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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 "Model/bidomainModel.hpp" |
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#include "Solver/CVGraphInterface.hpp" |
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namespace felisce { |
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BidomainModel::BidomainModel(): |
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Model(), |
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m_rom(nullptr), |
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m_verbose(0), |
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m_buildIonic(false), |
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m_buildCourt(false), |
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m_ionic(nullptr), |
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m_schaf(nullptr), |
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m_fhn(nullptr), |
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m_court(nullptr), |
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m_mv(nullptr), |
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m_paci(nullptr), |
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m_bcl(nullptr), |
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m_observations(nullptr), |
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m_extrapolateIsCreated(false) { |
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for(std::size_t i=0; i<m_linearProblemBidomain.size(); i++) { |
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m_linearProblemBidomain[i] = nullptr; |
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} |
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m_name = "Bidomain"; |
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} |
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BidomainModel::~BidomainModel() { |
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for(std::size_t i=0; i<m_linearProblemBidomain.size(); i++) { |
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m_linearProblemBidomain[i] = nullptr; |
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} |
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if(FelisceParam::instance().useROM) { |
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delete m_rom; |
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m_rom=nullptr; |
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} |
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if (m_buildIonic) { |
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delete m_ionic; |
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m_ionic=nullptr; |
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} |
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if (m_buildCourt) { |
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delete m_court; |
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m_court = nullptr; |
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} |
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if(m_observations) { |
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delete m_observations; |
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m_observations=nullptr; |
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} |
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for (std::size_t i=0; i<m_W_0.size(); i++) { |
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m_W_0[i].destroy(); |
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} |
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if ( (FelisceParam::instance().typeOfIonicModel == "courtAtriaSchafVent") || (FelisceParam::instance().typeOfIonicModel == "courtAtriaMvVent") ) { |
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m_m.destroy(); |
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m_h.destroy(); |
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m_j.destroy(); |
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m_ao.destroy(); |
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m_io.destroy(); |
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m_ua.destroy(); |
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m_ui.destroy(); |
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m_xr.destroy(); |
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m_xs.destroy(); |
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m_d.destroy(); |
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m_f.destroy(); |
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m_fca.destroy(); |
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m_urel.destroy(); |
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m_vrel.destroy(); |
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m_wrel.destroy(); |
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m_nai.destroy(); |
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m_nao.destroy(); |
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m_cao.destroy(); |
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m_ki.destroy(); |
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m_ko.destroy(); |
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m_cai.destroy(); |
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m_naiont.destroy(); |
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m_kiont.destroy(); |
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m_caiont.destroy(); |
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m_ileak.destroy(); |
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m_iup.destroy(); |
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m_itr.destroy(); |
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m_irel.destroy(); |
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m_cmdn.destroy(); |
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m_trpn.destroy(); |
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m_nsr.destroy(); |
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m_jsr.destroy(); |
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m_csqn.destroy(); |
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} |
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if (m_extrapolateIsCreated) |
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m_extrapolate.destroy(); |
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delete m_iApp; |
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if (FelisceParam::instance().hasAppliedExteriorCurrent) |
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delete m_iAppExt; |
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if(FelisceParam::instance().stateFilter) { |
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m_luenbFlter.destroy(); |
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m_Observ.destroy(); |
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} |
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if (FelisceParam::instance().restartSolution) { |
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if (FelisceParam::instance().orderBdfEdp > 0) |
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m_bdf_sol_n.destroy(); |
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if (FelisceParam::instance().orderBdfEdp > 1) |
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m_bdf_sol_n_1.destroy(); |
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if (FelisceParam::instance().orderBdfEdp > 2) |
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m_bdf_sol_n_2.destroy(); |
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if (FelisceParam::instance().orderBdfIonic > 0) { |
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for (std::size_t i=0; i<m_ionic_sol_n.size(); i++) { |
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m_ionic_sol_n[i].destroy(); |
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} |
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} |
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if (FelisceParam::instance().orderBdfIonic > 1) { |
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for (std::size_t i=0; i<m_ionic_sol_n_1.size(); i++) { |
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m_ionic_sol_n_1[i].destroy(); |
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} |
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} |
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if (FelisceParam::instance().orderBdfIonic > 2) { |
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for (std::size_t i=0; i<m_ionic_sol_n_2.size(); i++) { |
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m_ionic_sol_n_2[i].destroy(); |
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} |
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} |
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if ( (FelisceParam::instance().typeOfIonicModel == "courtAtriaSchafVent") || (FelisceParam::instance().typeOfIonicModel == "courtAtriaMvVent") ) { |
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for (int iCourt=0 ; iCourt<29; iCourt++) { |
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m_courtVarInit[iCourt].destroy(); |
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} |
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} |
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} |
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} |
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void BidomainModel::initializeDerivedLinearProblem() { |
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for (std::size_t i=0; i<m_linearProblem.size(); i++) { |
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m_linearProblemBidomain.push_back(static_cast<LinearProblemBidomain*>(m_linearProblem[i])); |
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} |
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} |
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//! Define m_ionic and m_bdfEdp (used in linearProblem). |
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void BidomainModel::initializeDerivedModel() { |
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m_verbose = FelisceParam::verbose(); |
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if ( FelisceParam::instance().withCVG ){ |
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m_linearProblemBidomain[0]->initPetscVectors(); |
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} |
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//Allocate m_ionic. |
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// Choose type of ionic model to be used. |
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if ((FelisceParam::instance().typeOfIonicModel == "schaf") || (FelisceParam::instance().typeOfIonicModel == "courtAtriaSchafVent")) { |
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// Initialize Mitchell and Schaeffer model. |
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m_schaf = new SchafSolver(m_fstransient); |
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m_ionic = m_schaf; |
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if (FelisceParam::instance().typeOfIonicModel == "courtAtriaSchafVent") { |
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// Initialize Courtemanche model |
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m_court = new CourtemancheSolver(m_fstransient); |
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} |
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} else if (FelisceParam::instance().typeOfIonicModel == "schafRev") { |
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// Initialize Mitchell and Schaeffer Revised model. |
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m_schaf = new SchafRevisedSolver(m_fstransient); |
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m_ionic = m_schaf; |
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} else if (FelisceParam::instance().typeOfIonicModel == "fhn") { |
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// Initialize Fitzhugh-Nagumo model |
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m_fhn = new FhNSolver(m_fstransient); |
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m_ionic =m_fhn; |
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} else if ( (FelisceParam::instance().typeOfIonicModel == "MV") || (FelisceParam::instance().typeOfIonicModel == "courtAtriaMvVent") ) { |
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// Initialize MV model |
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m_mv = new MVSolver(m_fstransient); |
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m_ionic = m_mv; |
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if (FelisceParam::instance().typeOfIonicModel == "courtAtriaMvVent") { |
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// Initialize Courtemanche model |
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m_court = new CourtemancheSolver(m_fstransient); |
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} |
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} else if (FelisceParam::instance().typeOfIonicModel == "Paci") { |
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// Initialize Paci model |
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m_paci = new PaciSolver(m_fstransient); |
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m_ionic = m_paci; |
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} else if (FelisceParam::instance().typeOfIonicModel == "BCL") { |
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// Initialize BCL model |
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m_bcl = new BCLSolver(m_fstransient); |
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m_ionic = m_bcl; |
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} |
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userDefinedIonicModel(); |
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//Fix order of bdf for ionic solver. |
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if ( (FelisceParam::instance().typeOfIonicModel == "MV") || (FelisceParam::instance().typeOfIonicModel == "courtAtriaMvVent") ) { |
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m_ionic->defineOrderBdf(FelisceParam::instance().orderBdfIonic,3); |
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m_W_0.resize(3); |
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} else if(FelisceParam::instance().typeOfIonicModel == "Paci") { |
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m_ionic->defineOrderBdf(FelisceParam::instance().orderBdfIonic,42); |
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m_W_0.resize(42); |
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} else if(FelisceParam::instance().typeOfIonicModel == "BCL") { |
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m_ionic->defineOrderBdf(FelisceParam::instance().orderBdfIonic,4); |
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m_W_0.resize(4); |
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} else |
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m_ionic->defineOrderBdf(FelisceParam::instance().orderBdfIonic,1); |
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//Define order for bdf used by EDP (linearProblem). |
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m_bdfEdp.defineOrder(FelisceParam::instance().orderBdfEdp); |
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initializeAppCurrent(); |
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if (FelisceParam::instance().hasAppliedExteriorCurrent) |
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initializeAppCurrentExt(); |
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if(FelisceParam::instance().stateFilter) { |
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m_observations = new EnsightCase(); |
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m_observations->read(FelisceParam::instance().observDir,FelisceParam::instance().observFileName); |
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} |
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} |
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void BidomainModel::initializeAppCurrent() { |
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std::unordered_map<std::string, int> mapOfType; |
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mapOfType["ellibi"] = 1; |
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mapOfType["zygote"] = 2; |
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bool warning_Iapp = true; |
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switch(mapOfType[FelisceParam::instance().typeOfAppliedCurrent]) { |
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case 1 : |
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m_iApp = new AppCurrent(); |
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warning_Iapp = false; |
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break; |
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case 2 : |
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m_iApp = new zygoteIapp(); |
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warning_Iapp = false; |
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break; |
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} |
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if (warning_Iapp) { |
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std::cout << "WARNING !\nApplied current not defined : used non pathological case for ellibi geometry.\n"; |
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m_iApp = new AppCurrent(); |
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} |
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m_iApp->initialize(m_fstransient); |
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} |
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void BidomainModel::initializeAppCurrentExt() { |
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m_iAppExt = new AppCurrent(); |
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m_iAppExt->initialize(m_fstransient); |
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} |
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void BidomainModel::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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// Warning: extra-data m_linearProblemBidomain[0]->EndocardiumDistance() size has to be numDof (not number of mesh points). |
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m_linearProblemBidomain[0]->evalFunctionOnDof(*m_iApp,m_fstransient->time,m_iAppValue,m_linearProblemBidomain[0]->EndocardiumDistance()); |
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} |
| 265 |
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else { |
| 266 |
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m_linearProblemBidomain[0]->evalFunctionOnDof(*m_iApp,m_fstransient->time,m_iAppValue); |
| 267 |
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} |
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} |
| 269 |
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void BidomainModel::evalIappExt() { |
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m_iAppValueExt.clear(); |
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m_linearProblemBidomain[0]->evalFunctionOnDof(*m_iAppExt,m_fstransient->time,m_iAppValueExt); |
| 273 |
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} |
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| 276 |
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//Calculate RHS std::vector to be multiplied by mass matrix. |
| 277 |
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void BidomainModel::finalizeRHSDP(int iProblem) |
| 278 |
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{ |
| 279 |
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int size = m_linearProblemBidomain[iProblem]->numDofLocalPerUnknown(potTransMemb); |
| 280 |
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double* valueForPetsc = new double[size]; |
| 281 |
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double* obsForPetsc = new double[size]; |
| 282 |
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felInt* idLocalValue = new felInt[size]; |
| 283 |
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felInt* idGlobalValue = new felInt[size]; |
| 284 |
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| 285 |
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double coefAm = FelisceParam::instance().Am; |
| 286 |
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double coefCm = FelisceParam::instance().Cm; |
| 287 |
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| 288 |
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double* observ=nullptr; |
| 289 |
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if (FelisceParam::instance().stateFilter ) { |
| 290 |
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//RHS of Luenb. filter |
| 291 |
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m_Observ.set(0.); |
| 292 |
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felInt sizeVar = m_linearProblemBidomain[iProblem]->numDofPerUnknown(potTransMemb); |
| 293 |
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int indexTime = m_observations->timeIndex(m_fstransient->time); |
| 294 |
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int idVariable = m_observations->variableIndex("potTransMemb"); |
| 295 |
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observ=new double[sizeVar]; |
| 296 |
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m_observations->readVariable(idVariable, indexTime,observ,sizeVar); |
| 297 |
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} |
| 298 |
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| 299 |
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// RHS = Am*Cm*BDF.RHS (Warning : bdf.RHS containes both problem variables). |
| 300 |
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m_linearProblemBidomain[iProblem]->vector().axpy(1.,m_bdfEdp.vector()); |
| 301 |
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m_linearProblemBidomain[iProblem]->vector().scale(coefAm*coefCm); |
| 302 |
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| 303 |
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// RHS = RHS + Am*Iapp |
| 304 |
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for (felInt i = 0; i < size; i++) { |
| 305 |
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idLocalValue[i] = i; |
| 306 |
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} |
| 307 |
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ISLocalToGlobalMappingApply(m_linearProblemBidomain[iProblem]->mappingDofLocalToDofGlobal(potTransMemb),size,&idLocalValue[0],&idGlobalValue[0]); |
| 308 |
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for (felInt i = 0; i < size; i++) { |
| 309 |
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felInt indexGlobal=idGlobalValue[i]; |
| 310 |
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#ifdef NDEBUG |
| 311 |
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valueForPetsc[i] = coefAm*m_iAppValue[indexGlobal]; |
| 312 |
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|
#else |
| 313 |
|
✗ |
valueForPetsc[i] = coefAm*m_iAppValue.at(indexGlobal); |
| 314 |
|
|
#endif |
| 315 |
|
✗ |
if (FelisceParam::instance().stateFilter ) { |
| 316 |
|
✗ |
AOPetscToApplication(m_linearProblemBidomain[iProblem]->ao(),1,&indexGlobal); |
| 317 |
|
✗ |
obsForPetsc[i] = observ[indexGlobal]; |
| 318 |
|
|
} |
| 319 |
|
|
} |
| 320 |
|
✗ |
m_linearProblemBidomain[iProblem]->vector().setValues(size,&idGlobalValue[0],&valueForPetsc[0],ADD_VALUES); |
| 321 |
|
|
|
| 322 |
|
✗ |
m_linearProblemBidomain[iProblem]->vector().assembly(); |
| 323 |
|
|
|
| 324 |
|
|
// For the second equation : RHS = 0 ( or applied exterior current ) |
| 325 |
|
✗ |
int sizePotExtraCell = m_linearProblemBidomain[iProblem]->numDofLocalPerUnknown(potExtraCell); |
| 326 |
|
✗ |
double* valueForPetscPotExtraCell = new double[sizePotExtraCell]; |
| 327 |
|
✗ |
felInt* idLocalValuePotExtraCell = new felInt[sizePotExtraCell]; |
| 328 |
|
✗ |
felInt* idGlobalValuePotExtraCell = new felInt[sizePotExtraCell]; |
| 329 |
|
|
|
| 330 |
|
✗ |
for (felInt i = 0; i < sizePotExtraCell; i++) { |
| 331 |
|
✗ |
idLocalValuePotExtraCell[i] = i; |
| 332 |
|
|
} |
| 333 |
|
✗ |
ISLocalToGlobalMappingApply(m_linearProblemBidomain[iProblem]->mappingDofLocalToDofGlobal(potExtraCell),sizePotExtraCell,&idLocalValuePotExtraCell[0],&idGlobalValuePotExtraCell[0]); |
| 334 |
|
✗ |
for (felInt i = 0; i < sizePotExtraCell; i++) { |
| 335 |
|
|
// For an applied exterior current |
| 336 |
|
✗ |
if (FelisceParam::instance().hasAppliedExteriorCurrent) { |
| 337 |
|
✗ |
valueForPetscPotExtraCell[i] = m_iAppValueExt[idGlobalValuePotExtraCell[i]]; |
| 338 |
|
|
} |
| 339 |
|
|
else { |
| 340 |
|
✗ |
valueForPetscPotExtraCell[i] = 0.0; |
| 341 |
|
|
} |
| 342 |
|
|
} |
| 343 |
|
✗ |
m_linearProblemBidomain[iProblem]->vector().setValues(sizePotExtraCell ,&idGlobalValuePotExtraCell[0],&valueForPetscPotExtraCell[0],INSERT_VALUES); |
| 344 |
|
|
|
| 345 |
|
✗ |
m_linearProblemBidomain[iProblem]->vector().assembly(); |
| 346 |
|
|
|
| 347 |
|
|
// RHS = RHS + Am*Iion |
| 348 |
|
✗ |
if ( (FelisceParam::instance().typeOfIonicModel == "courtAtriaSchafVent") || (FelisceParam::instance().typeOfIonicModel == "courtAtriaMvVent") ) { |
| 349 |
|
✗ |
m_linearProblemBidomain[iProblem]->vector().axpy(coefAm,m_ionic->ion()); |
| 350 |
|
✗ |
m_linearProblemBidomain[iProblem]->vector().axpy(-coefAm*0.001,m_court->ion()); |
| 351 |
|
|
} else { |
| 352 |
|
✗ |
m_linearProblemBidomain[iProblem]->vector().axpy(coefAm,m_ionic->ion()); |
| 353 |
|
|
} |
| 354 |
|
|
|
| 355 |
|
|
// Elisa, Dec. 2014 - Luenberger filter |
| 356 |
|
✗ |
if (FelisceParam::instance().electrodeControl) { |
| 357 |
|
✗ |
m_linearProblemBidomain[iProblem]->addElectrodeCondtrol(); |
| 358 |
|
|
} |
| 359 |
|
|
|
| 360 |
|
|
// RHS = RHS + Am*A2*A3*H*V_m |
| 361 |
|
✗ |
if (FelisceParam::instance().stateFilter ) { |
| 362 |
|
✗ |
m_Observ.setValues(size,&idGlobalValue[0],&obsForPetsc[0],INSERT_VALUES); |
| 363 |
|
✗ |
m_Observ.assembly(); |
| 364 |
|
✗ |
pointwiseMult(m_Observ,m_Observ,m_ionic->stabTerm()); |
| 365 |
|
✗ |
m_linearProblemBidomain[iProblem]->vector().axpy(coefAm,m_Observ); |
| 366 |
|
|
} |
| 367 |
|
|
|
| 368 |
|
|
// m_linearProblemBidomain[iProblem]->applyUserDefinedStimulation(m_fstransient->time); |
| 369 |
|
|
|
| 370 |
|
✗ |
delete [] valueForPetsc; |
| 371 |
|
✗ |
delete [] obsForPetsc; |
| 372 |
|
✗ |
delete [] idLocalValue; |
| 373 |
|
✗ |
delete [] idGlobalValue; |
| 374 |
|
✗ |
delete [] valueForPetscPotExtraCell; |
| 375 |
|
✗ |
delete [] idLocalValuePotExtraCell; |
| 376 |
|
✗ |
delete [] idGlobalValuePotExtraCell; |
| 377 |
|
|
|
| 378 |
|
|
} |
| 379 |
|
|
|
| 380 |
|
✗ |
void BidomainModel::preAssemblingMatrixRHS(std::size_t iProblem) { |
| 381 |
|
|
//Initialize vectors for ionic models and m_bdfEdp (with m_U_0) with a std::vector with same structure as m_RHS in linearProblem. |
| 382 |
|
|
//(in this case give PotTransMemb with value Vmin and 0 for PotExtraCell at time t == 0). |
| 383 |
|
|
|
| 384 |
|
|
// 1) initialize Vectors for ionic solver |
| 385 |
|
✗ |
if ( (FelisceParam::instance().typeOfIonicModel == "MV") || (FelisceParam::instance().typeOfIonicModel == "courtAtriaMvVent") ) { |
| 386 |
|
|
double valueByDofW0[3]; |
| 387 |
|
✗ |
valueByDofW0[0] = 1.; |
| 388 |
|
✗ |
valueByDofW0[1] = 1.; |
| 389 |
|
✗ |
valueByDofW0[2] = 0.; |
| 390 |
|
✗ |
for (felInt i=0; i<3; i++) { |
| 391 |
|
✗ |
m_W_0[i].duplicateFrom(m_linearProblemBidomain[iProblem]->vector()); |
| 392 |
|
✗ |
m_W_0[i].set(valueByDofW0[i]); |
| 393 |
|
|
} |
| 394 |
|
|
} |
| 395 |
|
✗ |
else if(FelisceParam::instance().typeOfIonicModel == "Paci") { |
| 396 |
|
|
double valueByDofW0[42]; |
| 397 |
|
|
|
| 398 |
|
✗ |
valueByDofW0[0] = 0.75; |
| 399 |
|
✗ |
valueByDofW0[1] = 0.75; |
| 400 |
|
✗ |
valueByDofW0[2] = 0.; |
| 401 |
|
✗ |
valueByDofW0[3] = 0.; |
| 402 |
|
✗ |
valueByDofW0[4] = 1.; |
| 403 |
|
✗ |
valueByDofW0[5] = 1.; |
| 404 |
|
✗ |
valueByDofW0[6] = 1.; |
| 405 |
|
✗ |
valueByDofW0[7] = 0.; |
| 406 |
|
✗ |
valueByDofW0[8] = 1.; |
| 407 |
|
✗ |
valueByDofW0[9] = 0.; |
| 408 |
|
✗ |
valueByDofW0[10] = 1.; |
| 409 |
|
✗ |
valueByDofW0[11] = 0.; |
| 410 |
|
✗ |
valueByDofW0[12] = 0.1; |
| 411 |
|
✗ |
valueByDofW0[13] = 1.; |
| 412 |
|
✗ |
valueByDofW0[14] = 0.0002; |
| 413 |
|
✗ |
valueByDofW0[15] = 0.3; |
| 414 |
|
✗ |
valueByDofW0[16] = 10.; |
| 415 |
|
✗ |
valueByDofW0[17] = 0.; |
| 416 |
|
✗ |
valueByDofW0[18] = 0.; |
| 417 |
|
✗ |
valueByDofW0[19] = 0.; |
| 418 |
|
✗ |
valueByDofW0[20] = 0.; |
| 419 |
|
✗ |
valueByDofW0[21] = 0.; |
| 420 |
|
✗ |
valueByDofW0[22] = 0.; |
| 421 |
|
✗ |
valueByDofW0[23] = 0.; |
| 422 |
|
✗ |
valueByDofW0[24] = 0.; |
| 423 |
|
✗ |
valueByDofW0[25] = 0.; |
| 424 |
|
✗ |
valueByDofW0[26] = 0.; |
| 425 |
|
✗ |
valueByDofW0[27] = 0.; |
| 426 |
|
✗ |
valueByDofW0[28] = 0.; |
| 427 |
|
✗ |
valueByDofW0[29] = 0.; |
| 428 |
|
✗ |
valueByDofW0[30] = 0.; |
| 429 |
|
✗ |
valueByDofW0[31] = 0.; |
| 430 |
|
✗ |
valueByDofW0[32] = 0.; |
| 431 |
|
✗ |
valueByDofW0[33] = 0.; |
| 432 |
|
✗ |
valueByDofW0[34] = 0.; |
| 433 |
|
✗ |
valueByDofW0[35] = 0.; |
| 434 |
|
✗ |
valueByDofW0[36] = 0.0074621; |
| 435 |
|
✗ |
valueByDofW0[37] = 0.692477; |
| 436 |
|
✗ |
valueByDofW0[38] = 0.692574; |
| 437 |
|
✗ |
valueByDofW0[39] = 0.692591; |
| 438 |
|
✗ |
valueByDofW0[40] = 0.496116; |
| 439 |
|
✗ |
valueByDofW0[41] = 0.000194015; |
| 440 |
|
|
|
| 441 |
|
|
|
| 442 |
|
✗ |
for (felInt i=0; i<42; i++) { |
| 443 |
|
✗ |
m_W_0[i].duplicateFrom(m_linearProblemBidomain[iProblem]->vector()); |
| 444 |
|
✗ |
m_W_0[i].set(valueByDofW0[i]); |
| 445 |
|
|
} |
| 446 |
|
|
} |
| 447 |
|
✗ |
else if (FelisceParam::instance().typeOfIonicModel == "BCL") { |
| 448 |
|
|
double valueByDofW0[4]; |
| 449 |
|
✗ |
valueByDofW0[0] = 1.; |
| 450 |
|
✗ |
valueByDofW0[1] = 1.; |
| 451 |
|
✗ |
valueByDofW0[2] = 0.; |
| 452 |
|
✗ |
valueByDofW0[3] = 1.; |
| 453 |
|
|
|
| 454 |
|
✗ |
for (felInt i=0; i<4; i++) { |
| 455 |
|
✗ |
m_W_0[i].duplicateFrom(m_linearProblemBidomain[iProblem]->vector()); |
| 456 |
|
✗ |
m_W_0[i].set(valueByDofW0[i]); |
| 457 |
|
|
} |
| 458 |
|
|
} |
| 459 |
|
|
// "schaf", "schafRev", "courtAtriaSchafVent", "fhn" |
| 460 |
|
|
else { |
| 461 |
|
✗ |
m_W_0.resize(1); |
| 462 |
|
✗ |
m_W_0[0].duplicateFrom(m_linearProblemBidomain[iProblem]->vector()); |
| 463 |
|
✗ |
if (FelisceParam::instance().typeOfIonicModel == "fhn") { |
| 464 |
|
✗ |
m_W_0[0].set(0.); |
| 465 |
|
|
} else { |
| 466 |
|
✗ |
double valueByDofW_0 = 1./((FelisceParam::instance().vMax - FelisceParam::instance().vMin)*(FelisceParam::instance().vMax - FelisceParam::instance().vMin)); |
| 467 |
|
✗ |
m_W_0[0].set(valueByDofW_0); |
| 468 |
|
|
} |
| 469 |
|
|
} |
| 470 |
|
|
|
| 471 |
|
✗ |
if ( (FelisceParam::instance().typeOfIonicModel == "courtAtriaSchafVent") || (FelisceParam::instance().typeOfIonicModel == "courtAtriaMvVent") ) { |
| 472 |
|
✗ |
double valueByDofm = 0.00291; |
| 473 |
|
✗ |
double valueByDofh = 0.965; |
| 474 |
|
✗ |
double valueByDofj = 0.978; |
| 475 |
|
✗ |
double valueByDofao = 0.0304; |
| 476 |
|
✗ |
double valueByDofio = 0.999; |
| 477 |
|
✗ |
double valueByDofua = 0.00496; |
| 478 |
|
✗ |
double valueByDofui = 0.999; |
| 479 |
|
✗ |
double valueByDofxr = 0.0000329; |
| 480 |
|
✗ |
double valueByDofxs = 0.0187; |
| 481 |
|
✗ |
double valueByDofd = 0.000137; |
| 482 |
|
✗ |
double valueByDoff = 0.999837; |
| 483 |
|
✗ |
double valueByDoffca = 0.775; |
| 484 |
|
✗ |
double valueByDofvrel = 1.00; |
| 485 |
|
✗ |
double valueByDofwrel = 0.999; |
| 486 |
|
✗ |
double valueByDofnai = 11.2; |
| 487 |
|
✗ |
double valueByDofnao = 140.0; |
| 488 |
|
✗ |
double valueByDofcao = 1.8; |
| 489 |
|
✗ |
double valueByDofki = 139.0; |
| 490 |
|
✗ |
double valueByDofko = 4.5; |
| 491 |
|
✗ |
double valueByDofcai = 0.000102; |
| 492 |
|
✗ |
double valueByDofcmdn = 0.00205; |
| 493 |
|
✗ |
double valueByDoftrpn = 0.0118; |
| 494 |
|
✗ |
double valueByDofnsr = 1.49; |
| 495 |
|
✗ |
double valueByDofjsr = 1.49; |
| 496 |
|
✗ |
double valueByDofcsqn = 6.51; |
| 497 |
|
|
|
| 498 |
|
✗ |
m_m.duplicateFrom(m_linearProblemBidomain[iProblem]->vector()); |
| 499 |
|
✗ |
m_m.set(valueByDofm); |
| 500 |
|
✗ |
m_h.duplicateFrom(m_linearProblemBidomain[iProblem]->vector()); |
| 501 |
|
✗ |
m_h.set(valueByDofh); |
| 502 |
|
✗ |
m_j.duplicateFrom(m_linearProblemBidomain[iProblem]->vector()); |
| 503 |
|
✗ |
m_j.set(valueByDofj); |
| 504 |
|
✗ |
m_ao.duplicateFrom(m_linearProblemBidomain[iProblem]->vector()); |
| 505 |
|
✗ |
m_ao.set(valueByDofao); |
| 506 |
|
✗ |
m_io.duplicateFrom(m_linearProblemBidomain[iProblem]->vector()); |
| 507 |
|
✗ |
m_io.set(valueByDofio); |
| 508 |
|
✗ |
m_ua.duplicateFrom(m_linearProblemBidomain[iProblem]->vector()); |
| 509 |
|
✗ |
m_ua.set(valueByDofua); |
| 510 |
|
✗ |
m_ui.duplicateFrom(m_linearProblemBidomain[iProblem]->vector()); |
| 511 |
|
✗ |
m_ui.set(valueByDofui); |
| 512 |
|
✗ |
m_xr.duplicateFrom(m_linearProblemBidomain[iProblem]->vector()); |
| 513 |
|
✗ |
m_xr.set(valueByDofxr); |
| 514 |
|
✗ |
m_xs.duplicateFrom(m_linearProblemBidomain[iProblem]->vector()); |
| 515 |
|
✗ |
m_xs.set(valueByDofxs); |
| 516 |
|
✗ |
m_d.duplicateFrom(m_linearProblemBidomain[iProblem]->vector()); |
| 517 |
|
✗ |
m_d.set(valueByDofd); |
| 518 |
|
✗ |
m_f.duplicateFrom(m_linearProblemBidomain[iProblem]->vector()); |
| 519 |
|
✗ |
m_f.set(valueByDoff); |
| 520 |
|
✗ |
m_fca.duplicateFrom(m_linearProblemBidomain[iProblem]->vector()); |
| 521 |
|
✗ |
m_fca.set(valueByDoffca); |
| 522 |
|
✗ |
m_urel.duplicateFrom(m_linearProblemBidomain[iProblem]->vector()); |
| 523 |
|
✗ |
m_urel.set(0.); |
| 524 |
|
✗ |
m_vrel.duplicateFrom(m_linearProblemBidomain[iProblem]->vector()); |
| 525 |
|
✗ |
m_vrel.set(valueByDofvrel); |
| 526 |
|
✗ |
m_wrel.duplicateFrom(m_linearProblemBidomain[iProblem]->vector()); |
| 527 |
|
✗ |
m_wrel.set(valueByDofwrel); |
| 528 |
|
✗ |
m_nai.duplicateFrom(m_linearProblemBidomain[iProblem]->vector()); |
| 529 |
|
✗ |
m_nai.set(valueByDofnai); |
| 530 |
|
✗ |
m_nao.duplicateFrom(m_linearProblemBidomain[iProblem]->vector()); |
| 531 |
|
✗ |
m_nao.set(valueByDofnao); |
| 532 |
|
✗ |
m_cao.duplicateFrom(m_linearProblemBidomain[iProblem]->vector()); |
| 533 |
|
✗ |
m_cao.set(valueByDofcao); |
| 534 |
|
✗ |
m_ki.duplicateFrom(m_linearProblemBidomain[iProblem]->vector()); |
| 535 |
|
✗ |
m_ki.set(valueByDofki); |
| 536 |
|
✗ |
m_ko.duplicateFrom(m_linearProblemBidomain[iProblem]->vector()); |
| 537 |
|
✗ |
m_ko.set(valueByDofko); |
| 538 |
|
✗ |
m_cai.duplicateFrom(m_linearProblemBidomain[iProblem]->vector()); |
| 539 |
|
✗ |
m_cai.set(valueByDofcai); |
| 540 |
|
✗ |
m_naiont.duplicateFrom(m_linearProblemBidomain[iProblem]->vector()); |
| 541 |
|
✗ |
m_naiont.set(0.); |
| 542 |
|
✗ |
m_kiont.duplicateFrom(m_linearProblemBidomain[iProblem]->vector()); |
| 543 |
|
✗ |
m_kiont.set(0.); |
| 544 |
|
✗ |
m_caiont.duplicateFrom(m_linearProblemBidomain[iProblem]->vector()); |
| 545 |
|
✗ |
m_caiont.set(0.); |
| 546 |
|
✗ |
m_ileak.duplicateFrom(m_linearProblemBidomain[iProblem]->vector()); |
| 547 |
|
✗ |
m_ileak.set(0.); |
| 548 |
|
✗ |
m_iup.duplicateFrom(m_linearProblemBidomain[iProblem]->vector()); |
| 549 |
|
✗ |
m_iup.set(0.); |
| 550 |
|
✗ |
m_itr.duplicateFrom(m_linearProblemBidomain[iProblem]->vector()); |
| 551 |
|
✗ |
m_itr.set(0.); |
| 552 |
|
✗ |
m_irel.duplicateFrom(m_linearProblemBidomain[iProblem]->vector()); |
| 553 |
|
✗ |
m_irel.set(0.); |
| 554 |
|
✗ |
m_cmdn.duplicateFrom(m_linearProblemBidomain[iProblem]->vector()); |
| 555 |
|
✗ |
m_cmdn.set(valueByDofcmdn); |
| 556 |
|
✗ |
m_trpn.duplicateFrom(m_linearProblemBidomain[iProblem]->vector()); |
| 557 |
|
✗ |
m_trpn.set(valueByDoftrpn); |
| 558 |
|
✗ |
m_nsr.duplicateFrom(m_linearProblemBidomain[iProblem]->vector()); |
| 559 |
|
✗ |
m_nsr.set(valueByDofnsr); |
| 560 |
|
✗ |
m_jsr.duplicateFrom(m_linearProblemBidomain[iProblem]->vector()); |
| 561 |
|
✗ |
m_jsr.set(valueByDofjsr); |
| 562 |
|
✗ |
m_csqn.duplicateFrom(m_linearProblemBidomain[iProblem]->vector()); |
| 563 |
|
✗ |
m_csqn.set(valueByDofcsqn); |
| 564 |
|
|
} |
| 565 |
|
|
|
| 566 |
|
|
|
| 567 |
|
|
|
| 568 |
|
|
// 2) copy structure in m_extrapolate (contains extrapolate values of linearProblem solution). |
| 569 |
|
✗ |
m_extrapolate.duplicateFrom(m_linearProblemBidomain[iProblem]->vector()); |
| 570 |
|
✗ |
m_extrapolate.set(0.); |
| 571 |
|
✗ |
m_extrapolateIsCreated = true; |
| 572 |
|
|
|
| 573 |
|
|
// Lun. filter |
| 574 |
|
✗ |
if(FelisceParam::instance().stateFilter) { |
| 575 |
|
✗ |
m_Observ.duplicateFrom(m_linearProblemBidomain[iProblem]->vector()); |
| 576 |
|
✗ |
m_Observ.set(0.); |
| 577 |
|
|
} |
| 578 |
|
|
|
| 579 |
|
|
// Read fibers and distance mapp (for Zygote geometry). |
| 580 |
|
✗ |
if(FelisceParam::instance().testCase == 1) { // Any testCase with fibers. |
| 581 |
|
✗ |
m_linearProblemBidomain[iProblem]->readData(*io()); |
| 582 |
|
|
} |
| 583 |
|
|
|
| 584 |
|
|
//Initialize heterogeneous parameters for schaf solver. |
| 585 |
|
✗ |
if ( (FelisceParam::instance().typeOfIonicModel == "schaf") || (FelisceParam::instance().typeOfIonicModel == "schafRev") || (FelisceParam::instance().typeOfIonicModel == "courtAtriaSchafVent") ) { |
| 586 |
|
✗ |
initializeSchafParameter(); |
| 587 |
|
✗ |
if (FelisceParam::instance().typeOfIonicModel == "courtAtriaSchafVent") |
| 588 |
|
✗ |
initializeCourtParameter(); |
| 589 |
|
|
} |
| 590 |
|
|
|
| 591 |
|
|
//Initialize heterogeneous parameters for MV solver. |
| 592 |
|
✗ |
if ( (FelisceParam::instance().typeOfIonicModel == "MV") || (FelisceParam::instance().typeOfIonicModel == "courtAtriaMvVent") ) { |
| 593 |
|
✗ |
initializeMVParameter(); |
| 594 |
|
✗ |
if (FelisceParam::instance().typeOfIonicModel == "courtAtriaMvVent") |
| 595 |
|
✗ |
initializeCourtParameter(); |
| 596 |
|
|
} |
| 597 |
|
|
|
| 598 |
|
|
//Initialize heterogeneous parameters for BCL solver. |
| 599 |
|
✗ |
if (FelisceParam::instance().typeOfIonicModel == "BCL") { |
| 600 |
|
✗ |
initializeBCLParameter(); |
| 601 |
|
|
} |
| 602 |
|
|
|
| 603 |
|
|
//Initialize heterogeneous parameters for FhN solver. |
| 604 |
|
✗ |
if (FelisceParam::instance().typeOfIonicModel == "fhn") { |
| 605 |
|
✗ |
initializeFhNParameter(); |
| 606 |
|
|
} |
| 607 |
|
|
|
| 608 |
|
✗ |
if(FelisceParam::instance().useROM) { |
| 609 |
|
✗ |
std::cout << "m_rom->initializeRom\n"; |
| 610 |
|
✗ |
m_rom = new RomPETSC(); |
| 611 |
|
✗ |
m_rom->initializeRom(m_fstransient, MpiInfo::petscComm(), m_linearProblemBidomain[iProblem]->ao()); |
| 612 |
|
✗ |
m_linearProblemBidomain[iProblem]->initializeROM(m_rom); |
| 613 |
|
✗ |
m_rom->initializeRomBasis(); |
| 614 |
|
|
} |
| 615 |
|
|
|
| 616 |
|
|
} |
| 617 |
|
|
|
| 618 |
|
✗ |
void BidomainModel::postAssemblingMatrixRHS(std::size_t iProblem) { |
| 619 |
|
|
|
| 620 |
|
|
// Evaluate applied current std::vector. |
| 621 |
|
✗ |
if (iProblem == 0) { |
| 622 |
|
✗ |
evalIapp(); |
| 623 |
|
✗ |
if (FelisceParam::instance().hasAppliedExteriorCurrent) |
| 624 |
|
✗ |
evalIappExt(); |
| 625 |
|
|
} |
| 626 |
|
|
|
| 627 |
|
|
|
| 628 |
|
|
// Calculate RHS std::vector (to be multiplied by mass matrix). |
| 629 |
|
|
// RHS = Am*Ion + Am*Iapp + ... |
| 630 |
|
✗ |
finalizeRHSDP(iProblem); |
| 631 |
|
|
|
| 632 |
|
|
// Calculate m_RHS : |
| 633 |
|
|
// if model == 'Bidomain' => m_RHS = mass * RHS. |
| 634 |
|
|
// if model == 'BidomainDecoupled' : |
| 635 |
|
|
// iProblem==0 => m_RHS=mass*RHS+Ksigmai*u_e |
| 636 |
|
|
// iProblem==1 => m_RHS=Ksigmai*V_m |
| 637 |
|
✗ |
m_linearProblemBidomain[iProblem]->addMatrixRHS(); |
| 638 |
|
|
|
| 639 |
|
|
//RHS of Luenb. filter (Cesare) |
| 640 |
|
✗ |
if (FelisceParam::instance().stateFilter) { |
| 641 |
|
✗ |
if (iProblem == 0) { |
| 642 |
|
✗ |
double coefAm = FelisceParam::instance().Am; |
| 643 |
|
✗ |
m_luenbFlter.zeroEntries(); |
| 644 |
|
✗ |
m_luenbFlter.copyFrom(m_linearProblemBidomain[iProblem]->matrix(1),SAME_NONZERO_PATTERN); |
| 645 |
|
✗ |
m_luenbFlter.assembly(MAT_FINAL_ASSEMBLY); |
| 646 |
|
|
// copy diagonal stabiliz. matrix in luenberger matrix |
| 647 |
|
✗ |
m_luenbFlter.diagonalScale(PetscVector::null(),m_ionic->stabTerm()); |
| 648 |
|
✗ |
m_luenbFlter.scale(coefAm); |
| 649 |
|
✗ |
m_linearProblemBidomain[iProblem]->matrix(0).axpy(1,m_luenbFlter,SAME_NONZERO_PATTERN); |
| 650 |
|
|
} |
| 651 |
|
|
} |
| 652 |
|
|
} |
| 653 |
|
|
|
| 654 |
|
|
// Re-define class to change clearMatrixRHS call |
| 655 |
|
✗ |
void BidomainModel::updateTime(const FlagMatrixRHS flagMatrixRHS) { |
| 656 |
|
✗ |
for(std::size_t i=0; i<m_linearProblem.size(); i++) { |
| 657 |
|
✗ |
m_linearProblemBidomain[i]->clearMatrixRHS(flagMatrixRHS); |
| 658 |
|
|
} |
| 659 |
|
✗ |
m_fstransient->iteration++; |
| 660 |
|
✗ |
m_fstransient->time +=m_fstransient->timeStep; |
| 661 |
|
|
} |
| 662 |
|
|
|
| 663 |
|
✗ |
void BidomainModel::initializeSchafParameter() { |
| 664 |
|
|
// Initialize TauClose. |
| 665 |
|
✗ |
if (FelisceParam::instance().hasHeteroTauClose) { |
| 666 |
|
✗ |
m_schaf->fctTauClose().initialize(m_fstransient); |
| 667 |
|
✗ |
if ( (FelisceParam::instance().typeOfAppliedCurrent == "zygote") || (FelisceParam::instance().typeOfAppliedCurrent == "heart") || (FelisceParam::instance().typeOfAppliedCurrent == "ellipseheart") ) { |
| 668 |
|
|
// Warning: extra-data m_linearProblemBidomain[0]->EndocardiumDistance() size has to be numDof (not number of mesh points). |
| 669 |
|
✗ |
m_linearProblemBidomain[0]->evalFunctionOnDof(m_schaf->fctTauClose(), m_schaf->tauClose(),m_linearProblemBidomain[0]->EndocardiumDistance()); |
| 670 |
|
|
} else { |
| 671 |
|
✗ |
m_linearProblemBidomain[0]->evalFunctionOnDof(m_schaf->fctTauClose(), m_schaf->tauClose()); |
| 672 |
|
|
} |
| 673 |
|
|
} |
| 674 |
|
|
// Initialize TauOut : heterogeneous in case of infarct. |
| 675 |
|
✗ |
if (FelisceParam::instance().hasInfarct) { |
| 676 |
|
✗ |
m_schaf->fctTauOut().initialize(m_fstransient); |
| 677 |
|
✗ |
m_linearProblemBidomain[0]->evalFunctionOnDof(m_schaf->fctTauOut(), m_schaf->tauOut()); |
| 678 |
|
|
} |
| 679 |
|
|
} |
| 680 |
|
|
|
| 681 |
|
✗ |
void BidomainModel::initializeMVParameter() { |
| 682 |
|
✗ |
if (FelisceParam::instance().CellsType == "hetero") { |
| 683 |
|
✗ |
m_mv->MVCoeff().initialize(m_fstransient); |
| 684 |
|
|
// Warning: extra-data m_linearProblemBidomain[0]->EndocardiumDistance() size has to be numDof (not number of mesh points). |
| 685 |
|
✗ |
m_linearProblemBidomain[0]->evalFunctionOnDof(m_mv->MVCoeff(), m_mv->cellType(),m_linearProblemBidomain[0]->EndocardiumDistance()); |
| 686 |
|
|
} |
| 687 |
|
|
// Initialize gfi |
| 688 |
|
✗ |
if (FelisceParam::instance().hasInfarct) { |
| 689 |
|
✗ |
m_mv->fctTauOut().initialize(m_fstransient); |
| 690 |
|
✗ |
m_linearProblemBidomain[0]->evalFunctionOnDof(m_mv->fctTauOut(), m_mv->tauOut()); |
| 691 |
|
|
} |
| 692 |
|
|
} |
| 693 |
|
|
|
| 694 |
|
✗ |
void BidomainModel::initializeBCLParameter() { |
| 695 |
|
✗ |
if (FelisceParam::instance().CellsType == "hetero") { |
| 696 |
|
✗ |
m_bcl->MVCoeff().initialize(m_fstransient); |
| 697 |
|
|
// Warning: extra-data m_linearProblemBidomain[0]->EndocardiumDistance() size has to be numDof (not number of mesh points). |
| 698 |
|
✗ |
m_linearProblemBidomain[0]->evalFunctionOnDof(m_bcl->MVCoeff(), m_bcl->cellType(),m_linearProblemBidomain[0]->EndocardiumDistance()); |
| 699 |
|
|
} |
| 700 |
|
|
} |
| 701 |
|
|
|
| 702 |
|
✗ |
void BidomainModel::initializeFhNParameter() { |
| 703 |
|
✗ |
if (FelisceParam::instance().hasInfarct) { |
| 704 |
|
✗ |
m_fhn->fctSpar().initialize(m_fstransient); |
| 705 |
|
✗ |
m_linearProblemBidomain[0]->evalFunctionOnDof(m_fhn->fctSpar(), m_fhn->f0Par()); |
| 706 |
|
|
} |
| 707 |
|
|
} |
| 708 |
|
|
|
| 709 |
|
✗ |
void BidomainModel::initializeCourtParameter() { |
| 710 |
|
|
// Initialize gToMax |
| 711 |
|
✗ |
m_court->fctCourtCondIto().initialize(m_fstransient); |
| 712 |
|
|
// Initialize gCaLMax |
| 713 |
|
✗ |
m_court->fctCourtCondICaL().initialize(m_fstransient); |
| 714 |
|
✗ |
if (FelisceParam::instance().hasHeteroCourtPar) { |
| 715 |
|
✗ |
m_linearProblemBidomain[0]->evalFunctionOnDof(m_court->fctCourtCondIto(), m_court->courtCondIto()); |
| 716 |
|
✗ |
m_linearProblemBidomain[0]->evalFunctionOnDof(m_court->fctCourtCondICaL(), m_court->courtCondICaL()); |
| 717 |
|
|
} |
| 718 |
|
|
// Initialize multiplicative coefficient |
| 719 |
|
✗ |
m_court->fctCourtCondMultCoeff().initialize(m_fstransient); |
| 720 |
|
|
// Warning: extra-data m_linearProblemBidomain[0]->Reference() size has to be numDof (not number of mesh points). |
| 721 |
|
✗ |
if (FelisceParam::instance().testCase == 1) |
| 722 |
|
✗ |
m_linearProblemBidomain[0]->evalFunctionOnDof(m_court->fctCourtCondMultCoeff(), m_court->courtCondMultCoeff(), m_linearProblemBidomain[0]->Reference()); |
| 723 |
|
|
else |
| 724 |
|
✗ |
m_linearProblemBidomain[0]->evalFunctionOnDof(m_court->fctCourtCondMultCoeff(), m_court->courtCondMultCoeff()); |
| 725 |
|
|
} |
| 726 |
|
|
|
| 727 |
|
|
// Pay attention on the call of this : |
| 728 |
|
|
// call BidomainModel::writeSolution() function instead of (non-virtual) Model::writeSolution() function |
| 729 |
|
✗ |
void BidomainModel::writeSolution() { |
| 730 |
|
✗ |
if (MpiInfo::rankProc() == 0) { |
| 731 |
|
✗ |
if (m_meshIsWritten == false) writeMesh(); |
| 732 |
|
|
} |
| 733 |
|
|
|
| 734 |
|
✗ |
if( (m_fstransient->iteration % FelisceParam::instance().frequencyWriteSolution == 0) or m_hasFinished) { |
| 735 |
|
✗ |
if(FelisceParam::verbose() > 1) PetscPrintf(MpiInfo::petscComm(),"Write solutions\n"); |
| 736 |
|
✗ |
for (std::size_t ipb = 0; ipb < m_linearProblem.size(); ipb++) { |
| 737 |
|
|
|
| 738 |
|
✗ |
m_linearProblemBidomain[ipb]->writeSolution(MpiInfo::rankProc(), m_ios, m_fstransient->time, m_fstransient->iteration); |
| 739 |
|
|
|
| 740 |
|
✗ |
if(FelisceParam::instance().printIonicVar) { |
| 741 |
|
|
int rankProc; |
| 742 |
|
✗ |
MPI_Comm_rank(MpiInfo::petscComm(),&rankProc); |
| 743 |
|
✗ |
if ( m_fstransient->iteration == 0 ) { |
| 744 |
|
✗ |
double * ionicSolToSave = new double[m_linearProblemBidomain[ipb]->numDofPerUnknown(0)]; |
| 745 |
|
✗ |
m_linearProblemBidomain[ipb]->fromVecToDoubleStar(ionicSolToSave, m_W_0[0], rankProc, 1, m_linearProblemBidomain[ipb]->numDofPerUnknown(0)); |
| 746 |
|
✗ |
if (rankProc == 0) { |
| 747 |
|
✗ |
m_linearProblemBidomain[ipb]->writeEnsightScalar(ionicSolToSave, static_cast<int>(m_fstransient->iteration/FelisceParam::instance().frequencyWriteSolution), "ionicVar"); |
| 748 |
|
✗ |
m_linearProblemBidomain[ipb]->writeEnsightCase(static_cast<int>(m_fstransient->iteration/FelisceParam::instance().frequencyWriteSolution)+1,"ionicVar"); |
| 749 |
|
|
} |
| 750 |
|
✗ |
delete [] ionicSolToSave; |
| 751 |
|
|
|
| 752 |
|
✗ |
if(FelisceParam::instance().typeOfIonicModel == "MV") { |
| 753 |
|
|
//MV |
| 754 |
|
✗ |
double * ionicSolToSaveV = new double[m_linearProblemBidomain[ipb]->numDofPerUnknown(0)]; |
| 755 |
|
✗ |
double * ionicSolToSaveW = new double[m_linearProblemBidomain[ipb]->numDofPerUnknown(0)]; |
| 756 |
|
✗ |
double * ionicSolToSaveS = new double[m_linearProblemBidomain[ipb]->numDofPerUnknown(0)]; |
| 757 |
|
|
|
| 758 |
|
✗ |
std::vector<std::string> varNames; |
| 759 |
|
✗ |
varNames.emplace_back("v"); |
| 760 |
|
✗ |
varNames.emplace_back("w"); |
| 761 |
|
✗ |
varNames.emplace_back("s"); |
| 762 |
|
|
|
| 763 |
|
✗ |
m_linearProblemBidomain[ipb]->fromVecToDoubleStar(ionicSolToSaveV, m_W_0[0], rankProc, 1, m_linearProblemBidomain[ipb]->numDofPerUnknown(0)); |
| 764 |
|
✗ |
m_linearProblemBidomain[ipb]->fromVecToDoubleStar(ionicSolToSaveW, m_W_0[1], rankProc, 1, m_linearProblemBidomain[ipb]->numDofPerUnknown(0)); |
| 765 |
|
✗ |
m_linearProblemBidomain[ipb]->fromVecToDoubleStar(ionicSolToSaveS, m_W_0[2], rankProc, 1, m_linearProblemBidomain[ipb]->numDofPerUnknown(0)); |
| 766 |
|
|
|
| 767 |
|
✗ |
if (MpiInfo::rankProc() == 0) { |
| 768 |
|
✗ |
m_linearProblemBidomain[ipb]->writeEnsightScalar(ionicSolToSaveV, static_cast<int>(m_fstransient->iteration/FelisceParam::instance().frequencyWriteSolution), varNames[0]); |
| 769 |
|
✗ |
m_linearProblemBidomain[ipb]->writeEnsightScalar(ionicSolToSaveW, static_cast<int>(m_fstransient->iteration/FelisceParam::instance().frequencyWriteSolution), varNames[1]); |
| 770 |
|
✗ |
m_linearProblemBidomain[ipb]->writeEnsightScalar(ionicSolToSaveS, static_cast<int>(m_fstransient->iteration/FelisceParam::instance().frequencyWriteSolution), varNames[2]); |
| 771 |
|
|
|
| 772 |
|
✗ |
m_linearProblemBidomain[ipb]->writeEnsightCaseCurrents(static_cast<int>(m_fstransient->iteration/FelisceParam::instance().frequencyWriteSolution)+1,varNames); |
| 773 |
|
|
|
| 774 |
|
|
} |
| 775 |
|
|
|
| 776 |
|
✗ |
delete [] ionicSolToSaveV; |
| 777 |
|
✗ |
delete [] ionicSolToSaveW; |
| 778 |
|
✗ |
delete [] ionicSolToSaveS; |
| 779 |
|
|
} |
| 780 |
|
|
|
| 781 |
|
✗ |
else if(FelisceParam::instance().typeOfIonicModel == "BCL") { |
| 782 |
|
|
//BCL |
| 783 |
|
✗ |
double * ionicSolToSaveH = new double[m_linearProblemBidomain[ipb]->numDofPerUnknown(0)]; |
| 784 |
|
✗ |
double * ionicSolToSaveF = new double[m_linearProblemBidomain[ipb]->numDofPerUnknown(0)]; |
| 785 |
|
✗ |
double * ionicSolToSaveR = new double[m_linearProblemBidomain[ipb]->numDofPerUnknown(0)]; |
| 786 |
|
✗ |
double * ionicSolToSaveS = new double[m_linearProblemBidomain[ipb]->numDofPerUnknown(0)]; |
| 787 |
|
|
|
| 788 |
|
✗ |
std::vector<std::string> varNames; |
| 789 |
|
✗ |
varNames.emplace_back("H"); |
| 790 |
|
✗ |
varNames.emplace_back("F"); |
| 791 |
|
✗ |
varNames.emplace_back("R"); |
| 792 |
|
✗ |
varNames.emplace_back("S"); |
| 793 |
|
|
|
| 794 |
|
✗ |
m_linearProblemBidomain[ipb]->fromVecToDoubleStar(ionicSolToSaveH, m_W_0[0], rankProc, 1, m_linearProblemBidomain[ipb]->numDofPerUnknown(0)); |
| 795 |
|
✗ |
m_linearProblemBidomain[ipb]->fromVecToDoubleStar(ionicSolToSaveF, m_W_0[1], rankProc, 1, m_linearProblemBidomain[ipb]->numDofPerUnknown(0)); |
| 796 |
|
✗ |
m_linearProblemBidomain[ipb]->fromVecToDoubleStar(ionicSolToSaveR, m_W_0[2], rankProc, 1, m_linearProblemBidomain[ipb]->numDofPerUnknown(0)); |
| 797 |
|
✗ |
m_linearProblemBidomain[ipb]->fromVecToDoubleStar(ionicSolToSaveS, m_W_0[3], rankProc, 1, m_linearProblemBidomain[ipb]->numDofPerUnknown(0)); |
| 798 |
|
|
|
| 799 |
|
✗ |
if (MpiInfo::rankProc() == 0) { |
| 800 |
|
✗ |
m_linearProblemBidomain[ipb]->writeEnsightScalar(ionicSolToSaveH, static_cast<int>(m_fstransient->iteration/FelisceParam::instance().frequencyWriteSolution), varNames[0]); |
| 801 |
|
✗ |
m_linearProblemBidomain[ipb]->writeEnsightScalar(ionicSolToSaveF, static_cast<int>(m_fstransient->iteration/FelisceParam::instance().frequencyWriteSolution), varNames[1]); |
| 802 |
|
✗ |
m_linearProblemBidomain[ipb]->writeEnsightScalar(ionicSolToSaveR, static_cast<int>(m_fstransient->iteration/FelisceParam::instance().frequencyWriteSolution), varNames[2]); |
| 803 |
|
✗ |
m_linearProblemBidomain[ipb]->writeEnsightScalar(ionicSolToSaveS, static_cast<int>(m_fstransient->iteration/FelisceParam::instance().frequencyWriteSolution), varNames[3]); |
| 804 |
|
|
|
| 805 |
|
✗ |
m_linearProblemBidomain[ipb]->writeEnsightCaseCurrents(static_cast<int>(m_fstransient->iteration/FelisceParam::instance().frequencyWriteSolution)+1,varNames); |
| 806 |
|
|
|
| 807 |
|
|
} |
| 808 |
|
|
|
| 809 |
|
✗ |
delete [] ionicSolToSaveH; |
| 810 |
|
✗ |
delete [] ionicSolToSaveF; |
| 811 |
|
✗ |
delete [] ionicSolToSaveR; |
| 812 |
|
✗ |
delete [] ionicSolToSaveS; |
| 813 |
|
|
|
| 814 |
|
|
} |
| 815 |
|
|
|
| 816 |
|
|
} else { |
| 817 |
|
✗ |
if(FelisceParam::instance().typeOfIonicModel == "MV") { |
| 818 |
|
✗ |
std::vector<std::string> varNames; |
| 819 |
|
✗ |
varNames.emplace_back("v"); |
| 820 |
|
✗ |
varNames.emplace_back("w"); |
| 821 |
|
✗ |
varNames.emplace_back("s"); |
| 822 |
|
|
|
| 823 |
|
✗ |
double * ionicSolToSave = new double[m_linearProblemBidomain[ipb]->numDofPerUnknown(0)]; |
| 824 |
|
|
|
| 825 |
|
✗ |
for (int iMvVar=0; iMvVar<3; iMvVar++) { |
| 826 |
|
✗ |
m_linearProblemBidomain[ipb]->fromVecToDoubleStar(ionicSolToSave, m_ionic->vec_sol()[iMvVar], rankProc, 1, m_linearProblemBidomain[ipb]->numDofPerUnknown(0)); |
| 827 |
|
✗ |
if (MpiInfo::rankProc() == 0) |
| 828 |
|
✗ |
m_linearProblemBidomain[ipb]->writeEnsightScalar(ionicSolToSave, static_cast<int>(m_fstransient->iteration/FelisceParam::instance().frequencyWriteSolution), varNames[iMvVar]); |
| 829 |
|
|
} |
| 830 |
|
|
|
| 831 |
|
✗ |
if (MpiInfo::rankProc() == 0) |
| 832 |
|
✗ |
m_linearProblemBidomain[ipb]->writeEnsightCaseCurrents(static_cast<int>(m_fstransient->iteration/FelisceParam::instance().frequencyWriteSolution)+1,varNames); |
| 833 |
|
|
|
| 834 |
|
✗ |
delete [] ionicSolToSave; |
| 835 |
|
✗ |
} else if(FelisceParam::instance().typeOfIonicModel == "BCL") { |
| 836 |
|
✗ |
std::vector<std::string> varNames; |
| 837 |
|
✗ |
varNames.emplace_back("H"); |
| 838 |
|
✗ |
varNames.emplace_back("F"); |
| 839 |
|
✗ |
varNames.emplace_back("R"); |
| 840 |
|
✗ |
varNames.emplace_back("S"); |
| 841 |
|
|
|
| 842 |
|
✗ |
double * ionicSolToSave = new double[m_linearProblemBidomain[ipb]->numDofPerUnknown(0)]; |
| 843 |
|
|
|
| 844 |
|
✗ |
for (int iMvVar=0; iMvVar<4; iMvVar++) { |
| 845 |
|
✗ |
m_linearProblemBidomain[ipb]->fromVecToDoubleStar(ionicSolToSave, m_ionic->vec_sol()[iMvVar], rankProc, 1, m_linearProblemBidomain[ipb]->numDofPerUnknown(0)); |
| 846 |
|
✗ |
if (MpiInfo::rankProc() == 0) |
| 847 |
|
✗ |
m_linearProblemBidomain[ipb]->writeEnsightScalar(ionicSolToSave, static_cast<int>(m_fstransient->iteration/FelisceParam::instance().frequencyWriteSolution), varNames[iMvVar]); |
| 848 |
|
|
} |
| 849 |
|
|
|
| 850 |
|
✗ |
if (MpiInfo::rankProc() == 0) |
| 851 |
|
✗ |
m_linearProblemBidomain[ipb]->writeEnsightCaseCurrents(static_cast<int>(m_fstransient->iteration/FelisceParam::instance().frequencyWriteSolution)+1,varNames); |
| 852 |
|
|
|
| 853 |
|
✗ |
delete [] ionicSolToSave; |
| 854 |
|
✗ |
} else if(FelisceParam::instance().typeOfIonicModel == "Paci") { |
| 855 |
|
✗ |
std::vector<std::string> varNames; |
| 856 |
|
✗ |
varNames.emplace_back("h"); |
| 857 |
|
✗ |
varNames.emplace_back("j"); |
| 858 |
|
✗ |
varNames.emplace_back("m"); |
| 859 |
|
✗ |
varNames.emplace_back("d"); |
| 860 |
|
✗ |
varNames.emplace_back("fCa"); |
| 861 |
|
✗ |
varNames.emplace_back("f1"); |
| 862 |
|
✗ |
varNames.emplace_back("f2"); |
| 863 |
|
✗ |
varNames.emplace_back("r"); |
| 864 |
|
✗ |
varNames.emplace_back("q"); |
| 865 |
|
✗ |
varNames.emplace_back("xr1"); |
| 866 |
|
✗ |
varNames.emplace_back("xr2"); |
| 867 |
|
✗ |
varNames.emplace_back("xs"); |
| 868 |
|
✗ |
varNames.emplace_back("xf"); |
| 869 |
|
✗ |
varNames.emplace_back("g"); |
| 870 |
|
✗ |
varNames.emplace_back("Cai"); |
| 871 |
|
✗ |
varNames.emplace_back("Casr"); |
| 872 |
|
✗ |
varNames.emplace_back("Nai"); |
| 873 |
|
✗ |
varNames.emplace_back("df1"); |
| 874 |
|
✗ |
varNames.emplace_back("INaCa"); |
| 875 |
|
✗ |
varNames.emplace_back("IpCa"); |
| 876 |
|
✗ |
varNames.emplace_back("IbCa"); |
| 877 |
|
✗ |
varNames.emplace_back("ENa"); |
| 878 |
|
✗ |
varNames.emplace_back("EKs"); |
| 879 |
|
✗ |
varNames.emplace_back("ECa"); |
| 880 |
|
✗ |
varNames.emplace_back("INa"); |
| 881 |
|
✗ |
varNames.emplace_back("ICaL"); |
| 882 |
|
✗ |
varNames.emplace_back("Ito"); |
| 883 |
|
✗ |
varNames.emplace_back("IKr"); |
| 884 |
|
✗ |
varNames.emplace_back("IKs"); |
| 885 |
|
✗ |
varNames.emplace_back("IK1"); |
| 886 |
|
✗ |
varNames.emplace_back("If"); |
| 887 |
|
✗ |
varNames.emplace_back("INaK"); |
| 888 |
|
✗ |
varNames.emplace_back("Irel"); |
| 889 |
|
✗ |
varNames.emplace_back("Iup"); |
| 890 |
|
✗ |
varNames.emplace_back("Ileak"); |
| 891 |
|
✗ |
varNames.emplace_back("IbNa"); |
| 892 |
|
|
|
| 893 |
|
✗ |
double * ionicSolToSave = new double[m_linearProblemBidomain[ipb]->numDofPerUnknown(0)]; |
| 894 |
|
|
|
| 895 |
|
✗ |
for (int iPaciVar=0; iPaciVar<42; iPaciVar++) { |
| 896 |
|
✗ |
m_linearProblemBidomain[ipb]->fromVecToDoubleStar(ionicSolToSave, m_ionic->vec_sol()[iPaciVar], rankProc, 1, m_linearProblemBidomain[ipb]->numDofPerUnknown(0)); |
| 897 |
|
✗ |
if (MpiInfo::rankProc() == 0) |
| 898 |
|
✗ |
m_linearProblemBidomain[ipb]->writeEnsightScalar(ionicSolToSave,static_cast<int>(m_fstransient->iteration/FelisceParam::instance().frequencyWriteSolution),varNames[iPaciVar]); |
| 899 |
|
|
} |
| 900 |
|
✗ |
if (MpiInfo::rankProc() == 0) |
| 901 |
|
✗ |
m_linearProblemBidomain[ipb]->writeEnsightCaseCurrents(static_cast<int>(m_fstransient->iteration/FelisceParam::instance().frequencyWriteSolution)+1,varNames); |
| 902 |
|
|
|
| 903 |
|
✗ |
delete [] ionicSolToSave; |
| 904 |
|
|
|
| 905 |
|
✗ |
} else { |
| 906 |
|
✗ |
double * ionicSolToSave = new double[m_linearProblemBidomain[ipb]->numDofPerUnknown(0)]; |
| 907 |
|
✗ |
m_linearProblemBidomain[ipb]->fromVecToDoubleStar(ionicSolToSave, m_ionic->sol(), rankProc, 1, m_linearProblemBidomain[ipb]->numDofPerUnknown(0)); |
| 908 |
|
✗ |
if (rankProc == 0) { |
| 909 |
|
✗ |
m_linearProblemBidomain[ipb]->writeEnsightScalar(ionicSolToSave, static_cast<int>(m_fstransient->iteration/FelisceParam::instance().frequencyWriteSolution), "ionicVar"); |
| 910 |
|
✗ |
m_linearProblemBidomain[ipb]->writeEnsightCase(static_cast<int>(m_fstransient->iteration/FelisceParam::instance().frequencyWriteSolution)+1,"ionicVar"); |
| 911 |
|
|
} |
| 912 |
|
✗ |
delete [] ionicSolToSave; |
| 913 |
|
|
} |
| 914 |
|
|
} |
| 915 |
|
|
} |
| 916 |
|
✗ |
if (MpiInfo::rankProc() == 0) { |
| 917 |
|
✗ |
for(std::size_t iio=0; iio<m_ios.size(); ++iio) { |
| 918 |
|
✗ |
if ( m_ios[iio]->typeOutput == 1 ) // 1 : ensight{ |
| 919 |
|
✗ |
m_ios[iio]->postProcess(m_fstransient->time/*, !m_sameGeometricMeshForVariable*/); |
| 920 |
|
|
} |
| 921 |
|
|
} |
| 922 |
|
|
} |
| 923 |
|
|
} |
| 924 |
|
|
|
| 925 |
|
✗ |
for (std::size_t ipb = 0; ipb < m_linearProblem.size(); ipb++) { |
| 926 |
|
✗ |
const int iMesh = m_linearProblem[ipb]->currentMesh(); |
| 927 |
|
|
|
| 928 |
|
✗ |
if( m_solutionBackup[ipb].hasToBackup(m_fstransient->iteration /*+ std::max(FelisceParam::instance().orderBdfEdp,FelisceParam::instance().orderBdfIonic)*/, FelisceParam::instance().frequencyBackup) && ( m_fstransient->iteration > ( std::max(FelisceParam::instance().orderBdfEdp,FelisceParam::instance().orderBdfIonic) - 1 ) ) ) { |
| 929 |
|
✗ |
if(FelisceParam::verbose() > 1) |
| 930 |
|
✗ |
PetscPrintf(MpiInfo::petscComm(),"Backup the solutions\n"); |
| 931 |
|
|
|
| 932 |
|
✗ |
double * supportVariable1 = nullptr; |
| 933 |
|
✗ |
double * supportVariable2 = nullptr; |
| 934 |
|
✗ |
double * supportVariable3 = nullptr; |
| 935 |
|
✗ |
double * supportVariable4 = nullptr; |
| 936 |
|
✗ |
double * supportVariable5 = nullptr; |
| 937 |
|
✗ |
double * supportVariable6 = nullptr; |
| 938 |
|
✗ |
std::vector<double*> supportVariableCourt; |
| 939 |
|
|
|
| 940 |
|
|
// Backup of linear problem variables |
| 941 |
|
✗ |
m_linearProblemBidomain[ipb]->writeSolutionBackup(m_initialCondition.listVariable(), MpiInfo::rankProc(), m_solutionBackup[ipb].listIO(), m_fstransient->time, m_fstransient->iteration); |
| 942 |
|
✗ |
felInt sizeSupportVariable = 0; |
| 943 |
|
|
|
| 944 |
|
|
// Backup of linear problem support variables (bdfEdp, bdfIonicModel, IonicModel variables, ... ) |
| 945 |
|
✗ |
if ( FelisceParam::instance().orderBdfEdp > 0 ) { |
| 946 |
|
✗ |
m_bdfEdp.sol_n().getSize(&sizeSupportVariable); |
| 947 |
|
✗ |
supportVariable1 = new double[sizeSupportVariable]; |
| 948 |
|
✗ |
m_linearProblemBidomain[ipb]->fromVecToDoubleStar(supportVariable1, m_bdfEdp.sol_n(), MpiInfo::rankProc(), 1); |
| 949 |
|
✗ |
m_linearProblem[ipb]->writeSupportVariableBackup("bdf_sol_n", supportVariable1, sizeSupportVariable, 1, MpiInfo::rankProc(), m_solutionBackup[ipb].io(iMesh), m_fstransient->time, m_fstransient->iteration); |
| 950 |
|
|
} |
| 951 |
|
|
|
| 952 |
|
✗ |
if ( FelisceParam::instance().orderBdfEdp > 1 ) { |
| 953 |
|
✗ |
m_bdfEdp.sol_n_1().getSize(&sizeSupportVariable); |
| 954 |
|
✗ |
supportVariable2 = new double[sizeSupportVariable]; |
| 955 |
|
✗ |
m_linearProblemBidomain[ipb]->fromVecToDoubleStar(supportVariable2, m_bdfEdp.sol_n_1(), MpiInfo::rankProc(), 1); |
| 956 |
|
✗ |
m_linearProblem[ipb]->writeSupportVariableBackup("bdf_sol_n_1", supportVariable2, sizeSupportVariable, 1, MpiInfo::rankProc(), m_solutionBackup[ipb].io(iMesh), m_fstransient->time, m_fstransient->iteration); |
| 957 |
|
|
} |
| 958 |
|
|
|
| 959 |
|
✗ |
if ( FelisceParam::instance().orderBdfEdp > 2 ) { |
| 960 |
|
✗ |
m_bdfEdp.sol_n_2().getSize(&sizeSupportVariable); |
| 961 |
|
✗ |
supportVariable3 = new double[sizeSupportVariable]; |
| 962 |
|
✗ |
m_linearProblemBidomain[ipb]->fromVecToDoubleStar(supportVariable3, m_bdfEdp.sol_n_2(), MpiInfo::rankProc(), 1); |
| 963 |
|
✗ |
m_linearProblem[ipb]->writeSupportVariableBackup("bdf_sol_n_2", supportVariable3, sizeSupportVariable, 1, MpiInfo::rankProc(), m_solutionBackup[ipb].io(iMesh), m_fstransient->time, m_fstransient->iteration); |
| 964 |
|
|
} |
| 965 |
|
|
|
| 966 |
|
✗ |
if ( (FelisceParam::instance().typeOfIonicModel == "MV") || (FelisceParam::instance().typeOfIonicModel == "courtAtriaMvVent") ) { |
| 967 |
|
|
//MV |
| 968 |
|
✗ |
double * ionicSolToSaveV = nullptr; |
| 969 |
|
✗ |
double * ionicSolToSaveW = nullptr; |
| 970 |
|
✗ |
double * ionicSolToSaveS = nullptr; |
| 971 |
|
✗ |
if ( FelisceParam::instance().orderBdfIonic > 0 ) { |
| 972 |
|
✗ |
m_ionic->vec_sol(0).getSize(&sizeSupportVariable); |
| 973 |
|
✗ |
ionicSolToSaveV = new double[sizeSupportVariable]; |
| 974 |
|
✗ |
m_ionic->vec_sol(1).getSize(&sizeSupportVariable); |
| 975 |
|
✗ |
ionicSolToSaveW = new double[sizeSupportVariable]; |
| 976 |
|
✗ |
m_ionic->vec_sol(2).getSize(&sizeSupportVariable); |
| 977 |
|
✗ |
ionicSolToSaveS = new double[sizeSupportVariable]; |
| 978 |
|
|
|
| 979 |
|
✗ |
m_linearProblemBidomain[ipb]->fromVecToDoubleStar(ionicSolToSaveV, m_ionic->vec_sol(0), MpiInfo::rankProc(), 1); |
| 980 |
|
✗ |
m_linearProblem[ipb]->writeSupportVariableBackup("ion_sol_v_n", ionicSolToSaveV, sizeSupportVariable, 1, MpiInfo::rankProc(), m_solutionBackup[ipb].io(iMesh), m_fstransient->time, m_fstransient->iteration); |
| 981 |
|
|
|
| 982 |
|
✗ |
m_linearProblemBidomain[ipb]->fromVecToDoubleStar(ionicSolToSaveW, m_ionic->vec_sol(1), MpiInfo::rankProc(), 1); |
| 983 |
|
✗ |
m_linearProblem[ipb]->writeSupportVariableBackup("ion_sol_w_n", ionicSolToSaveW, sizeSupportVariable, 1, MpiInfo::rankProc(), m_solutionBackup[ipb].io(iMesh), m_fstransient->time, m_fstransient->iteration); |
| 984 |
|
|
|
| 985 |
|
✗ |
m_linearProblemBidomain[ipb]->fromVecToDoubleStar(ionicSolToSaveS, m_ionic->vec_sol(2), MpiInfo::rankProc(), 1); |
| 986 |
|
✗ |
m_linearProblem[ipb]->writeSupportVariableBackup("ion_sol_s_n", ionicSolToSaveS, sizeSupportVariable, 1, MpiInfo::rankProc(), m_solutionBackup[ipb].io(iMesh), m_fstransient->time, m_fstransient->iteration); |
| 987 |
|
|
} |
| 988 |
|
|
|
| 989 |
|
✗ |
if ( FelisceParam::instance().orderBdfIonic > 1 ) { |
| 990 |
|
✗ |
m_linearProblemBidomain[ipb]->fromVecToDoubleStar(ionicSolToSaveV, m_ionic->vec_sol_n_1()[0], MpiInfo::rankProc(), 1); |
| 991 |
|
✗ |
m_linearProblem[ipb]->writeSupportVariableBackup("ion_sol_v_n_1", ionicSolToSaveV, sizeSupportVariable, 1, MpiInfo::rankProc(), m_solutionBackup[ipb].io(iMesh), m_fstransient->time, m_fstransient->iteration); |
| 992 |
|
|
|
| 993 |
|
✗ |
m_linearProblemBidomain[ipb]->fromVecToDoubleStar(ionicSolToSaveW, m_ionic->vec_sol_n_1()[1], MpiInfo::rankProc(), 1); |
| 994 |
|
✗ |
m_linearProblem[ipb]->writeSupportVariableBackup("ion_sol_w_n_1", ionicSolToSaveW, sizeSupportVariable, 1, MpiInfo::rankProc(), m_solutionBackup[ipb].io(iMesh), m_fstransient->time, m_fstransient->iteration); |
| 995 |
|
|
|
| 996 |
|
✗ |
m_linearProblemBidomain[ipb]->fromVecToDoubleStar(ionicSolToSaveS, m_ionic->vec_sol_n_1()[2], MpiInfo::rankProc(), 1); |
| 997 |
|
✗ |
m_linearProblem[ipb]->writeSupportVariableBackup("ion_sol_s_n_1", ionicSolToSaveS, sizeSupportVariable, 1, MpiInfo::rankProc(), m_solutionBackup[ipb].io(iMesh), m_fstransient->time, m_fstransient->iteration); |
| 998 |
|
|
} |
| 999 |
|
|
|
| 1000 |
|
✗ |
if ( FelisceParam::instance().orderBdfIonic > 2 ) { |
| 1001 |
|
✗ |
m_linearProblemBidomain[ipb]->fromVecToDoubleStar(ionicSolToSaveV, m_ionic->vec_sol_n_2()[0], MpiInfo::rankProc(), 1); |
| 1002 |
|
✗ |
m_linearProblem[ipb]->writeSupportVariableBackup("ion_sol_v_n_2", ionicSolToSaveV, sizeSupportVariable, 1, MpiInfo::rankProc(), m_solutionBackup[ipb].io(iMesh), m_fstransient->time, m_fstransient->iteration); |
| 1003 |
|
|
|
| 1004 |
|
✗ |
m_linearProblemBidomain[ipb]->fromVecToDoubleStar(ionicSolToSaveW, m_ionic->vec_sol_n_2()[1], MpiInfo::rankProc(), 1); |
| 1005 |
|
✗ |
m_linearProblem[ipb]->writeSupportVariableBackup("ion_sol_w_n_2", ionicSolToSaveW, sizeSupportVariable, 1, MpiInfo::rankProc(), m_solutionBackup[ipb].io(iMesh), m_fstransient->time, m_fstransient->iteration); |
| 1006 |
|
|
|
| 1007 |
|
✗ |
m_linearProblemBidomain[ipb]->fromVecToDoubleStar(ionicSolToSaveS, m_ionic->vec_sol_n_2()[2], MpiInfo::rankProc(), 1); |
| 1008 |
|
✗ |
m_linearProblem[ipb]->writeSupportVariableBackup("ion_sol_s_n_2", ionicSolToSaveS, sizeSupportVariable, 1, MpiInfo::rankProc(), m_solutionBackup[ipb].io(iMesh), m_fstransient->time, m_fstransient->iteration); |
| 1009 |
|
|
} |
| 1010 |
|
✗ |
if (ionicSolToSaveV) delete[] ionicSolToSaveV; |
| 1011 |
|
✗ |
if (ionicSolToSaveW) delete[] ionicSolToSaveW; |
| 1012 |
|
✗ |
if (ionicSolToSaveS) delete[] ionicSolToSaveS; |
| 1013 |
|
|
} |
| 1014 |
|
|
else { |
| 1015 |
|
✗ |
if ( FelisceParam::instance().orderBdfIonic > 0 ) { |
| 1016 |
|
✗ |
m_ionic->sol().getSize(&sizeSupportVariable); |
| 1017 |
|
✗ |
supportVariable4 = new double[sizeSupportVariable]; |
| 1018 |
|
✗ |
m_linearProblemBidomain[ipb]->fromVecToDoubleStar(supportVariable4, m_ionic->sol(), MpiInfo::rankProc(), 1); |
| 1019 |
|
✗ |
m_linearProblem[ipb]->writeSupportVariableBackup("ion_sol_n", supportVariable4, sizeSupportVariable, 1, MpiInfo::rankProc(), m_solutionBackup[ipb].io(iMesh), m_fstransient->time, m_fstransient->iteration); |
| 1020 |
|
|
} |
| 1021 |
|
|
|
| 1022 |
|
✗ |
if ( FelisceParam::instance().orderBdfIonic > 1 ) { |
| 1023 |
|
✗ |
m_ionic->sol_n_1().getSize(&sizeSupportVariable); |
| 1024 |
|
✗ |
supportVariable5 = new double[sizeSupportVariable]; |
| 1025 |
|
✗ |
m_linearProblemBidomain[ipb]->fromVecToDoubleStar(supportVariable5, m_ionic->sol_n_1(), MpiInfo::rankProc(), 1); |
| 1026 |
|
✗ |
m_linearProblem[ipb]->writeSupportVariableBackup("ion_sol_n_1", supportVariable5, sizeSupportVariable, 1, MpiInfo::rankProc(), m_solutionBackup[ipb].io(iMesh), m_fstransient->time, m_fstransient->iteration); |
| 1027 |
|
|
} |
| 1028 |
|
|
|
| 1029 |
|
✗ |
if ( FelisceParam::instance().orderBdfIonic > 2 ) { |
| 1030 |
|
✗ |
m_ionic->sol_n_2().getSize(&sizeSupportVariable); |
| 1031 |
|
✗ |
supportVariable6 = new double[sizeSupportVariable]; |
| 1032 |
|
✗ |
m_linearProblemBidomain[ipb]->fromVecToDoubleStar(supportVariable6, m_ionic->sol_n_2(), MpiInfo::rankProc(), 1); |
| 1033 |
|
✗ |
m_linearProblem[ipb]->writeSupportVariableBackup("ion_sol_n_2", supportVariable6, sizeSupportVariable, 1, MpiInfo::rankProc(), m_solutionBackup[ipb].io(iMesh), m_fstransient->time, m_fstransient->iteration); |
| 1034 |
|
|
} |
| 1035 |
|
|
} |
| 1036 |
|
|
|
| 1037 |
|
✗ |
if ( (FelisceParam::instance().typeOfIonicModel == "courtAtriaSchafVent") || (FelisceParam::instance().typeOfIonicModel == "courtAtriaMvVent") ) { |
| 1038 |
|
✗ |
std::string ionicVarFileName; |
| 1039 |
|
✗ |
for (int iCourt=0 ; iCourt<29; iCourt++) { |
| 1040 |
|
✗ |
supportVariableCourt.push_back(new double[sizeSupportVariable]); |
| 1041 |
|
✗ |
m_linearProblemBidomain[ipb]->fromVecToDoubleStar(supportVariableCourt[iCourt], m_court->ionicVariable(iCourt), MpiInfo::rankProc(), 1); |
| 1042 |
|
✗ |
ionicVarFileName = "court_ionic_var" + std::to_string(iCourt); |
| 1043 |
|
✗ |
m_linearProblem[ipb]->writeSupportVariableBackup(ionicVarFileName, supportVariableCourt[iCourt], sizeSupportVariable, 1, MpiInfo::rankProc(), m_solutionBackup[ipb].io(iMesh), m_fstransient->time, m_fstransient->iteration); |
| 1044 |
|
|
} |
| 1045 |
|
|
} |
| 1046 |
|
|
|
| 1047 |
|
✗ |
m_solutionBackup[ipb].backup(m_fstransient->time, m_mesh, MpiInfo::rankProc()); |
| 1048 |
|
|
|
| 1049 |
|
✗ |
if (supportVariable1 != nullptr) |
| 1050 |
|
✗ |
delete [] supportVariable1; |
| 1051 |
|
✗ |
if (supportVariable2 != nullptr) |
| 1052 |
|
✗ |
delete [] supportVariable2; |
| 1053 |
|
✗ |
if (supportVariable3 != nullptr) |
| 1054 |
|
✗ |
delete [] supportVariable3; |
| 1055 |
|
✗ |
if (supportVariable4 != nullptr) |
| 1056 |
|
✗ |
delete [] supportVariable4; |
| 1057 |
|
✗ |
if (supportVariable5 != nullptr) |
| 1058 |
|
✗ |
delete [] supportVariable5; |
| 1059 |
|
✗ |
if (supportVariable6 != nullptr) |
| 1060 |
|
✗ |
delete [] supportVariable6; |
| 1061 |
|
✗ |
if ( (FelisceParam::instance().typeOfIonicModel == "courtAtriaSchafVent") || (FelisceParam::instance().typeOfIonicModel == "courtAtriaMvVent") ) { |
| 1062 |
|
✗ |
for (int iCourt=0 ; iCourt<29; iCourt++) { |
| 1063 |
|
✗ |
if (supportVariableCourt[iCourt] != nullptr) |
| 1064 |
|
✗ |
delete [] supportVariableCourt[iCourt]; |
| 1065 |
|
|
} |
| 1066 |
|
|
} |
| 1067 |
|
|
} |
| 1068 |
|
|
} |
| 1069 |
|
|
} |
| 1070 |
|
|
|
| 1071 |
|
✗ |
void BidomainModel::userDefinedInitialConditions(std::size_t ipb) { |
| 1072 |
|
✗ |
if(FelisceParam::verbose() > 0) PetscPrintf(MpiInfo::petscComm(),"Restore solutions with previous simulation.\n"); |
| 1073 |
|
✗ |
double * supportVariable = nullptr; |
| 1074 |
|
|
// for (std::size_t ipb = 0; ipb < m_linearProblem.size(); ipb++) { |
| 1075 |
|
✗ |
int iterationToRead = FelisceParam::instance().restartSolutionIter + 1 - std::max(FelisceParam::instance().orderBdfEdp, FelisceParam::instance().orderBdfIonic); |
| 1076 |
|
|
|
| 1077 |
|
✗ |
int count = 0; |
| 1078 |
|
✗ |
supportVariable = new double[m_linearProblemBidomain[ipb]->numDof()]; |
| 1079 |
|
✗ |
m_initialCondition.readVariable(count, iterationToRead, supportVariable, m_linearProblemBidomain[ipb]->numDofPerUnknown(0) ); |
| 1080 |
|
✗ |
count++; |
| 1081 |
|
✗ |
for (felInt idof=0 ; idof<m_linearProblemBidomain[ipb]->numDofPerUnknown(0); idof++) { |
| 1082 |
|
✗ |
supportVariable[m_linearProblemBidomain[ipb]->numDofPerUnknown(0)+idof] = 0.0; |
| 1083 |
|
|
} |
| 1084 |
|
✗ |
m_linearProblemBidomain[ipb]->fromDoubleStarToVec(supportVariable,&m_U_0, m_linearProblemBidomain[ipb]->numDof()); |
| 1085 |
|
✗ |
if(FelisceParam::verbose() >= 40) |
| 1086 |
|
✗ |
m_U_0.view(); |
| 1087 |
|
✗ |
delete [] supportVariable; |
| 1088 |
|
✗ |
supportVariable = nullptr; |
| 1089 |
|
|
|
| 1090 |
|
✗ |
if ( FelisceParam::instance().orderBdfEdp > 0 ) { |
| 1091 |
|
✗ |
supportVariable = new double[m_linearProblemBidomain[ipb]->numDof()]; |
| 1092 |
|
✗ |
m_initialCondition.readVariable(count, iterationToRead, supportVariable, m_linearProblemBidomain[ipb]->numDofPerUnknown(0) ); |
| 1093 |
|
✗ |
for (felInt idof=0 ; idof<m_linearProblemBidomain[ipb]->numDofPerUnknown(0); idof++) { |
| 1094 |
|
✗ |
supportVariable[m_linearProblemBidomain[ipb]->numDofPerUnknown(0)+idof] = 0.0; |
| 1095 |
|
|
} |
| 1096 |
|
✗ |
count++; |
| 1097 |
|
✗ |
m_linearProblemBidomain[ipb]->fromDoubleStarToVec(supportVariable,&m_bdf_sol_n, m_linearProblemBidomain[ipb]->numDof()); |
| 1098 |
|
✗ |
if(FelisceParam::verbose() >= 40) |
| 1099 |
|
✗ |
m_bdf_sol_n.view(); |
| 1100 |
|
✗ |
delete [] supportVariable; |
| 1101 |
|
✗ |
supportVariable = nullptr; |
| 1102 |
|
|
} |
| 1103 |
|
|
|
| 1104 |
|
✗ |
if ( FelisceParam::instance().orderBdfEdp > 1 ) { |
| 1105 |
|
✗ |
supportVariable = new double[m_linearProblemBidomain[ipb]->numDof()]; |
| 1106 |
|
✗ |
m_initialCondition.readVariable(count, iterationToRead, supportVariable, m_linearProblemBidomain[ipb]->numDofPerUnknown(0) ); |
| 1107 |
|
✗ |
count++; |
| 1108 |
|
✗ |
for (felInt idof=0 ; idof<m_linearProblemBidomain[ipb]->numDofPerUnknown(0); idof++) { |
| 1109 |
|
✗ |
supportVariable[m_linearProblemBidomain[ipb]->numDofPerUnknown(0)+idof] = 0.0; |
| 1110 |
|
|
} |
| 1111 |
|
✗ |
m_linearProblemBidomain[ipb]->fromDoubleStarToVec(supportVariable,&m_bdf_sol_n_1, m_linearProblemBidomain[ipb]->numDof()); |
| 1112 |
|
✗ |
if(FelisceParam::verbose() >= 40) |
| 1113 |
|
✗ |
m_bdf_sol_n_1.view(); |
| 1114 |
|
✗ |
delete [] supportVariable; |
| 1115 |
|
✗ |
supportVariable = nullptr; |
| 1116 |
|
|
} |
| 1117 |
|
|
|
| 1118 |
|
✗ |
if ( FelisceParam::instance().orderBdfEdp > 2 ) { |
| 1119 |
|
✗ |
supportVariable = new double[m_linearProblemBidomain[ipb]->numDof()]; |
| 1120 |
|
✗ |
m_initialCondition.readVariable(count, iterationToRead, supportVariable, m_linearProblemBidomain[ipb]->numDofPerUnknown(0) ); |
| 1121 |
|
✗ |
count++; |
| 1122 |
|
✗ |
for (felInt idof=0 ; idof<m_linearProblemBidomain[ipb]->numDofPerUnknown(0); idof++) { |
| 1123 |
|
✗ |
supportVariable[m_linearProblemBidomain[ipb]->numDofPerUnknown(0)+idof] = 0.0; |
| 1124 |
|
|
} |
| 1125 |
|
✗ |
m_linearProblemBidomain[ipb]->fromDoubleStarToVec(supportVariable,&m_bdf_sol_n_2, m_linearProblemBidomain[ipb]->numDof()); |
| 1126 |
|
✗ |
if(FelisceParam::verbose() >= 40) |
| 1127 |
|
✗ |
m_bdf_sol_n_2.view(); |
| 1128 |
|
✗ |
delete [] supportVariable; |
| 1129 |
|
✗ |
supportVariable = nullptr; |
| 1130 |
|
|
} |
| 1131 |
|
|
|
| 1132 |
|
✗ |
if ( (FelisceParam::instance().typeOfIonicModel == "MV") || (FelisceParam::instance().typeOfIonicModel == "courtAtriaMvVent") ) { |
| 1133 |
|
✗ |
if ( FelisceParam::instance().orderBdfIonic > 0 ) { |
| 1134 |
|
✗ |
m_ionic_sol_n.resize(3); |
| 1135 |
|
✗ |
for (int iVar=0; iVar<3; iVar++) { |
| 1136 |
|
✗ |
supportVariable = new double[m_linearProblemBidomain[ipb]->numDof()]; |
| 1137 |
|
✗ |
m_initialCondition.readVariable(count, iterationToRead, supportVariable, m_linearProblemBidomain[ipb]->numDofPerUnknown(0) ); |
| 1138 |
|
✗ |
count++; |
| 1139 |
|
✗ |
for (felInt idof=0 ; idof<m_linearProblemBidomain[ipb]->numDofPerUnknown(0); idof++) { |
| 1140 |
|
✗ |
supportVariable[m_linearProblemBidomain[ipb]->numDofPerUnknown(0)+idof] = 0.0; |
| 1141 |
|
|
} |
| 1142 |
|
✗ |
m_linearProblemBidomain[ipb]->fromDoubleStarToVec(supportVariable,&m_ionic_sol_n[iVar], m_linearProblemBidomain[ipb]->numDof()); |
| 1143 |
|
✗ |
if(FelisceParam::verbose() >= 40) |
| 1144 |
|
✗ |
m_ionic_sol_n[iVar].view(); |
| 1145 |
|
✗ |
delete [] supportVariable; |
| 1146 |
|
✗ |
supportVariable = nullptr; |
| 1147 |
|
|
} |
| 1148 |
|
|
} |
| 1149 |
|
✗ |
if ( FelisceParam::instance().orderBdfIonic > 1 ) { |
| 1150 |
|
✗ |
m_ionic_sol_n_1.resize(3); |
| 1151 |
|
✗ |
for (int iVar=0; iVar<3; iVar++) { |
| 1152 |
|
✗ |
supportVariable = new double[m_linearProblemBidomain[ipb]->numDof()]; |
| 1153 |
|
✗ |
m_initialCondition.readVariable(count, iterationToRead, supportVariable, m_linearProblemBidomain[ipb]->numDofPerUnknown(0) ); |
| 1154 |
|
✗ |
count++; |
| 1155 |
|
✗ |
for (felInt idof=0 ; idof<m_linearProblemBidomain[ipb]->numDofPerUnknown(0); idof++) { |
| 1156 |
|
✗ |
supportVariable[m_linearProblemBidomain[ipb]->numDofPerUnknown(0)+idof] = 0.0; |
| 1157 |
|
|
} |
| 1158 |
|
✗ |
m_linearProblemBidomain[ipb]->fromDoubleStarToVec(supportVariable,&m_ionic_sol_n_1[iVar], m_linearProblemBidomain[ipb]->numDof()); |
| 1159 |
|
✗ |
if(FelisceParam::verbose() >= 40) |
| 1160 |
|
✗ |
m_ionic_sol_n_1[iVar].view(); |
| 1161 |
|
✗ |
delete [] supportVariable; |
| 1162 |
|
✗ |
supportVariable = nullptr; |
| 1163 |
|
|
} |
| 1164 |
|
|
} |
| 1165 |
|
✗ |
if ( FelisceParam::instance().orderBdfIonic > 2 ) { |
| 1166 |
|
✗ |
m_ionic_sol_n_2.resize(3); |
| 1167 |
|
✗ |
for (int iVar=0; iVar<3; iVar++) { |
| 1168 |
|
✗ |
supportVariable = new double[m_linearProblemBidomain[ipb]->numDof()]; |
| 1169 |
|
✗ |
m_initialCondition.readVariable(count, iterationToRead, supportVariable, m_linearProblemBidomain[ipb]->numDofPerUnknown(0) ); |
| 1170 |
|
✗ |
count++; |
| 1171 |
|
✗ |
for (felInt idof=0 ; idof<m_linearProblemBidomain[ipb]->numDofPerUnknown(0); idof++) { |
| 1172 |
|
✗ |
supportVariable[m_linearProblemBidomain[ipb]->numDofPerUnknown(0)+idof] = 0.0; |
| 1173 |
|
|
} |
| 1174 |
|
✗ |
m_linearProblemBidomain[ipb]->fromDoubleStarToVec(supportVariable,&m_ionic_sol_n_2[iVar], m_linearProblemBidomain[ipb]->numDof()); |
| 1175 |
|
✗ |
if(FelisceParam::verbose() >= 40) |
| 1176 |
|
✗ |
m_ionic_sol_n_2[iVar].view(); |
| 1177 |
|
✗ |
delete [] supportVariable; |
| 1178 |
|
✗ |
supportVariable = nullptr; |
| 1179 |
|
|
} |
| 1180 |
|
|
} |
| 1181 |
|
|
} |
| 1182 |
|
|
else { |
| 1183 |
|
✗ |
if ( FelisceParam::instance().orderBdfIonic > 0 ) { |
| 1184 |
|
✗ |
m_ionic_sol_n.resize(1); |
| 1185 |
|
✗ |
supportVariable = new double[m_linearProblemBidomain[ipb]->numDof()]; |
| 1186 |
|
✗ |
m_initialCondition.readVariable(count, iterationToRead, supportVariable, m_linearProblemBidomain[ipb]->numDofPerUnknown(0) ); |
| 1187 |
|
✗ |
count++; |
| 1188 |
|
✗ |
for (felInt idof=0 ; idof<m_linearProblemBidomain[ipb]->numDofPerUnknown(0); idof++) { |
| 1189 |
|
✗ |
supportVariable[m_linearProblemBidomain[ipb]->numDofPerUnknown(0)+idof] = 0.0; |
| 1190 |
|
|
} |
| 1191 |
|
✗ |
m_linearProblemBidomain[ipb]->fromDoubleStarToVec(supportVariable,&m_ionic_sol_n[0], m_linearProblemBidomain[ipb]->numDof()); |
| 1192 |
|
✗ |
if(FelisceParam::verbose() >= 40) |
| 1193 |
|
✗ |
m_ionic_sol_n[0].view(); |
| 1194 |
|
✗ |
delete [] supportVariable; |
| 1195 |
|
✗ |
supportVariable = nullptr; |
| 1196 |
|
|
} |
| 1197 |
|
|
|
| 1198 |
|
✗ |
if ( FelisceParam::instance().orderBdfIonic > 1 ) { |
| 1199 |
|
✗ |
m_ionic_sol_n_1.resize(1); |
| 1200 |
|
✗ |
supportVariable = new double[m_linearProblemBidomain[ipb]->numDof()]; |
| 1201 |
|
✗ |
m_initialCondition.readVariable(count, iterationToRead, supportVariable, m_linearProblemBidomain[ipb]->numDofPerUnknown(0) ); |
| 1202 |
|
✗ |
count++; |
| 1203 |
|
✗ |
for (felInt idof=0 ; idof<m_linearProblemBidomain[ipb]->numDofPerUnknown(0); idof++) { |
| 1204 |
|
✗ |
supportVariable[m_linearProblemBidomain[ipb]->numDofPerUnknown(0)+idof] = 0.0; |
| 1205 |
|
|
} |
| 1206 |
|
✗ |
m_linearProblemBidomain[ipb]->fromDoubleStarToVec(supportVariable,&m_ionic_sol_n_1[0], m_linearProblemBidomain[ipb]->numDof()); |
| 1207 |
|
✗ |
if(FelisceParam::verbose() >= 40) |
| 1208 |
|
✗ |
m_ionic_sol_n_1[0].view(); |
| 1209 |
|
✗ |
delete [] supportVariable; |
| 1210 |
|
✗ |
supportVariable = nullptr; |
| 1211 |
|
|
} |
| 1212 |
|
|
|
| 1213 |
|
✗ |
if ( FelisceParam::instance().orderBdfIonic > 2 ) { |
| 1214 |
|
✗ |
m_ionic_sol_n_2.resize(1); |
| 1215 |
|
✗ |
supportVariable = new double[m_linearProblemBidomain[ipb]->numDof()]; |
| 1216 |
|
✗ |
m_initialCondition.readVariable(count, iterationToRead, supportVariable, m_linearProblemBidomain[ipb]->numDofPerUnknown(0) ); |
| 1217 |
|
✗ |
count++; |
| 1218 |
|
✗ |
for (felInt idof=0 ; idof<m_linearProblemBidomain[ipb]->numDofPerUnknown(0); idof++) { |
| 1219 |
|
✗ |
supportVariable[m_linearProblemBidomain[ipb]->numDofPerUnknown(0)+idof] = 0.0; |
| 1220 |
|
|
} |
| 1221 |
|
✗ |
m_linearProblemBidomain[ipb]->fromDoubleStarToVec(supportVariable,&m_ionic_sol_n_2[0], m_linearProblemBidomain[ipb]->numDof()); |
| 1222 |
|
✗ |
if(FelisceParam::verbose() >= 40) |
| 1223 |
|
✗ |
m_ionic_sol_n_2[0].view(); |
| 1224 |
|
✗ |
delete [] supportVariable; |
| 1225 |
|
✗ |
supportVariable = nullptr; |
| 1226 |
|
|
} |
| 1227 |
|
|
} |
| 1228 |
|
|
|
| 1229 |
|
✗ |
if ( (FelisceParam::instance().typeOfIonicModel == "courtAtriaSchafVent") || (FelisceParam::instance().typeOfIonicModel == "courtAtriaMvVent") ) { |
| 1230 |
|
✗ |
std::string ionicVarFileName; |
| 1231 |
|
✗ |
m_courtVarInit.resize(29); |
| 1232 |
|
✗ |
for (int iCourt=0 ; iCourt<29; iCourt++) { |
| 1233 |
|
✗ |
supportVariable = new double[m_linearProblemBidomain[ipb]->numDof()]; |
| 1234 |
|
✗ |
m_initialCondition.readVariable(count, iterationToRead, supportVariable, m_linearProblemBidomain[ipb]->numDof()); |
| 1235 |
|
✗ |
count++; |
| 1236 |
|
✗ |
m_linearProblemBidomain[ipb]->fromDoubleStarToVec(supportVariable,&m_courtVarInit[iCourt], m_linearProblemBidomain[ipb]->numDof()); |
| 1237 |
|
✗ |
if(FelisceParam::verbose() >= 40) |
| 1238 |
|
✗ |
m_courtVarInit[iCourt].view(); |
| 1239 |
|
✗ |
delete [] supportVariable; |
| 1240 |
|
✗ |
supportVariable = nullptr; |
| 1241 |
|
|
} |
| 1242 |
|
|
} |
| 1243 |
|
|
|
| 1244 |
|
|
// } |
| 1245 |
|
|
|
| 1246 |
|
|
} |
| 1247 |
|
|
|
| 1248 |
|
✗ |
void BidomainModel::forward() |
| 1249 |
|
|
{ |
| 1250 |
|
|
|
| 1251 |
|
|
|
| 1252 |
|
|
//Write solution with ensight. |
| 1253 |
|
✗ |
BidomainModel::writeSolution(); |
| 1254 |
|
|
|
| 1255 |
|
|
//Advance time step. |
| 1256 |
|
✗ |
if (FelisceParam::instance().stateFilter) { |
| 1257 |
|
|
// clear RHS, and m_Matrix[0]. |
| 1258 |
|
✗ |
updateTime(FlagMatrixRHS::matrix_and_rhs); |
| 1259 |
|
|
} |
| 1260 |
|
|
else { |
| 1261 |
|
|
// clear only RHS, NOT m_Matrix[0]. |
| 1262 |
|
✗ |
updateTime(FlagMatrixRHS::only_rhs); |
| 1263 |
|
|
} |
| 1264 |
|
✗ |
printNewTimeIterationBanner(); |
| 1265 |
|
|
|
| 1266 |
|
|
|
| 1267 |
|
✗ |
if ( m_fstransient->iteration == 1 && !FelisceParam::instance().restartSolution) { |
| 1268 |
|
|
|
| 1269 |
|
|
//Initialization of bdf solver. |
| 1270 |
|
✗ |
m_bdfEdp.initialize(m_linearProblemBidomain[0]->solution()); |
| 1271 |
|
✗ |
m_linearProblemBidomain[0]->initializeTimeScheme(&m_bdfEdp); |
| 1272 |
|
|
|
| 1273 |
|
|
//m_extrapolate = initial solution. |
| 1274 |
|
✗ |
m_bdfEdp.extrapolate(m_extrapolate); |
| 1275 |
|
|
|
| 1276 |
|
|
//Initialization of Schaf solver. |
| 1277 |
|
✗ |
m_ionic->defineSizeAndMappingOfIonicProblem(m_linearProblemBidomain[0]->numDofLocalPerUnknown(potTransMemb), m_linearProblemBidomain[0]->mappingDofLocalToDofGlobal(potTransMemb), m_linearProblemBidomain[0]->ao()); |
| 1278 |
|
|
|
| 1279 |
|
✗ |
m_ionic->initializeExtrap(m_extrapolate); |
| 1280 |
|
✗ |
m_ionic->initialize(m_W_0); |
| 1281 |
|
✗ |
m_buildIonic = true; |
| 1282 |
|
✗ |
if ( (FelisceParam::instance().typeOfIonicModel == "courtAtriaSchafVent") || (FelisceParam::instance().typeOfIonicModel == "courtAtriaMvVent") ) { |
| 1283 |
|
✗ |
m_court->defineSizeAndMappingOfIonicProblem(m_linearProblemBidomain[0]->numDofLocalPerUnknown(potTransMemb), m_linearProblemBidomain[0]->mappingDofLocalToDofGlobal(potTransMemb), m_linearProblemBidomain[0]->ao()); |
| 1284 |
|
✗ |
m_court->initializeExtrap(m_extrapolate); |
| 1285 |
|
✗ |
m_court->initializeConcentrationsAndGateConditions(m_m, m_h, m_j, m_ao, m_io, m_ua, m_ui, m_xr, m_xs, m_d, m_f, m_fca, m_urel, m_vrel, m_wrel, m_nai, m_nao, m_cao, m_ki, m_ko, m_cai, m_naiont, m_kiont, m_caiont, m_ileak, m_iup, m_itr, m_irel, m_cmdn, m_trpn, m_nsr, m_jsr, m_csqn); |
| 1286 |
|
✗ |
m_buildCourt = true; |
| 1287 |
|
|
} |
| 1288 |
|
|
|
| 1289 |
|
|
} |
| 1290 |
|
✗ |
else if ( m_fstransient->iteration == 1 && FelisceParam::instance().restartSolution) { |
| 1291 |
|
|
// Read vectors: |
| 1292 |
|
|
//Initialization of bdf solver. |
| 1293 |
|
✗ |
if (FelisceParam::instance().orderBdfEdp == 1) { |
| 1294 |
|
✗ |
m_bdfEdp.initialize(m_bdf_sol_n); |
| 1295 |
|
|
} |
| 1296 |
|
✗ |
else if (FelisceParam::instance().orderBdfEdp == 2) { |
| 1297 |
|
✗ |
m_bdfEdp.initialize(m_bdf_sol_n_1,m_bdf_sol_n); |
| 1298 |
|
|
} |
| 1299 |
|
✗ |
else if (FelisceParam::instance().orderBdfEdp == 2) { |
| 1300 |
|
✗ |
m_bdfEdp.initialize(m_bdf_sol_n_2,m_bdf_sol_n_1,m_bdf_sol_n); |
| 1301 |
|
|
} |
| 1302 |
|
✗ |
m_linearProblemBidomain[0]->initializeTimeScheme(&m_bdfEdp); |
| 1303 |
|
|
//m_extrapolate = initial solution. |
| 1304 |
|
✗ |
m_bdfEdp.extrapolate(m_extrapolate); |
| 1305 |
|
|
|
| 1306 |
|
|
|
| 1307 |
|
|
//Initialization of ionic solver. |
| 1308 |
|
✗ |
m_ionic->defineSizeAndMappingOfIonicProblem(m_linearProblemBidomain[0]->numDofLocalPerUnknown(potTransMemb), m_linearProblemBidomain[0]->mappingDofLocalToDofGlobal(potTransMemb), m_linearProblemBidomain[0]->ao()); |
| 1309 |
|
|
|
| 1310 |
|
✗ |
if (FelisceParam::instance().orderBdfIonic == 1) { |
| 1311 |
|
✗ |
m_ionic->initialize(m_ionic_sol_n); |
| 1312 |
|
|
} |
| 1313 |
|
✗ |
else if (FelisceParam::instance().orderBdfIonic == 2) { |
| 1314 |
|
✗ |
m_ionic->initialize(m_ionic_sol_n, m_ionic_sol_n_1); |
| 1315 |
|
|
} |
| 1316 |
|
✗ |
else if (FelisceParam::instance().orderBdfIonic == 3) { |
| 1317 |
|
✗ |
m_ionic->initialize(m_ionic_sol_n, m_ionic_sol_n_1, m_ionic_sol_n_2); |
| 1318 |
|
|
} |
| 1319 |
|
✗ |
m_ionic->initializeExtrap(m_extrapolate); |
| 1320 |
|
✗ |
m_buildIonic = true; |
| 1321 |
|
|
|
| 1322 |
|
✗ |
if ( (FelisceParam::instance().typeOfIonicModel == "courtAtriaSchafVent") || (FelisceParam::instance().typeOfIonicModel == "courtAtriaMvVent") ) { |
| 1323 |
|
✗ |
m_court->defineSizeAndMappingOfIonicProblem(m_linearProblemBidomain[0]->numDofLocalPerUnknown(potTransMemb), m_linearProblemBidomain[0]->mappingDofLocalToDofGlobal(potTransMemb), m_linearProblemBidomain[0]->ao()); |
| 1324 |
|
✗ |
m_court->initializeExtrap(m_extrapolate); |
| 1325 |
|
✗ |
m_court->initializeConcentrationsAndGateConditions(m_courtVarInit[0], m_courtVarInit[1], m_courtVarInit[2], m_courtVarInit[3], m_courtVarInit[4], m_courtVarInit[5], m_courtVarInit[6], m_courtVarInit[7], m_courtVarInit[8], m_courtVarInit[9], m_courtVarInit[10], m_courtVarInit[11], m_courtVarInit[12], m_courtVarInit[13], m_courtVarInit[14], m_courtVarInit[15], m_courtVarInit[16], m_courtVarInit[17], m_courtVarInit[18], m_courtVarInit[19], m_courtVarInit[20], m_courtVarInit[21], m_courtVarInit[22], m_courtVarInit[23], m_courtVarInit[23], m_courtVarInit[23], m_courtVarInit[23], m_courtVarInit[23], m_courtVarInit[24], m_courtVarInit[25], m_courtVarInit[26], m_courtVarInit[27], m_courtVarInit[28]); |
| 1326 |
|
✗ |
m_buildCourt = true; |
| 1327 |
|
|
} |
| 1328 |
|
|
|
| 1329 |
|
|
} |
| 1330 |
|
|
else { |
| 1331 |
|
✗ |
m_bdfEdp.update(m_linearProblemBidomain[0]->solution()); |
| 1332 |
|
✗ |
m_bdfEdp.extrapolate(m_extrapolate); |
| 1333 |
|
✗ |
m_ionic->update(m_extrapolate); |
| 1334 |
|
|
|
| 1335 |
|
✗ |
if ( (FelisceParam::instance().typeOfIonicModel == "courtAtriaSchafVent") || (FelisceParam::instance().typeOfIonicModel == "courtAtriaMvVent") ) { |
| 1336 |
|
✗ |
m_court->updateExtrap(m_extrapolate); |
| 1337 |
|
|
} |
| 1338 |
|
|
} |
| 1339 |
|
|
|
| 1340 |
|
|
// Long QT segment during period [torsadeTimeBegin,torsadeTimeEnd] |
| 1341 |
|
✗ |
if (FelisceParam::instance().torsade) { |
| 1342 |
|
✗ |
if ( std::abs( m_fstransient->time - FelisceParam::instance().torsadeTimeBegin ) < 2*FelisceParam::instance().timeStep ) { |
| 1343 |
|
|
// Warning: extra-data m_linearProblemBidomain[0]->EndocardiumDistance() size has to be numDof (not number of mesh points). |
| 1344 |
|
✗ |
m_linearProblemBidomain[0]->evalFunctionOnDof(m_schaf->fctTauClose(), m_schaf->tauClose(),m_linearProblemBidomain[0]->EndocardiumDistance(), m_fstransient->time); |
| 1345 |
|
|
} |
| 1346 |
|
✗ |
if ( std::abs( m_fstransient->time - FelisceParam::instance().torsadeTimeEnd ) < 2*FelisceParam::instance().timeStep ) { |
| 1347 |
|
|
// Warning: extra-data m_linearProblemBidomain[0]->EndocardiumDistance() size has to be numDof (not number of mesh points). |
| 1348 |
|
✗ |
m_linearProblemBidomain[0]->evalFunctionOnDof(m_schaf->fctTauClose(), m_schaf->tauClose(),m_linearProblemBidomain[0]->EndocardiumDistance(), m_fstransient->time); |
| 1349 |
|
|
} |
| 1350 |
|
|
} |
| 1351 |
|
|
|
| 1352 |
|
|
//Solve ionic model(s) and calculate Iion. |
| 1353 |
|
|
|
| 1354 |
|
✗ |
m_ionic->computeRHS(); |
| 1355 |
|
✗ |
m_ionic->solveEDO(); |
| 1356 |
|
✗ |
m_ionic->computeIon(); |
| 1357 |
|
✗ |
if ( (FelisceParam::instance().typeOfIonicModel != "BCL") && (FelisceParam::instance().typeOfIonicModel != "Paci")) { |
| 1358 |
|
✗ |
m_ionic->updateBdf(); |
| 1359 |
|
|
} |
| 1360 |
|
|
|
| 1361 |
|
|
|
| 1362 |
|
|
|
| 1363 |
|
✗ |
if ( (FelisceParam::instance().typeOfIonicModel == "courtAtriaSchafVent") || (FelisceParam::instance().typeOfIonicModel == "courtAtriaMvVent") ) { |
| 1364 |
|
✗ |
m_court->computeIon(); |
| 1365 |
|
|
} |
| 1366 |
|
|
|
| 1367 |
|
✗ |
m_bdfEdp.computeRHSTime(m_fstransient->timeStep); |
| 1368 |
|
|
|
| 1369 |
|
|
// Assembling of matrices at first iteration (because of needs some coefficients not defined at iteration 0). |
| 1370 |
|
|
|
| 1371 |
|
✗ |
if ( m_fstransient->iteration == 1 ) { |
| 1372 |
|
✗ |
if (FelisceParam::instance().hasMoveMesh) { |
| 1373 |
|
✗ |
m_linearProblemBidomain[0]->readDataDisplacement(m_ios,m_fstransient->iteration); |
| 1374 |
|
✗ |
m_linearProblemBidomain[0]->meshLocal()->moveMesh(m_linearProblemBidomain[0]->Displacement(),1.0); |
| 1375 |
|
✗ |
m_linearProblemBidomain[0]->assembleMatrixRHS(MpiInfo::rankProc()); |
| 1376 |
|
|
} |
| 1377 |
|
|
else { |
| 1378 |
|
✗ |
if ( FelisceParam::instance().hasCoupledAtriaVent ) { |
| 1379 |
|
✗ |
m_linearProblemBidomain[0]->assembleMatrixRHSCurrentAndCurvilinearElement(MpiInfo::rankProc()); |
| 1380 |
|
|
//m_linearProblemBidomain[0]->initAndStoreMassMatrix(); |
| 1381 |
|
|
} |
| 1382 |
|
|
else { |
| 1383 |
|
✗ |
m_linearProblemBidomain[0]->assembleMatrixRHS(MpiInfo::rankProc()); |
| 1384 |
|
|
} |
| 1385 |
|
|
|
| 1386 |
|
✗ |
if(FelisceParam::instance().stateFilter) { |
| 1387 |
|
✗ |
m_luenbFlter.duplicateFrom(m_linearProblemBidomain[0]->matrix(1),MAT_COPY_VALUES); |
| 1388 |
|
✗ |
m_luenbFlter.assembly(MAT_FINAL_ASSEMBLY); |
| 1389 |
|
✗ |
m_luenbFlter.zeroEntries(); |
| 1390 |
|
|
} |
| 1391 |
|
|
} |
| 1392 |
|
|
} |
| 1393 |
|
|
else { |
| 1394 |
|
✗ |
if (FelisceParam::instance().hasMoveMesh) { |
| 1395 |
|
✗ |
m_linearProblemBidomain[0]->clearMatrixRHS(FlagMatrixRHS::matrix_and_rhs); |
| 1396 |
|
✗ |
m_linearProblemBidomain[0]->clearMatrix(1); |
| 1397 |
|
✗ |
m_linearProblemBidomain[0]->readDataDisplacement(m_ios,m_fstransient->iteration); |
| 1398 |
|
✗ |
if (FelisceParam::instance().hasMoveFibers) |
| 1399 |
|
✗ |
m_linearProblemBidomain[0]->updateFibers(*io(),m_fstransient->iteration*m_fstransient->timeStep); |
| 1400 |
|
✗ |
m_linearProblemBidomain[0]->meshLocal()->moveMesh(m_linearProblemBidomain[0]->Displacement(),1.0); |
| 1401 |
|
✗ |
m_linearProblemBidomain[0]->assembleMatrixRHS(MpiInfo::rankProc()); |
| 1402 |
|
|
|
| 1403 |
|
|
} |
| 1404 |
|
|
} |
| 1405 |
|
|
|
| 1406 |
|
|
|
| 1407 |
|
|
|
| 1408 |
|
|
//Specific operations before solve the system : calculate m_RHS std::vector used in solve(). |
| 1409 |
|
✗ |
postAssemblingMatrixRHS(); |
| 1410 |
|
|
|
| 1411 |
|
|
|
| 1412 |
|
|
//Simulation of MEA experimentation |
| 1413 |
|
✗ |
if(FelisceParam::instance().bc_potExtraCell == "MEA_grounds") { |
| 1414 |
|
✗ |
m_linearProblem[0]->finalizeEssBCTransient(); |
| 1415 |
|
✗ |
m_linearProblem[0]->applyBC(FelisceParam::instance().essentialBoundaryConditionsMethod, MpiInfo::rankProc()); |
| 1416 |
|
|
} |
| 1417 |
|
|
|
| 1418 |
|
|
|
| 1419 |
|
|
//Solve the system m_Matrix[0]*m_sol=m_RHS. |
| 1420 |
|
|
//std::cout << "MPI INFO : " << MpiInfo::rankProc() << " " << MpiInfo::numProc() << std::endl; |
| 1421 |
|
✗ |
m_linearProblemBidomain[0]->solve(MpiInfo::rankProc(), MpiInfo::numProc()); |
| 1422 |
|
|
|
| 1423 |
|
|
// Choose zero mean value solution. |
| 1424 |
|
✗ |
if(FelisceParam::instance().bc_potExtraCell != "MEA_grounds") { |
| 1425 |
|
✗ |
m_linearProblemBidomain[0]->removeAverageFromSolution(potExtraCell, MpiInfo::rankProc()); |
| 1426 |
|
|
} |
| 1427 |
|
|
//m_linearProblemBidomain[0]->removeAverageForPotExtraCell(); |
| 1428 |
|
|
|
| 1429 |
|
|
|
| 1430 |
|
|
} |
| 1431 |
|
|
|
| 1432 |
|
✗ |
void BidomainModel::forwardROM() { |
| 1433 |
|
|
//Write solution with ensight. |
| 1434 |
|
✗ |
BidomainModel::writeSolution(); |
| 1435 |
|
|
//Advance time step. |
| 1436 |
|
✗ |
updateTime(FlagMatrixRHS::only_rhs); |
| 1437 |
|
✗ |
printNewTimeIterationBanner(); |
| 1438 |
|
|
|
| 1439 |
|
✗ |
if ( m_fstransient->iteration == 1) { |
| 1440 |
|
|
//Initialization of bdf solver. |
| 1441 |
|
✗ |
m_bdfEdp.initialize(m_linearProblemBidomain[0]->solution()); |
| 1442 |
|
✗ |
m_linearProblemBidomain[0]->initializeTimeScheme(&m_bdfEdp); |
| 1443 |
|
|
//m_extrapolate = initial solution. |
| 1444 |
|
✗ |
m_bdfEdp.extrapolate(m_extrapolate); |
| 1445 |
|
|
//Initialization of Schaf solver. |
| 1446 |
|
✗ |
m_ionic->defineSizeAndMappingOfIonicProblem(m_linearProblemBidomain[0]->numDofLocalPerUnknown(potTransMemb), m_linearProblemBidomain[0]->mappingDofLocalToDofGlobal(potTransMemb), m_linearProblemBidomain[0]->ao()); |
| 1447 |
|
✗ |
m_ionic->initializeExtrap(m_extrapolate); |
| 1448 |
|
✗ |
m_ionic->initialize(m_W_0[0]); |
| 1449 |
|
✗ |
m_buildIonic = true; |
| 1450 |
|
|
} else { |
| 1451 |
|
✗ |
m_bdfEdp.update(m_linearProblemBidomain[0]->solution()); |
| 1452 |
|
✗ |
m_bdfEdp.extrapolate(m_extrapolate); |
| 1453 |
|
✗ |
m_ionic->update(m_extrapolate); |
| 1454 |
|
|
} |
| 1455 |
|
|
|
| 1456 |
|
|
//Solve Mithcell and Schaeffer model and calculate Iion. |
| 1457 |
|
✗ |
m_ionic->computeRHS(); |
| 1458 |
|
✗ |
m_ionic->solveEDO(); |
| 1459 |
|
✗ |
m_ionic->computeIon(); |
| 1460 |
|
✗ |
m_ionic->updateBdf(); |
| 1461 |
|
|
|
| 1462 |
|
✗ |
m_bdfEdp.computeRHSTime(m_fstransient->timeStep); |
| 1463 |
|
|
|
| 1464 |
|
|
// Assembling of matrices at first iteration (because of needs some coefficients not defined at iteration 0). |
| 1465 |
|
✗ |
if ( m_fstransient->iteration == 1 ) { |
| 1466 |
|
✗ |
m_linearProblemBidomain[0]->assembleMatrixRHS(MpiInfo::rankProc()); |
| 1467 |
|
✗ |
if(FelisceParam::instance().stateFilter) { |
| 1468 |
|
✗ |
m_luenbFlter.duplicateFrom(m_linearProblemBidomain[0]->matrix(1),MAT_COPY_VALUES); |
| 1469 |
|
✗ |
m_luenbFlter.assembly(MAT_FINAL_ASSEMBLY); |
| 1470 |
|
✗ |
m_luenbFlter.zeroEntries(); |
| 1471 |
|
|
} |
| 1472 |
|
|
} |
| 1473 |
|
|
//Specific operations before solve the system : calculate m_RHS std::vector used in solve(). |
| 1474 |
|
✗ |
postAssemblingMatrixRHS(); |
| 1475 |
|
|
//Solve the system m_Matrix[0]*m_sol=m_RHS. |
| 1476 |
|
✗ |
m_rom->solveROM(m_linearProblemBidomain[0]->solution()); |
| 1477 |
|
|
|
| 1478 |
|
✗ |
m_linearProblemBidomain[0]->removeAverageFromSolution(potExtraCell, MpiInfo::rankProc()); |
| 1479 |
|
|
|
| 1480 |
|
|
} |
| 1481 |
|
|
|
| 1482 |
|
✗ |
MVSolver* BidomainModel::getMVSolver() { |
| 1483 |
|
✗ |
return m_mv; |
| 1484 |
|
|
} |
| 1485 |
|
|
#ifdef FELISCE_WITH_CVGRAPH |
| 1486 |
|
✗ |
void BidomainModel::forwardLight() { |
| 1487 |
|
|
|
| 1488 |
|
|
//Advance time step. |
| 1489 |
|
✗ |
std::stringstream msg; |
| 1490 |
|
✗ |
msg<<"Starting a new time step, preparing forward"<<std::endl; |
| 1491 |
|
✗ |
PetscPrintf(MpiInfo::petscComm(),"%s",msg.str().c_str()); |
| 1492 |
|
✗ |
BidomainModel::writeSolution(); |
| 1493 |
|
✗ |
updateTime(FlagMatrixRHS::only_rhs); |
| 1494 |
|
✗ |
printNewTimeIterationBanner(); |
| 1495 |
|
|
|
| 1496 |
|
|
// Initialize a bunch of stuff. Should be moved elsewhere. |
| 1497 |
|
✗ |
if (m_fstransient->iteration == 1) { |
| 1498 |
|
|
//Initialization of bdf solver. |
| 1499 |
|
✗ |
m_bdfEdp.initialize(m_linearProblemBidomain[0]->solution()); |
| 1500 |
|
✗ |
m_linearProblemBidomain[0]->initializeTimeScheme(&m_bdfEdp); |
| 1501 |
|
|
//m_extrapolate = initial solution. |
| 1502 |
|
✗ |
m_bdfEdp.extrapolate(m_extrapolate); |
| 1503 |
|
|
//Initialization of ionic solver. |
| 1504 |
|
✗ |
m_ionic->defineSizeAndMappingOfIonicProblem(m_linearProblemBidomain[0]->numDofLocalPerUnknown(potTransMemb), m_linearProblemBidomain[0]->mappingDofLocalToDofGlobal(potTransMemb), m_linearProblemBidomain[0]->ao()); |
| 1505 |
|
✗ |
m_ionic->initializeExtrap(m_extrapolate); |
| 1506 |
|
✗ |
m_ionic->initialize(m_W_0); |
| 1507 |
|
✗ |
m_buildIonic = true; |
| 1508 |
|
|
} else { |
| 1509 |
|
✗ |
m_bdfEdp.update(m_linearProblemBidomain[0]->solution()); |
| 1510 |
|
✗ |
m_bdfEdp.extrapolate(m_extrapolate); |
| 1511 |
|
✗ |
m_ionic->update(m_extrapolate); |
| 1512 |
|
|
} |
| 1513 |
|
|
|
| 1514 |
|
✗ |
m_ionic->computeRHS(); |
| 1515 |
|
✗ |
m_ionic->solveEDO(); |
| 1516 |
|
✗ |
m_ionic->computeIon(); |
| 1517 |
|
✗ |
m_ionic->updateBdf(); |
| 1518 |
|
✗ |
m_bdfEdp.computeRHSTime(m_fstransient->timeStep); |
| 1519 |
|
|
|
| 1520 |
|
✗ |
if (m_fstransient->iteration == 1){ |
| 1521 |
|
✗ |
m_linearProblemBidomain[0]->assembleMatrixRHSCurrentAndCurvilinearElement(MpiInfo::rankProc()); |
| 1522 |
|
|
//m_linearProblem[0]->createAndCopyMatrixRHSWithoutBC(FlagMatrixRHS::only_matrix); |
| 1523 |
|
✗ |
m_linearProblemBidomain[0]->initAndStoreMassMatrix(); |
| 1524 |
|
|
} |
| 1525 |
|
|
|
| 1526 |
|
|
//Specific operations before solve the system : calculate m_RHS std::vector used in solve(). |
| 1527 |
|
✗ |
postAssemblingMatrixRHS(); |
| 1528 |
|
|
|
| 1529 |
|
|
// Apply the BC |
| 1530 |
|
✗ |
m_linearProblem[0]->finalizeEssBCConstantInT(); |
| 1531 |
|
✗ |
m_linearProblem[0]->finalizeEssBCTransient(); |
| 1532 |
|
✗ |
if (m_fstransient->iteration == 1){ |
| 1533 |
|
✗ |
m_linearProblem[0]->applyBC(FelisceParam::instance().essentialBoundaryConditionsMethod, MpiInfo::rankProc(),FlagMatrixRHS::matrix_and_rhs, FlagMatrixRHS::matrix_and_rhs, 0, true, ApplyNaturalBoundaryConditions::no); |
| 1534 |
|
|
} else { |
| 1535 |
|
✗ |
m_linearProblem[0]->applyBC(FelisceParam::instance().essentialBoundaryConditionsMethod, MpiInfo::rankProc(),FlagMatrixRHS::only_rhs, FlagMatrixRHS::only_rhs, 0, true, ApplyNaturalBoundaryConditions::no); |
| 1536 |
|
|
} |
| 1537 |
|
|
|
| 1538 |
|
|
|
| 1539 |
|
|
//Solve the system m_Matrix[0]*m_sol=m_RHS. |
| 1540 |
|
✗ |
m_linearProblemBidomain[0]->solve(MpiInfo::rankProc(), MpiInfo::numProc()); |
| 1541 |
|
|
// Remove average |
| 1542 |
|
✗ |
m_linearProblemBidomain[0]->removeAverageForPotExtraCell(); |
| 1543 |
|
|
//m_linearProblemBidomain[0]->removeAverageFromSolution(potExtraCell, MpiInfo::rankProc()); |
| 1544 |
|
|
|
| 1545 |
|
|
} |
| 1546 |
|
|
|
| 1547 |
|
|
|
| 1548 |
|
✗ |
void BidomainModel::startIterationCVG() { |
| 1549 |
|
✗ |
cvgMainSlave* slave=m_linearProblem[0]->slave(); |
| 1550 |
|
✗ |
if (slave==nullptr) { |
| 1551 |
|
✗ |
FEL_ERROR("slave not initialized"); |
| 1552 |
|
|
} |
| 1553 |
|
|
//Advance time step. |
| 1554 |
|
✗ |
if( slave->newTimeStep() ) { |
| 1555 |
|
✗ |
m_kount = 0; |
| 1556 |
|
✗ |
std::stringstream msg; |
| 1557 |
|
✗ |
msg<<"Starting a new time step, preparing forward"<<std::endl; |
| 1558 |
|
✗ |
PetscPrintf(MpiInfo::petscComm(),"%s",msg.str().c_str()); |
| 1559 |
|
✗ |
BidomainModel::writeSolution(); |
| 1560 |
|
✗ |
updateTime(FlagMatrixRHS::only_rhs); |
| 1561 |
|
✗ |
printNewTimeIterationBanner(); |
| 1562 |
|
✗ |
} else if( slave->redoTimeStep() ){ |
| 1563 |
|
✗ |
m_kount++; |
| 1564 |
|
✗ |
std::stringstream msg; |
| 1565 |
|
✗ |
msg << "......................................" << std::endl; |
| 1566 |
|
✗ |
msg << "Redo time step at time t= " << m_fstransient->time << std::endl; |
| 1567 |
|
✗ |
PetscPrintf(MpiInfo::petscComm(),"%s",msg.str().c_str()); |
| 1568 |
|
✗ |
m_linearProblemBidomain[0]->clearMatrixRHS(FlagMatrixRHS::only_rhs); |
| 1569 |
|
✗ |
} else { |
| 1570 |
|
✗ |
slave->msgInfo().print(1); |
| 1571 |
|
✗ |
FEL_ERROR("Error: strange timeStatus"); |
| 1572 |
|
|
} |
| 1573 |
|
|
|
| 1574 |
|
|
|
| 1575 |
|
|
// Initialize a bunch of stuff. Should be moved elsewhere. |
| 1576 |
|
✗ |
if ( ( m_fstransient->iteration == 1) && slave->newTimeStep()) { |
| 1577 |
|
|
//Initialization of bdf solver. |
| 1578 |
|
✗ |
m_bdfEdp.initialize(m_linearProblemBidomain[0]->solution()); |
| 1579 |
|
✗ |
m_linearProblemBidomain[0]->initializeTimeScheme(&m_bdfEdp); |
| 1580 |
|
|
//m_extrapolate = initial solution. |
| 1581 |
|
✗ |
m_bdfEdp.extrapolate(m_extrapolate); |
| 1582 |
|
|
//Initialization of ionic solver. |
| 1583 |
|
✗ |
m_ionic->defineSizeAndMappingOfIonicProblem(m_linearProblemBidomain[0]->numDofLocalPerUnknown(potTransMemb), m_linearProblemBidomain[0]->mappingDofLocalToDofGlobal(potTransMemb), m_linearProblemBidomain[0]->ao()); |
| 1584 |
|
✗ |
m_ionic->initializeExtrap(m_extrapolate); |
| 1585 |
|
✗ |
m_ionic->initialize(m_W_0); |
| 1586 |
|
✗ |
m_buildIonic = true; |
| 1587 |
|
✗ |
} else if (slave->newTimeStep()) { |
| 1588 |
|
✗ |
m_bdfEdp.update(m_linearProblemBidomain[0]->solution()); |
| 1589 |
|
✗ |
m_bdfEdp.extrapolate(m_extrapolate); |
| 1590 |
|
✗ |
m_ionic->update(m_extrapolate); |
| 1591 |
|
|
} |
| 1592 |
|
|
|
| 1593 |
|
✗ |
if (slave->newTimeStep()){ |
| 1594 |
|
✗ |
m_ionic->computeRHS(); |
| 1595 |
|
✗ |
m_ionic->solveEDO(); |
| 1596 |
|
✗ |
m_ionic->computeIon(); |
| 1597 |
|
✗ |
m_ionic->updateBdf(); |
| 1598 |
|
✗ |
m_bdfEdp.computeRHSTime(m_fstransient->timeStep); |
| 1599 |
|
|
} |
| 1600 |
|
|
|
| 1601 |
|
|
|
| 1602 |
|
✗ |
if ( (m_fstransient->iteration == 1) && slave->newTimeStep() ){ |
| 1603 |
|
✗ |
m_linearProblemBidomain[0]->assembleMatrixRHSCurrentAndCurvilinearElement(MpiInfo::rankProc()); |
| 1604 |
|
✗ |
m_linearProblem[0]->createAndCopyMatrixRHSWithoutBC(FlagMatrixRHS::only_matrix); |
| 1605 |
|
✗ |
m_linearProblemBidomain[0]->initAndStoreMassMatrix(); |
| 1606 |
|
|
} |
| 1607 |
|
|
|
| 1608 |
|
|
//Specific operations before solve the system : calculate m_RHS std::vector used in solve(). |
| 1609 |
|
✗ |
postAssemblingMatrixRHS(); |
| 1610 |
|
✗ |
m_linearProblemBidomain[0]->applyUserDefinedStimulation(m_fstransient->time); |
| 1611 |
|
✗ |
m_linearProblem[0]->createAndCopyMatrixRHSWithoutBC(FlagMatrixRHS::only_rhs); |
| 1612 |
|
|
|
| 1613 |
|
|
// Apply the BC |
| 1614 |
|
✗ |
m_linearProblem[0]->finalizeEssBCConstantInT(); |
| 1615 |
|
✗ |
m_linearProblem[0]->finalizeEssBCTransient(); |
| 1616 |
|
✗ |
if (( m_fstransient->iteration == 1) && slave->newTimeStep() ){ |
| 1617 |
|
|
//std::cout << "BidomainModel::startIterationCVG(): FIRST TIME STEP" <<std::endl; |
| 1618 |
|
✗ |
if (slave->thereIsAtLeastOneRobinCondition()){ |
| 1619 |
|
|
//std::cout << " CVG Robin: we apply the robin condition in the MATRIX ONLY. The RHS parts are handled in cvgAddExternalResidualToRHS() and cvgAddRobinToRHS()." << std::endl; |
| 1620 |
|
✗ |
m_linearProblem[0]->applyBC(FelisceParam::instance().essentialBoundaryConditionsMethod,MpiInfo::rankProc(),FlagMatrixRHS::matrix_and_rhs, FlagMatrixRHS::only_matrix, 0, true, ApplyNaturalBoundaryConditions::yes); |
| 1621 |
|
|
} else { |
| 1622 |
|
|
//std::cout << " CVG Neumann: Neumann from other compartment handled in cvgAddExternalResidualToRHS()" << std::endl; |
| 1623 |
|
✗ |
m_linearProblem[0]->applyBC(FelisceParam::instance().essentialBoundaryConditionsMethod, MpiInfo::rankProc(),FlagMatrixRHS::matrix_and_rhs, FlagMatrixRHS::matrix_and_rhs, 0, true, ApplyNaturalBoundaryConditions::no); |
| 1624 |
|
|
} |
| 1625 |
|
|
} else { |
| 1626 |
|
✗ |
m_linearProblem[0]->applyBC(FelisceParam::instance().essentialBoundaryConditionsMethod, MpiInfo::rankProc(),FlagMatrixRHS::only_rhs, FlagMatrixRHS::only_rhs, 0, true, ApplyNaturalBoundaryConditions::no); |
| 1627 |
|
|
} |
| 1628 |
|
|
|
| 1629 |
|
✗ |
if (slave->thereIsAtLeastOneRobinCondition()){ |
| 1630 |
|
|
//std::cout << " CVG Robin: Add remaining term in RHS: beta_torso*massBD*u_torso" << std::endl; |
| 1631 |
|
✗ |
m_linearProblemBidomain[0]->cvgAddRobinToRHS(); |
| 1632 |
|
|
} |
| 1633 |
|
|
// Add current from other compartment |
| 1634 |
|
|
//m_linearProblemBidomain[0]->addCurrentToRHS(); |
| 1635 |
|
|
//Solve the system m_Matrix[0]*m_sol=m_RHS. |
| 1636 |
|
|
double tic, toc, tsolve; |
| 1637 |
|
✗ |
tic = clock(); |
| 1638 |
|
✗ |
m_linearProblemBidomain[0]->solve(MpiInfo::rankProc(), MpiInfo::numProc()); |
| 1639 |
|
✗ |
toc = clock(); |
| 1640 |
|
✗ |
tsolve = (toc-tic)/CLOCKS_PER_SEC; |
| 1641 |
|
|
// Remove average |
| 1642 |
|
|
//double trmvav, trmvav2; |
| 1643 |
|
|
//m_linearProblemBidomain[0]->removeAverageFromSolution(potExtraCell, MpiInfo::rankProc()); |
| 1644 |
|
|
//toc = clock(); |
| 1645 |
|
|
//trmvav = (toc-tic)/CLOCKS_PER_SEC; |
| 1646 |
|
|
//tic = clock(); |
| 1647 |
|
|
|
| 1648 |
|
✗ |
m_linearProblemBidomain[0]->removeAverageForPotExtraCell(); |
| 1649 |
|
|
|
| 1650 |
|
|
//toc = clock(); |
| 1651 |
|
|
//trmvav = (toc-tic)/CLOCKS_PER_SEC; |
| 1652 |
|
✗ |
std::cout << "Tsolve = " << tsolve << std::endl;// ",Trmvav2=" << trmvav2<< std::endl; |
| 1653 |
|
|
} |
| 1654 |
|
|
#endif |
| 1655 |
|
|
|
| 1656 |
|
|
} |
| 1657 |
|
|
|