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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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#include <iostream> |
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#include <fstream> |
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// External includes |
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// Project includes |
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#include "Solver/linearProblemBidomain.hpp" |
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#include "InputOutput/io.hpp" |
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#include "Core/felisceTools.hpp" |
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#include "Core/filesystemUtil.hpp" |
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#include "Tools/fe_utilities.hpp" |
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namespace felisce |
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{ |
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LinearProblemBidomain::LinearProblemBidomain(): |
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LinearProblem("Problem cardiac Bidomain",2), |
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m_rom(nullptr), |
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m_fePotTransMemb(nullptr), |
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m_fePotExtraCell(nullptr), |
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m_fePotTransMembCurv(nullptr), |
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m_fePotExtraCellCurv(nullptr), |
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m_sortedSol(nullptr), |
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m_bdf(nullptr), |
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m_initializeCVGraphInterface(false), |
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m_electrodeNode(nullptr), |
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m_electrodeMeasure(nullptr) { |
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if (FelisceParam::instance().stateFilter) |
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this->setNumberOfMatrix(3); |
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if ( FelisceParam::instance().withCVG ) { |
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#ifdef FELISCE_WITH_CVGRAPH |
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m_cvgDirichletVariable = "cvgraphPOTENTIAL"; |
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#endif |
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m_seqVecs.Init("cvgraphPOTENTIAL"); |
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m_seqVecs.Init("cvgraphCURRENT"); |
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} |
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} |
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LinearProblemBidomain::~LinearProblemBidomain() { |
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m_rom = nullptr; |
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m_fstransient = nullptr; |
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m_fePotTransMemb = nullptr; |
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m_fePotExtraCell = nullptr; |
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m_bdf = nullptr; |
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delete [] m_sortedSol; |
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// Elisa, Dec. 2014 - Luenberger filter |
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if (FelisceParam::instance().electrodeControl) { |
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delete [] m_electrodeNode; |
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for (felInt i=0; i<m_numElectrodeNode+1; i++) { |
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delete [] m_electrodeMeasure[i]; |
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} |
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delete [] m_electrodeMeasure; |
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m_electrodeControl.destroy(); |
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} |
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} |
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void LinearProblemBidomain::initialize(std::vector<GeometricMeshRegion::Pointer>& mesh, FelisceTransient::Pointer fstransient, MPI_Comm& comm, bool doUseSNES) { |
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LinearProblem::initialize(mesh,comm, doUseSNES); |
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m_fstransient = fstransient; |
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std::vector<PhysicalVariable> listVariable(2); |
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std::vector<std::size_t> listNumComp(2); |
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listVariable[0] = potTransMemb; |
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listNumComp[0] = 1; |
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listVariable[1] = potExtraCell; |
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listNumComp[1] = 1; |
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//define unknown of the linear system. |
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m_listUnknown.push_back(potTransMemb); |
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m_listUnknown.push_back(potExtraCell); |
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definePhysicalVariable(listVariable,listNumComp); |
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} |
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void LinearProblemBidomain::readData(IO& io) { |
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// Read fibers file (*.00000.vct) |
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m_vectorFiber.resize(m_mesh[m_currentMesh]->numPoints()*3); |
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io.readVariable(0, 0.,&m_vectorFiber[0], m_vectorFiber.size()); |
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// Read distance from endocardium file for Zygote geometry (*.00000.scl) |
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if ( (FelisceParam::instance().typeOfAppliedCurrent == "zygote") || (FelisceParam::instance().typeOfAppliedCurrent == "zygoteImproved") || (FelisceParam::instance().typeOfAppliedCurrent == "heart") || (FelisceParam::instance().typeOfAppliedCurrent == "ellipseheart") ) { |
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m_vectorDistance.resize(m_numDof,0.); |
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io.readVariable(1, 0.,&m_vectorDistance[0],m_mesh[m_currentMesh]->numPoints()); |
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if ( (FelisceParam::instance().typeOfAppliedCurrent == "heart") || (FelisceParam::instance().typeOfAppliedCurrent == "ellipseheart") ) { |
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if (FelisceParam::instance().hasCoupledAtriaVent) { |
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m_vectorAngle.resize(m_numDof,0.); |
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io.readVariable(2, 0.,&m_vectorAngle[0],m_mesh[m_currentMesh]->numPoints()); |
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m_vectorRef.resize(m_numDof,0.); |
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io.readVariable(3, 0.,&m_vectorRef[0],m_mesh[m_currentMesh]->numPoints()); |
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} |
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} |
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} |
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} |
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void LinearProblemBidomain::updateFibers(IO& io,double iteration) { //when the mesh moves |
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m_vectorFiber.resize(m_mesh[m_currentMesh]->numPoints()*3); |
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io.readVariable(0, iteration,&m_vectorFiber[0], m_vectorFiber.size()); |
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} |
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void LinearProblemBidomain::readDataDisplacement(std::vector<IO::Pointer>& io,double iteration) { |
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// Read displacement file (*.00000.vct) |
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if ((FelisceParam::instance().typeOfAppliedCurrent == "zygote")&&(FelisceParam::instance().typeOfAppliedCurrent == "planarWave")){ |
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const int iMesh = m_listVariable[2].idMesh(); |
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m_vectorDisp.resize(m_mesh[iMesh]->numPoints()*3,0.); |
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io[iMesh]->readVariable(2, iteration,&m_vectorDisp[0], m_vectorDisp.size()); |
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} |
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else{ |
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const int iMesh = m_listVariable[1].idMesh(); |
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m_vectorDisp.resize(m_mesh[iMesh]->numPoints()*3,0.); |
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io[iMesh]->readVariable(1, iteration,&m_vectorDisp[0], m_vectorDisp.size()); |
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} |
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std::transform(m_vectorDisp.begin(), m_vectorDisp.end(), m_vectorDisp.begin(),std::bind(std::multiplies<double>(),FelisceParam::instance().spaceUnit, std::placeholders::_1)); |
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} |
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void LinearProblemBidomain::writeEnsightScalar(double* solValue, int idIter, std::string varName) { |
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std::string iteration; |
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if (idIter < 10) |
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iteration = "0000" + std::to_string(idIter); |
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else if (idIter < 100) |
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iteration = "000" + std::to_string(idIter); |
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else if (idIter < 1000) |
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iteration = "00" + std::to_string(idIter); |
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else if (idIter < 10000) |
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iteration = "0" + std::to_string(idIter); |
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else if (idIter < 100000) |
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iteration = std::to_string(idIter); |
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std::string fileName = FelisceParam::instance().resultDir + "/" + varName + "." + iteration + ".scl"; |
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FILE * solFile; |
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solFile = fopen(fileName.c_str(),"w"); |
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fprintf(solFile, "Scalar per node\n"); |
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int count = 0; |
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for(int j=0; j < static_cast<int>(m_numDof/2); j++) { |
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fprintf(solFile,"%12.5e", solValue[j]); |
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count++; |
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if(count == 6) { |
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fprintf(solFile,"\n"); |
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count = 0; |
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} |
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} |
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fprintf(solFile,"\n"); |
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fclose(solFile); |
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} |
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double LinearProblemBidomain::conductivityHom(int currentLabel) { |
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double conductivity = 1.0; |
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if (FelisceParam::instance().hasHeteroCondAtria) { |
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if (std::fabs(currentLabel - 31.0) < 1.0e-12) { //SN |
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conductivity = 0.3; |
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} else if (std::fabs(currentLabel - 32.0) < 1.0e-12) { //CT |
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conductivity = 3.0; |
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} else if (std::fabs(currentLabel - 33.0) < 1.0e-12) { //BB |
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conductivity = 4.75; |
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} else if (std::fabs(currentLabel - 34.0) < 1.0e-12) { //RAI |
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conductivity = 0.375; |
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} else if (std::fabs(currentLabel - 35.0) < 1.0e-12) { //PM |
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conductivity = 1.5; |
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} else { //regular atria and F0 |
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conductivity = 1.0; |
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} |
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} |
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return conductivity; |
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} |
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double LinearProblemBidomain::conductivityHet(int currentLabel) { |
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double conductivity = 1.0; |
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if (FelisceParam::instance().hasHeteroCondAtria) { |
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if (std::fabs(currentLabel - 31.0) < 1.0e-12) { //SN |
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conductivity = 0.36; |
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} else if (std::fabs(currentLabel - 32.0) < 1.0e-12) { //CT |
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conductivity = 4.5; |
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} else if (std::fabs(currentLabel - 33.0) < 1.0e-12) { //BB |
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conductivity = 7.75; |
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} else if (std::fabs(currentLabel - 34.0) < 1.0e-12) { //RAI |
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conductivity = 0.45; |
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} else if (std::fabs(currentLabel - 35.0) < 1.0e-12) { //PM |
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conductivity = 1.8; |
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} else if (std::fabs(currentLabel - 36.0) < 1.0e-12) { //F0 |
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conductivity = 0.9; |
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} else { //regular atria |
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conductivity = 1.0; |
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} |
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} |
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return conductivity; |
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} |
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void LinearProblemBidomain::writeEnsightCase(int numIt, std::string varName) { |
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FILE * pFile; |
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std::string caseName = FelisceParam::instance().resultDir + "/" + varName + ".case"; |
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pFile = fopen(caseName.c_str(),"w"); |
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fprintf(pFile,"FORMAT\n"); |
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fprintf(pFile,"type: ensight\n"); |
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fprintf(pFile, "GEOMETRY\n"); |
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std::string nameGeo = "model: 1 " + FelisceParam::instance().outputMesh[0] + "\n"; |
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fprintf(pFile,"%s", nameGeo.c_str()); |
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fprintf(pFile, "VARIABLE\n"); |
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std::string secName = "scalar per node: 1 " + varName + " " + varName +".*****.scl\n"; |
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fprintf(pFile, "%s", secName.c_str()); |
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fprintf(pFile, "TIME\n"); |
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fprintf(pFile, "time std::set: %d \n", 1); |
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fprintf(pFile, "number of steps: %d \n", numIt); |
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fprintf(pFile, "filename start number: %d\n", 0); |
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fprintf(pFile, "filename increment: %d\n", 1); |
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fprintf(pFile, "time values:\n"); |
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const double dt = FelisceParam::instance().timeStep * FelisceParam::instance().frequencyWriteSolution; |
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int count=0; |
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for(int j=0; j < numIt; j++) { |
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double valT = j*dt; |
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fprintf(pFile,"%lf ",valT); |
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count++; |
| 235 |
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if(count == 6) { |
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fprintf(pFile,"\n"); |
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count=0; |
| 238 |
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} |
| 239 |
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} |
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fclose(pFile); |
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} |
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void LinearProblemBidomain::writeEnsightCaseCurrents(int numIt, std::vector<std::string> varName) { |
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FILE * pFile; |
| 247 |
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std::string caseName = FelisceParam::instance().resultDir + "/" + "courants" + ".case"; |
| 248 |
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pFile = fopen(caseName.c_str(),"w"); |
| 249 |
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fprintf(pFile,"FORMAT\n"); |
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fprintf(pFile,"type: ensight\n"); |
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fprintf(pFile, "GEOMETRY\n"); |
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std::string nameGeo = "model: 1 " + FelisceParam::instance().outputMesh[currentMesh()] + "\n"; |
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fprintf(pFile,"%s", nameGeo.c_str()); |
| 254 |
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fprintf(pFile, "VARIABLE\n"); |
| 255 |
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| 256 |
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const double nbvarName = varName.size(); |
| 257 |
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for(int i=0; i<nbvarName; i++) { |
| 258 |
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std::string secName = "scalar per node: 1 " + varName[i] + " " + varName[i] +".*****.scl\n"; |
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fprintf(pFile, "%s", secName.c_str()); |
| 260 |
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} |
| 261 |
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| 262 |
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fprintf(pFile, "TIME\n"); |
| 263 |
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fprintf(pFile, "time std::set: %d \n", 1); |
| 264 |
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fprintf(pFile, "number of steps: %d \n", numIt); |
| 265 |
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fprintf(pFile, "filename start number: %d\n", 0); |
| 266 |
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fprintf(pFile, "filename increment: %d\n", 1); |
| 267 |
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fprintf(pFile, "time values:\n"); |
| 268 |
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| 269 |
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const double dt = FelisceParam::instance().timeStep * FelisceParam::instance().frequencyWriteSolution; |
| 270 |
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int count=0; |
| 271 |
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for(int j=0; j < numIt; j++) { |
| 272 |
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double valT = j*dt; |
| 273 |
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fprintf(pFile,"%lf ",valT); |
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count++; |
| 275 |
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if(count == 6) { |
| 276 |
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fprintf(pFile,"\n"); |
| 277 |
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count=0; |
| 278 |
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} |
| 279 |
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} |
| 280 |
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fclose(pFile); |
| 281 |
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} |
| 282 |
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| 284 |
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void LinearProblemBidomain::writeSolution(int rank, std::vector<IO::Pointer>& io, double& time, int iteration) { |
| 285 |
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LinearProblem::writeSolution(rank,io, time, iteration); |
| 286 |
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// Add fiber as an output variable. |
| 287 |
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/* |
| 288 |
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io.writeSolution(rank, time, iteration, 1, "fiber", m_fiber, m_supportDofUnknown[0].listNode().size(), m_dimension); |
| 289 |
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if (FelisceParam::instance().typeOfAppliedCurrent == "zygote") |
| 290 |
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{ |
| 291 |
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// Add distance std::unordered_map as an output variable. |
| 292 |
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io.writeSolution(rank, time, iteration, 0, "distance", m_endocardiumDistance, m_supportDofUnknown[0].listNode().size(), m_dimension); |
| 293 |
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} |
| 294 |
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*/ |
| 295 |
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} |
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| 297 |
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| 298 |
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void LinearProblemBidomain::getFiberDirection(felInt iel, int iUnknown, std::vector<double>& elemFiber) { |
| 299 |
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//Warning: the fibers must be normalized. |
| 300 |
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✗ |
int numSupport = static_cast<int>(supportDofUnknown(iUnknown).iEle()[iel+1] - supportDofUnknown(iUnknown).iEle()[iel]); |
| 301 |
|
✗ |
elemFiber.resize( numSupport*3,0.); |
| 302 |
|
✗ |
for (int i = 0; i < numSupport; i++) { |
| 303 |
|
✗ |
elemFiber[i*3] = m_vectorFiber[3*(supportDofUnknown(iUnknown).iSupportDof()[supportDofUnknown(iUnknown).iEle()[iel]+i])]; |
| 304 |
|
✗ |
elemFiber[i*3+1] = m_vectorFiber[3*(supportDofUnknown(iUnknown).iSupportDof()[supportDofUnknown(iUnknown).iEle()[iel]+i])+1]; |
| 305 |
|
✗ |
elemFiber[i*3+2] = m_vectorFiber[3*(supportDofUnknown(iUnknown).iSupportDof()[supportDofUnknown(iUnknown).iEle()[iel]+i])+2]; |
| 306 |
|
|
} |
| 307 |
|
|
} |
| 308 |
|
|
|
| 309 |
|
✗ |
void LinearProblemBidomain::getAngle(felInt iel, int iUnknown, std::vector<double>& elemAngle) { |
| 310 |
|
✗ |
int numSupport = static_cast<int>(supportDofUnknown(iUnknown).iEle()[iel+1] - supportDofUnknown(iUnknown).iEle()[iel]); |
| 311 |
|
✗ |
elemAngle.resize(numSupport,0.); |
| 312 |
|
✗ |
for (int i = 0; i < numSupport; i++) { |
| 313 |
|
✗ |
elemAngle[i] = m_vectorAngle[(supportDofUnknown(iUnknown).iSupportDof()[supportDofUnknown(iUnknown).iEle()[iel]+i])]; |
| 314 |
|
|
} |
| 315 |
|
|
} |
| 316 |
|
|
|
| 317 |
|
✗ |
void LinearProblemBidomain::initPerElementType(ElementType eltType, FlagMatrixRHS flagMatrixRHS) { |
| 318 |
|
|
IGNORE_UNUSED_ELT_TYPE; |
| 319 |
|
|
IGNORE_UNUSED_FLAG_MATRIX_RHS; |
| 320 |
|
|
//Init pointer on Finite Element, Variable or idVariable |
| 321 |
|
✗ |
m_ipotTransMemb = m_listVariable.getVariableIdList(potTransMemb); |
| 322 |
|
✗ |
m_ipotExtraCell = m_listVariable.getVariableIdList(potExtraCell); |
| 323 |
|
✗ |
m_fePotTransMemb = m_listCurrentFiniteElement[m_ipotTransMemb]; |
| 324 |
|
✗ |
m_fePotExtraCell = m_fePotTransMemb; |
| 325 |
|
|
|
| 326 |
|
|
} |
| 327 |
|
|
|
| 328 |
|
✗ |
void LinearProblemBidomain::computeElementArray(const std::vector<Point*>& elemPoint, const std::vector<felInt>& elemIdPoint, felInt& iel, FlagMatrixRHS flagMatrixRHS) { |
| 329 |
|
|
IGNORE_UNUSED_FLAG_MATRIX_RHS; |
| 330 |
|
|
IGNORE_UNUSED_ELEM_ID_POINT; |
| 331 |
|
✗ |
m_fePotTransMemb->updateMeasQuadPt(0, elemPoint); |
| 332 |
|
✗ |
m_fePotTransMemb->updateFirstDeriv(0, elemPoint); |
| 333 |
|
|
|
| 334 |
|
|
// Assembling matrices[0] |
| 335 |
|
✗ |
double coefTime = 1./m_fstransient->timeStep; |
| 336 |
|
✗ |
double coefAm = FelisceParam::instance().Am; |
| 337 |
|
✗ |
double coefCm = FelisceParam::instance().Cm; |
| 338 |
|
✗ |
double coef = m_bdf->coeffDeriv0()*coefTime*coefAm*coefCm; |
| 339 |
|
|
|
| 340 |
|
|
//1st equation : Am*Cm/dt V_m |
| 341 |
|
✗ |
m_elementMat[0]->phi_i_phi_j(coef,*m_fePotTransMemb,0,0,1); |
| 342 |
|
|
|
| 343 |
|
✗ |
if (FelisceParam::instance().testCase == 1) { |
| 344 |
|
✗ |
std::vector<double> elemFiber; |
| 345 |
|
✗ |
getFiberDirection(iel,m_ipotTransMemb, elemFiber); |
| 346 |
|
|
|
| 347 |
|
✗ |
if (FelisceParam::instance().model == "Bidomain") { |
| 348 |
|
|
//1st equation : \sigma_i^t \grad V_m |
| 349 |
|
✗ |
m_elementMat[0]->grad_phi_i_grad_phi_j(FelisceParam::instance().intraTransvTensor,*m_fePotTransMemb,0,0,1); |
| 350 |
|
|
|
| 351 |
|
|
//1st equation : (\sigma_i^l-\sigma_i^t) a vec a \grad V_m |
| 352 |
|
✗ |
m_elementMat[0]->tau_grad_phi_i_tau_grad_phi_j(FelisceParam::instance().intraFiberTensor-FelisceParam::instance().intraTransvTensor,elemFiber,*m_fePotTransMemb,0,0,1); |
| 353 |
|
|
|
| 354 |
|
|
//1st equation : \sigma_i^t \grad u_e |
| 355 |
|
✗ |
m_elementMat[0]->grad_phi_i_grad_phi_j(FelisceParam::instance().intraTransvTensor,*m_fePotExtraCell,0,1,1); |
| 356 |
|
|
|
| 357 |
|
|
//1st equation : (\sigma_i^l-\sigma_i^t) a vec a \grad u_e |
| 358 |
|
✗ |
m_elementMat[0]->tau_grad_phi_i_tau_grad_phi_j(FelisceParam::instance().intraFiberTensor-FelisceParam::instance().intraTransvTensor,elemFiber,*m_fePotExtraCell,0,1,1); |
| 359 |
|
|
|
| 360 |
|
|
//2nd equation : \sigma_i^t \grad V_m |
| 361 |
|
✗ |
m_elementMat[0]->grad_phi_i_grad_phi_j(FelisceParam::instance().intraTransvTensor,*m_fePotTransMemb,1,0,1); |
| 362 |
|
|
|
| 363 |
|
|
//2nd equation : (\sigma_i^l-\sigma_i^t) a vec a \grad V_m |
| 364 |
|
✗ |
m_elementMat[0]->tau_grad_phi_i_tau_grad_phi_j(FelisceParam::instance().intraFiberTensor-FelisceParam::instance().intraTransvTensor,elemFiber,*m_fePotTransMemb,1,0,1); |
| 365 |
|
|
|
| 366 |
|
|
//2nd equation : (\sigma_i^t+\sigma_e^t) \grad u_e |
| 367 |
|
✗ |
m_elementMat[0]->grad_phi_i_grad_phi_j(FelisceParam::instance().intraTransvTensor+FelisceParam::instance().extraTransvTensor,*m_fePotExtraCell,1,1,1); |
| 368 |
|
|
|
| 369 |
|
|
//2nd equation : ((\sigma_i^l-\sigma_i^t)+(\sigma_e^l-\sigma_e^t)) a vec a \grad u_e |
| 370 |
|
✗ |
m_elementMat[0]->tau_grad_phi_i_tau_grad_phi_j(FelisceParam::instance().intraFiberTensor-FelisceParam::instance().intraTransvTensor+FelisceParam::instance().extraFiberTensor-FelisceParam::instance().extraTransvTensor,elemFiber,*m_fePotExtraCell,1,1,1); |
| 371 |
|
|
|
| 372 |
|
|
} |
| 373 |
|
✗ |
else if (FelisceParam::instance().model == "Monodomain") { |
| 374 |
|
|
//1st equation : \sigma_i^t \grad V_m |
| 375 |
|
✗ |
m_elementMat[0]->grad_phi_i_grad_phi_j(FelisceParam::instance().intraTransvTensor,*m_fePotTransMemb,0,0,1); |
| 376 |
|
|
|
| 377 |
|
|
//1st equation : (\sigma_i^l-\sigma_i^t) a vec a \grad V_m |
| 378 |
|
✗ |
m_elementMat[0]->tau_grad_phi_i_tau_grad_phi_j(FelisceParam::instance().intraFiberTensor-FelisceParam::instance().intraTransvTensor,elemFiber,*m_fePotTransMemb,0,0,1); |
| 379 |
|
|
|
| 380 |
|
|
//2nd equation : (\sigma_i^t+\sigma_e^t) \grad u_e |
| 381 |
|
✗ |
m_elementMat[0]->grad_phi_i_grad_phi_j(FelisceParam::instance().intraTransvTensor+FelisceParam::instance().extraTransvTensor,*m_fePotExtraCell,1,1,1); |
| 382 |
|
|
|
| 383 |
|
|
//2nd equation : ((\sigma_i^l-\sigma_i^t)+(\sigma_e^l-\sigma_e^t)) a vec a \grad u_e |
| 384 |
|
✗ |
m_elementMat[0]->tau_grad_phi_i_tau_grad_phi_j(FelisceParam::instance().intraFiberTensor-FelisceParam::instance().intraTransvTensor+FelisceParam::instance().extraFiberTensor-FelisceParam::instance().extraTransvTensor,elemFiber,*m_fePotExtraCell,1,1,1); |
| 385 |
|
|
} |
| 386 |
|
|
} |
| 387 |
|
|
else { |
| 388 |
|
✗ |
if (FelisceParam::instance().model == "Bidomain") { |
| 389 |
|
|
//1st equation : \sigma_i^t \grad V_m |
| 390 |
|
✗ |
m_elementMat[0]->grad_phi_i_grad_phi_j(FelisceParam::instance().intraTransvTensor,*m_fePotTransMemb,0,0,1); |
| 391 |
|
|
|
| 392 |
|
|
//1st equation : \sigma_i^t \grad u_e |
| 393 |
|
✗ |
m_elementMat[0]->grad_phi_i_grad_phi_j(FelisceParam::instance().intraTransvTensor,*m_fePotExtraCell,0,1,1); |
| 394 |
|
|
|
| 395 |
|
|
//2nd equation : \sigma_i^t \grad V_m |
| 396 |
|
✗ |
m_elementMat[0]->grad_phi_i_grad_phi_j(FelisceParam::instance().intraTransvTensor,*m_fePotTransMemb,1,0,1); |
| 397 |
|
|
|
| 398 |
|
|
//2nd equation : (\sigma_i^t+\sigma_e^t) \grad u_e |
| 399 |
|
✗ |
m_elementMat[0]->grad_phi_i_grad_phi_j(FelisceParam::instance().intraTransvTensor+FelisceParam::instance().extraTransvTensor,*m_fePotExtraCell,1,1,1); |
| 400 |
|
|
|
| 401 |
|
|
} |
| 402 |
|
✗ |
else if (FelisceParam::instance().model == "Monodomain") { |
| 403 |
|
|
//1st equation : \sigma_i^t \grad V_m |
| 404 |
|
✗ |
m_elementMat[0]->grad_phi_i_grad_phi_j(FelisceParam::instance().intraTransvTensor,*m_fePotTransMemb,0,0,1); |
| 405 |
|
|
|
| 406 |
|
|
//2nd equation : (\sigma_i^t+\sigma_e^t) \grad u_e |
| 407 |
|
✗ |
m_elementMat[0]->grad_phi_i_grad_phi_j(FelisceParam::instance().intraTransvTensor+FelisceParam::instance().extraTransvTensor,*m_fePotExtraCell,1,1,1); |
| 408 |
|
|
} |
| 409 |
|
|
} |
| 410 |
|
|
//Assembling matrix(1) = mass (only first quadrant). |
| 411 |
|
✗ |
m_elementMat[1]->phi_i_phi_j(1.,*m_fePotTransMemb,0,0,1); |
| 412 |
|
✗ |
m_elementMat[1]->phi_i_phi_j(1.,*m_fePotTransMemb,1,1,1); |
| 413 |
|
|
|
| 414 |
|
✗ |
if (FelisceParam::instance().stateFilter) { |
| 415 |
|
✗ |
*m_elementMat[2]=*m_elementMat[0]; |
| 416 |
|
|
} |
| 417 |
|
|
} |
| 418 |
|
|
|
| 419 |
|
✗ |
void LinearProblemBidomain::computeElementArraySurfaceModel(const std::vector<Point*>& elemPoint, const std::vector<felInt>& elemIdPoint, felInt& iel, FlagMatrixRHS flagMatrixRHS) { |
| 420 |
|
|
(void) elemIdPoint; |
| 421 |
|
|
(void) flagMatrixRHS; |
| 422 |
|
✗ |
m_ipotTransMemb = m_listVariable.getVariableIdList(potTransMemb); |
| 423 |
|
✗ |
m_fePotTransMembCurv = m_listCurvilinearFiniteElement[m_ipotTransMemb]; |
| 424 |
|
✗ |
m_fePotExtraCellCurv = m_fePotTransMembCurv; |
| 425 |
|
|
|
| 426 |
|
✗ |
m_fePotTransMembCurv->updateMeasNormalContra(0, elemPoint); |
| 427 |
|
|
|
| 428 |
|
✗ |
auto bndRefIt = find(FelisceParam::instance().notBoundarySurfaceLabels.begin(), FelisceParam::instance().notBoundarySurfaceLabels.end(), m_currentLabel); |
| 429 |
|
|
|
| 430 |
|
✗ |
if(bndRefIt != FelisceParam::instance().notBoundarySurfaceLabels.end()) { |
| 431 |
|
|
// if ((m_currentLabel > 29) && (m_currentLabel < 41)) { |
| 432 |
|
✗ |
std::vector<double> elemAngle; |
| 433 |
|
✗ |
getAngle(iel,m_ipotTransMemb,elemAngle); |
| 434 |
|
|
|
| 435 |
|
✗ |
std::vector<double> elemFiber; |
| 436 |
|
✗ |
getFiberDirection(iel,m_ipotTransMemb,elemFiber); |
| 437 |
|
|
|
| 438 |
|
|
// Assembling matrix(0) |
| 439 |
|
✗ |
double coefTime = 1./m_fstransient->timeStep; |
| 440 |
|
✗ |
double coefAm = FelisceParam::instance().Am; |
| 441 |
|
✗ |
double coefCm = FelisceParam::instance().Cm; |
| 442 |
|
✗ |
double coef = m_bdf->coeffDeriv0()*coefTime*coefAm*coefCm; |
| 443 |
|
|
|
| 444 |
|
✗ |
double atriaThick=0.2; // cm - atria thickness |
| 445 |
|
|
|
| 446 |
|
|
//1st equation : Am*Cm/dt V_m |
| 447 |
|
✗ |
m_elementMatBD[0]->phi_i_phi_j(atriaThick*coef,*m_fePotTransMembCurv,0,0,1); |
| 448 |
|
|
|
| 449 |
|
|
//1st equation : \sigma_i^t \grad V_m |
| 450 |
|
✗ |
if (m_currentLabel < 40) { // regular atrial myocardium |
| 451 |
|
✗ |
m_elementMatBD[0]->grad_phi_i_grad_phi_j(atriaThick*FelisceParam::instance().intraTransvTensorAtria*conductivityHom(m_currentLabel),*m_fePotTransMembCurv,0,0,1); |
| 452 |
|
✗ |
m_elementMatBD[0]->tau_orthotau_grad_phi_i_grad_phi_j(atriaThick*(FelisceParam::instance().intraFiberTensorAtria - FelisceParam::instance().intraTransvTensorAtria)*conductivityHet(m_currentLabel),elemFiber,elemAngle,*m_fePotTransMembCurv,0,0,1); |
| 453 |
|
|
} |
| 454 |
|
|
|
| 455 |
|
|
//1st equation : \sigma_i^t \grad u_e |
| 456 |
|
✗ |
if (m_currentLabel < 40) { // regular atrial myocardium |
| 457 |
|
✗ |
m_elementMatBD[0]->grad_phi_i_grad_phi_j(atriaThick*FelisceParam::instance().intraTransvTensorAtria*conductivityHom(m_currentLabel),*m_fePotExtraCellCurv,0,1,1); |
| 458 |
|
✗ |
m_elementMatBD[0]->tau_orthotau_grad_phi_i_grad_phi_j(atriaThick*(FelisceParam::instance().intraFiberTensorAtria - FelisceParam::instance().intraTransvTensorAtria)*conductivityHet(m_currentLabel),elemFiber,elemAngle,*m_fePotExtraCellCurv,0,1,1); |
| 459 |
|
|
} |
| 460 |
|
|
|
| 461 |
|
|
//2nd equation : \sigma_i^t \grad V_m |
| 462 |
|
✗ |
if (m_currentLabel < 40) { // regular atrial myocardium |
| 463 |
|
✗ |
m_elementMatBD[0]->grad_phi_i_grad_phi_j(atriaThick*FelisceParam::instance().intraTransvTensorAtria*conductivityHom(m_currentLabel),*m_fePotTransMembCurv,1,0,1); |
| 464 |
|
✗ |
m_elementMatBD[0]->tau_orthotau_grad_phi_i_grad_phi_j(atriaThick*(FelisceParam::instance().intraFiberTensorAtria - FelisceParam::instance().intraTransvTensorAtria)*conductivityHet(m_currentLabel),elemFiber,elemAngle,*m_fePotTransMembCurv,1,0,1); |
| 465 |
|
|
} |
| 466 |
|
|
|
| 467 |
|
|
//2nd equation : (\sigma_i^t+\sigma_e^t) \grad u_e |
| 468 |
|
✗ |
double connectionCoeff = 3.e-4; // 0.0003 |
| 469 |
|
✗ |
if (m_currentLabel < 40) { // atrial myocardium |
| 470 |
|
✗ |
m_elementMatBD[0]->grad_phi_i_grad_phi_j(atriaThick*(FelisceParam::instance().intraTransvTensorAtria+FelisceParam::instance().extraTransvTensorAtria)*conductivityHom(m_currentLabel),*m_fePotExtraCellCurv,1,1,1); |
| 471 |
|
✗ |
m_elementMatBD[0]->tau_orthotau_grad_phi_i_grad_phi_j(atriaThick*(FelisceParam::instance().intraFiberTensorAtria - FelisceParam::instance().intraTransvTensorAtria + FelisceParam::instance().extraFiberTensorAtria - FelisceParam::instance().extraTransvTensorAtria)*conductivityHet(m_currentLabel),elemFiber,elemAngle,*m_fePotExtraCellCurv,1,1,1); |
| 472 |
|
✗ |
} else if (std::fabs(m_currentLabel - 40) < 1.0e-8) { // connection aera |
| 473 |
|
✗ |
m_elementMatBD[0]->grad_phi_i_grad_phi_j(atriaThick*(FelisceParam::instance().extraTransvTensorAtria)*connectionCoeff,*m_fePotExtraCellCurv,1,1,1); |
| 474 |
|
|
} |
| 475 |
|
|
|
| 476 |
|
|
//Assembling matrix(1) = mass (only first quadrant if hasAppliedExteriorCurrent = false) |
| 477 |
|
✗ |
m_elementMatBD[1]->phi_i_phi_j(atriaThick*1.,*m_fePotTransMembCurv,0,0,1); |
| 478 |
|
✗ |
m_elementMatBD[1]->phi_i_phi_j(atriaThick*1.,*m_fePotTransMembCurv,1,1,1); |
| 479 |
|
|
} |
| 480 |
|
|
} |
| 481 |
|
|
|
| 482 |
|
✗ |
void LinearProblemBidomain::computeElementArrayBoundaryCondition(const std::vector<Point*>& elemPoint, const std::vector<felInt>& /*elemIdPoint*/, felInt& iel, FlagMatrixRHS /*flagMatrixRHS*/) { |
| 483 |
|
|
|
| 484 |
|
|
(void)iel; |
| 485 |
|
|
|
| 486 |
|
✗ |
m_curvFe->updateMeas(0,elemPoint); |
| 487 |
|
|
// #ifdef FELISCE_WITH_CVGRAPH |
| 488 |
|
|
// if (FelisceParam::instance().withCVG ) { |
| 489 |
|
|
// this->cvgraphNaturalBC(iel); |
| 490 |
|
|
// } |
| 491 |
|
|
// #endif |
| 492 |
|
|
} |
| 493 |
|
|
|
| 494 |
|
✗ |
void LinearProblemBidomain::addMatrixRHS() { |
| 495 |
|
|
|
| 496 |
|
|
//Rebuild the matrix with the filter |
| 497 |
|
✗ |
if (FelisceParam::instance().stateFilter ) { |
| 498 |
|
✗ |
matrix(0).copyFrom(matrix(2),SAME_NONZERO_PATTERN); |
| 499 |
|
|
} |
| 500 |
|
|
|
| 501 |
|
|
// _RHS = m_mass * _RHS. |
| 502 |
|
✗ |
PetscVector tmpB; |
| 503 |
|
✗ |
tmpB.duplicateFrom(vector()); |
| 504 |
|
✗ |
tmpB.copyFrom(vector()); |
| 505 |
|
✗ |
mult(matrix(1),tmpB,vector()); // _RHS = m_mass * tmpB |
| 506 |
|
✗ |
tmpB.destroy(); |
| 507 |
|
|
|
| 508 |
|
✗ |
if (m_initializeCVGraphInterface) { |
| 509 |
|
✗ |
vector(1).copyFrom(vector()); |
| 510 |
|
|
} |
| 511 |
|
|
|
| 512 |
|
✗ |
if(FelisceParam::instance().useROM) { |
| 513 |
|
✗ |
if (m_fstransient->iteration == 1) { |
| 514 |
|
✗ |
m_rom->fullToReducedMatrix(matrix(0)); |
| 515 |
|
|
} |
| 516 |
|
✗ |
m_rom->fullToReducedRHS(vector()); |
| 517 |
|
|
} |
| 518 |
|
|
|
| 519 |
|
|
} |
| 520 |
|
|
|
| 521 |
|
✗ |
void LinearProblemBidomain::readMatch() { |
| 522 |
|
|
// Input files. |
| 523 |
|
✗ |
std::string matchFileName = FelisceParam::instance().inputDirectory + "/" + FelisceParam::instance().ECGmatchFile;// load the match file (heart nodes) |
| 524 |
|
|
|
| 525 |
|
✗ |
std::ifstream matchFile(matchFileName.c_str()); |
| 526 |
|
✗ |
if(!matchFile) { |
| 527 |
|
✗ |
FEL_ERROR("Fatal error: cannot open match file " + matchFileName ); |
| 528 |
|
|
} |
| 529 |
|
✗ |
if (FelisceParam::verbose() > 0) { |
| 530 |
|
✗ |
std::cout << "Reading " << matchFileName << std::endl; |
| 531 |
|
|
} |
| 532 |
|
✗ |
matchFile >> m_numElectrodeNode; |
| 533 |
|
✗ |
m_electrodeNode = new felInt[m_numElectrodeNode]; |
| 534 |
|
|
felInt value; |
| 535 |
|
✗ |
for(int j=0; j<m_numElectrodeNode; j++) { |
| 536 |
|
✗ |
matchFile >> value; |
| 537 |
|
✗ |
m_electrodeNode[j] = value; |
| 538 |
|
|
} |
| 539 |
|
✗ |
matchFile.close(); |
| 540 |
|
|
} |
| 541 |
|
|
|
| 542 |
|
|
// Elisa, Dec. 2014 - read measures for Luenberger filter |
| 543 |
|
✗ |
void LinearProblemBidomain::readElectrodeMeasure() { |
| 544 |
|
|
// load the measures |
| 545 |
|
✗ |
std::string inputFileName = FelisceParam::instance().inputDirectory + "/" + FelisceParam::instance().ECGfileName + ".tab"; |
| 546 |
|
✗ |
std::string outputFileName = FelisceParam::instance().resultDir + "/" + FelisceParam::instance().ECGfileName + "_control.tab"; |
| 547 |
|
✗ |
int ierr = 0; |
| 548 |
|
✗ |
if ( !filesystemUtil::directoryExists(FelisceParam::instance().resultDir.c_str()) ) { |
| 549 |
|
✗ |
std::string command = "mkdir -p " + FelisceParam::instance().resultDir; |
| 550 |
|
✗ |
ierr = system(command.c_str()); |
| 551 |
|
✗ |
if (ierr) { |
| 552 |
|
✗ |
std::cout << "Cannot copy control file in resultDir." << std::endl; |
| 553 |
|
|
} |
| 554 |
|
|
} |
| 555 |
|
✗ |
if (ierr == 0) { |
| 556 |
|
✗ |
filesystemUtil::copyFileSomewhereElse(inputFileName,outputFileName); |
| 557 |
|
|
} |
| 558 |
|
|
|
| 559 |
|
✗ |
std::ifstream ecgFile(inputFileName.c_str(), std::ios_base::in); |
| 560 |
|
✗ |
if ( !ecgFile.is_open() ) { |
| 561 |
|
✗ |
FEL_ERROR(" ERROR: Can not open file " + inputFileName); |
| 562 |
|
|
} |
| 563 |
|
|
|
| 564 |
|
✗ |
m_electrodeMeasure = new double* [m_numElectrodeNode+1]; |
| 565 |
|
✗ |
for (int i=0; i<m_numElectrodeNode+1; i++) { |
| 566 |
|
✗ |
m_electrodeMeasure[i] = new double [FelisceParam::instance().timeIterationMax]; |
| 567 |
|
|
} |
| 568 |
|
|
|
| 569 |
|
✗ |
for (int j=0; j<FelisceParam::instance().timeIterationMax; j++) { |
| 570 |
|
✗ |
for(int i=0; i<m_numElectrodeNode+1; i++) { |
| 571 |
|
✗ |
ecgFile >> m_electrodeMeasure[i][j]; |
| 572 |
|
|
} |
| 573 |
|
|
} |
| 574 |
|
✗ |
ecgFile.close(); |
| 575 |
|
|
|
| 576 |
|
✗ |
m_electrodeControl.duplicateFrom(vector()); |
| 577 |
|
|
} |
| 578 |
|
|
|
| 579 |
|
|
// Elisa, Dec. 2014 - Luenberger filter |
| 580 |
|
✗ |
void LinearProblemBidomain::addElectrodeCondtrol() { |
| 581 |
|
✗ |
if (m_electrodeNode == nullptr) { |
| 582 |
|
✗ |
readMatch(); |
| 583 |
|
|
} |
| 584 |
|
✗ |
if (m_electrodeMeasure == nullptr) { |
| 585 |
|
✗ |
readElectrodeMeasure(); |
| 586 |
|
|
} |
| 587 |
|
|
|
| 588 |
|
✗ |
if (FelisceParam::instance().electrodeControl) { |
| 589 |
|
✗ |
if ( !Tools::almostEqual(m_electrodeMeasure[0][m_fstransient->iteration-1], m_fstransient->time-m_fstransient->timeStep, m_fstransient->timeStep/10.) ) { |
| 590 |
|
✗ |
FEL_WARNING("Measures physical time different from solver physical time.\n"); |
| 591 |
|
|
} |
| 592 |
|
|
} |
| 593 |
|
|
|
| 594 |
|
✗ |
m_electrodeControl.set(0.); |
| 595 |
|
|
|
| 596 |
|
✗ |
int sizePot = numDofLocalPerUnknown(potExtraCell); |
| 597 |
|
✗ |
double value[sizePot]; |
| 598 |
|
✗ |
felInt idLocalUe[sizePot]; |
| 599 |
|
✗ |
felInt idGlobalUe[sizePot]; |
| 600 |
|
✗ |
felInt idLocalVm[sizePot]; |
| 601 |
|
✗ |
felInt idGlobalVm[sizePot]; |
| 602 |
|
|
|
| 603 |
|
✗ |
for (felInt i = 0; i < sizePot; i++) { |
| 604 |
|
✗ |
idLocalUe[i] = i; |
| 605 |
|
✗ |
idLocalVm[i] = i; |
| 606 |
|
✗ |
value[i] = 0.; |
| 607 |
|
|
} |
| 608 |
|
✗ |
ISLocalToGlobalMappingApply(mappingDofLocalToDofGlobal(potTransMemb),sizePot,&idLocalVm[0],&idGlobalVm[0]); |
| 609 |
|
✗ |
ISLocalToGlobalMappingApply(mappingDofLocalToDofGlobal(potExtraCell),sizePot,&idLocalUe[0],&idGlobalUe[0]); |
| 610 |
|
|
|
| 611 |
|
✗ |
for (felInt i = 0; i < m_numElectrodeNode; i++) { |
| 612 |
|
✗ |
felInt idElectrode = m_electrodeNode[i]-1; |
| 613 |
|
✗ |
value[idGlobalVm[idElectrode]] = m_electrodeMeasure[i+1][m_fstransient->iteration-1]; |
| 614 |
|
|
double valuePot; |
| 615 |
|
✗ |
this->solution().getValues(1,&idGlobalUe[idElectrode],&valuePot); |
| 616 |
|
✗ |
value[idGlobalVm[idElectrode]] -= valuePot; |
| 617 |
|
|
} |
| 618 |
|
|
|
| 619 |
|
✗ |
m_electrodeControl.setValues(sizePot,&idGlobalVm[0],&value[0],INSERT_VALUES); |
| 620 |
|
|
|
| 621 |
|
✗ |
m_electrodeControl.assembly(); |
| 622 |
|
|
|
| 623 |
|
✗ |
vector().axpy(-FelisceParam::instance().aFilter,m_electrodeControl); |
| 624 |
|
|
|
| 625 |
|
✗ |
vector().assembly(); |
| 626 |
|
|
|
| 627 |
|
|
} |
| 628 |
|
|
|
| 629 |
|
✗ |
void LinearProblemBidomain::assembleOnlyMassMatrix(PetscMatrix& mass) |
| 630 |
|
|
{ |
| 631 |
|
|
// Allocation |
| 632 |
|
✗ |
mass.duplicateFrom(matrix(0),MAT_DO_NOT_COPY_VALUES); |
| 633 |
|
✗ |
mass.zeroEntries(); |
| 634 |
|
|
|
| 635 |
|
|
/* Loop function */ |
| 636 |
|
✗ |
auto function = [this,&mass](ElementType& eltType, felInt iel, std::vector<Point*>& elemPoint, std::vector<felInt>& elemIdPoint, felInt& ielSupportDof) { |
| 637 |
|
✗ |
setElemPoint(eltType, iel, elemPoint, elemIdPoint, &ielSupportDof); |
| 638 |
|
✗ |
m_elementMat[0]->zero(); |
| 639 |
|
✗ |
userComputeMass(elemPoint, elemIdPoint, ielSupportDof); |
| 640 |
|
✗ |
setValueCustomMatrix(ielSupportDof, ielSupportDof, mass); |
| 641 |
|
✗ |
return 0.0; |
| 642 |
|
✗ |
}; |
| 643 |
|
|
/* Pre-function */ |
| 644 |
|
✗ |
auto functionpre = [this](ElementType& eltType) { |
| 645 |
|
✗ |
defineFiniteElement(eltType); |
| 646 |
|
✗ |
initElementArray(); |
| 647 |
|
✗ |
allocateArrayForAssembleMatrixRHS(FlagMatrixRHS::only_matrix); |
| 648 |
|
✗ |
}; |
| 649 |
|
|
/* Post-function */ |
| 650 |
|
✗ |
auto functionpost = [this](ElementType& eltType) { |
| 651 |
|
|
IGNORE_UNUSED_ARGUMENT(eltType); |
| 652 |
|
✗ |
desallocateArrayForAssembleMatrixRHS(FlagMatrixRHS::only_matrix); |
| 653 |
|
✗ |
}; |
| 654 |
|
✗ |
FEUtilities::LoopOverElements(*m_meshLocal[m_currentMesh], m_meshLocal[m_currentMesh]->bagElementTypeDomain(), &function, &functionpre, &functionpost); |
| 655 |
|
|
|
| 656 |
|
|
// Final assembly |
| 657 |
|
✗ |
mass.assembly(MAT_FINAL_ASSEMBLY); |
| 658 |
|
|
} |
| 659 |
|
|
|
| 660 |
|
✗ |
void LinearProblemBidomain::initAndStoreMassMatrix() { |
| 661 |
|
✗ |
assembleOnlyMassMatrix(m_massMatrix); |
| 662 |
|
|
// TO DO: This should not be here, it's only temporary. Should be moved to prepareCVGRobin(). |
| 663 |
|
✗ |
initMassBoundaryForStimulation(); |
| 664 |
|
|
#ifdef FELISCE_WITH_CVGRAPH |
| 665 |
|
✗ |
if ( FelisceParam::instance().withCVG ) { |
| 666 |
|
✗ |
initMassBoundaryForCVG(); |
| 667 |
|
|
} |
| 668 |
|
|
#endif |
| 669 |
|
|
} |
| 670 |
|
|
|
| 671 |
|
|
#ifdef FELISCE_WITH_CVGRAPH |
| 672 |
|
✗ |
void LinearProblemBidomain::initMassBoundaryForCVG() { |
| 673 |
|
✗ |
this->assembleMassBoundaryOnly(&LinearProblemBidomain::massMatrixComputer, |
| 674 |
|
✗ |
this->slave()->interfaceLabels(/*iConn*/0), |
| 675 |
|
|
&LinearProblemBidomain::initPerETMass, |
| 676 |
|
|
&LinearProblemBidomain::updateFE, |
| 677 |
|
✗ |
this->dofBD(/*iConn*/0), this->massBDVec()[/*iConn*/0]); |
| 678 |
|
|
} |
| 679 |
|
|
|
| 680 |
|
|
/*! \brief Function to assemble the mass matrix |
| 681 |
|
|
* Function to be called in the assemblyLoopBoundaryGeneral |
| 682 |
|
|
*/ |
| 683 |
|
✗ |
void LinearProblemBidomain::massMatrixComputer(felInt ielSupportDof) { |
| 684 |
|
✗ |
this->m_elementMatBD[0]->zero(); |
| 685 |
|
✗ |
this->m_elementMatBD[0]->phi_i_phi_j(/*coef*/1.,*m_curvFe,1,1,1); |
| 686 |
|
✗ |
this->setValueMatrixBD(ielSupportDof); |
| 687 |
|
|
} |
| 688 |
|
|
void |
| 689 |
|
✗ |
LinearProblemBidomain::initPerETMass() { |
| 690 |
|
✗ |
felInt numDofTotal = 0; |
| 691 |
|
|
//pay attention this numDofTotal is bigger than expected since it counts for all the VARIABLES |
| 692 |
|
✗ |
for (std::size_t iFe = 0; iFe < this->m_listCurvilinearFiniteElement.size(); iFe++) {//this loop is on variables while it should be on unknown |
| 693 |
|
✗ |
numDofTotal += this->m_listCurvilinearFiniteElement[iFe]->numDof()*this->m_listVariable[iFe].numComponent(); |
| 694 |
|
|
} |
| 695 |
|
✗ |
m_globPosColumn.resize(numDofTotal); m_globPosRow.resize(numDofTotal); m_matrixValues.resize(numDofTotal*numDofTotal); |
| 696 |
|
|
|
| 697 |
|
✗ |
m_curvFe = this->m_listCurvilinearFiniteElement[ m_ipotExtraCell ]; |
| 698 |
|
|
} |
| 699 |
|
|
void |
| 700 |
|
✗ |
LinearProblemBidomain::updateFE(const std::vector<Point*>& elemPoint, const std::vector<int>&) { |
| 701 |
|
✗ |
m_curvFe->updateMeasNormal(0, elemPoint); |
| 702 |
|
|
} |
| 703 |
|
|
#endif |
| 704 |
|
|
|
| 705 |
|
|
#ifdef FELISCE_WITH_CVGRAPH |
| 706 |
|
✗ |
void LinearProblemBidomain::readData() { |
| 707 |
|
✗ |
for ( std::size_t iConn(0); iConn<this->slave()->numConnections(); ++iConn ) { |
| 708 |
|
|
//std::cout << "####### LinearProblemBidomain::readData(): " << this->slave()->numVarToRead(iConn) << " variables to read" << std::endl; |
| 709 |
|
✗ |
std::vector<PetscVector> vecs; |
| 710 |
|
✗ |
for ( std::size_t cVar(0); cVar<this->slave()->numVarToRead(iConn); ++cVar) { |
| 711 |
|
✗ |
std::string varToRead = this->slave()->readVariable(iConn,cVar); |
| 712 |
|
✗ |
if ( varToRead == "CURRENT" ) { |
| 713 |
|
✗ |
vecs.push_back(m_seqVecs.Get("cvgraphCURRENT")); |
| 714 |
|
✗ |
} else if ( varToRead == "POTENTIAL" ) { |
| 715 |
|
✗ |
vecs.push_back(m_seqVecs.Get("cvgraphPOTENTIAL")); |
| 716 |
|
|
} else { |
| 717 |
|
✗ |
std::cout<<"Connection: "<<iConn<<"--variable to read: "<< varToRead << std::endl; |
| 718 |
|
✗ |
FEL_ERROR("Error in variable to read"); |
| 719 |
|
|
} |
| 720 |
|
|
} |
| 721 |
|
✗ |
this->slave()->receiveData(vecs,iConn); |
| 722 |
|
|
} |
| 723 |
|
|
} |
| 724 |
|
✗ |
void LinearProblemBidomain::sendData() { |
| 725 |
|
|
//std::cout << "LinearProblemBidomain::sendData()" <<std::endl; |
| 726 |
|
✗ |
this->gatherSolution(); |
| 727 |
|
✗ |
for ( std::size_t iConn(0); iConn<this->slave()->numConnections(); ++iConn ) { |
| 728 |
|
✗ |
std::vector<PetscVector> vecs; |
| 729 |
|
✗ |
for ( std::size_t cVar(0); cVar<this->slave()->numVarToSend(iConn); ++cVar) { |
| 730 |
|
✗ |
std::string varToSend = this->slave()->sendVariable(iConn, cVar); |
| 731 |
|
✗ |
if ( varToSend == "POTENTIAL" ) { |
| 732 |
|
✗ |
vecs.push_back(this->sequentialSolution()); |
| 733 |
|
✗ |
} else if ( varToSend == "CURRENT" ) { |
| 734 |
|
|
// TODO: Add prepareResidual() and move this to startIterationCVG |
| 735 |
|
✗ |
this->computeResidual(); |
| 736 |
|
✗ |
vecs.push_back(this->seqResidual()); |
| 737 |
|
|
} else { |
| 738 |
|
|
//std::cout<<"Connection: "<<iConn<<"--variable to send: "<< varToSend << std::endl; |
| 739 |
|
✗ |
FEL_ERROR("Error in variable to read"); |
| 740 |
|
|
} |
| 741 |
|
|
} |
| 742 |
|
✗ |
this->slave()->sendData(vecs,iConn); |
| 743 |
|
|
} |
| 744 |
|
|
} |
| 745 |
|
✗ |
void LinearProblemBidomain::addCurrentToRHS() { |
| 746 |
|
|
//! for each dof on the boundary on this proc. |
| 747 |
|
✗ |
felInt numLocalDofInterface=this->dofBD(/*iBD*/0).numLocalDofInterface(); |
| 748 |
|
✗ |
std::vector<double> tmp(numLocalDofInterface); |
| 749 |
|
✗ |
m_seqVecs.Get("cvgraphCURRENT").getValues( numLocalDofInterface, this->dofBD(/*iBD*/0).loc2PetscVolPtr(), tmp.data() ); |
| 750 |
|
✗ |
this->vector().setValues(numLocalDofInterface,this->dofBD(/*iBD*/0).loc2PetscVolPtr(),tmp.data(),ADD_VALUES); |
| 751 |
|
✗ |
this->vector().assembly(); |
| 752 |
|
|
} |
| 753 |
|
|
|
| 754 |
|
✗ |
void LinearProblemBidomain::cvgAddRobinToRHS(){ |
| 755 |
|
|
//std::cout << "LinearProblemBidomain::cvgAddRobinToRHS()" << std::endl; |
| 756 |
|
|
//std::cout << " alpha_robin = " << FelisceParam::instance().alphaRobin[0/*iRobin*/] << std::endl; |
| 757 |
|
|
} |
| 758 |
|
|
|
| 759 |
|
|
#endif |
| 760 |
|
|
|
| 761 |
|
|
} |
| 762 |
|
|
|