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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: Julien Castelneau, Dominique Chapelle, Miguel Fernandez |
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// |
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// System includes |
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#include <stack> |
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// External includes |
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// Project includes |
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#include "linearProblemNSContinuation.hpp" |
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#include "Core/felisceTransient.hpp" |
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#include "FiniteElement/elementVector.hpp" |
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#include "FiniteElement/elementMatrix.hpp" |
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#include "InputOutput/io.hpp" |
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#include "DegreeOfFreedom/boundaryCondition.hpp" |
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/*! |
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\file linearProblemNSContinuation.cpp |
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\date 22/02/2022 |
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\brief Continuation method for FSI, monolithic |
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*/ |
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namespace felisce { |
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LinearProblemNSContinuation::LinearProblemNSContinuation(): |
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LinearProblem() |
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{ |
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m_useDataPreviousVelocity = true ; |
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m_previousVelocity = &m_oldVelocity; |
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m_aoPreviousVelocity = &m_ao; |
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m_dofPreviousVelocity = &m_dof; |
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} |
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void LinearProblemNSContinuation::setPreviousVelocity(PetscVector & previousVelocityCandidate, AO & aoPreviousVelocity, Dof & dofPreviousVelocity) |
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{ |
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m_previousVelocity = &previousVelocityCandidate; |
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m_aoPreviousVelocity = &aoPreviousVelocity; |
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m_dofPreviousVelocity = &dofPreviousVelocity; |
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m_useDataPreviousVelocity = false ; |
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} |
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void LinearProblemNSContinuation::readVelocityData(IO& io,double iteration) { |
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// Read velocity variable from the .case file |
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// store previous velocity from data |
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if(m_useDataPreviousVelocity) // validation |
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{ |
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if(iteration==0 || (m_velocityData.isNull()) ) |
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{ |
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m_oldVelocity.duplicateFrom(this->sequentialSolution()); |
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m_oldVelocity.set(0.); |
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}else{ |
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m_oldVelocity.copyFrom(m_velocityData); |
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} |
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} |
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if(iteration==0 || (m_velocityData.isNull()) ) |
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m_velocityData.duplicateFrom(this->sequentialSolution()); |
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std::vector<double> dataVelocity; |
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dataVelocity.resize(m_mesh[m_currentMesh]->numPoints()*3, 0.); |
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io.readVariable(0,iteration, dataVelocity.data(), dataVelocity.size()); |
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int dim = this->dimension(); |
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m_vectorVelocityData.resize(m_mesh[m_currentMesh]->numPoints()*dim, 0.); |
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for (int i=0; i < m_mesh[m_currentMesh]->numPoints(); ++i) { |
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for(int icomp=0; icomp<dim; icomp++) { |
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m_vectorVelocityData[dim*i+icomp]=dataVelocity[3*i+icomp]; |
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} |
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} |
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std::vector<PetscInt> ao_potData( m_vectorVelocityData.size()); |
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for (size_t i=0; i < m_vectorVelocityData.size(); ++i) { |
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ao_potData[i]=i; |
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} |
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AOApplicationToPetsc(this->ao(),m_vectorVelocityData.size(),ao_potData.data()); |
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VecSetValues(m_velocityData.toPetsc(),m_vectorVelocityData.size(),ao_potData.data(), m_vectorVelocityData.data(), INSERT_VALUES); |
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//m_velocityData.view(PETSC_VIEWER_STDOUT_SELF); |
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} |
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void LinearProblemNSContinuation::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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this->m_fstransient = fstransient; |
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std::vector<PhysicalVariable> listVariable; |
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std::vector<std::size_t> listNumComp; |
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// primal variables |
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listVariable.push_back(velocity); |
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listNumComp.push_back(this->dimension()); |
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listVariable.push_back(pressure); |
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listNumComp.push_back(1); |
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// dual variables with dummy names |
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listVariable.push_back(velocityDiv); |
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listNumComp.push_back(this->dimension()); |
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listVariable.push_back(potThorax); |
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listNumComp.push_back(1); |
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if(FelisceParam::instance(this->instanceIndex()).useALEformulation) |
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{ |
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listVariable.push_back(displacement); |
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listNumComp.push_back(this->dimension()); |
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} |
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//define unknown of the linear system. |
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m_listUnknown.push_back(velocity); |
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m_listUnknown.push_back(pressure); |
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m_listUnknown.push_back(velocityDiv); |
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m_listUnknown.push_back(potThorax); |
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userAddOtherUnknowns(listVariable,listNumComp); |
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userAddOtherVariables(listVariable,listNumComp); |
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definePhysicalVariable(listVariable,listNumComp); |
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m_iVelocity = m_listVariable.getVariableIdList(velocity); |
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m_iPressure = m_listVariable.getVariableIdList(pressure); |
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m_iVelocityDiv = m_listVariable.getVariableIdList(velocityDiv); |
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m_iPotThorax = m_listVariable.getVariableIdList(potThorax); |
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m_viscosity = FelisceParam::instance(this->instanceIndex()).viscosity; |
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m_useSymmetricStress = FelisceParam::instance(this->instanceIndex()).useSymmetricStress; |
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} |
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void LinearProblemNSContinuation::initPerElementType(ElementType eltType, FlagMatrixRHS flagMatrixRHS) { |
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IGNORE_UNUSED_ARGUMENT(eltType); |
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IGNORE_UNUSED_ARGUMENT(flagMatrixRHS); |
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m_feVel = m_listCurrentFiniteElement[m_iVelocity]; |
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m_fePres = m_listCurrentFiniteElement[m_iPressure]; |
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// for the convective term + ALE |
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m_elemFieldAdv.initialize(DOF_FIELD, *m_feVel, this->dimension()); |
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// define elemField to store the given velocity measurements and the source terms |
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m_dataTerm.initialize(DOF_FIELD, *m_feVel, this->dimension()); |
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m_sourceTerm.initialize(DOF_FIELD, *m_feVel, this->dimension()); |
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//========= |
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// ALE |
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//========= |
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if(FelisceParam::instance(this->instanceIndex()).useALEformulation) { |
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m_iDisplacement = m_listVariable.getVariableIdList(displacement); |
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m_elemFieldVelMesh.initialize(DOF_FIELD, *m_feVel, this->dimension()); |
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m_beta.initialize(DOF_FIELD, *m_feVel, this->dimension()); |
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numDofExtensionProblem = m_externalDof[0]->numDof(); |
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m_petscToGlobal1.resize(numDofExtensionProblem); |
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m_petscToGlobal2.resize(numDofExtensionProblem); |
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m_auxvec.resize(numDofExtensionProblem); |
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for (int i=0; i<numDofExtensionProblem; i++) { |
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m_petscToGlobal1[i]=i; |
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m_petscToGlobal2[i]=i; |
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} |
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AOApplicationToPetsc(m_externalAO[0],numDofExtensionProblem,m_petscToGlobal1.data()); |
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AOApplicationToPetsc(m_ao,numDofExtensionProblem,m_petscToGlobal2.data()); |
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} |
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} |
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void LinearProblemNSContinuation::computeElementArray(const std::vector<Point*>& elemPoint, const std::vector<felInt>& /*elemIdPoint*/, felInt& iel, FlagMatrixRHS flagMatrixRHS) { |
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m_feVel->updateFirstDeriv(0, elemPoint); |
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m_fePres->updateFirstDeriv(0, elemPoint); |
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double hK = m_feVel->diameter(); |
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// stabilization parameters |
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double gamma_M = FelisceParam::instance(this->instanceIndex()).referenceValue2; // data fidelity coefficient |
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double gamma_p = hK*hK*FelisceParam::instance(this->instanceIndex()).referenceValue3; // Brezzi-Pitkaranta coefficient |
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double gamma_p_star = FelisceParam::instance(this->instanceIndex()).referenceValue4; // dual pressure coefficient |
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double gamma_div = 0.1; |
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double gamma_u_star = 0.1; |
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// Luenberger parameter |
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double gamma_L = FelisceParam::instance(this->instanceIndex()).NS_gamma; |
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// time derivative coefficient |
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double rhof = FelisceParam::instance(this->instanceIndex()).density; |
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double coef_time = rhof/m_fstransient->timeStep; |
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// defining the block matrix of the system |
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if (flagMatrixRHS == FlagMatrixRHS::matrix_and_rhs || flagMatrixRHS == FlagMatrixRHS::only_matrix) { |
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/// div stabilizing term acting on u, int \nabla \cdot u \nabla \cdot v |
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m_elementMat[0]->div_phi_j_div_phi_i(gamma_div, *m_feVel, 0, 0, this->dimension()); // block (0,0) |
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// data term, int_\Omega uv. to this block we will also add the cip stabilization |
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m_elementMat[0]->phi_i_phi_j(gamma_M, *m_feVel, 0, 0, this->dimension()); // block (0,0) |
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// stabilizing term acting on p |
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m_elementMat[0]->grad_phi_i_grad_phi_j(gamma_p, *m_fePres, this->dimension(), this->dimension(), 1); // block (1,1) |
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// time discretization for z |
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m_elementMat[0]->phi_i_phi_j(coef_time, *m_feVel, 0, 1+this->dimension(), this->dimension()); // block (0,2) |
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// Stokes blocks for z and y, int_\Omega \epsilon v : \epsilon z or int_\Omega \nabla v : \nabla z |
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if (m_useSymmetricStress) |
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m_elementMat[0]->eps_phi_i_eps_phi_j(2*m_viscosity, *m_feVel, 0, 1+this->dimension(), this->dimension()); // block (0,2) |
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else |
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m_elementMat[0]->grad_phi_i_grad_phi_j(m_viscosity, *m_feVel, 0, 1+this->dimension(), this->dimension()); // block (0,2) |
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// \int y \nabla \cdot v and -\int q \nabla \cdot z |
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m_elementMat[0]->psi_j_div_phi_i(1., *m_feVel, *m_fePres, 0, 1+2*this->dimension()); // block (0,3) |
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m_elementMat[0]->psi_i_div_phi_j(-1., *m_feVel, *m_fePres, this->dimension(), 1+this->dimension()); // block (1,2) |
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// time discretization for u |
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m_elementMat[0]->phi_i_phi_j(coef_time, *m_feVel, 1+this->dimension(), 0, this->dimension()); // block (2,0) |
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// Stokes blocks for u and p, int_\Omega \epsilon u : \epsilon v or int_\Omega \nabla u : \nabla v |
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if (m_useSymmetricStress) |
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m_elementMat[0]->eps_phi_i_eps_phi_j(2*m_viscosity, *m_feVel, 1+this->dimension(), 0, this->dimension()); // block (2,0) |
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else |
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m_elementMat[0]->grad_phi_i_grad_phi_j(m_viscosity, *m_feVel, 1+this->dimension(), 0, this->dimension()); // block (2,0) |
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// -int p \nabla \cdot w and \int x \nabla \cdot u |
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m_elementMat[0]->psi_j_div_phi_i(-1., *m_feVel, *m_fePres, 1+this->dimension(), this->dimension()); // block (2,1) |
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m_elementMat[0]->psi_i_div_phi_j(1., *m_feVel, *m_fePres, 1+2*this->dimension(), 0); // block (3,0) |
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// stabilizing term acting on z, -int_\Omega grad z : grad w |
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m_elementMat[0]->grad_phi_i_grad_phi_j(-gamma_u_star, *m_feVel, 1+this->dimension(), 1+this->dimension(), this->dimension()); // block (2,2) |
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// stabilizing term acting on y, -int_\Omega y * x |
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m_elementMat[0]->phi_i_phi_j(-gamma_p_star, *m_fePres, 1+2*this->dimension(), 1+2*this->dimension(), 1); // block (3,3) |
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// ALE |
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if(FelisceParam::instance(this->instanceIndex()).useALEformulation) { |
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// m_elemFielVelMesh -> -w^{n} |
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m_elemFieldVelMesh.setValue(externalVec(0), *m_feVel, iel, m_iDisplacement, m_externalAO[0], *m_externalDof[0]); |
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// ALE term for u |
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m_elementMat[0]->div_u_phi_j_phi_i(rhof, m_elemFieldVelMesh, *m_feVel, 1+this->dimension(), 0, this->dimension()); // block (2,0) |
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// ALE term for z |
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m_elementMat[0]->div_u_phi_j_phi_i(rhof, m_elemFieldVelMesh, *m_feVel, 0, 1+this->dimension(), this->dimension()); // block (0,2) |
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m_beta.setValue(previousVelocity(), *m_feVel, iel, m_iVelocity, *m_aoPreviousVelocity, *m_dofPreviousVelocity); |
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// Construction of m_beta = u^{n-1} - w^{n}; Recall that externalVec(0) = - w^{n} |
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m_beta.get_val() = m_beta.get_val() + m_elemFieldVelMesh.get_val(); |
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if(FelisceParam::instance(this->instanceIndex()).NSequationFlag) { // for Navier-Stokes |
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// Temam's stabilization trick |
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m_elemFieldAdv.setValue(previousVelocity(), *m_feVel, iel, m_iVelocity, aoPreviousVelocity(), dofPreviousVelocity()); |
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m_elementMat[0]->div_u_phi_j_phi_i(0.5*rhof, m_elemFieldAdv, *m_feVel, 1+this->dimension(), 0, this->dimension()); // block (2,0) |
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m_elementMat[0]->div_u_phi_j_phi_i(0.5*rhof, m_elemFieldAdv, *m_feVel, 0, 1+this->dimension(), this->dimension()); // block (0,2) |
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//convective term for u |
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m_elementMat[0]->u_grad_phi_j_phi_i(rhof, m_beta, *m_feVel, 1+this->dimension(), 0, this->dimension()); // block (2,0) |
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//convective term for z |
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m_elementMat[0]->u_grad_phi_j_phi_i(rhof, m_beta, *m_feVel, 0, 1+this->dimension(), this->dimension(), true); // block (0,2) |
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} |
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else { // for Stokes |
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//convective ALE term for u |
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m_elementMat[0]->u_grad_phi_j_phi_i(rhof, m_elemFieldVelMesh, *m_feVel, 1+this->dimension(), 0, this->dimension()); // block (2,0) |
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//convective ALE term for z |
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m_elementMat[0]->u_grad_phi_j_phi_i(rhof, m_elemFieldVelMesh, *m_feVel, 0, 1+this->dimension(), this->dimension(), true); // block (0,2) |
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} |
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} |
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else { |
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if(FelisceParam::instance(this->instanceIndex()).NSequationFlag) { // for Navier-Stokes, no ALE |
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// Temam's stabilization trick |
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m_elemFieldAdv.setValue(previousVelocity(), *m_feVel, iel, m_iVelocity, aoPreviousVelocity(), dofPreviousVelocity()); |
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|
✗ |
m_elementMat[0]->div_u_phi_j_phi_i(0.5*rhof, m_elemFieldAdv, *m_feVel, 1+this->dimension(), 0, this->dimension()); // block (2,0) |
| 280 |
|
✗ |
m_elementMat[0]->div_u_phi_j_phi_i(0.5*rhof, m_elemFieldAdv, *m_feVel, 0, 1+this->dimension(), this->dimension()); // block (0,2) |
| 281 |
|
|
|
| 282 |
|
|
// linearized convective term |
| 283 |
|
✗ |
m_elementMat[0]->u_grad_phi_j_phi_i(rhof, m_elemFieldAdv, *m_feVel, 1+this->dimension(), 0, this->dimension()); // block (2,0) |
| 284 |
|
✗ |
m_elementMat[0]->u_grad_phi_j_phi_i(rhof, m_elemFieldAdv, *m_feVel, 0,1+this->dimension(),this->dimension(),true); // block (0,2) |
| 285 |
|
|
} |
| 286 |
|
|
} |
| 287 |
|
|
|
| 288 |
|
|
// Luenberger terms |
| 289 |
|
|
// int_\Omega v * z |
| 290 |
|
✗ |
m_elementMat[0]->phi_i_phi_j(gamma_L, *m_feVel, 0, 1+this->dimension(), this->dimension()); // block (0,2) |
| 291 |
|
|
// int_\Omega u * w |
| 292 |
|
✗ |
m_elementMat[0]->phi_i_phi_j(gamma_L, *m_feVel, 1+this->dimension(), 0, this->dimension()); // block (2,0) |
| 293 |
|
|
} |
| 294 |
|
|
|
| 295 |
|
|
// rhs terms in the current configuration |
| 296 |
|
✗ |
if (flagMatrixRHS == FlagMatrixRHS::matrix_and_rhs) { |
| 297 |
|
|
//rhs data terms, using the measurements |
| 298 |
|
✗ |
m_dataTerm.setValue(m_velocityData, *m_feVel, iel, m_iVelocity, m_ao, dof()); |
| 299 |
|
|
|
| 300 |
|
|
// gamma_M int_\Omega u_M * v |
| 301 |
|
✗ |
m_elementVector[0]->source(gamma_M, *m_feVel, m_dataTerm, 0, this->dimension()); |
| 302 |
|
|
|
| 303 |
|
|
// gamma_L int_\Omega u_M * w |
| 304 |
|
✗ |
m_elementVector[0]->source(gamma_L, *m_feVel, m_dataTerm, 1+this->dimension(), this->dimension()); // Luenberger term |
| 305 |
|
|
} |
| 306 |
|
|
|
| 307 |
|
|
// rhs terms in the previous configuration |
| 308 |
|
✗ |
if (flagMatrixRHS == FlagMatrixRHS::only_rhs) { |
| 309 |
|
|
// rhof/tau int_\Omega u^{n-1} * w |
| 310 |
|
✗ |
m_sourceTerm.setValue(previousVelocity(), *m_feVel, iel, m_iVelocity, aoPreviousVelocity(), dofPreviousVelocity()); |
| 311 |
|
|
|
| 312 |
|
✗ |
m_elementVector[0]->source(coef_time, *m_feVel, m_sourceTerm, 1+this->dimension(), this->dimension()); |
| 313 |
|
|
// rhs f term, zero |
| 314 |
|
|
} |
| 315 |
|
|
} |
| 316 |
|
|
|
| 317 |
|
✗ |
void LinearProblemNSContinuation::userChangePattern(int numProc, int rankProc) { |
| 318 |
|
|
IGNORE_UNUSED_ARGUMENT(numProc); |
| 319 |
|
|
IGNORE_UNUSED_ARGUMENT(rankProc); |
| 320 |
|
|
// compute initial (uniform) repartition of dof on processes |
| 321 |
|
✗ |
felInt numDofByProc = m_numDof/MpiInfo::numProc(); |
| 322 |
|
✗ |
std::vector<felInt> numDofPerProc(MpiInfo::numProc()); |
| 323 |
|
✗ |
for(felInt i=0; i<MpiInfo::numProc(); ++i) { |
| 324 |
|
✗ |
if(i == MpiInfo::numProc() - 1) |
| 325 |
|
✗ |
numDofPerProc[i] = m_numDof - i*numDofByProc; |
| 326 |
|
|
else |
| 327 |
|
✗ |
numDofPerProc[i] = numDofByProc; |
| 328 |
|
|
} |
| 329 |
|
|
|
| 330 |
|
✗ |
felInt shiftDof = 0; |
| 331 |
|
✗ |
for(felInt i=0; i<MpiInfo::rankProc(); ++i) |
| 332 |
|
✗ |
shiftDof += numDofPerProc[i]; |
| 333 |
|
|
|
| 334 |
|
✗ |
std::vector<felInt> rankDof(m_numDof, -1); |
| 335 |
|
✗ |
for(felInt i=0; i<numDofPerProc[MpiInfo::rankProc()]; ++i) |
| 336 |
|
✗ |
rankDof[i + shiftDof] = MpiInfo::rankProc(); |
| 337 |
|
|
|
| 338 |
|
|
// build the edges or faces depending on the dimension (for the global mesh) |
| 339 |
|
|
// In this function, "faces" refers to either edges or faces. |
| 340 |
|
✗ |
if(dimension() == 2) |
| 341 |
|
✗ |
m_mesh[m_currentMesh]->buildEdges(); |
| 342 |
|
|
else |
| 343 |
|
✗ |
m_mesh[m_currentMesh]->buildFaces(); |
| 344 |
|
|
|
| 345 |
|
|
// variables |
| 346 |
|
|
GeometricMeshRegion::ElementType eltType, eltTypeOpp; |
| 347 |
|
|
felInt idVar1, idVar2; |
| 348 |
|
|
felInt node1, node2; |
| 349 |
|
|
felInt numFacesPerElement, numEltPerLabel; |
| 350 |
|
|
felInt ielSupport, jelSupport; |
| 351 |
|
|
felInt ielCurrentGeo, ielOppositeGeo; |
| 352 |
|
✗ |
std::vector<felInt> vecSupport, vecSupportOpposite; |
| 353 |
|
✗ |
std::vector<felInt> numElement(m_mesh[m_currentMesh]->m_numTypesOfElement, 0); |
| 354 |
|
✗ |
std::vector< std::set<felInt> > nodesNeighborhood(m_numDof); |
| 355 |
|
|
|
| 356 |
|
|
|
| 357 |
|
|
// zeroth loop on the unknown of the linear problem |
| 358 |
|
✗ |
for (size_t iUnknown1 = 0; iUnknown1 < m_listUnknown.size(); ++iUnknown1) { |
| 359 |
|
✗ |
idVar1 = m_listUnknown.idVariable(iUnknown1); |
| 360 |
|
|
|
| 361 |
|
✗ |
ielCurrentGeo = 0; |
| 362 |
|
|
|
| 363 |
|
|
// first loop on element type |
| 364 |
|
✗ |
for (size_t i=0; i<m_mesh[m_currentMesh]->bagElementTypeDomain().size(); ++i) { |
| 365 |
|
✗ |
eltType = m_mesh[m_currentMesh]->bagElementTypeDomain()[i]; |
| 366 |
|
✗ |
const GeoElement* geoEle = GeometricMeshRegion::eltEnumToFelNameGeoEle[eltType].second; |
| 367 |
|
✗ |
numElement[eltType] = 0; |
| 368 |
|
✗ |
numFacesPerElement = geoEle->numBdEle(); |
| 369 |
|
|
|
| 370 |
|
|
// second loop on region of the mesh. |
| 371 |
|
✗ |
for(GeometricMeshRegion::IntRefToBegEndIndex_type::const_iterator itRef =m_mesh[m_currentMesh]->intRefToBegEndMaps[eltType].begin(); itRef !=m_mesh[m_currentMesh]->intRefToBegEndMaps[eltType].end(); itRef++) { |
| 372 |
|
✗ |
numEltPerLabel = itRef->second.second; |
| 373 |
|
|
|
| 374 |
|
|
// Third loop on element |
| 375 |
|
✗ |
for (felInt iel = 0; iel < numEltPerLabel; iel++) { |
| 376 |
|
✗ |
m_supportDofUnknown[iUnknown1].getIdElementSupport(eltType, numElement[eltType], vecSupport); |
| 377 |
|
|
|
| 378 |
|
✗ |
for(size_t ielSup=0; ielSup<vecSupport.size(); ++ielSup) { |
| 379 |
|
✗ |
ielSupport = vecSupport[ielSup]; |
| 380 |
|
|
|
| 381 |
|
|
// for all support dof in this support element |
| 382 |
|
✗ |
for (felInt iSup = 0; iSup < m_supportDofUnknown[iUnknown1].getNumSupportDof(ielSupport); ++iSup) { |
| 383 |
|
|
// for all component of the unknown |
| 384 |
|
✗ |
for (size_t iComp = 0; iComp < m_listVariable[idVar1].numComponent(); iComp++) { |
| 385 |
|
|
// get the global id of the support dof |
| 386 |
|
✗ |
dof().loc2glob(ielSupport, iSup, idVar1, iComp, node1); |
| 387 |
|
|
|
| 388 |
|
|
// if this node is on this process |
| 389 |
|
✗ |
if(rankDof[node1] == MpiInfo::rankProc()) { |
| 390 |
|
|
// loop over the boundaries of the element |
| 391 |
|
✗ |
for(felInt iface=0; iface < numFacesPerElement; ++iface) { |
| 392 |
|
|
// check if this face is an inner face or a boundary |
| 393 |
|
✗ |
ielOppositeGeo = ielCurrentGeo; |
| 394 |
|
✗ |
eltTypeOpp = eltType; |
| 395 |
|
✗ |
bool isAnInnerFace =m_mesh[m_currentMesh]->getAdjElement(eltTypeOpp, ielOppositeGeo, iface); |
| 396 |
|
|
|
| 397 |
|
✗ |
if(isAnInnerFace) { |
| 398 |
|
|
// for all unknown |
| 399 |
|
✗ |
for (size_t iUnknown2 = 0; iUnknown2 < m_listUnknown.size(); ++iUnknown2) { |
| 400 |
|
✗ |
idVar2 = m_listUnknown.idVariable(iUnknown2); |
| 401 |
|
|
|
| 402 |
|
|
// get the support element of the opposite element |
| 403 |
|
✗ |
m_supportDofUnknown[iUnknown2].getIdElementSupport(ielOppositeGeo, vecSupportOpposite); |
| 404 |
|
|
|
| 405 |
|
|
// for all support element |
| 406 |
|
✗ |
for(size_t jelSup=0; jelSup<vecSupportOpposite.size(); ++jelSup) { |
| 407 |
|
✗ |
jelSupport = vecSupportOpposite[jelSup]; |
| 408 |
|
|
|
| 409 |
|
|
// for all support dof in this support element |
| 410 |
|
✗ |
for (felInt jSup = 0; jSup < m_supportDofUnknown[iUnknown2].getNumSupportDof(jelSupport); ++jSup) { |
| 411 |
|
|
|
| 412 |
|
|
// for all component of the second unknown |
| 413 |
|
✗ |
for (size_t jComp = 0; jComp < m_listVariable[idVar2].numComponent(); jComp++) { |
| 414 |
|
|
|
| 415 |
|
|
// If the two current components are connected |
| 416 |
|
✗ |
felInt iConnect = dof().getNumGlobComp(iUnknown1, iComp); |
| 417 |
|
✗ |
felInt jConnect = dof().getNumGlobComp(iUnknown2, jComp); |
| 418 |
|
✗ |
if (m_listUnknown.mask()(iConnect, jConnect) > 0) { |
| 419 |
|
|
// get the global id of the second support dof |
| 420 |
|
✗ |
dof().loc2glob(jelSupport, jSup, idVar2, jComp, node2); |
| 421 |
|
|
|
| 422 |
|
|
// remove diagonal term to define pattern and use it in Parmetis. |
| 423 |
|
|
// if the two global ids are different, they are neighboors |
| 424 |
|
✗ |
if(node1 != node2) |
| 425 |
|
✗ |
nodesNeighborhood[node1].insert(node2); |
| 426 |
|
|
} |
| 427 |
|
|
} |
| 428 |
|
|
} |
| 429 |
|
|
} |
| 430 |
|
|
} |
| 431 |
|
|
} |
| 432 |
|
|
} |
| 433 |
|
|
} |
| 434 |
|
|
} |
| 435 |
|
|
} |
| 436 |
|
|
} |
| 437 |
|
✗ |
++ielCurrentGeo; |
| 438 |
|
✗ |
++numElement[eltType]; |
| 439 |
|
|
} |
| 440 |
|
|
} |
| 441 |
|
|
} |
| 442 |
|
|
} |
| 443 |
|
|
|
| 444 |
|
|
// Store the pattern in CSR style |
| 445 |
|
✗ |
std::vector<felInt> iCSR, jCSR; |
| 446 |
|
✗ |
felInt dofSize = 0; |
| 447 |
|
✗ |
felInt cptDof = 0; |
| 448 |
|
|
felInt pos; |
| 449 |
|
|
|
| 450 |
|
✗ |
iCSR.resize(dof().pattern().numRows() + 1, 0); |
| 451 |
|
✗ |
for(size_t iNode=0; iNode<nodesNeighborhood.size(); ++iNode) |
| 452 |
|
✗ |
dofSize += nodesNeighborhood[iNode].size(); |
| 453 |
|
|
|
| 454 |
|
✗ |
jCSR.resize(dofSize, 0); |
| 455 |
|
✗ |
for(size_t iNode=0; iNode<nodesNeighborhood.size(); ++iNode) { |
| 456 |
|
✗ |
if(rankDof[iNode] == MpiInfo::rankProc()) { |
| 457 |
|
✗ |
iCSR[cptDof + 1] = iCSR[cptDof] + nodesNeighborhood[iNode].size(); |
| 458 |
|
✗ |
pos = 0; |
| 459 |
|
✗ |
for(std::set<felInt>::iterator it=nodesNeighborhood[iNode].begin(); it != nodesNeighborhood[iNode].end(); ++it) { |
| 460 |
|
✗ |
jCSR[iCSR[cptDof] + pos] = *it; |
| 461 |
|
✗ |
++pos; |
| 462 |
|
|
} |
| 463 |
|
✗ |
++cptDof; |
| 464 |
|
|
} |
| 465 |
|
|
} |
| 466 |
|
|
|
| 467 |
|
|
// Now, call merge pattern |
| 468 |
|
✗ |
dof().mergeGlobalPattern(iCSR, jCSR); |
| 469 |
|
|
//std::cout<<"After global merge"<<std::endl; |
| 470 |
|
|
//dof().pattern().print(1, std::cout); |
| 471 |
|
|
} |
| 472 |
|
|
|
| 473 |
|
|
// compared to the function linearProblemNS::assembleFaceOrientedStabilization, here we use different blocks and only the jumps in the velocity |
| 474 |
|
✗ |
void LinearProblemNSContinuation::assembleCIPStabilization() { |
| 475 |
|
|
// definition of variables |
| 476 |
|
✗ |
std::pair<bool, GeometricMeshRegion::ElementType> adjElt; |
| 477 |
|
|
GeometricMeshRegion::ElementType eltType; // Type of element |
| 478 |
|
|
|
| 479 |
|
✗ |
felInt ielCurrentLocalGeo = 0; // local geometric id of the current element |
| 480 |
|
✗ |
felInt ielCurrentGlobalGeo = 0; // global geometric id of the current element |
| 481 |
|
✗ |
felInt ielOppositeGlobalGeo = 0; // global geometric id of the opposite element |
| 482 |
|
|
felInt numFacesPerType; // number of faces of an element of a given type |
| 483 |
|
|
felInt numPointPerElt; // number of vertices by element |
| 484 |
|
|
felInt ielCurrentGlobalSup; // global support element id of the current element |
| 485 |
|
|
felInt ielOppositeGlobalSup; // global support element id of the opposite element |
| 486 |
|
|
|
| 487 |
|
✗ |
std::vector<felInt> idOfFacesCurrent; // ids of the current element edges |
| 488 |
|
✗ |
std::vector<felInt> idOfFacesOpposite; // ids of the opposite element edges |
| 489 |
|
✗ |
std::vector<felInt> currentElemIdPoint; // ids of the vertices of the current element |
| 490 |
|
✗ |
std::vector<felInt> oppositeElemIdPoint; // ids of the vertices of the opposite element |
| 491 |
|
✗ |
std::vector<Point*> currentElemPoint; // point coordinates of the current element vertices |
| 492 |
|
✗ |
std::vector<Point*> oppositeElemPoint; // point coordinates of the opposite element vertices |
| 493 |
|
|
|
| 494 |
|
✗ |
FlagMatrixRHS flag = FlagMatrixRHS::only_matrix; // flag to only assemble the matrix |
| 495 |
|
|
felInt idFaceToDo; |
| 496 |
|
✗ |
bool allDone = false; |
| 497 |
|
|
|
| 498 |
|
✗ |
ElementField elemFieldAdvFace; |
| 499 |
|
|
|
| 500 |
|
|
felInt rank; |
| 501 |
|
✗ |
MPI_Comm_rank(PETSC_COMM_WORLD, &rank); |
| 502 |
|
|
|
| 503 |
|
|
// bag element type vector |
| 504 |
|
✗ |
const std::vector<ElementType>& bagElementTypeDomain = m_meshLocal[m_currentMesh]->bagElementTypeDomain(); |
| 505 |
|
✗ |
eltType = bagElementTypeDomain[0]; |
| 506 |
|
|
|
| 507 |
|
|
|
| 508 |
|
|
// Finite Element With Bd for the opposite element |
| 509 |
|
|
CurrentFiniteElementWithBd* ptmp; |
| 510 |
|
|
CurrentFiniteElementWithBd* oppositeFEWithBd; |
| 511 |
|
|
|
| 512 |
|
✗ |
m_velocity = &m_listVariable[m_listVariable.getVariableIdList(velocity)]; |
| 513 |
|
|
|
| 514 |
|
✗ |
const GeoElement *geoEle = m_mesh[m_currentMesh]->eltEnumToFelNameGeoEle[eltType].second; |
| 515 |
|
✗ |
felInt typeOfFEVel = m_velocity->finiteElementType(); |
| 516 |
|
|
|
| 517 |
|
✗ |
const RefElement *refEleVel = geoEle->defineFiniteEle(eltType, typeOfFEVel, *m_mesh[m_currentMesh]); |
| 518 |
|
✗ |
oppositeFEWithBd = new CurrentFiniteElementWithBd(*refEleVel, *geoEle, m_velocity->degreeOfExactness(), m_velocity->degreeOfExactness()); |
| 519 |
|
|
|
| 520 |
|
|
// initializing variables |
| 521 |
|
✗ |
numPointPerElt = m_meshLocal[m_currentMesh]->m_numPointsPerElt[eltType]; |
| 522 |
|
✗ |
numFacesPerType = GeometricMeshRegion::eltEnumToFelNameGeoEle[eltType].second->numBdEle(); |
| 523 |
|
|
|
| 524 |
|
|
// resize of vectors |
| 525 |
|
✗ |
idOfFacesCurrent.resize(numFacesPerType, -1); |
| 526 |
|
✗ |
idOfFacesOpposite.resize(numFacesPerType, -1); |
| 527 |
|
✗ |
currentElemIdPoint.resize(numPointPerElt, -1); |
| 528 |
|
✗ |
oppositeElemIdPoint.resize(numPointPerElt, -1); |
| 529 |
|
✗ |
currentElemPoint.resize(numPointPerElt, NULL); |
| 530 |
|
✗ |
oppositeElemPoint.resize(numPointPerElt, NULL); |
| 531 |
|
|
|
| 532 |
|
|
// define finite element |
| 533 |
|
✗ |
defineFiniteElement(eltType); |
| 534 |
|
✗ |
initElementArray(); |
| 535 |
|
✗ |
defineCurrentFiniteElementWithBd(eltType); |
| 536 |
|
|
|
| 537 |
|
|
// allocate arrays for assembling the matrix |
| 538 |
|
✗ |
allocateArrayForAssembleMatrixRHS(flag); |
| 539 |
|
|
|
| 540 |
|
|
// init variables |
| 541 |
|
✗ |
initPerElementType(eltType, flag); |
| 542 |
|
✗ |
CurrentFiniteElementWithBd* feWithBd = m_listCurrentFiniteElementWithBd[m_iVelocity]; |
| 543 |
|
|
|
| 544 |
|
✗ |
CurrentFiniteElementWithBd* firstCurrentFe = feWithBd; |
| 545 |
|
✗ |
CurrentFiniteElementWithBd* firstOppositeFe = oppositeFEWithBd; |
| 546 |
|
|
|
| 547 |
|
|
// get informations on the current element |
| 548 |
|
✗ |
setElemPoint(eltType, 0, currentElemPoint, currentElemIdPoint, &ielCurrentGlobalSup); |
| 549 |
|
|
|
| 550 |
|
|
// update the finite elements |
| 551 |
|
✗ |
feWithBd->updateFirstDeriv(0, currentElemPoint); |
| 552 |
|
✗ |
feWithBd->updateBdMeasNormal(); |
| 553 |
|
|
|
| 554 |
|
|
// get the global id of the first geometric element |
| 555 |
|
✗ |
ISLocalToGlobalMappingApply(m_mappingElem[m_currentMesh], 1, &ielCurrentLocalGeo, &ielCurrentGlobalGeo); |
| 556 |
|
|
|
| 557 |
|
|
// the map to remember what contribution have already been computed |
| 558 |
|
✗ |
std::map<felInt, std::vector<bool> > contribDone; |
| 559 |
|
✗ |
addNewFaceOrientedContributor(numFacesPerType, ielCurrentGlobalGeo, contribDone[ielCurrentGlobalGeo]); |
| 560 |
|
|
|
| 561 |
|
|
// build the stack to know what is the next element |
| 562 |
|
✗ |
std::stack<felInt> nextInStack; |
| 563 |
|
✗ |
nextInStack.push(ielCurrentGlobalGeo); |
| 564 |
|
|
|
| 565 |
|
|
// get all the faces of the element |
| 566 |
|
✗ |
if(dimension() == 2) |
| 567 |
|
✗ |
m_mesh[m_currentMesh]->getAllEdgeOfElement(ielCurrentGlobalGeo, idOfFacesCurrent); |
| 568 |
|
|
else |
| 569 |
|
✗ |
m_mesh[m_currentMesh]->getAllFaceOfElement(ielCurrentGlobalGeo, idOfFacesCurrent); |
| 570 |
|
|
|
| 571 |
|
|
// loop over all the element (snake style) |
| 572 |
|
✗ |
while(!nextInStack.empty()) { |
| 573 |
|
|
// check the faces and use the first one that is an inner face and that has not been done yet. |
| 574 |
|
✗ |
idFaceToDo = -1; |
| 575 |
|
✗ |
allDone = true; |
| 576 |
|
✗ |
for(size_t iface=0; iface<contribDone[ielCurrentGlobalGeo].size(); ++iface) { |
| 577 |
|
✗ |
if(!contribDone[ielCurrentGlobalGeo][iface]) { |
| 578 |
|
|
// This is an inner face, check if the contribution has already been computed or not |
| 579 |
|
✗ |
if(idFaceToDo == -1) { |
| 580 |
|
✗ |
idFaceToDo = iface; |
| 581 |
|
|
} else { |
| 582 |
|
✗ |
allDone = false; |
| 583 |
|
|
} |
| 584 |
|
|
} |
| 585 |
|
|
} |
| 586 |
|
|
|
| 587 |
|
|
// update the stack |
| 588 |
|
✗ |
if(!allDone) |
| 589 |
|
✗ |
nextInStack.push(ielCurrentGlobalGeo); |
| 590 |
|
|
|
| 591 |
|
✗ |
if(nextInStack.top() == ielCurrentGlobalGeo && allDone) |
| 592 |
|
✗ |
nextInStack.pop(); |
| 593 |
|
|
|
| 594 |
|
|
|
| 595 |
|
|
// assemble terms |
| 596 |
|
✗ |
if(idFaceToDo != -1) { |
| 597 |
|
|
// get the opposite id of the element |
| 598 |
|
✗ |
ielOppositeGlobalGeo = ielCurrentGlobalGeo; |
| 599 |
|
✗ |
adjElt =m_mesh[m_currentMesh]->getAdjElement(ielOppositeGlobalGeo, idFaceToDo); |
| 600 |
|
|
|
| 601 |
|
|
// get the type of the opposite element |
| 602 |
|
|
// eltTypeOpp = adjElt.second; |
| 603 |
|
|
|
| 604 |
|
|
// update the opposite finite element and set ielOppositeGlobalSup |
| 605 |
|
✗ |
updateFaceOrientedFEWithBd(oppositeFEWithBd, idOfFacesOpposite, numPointPerElt, ielOppositeGlobalGeo, ielOppositeGlobalSup); |
| 606 |
|
|
|
| 607 |
|
|
// find the local id of the edge in the opposite element |
| 608 |
|
✗ |
felInt localIdFaceOpposite = -1; |
| 609 |
|
✗ |
for(size_t jface=0; jface<idOfFacesOpposite.size(); ++jface) { |
| 610 |
|
✗ |
if(idOfFacesCurrent[idFaceToDo] == idOfFacesOpposite[jface]) { |
| 611 |
|
✗ |
localIdFaceOpposite = jface; |
| 612 |
|
|
} |
| 613 |
|
|
} |
| 614 |
|
|
|
| 615 |
|
|
// compute coefficients |
| 616 |
|
✗ |
CurvilinearFiniteElement* curvFe = &feWithBd->bdEle(idFaceToDo); |
| 617 |
|
|
//CurvilinearFiniteElement* curvFeOP = &oppositeFEWithBd->bdEle(localIdFaceOpposite); |
| 618 |
|
✗ |
double hK = curvFe->diameter(); //0.5 * (feWithBd->diameter() + oppositeFEWithBd->diameter()); |
| 619 |
|
|
//cout << hK - curvFeOP->diameter() << endl; |
| 620 |
|
✗ |
double gamma_u = FelisceParam::instance(this->instanceIndex()).referenceValue1; // cip coefficient |
| 621 |
|
✗ |
double gamma = hK*gamma_u; |
| 622 |
|
|
|
| 623 |
|
|
// We can now compute all the integrals. |
| 624 |
|
|
// current element for phi_i and phi_j |
| 625 |
|
✗ |
m_elementMat[0]->zero(); |
| 626 |
|
✗ |
m_elementMat[0]->grad_phi_j_dot_n_grad_psi_i_dot_n(gamma, *feWithBd, *feWithBd, idFaceToDo, idFaceToDo, 0, 0, this->dimension()); // block (0,0) |
| 627 |
|
✗ |
setValueMatrixRHS(ielCurrentGlobalSup, ielCurrentGlobalSup, flag); |
| 628 |
|
|
|
| 629 |
|
|
// current element for phi_i and opposite element for phi_j |
| 630 |
|
✗ |
m_elementMat[0]->zero(); |
| 631 |
|
✗ |
m_elementMat[0]->grad_phi_j_dot_n_grad_psi_i_dot_n(gamma, *oppositeFEWithBd, *feWithBd, localIdFaceOpposite, idFaceToDo, 0, 0, this->dimension()); // block (0,0) |
| 632 |
|
✗ |
setValueMatrixRHS(ielCurrentGlobalSup, ielOppositeGlobalSup, flag); |
| 633 |
|
|
|
| 634 |
|
|
// opposite element for phi_i and current element for phi_j |
| 635 |
|
✗ |
m_elementMat[0]->zero(); |
| 636 |
|
✗ |
m_elementMat[0]->grad_phi_j_dot_n_grad_psi_i_dot_n(gamma, *feWithBd, *oppositeFEWithBd, idFaceToDo, localIdFaceOpposite, 0, 0, this->dimension()); // block (0,0) |
| 637 |
|
✗ |
setValueMatrixRHS(ielOppositeGlobalSup, ielCurrentGlobalSup, flag); |
| 638 |
|
|
|
| 639 |
|
|
// opposite element for phi_i and phi_j |
| 640 |
|
✗ |
m_elementMat[0]->zero(); |
| 641 |
|
✗ |
m_elementMat[0]->grad_phi_j_dot_n_grad_psi_i_dot_n(gamma, *oppositeFEWithBd, *oppositeFEWithBd, localIdFaceOpposite, localIdFaceOpposite, 0, 0, this->dimension()); // block (0,0) |
| 642 |
|
✗ |
setValueMatrixRHS(ielOppositeGlobalSup, ielOppositeGlobalSup, flag); |
| 643 |
|
|
|
| 644 |
|
|
// update the map to say that this face is done |
| 645 |
|
✗ |
contribDone[ielCurrentGlobalGeo][idFaceToDo] = true; |
| 646 |
|
|
|
| 647 |
|
|
// check if the opposite element is on this proc |
| 648 |
|
✗ |
if(m_eltPart[m_currentMesh][ielOppositeGlobalGeo] == rank) { |
| 649 |
|
✗ |
if(contribDone.find(ielOppositeGlobalGeo) == contribDone.end()) { |
| 650 |
|
|
// not found in the map, add it and initialize it. |
| 651 |
|
✗ |
addNewFaceOrientedContributor(numFacesPerType, ielOppositeGlobalGeo, contribDone[ielOppositeGlobalGeo]); |
| 652 |
|
|
} |
| 653 |
|
✗ |
contribDone[ielOppositeGlobalGeo][localIdFaceOpposite] = true; |
| 654 |
|
|
|
| 655 |
|
|
// update the finite element as the opposite finite element. |
| 656 |
|
✗ |
ptmp = feWithBd; |
| 657 |
|
✗ |
feWithBd = oppositeFEWithBd; |
| 658 |
|
✗ |
oppositeFEWithBd = ptmp; |
| 659 |
|
|
|
| 660 |
|
✗ |
ielCurrentGlobalGeo = ielOppositeGlobalGeo; |
| 661 |
|
✗ |
ielCurrentGlobalSup = ielOppositeGlobalSup; |
| 662 |
|
✗ |
idOfFacesCurrent = idOfFacesOpposite; |
| 663 |
|
|
} |
| 664 |
|
|
else { |
| 665 |
|
|
// not on this rank, take the next one in the stack |
| 666 |
|
✗ |
if(!nextInStack.empty()) { |
| 667 |
|
✗ |
ielCurrentGlobalGeo = nextInStack.top(); |
| 668 |
|
✗ |
updateFaceOrientedFEWithBd(feWithBd, idOfFacesCurrent, numPointPerElt, ielCurrentGlobalGeo, ielCurrentGlobalSup); |
| 669 |
|
|
} |
| 670 |
|
|
} |
| 671 |
|
|
} |
| 672 |
|
|
else { |
| 673 |
|
|
// All contribution have been already computed on this element |
| 674 |
|
|
// take the next element in the stack |
| 675 |
|
✗ |
if(!nextInStack.empty()) { |
| 676 |
|
✗ |
ielCurrentGlobalGeo = nextInStack.top(); |
| 677 |
|
✗ |
updateFaceOrientedFEWithBd(feWithBd, idOfFacesCurrent, numPointPerElt, ielCurrentGlobalGeo, ielCurrentGlobalSup); |
| 678 |
|
|
} |
| 679 |
|
|
} |
| 680 |
|
|
} |
| 681 |
|
|
|
| 682 |
|
|
// desallocate array use for assemble with petsc. |
| 683 |
|
✗ |
desallocateArrayForAssembleMatrixRHS(flag); |
| 684 |
|
|
|
| 685 |
|
|
// desallocate opposite finite elements |
| 686 |
|
✗ |
feWithBd = firstCurrentFe; |
| 687 |
|
✗ |
delete firstOppositeFe; |
| 688 |
|
|
} |
| 689 |
|
|
|
| 690 |
|
✗ |
void LinearProblemNSContinuation::addNewFaceOrientedContributor(felInt size, felInt idElt, std::vector<bool>& vec) { |
| 691 |
|
|
felInt ielTmp; |
| 692 |
|
✗ |
std::pair<bool, GeometricMeshRegion::ElementType> adjElt; |
| 693 |
|
|
|
| 694 |
|
✗ |
vec.resize(size, false); |
| 695 |
|
✗ |
for(felInt iface=0; iface<size; ++iface) { |
| 696 |
|
|
// check if this face is an inner face or a boundary |
| 697 |
|
✗ |
ielTmp = idElt; |
| 698 |
|
✗ |
adjElt =m_mesh[m_currentMesh]->getAdjElement(ielTmp, iface); |
| 699 |
|
|
|
| 700 |
|
✗ |
if(!adjElt.first) { |
| 701 |
|
|
// not an inner face, set the contribution to done. |
| 702 |
|
✗ |
vec[iface] = true; |
| 703 |
|
|
} |
| 704 |
|
|
} |
| 705 |
|
|
} |
| 706 |
|
|
|
| 707 |
|
✗ |
void LinearProblemNSContinuation::updateFaceOrientedFEWithBd(CurrentFiniteElementWithBd* fe, std::vector<felInt>& idOfFaces, felInt numPoints, felInt idElt, felInt& idSup) { |
| 708 |
|
✗ |
std::vector<felInt> elemIdPoint(numPoints, -1); |
| 709 |
|
✗ |
std::vector<Point*> elemPoint(numPoints, NULL); |
| 710 |
|
|
|
| 711 |
|
|
// get information on the opposite element |
| 712 |
|
|
// same as the function "setElemPoint" but here ielOppositeGlobalGeo is global |
| 713 |
|
|
// we assume that the supportDofMesh is the same for all unknown (like in setElemPoint) |
| 714 |
|
✗ |
m_supportDofUnknown[0].getIdElementSupport(idElt, idSup); |
| 715 |
|
✗ |
m_mesh[m_currentMesh]->getOneElement(idElt, elemIdPoint); |
| 716 |
|
✗ |
for (felInt iPoint=0; iPoint<numPoints; ++iPoint) |
| 717 |
|
✗ |
elemPoint[iPoint] = &(m_mesh[m_currentMesh]->listPoints()[elemIdPoint[iPoint]]); |
| 718 |
|
|
|
| 719 |
|
|
// update the finite elements |
| 720 |
|
✗ |
fe->updateFirstDeriv(0, elemPoint); |
| 721 |
|
✗ |
fe->updateBdMeasNormal(); |
| 722 |
|
|
|
| 723 |
|
|
// get all the faces of the element |
| 724 |
|
✗ |
if(dimension() == 2) |
| 725 |
|
✗ |
m_mesh[m_currentMesh]->getAllEdgeOfElement(idElt, idOfFaces); |
| 726 |
|
|
else |
| 727 |
|
✗ |
m_mesh[m_currentMesh]->getAllFaceOfElement(idElt, idOfFaces); |
| 728 |
|
|
} |
| 729 |
|
|
} |
| 730 |
|
|
|