NonlinearEigenSystem.C

Go to the documentation of this file.

//* This file is part of the MOOSE framework
//* https://mooseframework.inl.gov
//*
//* All rights reserved, see COPYRIGHT for full restrictions
//* https://github.com/idaholab/moose/blob/master/COPYRIGHT
//*
//* Licensed under LGPL 2.1, please see LICENSE for details
//* https://www.gnu.org/licenses/lgpl-2.1.html
 
#include "NonlinearEigenSystem.h"
 
// MOOSE includes
#include "DirichletBC.h"
#include "EigenDirichletBC.h"
#include "ArrayDirichletBC.h"
#include "EigenArrayDirichletBC.h"
#include "EigenProblem.h"
#include "IntegratedBC.h"
#include "KernelBase.h"
#include "NodalBC.h"
#include "TimeIntegrator.h"
#include "SlepcSupport.h"
#include "DGKernelBase.h"
#include "ScalarKernelBase.h"
#include "MooseVariableScalar.h"
#include "ResidualObject.h"
 
#include "libmesh/libmesh_config.h"
#include "libmesh/petsc_matrix.h"
#include "libmesh/sparse_matrix.h"
#include "libmesh/diagonal_matrix.h"
#include "libmesh/petsc_shell_matrix.h"
#include "libmesh/petsc_solver_exception.h"
#include "libmesh/slepc_eigen_solver.h"
 
#ifdef LIBMESH_HAVE_SLEPC
 
namespace Moose
{
 
void
assemble_matrix(EquationSystems & es, const std::string & system_name)
{
  EigenProblem * p = es.parameters.get<EigenProblem *>("_eigen_problem");
  auto & eigen_system = es.get_system<libMesh::CondensedEigenSystem>(system_name);
  NonlinearEigenSystem & eigen_nl =
      p->getNonlinearEigenSystem(/*nl_sys_num=*/eigen_system.number());
 
  // If this is a nonlinear eigenvalue problem,
  // we do not need to assemble anything
  if (p->isNonlinearEigenvalueSolver(eigen_nl.number()))
  {
    // If you want an efficient eigensolver,
    // please use PETSc 3.13 or newer.
    // We need to do an unnecessary assembly,
    // if you use PETSc that is older than 3.13.
#if PETSC_RELEASE_LESS_THAN(3, 13, 0)
    if (eigen_system.has_matrix_B())
      p->computeJacobianTag(*eigen_system.current_local_solution,
                            eigen_system.get_matrix_B(),
                            eigen_nl.eigenMatrixTag());
#endif
    return;
  }
 
#if !PETSC_RELEASE_LESS_THAN(3, 13, 0)
  // If we use shell matrices and do not use a shell preconditioning matrix,
  // we only need to form a preconditioning matrix
  if (eigen_system.use_shell_matrices() && !eigen_system.use_shell_precond_matrix())
  {
    p->computeJacobianTag(*eigen_system.current_local_solution,
                          eigen_system.get_precond_matrix(),
                          eigen_nl.precondMatrixTag());
    return;
  }
#endif
  // If it is a linear generalized eigenvalue problem,
  // we assemble A and B together
  if (eigen_system.generalized())
  {
    p->computeJacobianAB(*eigen_system.current_local_solution,
                         eigen_system.get_matrix_A(),
                         eigen_system.get_matrix_B(),
                         eigen_nl.nonEigenMatrixTag(),
                         eigen_nl.eigenMatrixTag());
#if LIBMESH_HAVE_SLEPC
    if (p->negativeSignEigenKernel())
      LibmeshPetscCallA(
          p->comm().get(),
          MatScale(cast_ref<PetscMatrix<Number> &>(eigen_system.get_matrix_B()).mat(), -1.0));
#endif
    return;
  }
 
  // If it is a linear eigenvalue problem, we assemble matrix A
  {
    p->computeJacobianTag(*eigen_system.current_local_solution,
                          eigen_system.get_matrix_A(),
                          eigen_nl.nonEigenMatrixTag());
 
    return;
  }
}
}
 
NonlinearEigenSystem::NonlinearEigenSystem(EigenProblem & eigen_problem, const std::string & name)
  : NonlinearSystemBase(
        eigen_problem, eigen_problem.es().add_system<libMesh::CondensedEigenSystem>(name), name),
    _eigen_sys(eigen_problem.es().get_system<libMesh::CondensedEigenSystem>(name)),
    _eigen_problem(eigen_problem),
    _solver_configuration(nullptr),
    _n_eigen_pairs_required(eigen_problem.getNEigenPairsRequired()),
    _work_rhs_vector_AX(addVector("work_rhs_vector_Ax", false, PARALLEL)),
    _work_rhs_vector_BX(addVector("work_rhs_vector_Bx", false, PARALLEL)),
    _precond_matrix_includes_eigen(false),
    _preconditioner(nullptr),
    _num_constrained_dofs(0)
{
  libMesh::SlepcEigenSolver<Number> * solver =
      cast_ptr<libMesh::SlepcEigenSolver<Number> *>(_eigen_sys.eigen_solver.get());
 
  if (!solver)
    mooseError("A slepc eigen solver is required");
 
  // setup of our class @SlepcSolverConfiguration
  _solver_configuration =
      std::make_unique<SlepcEigenSolverConfiguration>(eigen_problem, *solver, *this);
 
  solver->set_solver_configuration(*_solver_configuration);
 
  _Ax_tag = eigen_problem.addVectorTag("Ax_tag");
 
  _Bx_tag = eigen_problem.addVectorTag("Eigen");
 
  _A_tag = eigen_problem.addMatrixTag("A_tag");
 
  _B_tag = eigen_problem.addMatrixTag("Eigen");
 
  // By default, _precond_tag and _A_tag will share the same
  // objects. If we want to include eigen contributions to
  // the preconditioning matrix, and then _precond_tag will
  // point to part of "B" objects
  _precond_tag = eigen_problem.addMatrixTag("Eigen_precond");
 
  // We do not rely on creating submatrices in the solve routine
  _eigen_sys.dont_create_submatrices_in_solve();
}
 
void
NonlinearEigenSystem::postAddResidualObject(ResidualObject & object)
{
  // If it is an eigen dirichlet boundary condition, we should skip it because their
  // contributions should be zero. If we do not skip it, preconditioning matrix will
  // be singular because boundary elements are zero.
  if (_precond_matrix_includes_eigen && !dynamic_cast<EigenDirichletBC *>(&object) &&
      !dynamic_cast<EigenArrayDirichletBC *>(&object))
    object.useMatrixTag(_precond_tag, {});
 
  auto & vtags = object.getVectorTags({});
  auto & mtags = object.getMatrixTags({});
 
  const bool eigen = (vtags.find(_Bx_tag) != vtags.end()) || (mtags.find(_B_tag) != mtags.end());
 
  if (eigen && !_eigen_sys.generalized())
    object.mooseError("This object has been marked as contributing to B or Bx but the eigen "
                      "problem type is not a generalized one");
 
  // If it is an eigen kernel, mark its variable as eigen
  if (eigen)
  {
    // Note: the object may be on the displaced system
    auto sys = object.parameters().get<SystemBase *>("_sys");
    auto vname = object.variable().name();
    if (hasScalarVariable(vname))
      sys->getScalarVariable(0, vname).eigen(true);
    else
      sys->getVariable(0, vname).eigen(true);
 
    // Associate the eigen matrix tag and the vector tag
    // if this is a eigen kernel
    object.useMatrixTag(_B_tag, {});
    object.useVectorTag(_Bx_tag, {});
  }
  else
  {
    // Noneigen Vector tag
    object.useVectorTag(_Ax_tag, {});
    // Noneigen Matrix tag
    object.useMatrixTag(_A_tag, {});
    // Noneigen Kernels
    object.useMatrixTag(_precond_tag, {});
  }
}
 
void
NonlinearEigenSystem::initializeCondensedMatrices()
{
  if (!(_num_constrained_dofs = dofMap().n_constrained_dofs()))
    return;
 
  _eigen_sys.initialize_condensed_dofs();
  const auto m = cast_int<numeric_index_type>(_eigen_sys.local_non_condensed_dofs_vector.size());
  auto M = m;
  _communicator.sum(M);
  if (_eigen_sys.has_condensed_matrix_A())
  {
    _eigen_sys.get_condensed_matrix_A().init(M, M, m, m);
    // A bit ludicrously MatCopy requires the matrix being copied to to be assembled
    _eigen_sys.get_condensed_matrix_A().close();
  }
  if (_eigen_sys.has_condensed_matrix_B())
  {
    _eigen_sys.get_condensed_matrix_B().init(M, M, m, m);
    _eigen_sys.get_condensed_matrix_B().close();
  }
  if (_eigen_sys.has_condensed_precond_matrix())
  {
    _eigen_sys.get_condensed_precond_matrix().init(M, M, m, m);
    _eigen_sys.get_condensed_precond_matrix().close();
  }
}
 
void
NonlinearEigenSystem::postInit()
{
  NonlinearSystemBase::postInit();
  initializeCondensedMatrices();
}
 
void
NonlinearEigenSystem::reinit()
{
  NonlinearSystemBase::reinit();
  initializeCondensedMatrices();
}
 
void
NonlinearEigenSystem::solve()
{
  const bool presolve_succeeded = preSolve();
  if (!presolve_succeeded)
    return;
 
  std::unique_ptr<NumericVector<Number>> subvec;
 
  // We apply initial guess for only nonlinear solver
  if (_eigen_problem.isNonlinearEigenvalueSolver(number()))
  {
    if (_num_constrained_dofs)
    {
      subvec = solution().get_subvector(_eigen_sys.local_non_condensed_dofs_vector);
      _eigen_sys.set_initial_space(*subvec);
    }
    else
      _eigen_sys.set_initial_space(solution());
  }
 
  const bool time_integrator_solve = std::any_of(_time_integrators.begin(),
                                                 _time_integrators.end(),
                                                 [](auto & ti) { return ti->overridesSolve(); });
  if (time_integrator_solve)
    mooseAssert(_time_integrators.size() == 1,
                "If solve is overridden, then there must be only one time integrator");
 
  if (time_integrator_solve)
    _time_integrators.front()->solve();
  else
    system().solve();
 
  for (auto & ti : _time_integrators)
  {
    if (!ti->overridesSolve())
      ti->setNumIterationsLastSolve();
    ti->postSolve();
  }
 
  // store solve information
  if (_eigen_problem.isNonlinearEigenvalueSolver(number()))
  {
    auto snes = getSNES();
 
    // nonlinear iterations
    PetscInt nl_its;
    LibmeshPetscCallA(_eigen_problem.comm().get(), SNESGetIterationNumber(snes, &nl_its));
    _n_iters = nl_its;
 
    // linear iterations
    PetscInt l_its;
    LibmeshPetscCallA(_eigen_problem.comm().get(), SNESGetLinearSolveIterations(snes, &l_its));
    _n_linear_iters = l_its;
 
    // final residual
    PetscReal norm;
    LibmeshPetscCall(SNESGetFunctionNorm(snes, &norm));
    _final_residual = norm;
  }
 
  // store eigenvalues
  unsigned int n_converged_eigenvalues = getNumConvergedEigenvalues();
 
  _n_eigen_pairs_required = _eigen_problem.getNEigenPairsRequired();
 
  if (_n_eigen_pairs_required < n_converged_eigenvalues)
    n_converged_eigenvalues = _n_eigen_pairs_required;
 
  _eigen_values.resize(n_converged_eigenvalues);
  for (unsigned int n = 0; n < n_converged_eigenvalues; n++)
    _eigen_values[n] = getConvergedEigenvalue(n);
 
  // Update the solution vector to the active eigenvector
  if (n_converged_eigenvalues)
    getConvergedEigenpair(_eigen_problem.activeEigenvalueIndex());
 
  if (_eigen_problem.isNonlinearEigenvalueSolver(number()) && _num_constrained_dofs)
    solution().restore_subvector(std::move(subvec), _eigen_sys.local_non_condensed_dofs_vector);
}
 
unsigned int
NonlinearEigenSystem::nNonlinearIterations() const
{
  if (!_time_integrators.empty())
    mooseError("Not implemented for time integrators.");
  if (!_eigen_problem.isNonlinearEigenvalueSolver(number()))
    mooseError("Only implemented for nonlinear eigenvalue solvers.");
 
  return _n_iters;
}
 
unsigned int
NonlinearEigenSystem::nLinearIterations() const
{
  if (!_time_integrators.empty())
    mooseError("Not implemented for time integrators.");
  if (!_eigen_problem.isNonlinearEigenvalueSolver(number()))
    mooseError("Only implemented for nonlinear eigenvalue solvers.");
 
  return _n_linear_iters;
}
 
Real
NonlinearEigenSystem::finalNonlinearResidual() const
{
  if (!_eigen_problem.isNonlinearEigenvalueSolver(number()))
    mooseError("Only implemented for nonlinear eigenvalue solvers.");
 
  return _final_residual;
}
 
void
NonlinearEigenSystem::attachSLEPcCallbacks()
{
  // Tell libmesh not to close matrices before solve
  _eigen_sys.get_eigen_solver().set_close_matrix_before_solve(false);
 
  if (_num_constrained_dofs)
  {
    // Condensed Matrix A
    if (_eigen_sys.has_condensed_matrix_A())
    {
      Mat mat = cast_ref<PetscMatrix<Number> &>(_eigen_sys.get_condensed_matrix_A()).mat();
 
      Moose::SlepcSupport::attachCallbacksToMat(_eigen_problem, mat, false);
    }
 
    // Condensed Matrix B
    if (_eigen_sys.has_condensed_matrix_B())
    {
      Mat mat = cast_ref<PetscMatrix<Number> &>(_eigen_sys.get_condensed_matrix_B()).mat();
 
      Moose::SlepcSupport::attachCallbacksToMat(_eigen_problem, mat, true);
    }
 
    // Condensed Preconditioning matrix
    if (_eigen_sys.has_condensed_precond_matrix())
    {
      Mat mat = cast_ref<PetscMatrix<Number> &>(_eigen_sys.get_condensed_precond_matrix()).mat();
 
      Moose::SlepcSupport::attachCallbacksToMat(_eigen_problem, mat, true);
    }
  }
  else
  {
    // Matrix A
    if (_eigen_sys.has_matrix_A())
    {
      Mat mat = cast_ref<PetscMatrix<Number> &>(_eigen_sys.get_matrix_A()).mat();
 
      Moose::SlepcSupport::attachCallbacksToMat(_eigen_problem, mat, false);
    }
 
    // Matrix B
    if (_eigen_sys.has_matrix_B())
    {
      Mat mat = cast_ref<PetscMatrix<Number> &>(_eigen_sys.get_matrix_B()).mat();
 
      Moose::SlepcSupport::attachCallbacksToMat(_eigen_problem, mat, true);
    }
 
    // Preconditioning matrix
    if (_eigen_sys.has_precond_matrix())
    {
      Mat mat = cast_ref<PetscMatrix<Number> &>(_eigen_sys.get_precond_matrix()).mat();
 
      Moose::SlepcSupport::attachCallbacksToMat(_eigen_problem, mat, true);
    }
  }
 
  // Shell matrix A
  if (_eigen_sys.has_shell_matrix_A())
  {
    Mat mat = cast_ref<libMesh::PetscShellMatrix<Number> &>(_eigen_sys.get_shell_matrix_A()).mat();
 
    // Attach callbacks for nonlinear eigenvalue solver
    Moose::SlepcSupport::attachCallbacksToMat(_eigen_problem, mat, false);
 
    // Set MatMult operations for shell
    Moose::SlepcSupport::setOperationsForShellMat(_eigen_problem, mat, false);
  }
 
  // Shell matrix B
  if (_eigen_sys.has_shell_matrix_B())
  {
    Mat mat = cast_ref<libMesh::PetscShellMatrix<Number> &>(_eigen_sys.get_shell_matrix_B()).mat();
 
    Moose::SlepcSupport::attachCallbacksToMat(_eigen_problem, mat, true);
 
    // Set MatMult operations for shell
    Moose::SlepcSupport::setOperationsForShellMat(_eigen_problem, mat, true);
  }
 
  // Shell preconditioning matrix
  if (_eigen_sys.has_shell_precond_matrix())
  {
    Mat mat =
        cast_ref<libMesh::PetscShellMatrix<Number> &>(_eigen_sys.get_shell_precond_matrix()).mat();
 
    Moose::SlepcSupport::attachCallbacksToMat(_eigen_problem, mat, true);
  }
}
 
void
NonlinearEigenSystem::stopSolve(const ExecFlagType &, const std::set<TagID> &)
{
  mooseError("did not implement yet \n");
}
 
void
NonlinearEigenSystem::setupFiniteDifferencedPreconditioner()
{
  mooseError("did not implement yet \n");
}
 
bool
NonlinearEigenSystem::converged()
{
  return _eigen_sys.get_n_converged();
}
 
unsigned int
NonlinearEigenSystem::getCurrentNonlinearIterationNumber()
{
  mooseError("did not implement yet \n");
  return 0;
}
 
NumericVector<Number> &
NonlinearEigenSystem::RHS()
{
  return _work_rhs_vector_BX;
}
 
NumericVector<Number> &
NonlinearEigenSystem::residualVectorAX()
{
  return _work_rhs_vector_AX;
}
 
NumericVector<Number> &
NonlinearEigenSystem::residualVectorBX()
{
  return _work_rhs_vector_BX;
}
 
libMesh::NonlinearSolver<Number> *
NonlinearEigenSystem::nonlinearSolver()
{
  mooseError("did not implement yet \n");
  return NULL;
}
 
SNES
NonlinearEigenSystem::getSNES()
{
  EPS eps = getEPS();
 
  if (_eigen_problem.isNonlinearEigenvalueSolver(number()))
  {
    SNES snes = nullptr;
    LibmeshPetscCall(Moose::SlepcSupport::mooseSlepcEPSGetSNES(eps, &snes));
    return snes;
  }
  else
    mooseError("There is no SNES in linear eigen solver");
}
 
EPS
NonlinearEigenSystem::getEPS()
{
  libMesh::SlepcEigenSolver<Number> * solver =
      cast_ptr<libMesh::SlepcEigenSolver<Number> *>(&(*_eigen_sys.eigen_solver));
 
  if (!solver)
    mooseError("Unable to retrieve eigen solver");
 
  return solver->eps();
}
 
void
NonlinearEigenSystem::checkIntegrity()
{
  if (_nodal_bcs.hasActiveObjects())
  {
    const auto & nodal_bcs = _nodal_bcs.getActiveObjects();
    for (const auto & nodal_bc : nodal_bcs)
    {
      // If this is a dirichlet boundary condition
      auto nbc = std::dynamic_pointer_cast<DirichletBC>(nodal_bc);
      // If this is a eigen Dirichlet boundary condition
      auto eigen_nbc = std::dynamic_pointer_cast<EigenDirichletBC>(nodal_bc);
      // ArrayDirichletBC
      auto anbc = std::dynamic_pointer_cast<ArrayDirichletBC>(nodal_bc);
      // EigenArrayDirichletBC
      auto aeigen_nbc = std::dynamic_pointer_cast<EigenArrayDirichletBC>(nodal_bc);
      // If it is a Dirichlet boundary condition, then value has to be zero
      if (nbc && nbc->variable().eigen() && nbc->getParam<Real>("value"))
        mooseError(
            "Can't set an inhomogeneous Dirichlet boundary condition for eigenvalue problems.");
      // If it is an array Dirichlet boundary condition, all values should be zero
      else if (anbc)
      {
        auto & values = anbc->getParam<RealEigenVector>("values");
        for (MooseIndex(values) i = 0; i < values.size(); i++)
        {
          if (values(i))
            mooseError("Can't set an inhomogeneous array Dirichlet boundary condition for "
                       "eigenvalue problems.");
        }
      }
      else if (!nbc && !eigen_nbc && !anbc && !aeigen_nbc)
        mooseError(
            "Invalid NodalBC for eigenvalue problems, please use homogeneous (array) Dirichlet.");
    }
  }
}
 
std::pair<Real, Real>
NonlinearEigenSystem::getConvergedEigenvalue(dof_id_type n) const
{
  unsigned int n_converged_eigenvalues = getNumConvergedEigenvalues();
  if (n >= n_converged_eigenvalues)
    mooseError(n, " not in [0, ", n_converged_eigenvalues, ")");
  return _eigen_sys.get_eigenvalue(n);
}
 
std::pair<Real, Real>
NonlinearEigenSystem::getConvergedEigenpair(dof_id_type n) const
{
  unsigned int n_converged_eigenvalues = getNumConvergedEigenvalues();
 
  if (n >= n_converged_eigenvalues)
    mooseError(n, " not in [0, ", n_converged_eigenvalues, ")");
 
  return _eigen_sys.get_eigenpair(n);
}
 
void
NonlinearEigenSystem::attachPreconditioner(Preconditioner<Number> * preconditioner)
{
  _preconditioner = preconditioner;
 
  // If we have a customized preconditioner,
  // We need to let PETSc know that
  if (_preconditioner)
  {
    LibmeshPetscCall(Moose::SlepcSupport::registerPCToPETSc());
    // Mark this, and then we can setup correct petsc options
    _eigen_problem.solverParams(number())._customized_pc_for_eigen = true;
    _eigen_problem.solverParams(number())._type = Moose::ST_JFNK;
  }
}
 
void
NonlinearEigenSystem::turnOffJacobian()
{
  // Let us do nothing at the current moment
}
 
void
NonlinearEigenSystem::residualAndJacobianTogether()
{
  mooseError(
      "NonlinearEigenSystem::residualAndJacobianTogether is not implemented. It might even be "
      "nonsensical. If it is sensical and you want this capability, please contact a MOOSE "
      "developer.");
}
 
void
NonlinearEigenSystem::computeScalingJacobian()
{
  _eigen_problem.computeJacobianTag(*_current_solution, *_scaling_matrix, precondMatrixTag());
}
 
void
NonlinearEigenSystem::computeScalingResidual()
{
  _eigen_problem.computeResidualTag(*_current_solution, RHS(), nonEigenVectorTag());
}
 
std::set<TagID>
NonlinearEigenSystem::defaultVectorTags() const
{
  auto tags = NonlinearSystemBase::defaultVectorTags();
  tags.insert(eigenVectorTag());
  tags.insert(nonEigenVectorTag());
  return tags;
}
 
std::set<TagID>
NonlinearEigenSystem::defaultMatrixTags() const
{
  auto tags = NonlinearSystemBase::defaultMatrixTags();
  tags.insert(eigenMatrixTag());
  tags.insert(nonEigenMatrixTag());
  return tags;
}
 
#else
 
NonlinearEigenSystem::NonlinearEigenSystem(EigenProblem & eigen_problem,
                                           const std::string & /*name*/)
  : libMesh::ParallelObject(eigen_problem)
{
  mooseError("Need to install SLEPc to solve eigenvalue problems, please reconfigure libMesh\n");
}
 
#endif /* LIBMESH_HAVE_SLEPC */