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// ______ ______ _ _ _____ ______ |
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// | ____| ____| | (_)/ ____| | ____| |
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// | |__ | |__ | | _| (___ ___| |__ |
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// | __| | __| | | | |\___ \ / __| __| |
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// | | | |____| |____| |____) | (__| |____ |
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// |_| |______|______|_|_____/ \___|______| |
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// Finite Elements for Life Sciences and Engineering |
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// |
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// License: LGL2.1 License |
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// FELiScE default license: LICENSE in root folder |
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// |
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// Main authors: E.Schenone D. Lombardi |
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// |
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// System includes |
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// External includes |
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// Project includes |
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#include "Solver/eigenProblemPOD.hpp" |
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#include "FiniteElement/elementMatrix.hpp" |
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#include "FiniteElement/elementField.hpp" |
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#include "Core/felisceParam.hpp" |
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#include "Core/felisceTools.hpp" |
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namespace felisce |
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{ |
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/*! Constructor |
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*/ |
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EigenProblemPOD::EigenProblemPOD(): |
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EigenProblem(), |
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m_fePotTransMemb(nullptr), |
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m_eigenValue(nullptr), |
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m_dimRomBasis(0), |
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m_beta(nullptr), |
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m_mu(nullptr), |
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m_gamma(nullptr), |
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m_eta(nullptr), |
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m_modeMean(nullptr), |
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m_fiber(nullptr), |
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m_source(nullptr), |
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m_solutionInitialized(false), |
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m_tensorCs(nullptr), |
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m_tensorE(nullptr), |
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m_tensorT(nullptr), |
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m_tensorTs(nullptr), |
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m_tensorY(nullptr) |
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{} |
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EigenProblemPOD::~EigenProblemPOD() { |
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delete [] m_fePotTransMemb; |
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delete [] m_eigenValue; |
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for (int i=0; i<m_dimRomBasis; i++) { |
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m_basis[i].destroy(); |
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} |
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m_U_0.destroy(); |
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m_U_0_seq.destroy(); |
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m_W_0.destroy(); |
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if (m_solutionInitialized) { |
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delete [] m_beta; |
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delete [] m_mu; |
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delete [] m_gamma; |
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delete [] m_eta; |
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delete [] m_modeMean; |
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} |
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if (m_fiber) { |
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delete [] m_fiber; |
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} |
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m_autocorr.destroy(); |
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} |
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void EigenProblemPOD::initialize(const GeometricMeshRegion::Pointer& mesh, FelisceTransient::Pointer fstransient, MPI_Comm& comm) { |
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EigenProblem::initialize(mesh, fstransient, comm); |
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std::unordered_map<std::string, int> mapOfPbm; |
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mapOfPbm["FKPP"] = 0; |
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mapOfPbm["Monodomain"] = 1; |
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mapOfPbm["Bidomain"] = 2; |
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m_problem = mapOfPbm[FelisceParam::instance().model]; |
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m_dimRomBasis = FelisceParam::instance().dimRomBasis; |
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m_numSource = FelisceParam::instance().numberOfSource; |
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// m_numSnapshot = FelisceParam::instance().numberOfSnapshot; |
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// m_samplingFreq = FelisceParam::instance().samplingFrequency; |
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int id=0; |
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m_idG = id; |
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id++; |
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m_idK = id; |
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id++; |
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if (FelisceParam::instance().hasInfarct) { |
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m_idGs = id; |
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id++; |
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} |
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m_numberOfMatrix = id; |
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std::vector<PhysicalVariable> listVariable; |
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std::vector<std::size_t> listNumComp; |
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if (m_problem==1) { |
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nameOfTheProblem = "Problem cardiac Monodomain"; |
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listVariable.push_back(potTransMemb); |
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listNumComp.push_back(1); |
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m_listUnknown.push_back(potTransMemb); |
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} |
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definePhysicalVariable(listVariable,listNumComp); |
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} |
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// Define Physical Variable associate to the problem |
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void EigenProblemPOD::initPerElementType() { |
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if (m_problem==1) { |
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//Init pointer on Finite Element, Variable or idVariable |
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m_ipotTransMemb = m_listVariable.getVariableIdList(potTransMemb); |
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m_fePotTransMemb = m_listCurrentFiniteElement[m_ipotTransMemb]; |
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m_elemFieldU0.initialize(DOF_FIELD,*m_fePotTransMemb); |
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if (FelisceParam::instance().hasInfarct) { |
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m_elemFieldFhNf0.initialize(DOF_FIELD,*m_fePotTransMemb); |
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} |
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} |
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} |
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// Assemble Matrix |
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// mass matrix |
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void EigenProblemPOD::computeElementArray(const std::vector<Point*>& elemPoint, const std::vector<felInt>& elemIdPoint, felInt& iel, FlagMatrixRHS flagMatrixRHS) { |
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IGNORE_UNUSED_ELEM_ID_POINT; |
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IGNORE_UNUSED_FLAG_MATRIX_RHS; |
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if (m_problem==1) { |
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m_fePotTransMemb->updateMeasQuadPt(0, elemPoint); |
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m_fePotTransMemb->updateFirstDeriv(0, elemPoint); |
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// Matrix[0] = phi_i * phi_j |
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m_elementMat[m_idG]->phi_i_phi_j(1.,*m_fePotTransMemb,0,0,1); |
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m_elementMat[m_idK]->grad_phi_i_grad_phi_j(FelisceParam::instance().intraTransvTensor,*m_fePotTransMemb,0,0,1); |
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if (FelisceParam::instance().hasInfarct) { |
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// m_Matrix[] = s * phi_i * phi_j |
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m_elemFieldFhNf0.setValue(m_FhNf0, *m_fePotTransMemb, iel, m_ipotTransMemb, m_ao, m_dof); |
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m_elementMat[m_idGs]->a_phi_i_phi_j(1.,m_elemFieldFhNf0,*m_fePotTransMemb,0,0,1); |
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} |
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} |
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} |
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void EigenProblemPOD::readSnapshot(IO& io) { |
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m_snapshot.resize(m_numSnapshot); |
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for(int i=0; i<m_numSnapshot; i++) { |
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double* snap = nullptr; |
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snap = new double[m_mesh->numPoints()]; |
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double timeVar = 0.; |
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m_Matrix[m_idG].getVecs(m_snapshot[i],nullPetscVector); |
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m_snapshot[i].setFromOptions(); |
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PetscVector tmpSeq; |
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tmpSeq.createSeq(PETSC_COMM_SELF,m_numDof); |
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tmpSeq.setFromOptions(); |
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timeVar = i*m_samplingFreq*FelisceParam::instance().timeStep; |
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io.readVariable(0, timeVar,snap, m_mesh->numPoints()); |
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felInt ia; |
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for (felInt j=0; j< m_numDof; j++) { |
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ia = j; |
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AOApplicationToPetsc(m_ao,1,&ia); |
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tmpSeq.setValues(1,&ia,&snap[j],INSERT_VALUES); |
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} |
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tmpSeq.assembly(); |
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fromDoubleStarToVec(snap,m_snapshot[i] , m_mesh->numPoints()); |
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tmpSeq.destroy(); |
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delete [] snap; |
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} |
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} |
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void EigenProblemPOD::computeAutocorr() { |
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m_autocorr.createAIJ(PETSC_COMM_WORLD, PETSC_DECIDE, PETSC_DECIDE, m_numSnapshot, m_numSnapshot,PETSC_DECIDE, nullptr, PETSC_DECIDE, nullptr); |
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for(int i=0; i<m_numSnapshot; i++) { |
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for(int j=0; j<=i; j++) { |
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double prod = 0.0; |
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scalarProduct(m_snapshot[i],m_snapshot[j],prod,true); |
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m_autocorr.setValues(1,&i,1,&j,&prod,INSERT_VALUES); |
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m_autocorr.setValues(1,&j,1,&i,&prod,INSERT_VALUES); |
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} |
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} |
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m_autocorr.assembly(MAT_FINAL_ASSEMBLY); |
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} |
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// Visualize modes as a variable |
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void EigenProblemPOD::writeMode(const int iter) { |
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int rankProc; |
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MPI_Comm_rank(m_petscComm,&rankProc); |
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std::string fileName; |
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if (iter > 0) |
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fileName = "basis" + std::to_string(iter); |
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else |
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fileName = "basis"; |
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double* tmpSolToSave = nullptr; |
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tmpSolToSave = new double[m_numDof]; |
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for (int iBasis=0; iBasis<m_dimRomBasis; iBasis++) { |
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fromVecToDoubleStar(tmpSolToSave, m_basisPOD[iBasis], rankProc, 1); |
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writeEnsightVector(tmpSolToSave, iBasis, fileName); |
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} |
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delete [] tmpSolToSave; |
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if (rankProc == 0) |
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writeEnsightCase(m_dimRomBasis, 1.,fileName); |
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} |
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void EigenProblemPOD::writeEnsightSolution(const int iter) { |
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PetscVector solUe; |
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solUe.duplicateFrom(m_U_0); |
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if (iter > 0) { |
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projectOnDof(m_beta,m_sol,m_dimRomBasis); |
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if (FelisceParam::instance().model == "Bidomain") { |
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std::cout << "Bidomain still to be defined with POD"<<std::endl; |
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} |
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} else { |
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m_sol.copyFrom(m_U_0); |
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if (FelisceParam::instance().model == "Bidomain") { |
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std::cout << "Bidomain still to be defined with POD"<<std::endl; |
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} |
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} |
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int rankProc; |
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MPI_Comm_rank(m_petscComm,&rankProc); |
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double* tmpSolToSave = nullptr; |
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tmpSolToSave = new double[m_numDof]; |
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if ( (FelisceParam::instance().model == "FKPP") ) { |
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fromVecToDoubleStar(tmpSolToSave, m_sol, rankProc, 1); |
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writeEnsightVector(tmpSolToSave, iter, "sol"); |
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} |
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if ( (FelisceParam::instance().model == "Monodomain") || (FelisceParam::instance().model == "Bidomain") ) { |
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fromVecToDoubleStar(tmpSolToSave, m_sol, rankProc, 1); |
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writeEnsightVector(tmpSolToSave, iter, "potTransMemb"); |
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} |
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if (FelisceParam::instance().model == "Bidomain") { |
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fromVecToDoubleStar(tmpSolToSave, solUe, rankProc, 1); |
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writeEnsightVector(tmpSolToSave, iter, "potExtraCell"); |
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} |
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delete [] tmpSolToSave; |
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if ( (FelisceParam::instance().model == "FKPP") ) { |
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if (rankProc == 0) |
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writeEnsightCase(iter+1, FelisceParam::instance().timeStep * FelisceParam::instance().frequencyWriteSolution,"sol", FelisceParam::instance().time); |
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} |
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if ( (FelisceParam::instance().model == "Monodomain") || (FelisceParam::instance().model == "Bidomain") ) { |
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if (rankProc == 0) |
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writeEnsightCase(iter+1, FelisceParam::instance().timeStep * FelisceParam::instance().frequencyWriteSolution,"potTransMemb", FelisceParam::instance().time); |
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} |
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if (FelisceParam::instance().model == "Bidomain") { |
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std::vector<std::string> varNames; |
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varNames.resize(2); |
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varNames[0] = "potTransMemb"; |
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varNames[1] = "potExtraCell"; |
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if (rankProc == 0) |
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writeEnsightCase(iter+1, FelisceParam::instance().timeStep * FelisceParam::instance().frequencyWriteSolution,varNames, FelisceParam::instance().time); |
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} |
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} |
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// Solve eigenproblem to build rom basis |
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void EigenProblemPOD::buildSolver() { |
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if (FelisceParam::verbose()) PetscPrintf(PETSC_COMM_WORLD,"\nBuilding Slepc Solver.\n"); |
| 302 |
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#ifdef FELISCE_WITH_SLEPC |
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EPSSetOperators(m_eps,m_autocorr.toPetsc(),nullptr); |
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EPSSetDimensions(m_eps,m_numSnapshot,PETSC_DECIDE,PETSC_DECIDE); |
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EPSSetProblemType(m_eps,EPS_HEP); |
| 307 |
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EPSSetType(m_eps, EPSKRYLOVSCHUR); //EPSARNOLDI); |
| 308 |
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EPSSetTolerances(m_eps,1.0e-5,200); |
| 309 |
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EPSKrylovSchurSetRestart(m_eps,0.6); |
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EPSSetFromOptions(m_eps); |
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#endif |
| 312 |
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} |
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| 315 |
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✗ |
void EigenProblemPOD::solve() { |
| 316 |
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if (FelisceParam::verbose()) PetscPrintf(PETSC_COMM_WORLD,"\nSolve eigenvalue problem.\n"); |
| 317 |
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#ifdef FELISCE_WITH_SLEPC |
| 318 |
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PetscInt nconv; |
| 319 |
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//First request a singular value from one end of the spectrum |
| 320 |
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EPSSetWhichEigenpairs(m_eps,EPS_LARGEST_REAL); |
| 321 |
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if (m_verbose >= 10) { |
| 322 |
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m_autocorr.view(); |
| 323 |
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EPSView(m_eps,PETSC_VIEWER_STDOUT_WORLD); |
| 324 |
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} |
| 325 |
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| 326 |
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✗ |
EPSSolve(m_eps); |
| 327 |
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| 328 |
|
|
//Get number of converged singular values |
| 329 |
|
✗ |
EPSGetConverged(m_eps,&nconv); |
| 330 |
|
✗ |
PetscPrintf(PETSC_COMM_WORLD," Number of converged values = %d.\n", nconv); |
| 331 |
|
|
|
| 332 |
|
✗ |
if ( m_dimRomBasis > m_numDof ) { |
| 333 |
|
✗ |
PetscPrintf(PETSC_COMM_WORLD," Warning! Number of function basis bigger than number of dof.\n"); |
| 334 |
|
✗ |
m_dimRomBasis = m_numDof; |
| 335 |
|
|
} |
| 336 |
|
|
|
| 337 |
|
✗ |
if ( m_dimRomBasis > nconv ) { |
| 338 |
|
✗ |
PetscPrintf(PETSC_COMM_WORLD," Warning! Number of function basis bigger than number of converged values.\n"); |
| 339 |
|
✗ |
m_dimRomBasis = nconv; |
| 340 |
|
|
} |
| 341 |
|
|
|
| 342 |
|
|
double sigma; |
| 343 |
|
|
//Get converged singular values: largest singular value is stored in sigma. |
| 344 |
|
✗ |
if (nconv > 0) { |
| 345 |
|
✗ |
for (int i=0; i < m_dimRomBasis; i++) { |
| 346 |
|
✗ |
EPSGetEigenpair(m_eps,i,&sigma,FELISCE_PETSC_NULLPTR,FELISCE_PETSC_NULLPTR,FELISCE_PETSC_NULLPTR); |
| 347 |
|
|
} |
| 348 |
|
|
} else { |
| 349 |
|
✗ |
m_dimRomBasis = 0; |
| 350 |
|
✗ |
PetscPrintf(PETSC_COMM_WORLD," Unable to compute smallest singular value!\n\n"); |
| 351 |
|
✗ |
exit(1); |
| 352 |
|
|
} |
| 353 |
|
✗ |
PetscPrintf(PETSC_COMM_WORLD, "m_dimRomBasis = %d \n", m_dimRomBasis); |
| 354 |
|
|
|
| 355 |
|
✗ |
if (m_eigenValue == nullptr) |
| 356 |
|
✗ |
m_eigenValue = new double[m_dimRomBasis]; |
| 357 |
|
|
|
| 358 |
|
|
//m_basis.clear(); |
| 359 |
|
|
//m_basis.resize(m_dimRomBasis); |
| 360 |
|
✗ |
m_basisPOD.resize(m_dimRomBasis); |
| 361 |
|
✗ |
m_eigenvector.resize(m_dimRomBasis); |
| 362 |
|
|
double norm2; |
| 363 |
|
|
|
| 364 |
|
✗ |
double imgpart = 0.; |
| 365 |
|
✗ |
for (int i=0; i < m_dimRomBasis; i++) { |
| 366 |
|
✗ |
m_autocorr.getVecs(nullPetscVector,m_eigenvector[i]); |
| 367 |
|
✗ |
EPSGetEigenpair(m_eps,i,&m_eigenValue[i],&imgpart,m_eigenvector[i].toPetsc(),FELISCE_PETSC_NULLPTR); |
| 368 |
|
✗ |
if (Tools::notEqual(imgpart,0.0)) { |
| 369 |
|
✗ |
PetscPrintf(PETSC_COMM_WORLD, "Warning! Im(m_eigenValue[%d]) = %e \n", i, imgpart); |
| 370 |
|
|
} |
| 371 |
|
✗ |
m_eigenvector[i].norm(NORM_2,&norm2); |
| 372 |
|
|
|
| 373 |
|
✗ |
if (m_verbose >= 1) { |
| 374 |
|
✗ |
PetscPrintf(PETSC_COMM_WORLD, "m_eigenValue[%d] = %e \n", i, m_eigenValue[i]); |
| 375 |
|
✗ |
PetscPrintf(PETSC_COMM_WORLD, "norm2[%d] = %e \n", i, norm2); |
| 376 |
|
|
} |
| 377 |
|
|
} |
| 378 |
|
|
|
| 379 |
|
|
felInt ia; |
| 380 |
|
✗ |
for (int i=0; i<m_dimRomBasis; i++) { |
| 381 |
|
✗ |
m_Matrix[0].getVecs(nullPetscVector,m_basisPOD[i]); |
| 382 |
|
✗ |
for(int h=0; h<m_numSnapshot; h++) { |
| 383 |
|
✗ |
ia = h; |
| 384 |
|
✗ |
AOApplicationToPetsc(m_ao,1,&ia); |
| 385 |
|
✗ |
double tmpCoeff = 0.0; |
| 386 |
|
✗ |
m_eigenvector[i].getValues(1,&ia,&tmpCoeff); |
| 387 |
|
✗ |
m_basisPOD[i].axpy( tmpCoeff, m_snapshot[h]); |
| 388 |
|
|
}; |
| 389 |
|
✗ |
double tmpRescale = m_eigenValue[i]; |
| 390 |
|
✗ |
tmpRescale = std::sqrt(tmpRescale); |
| 391 |
|
✗ |
tmpRescale = 1.0/tmpRescale; |
| 392 |
|
✗ |
m_basisPOD[i].scale(tmpRescale); |
| 393 |
|
|
}; |
| 394 |
|
|
|
| 395 |
|
✗ |
std::string fileName = FelisceParam::instance().resultDir + "/eigenValue"; |
| 396 |
|
✗ |
viewPOD(m_eigenValue,m_dimRomBasis,fileName); |
| 397 |
|
|
#endif |
| 398 |
|
|
} |
| 399 |
|
|
|
| 400 |
|
|
|
| 401 |
|
|
|
| 402 |
|
|
|
| 403 |
|
|
// Reduced model functions |
| 404 |
|
|
//======================== |
| 405 |
|
|
// Initialization |
| 406 |
|
✗ |
void EigenProblemPOD::readData(IO& io) { |
| 407 |
|
✗ |
m_Matrix[0].getVecs(m_U_0,nullPetscVector); |
| 408 |
|
✗ |
m_U_0.setFromOptions(); |
| 409 |
|
|
|
| 410 |
|
✗ |
m_W_0.duplicateFrom(m_U_0); |
| 411 |
|
✗ |
m_W_0.copyFrom(m_U_0); |
| 412 |
|
|
|
| 413 |
|
✗ |
m_U_0_seq.createSeq(PETSC_COMM_SELF,m_numDof); |
| 414 |
|
✗ |
m_U_0_seq.setFromOptions(); |
| 415 |
|
✗ |
if (FelisceParam::instance().hasInitialCondition) { |
| 416 |
|
|
// Read initial solution file (*.00000.scl) |
| 417 |
|
✗ |
double* initialSolution = nullptr; |
| 418 |
|
✗ |
initialSolution = new double[m_mesh->numPoints()]; |
| 419 |
|
✗ |
double* ionicSolution = nullptr; |
| 420 |
|
✗ |
ionicSolution = new double[m_mesh->numPoints()]; |
| 421 |
|
|
// potTransMemb |
| 422 |
|
✗ |
io.readVariable(0, 0.,initialSolution, m_mesh->numPoints()); |
| 423 |
|
|
// ionicVar |
| 424 |
|
✗ |
io.readVariable(1, 0.,ionicSolution, m_mesh->numPoints()); |
| 425 |
|
|
felInt ia; |
| 426 |
|
✗ |
for (felInt i=0; i< m_numDof; i++) { |
| 427 |
|
✗ |
ia = i; |
| 428 |
|
✗ |
AOApplicationToPetsc(m_ao,1,&ia); |
| 429 |
|
✗ |
m_U_0_seq.setValues(1,&ia,&initialSolution[i],INSERT_VALUES); |
| 430 |
|
|
} |
| 431 |
|
✗ |
m_U_0_seq.assembly(); |
| 432 |
|
✗ |
fromDoubleStarToVec(initialSolution, m_U_0, m_mesh->numPoints()); |
| 433 |
|
✗ |
fromDoubleStarToVec(ionicSolution, m_W_0, m_mesh->numPoints()); |
| 434 |
|
✗ |
delete [] initialSolution; |
| 435 |
|
✗ |
delete [] ionicSolution; |
| 436 |
|
|
// Read fibers file (*.00000.vct) |
| 437 |
|
✗ |
if (FelisceParam::instance().testCase == 1) { |
| 438 |
|
✗ |
if (m_fiber == nullptr) |
| 439 |
|
✗ |
m_fiber = new double[m_mesh->numPoints()*3]; |
| 440 |
|
✗ |
io.readVariable(2, 0.,m_fiber, m_mesh->numPoints()*3); |
| 441 |
|
|
} |
| 442 |
|
|
} else { |
| 443 |
|
✗ |
PetscPrintf(PETSC_COMM_WORLD, "U_0 not read from file (zero vector)."); |
| 444 |
|
✗ |
m_U_0.set( 0.); |
| 445 |
|
✗ |
m_U_0.assembly(); |
| 446 |
|
✗ |
m_W_0.set( 0.); |
| 447 |
|
✗ |
m_W_0.assembly(); |
| 448 |
|
✗ |
m_U_0_seq.set( 0.); |
| 449 |
|
✗ |
m_U_0_seq.assembly(); |
| 450 |
|
|
} |
| 451 |
|
|
} |
| 452 |
|
|
|
| 453 |
|
✗ |
void EigenProblemPOD::getFiberDirection(felInt iel, int iUnknown, std::vector<double>& elemFiber) { |
| 454 |
|
✗ |
int numSupport = static_cast<int>(m_supportDofUnknown[iUnknown].iEle()[iel+1] - m_supportDofUnknown[iUnknown].iEle()[iel]); |
| 455 |
|
✗ |
elemFiber.resize( numSupport*3,0.); |
| 456 |
|
✗ |
for (int i = 0; i < numSupport; i++) { |
| 457 |
|
✗ |
elemFiber[i*3] = m_fiber[3*(m_supportDofUnknown[iUnknown].iSupportDof()[m_supportDofUnknown[iUnknown].iEle()[iel]+i])]; |
| 458 |
|
✗ |
elemFiber[i*3+1] = m_fiber[3*(m_supportDofUnknown[iUnknown].iSupportDof()[m_supportDofUnknown[iUnknown].iEle()[iel]+i])+1]; |
| 459 |
|
✗ |
elemFiber[i*3+2] = m_fiber[3*(m_supportDofUnknown[iUnknown].iSupportDof()[m_supportDofUnknown[iUnknown].iEle()[iel]+i])+2]; |
| 460 |
|
|
} |
| 461 |
|
|
} |
| 462 |
|
|
|
| 463 |
|
✗ |
void EigenProblemPOD::initializeROM() { |
| 464 |
|
✗ |
if (FelisceParam::verbose() > 10 ) PetscPrintf(PETSC_COMM_WORLD,"\nEigenProblemPOD::initializeROM()\n"); |
| 465 |
|
|
|
| 466 |
|
✗ |
m_basisPOD.resize(m_dimRomBasis); |
| 467 |
|
✗ |
for (int i=0; i<m_dimRomBasis; i++) { |
| 468 |
|
✗ |
m_Matrix[m_idG].getVecs(m_basisPOD[i],nullPetscVector); |
| 469 |
|
✗ |
m_basisPOD[i].setFromOptions(); |
| 470 |
|
✗ |
double* vec = new double[m_numDof]; |
| 471 |
|
✗ |
readEnsightFile(vec,"basis",i,m_numDof); |
| 472 |
|
✗ |
fromDoubleStarToVec(vec, m_basisPOD[i], m_numDof); |
| 473 |
|
✗ |
delete [] vec; |
| 474 |
|
✗ |
if (FelisceParam::verbose() > 40) m_basisPOD[i].view(); |
| 475 |
|
|
} |
| 476 |
|
|
|
| 477 |
|
✗ |
readEigenValueFromFile(); |
| 478 |
|
|
|
| 479 |
|
✗ |
initializeSolution(); |
| 480 |
|
|
} |
| 481 |
|
|
|
| 482 |
|
✗ |
void EigenProblemPOD::readEnsightFile(double* vec, std::string varName, int idIter, felInt size) { |
| 483 |
|
✗ |
std::string iteration; |
| 484 |
|
✗ |
if (idIter < 10) |
| 485 |
|
✗ |
iteration = "0000" + std::to_string(idIter); |
| 486 |
|
✗ |
else if (idIter < 100) |
| 487 |
|
✗ |
iteration = "000" + std::to_string(idIter); |
| 488 |
|
✗ |
else if (idIter < 1000) |
| 489 |
|
✗ |
iteration = "00" + std::to_string(idIter); |
| 490 |
|
✗ |
else if (idIter < 10000) |
| 491 |
|
✗ |
iteration = "0" + std::to_string(idIter); |
| 492 |
|
✗ |
else if (idIter < 100000) |
| 493 |
|
✗ |
iteration = std::to_string(idIter); |
| 494 |
|
|
|
| 495 |
|
✗ |
std::string fileName = FelisceParam::instance().inputDirectory + "/" + varName + "." + iteration + ".scl"; |
| 496 |
|
✗ |
if (FelisceParam::verbose() > 1) PetscPrintf(PETSC_COMM_WORLD, "Read file %s\n", fileName.c_str()); |
| 497 |
|
✗ |
FILE* pFile = fopen (fileName.c_str(),"r"); |
| 498 |
|
✗ |
if (pFile==nullptr) { |
| 499 |
|
✗ |
FEL_ERROR("Impossible to read "+fileName +"."); |
| 500 |
|
|
} |
| 501 |
|
|
char str[80]; |
| 502 |
|
✗ |
std::string display; |
| 503 |
|
✗ |
if ( fscanf(pFile,"%s", str) !=1 ) { |
| 504 |
|
✗ |
FEL_WARNING("Failed ot read str"); |
| 505 |
|
|
} |
| 506 |
|
✗ |
display = str; |
| 507 |
|
✗ |
if ( fscanf(pFile,"%s", str) !=1 ) { |
| 508 |
|
✗ |
FEL_WARNING("Failed ot read str"); |
| 509 |
|
|
} |
| 510 |
|
✗ |
display = str; |
| 511 |
|
✗ |
if ( fscanf(pFile,"%s", str) !=1) { |
| 512 |
|
✗ |
FEL_WARNING("Failed ot read str"); |
| 513 |
|
|
} |
| 514 |
|
✗ |
display = str; |
| 515 |
|
|
//Read values |
| 516 |
|
✗ |
int count = 0; |
| 517 |
|
✗ |
for ( felInt i = 0; i < size; i++) { |
| 518 |
|
✗ |
if ( fscanf(pFile,"%lf", &vec[i]) !=1 ) { |
| 519 |
|
✗ |
FEL_WARNING("Failed ot read vec"); |
| 520 |
|
|
} |
| 521 |
|
✗ |
if ( count == 6 ) { |
| 522 |
|
✗ |
if ( fscanf( pFile, "\n" ) !=0 ) { |
| 523 |
|
✗ |
FEL_WARNING("Failed ot read"); |
| 524 |
|
|
} |
| 525 |
|
✗ |
count=0; |
| 526 |
|
|
} |
| 527 |
|
✗ |
count++; |
| 528 |
|
|
} |
| 529 |
|
✗ |
fclose(pFile); |
| 530 |
|
|
} |
| 531 |
|
|
|
| 532 |
|
✗ |
void EigenProblemPOD::readEigenValueFromFile() { |
| 533 |
|
✗ |
std::string fileName = FelisceParam::instance().inputDirectory + "/eigenValue"; |
| 534 |
|
✗ |
if (FelisceParam::verbose() > 1) PetscPrintf(PETSC_COMM_WORLD, "Read file %s\n", fileName.c_str()); |
| 535 |
|
✗ |
FILE* pFile = fopen (fileName.c_str(),"r"); |
| 536 |
|
✗ |
if (pFile==nullptr) { |
| 537 |
|
✗ |
FEL_ERROR("Impossible to read "+fileName +"."); |
| 538 |
|
|
} |
| 539 |
|
|
//Read values |
| 540 |
|
✗ |
m_eigenValue = new double[m_dimRomBasis]; |
| 541 |
|
✗ |
for ( felInt i = 0; i < m_dimRomBasis; i++) { |
| 542 |
|
✗ |
if ( fscanf(pFile,"%lf", &m_eigenValue[i]) !=1 ) { |
| 543 |
|
✗ |
FEL_WARNING("Failed ot read vec"); |
| 544 |
|
|
} |
| 545 |
|
✗ |
if ( fscanf( pFile, "\n" ) !=0 ) { |
| 546 |
|
✗ |
FEL_WARNING("Failed ot read"); |
| 547 |
|
|
} |
| 548 |
|
|
} |
| 549 |
|
✗ |
fclose(pFile); |
| 550 |
|
|
|
| 551 |
|
✗ |
if (FelisceParam::verbose() > 10) { |
| 552 |
|
✗ |
PetscPrintf(PETSC_COMM_WORLD, "EigenValues:\n"); |
| 553 |
|
✗ |
for ( felInt i = 0; i < m_dimRomBasis; i++) { |
| 554 |
|
✗ |
PetscPrintf(PETSC_COMM_WORLD, "[%d] %e \n", i, m_eigenValue[i]); |
| 555 |
|
|
} |
| 556 |
|
|
} |
| 557 |
|
|
|
| 558 |
|
|
} |
| 559 |
|
|
|
| 560 |
|
|
|
| 561 |
|
✗ |
void EigenProblemPOD::computeGamma() { |
| 562 |
|
✗ |
if (FelisceParam::verbose() > 10 ) PetscPrintf(PETSC_COMM_WORLD,"\nEigenProblemPOD::computeGamma()\n"); |
| 563 |
|
|
|
| 564 |
|
|
// Warning: for Monodomain heart potential problem coupled with FhN |
| 565 |
|
|
// todo To be generalized |
| 566 |
|
|
|
| 567 |
|
✗ |
double Am = FelisceParam::instance().Am; |
| 568 |
|
✗ |
double Cm = FelisceParam::instance().Cm; |
| 569 |
|
✗ |
double s = FelisceParam::instance().f0; |
| 570 |
|
✗ |
double a = FelisceParam::instance().alpha; |
| 571 |
|
✗ |
double eps = FelisceParam::instance().epsilon; |
| 572 |
|
✗ |
double gam = FelisceParam::instance().gammaEl; |
| 573 |
|
|
|
| 574 |
|
✗ |
if (m_gamma == nullptr) |
| 575 |
|
✗ |
m_gamma = new double[m_dimRomBasis]; |
| 576 |
|
✗ |
if (m_eta == nullptr) |
| 577 |
|
✗ |
m_eta = new double[m_dimRomBasis]; |
| 578 |
|
|
|
| 579 |
|
✗ |
for (int p=0; p<m_dimRomBasis; p++) { |
| 580 |
|
✗ |
m_gamma[p] = 0.0; |
| 581 |
|
|
}; |
| 582 |
|
|
|
| 583 |
|
✗ |
if ( !FelisceParam::instance().hasInfarct ) { |
| 584 |
|
✗ |
for (int p=0; p<m_dimRomBasis; p++) { |
| 585 |
|
✗ |
m_gamma[p] = - ( s*a*Am ) * m_beta[p]; |
| 586 |
|
✗ |
m_gamma[p] += - Am * m_mu[p]; |
| 587 |
|
✗ |
for (int i=0; i<m_dimRomBasis; i++) { |
| 588 |
|
✗ |
m_gamma[p] -= m_beta[i]*m_tensorE[secondOrderGlobalIndex(p,i)]; |
| 589 |
|
✗ |
for (int j=0; j<m_dimRomBasis; j++) { |
| 590 |
|
✗ |
m_gamma[p] += ( s*(a+1)*Am) * m_beta[i] * m_beta[j] * m_tensorT[thirdOrderGlobalIndex(i,j,p)]; |
| 591 |
|
✗ |
for (int k=0; k<m_dimRomBasis; k++) { |
| 592 |
|
✗ |
m_gamma[p] += - s*Am * m_beta[i] * m_beta[j] * m_beta[k] * m_tensorY[fourthOrderGlobalIndex(i,j,k,p)]; |
| 593 |
|
|
} |
| 594 |
|
|
} |
| 595 |
|
|
} |
| 596 |
|
|
|
| 597 |
|
✗ |
if (FelisceParam::instance().hasSource) { |
| 598 |
|
✗ |
double delay[m_numSource]; |
| 599 |
|
✗ |
for (int iS=0; iS<m_numSource; iS++) { |
| 600 |
|
✗ |
delay[iS] = FelisceParam::instance().delayStim[iS]; |
| 601 |
|
|
} |
| 602 |
|
✗ |
double tPeriod=fmod(m_fstransient->time,FelisceParam::instance().timePeriod); |
| 603 |
|
✗ |
for (int iS=0; iS<m_numSource; iS++) { |
| 604 |
|
✗ |
if ((tPeriod>=delay[iS])&&(tPeriod<=(delay[iS]+FelisceParam::instance().stimTime))) |
| 605 |
|
✗ |
m_gamma[p] += Am*m_source[iS][p]; |
| 606 |
|
|
} |
| 607 |
|
|
} |
| 608 |
|
|
|
| 609 |
|
✗ |
m_gamma[p] = m_gamma[p] / (Am*Cm); |
| 610 |
|
|
|
| 611 |
|
✗ |
m_eta[p] = eps * ( gam * m_beta[p] - m_mu[p] ); |
| 612 |
|
|
|
| 613 |
|
|
} |
| 614 |
|
✗ |
} else if (FelisceParam::instance().hasInfarct) { |
| 615 |
|
✗ |
for (int p=0; p<m_dimRomBasis; p++) { |
| 616 |
|
✗ |
m_gamma[p] += - Am * m_mu[p]; |
| 617 |
|
✗ |
for (int i=0; i<m_dimRomBasis; i++) { |
| 618 |
|
✗ |
m_gamma[p] -= m_beta[i]*m_tensorE[secondOrderGlobalIndex(p,i)]; |
| 619 |
|
✗ |
m_gamma[p] += - a*Am * m_beta[i] * m_tensorCs[secondOrderGlobalIndex(i,p)]; |
| 620 |
|
✗ |
for (int j=0; j<m_dimRomBasis; j++) { |
| 621 |
|
✗ |
m_gamma[p] += (a+1)*Am * m_beta[i] * m_beta[j] * m_tensorTs[thirdOrderGlobalIndex(i,j,p)]; |
| 622 |
|
✗ |
for (int k=0; k<m_dimRomBasis; k++) { |
| 623 |
|
✗ |
m_gamma[p] += - Am * m_beta[i] * m_beta[j] * m_beta[k] * m_tensorY[fourthOrderGlobalIndex(i,j,k,p)]; |
| 624 |
|
|
} |
| 625 |
|
|
} |
| 626 |
|
|
} |
| 627 |
|
|
|
| 628 |
|
✗ |
if (FelisceParam::instance().hasSource) { |
| 629 |
|
✗ |
double delay[m_numSource]; |
| 630 |
|
✗ |
for (int iS=0; iS<m_numSource; iS++) { |
| 631 |
|
✗ |
delay[iS] = FelisceParam::instance().delayStim[iS]; |
| 632 |
|
|
} |
| 633 |
|
✗ |
double tPeriod=fmod(m_fstransient->time,FelisceParam::instance().timePeriod); |
| 634 |
|
✗ |
for (int iS=0; iS<m_numSource; iS++) { |
| 635 |
|
✗ |
if ((tPeriod>=delay[iS])&&(tPeriod<=(delay[iS]+FelisceParam::instance().stimTime))) |
| 636 |
|
✗ |
m_gamma[p] += Am*m_source[iS][p]; |
| 637 |
|
|
} |
| 638 |
|
|
} |
| 639 |
|
|
|
| 640 |
|
✗ |
m_gamma[p] = m_gamma[p] / (Am*Cm); |
| 641 |
|
|
|
| 642 |
|
✗ |
m_eta[p] = eps * ( gam * m_beta[p] - m_mu[p] ); |
| 643 |
|
|
|
| 644 |
|
|
} |
| 645 |
|
|
} |
| 646 |
|
|
|
| 647 |
|
|
} |
| 648 |
|
|
|
| 649 |
|
|
|
| 650 |
|
|
|
| 651 |
|
|
|
| 652 |
|
|
|
| 653 |
|
✗ |
void EigenProblemPOD::initializeSolution() { |
| 654 |
|
✗ |
if (FelisceParam::verbose() > 10 ) PetscPrintf(PETSC_COMM_WORLD,"\nEigenProblemPOD::initializeSolution()\n"); |
| 655 |
|
|
|
| 656 |
|
✗ |
if ( !m_solutionInitialized) { |
| 657 |
|
✗ |
if (m_beta == nullptr) |
| 658 |
|
✗ |
m_beta = new double[m_dimRomBasis]; |
| 659 |
|
|
|
| 660 |
|
✗ |
projectOnBasis(m_U_0,m_beta,true); |
| 661 |
|
|
|
| 662 |
|
✗ |
if (m_mu == nullptr) |
| 663 |
|
✗ |
m_mu = new double[m_dimRomBasis]; |
| 664 |
|
|
|
| 665 |
|
✗ |
projectOnBasis(m_W_0,m_mu,true); |
| 666 |
|
|
|
| 667 |
|
✗ |
m_solutionInitialized = true; |
| 668 |
|
|
} |
| 669 |
|
|
} |
| 670 |
|
|
|
| 671 |
|
|
|
| 672 |
|
✗ |
void EigenProblemPOD::setFhNf0(std::vector<double>& valuef0) { |
| 673 |
|
✗ |
m_FhNf0.createSeq(PETSC_COMM_SELF,m_numDof); |
| 674 |
|
✗ |
m_FhNf0.setFromOptions(); |
| 675 |
|
|
|
| 676 |
|
|
// initialize SEQUENTIAL vectors (in order to use elemField) |
| 677 |
|
|
felInt ia; |
| 678 |
|
✗ |
for (felInt i=0; i< m_numDof; i++) { |
| 679 |
|
✗ |
ia = i; |
| 680 |
|
✗ |
AOApplicationToPetsc(m_ao,1,&ia); |
| 681 |
|
✗ |
m_FhNf0.setValues(1,&ia,&valuef0[i],INSERT_VALUES); |
| 682 |
|
|
} |
| 683 |
|
✗ |
m_FhNf0.assembly(); |
| 684 |
|
|
|
| 685 |
|
|
} |
| 686 |
|
|
|
| 687 |
|
✗ |
void EigenProblemPOD::setIapp(std::vector<double>& iApp, int& idS) { |
| 688 |
|
✗ |
if (m_source == nullptr) { |
| 689 |
|
✗ |
m_source = new double*[m_numSource]; |
| 690 |
|
✗ |
for (int i=0; i<m_numSource; i++) { |
| 691 |
|
✗ |
m_source[i] = new double[m_dimRomBasis]; |
| 692 |
|
|
} |
| 693 |
|
|
} |
| 694 |
|
|
|
| 695 |
|
✗ |
PetscVector RHS; |
| 696 |
|
✗ |
RHS.createSeq(PETSC_COMM_SELF,m_numDof); |
| 697 |
|
✗ |
RHS.setFromOptions(); |
| 698 |
|
|
// initialize SEQUENTIAL vectors (in order to use elemField) |
| 699 |
|
|
felInt ia; |
| 700 |
|
✗ |
for (felInt i=0; i< m_numDof; i++) { |
| 701 |
|
✗ |
ia = i; |
| 702 |
|
✗ |
AOApplicationToPetsc(m_ao,1,&ia); |
| 703 |
|
✗ |
RHS.setValues(1,&ia,&iApp[i],INSERT_VALUES); |
| 704 |
|
|
} |
| 705 |
|
✗ |
RHS.assembly(); |
| 706 |
|
|
|
| 707 |
|
✗ |
projectOnBasis(RHS, m_source[idS], true); |
| 708 |
|
|
|
| 709 |
|
✗ |
RHS.destroy(); |
| 710 |
|
|
} |
| 711 |
|
|
|
| 712 |
|
|
|
| 713 |
|
|
|
| 714 |
|
|
|
| 715 |
|
|
|
| 716 |
|
|
|
| 717 |
|
✗ |
void EigenProblemPOD::checkSolution(PetscVector& solution, PetscVector& refSol, double & error) { |
| 718 |
|
|
|
| 719 |
|
✗ |
PetscVector tmpVec1; |
| 720 |
|
✗ |
tmpVec1.duplicateFrom(refSol); |
| 721 |
|
|
|
| 722 |
|
✗ |
PetscVector tmpVec2; |
| 723 |
|
✗ |
tmpVec2.duplicateFrom(refSol); |
| 724 |
|
|
|
| 725 |
|
✗ |
waxpy(tmpVec1,-1.0,refSol,solution); |
| 726 |
|
|
|
| 727 |
|
✗ |
mult(m_Matrix[m_idG],tmpVec1,tmpVec2); |
| 728 |
|
|
|
| 729 |
|
✗ |
dot(tmpVec1,tmpVec2,&error); |
| 730 |
|
|
|
| 731 |
|
✗ |
tmpVec1.destroy(); |
| 732 |
|
✗ |
tmpVec2.destroy(); |
| 733 |
|
|
} |
| 734 |
|
|
|
| 735 |
|
|
|
| 736 |
|
|
|
| 737 |
|
✗ |
void EigenProblemPOD::checkBasis() { |
| 738 |
|
|
|
| 739 |
|
✗ |
if (!m_solutionInitialized) { |
| 740 |
|
✗ |
initializeSolution(); |
| 741 |
|
|
} |
| 742 |
|
|
|
| 743 |
|
✗ |
double convergence[m_dimRomBasis]; |
| 744 |
|
|
int rankProc; |
| 745 |
|
✗ |
MPI_Comm_rank(m_petscComm,&rankProc); |
| 746 |
|
✗ |
PetscVector tmpSol; |
| 747 |
|
✗ |
tmpSol.duplicateFrom(m_snapshot[m_numSnapshot-1]); |
| 748 |
|
|
|
| 749 |
|
|
// Check convergence on the last snapshot |
| 750 |
|
✗ |
double* tmpSolToSave = nullptr; |
| 751 |
|
✗ |
tmpSolToSave = new double[m_numDof]; |
| 752 |
|
✗ |
for (int iBasis=0; iBasis < m_dimRomBasis; iBasis++) { |
| 753 |
|
✗ |
double tmpCoeff[iBasis]; |
| 754 |
|
✗ |
for (int jBasis=0; jBasis<iBasis+1; jBasis++) { |
| 755 |
|
✗ |
tmpCoeff[jBasis] = 0.0; |
| 756 |
|
✗ |
scalarProduct(m_snapshot[m_numSnapshot-1], m_basisPOD[jBasis], tmpCoeff[jBasis],true); |
| 757 |
|
|
} |
| 758 |
|
|
|
| 759 |
|
✗ |
projectOnDof(tmpCoeff,tmpSol,iBasis); |
| 760 |
|
|
|
| 761 |
|
✗ |
checkSolution(tmpSol,m_snapshot[m_numSnapshot-1],convergence[iBasis]); |
| 762 |
|
|
|
| 763 |
|
✗ |
fromVecToDoubleStar(tmpSolToSave, tmpSol, rankProc, 1); |
| 764 |
|
✗ |
writeEnsightVector(tmpSolToSave, iBasis, "potTransMembConv"); |
| 765 |
|
|
|
| 766 |
|
✗ |
PetscPrintf(PETSC_COMM_WORLD, "convergence[%d] = %e \n", iBasis, convergence[iBasis]); |
| 767 |
|
|
} |
| 768 |
|
✗ |
if (rankProc == 0) |
| 769 |
|
✗ |
writeEnsightCase(m_dimRomBasis, 1., "potTransMembConv"); |
| 770 |
|
✗ |
std::string fileName = FelisceParam::instance().resultDir + "/convergence"; |
| 771 |
|
✗ |
viewPOD(convergence,m_dimRomBasis,fileName); |
| 772 |
|
|
|
| 773 |
|
✗ |
delete [] tmpSolToSave; |
| 774 |
|
✗ |
tmpSol.destroy(); |
| 775 |
|
|
} |
| 776 |
|
|
|
| 777 |
|
|
|
| 778 |
|
✗ |
void EigenProblemPOD::checkOrthonormality() { |
| 779 |
|
✗ |
std::ofstream fOrth; |
| 780 |
|
✗ |
fOrth.open("Orthonormality.log"); |
| 781 |
|
|
|
| 782 |
|
✗ |
std::cout << "Checking basis orthonormality: " <<std::endl; |
| 783 |
|
✗ |
for(int i=0; i<m_dimRomBasis; i++) { |
| 784 |
|
✗ |
for(int j=0; j<i+1; j++) { |
| 785 |
|
✗ |
double prod = 0.0; |
| 786 |
|
✗ |
scalarProduct(m_basisPOD[i], m_basisPOD[j], prod, true); |
| 787 |
|
✗ |
fOrth << "Mass("<<i<<","<<j<<") = " << prod <<std::endl; |
| 788 |
|
|
}; |
| 789 |
|
|
}; |
| 790 |
|
✗ |
fOrth.close(); |
| 791 |
|
|
} |
| 792 |
|
|
|
| 793 |
|
|
|
| 794 |
|
|
|
| 795 |
|
✗ |
void EigenProblemPOD::scalarProduct(PetscVector& firstVec, PetscVector& secondVec, double& prod, bool flagMass) { |
| 796 |
|
✗ |
PetscVector tmpVec; |
| 797 |
|
✗ |
tmpVec.duplicateFrom(firstVec); |
| 798 |
|
|
|
| 799 |
|
✗ |
if (flagMass) { |
| 800 |
|
✗ |
mult(m_Matrix[m_idG], firstVec, tmpVec); |
| 801 |
|
✗ |
dot(tmpVec,secondVec,&prod); |
| 802 |
|
|
} else { |
| 803 |
|
✗ |
dot( firstVec,secondVec,&prod); |
| 804 |
|
|
} |
| 805 |
|
|
|
| 806 |
|
✗ |
tmpVec.destroy(); |
| 807 |
|
✗ |
}; |
| 808 |
|
|
|
| 809 |
|
|
|
| 810 |
|
|
|
| 811 |
|
|
// Modified Gram-Schmidt (see Golub & Van Loan) |
| 812 |
|
✗ |
void EigenProblemPOD::MGS(std::vector<PetscVector>& subspace) { |
| 813 |
|
✗ |
PetscVector tmpVec; |
| 814 |
|
✗ |
tmpVec.duplicateFrom(subspace[0]); |
| 815 |
|
✗ |
int dimSubSpace = subspace.size(); |
| 816 |
|
|
|
| 817 |
|
✗ |
for(int iBasis=0; iBasis<dimSubSpace; iBasis++) { |
| 818 |
|
✗ |
mult(m_Matrix[0],subspace[iBasis],tmpVec); |
| 819 |
|
✗ |
double rii = 0.0; |
| 820 |
|
✗ |
dot(tmpVec,subspace[iBasis],&rii); |
| 821 |
|
✗ |
rii = 1.0/std::sqrt(rii); |
| 822 |
|
✗ |
subspace[iBasis].scale(rii); |
| 823 |
|
|
|
| 824 |
|
✗ |
mult(m_Matrix[0],subspace[iBasis],tmpVec); |
| 825 |
|
|
|
| 826 |
|
✗ |
for(int j=iBasis+1; j<m_dimRomBasis; j++) { |
| 827 |
|
✗ |
double rij = 0.0; |
| 828 |
|
✗ |
dot(tmpVec,subspace[j],&rij); |
| 829 |
|
✗ |
rij = -1.0 * rij; |
| 830 |
|
✗ |
subspace[j].axpy(rij,subspace[iBasis]); |
| 831 |
|
|
} |
| 832 |
|
|
} |
| 833 |
|
✗ |
tmpVec.destroy(); |
| 834 |
|
|
} |
| 835 |
|
|
|
| 836 |
|
|
|
| 837 |
|
|
|
| 838 |
|
✗ |
void EigenProblemPOD::computeMatrixZeta() { |
| 839 |
|
✗ |
if (FelisceParam::verbose() > 10 ) PetscPrintf(PETSC_COMM_WORLD,"\nEigenProblemPOD::computeMatrixZeta()\n"); |
| 840 |
|
✗ |
if ( m_zeta.size() == 0 ) { |
| 841 |
|
✗ |
m_size2 = static_cast<int>(m_dimRomBasis*(m_dimRomBasis+1)/2); |
| 842 |
|
✗ |
m_zeta.resize(m_size2); |
| 843 |
|
✗ |
for (int i=0; i<m_size2; i++) |
| 844 |
|
✗ |
m_zeta[i].duplicateFrom(m_basisPOD[0]); |
| 845 |
|
|
} |
| 846 |
|
|
|
| 847 |
|
✗ |
for (int i=0; i<m_dimRomBasis; i++) { // row |
| 848 |
|
✗ |
for (int j=0; j<i+1; j++) { // column |
| 849 |
|
|
// secondOrderGlobalIndex(i,j) = i*(i+1)/2 + j |
| 850 |
|
✗ |
pointwiseMult(m_zeta[secondOrderGlobalIndex(i,j)],m_basisPOD[i],m_basisPOD[j]); |
| 851 |
|
|
} |
| 852 |
|
|
} |
| 853 |
|
|
|
| 854 |
|
|
} |
| 855 |
|
|
|
| 856 |
|
|
|
| 857 |
|
|
|
| 858 |
|
✗ |
int EigenProblemPOD::secondOrderGlobalIndex(int& i, int& j) { |
| 859 |
|
|
int id; |
| 860 |
|
|
|
| 861 |
|
✗ |
if (i >= j) { |
| 862 |
|
✗ |
id = static_cast<int>(i*(i+1)/2+j); |
| 863 |
|
|
} else { |
| 864 |
|
✗ |
id = static_cast<int>(j*(j+1)/2+i); |
| 865 |
|
|
} |
| 866 |
|
|
|
| 867 |
|
✗ |
return id; |
| 868 |
|
|
} |
| 869 |
|
|
|
| 870 |
|
✗ |
int EigenProblemPOD::thirdOrderGlobalIndex(int& i, int& j, int& k) { |
| 871 |
|
|
int id; |
| 872 |
|
|
int s[3]; |
| 873 |
|
✗ |
s[0] = i; |
| 874 |
|
✗ |
s[1] = j; |
| 875 |
|
✗ |
s[2] = k; |
| 876 |
|
|
int temp; |
| 877 |
|
✗ |
for (int ii=0; ii<3; ii++) { |
| 878 |
|
✗ |
for (int jj=0; jj<2; jj++) { |
| 879 |
|
✗ |
if (s[jj] < s[jj+1]) { |
| 880 |
|
✗ |
temp = s[jj]; |
| 881 |
|
✗ |
s[jj] = s[jj+1]; |
| 882 |
|
✗ |
s[jj+1] = temp; |
| 883 |
|
|
} |
| 884 |
|
|
} |
| 885 |
|
|
} |
| 886 |
|
✗ |
id = static_cast<int>(s[0]*(s[0]+1)*(s[0]+2)/6); |
| 887 |
|
✗ |
id += static_cast<int>(s[1]*(s[1]+1)/2); |
| 888 |
|
✗ |
id += s[2]; |
| 889 |
|
✗ |
return id; |
| 890 |
|
|
} |
| 891 |
|
|
|
| 892 |
|
✗ |
int EigenProblemPOD::fourthOrderGlobalIndex(int& i, int& j, int& k, int& h) { |
| 893 |
|
|
int id; |
| 894 |
|
|
int s[4]; |
| 895 |
|
✗ |
s[0] = i; |
| 896 |
|
✗ |
s[1] = j; |
| 897 |
|
✗ |
s[2] = k; |
| 898 |
|
✗ |
s[3] = h; |
| 899 |
|
|
int temp; |
| 900 |
|
✗ |
for (int ii=0; ii<4; ii++) { |
| 901 |
|
✗ |
for (int jj=0; jj<3; jj++) { |
| 902 |
|
✗ |
if (s[jj] < s[jj+1]) { |
| 903 |
|
✗ |
temp = s[jj]; |
| 904 |
|
✗ |
s[jj] = s[jj+1]; |
| 905 |
|
✗ |
s[jj+1] = temp; |
| 906 |
|
|
} |
| 907 |
|
|
} |
| 908 |
|
|
} |
| 909 |
|
✗ |
id = static_cast<int>(s[0]*(s[0]+1)*(s[0]*s[0]+5*s[0]+6)/24); |
| 910 |
|
✗ |
id += static_cast<int>(s[1]*(s[1]+1)*(s[1]+2)/6); |
| 911 |
|
✗ |
id += static_cast<int>(s[2]*(s[2]+1)/2); |
| 912 |
|
✗ |
id += s[3]; |
| 913 |
|
✗ |
return id; |
| 914 |
|
|
} |
| 915 |
|
|
|
| 916 |
|
|
|
| 917 |
|
✗ |
void EigenProblemPOD::computeTensor() { |
| 918 |
|
✗ |
int n = m_dimRomBasis; |
| 919 |
|
|
|
| 920 |
|
✗ |
if ( !FelisceParam::instance().hasInfarct) { |
| 921 |
|
|
// T_ijk = < phi_i, zeta_jk > |
| 922 |
|
✗ |
m_size3 = static_cast<int>(n*(n+1)*(n+2)/6); |
| 923 |
|
✗ |
if (m_tensorT == nullptr) |
| 924 |
|
✗ |
m_tensorT = new double [m_size3]; |
| 925 |
|
|
// Y_ijkh = < zeta_ij, zeta_kh > |
| 926 |
|
✗ |
m_size4 = static_cast<int>(n*(n+1)*(n*n+5*n+6)/24); |
| 927 |
|
✗ |
if (m_tensorY == nullptr) |
| 928 |
|
✗ |
m_tensorY = new double [m_size4]; |
| 929 |
|
✗ |
if (m_tensorE == nullptr) |
| 930 |
|
✗ |
m_tensorE = new double [m_size2]; |
| 931 |
|
|
|
| 932 |
|
|
|
| 933 |
|
|
double valueT; |
| 934 |
|
|
double valueY; |
| 935 |
|
|
double valueE; |
| 936 |
|
✗ |
PetscVector phiG; |
| 937 |
|
✗ |
phiG.duplicateFrom(m_basisPOD[0]); |
| 938 |
|
✗ |
PetscVector phiK; |
| 939 |
|
✗ |
phiK.duplicateFrom(m_basisPOD[0]); |
| 940 |
|
|
|
| 941 |
|
✗ |
for (int i=0; i<m_dimRomBasis; i++) { |
| 942 |
|
|
// phiK = phi_i^T * K |
| 943 |
|
✗ |
mult(m_Matrix[m_idK],m_basisPOD[i],phiK); |
| 944 |
|
✗ |
for (int j=0; j<i+1; j++) { |
| 945 |
|
|
// phiG = zeta_ij^T * G |
| 946 |
|
✗ |
mult(m_Matrix[m_idG],m_zeta[secondOrderGlobalIndex(i,j)],phiG); |
| 947 |
|
|
// valueE |
| 948 |
|
✗ |
dot(m_basisPOD[j],phiK,&valueE); |
| 949 |
|
✗ |
m_tensorE[secondOrderGlobalIndex(i,j)] = valueE; |
| 950 |
|
|
|
| 951 |
|
✗ |
for (int k=0; k<j+1; k++) { |
| 952 |
|
|
// valueT = zeta_ij^T * G * phi_k |
| 953 |
|
✗ |
dot(m_basisPOD[k],phiG,&valueT); |
| 954 |
|
✗ |
m_tensorT[thirdOrderGlobalIndex(i,j,k)] = valueT; |
| 955 |
|
✗ |
for (int h=0; h<k+1; h++) { |
| 956 |
|
|
// valueY = zeta_ij^T * G * zeta_kh |
| 957 |
|
✗ |
dot(m_zeta[secondOrderGlobalIndex(k,h)],phiG,&valueY); |
| 958 |
|
✗ |
m_tensorY[fourthOrderGlobalIndex(i,j,k,h)] = valueY; |
| 959 |
|
|
} |
| 960 |
|
|
} |
| 961 |
|
|
} |
| 962 |
|
|
} |
| 963 |
|
✗ |
phiG.destroy(); |
| 964 |
|
✗ |
} else if (FelisceParam::instance().hasInfarct) { |
| 965 |
|
|
// Cs_ij = < s phi_i, phi_j > |
| 966 |
|
✗ |
if (m_tensorCs == nullptr) |
| 967 |
|
✗ |
m_tensorCs = new double [m_size2]; |
| 968 |
|
|
// T_ijk = < phi_i, zeta_jk > |
| 969 |
|
✗ |
m_size3 = static_cast<int>(n*(n+1)*(n+2)/6); |
| 970 |
|
✗ |
if (m_tensorT == nullptr) |
| 971 |
|
✗ |
m_tensorT = new double [m_size3]; |
| 972 |
|
|
// Ts_ijk = < s phi_i, zeta_jk > |
| 973 |
|
✗ |
m_size3 = static_cast<int>(n*(n+1)*(n+2)/6); |
| 974 |
|
✗ |
if (m_tensorTs == nullptr) |
| 975 |
|
✗ |
m_tensorTs = new double [m_size3]; |
| 976 |
|
|
// Y_ijkh = < zeta_ij, zeta_kh > |
| 977 |
|
✗ |
m_size4 = static_cast<int>(n*(n+1)*(n*n+5*n+6)/24); |
| 978 |
|
✗ |
if (m_tensorY == nullptr) |
| 979 |
|
✗ |
m_tensorY = new double [m_size4]; |
| 980 |
|
✗ |
if (m_tensorE == nullptr) |
| 981 |
|
✗ |
m_tensorE = new double [m_size2]; |
| 982 |
|
|
|
| 983 |
|
|
double valueCs; |
| 984 |
|
|
double valueT; |
| 985 |
|
|
double valueTs; |
| 986 |
|
|
double valueY; |
| 987 |
|
|
double valueE; |
| 988 |
|
✗ |
PetscVector phiGs; |
| 989 |
|
✗ |
PetscVector zetaG; |
| 990 |
|
✗ |
PetscVector zetaGs; |
| 991 |
|
✗ |
PetscVector phiK; |
| 992 |
|
✗ |
phiGs.duplicateFrom(m_basisPOD[0]); |
| 993 |
|
✗ |
zetaG.duplicateFrom(m_basisPOD[0]); |
| 994 |
|
✗ |
zetaGs.duplicateFrom(m_basisPOD[0]); |
| 995 |
|
✗ |
phiK.duplicateFrom(m_basisPOD[0]); |
| 996 |
|
✗ |
for (int i=0; i<m_dimRomBasis; i++) { |
| 997 |
|
|
// phiGs = phi_i^T * Gs |
| 998 |
|
✗ |
mult(m_Matrix[m_idGs],m_basisPOD[i],phiGs); |
| 999 |
|
✗ |
mult(m_Matrix[m_idK],m_basisPOD[i],phiK); |
| 1000 |
|
✗ |
for (int j=0; j<i+1; j++) { |
| 1001 |
|
|
// valueCs = phi_i^T * Gs * phi_j |
| 1002 |
|
✗ |
dot(m_basisPOD[j],phiGs,&valueCs); |
| 1003 |
|
✗ |
m_tensorCs[secondOrderGlobalIndex(i,j)] = valueCs; |
| 1004 |
|
|
|
| 1005 |
|
|
//valueE |
| 1006 |
|
✗ |
dot(m_basisPOD[j],phiK,&valueE); |
| 1007 |
|
✗ |
m_tensorE[secondOrderGlobalIndex(i,j)] = valueE; |
| 1008 |
|
|
|
| 1009 |
|
|
// zetaG = zeta_ij^T * G |
| 1010 |
|
✗ |
mult(m_Matrix[m_idG],m_zeta[secondOrderGlobalIndex(i,j)],zetaG); |
| 1011 |
|
|
// zetaGs = zeta_i^T * Gs |
| 1012 |
|
✗ |
mult(m_Matrix[m_idGs],m_zeta[secondOrderGlobalIndex(i,j)],zetaGs); |
| 1013 |
|
✗ |
for (int k=0; k<j+1; k++) { |
| 1014 |
|
|
// valueT = zeta_ij^T * G * phi_k |
| 1015 |
|
✗ |
dot(m_basisPOD[k],zetaG,&valueT); |
| 1016 |
|
✗ |
m_tensorT[thirdOrderGlobalIndex(i,j,k)] = valueT; |
| 1017 |
|
|
// valueTs = zeta_ij^T * Gs * phi_k |
| 1018 |
|
✗ |
dot(m_basisPOD[k],zetaGs,&valueTs); |
| 1019 |
|
✗ |
m_tensorTs[thirdOrderGlobalIndex(i,j,k)] = valueTs; |
| 1020 |
|
✗ |
for (int h=0; h<k+1; h++) { |
| 1021 |
|
|
// valueY = zeta_ij^T * Gs * zeta_kh |
| 1022 |
|
✗ |
dot(m_zeta[secondOrderGlobalIndex(k,h)],zetaGs,&valueY); |
| 1023 |
|
✗ |
m_tensorY[fourthOrderGlobalIndex(i,j,k,h)] = valueY; |
| 1024 |
|
|
} |
| 1025 |
|
|
} |
| 1026 |
|
|
} |
| 1027 |
|
|
} |
| 1028 |
|
✗ |
phiGs.destroy(); |
| 1029 |
|
✗ |
zetaG.destroy(); |
| 1030 |
|
✗ |
zetaGs.destroy(); |
| 1031 |
|
|
} |
| 1032 |
|
✗ |
}; |
| 1033 |
|
|
|
| 1034 |
|
|
|
| 1035 |
|
|
|
| 1036 |
|
✗ |
void EigenProblemPOD::updateBeta() { |
| 1037 |
|
✗ |
if (FelisceParam::verbose() > 10 ) PetscPrintf(PETSC_COMM_WORLD,"\nEigenProblemPOD::updateBeta()\n"); |
| 1038 |
|
|
|
| 1039 |
|
✗ |
double dt = FelisceParam::instance().timeStep; |
| 1040 |
|
✗ |
double newBeta[m_dimRomBasis]; |
| 1041 |
|
|
// beta^{n+1} = beta^n + dt * gamma^n |
| 1042 |
|
✗ |
for (int i=0; i<m_dimRomBasis; i++) { |
| 1043 |
|
✗ |
newBeta[i] = m_gamma[i]; |
| 1044 |
|
|
} |
| 1045 |
|
✗ |
for (int i=0; i<m_dimRomBasis; i++) { |
| 1046 |
|
✗ |
m_beta[i] += dt * newBeta[i]; |
| 1047 |
|
|
} |
| 1048 |
|
|
|
| 1049 |
|
✗ |
double newMu[m_dimRomBasis]; |
| 1050 |
|
|
// mu^{n+1} = mu^n + dt * eta^n |
| 1051 |
|
✗ |
for (int i=0; i<m_dimRomBasis; i++) { |
| 1052 |
|
✗ |
newMu[i] = m_eta[i]; |
| 1053 |
|
|
} |
| 1054 |
|
✗ |
for (int i=0; i<m_dimRomBasis; i++) { |
| 1055 |
|
✗ |
m_mu[i] += dt * newMu[i]; |
| 1056 |
|
|
} |
| 1057 |
|
|
} |
| 1058 |
|
|
|
| 1059 |
|
|
|
| 1060 |
|
|
|
| 1061 |
|
|
// Projection functions from FE space to RO one |
| 1062 |
|
✗ |
void EigenProblemPOD::projectOnBasis(PetscVector& vectorDof, double* vectorBasis, bool flagMass) { |
| 1063 |
|
✗ |
PetscVector tmpVec; |
| 1064 |
|
✗ |
tmpVec.duplicateFrom(vectorDof); |
| 1065 |
|
|
|
| 1066 |
|
✗ |
if (flagMass) { |
| 1067 |
|
✗ |
for (int iBasis=0; iBasis<m_dimRomBasis; iBasis++) { |
| 1068 |
|
✗ |
mult(m_Matrix[m_idG], m_basisPOD[iBasis], tmpVec); |
| 1069 |
|
✗ |
dot(tmpVec,vectorDof,&vectorBasis[iBasis]); |
| 1070 |
|
|
} |
| 1071 |
|
|
} else { |
| 1072 |
|
✗ |
for (int iBasis=0; iBasis<m_dimRomBasis; iBasis++) { |
| 1073 |
|
✗ |
dot( m_basisPOD[iBasis],vectorDof,&vectorBasis[iBasis]); |
| 1074 |
|
|
} |
| 1075 |
|
|
} |
| 1076 |
|
|
|
| 1077 |
|
✗ |
tmpVec.destroy(); |
| 1078 |
|
|
} |
| 1079 |
|
|
|
| 1080 |
|
|
// Projection functions from RO space to FE one |
| 1081 |
|
✗ |
void EigenProblemPOD::projectOnDof(double* vectorBasis, PetscVector& vectorDof, int size) { |
| 1082 |
|
✗ |
vectorDof.set(0.); |
| 1083 |
|
✗ |
for (int iBasis=0; iBasis<size; iBasis++) { |
| 1084 |
|
✗ |
vectorDof.axpy(vectorBasis[iBasis],m_basisPOD[iBasis]); |
| 1085 |
|
|
} |
| 1086 |
|
|
} |
| 1087 |
|
|
|
| 1088 |
|
|
|
| 1089 |
|
|
// Auxiliary function to debug purposes. |
| 1090 |
|
✗ |
void EigenProblemPOD::viewPOD(double* vToPrint, int vSize, std::ofstream outStream) { |
| 1091 |
|
|
int rankProc; |
| 1092 |
|
✗ |
MPI_Comm_rank(m_petscComm,&rankProc); |
| 1093 |
|
✗ |
if (rankProc == 0) { |
| 1094 |
|
✗ |
for(int i=0; i<vSize; i++) { |
| 1095 |
|
✗ |
outStream << vToPrint[i] << std::endl; |
| 1096 |
|
|
} |
| 1097 |
|
✗ |
outStream.close(); |
| 1098 |
|
|
} |
| 1099 |
|
|
} |
| 1100 |
|
|
|
| 1101 |
|
|
|
| 1102 |
|
✗ |
void EigenProblemPOD::viewPOD(double* vToPrint, int vSize, std::string fName) { |
| 1103 |
|
|
int rankProc; |
| 1104 |
|
✗ |
MPI_Comm_rank(m_petscComm,&rankProc); |
| 1105 |
|
✗ |
if (rankProc == 0) { |
| 1106 |
|
✗ |
std::ofstream outStream(fName.c_str()); |
| 1107 |
|
✗ |
for(int i=0; i<vSize; i++) { |
| 1108 |
|
✗ |
outStream << vToPrint[i] << std::endl; |
| 1109 |
|
|
} |
| 1110 |
|
✗ |
outStream.close(); |
| 1111 |
|
|
} |
| 1112 |
|
|
} |
| 1113 |
|
|
|
| 1114 |
|
|
} |
| 1115 |
|
|
|