParam::instance().intraFiberTensor - FelisceParam::instance().intraTransvTensor),elemFiber,*m_fePotExtraCell,0,1,1); |
| 397 |
|
|
|
| 398 |
|
|
//2nd equation : \sigma_i^t \grad V_m |
| 399 |
|
✗ |
m_elementMatBD[0]->grad_phi_i_grad_phi_j(FelisceParam::instance().intraTransvTensor*conductivityHom(m_currentLabel),*m_fePotTransMemb,1,0,1); |
| 400 |
|
✗ |
m_elementMatBD[0]->tau_orthotau_grad_phi_i_grad_phi_j((FelisceParam::instance().intraFiberTensor - FelisceParam::instance().intraTransvTensor)*conductivityHet(m_currentLabel),elemFiber,elemAngle,*m_fePotTransMemb,1,0,1); |
| 401 |
|
|
//m_elementMatBD[0]->tau_grad_phi_i_tau_grad_phi_j((FelisceParam::instance().intraFiberTensor - FelisceParam::instance().intraTransvTensor),elemFiber,*m_fePotTransMemb,1,0,1); |
| 402 |
|
|
|
| 403 |
|
|
//2nd equation : \eps u_e |
| 404 |
|
✗ |
double eps = 1.0e-6; |
| 405 |
|
✗ |
m_elementMatBD[0]->phi_i_phi_j(eps,*m_fePotExtraCell,1,1,1); |
| 406 |
|
|
|
| 407 |
|
|
//2nd equation : (\sigma_i^t+\sigma_e^t) \grad u_e |
| 408 |
|
✗ |
m_elementMatBD[0]->grad_phi_i_grad_phi_j((FelisceParam::instance().intraTransvTensor+FelisceParam::instance().extraTransvTensor)*conductivityHom(m_currentLabel),*m_fePotExtraCell,1,1,1); |
| 409 |
|
✗ |
m_elementMatBD[0]->tau_orthotau_grad_phi_i_grad_phi_j((FelisceParam::instance().intraFiberTensor - FelisceParam::instance().intraTransvTensor + FelisceParam::instance().extraFiberTensor - FelisceParam::instance().extraTransvTensor)*conductivityHet(m_currentLabel),elemFiber,elemAngle,*m_fePotExtraCell,1,1,1); |
| 410 |
|
|
//m_elementMatBD[0]->tau_grad_phi_i_tau_grad_phi_j((FelisceParam::instance().intraFiberTensor - FelisceParam::instance().intraTransvTensor + FelisceParam::instance().extraFiberTensor - FelisceParam::instance().extraTransvTensor),elemFiber,*m_fePotExtraCell,1,1,1); |
| 411 |
|
✗ |
} else { |
| 412 |
|
|
//1st equation : \sigma_i^t \grad V_m |
| 413 |
|
✗ |
m_elementMatBD[0]->grad_phi_i_grad_phi_j(FelisceParam::instance().intraTransvTensor,*m_fePotTransMemb,0,0,1); |
| 414 |
|
|
|
| 415 |
|
|
//1st equation : \sigma_i^t \grad u_e |
| 416 |
|
✗ |
m_elementMatBD[0]->grad_phi_i_grad_phi_j(FelisceParam::instance().intraTransvTensor,*m_fePotExtraCell,0,1,1); |
| 417 |
|
|
|
| 418 |
|
|
//2nd equation : \sigma_i^t \grad V_m |
| 419 |
|
✗ |
m_elementMatBD[0]->grad_phi_i_grad_phi_j(FelisceParam::instance().intraTransvTensor,*m_fePotTransMemb,1,0,1); |
| 420 |
|
|
|
| 421 |
|
|
//2nd equation : \eps u_e |
| 422 |
|
✗ |
double eps = 1.0e-6; |
| 423 |
|
✗ |
m_elementMatBD[0]->phi_i_phi_j(eps,*m_fePotExtraCell,1,1,1); |
| 424 |
|
|
|
| 425 |
|
|
//2nd equation : (\sigma_i^t+\sigma_e^t) \grad u_e |
| 426 |
|
✗ |
m_elementMatBD[0]->grad_phi_i_grad_phi_j((FelisceParam::instance().intraTransvTensor+FelisceParam::instance().extraTransvTensor),*m_fePotExtraCell,1,1,1); |
| 427 |
|
|
|
| 428 |
|
|
} |
| 429 |
|
|
|
| 430 |
|
|
//Assembling matrix(1) = mass (only first quadrant if hasAppliedExteriorCurrent = false) |
| 431 |
|
✗ |
m_elementMatBD[1]->phi_i_phi_j(1.,*m_fePotTransMemb,0,0,1); |
| 432 |
|
✗ |
if (FelisceParam::instance().hasAppliedExteriorCurrent) |
| 433 |
|
✗ |
m_elementMatBD[1]->phi_i_phi_j(1.,*m_fePotTransMemb,1,1,1); |
| 434 |
|
|
|
| 435 |
|
✗ |
if (FelisceParam::instance().dataAssimilation) { |
| 436 |
|
✗ |
std::vector<double> elemData; |
| 437 |
|
✗ |
getData(iel,m_ipotTransMemb,elemData); |
| 438 |
|
✗ |
m_elemFieldVm.setValue(this->sequentialSolution(), *m_fePotTransMemb, iel, m_ipotTransMemb, m_ao, dof()); |
| 439 |
|
|
|
| 440 |
|
✗ |
m_elemFieldLSVm.setValue(m_levelSetSeq, *m_fePotTransMemb, iel, m_ipotTransMemb, m_ao, dof()); |
| 441 |
|
✗ |
m_elementVectorBD[0]->grad_u_dot_grad_LSu_v(1.0, m_elemFieldVm, m_elemFieldLSVm, elemData, m_avHeavU0, m_avHeavMinusU0, FelisceParam::instance().insidePar, FelisceParam::instance().outsidePar, *m_fePotTransMemb,0); |
| 442 |
|
|
} |
| 443 |
|
|
} |
| 444 |
|
|
|
| 445 |
|
|
|
| 446 |
|
|
} |
| 447 |
|
|
|
| 448 |
|
✗ |
void LinearProblemBidomainCurv::addMatrixRHS() { |
| 449 |
|
|
// _RHS = m_mass * _RHS. |
| 450 |
|
✗ |
PetscVector tmpB; |
| 451 |
|
✗ |
tmpB.duplicateFrom(vector()); |
| 452 |
|
✗ |
tmpB.copyFrom(vector()); |
| 453 |
|
✗ |
mult(matrix(1),tmpB,vector()); |
| 454 |
|
✗ |
tmpB.destroy(); |
| 455 |
|
|
} |
| 456 |
|
|
|
| 457 |
|
✗ |
void LinearProblemBidomainCurv::writeEnsightScalar(double* solValue, int idIter, std::string varName) { |
| 458 |
|
✗ |
std::string iteration; |
| 459 |
|
✗ |
if (idIter < 10) |
| 460 |
|
✗ |
iteration = "0000" + std::to_string(idIter); |
| 461 |
|
✗ |
else if (idIter < 100) |
| 462 |
|
✗ |
iteration = "000" + std::to_string(idIter); |
| 463 |
|
✗ |
else if (idIter < 1000) |
| 464 |
|
✗ |
iteration = "00" + std::to_string(idIter); |
| 465 |
|
✗ |
else if (idIter < 10000) |
| 466 |
|
✗ |
iteration = "0" + std::to_string(idIter); |
| 467 |
|
✗ |
else if (idIter < 100000) |
| 468 |
|
✗ |
iteration = std::to_string(idIter); |
| 469 |
|
|
|
| 470 |
|
✗ |
std::string fileName = FelisceParam::instance().resultDir + "/" + varName + "." + iteration + ".scl"; |
| 471 |
|
|
FILE * solFile; |
| 472 |
|
✗ |
solFile = fopen(fileName.c_str(),"w"); |
| 473 |
|
✗ |
fprintf(solFile, "Scalar per node\n"); |
| 474 |
|
✗ |
int count = 0; |
| 475 |
|
✗ |
for(int j=0; j < static_cast<int>(m_numDof/2); j++) { |
| 476 |
|
✗ |
fprintf(solFile,"%12.5e", solValue[j]); |
| 477 |
|
✗ |
count++; |
| 478 |
|
✗ |
if(count == 6) { |
| 479 |
|
✗ |
fprintf(solFile,"\n"); |
| 480 |
|
✗ |
count = 0; |
| 481 |
|
|
} |
| 482 |
|
|
} |
| 483 |
|
✗ |
fprintf(solFile,"\n"); |
| 484 |
|
✗ |
fclose(solFile); |
| 485 |
|
|
} |
| 486 |
|
|
|
| 487 |
|
✗ |
void LinearProblemBidomainCurv::writeEnsightCase(int numIt, std::string varName) { |
| 488 |
|
|
|
| 489 |
|
|
FILE * pFile; |
| 490 |
|
✗ |
std::string caseName = FelisceParam::instance().resultDir + "/" + varName + ".case"; |
| 491 |
|
✗ |
pFile = fopen(caseName.c_str(),"w"); |
| 492 |
|
✗ |
fprintf(pFile,"FORMAT\n"); |
| 493 |
|
✗ |
fprintf(pFile,"type: ensight\n"); |
| 494 |
|
✗ |
fprintf(pFile, "GEOMETRY\n"); |
| 495 |
|
✗ |
std::string nameGeo = "model: 1 " + FelisceParam::instance().outputMesh[0] + "\n"; |
| 496 |
|
✗ |
fprintf(pFile,"%s", nameGeo.c_str()); |
| 497 |
|
✗ |
fprintf(pFile, "VARIABLE\n"); |
| 498 |
|
✗ |
std::string secName = "scalar per node: 1 " + varName + " " + varName +".*****.scl\n"; |
| 499 |
|
✗ |
fprintf(pFile, "%s", secName.c_str()); |
| 500 |
|
✗ |
fprintf(pFile, "TIME\n"); |
| 501 |
|
✗ |
fprintf(pFile, "time std::set: %d \n", 1); |
| 502 |
|
✗ |
fprintf(pFile, "number of steps: %d \n", numIt); |
| 503 |
|
✗ |
fprintf(pFile, "filename start number: %d\n", 0); |
| 504 |
|
✗ |
fprintf(pFile, "filename increment: %d\n", 1); |
| 505 |
|
✗ |
fprintf(pFile, "time values:\n"); |
| 506 |
|
|
|
| 507 |
|
✗ |
const double dt = FelisceParam::instance().timeStep * FelisceParam::instance().frequencyWriteSolution; |
| 508 |
|
✗ |
int count=0; |
| 509 |
|
✗ |
for(int j=0; j < numIt; j++) { |
| 510 |
|
✗ |
double valT = j*dt; |
| 511 |
|
✗ |
fprintf(pFile,"%lf ",valT); |
| 512 |
|
✗ |
count++; |
| 513 |
|
✗ |
if(count == 6) { |
| 514 |
|
✗ |
fprintf(pFile,"\n"); |
| 515 |
|
✗ |
count=0; |
| 516 |
|
|
} |
| 517 |
|
|
} |
| 518 |
|
✗ |
fclose(pFile); |
| 519 |
|
|
} |
| 520 |
|
|
} |
| 521 |
|
|
|