PhysicsBasedPreconditioner.C

Go to the documentation of this file.

//* This file is part of the MOOSE framework
//* https://www.mooseframework.org
//*
//* 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 "PhysicsBasedPreconditioner.h"
 
// MOOSE includes
#include "ComputeJacobianBlocksThread.h"
#include "FEProblem.h"
#include "MooseEnum.h"
#include "MooseVariableFE.h"
#include "NonlinearSystem.h"
#include "PetscSupport.h"
 
#include "libmesh/libmesh_common.h"
#include "libmesh/equation_systems.h"
#include "libmesh/nonlinear_implicit_system.h"
#include "libmesh/nonlinear_solver.h"
#include "libmesh/linear_implicit_system.h"
#include "libmesh/transient_system.h"
#include "libmesh/numeric_vector.h"
#include "libmesh/sparse_matrix.h"
#include "libmesh/string_to_enum.h"
#include "libmesh/coupling_matrix.h"
 
registerMooseObjectAliased("MooseApp", PhysicsBasedPreconditioner, "PBP");
 
defineLegacyParams(PhysicsBasedPreconditioner);
 
InputParameters
PhysicsBasedPreconditioner::validParams()
{
  InputParameters params = MoosePreconditioner::validParams();
 
  params.addRequiredParam<std::vector<std::string>>(
      "solve_order",
      "The order the block rows will be solved in.  Put the name of variables here "
      "to stand for solving that variable's block row.  A variable may appear more "
      "than once (to create cylces if you like).");
  params.addRequiredParam<std::vector<std::string>>("preconditioner", "TODO: docstring");
 
  params.addParam<std::vector<std::string>>(
      "off_diag_row",
      "The off diagonal row you want to add into the matrix, it will be associated "
      "with an off diagonal column from the same position in off_diag_colum.");
  params.addParam<std::vector<std::string>>("off_diag_column",
                                            "The off diagonal column you want to add into the "
                                            "matrix, it will be associated with an off diagonal "
                                            "row from the same position in off_diag_row.");
 
  return params;
}
 
PhysicsBasedPreconditioner::PhysicsBasedPreconditioner(const InputParameters & params)
  : MoosePreconditioner(params),
    Preconditioner<Number>(MoosePreconditioner::_communicator),
    _nl(_fe_problem.getNonlinearSystemBase()),
    _init_timer(registerTimedSection("init", 2)),
    _apply_timer(registerTimedSection("apply", 1))
{
  unsigned int num_systems = _nl.system().n_vars();
  _systems.resize(num_systems);
  _preconditioners.resize(num_systems);
  _off_diag.resize(num_systems);
  _off_diag_mats.resize(num_systems);
  _pre_type.resize(num_systems);
 
  { // Setup the Coupling Matrix so MOOSE knows what we're doing
    NonlinearSystemBase & nl = _fe_problem.getNonlinearSystemBase();
    unsigned int n_vars = nl.nVariables();
 
    // The coupling matrix is held and released by FEProblemBase, so it is not released in this
    // object
    std::unique_ptr<CouplingMatrix> cm = libmesh_make_unique<CouplingMatrix>(n_vars);
 
    bool full = false; // getParam<bool>("full"); // TODO: add a FULL option for PBP
 
    if (!full)
    {
      // put 1s on diagonal
      for (unsigned int i = 0; i < n_vars; i++)
        (*cm)(i, i) = 1;
 
      // off-diagonal entries
      std::vector<std::vector<unsigned int>> off_diag(n_vars);
      for (unsigned int i = 0; i < getParam<std::vector<std::string>>("off_diag_row").size(); i++)
      {
        unsigned int row =
            nl.getVariable(0, getParam<std::vector<std::string>>("off_diag_row")[i]).number();
        unsigned int column =
            nl.getVariable(0, getParam<std::vector<std::string>>("off_diag_column")[i]).number();
        (*cm)(row, column) = 1;
      }
 
      // TODO: handle coupling entries between NL-vars and SCALAR-vars
    }
    else
    {
      for (unsigned int i = 0; i < n_vars; i++)
        for (unsigned int j = 0; j < n_vars; j++)
          (*cm)(i, j) = 1;
    }
 
    _fe_problem.setCouplingMatrix(std::move(cm));
  }
 
  // PC types
  const std::vector<std::string> & pc_types = getParam<std::vector<std::string>>("preconditioner");
  for (unsigned int i = 0; i < num_systems; i++)
    _pre_type[i] = Utility::string_to_enum<PreconditionerType>(pc_types[i]);
 
  // solve order
  const std::vector<std::string> & solve_order = getParam<std::vector<std::string>>("solve_order");
  _solve_order.resize(solve_order.size());
  for (unsigned int i = 0; i < solve_order.size(); i++)
    _solve_order[i] = _nl.system().variable_number(solve_order[i]);
 
  // diag and off-diag systems
  unsigned int n_vars = _nl.system().n_vars();
 
  // off-diagonal entries
  const std::vector<std::string> & odr = getParam<std::vector<std::string>>("off_diag_row");
  const std::vector<std::string> & odc = getParam<std::vector<std::string>>("off_diag_column");
  std::vector<std::vector<unsigned int>> off_diag(n_vars);
  for (unsigned int i = 0; i < odr.size(); i++)
  {
    unsigned int row = _nl.system().variable_number(odr[i]);
    unsigned int column = _nl.system().variable_number(odc[i]);
    off_diag[row].push_back(column);
  }
  // Add all of the preconditioning systems
  for (unsigned int var = 0; var < n_vars; var++)
    addSystem(var, off_diag[var], _pre_type[var]);
 
  _nl.nonlinearSolver()->attach_preconditioner(this);
 
  if (_fe_problem.solverParams()._type != Moose::ST_JFNK)
    mooseError("PBP must be used with JFNK solve type");
}
 
PhysicsBasedPreconditioner::~PhysicsBasedPreconditioner() { this->clear(); }
 
void
PhysicsBasedPreconditioner::addSystem(unsigned int var,
                                      std::vector<unsigned int> off_diag,
                                      PreconditionerType type)
{
  std::string var_name = _nl.system().variable_name(var);
 
  LinearImplicitSystem & precond_system =
      _fe_problem.es().add_system<LinearImplicitSystem>(var_name + "_system");
  precond_system.assemble_before_solve = false;
 
  const std::set<SubdomainID> * active_subdomains = _nl.getVariableBlocks(var);
  precond_system.add_variable(
      var_name + "_prec", _nl.system().variable(var).type(), active_subdomains);
 
  _systems[var] = &precond_system;
  _pre_type[var] = type;
 
  _off_diag_mats[var].resize(off_diag.size());
  for (unsigned int i = 0; i < off_diag.size(); i++)
  {
    // Add the matrix to hold the off-diagonal piece
    _off_diag_mats[var][i] = &precond_system.add_matrix(_nl.system().variable_name(off_diag[i]));
  }
 
  _off_diag[var] = off_diag;
}
 
void
PhysicsBasedPreconditioner::init()
{
  TIME_SECTION(_init_timer);
 
  // Tell libMesh that this is initialized!
  _is_initialized = true;
 
  const unsigned int num_systems = _systems.size();
 
  // If no order was specified, just solve them in increasing order
  if (_solve_order.size() == 0)
  {
    _solve_order.resize(num_systems);
    for (unsigned int i = 0; i < num_systems; i++)
      _solve_order[i] = i;
  }
 
  // Loop over variables
  for (unsigned int system_var = 0; system_var < num_systems; system_var++)
  {
    LinearImplicitSystem & u_system = *_systems[system_var];
 
    if (!_preconditioners[system_var])
      _preconditioners[system_var] =
          Preconditioner<Number>::build_preconditioner(MoosePreconditioner::_communicator);
 
    // we have to explicitly set the matrix in the preconditioner, because h-adaptivity could have
    // changed it and we have to work with the current one
    Preconditioner<Number> * preconditioner = _preconditioners[system_var].get();
    preconditioner->set_matrix(*u_system.matrix);
    preconditioner->set_type(_pre_type[system_var]);
 
    preconditioner->init();
  }
}
 
void
PhysicsBasedPreconditioner::setup()
{
  const unsigned int num_systems = _systems.size();
 
  std::vector<JacobianBlock *> blocks;
 
  // Loop over variables
  for (unsigned int system_var = 0; system_var < num_systems; system_var++)
  {
    LinearImplicitSystem & u_system = *_systems[system_var];
 
    {
      JacobianBlock * block = new JacobianBlock(u_system, *u_system.matrix, system_var, system_var);
      blocks.push_back(block);
    }
 
    for (unsigned int diag = 0; diag < _off_diag[system_var].size(); diag++)
    {
      unsigned int coupled_var = _off_diag[system_var][diag];
      std::string coupled_name = _nl.system().variable_name(coupled_var);
 
      JacobianBlock * block =
          new JacobianBlock(u_system, *_off_diag_mats[system_var][diag], system_var, coupled_var);
      blocks.push_back(block);
    }
  }
 
  _fe_problem.computeJacobianBlocks(blocks);
 
  // cleanup
  for (auto & block : blocks)
    delete block;
}
 
void
PhysicsBasedPreconditioner::apply(const NumericVector<Number> & x, NumericVector<Number> & y)
{
  TIME_SECTION(_apply_timer);
 
  const unsigned int num_systems = _systems.size();
 
  MooseMesh & mesh = _fe_problem.mesh();
 
  // Zero out the solution vectors
  for (unsigned int sys = 0; sys < num_systems; sys++)
    _systems[sys]->solution->zero();
 
  // Loop over solve order
  for (unsigned int i = 0; i < _solve_order.size(); i++)
  {
    unsigned int system_var = _solve_order[i];
 
    LinearImplicitSystem & u_system = *_systems[system_var];
 
    // Copy rhs from the big system into the small one
    MoosePreconditioner::copyVarValues(
        mesh, _nl.system().number(), system_var, x, u_system.number(), 0, *u_system.rhs);
 
    // Modify the RHS by subtracting off the matvecs of the solutions for the other preconditioning
    // systems with the off diagonal blocks in this system.
    for (unsigned int diag = 0; diag < _off_diag[system_var].size(); diag++)
    {
      unsigned int coupled_var = _off_diag[system_var][diag];
      LinearImplicitSystem & coupled_system = *_systems[coupled_var];
      SparseMatrix<Number> & off_diag = *_off_diag_mats[system_var][diag];
      NumericVector<Number> & rhs = *u_system.rhs;
 
      // This next bit computes rhs -= A*coupled_solution
      // It does what it does because there is no vector_mult_sub()
      rhs.close();
      rhs.scale(-1.0);
      rhs.close();
      off_diag.vector_mult_add(rhs, *coupled_system.solution);
      rhs.close();
      rhs.scale(-1.0);
      rhs.close();
    }
 
    // Apply the preconditioner to the small system
    _preconditioners[system_var]->apply(*u_system.rhs, *u_system.solution);
 
    // Copy solution from small system into the big one
    // copyVarValues(mesh,system,0,*u_system.solution,0,system_var,y);
  }
 
  // Copy the solutions out
  for (unsigned int system_var = 0; system_var < num_systems; system_var++)
  {
    LinearImplicitSystem & u_system = *_systems[system_var];
 
    MoosePreconditioner::copyVarValues(
        mesh, u_system.number(), 0, *u_system.solution, _nl.system().number(), system_var, y);
  }
 
  y.close();
}
 
void
PhysicsBasedPreconditioner::clear()
{
}