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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 "Model/bidomainDecoupledModel.hpp" |
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namespace felisce { |
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BidomainDecoupledModel::BidomainDecoupledModel(): |
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BidomainModel(), |
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m_linearProblemBidomainTransMemb(nullptr), |
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m_linearProblemBidomainExtraCell(nullptr) { |
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m_name = "BidomainDecoupled"; |
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} |
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BidomainDecoupledModel::~BidomainDecoupledModel() { |
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m_linearProblemBidomainTransMemb = nullptr; |
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m_linearProblemBidomainExtraCell = nullptr; |
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m_Ue_0.destroy(); |
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m_extrapolatePotTransMemb.destroy(); |
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if(!FelisceParam::instance().monodomain) |
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m_extrapolatePotExtraCell.destroy(); |
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} |
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//! Define m_ionic and m_bdfEdp (used in linearProblem). |
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void BidomainDecoupledModel::initializeDerivedModel() { |
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BidomainModel::initializeDerivedModel(); |
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//Define order for bdf used to calculate m_extrapolateExtraCell. |
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if(!FelisceParam::instance().monodomain) |
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m_bdfExtraCell.defineOrder(FelisceParam::instance().orderBdfEdp); |
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} |
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void BidomainDecoupledModel::initializeDerivedLinearProblem() { |
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m_linearProblemBidomainTransMemb = dynamic_cast<LinearProblemBidomainTransMemb*>(m_linearProblem[0]); |
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m_linearProblemBidomainExtraCell = dynamic_cast<LinearProblemBidomainExtraCell*>(m_linearProblem[1]); |
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initializeAppCurrent(); |
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} |
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void BidomainDecoupledModel::initializeAppCurrent() { |
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m_iApp = new AppCurrent(); |
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m_iApp->initialize(m_fstransient); |
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} |
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void BidomainDecoupledModel::evalIapp() { |
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m_iAppValue.clear(); |
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if ( (FelisceParam::instance().typeOfAppliedCurrent == "zygote") || (FelisceParam::instance().typeOfAppliedCurrent == "heart") || (FelisceParam::instance().typeOfAppliedCurrent == "ellipseheart") ) { |
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m_linearProblemBidomainTransMemb->evalFunctionOnDof(*m_iApp,m_fstransient->time,m_iAppValue,m_linearProblemBidomainTransMemb->EndocardiumDistance()); |
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} else { |
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m_linearProblemBidomainTransMemb->evalFunctionOnDof(*m_iApp,m_fstransient->time,m_iAppValue); |
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} |
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} |
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void BidomainDecoupledModel::finalizeRHSDP(int iProblem) { |
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if (iProblem == 0) { |
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int size = m_linearProblem[iProblem]->numDofLocalPerUnknown(potTransMemb); |
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double valueForPetsc[size]; |
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felInt idLocalValue[size]; |
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felInt idGlobalValue[size]; |
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double coefAm = FelisceParam::instance().Am; |
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double coefCm = FelisceParam::instance().Cm; |
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// m_massRHS = Am * Cm * m_bdfEdp.RHS |
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m_linearProblemBidomainTransMemb->massRHS().axpy(coefAm*coefCm, m_bdfEdp.vector()); |
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for (felInt i = 0; i < size; i++) { |
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idLocalValue[i] = i; |
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} |
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ISLocalToGlobalMappingApply(m_linearProblem[iProblem]->mappingDofLocalToDofGlobal(potTransMemb),size,&idLocalValue[0],&idGlobalValue[0]); |
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for (felInt i = 0; i < size; i++) { |
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valueForPetsc[i] = coefAm*m_iAppValue[idGlobalValue[i]]; |
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} |
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// m_massRHS = m_massRHS + Am * Iapp |
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m_linearProblemBidomainTransMemb->massRHS().setValues(size,&idGlobalValue[0],&valueForPetsc[0],ADD_VALUES); |
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m_linearProblemBidomainTransMemb->massRHS().assembly(); |
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// m_massRHS = m_massRHS + Am * Iion |
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m_linearProblemBidomainTransMemb->massRHS().axpy(coefAm,m_ionic->ion()); |
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if(!FelisceParam::instance().monodomain) { |
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// _KsigmaiRHS = m_extrapolatePotExtraCell |
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m_linearProblemBidomainTransMemb->ksigmaiRHS().axpy(1.,m_extrapolatePotExtraCell); |
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} |
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} else if (iProblem == 1) { |
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m_linearProblemBidomainExtraCell->vector().axpy(1.0,m_linearProblem[0]->solution()); |
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} |
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} |
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void BidomainDecoupledModel::preAssemblingMatrixRHS(std::size_t iProblem) { |
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// Initialize useful vectors of initial solution and initial extrapolate with a std::vector with same structure of _RHS for each linearProblem. |
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if (iProblem == 0) { // First problem solves first equation on potTransMemb |
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// Give _U_0 and m_W_0 values: |
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// initialize PotTransMemb with value Vmin |
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// and W_0 with 1/(vMax-vMin)^2. |
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// 1) copy structure in _U_0 and in m_extrapolatePotTransMemb. |
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m_U_0.duplicateFrom(m_linearProblem[iProblem]->vector()); |
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m_U_0.set(FelisceParam::instance().vMin); |
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// 2) copy structure in m_W_0 (initialize solution at time 0 of EDO in schaf solver) - only for first equation. |
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m_W_0.resize(1); |
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m_W_0[0].duplicateFrom(m_linearProblem[iProblem]->vector()); |
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double valueByDofW_0 = 1./((FelisceParam::instance().vMax - FelisceParam::instance().vMin)*(FelisceParam::instance().vMax - FelisceParam::instance().vMin)); |
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m_W_0[0].set(valueByDofW_0); |
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// 3) copy structure in m_extrapolatePotTransMemb (contains extrapolate values of linearProblem[0] solution). |
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m_extrapolatePotTransMemb.duplicateFrom(m_linearProblem[iProblem]->vector()); |
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m_extrapolatePotTransMemb.zeroEntries(); |
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// 3) copy structure in m_massRHS and _KsigmaiRHS. |
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m_linearProblemBidomainTransMemb->massRHS().duplicateFrom(m_linearProblem[iProblem]->vector()); |
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m_linearProblemBidomainTransMemb->massRHS().set(0.); |
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m_linearProblemBidomainTransMemb->ksigmaiRHS().duplicateFrom(m_linearProblem[iProblem]->vector()); |
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m_linearProblemBidomainTransMemb->ksigmaiRHS().set(0.); |
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//Initialize solution for solver. |
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m_linearProblem[iProblem]->solution().copyFrom(m_U_0); |
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// Read fibers and distance mapp (for Zygote geometry). |
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m_linearProblem[iProblem]->readData(*io()); |
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//Initialize heterogeneous parameters for schaf solver (useful only for first problem). |
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if (FelisceParam::instance().typeOfIonicModel == "schaf") { |
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initializeSchafParameter(); |
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} |
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} else if (iProblem == 1) { |
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// 1) copy structure in _Ue_0. |
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m_Ue_0.duplicateFrom(m_linearProblem[iProblem]->vector()); |
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m_Ue_0.set(0.0); |
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// 2) copy structure in m_extrapolatePotExtraCell (contains extrapolate values of linearProblem[1] solution). |
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if(!FelisceParam::instance().monodomain) { |
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m_extrapolatePotExtraCell.duplicateFrom(m_linearProblem[iProblem]->vector()); |
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m_extrapolatePotExtraCell.set(0.); |
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} |
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//Initialize solution for solver. |
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m_linearProblem[iProblem]->solution().copyFrom(m_Ue_0); |
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// Read fibers and distance mapp (for Zygote geometry). |
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m_linearProblem[iProblem]->readData(*io()); |
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} |
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//Debug print. |
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// /todo fix value of verbose |
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if (m_verbose > 2 && iProblem == 0) { |
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PetscPrintf(MpiInfo::petscComm(),"\n\t\t _U_0 (==m_sol (linearProblem[0]) at time == 0):\n"); |
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m_U_0.view(); |
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PetscPrintf(MpiInfo::petscComm(),"\n\t\t m_W_0 (==m_solEDO (ionicSolver) at time == 0):\n"); |
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m_W_0[0].view(); |
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} else if (m_verbose > 2 && iProblem == 1) { |
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PetscPrintf(MpiInfo::petscComm(),"\n\t\t m_Ue_0 (==m_sol (linearProblem[1]) at time == 0):\n"); |
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m_Ue_0.view(); |
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} |
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} |
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void BidomainDecoupledModel::postAssemblingMatrixRHS(std::size_t iProblem) { |
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// Evaluate applied current std::vector. |
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if (iProblem == 0) { |
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evalIapp(); |
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} |
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// Calculate RHS std::vector (to be multiplied by mass matrix). |
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finalizeRHSDP(iProblem); |
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// Calculate _RHS : |
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// if model == 'Bidomain' => _RHS = mass * RHS. |
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// if model == 'BidomainDecoupled' : |
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// iProblem==0 => _RHS=mass*RHS+Ksigmai*u_e |
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// iProblem==1 => _RHS=Ksigmai*V_m |
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m_linearProblem[iProblem]->addMatrixRHS(); |
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//RHS of Luenb. filter |
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if (FelisceParam::instance().stateFilter) { |
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if (iProblem == 0) { |
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double coefAm = FelisceParam::instance().Am; |
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m_luenbFlter.zeroEntries(); |
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m_luenbFlter.copyFrom(m_linearProblem[iProblem]->matrix(1),SAME_NONZERO_PATTERN); |
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m_luenbFlter.assembly(MAT_FINAL_ASSEMBLY); |
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// copy diagonal stabiliz. matrix in luenberger matrix |
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m_luenbFlter.diagonalScale(PetscVector::null(),m_ionic->stabTerm()); |
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m_luenbFlter.scale(coefAm); |
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m_linearProblem[iProblem]->matrix(0).axpy(1,m_luenbFlter,SAME_NONZERO_PATTERN); |
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} |
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} |
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} |
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void BidomainDecoupledModel::initializeSchafParameter() { |
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// Initialize TauClose. |
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if (FelisceParam::instance().hasHeteroTauClose) { |
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m_schaf->fctTauClose().initialize(m_fstransient); |
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if ( (FelisceParam::instance().typeOfAppliedCurrent == "zygote") || (FelisceParam::instance().typeOfAppliedCurrent == "heart") || (FelisceParam::instance().typeOfAppliedCurrent == "ellipseheart") ) { |
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m_linearProblemBidomainTransMemb->evalFunctionOnDof(m_schaf->fctTauClose(), m_schaf->tauClose(),m_linearProblemBidomainTransMemb->EndocardiumDistance()); |
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} |
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else { |
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m_linearProblemBidomainTransMemb->evalFunctionOnDof(m_schaf->fctTauClose(), m_schaf->tauClose()); |
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} |
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} |
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// Initialize TauOut : heterogeneous in case of infarct. |
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if (FelisceParam::instance().hasInfarct) { |
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m_schaf->fctTauOut().initialize(m_fstransient); |
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m_linearProblemBidomainTransMemb->evalFunctionOnDof(m_schaf->fctTauOut(), m_schaf->tauOut()); |
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} |
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} |
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// Pay attention on the call of this : |
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// call BidomainModel::writeSolution() function instead of (non-virtual) Model::writeSolution() function |
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void BidomainDecoupledModel::writeSolution() |
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{ |
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Model::writeSolution(); |
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} |
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void BidomainDecoupledModel::forward() { |
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//Write solution with ensight. |
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BidomainDecoupledModel::writeSolution(); |
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//Advance time step. |
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updateTime(FlagMatrixRHS::only_rhs); |
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printNewTimeIterationBanner(); |
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if ( m_fstransient->iteration == 1) { |
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//Initialization of bdf solvers. |
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m_bdfEdp.initialize(m_linearProblem[0]->solution()); |
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if(!FelisceParam::instance().monodomain) |
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m_bdfExtraCell.initialize(m_linearProblem[1]->solution()); |
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m_linearProblemBidomainTransMemb->initializeTimeScheme(&m_bdfEdp); |
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//m_extrapolate = initial solution. |
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m_bdfEdp.extrapolate(m_extrapolatePotTransMemb); |
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if(!FelisceParam::instance().monodomain) { |
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m_bdfExtraCell.extrapolate(m_extrapolatePotExtraCell); |
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} |
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//Initialization of ionic solver. |
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m_ionic->defineSizeAndMappingOfIonicProblem(m_linearProblem[0]->numDofLocalPerUnknown(potTransMemb), m_linearProblem[0]->mappingDofLocalToDofGlobal(potTransMemb), m_linearProblemBidomain[0]->ao()); |
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m_ionic->initializeExtrap(m_extrapolatePotTransMemb); |
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m_ionic->initialize(m_W_0[0]); |
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m_buildIonic = true; |
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} else { |
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m_bdfEdp.update(m_linearProblem[0]->solution()); |
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if(!FelisceParam::instance().monodomain) |
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m_bdfExtraCell.update(m_linearProblem[1]->solution()); |
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m_bdfEdp.extrapolate(m_extrapolatePotTransMemb); |
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if(!FelisceParam::instance().monodomain) { |
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m_bdfExtraCell.extrapolate(m_extrapolatePotExtraCell); |
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} |
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m_ionic->update(m_extrapolatePotTransMemb); |
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} |
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//Solve Mitchell and Schaeffer model and calculate Iion. |
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m_ionic->computeRHS(); |
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m_ionic->solveEDO(); |
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m_ionic->computeIon(); |
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m_ionic->updateBdf(); |
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m_bdfEdp.computeRHSTime(m_fstransient->timeStep); |
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// Assembling of matrices at first iteration (because of needs some coefficients not defined at iteration 0). |
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if ( m_fstransient->iteration == 1 ) { |
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if ( FelisceParam::instance().hasCoupledAtriaVent ) |
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m_linearProblemBidomainTransMemb->assembleMatrixRHSCurrentAndCurvilinearElement(MpiInfo::rankProc()); |
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else |
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m_linearProblemBidomainTransMemb->assembleMatrixRHS(MpiInfo::rankProc()); |
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} |
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//Specific operations before solve the system : calculate _RHS std::vector used in solve(). |
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postAssemblingMatrixRHS(0); |
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//Solve the system _Matrix[0]*_V_m=_RHS. |
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m_linearProblem[0]->solve(MpiInfo::rankProc(), MpiInfo::numProc()); |
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// Assemble Matrix of linearProblem. |
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|
✗ |
if ( m_fstransient->iteration == 1 ) { |
| 293 |
|
✗ |
if ( FelisceParam::instance().hasCoupledAtriaVent ) |
| 294 |
|
✗ |
m_linearProblemBidomainExtraCell->assembleMatrixRHSCurrentAndCurvilinearElement(MpiInfo::rankProc()); |
| 295 |
|
|
else |
| 296 |
|
✗ |
m_linearProblemBidomainExtraCell->assembleMatrixRHS(MpiInfo::rankProc()); |
| 297 |
|
|
} |
| 298 |
|
|
|
| 299 |
|
|
//Specific operations before solve the system : calculate _RHS std::vector used in solve(). |
| 300 |
|
✗ |
postAssemblingMatrixRHS(1); |
| 301 |
|
|
|
| 302 |
|
|
//Solve the system _Matrix[0]*m_u_e=_RHS. |
| 303 |
|
✗ |
m_linearProblem[1]->solve(MpiInfo::rankProc(), MpiInfo::numProc()); |
| 304 |
|
|
|
| 305 |
|
✗ |
if ( FelisceParam::instance().hasCoupledAtriaVent == false ) |
| 306 |
|
✗ |
m_linearProblem[1]->removeAverageFromSolution(potExtraCell, MpiInfo::rankProc()); |
| 307 |
|
|
|
| 308 |
|
|
} |
| 309 |
|
|
|
| 310 |
|
|
} |
| 311 |
|
|
|