/
FEProblemBase.C
8337 lines (7096 loc) · 283 KB
/
FEProblemBase.C
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//* 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 "FEProblemBase.h"
#include "AuxiliarySystem.h"
#include "MaterialPropertyStorage.h"
#include "MooseEnum.h"
#include "Factory.h"
#include "MooseUtils.h"
#include "DisplacedProblem.h"
#include "SystemBase.h"
#include "MaterialData.h"
#include "ComputeUserObjectsThread.h"
#include "ComputeNodalUserObjectsThread.h"
#include "ComputeThreadedGeneralUserObjectsThread.h"
#include "ComputeMaterialsObjectThread.h"
#include "ProjectMaterialProperties.h"
#include "ComputeIndicatorThread.h"
#include "ComputeMarkerThread.h"
#include "ComputeInitialConditionThread.h"
#include "ComputeFVInitialConditionThread.h"
#include "ComputeBoundaryInitialConditionThread.h"
#include "MaxQpsThread.h"
#include "ActionWarehouse.h"
#include "Conversion.h"
#include "Material.h"
#include "FunctorMaterial.h"
#include "ConstantIC.h"
#include "Parser.h"
#include "ElementH1Error.h"
#include "Function.h"
#include "NonlinearSystem.h"
#include "Distribution.h"
#include "Sampler.h"
#include "PetscSupport.h"
#include "RandomInterface.h"
#include "RandomData.h"
#include "MooseEigenSystem.h"
#include "MooseParsedFunction.h"
#include "MeshChangedInterface.h"
#include "ComputeJacobianBlocksThread.h"
#include "ScalarInitialCondition.h"
#include "FVInitialConditionTempl.h"
#include "ElementPostprocessor.h"
#include "NodalPostprocessor.h"
#include "SidePostprocessor.h"
#include "InternalSidePostprocessor.h"
#include "InterfacePostprocessor.h"
#include "GeneralPostprocessor.h"
#include "ElementVectorPostprocessor.h"
#include "NodalVectorPostprocessor.h"
#include "SideVectorPostprocessor.h"
#include "InternalSideVectorPostprocessor.h"
#include "GeneralVectorPostprocessor.h"
#include "Positions.h"
#include "Indicator.h"
#include "Marker.h"
#include "MultiApp.h"
#include "MultiAppTransfer.h"
#include "TransientMultiApp.h"
#include "ElementUserObject.h"
#include "DomainUserObject.h"
#include "NodalUserObject.h"
#include "SideUserObject.h"
#include "InternalSideUserObject.h"
#include "InterfaceUserObject.h"
#include "GeneralUserObject.h"
#include "ThreadedGeneralUserObject.h"
#include "InternalSideIndicator.h"
#include "Transfer.h"
#include "MultiAppTransfer.h"
#include "MultiMooseEnum.h"
#include "Predictor.h"
#include "Assembly.h"
#include "Control.h"
#include "XFEMInterface.h"
#include "ConsoleUtils.h"
#include "NonlocalKernel.h"
#include "NonlocalIntegratedBC.h"
#include "ShapeElementUserObject.h"
#include "ShapeSideUserObject.h"
#include "MooseVariableFE.h"
#include "MooseVariableScalar.h"
#include "InputParameterWarehouse.h"
#include "TimeIntegrator.h"
#include "LineSearch.h"
#include "FloatingPointExceptionGuard.h"
#include "MaxVarNDofsPerElem.h"
#include "MaxVarNDofsPerNode.h"
#include "FVKernel.h"
#include "FVTimeKernel.h"
#include "MooseVariableFV.h"
#include "FVBoundaryCondition.h"
#include "FVInterfaceKernel.h"
#include "Reporter.h"
#include "ADUtils.h"
#include "Executioner.h"
#include "VariadicTable.h"
#include "BoundaryNodeIntegrityCheckThread.h"
#include "BoundaryElemIntegrityCheckThread.h"
#include "NodalBCBase.h"
#include "MortarUserObject.h"
#include "MortarUserObjectThread.h"
#include "RedistributeProperties.h"
#include "Checkpoint.h"
#include "libmesh/exodusII_io.h"
#include "libmesh/quadrature.h"
#include "libmesh/coupling_matrix.h"
#include "libmesh/nonlinear_solver.h"
#include "libmesh/sparse_matrix.h"
#include "libmesh/string_to_enum.h"
#include "libmesh/fe_interface.h"
#include "libmesh/enum_norm_type.h"
#include "metaphysicl/dualnumber.h"
// Anonymous namespace for helper function
namespace
{
/**
* Method for sorting the MooseVariableFEBases based on variable numbers
*/
bool
sortMooseVariables(const MooseVariableFEBase * a, const MooseVariableFEBase * b)
{
return a->number() < b->number();
}
} // namespace
Threads::spin_mutex get_function_mutex;
InputParameters
FEProblemBase::validParams()
{
InputParameters params = SubProblem::validParams();
params.addParam<unsigned int>("null_space_dimension", 0, "The dimension of the nullspace");
params.addParam<unsigned int>(
"transpose_null_space_dimension", 0, "The dimension of the transpose nullspace");
params.addParam<unsigned int>(
"near_null_space_dimension", 0, "The dimension of the near nullspace");
params.addParam<bool>("solve",
true,
"Whether or not to actually solve the Nonlinear system. "
"This is handy in the case that all you want to do is "
"execute AuxKernels, Transfers, etc. without actually "
"solving anything");
params.addParam<bool>("use_nonlinear",
true,
"Determines whether to use a Nonlinear vs a "
"Eigenvalue system (Automatically determined based "
"on executioner)");
params.addParam<bool>("error_on_jacobian_nonzero_reallocation",
"This causes PETSc to error if it had to reallocate memory in the Jacobian "
"matrix due to not having enough nonzeros");
params.addParam<bool>("ignore_zeros_in_jacobian",
false,
"Do not explicitly store zero values in "
"the Jacobian matrix if true");
params.addParam<bool>("force_restart",
false,
"EXPERIMENTAL: If true, a sub_app may use a "
"restart file instead of using of using the master "
"backup file");
params.addDeprecatedParam<bool>("skip_additional_restart_data",
false,
"True to skip additional data in equation system for restart.",
"This parameter is no longer used, as we do not load additional "
"vectors by default with restart");
params.addParam<bool>("skip_nl_system_check",
false,
"True to skip the NonlinearSystem check for work to do (e.g. Make sure "
"that there are variables to solve for).");
params.addParam<bool>("allow_initial_conditions_with_restart",
false,
"True to allow the user to specify initial conditions when restarting. "
"Initial conditions can override any restarted field");
/// One entry of coord system per block, the size of _blocks and _coord_sys has to match, except:
/// 1. _blocks.size() == 0, then there needs to be just one entry in _coord_sys, which will
/// be set for the whole domain
/// 2. _blocks.size() > 0 and no coordinate system was specified, then the whole domain will be XYZ.
/// 3. _blocks.size() > 0 and one coordinate system was specified, then the whole domain will be that system.
params.addDeprecatedParam<std::vector<SubdomainName>>(
"block", "Block IDs for the coordinate systems", "Please use 'Mesh/coord_block' instead");
MultiMooseEnum coord_types("XYZ RZ RSPHERICAL", "XYZ");
MooseEnum rz_coord_axis("X=0 Y=1", "Y");
params.addDeprecatedParam<MultiMooseEnum>("coord_type",
coord_types,
"Type of the coordinate system per block param",
"Please use 'Mesh/coord_type' instead");
params.addDeprecatedParam<MooseEnum>("rz_coord_axis",
rz_coord_axis,
"The rotation axis (X | Y) for axisymetric coordinates",
"Please use 'Mesh/rz_coord_axis' instead");
params.addParam<bool>(
"kernel_coverage_check", true, "Set to false to disable kernel->subdomain coverage check");
params.addParam<bool>(
"boundary_restricted_node_integrity_check",
true,
"Set to false to disable checking of boundary restricted nodal object variable dependencies, "
"e.g. are the variable dependencies defined on the selected boundaries?");
params.addParam<bool>("boundary_restricted_elem_integrity_check",
true,
"Set to false to disable checking of boundary restricted elemental object "
"variable dependencies, e.g. are the variable dependencies defined on the "
"selected boundaries?");
params.addParam<bool>("material_coverage_check",
true,
"Set to false to disable material->subdomain coverage check");
params.addParam<bool>("fv_bcs_integrity_check",
true,
"Set to false to disable checking of overlapping Dirichlet and Flux BCs "
"and/or multiple DirichletBCs per sideset");
params.addParam<bool>(
"material_dependency_check", true, "Set to false to disable material dependency check");
params.addParam<bool>("parallel_barrier_messaging",
false,
"Displays messaging from parallel "
"barrier notifications when executing "
"or transferring to/from Multiapps "
"(default: false)");
params.addParam<bool>(
"verbose_setup", false, "Set to True to have the problem report on any object created");
params.addParam<bool>("verbose_multiapps",
false,
"Set to True to enable verbose screen printing related to MultiApps");
params.addParam<FileNameNoExtension>("restart_file_base",
"File base name used for restart (e.g. "
"<path>/<filebase> or <path>/LATEST to "
"grab the latest file available)");
params.addParam<std::vector<std::vector<TagName>>>(
"extra_tag_vectors",
"Extra vectors to add to the system that can be filled by objects which compute residuals "
"and Jacobians (Kernels, BCs, etc.) by setting tags on them. The outer index is for which "
"nonlinear system the extra tag vectors should be added for");
params.addParam<std::vector<std::vector<TagName>>>(
"extra_tag_matrices",
"Extra matrices to add to the system that can be filled "
"by objects which compute residuals and Jacobians "
"(Kernels, BCs, etc.) by setting tags on them. The outer index is for which "
"nonlinear system the extra tag vectors should be added for");
params.addParam<std::vector<TagName>>(
"extra_tag_solutions",
"Extra solution vectors to add to the system that can be used by "
"objects for coupling variable values stored in them.");
params.addParam<bool>("previous_nl_solution_required",
false,
"True to indicate that this calculation requires a solution vector for "
"storing the previous nonlinear iteration.");
params.addParam<std::vector<NonlinearSystemName>>(
"nl_sys_names", std::vector<NonlinearSystemName>{"nl0"}, "The nonlinear system names");
params.addParam<bool>("check_uo_aux_state",
false,
"True to turn on a check that no state presents during the evaluation of "
"user objects and aux kernels");
params.addPrivateParam<MooseMesh *>("mesh");
params.declareControllable("solve");
params.addParam<bool>(
"allow_invalid_solution",
false,
"Set to true to allow convergence even though the solution has been marked as 'invalid'");
params.addParam<bool>("immediately_print_invalid_solution",
false,
"Whether or not to report invalid solution warnings at the time the "
"warning is produced instead of after the calculation");
params.addParamNamesToGroup(
"skip_nl_system_check kernel_coverage_check boundary_restricted_node_integrity_check "
"boundary_restricted_elem_integrity_check material_coverage_check fv_bcs_integrity_check "
"material_dependency_check check_uo_aux_state error_on_jacobian_nonzero_reallocation",
"Simulation checks");
params.addParamNamesToGroup("use_nonlinear previous_nl_solution_required nl_sys_names "
"ignore_zeros_in_jacobian",
"Nonlinear system(s)");
params.addParamNamesToGroup(
"restart_file_base force_restart allow_initial_conditions_with_restart", "Restart");
params.addParamNamesToGroup("verbose_setup verbose_multiapps parallel_barrier_messaging",
"Verbosity");
params.addParamNamesToGroup(
"null_space_dimension transpose_null_space_dimension near_null_space_dimension",
"Null space removal");
params.addParamNamesToGroup("extra_tag_vectors extra_tag_matrices extra_tag_solutions",
"Tagging");
params.addParamNamesToGroup("allow_invalid_solution immediately_print_invalid_solution",
"Solution validity control");
return params;
}
FEProblemBase::FEProblemBase(const InputParameters & parameters)
: SubProblem(parameters),
Restartable(this, "FEProblemBase"),
_mesh(*getCheckedPointerParam<MooseMesh *>("mesh")),
_req(declareManagedRestartableDataWithContext<RestartableEquationSystems>(
"equation_systems", nullptr, _mesh)),
_initialized(false),
_solve(getParam<bool>("solve")),
_transient(false),
_time(declareRestartableData<Real>("time")),
_time_old(declareRestartableData<Real>("time_old")),
_t_step(declareRecoverableData<int>("t_step")),
_dt(declareRestartableData<Real>("dt")),
_dt_old(declareRestartableData<Real>("dt_old")),
_nl_sys_names(getParam<std::vector<NonlinearSystemName>>("nl_sys_names")),
_num_nl_sys(_nl_sys_names.size()),
_nl(_num_nl_sys, nullptr),
_current_nl_sys(nullptr),
_aux(nullptr),
_coupling(Moose::COUPLING_DIAG),
_mesh_divisions(/*threaded=*/true),
_material_props(declareRestartableDataWithContext<MaterialPropertyStorage>(
"material_props", &_mesh, _material_prop_registry)),
_bnd_material_props(declareRestartableDataWithContext<MaterialPropertyStorage>(
"bnd_material_props", &_mesh, _material_prop_registry)),
_neighbor_material_props(declareRestartableDataWithContext<MaterialPropertyStorage>(
"neighbor_material_props", &_mesh, _material_prop_registry)),
_reporter_data(_app),
// TODO: delete the following line after apps have been updated to not call getUserObjects
_all_user_objects(_app.getExecuteOnEnum()),
_multi_apps(_app.getExecuteOnEnum()),
_transient_multi_apps(_app.getExecuteOnEnum()),
_transfers(_app.getExecuteOnEnum(), /*threaded=*/false),
_to_multi_app_transfers(_app.getExecuteOnEnum(), /*threaded=*/false),
_from_multi_app_transfers(_app.getExecuteOnEnum(), /*threaded=*/false),
_between_multi_app_transfers(_app.getExecuteOnEnum(), /*threaded=*/false),
#ifdef LIBMESH_ENABLE_AMR
_adaptivity(*this),
_cycles_completed(0),
#endif
_displaced_mesh(nullptr),
_geometric_search_data(*this, _mesh),
_mortar_data(*this),
_reinit_displaced_elem(false),
_reinit_displaced_face(false),
_reinit_displaced_neighbor(false),
_input_file_saved(false),
_has_dampers(false),
_has_constraints(false),
_snesmf_reuse_base(true),
_skip_exception_check(false),
_snesmf_reuse_base_set_by_user(false),
_has_initialized_stateful(false),
_const_jacobian(false),
_has_jacobian(false),
_needs_old_newton_iter(false),
_has_nonlocal_coupling(false),
_calculate_jacobian_in_uo(false),
_kernel_coverage_check(getParam<bool>("kernel_coverage_check")),
_boundary_restricted_node_integrity_check(
getParam<bool>("boundary_restricted_node_integrity_check")),
_boundary_restricted_elem_integrity_check(
getParam<bool>("boundary_restricted_elem_integrity_check")),
_material_coverage_check(getParam<bool>("material_coverage_check")),
_fv_bcs_integrity_check(getParam<bool>("fv_bcs_integrity_check")),
_material_dependency_check(getParam<bool>("material_dependency_check")),
_uo_aux_state_check(getParam<bool>("check_uo_aux_state")),
_max_qps(std::numeric_limits<unsigned int>::max()),
_max_scalar_order(INVALID_ORDER),
_has_time_integrator(false),
_has_exception(false),
_parallel_barrier_messaging(getParam<bool>("parallel_barrier_messaging")),
_verbose_setup(getParam<bool>("verbose_setup")),
_verbose_multiapps(getParam<bool>("verbose_multiapps")),
_current_execute_on_flag(EXEC_NONE),
_control_warehouse(_app.getExecuteOnEnum(), /*threaded=*/false),
_is_petsc_options_inserted(false),
_line_search(nullptr),
_using_ad_mat_props(false),
_error_on_jacobian_nonzero_reallocation(
isParamValid("error_on_jacobian_nonzero_reallocation")
? getParam<bool>("error_on_jacobian_nonzero_reallocation")
: _app.errorOnJacobianNonzeroReallocation()),
_ignore_zeros_in_jacobian(getParam<bool>("ignore_zeros_in_jacobian")),
_force_restart(getParam<bool>("force_restart")),
_allow_ics_during_restart(getParam<bool>("allow_initial_conditions_with_restart")),
_skip_nl_system_check(getParam<bool>("skip_nl_system_check")),
_fail_next_nonlinear_convergence_check(false),
_allow_invalid_solution(getParam<bool>("allow_invalid_solution")),
_immediately_print_invalid_solution(getParam<bool>("immediately_print_invalid_solution")),
_started_initial_setup(false),
_has_internal_edge_residual_objects(false),
_u_dot_requested(false),
_u_dotdot_requested(false),
_u_dot_old_requested(false),
_u_dotdot_old_requested(false),
_has_mortar(false),
_num_grid_steps(0),
_print_execution_on()
{
// Initialize static do_derivatives member. We initialize this to true so that all the default AD
// things that we setup early in the simulation actually get their derivative vectors initalized.
// We will toggle this to false when doing residual evaluations
ADReal::do_derivatives = true;
for (const auto i : index_range(_nl_sys_names))
_nl_sys_name_to_num[_nl_sys_names[i]] = i;
_nonlocal_cm.resize(_nl_sys_names.size());
_cm.resize(_nl_sys_names.size());
_time = 0.0;
_time_old = 0.0;
_t_step = 0;
_dt = 0;
_dt_old = _dt;
unsigned int n_threads = libMesh::n_threads();
_real_zero.resize(n_threads, 0.);
_scalar_zero.resize(n_threads);
_zero.resize(n_threads);
_phi_zero.resize(n_threads);
_ad_zero.resize(n_threads);
_grad_zero.resize(n_threads);
_ad_grad_zero.resize(n_threads);
_grad_phi_zero.resize(n_threads);
_second_zero.resize(n_threads);
_ad_second_zero.resize(n_threads);
_second_phi_zero.resize(n_threads);
_point_zero.resize(n_threads);
_vector_zero.resize(n_threads);
_vector_curl_zero.resize(n_threads);
_uo_jacobian_moose_vars.resize(n_threads);
_active_elemental_moose_variables.resize(n_threads);
_block_mat_side_cache.resize(n_threads);
_bnd_mat_side_cache.resize(n_threads);
_interface_mat_side_cache.resize(n_threads);
es().parameters.set<FEProblemBase *>("_fe_problem_base") = this;
if (parameters.isParamSetByUser("coord_type"))
setCoordSystem(getParam<std::vector<SubdomainName>>("block"),
getParam<MultiMooseEnum>("coord_type"));
if (parameters.isParamSetByUser("rz_coord_axis"))
setAxisymmetricCoordAxis(getParam<MooseEnum>("rz_coord_axis"));
if (isParamValid("restart_file_base"))
{
std::string restart_file_base = getParam<FileNameNoExtension>("restart_file_base");
// This check reverts to old behavior of providing "restart_file_base=" to mean
// don't restart... BISON currently relies on this. It could probably be removed.
// The new MooseUtils::convertLatestCheckpoint will error out if a checkpoint file
// is not found, which I think makes sense. Which means, without this, if you
// set "restart_file_base=", you'll get a "No checkpoint file found" error
if (restart_file_base.size())
{
restart_file_base = MooseUtils::convertLatestCheckpoint(restart_file_base);
setRestartFile(restart_file_base);
}
}
// // Generally speaking, the mesh is prepared for use, and consequently remote elements are deleted
// // well before our Problem(s) are constructed. Historically, in MooseMesh we have a bunch of
// // needs_prepare type flags that make it so we never call prepare_for_use (and consequently
// // delete_remote_elements) again. So the below line, historically, has had no impact. HOWEVER:
// // I've added some code in SetupMeshCompleteAction for deleting remote elements post
// // EquationSystems::init. If I execute that code without default ghosting, then I get > 40 MOOSE
// // test failures, so we clearly have some simulations that are not yet covered properly by
// // relationship managers. Until that is resolved, I am going to retain default geometric ghosting
// if (!_default_ghosting)
// _mesh.getMesh().remove_ghosting_functor(_mesh.getMesh().default_ghosting());
#if !PETSC_RELEASE_LESS_THAN(3, 12, 0)
// Main app should hold the default database to handle system petsc options
if (!_app.isUltimateMaster())
PetscOptionsCreate(&_petsc_option_data_base);
#endif
}
const MooseMesh &
FEProblemBase::mesh(bool use_displaced) const
{
if (use_displaced && !_displaced_problem)
mooseWarning("Displaced mesh was requested but the displaced problem does not exist. "
"Regular mesh will be returned");
return ((use_displaced && _displaced_problem) ? _displaced_problem->mesh() : mesh());
}
void
FEProblemBase::createTagVectors()
{
// add vectors and their tags to system
auto & vectors = getParam<std::vector<std::vector<TagName>>>("extra_tag_vectors");
for (const auto nl_sys_num : index_range(vectors))
for (auto & vector : vectors[nl_sys_num])
{
auto tag = addVectorTag(vector);
_nl[nl_sys_num]->addVector(tag, false, GHOSTED);
}
// add matrices and their tags
auto & matrices = getParam<std::vector<std::vector<TagName>>>("extra_tag_matrices");
for (const auto nl_sys_num : index_range(matrices))
for (auto & matrix : matrices[nl_sys_num])
{
auto tag = addMatrixTag(matrix);
_nl[nl_sys_num]->addMatrix(tag);
}
}
void
FEProblemBase::createTagSolutions()
{
auto & vectors = getParam<std::vector<TagName>>("extra_tag_solutions");
for (auto & vector : vectors)
{
auto tag = addVectorTag(vector, Moose::VECTOR_TAG_SOLUTION);
for (auto & nl : _nl)
nl->addVector(tag, false, GHOSTED);
_aux->addVector(tag, false, GHOSTED);
}
if (getParam<bool>("previous_nl_solution_required"))
{
// We'll populate the zeroth state of the nonlinear iterations with the current solution for
// ease of use in doing things like copying solutions backwards. We're just storing pointers in
// the solution states containers so populating the zeroth state does not cost us the memory of
// a new vector
for (const auto i : make_range(0, 2))
{
for (auto & nl : _nl)
nl->needSolutionState(i, Moose::SolutionIterationType::Nonlinear);
_aux->needSolutionState(i, Moose::SolutionIterationType::Nonlinear);
}
}
auto tag = addVectorTag(Moose::SOLUTION_TAG, Moose::VECTOR_TAG_SOLUTION);
for (auto & nl : _nl)
nl->associateVectorToTag(*nl->system().current_local_solution.get(), tag);
_aux->associateVectorToTag(*_aux->system().current_local_solution.get(), tag);
}
void
FEProblemBase::newAssemblyArray(std::vector<std::shared_ptr<NonlinearSystemBase>> & nls)
{
unsigned int n_threads = libMesh::n_threads();
_assembly.resize(n_threads);
for (const auto i : make_range(n_threads))
{
_assembly[i].resize(nls.size());
for (const auto j : index_range(nls))
_assembly[i][j] = std::make_unique<Assembly>(*nls[j], i);
}
}
void
FEProblemBase::initNullSpaceVectors(const InputParameters & parameters,
std::vector<std::shared_ptr<NonlinearSystemBase>> & nls)
{
TIME_SECTION("initNullSpaceVectors", 5, "Initializing Null Space Vectors");
unsigned int dimNullSpace = parameters.get<unsigned int>("null_space_dimension");
unsigned int dimTransposeNullSpace =
parameters.get<unsigned int>("transpose_null_space_dimension");
unsigned int dimNearNullSpace = parameters.get<unsigned int>("near_null_space_dimension");
for (unsigned int i = 0; i < dimNullSpace; ++i)
{
std::ostringstream oss;
oss << "_" << i;
// do not project, since this will be recomputed, but make it ghosted, since the near nullspace
// builder might march over all nodes
for (auto & nl : nls)
nl->addVector("NullSpace" + oss.str(), false, GHOSTED);
}
_subspace_dim["NullSpace"] = dimNullSpace;
for (unsigned int i = 0; i < dimTransposeNullSpace; ++i)
{
std::ostringstream oss;
oss << "_" << i;
// do not project, since this will be recomputed, but make it ghosted, since the near nullspace
// builder might march over all nodes
for (auto & nl : nls)
nl->addVector("TransposeNullSpace" + oss.str(), false, GHOSTED);
}
_subspace_dim["TransposeNullSpace"] = dimTransposeNullSpace;
for (unsigned int i = 0; i < dimNearNullSpace; ++i)
{
std::ostringstream oss;
oss << "_" << i;
// do not project, since this will be recomputed, but make it ghosted, since the near-nullspace
// builder might march over all semilocal nodes
for (auto & nl : nls)
nl->addVector("NearNullSpace" + oss.str(), false, GHOSTED);
}
_subspace_dim["NearNullSpace"] = dimNearNullSpace;
}
FEProblemBase::~FEProblemBase()
{
// Flush the Console stream, the underlying call to Console::mooseConsole
// relies on a call to Output::checkInterval that has references to
// _time, etc. If it is not flushed here memory problems arise if you have
// an unflushed stream and start destructing things.
_console << std::flush;
unsigned int n_threads = libMesh::n_threads();
for (unsigned int i = 0; i < n_threads; i++)
{
_zero[i].release();
_phi_zero[i].release();
_scalar_zero[i].release();
_grad_zero[i].release();
_grad_phi_zero[i].release();
_second_zero[i].release();
_second_phi_zero[i].release();
_vector_zero[i].release();
_vector_curl_zero[i].release();
_ad_zero[i].release();
_ad_grad_zero[i].release();
_ad_second_zero[i].release();
}
#if !PETSC_RELEASE_LESS_THAN(3, 12, 0)
if (!_app.isUltimateMaster())
PetscOptionsDestroy(&_petsc_option_data_base);
#endif
}
void
FEProblemBase::setCoordSystem(const std::vector<SubdomainName> & blocks,
const MultiMooseEnum & coord_sys)
{
TIME_SECTION("setCoordSystem", 5, "Setting Coordinate System");
_mesh.setCoordSystem(blocks, coord_sys);
}
void
FEProblemBase::setAxisymmetricCoordAxis(const MooseEnum & rz_coord_axis)
{
_mesh.setAxisymmetricCoordAxis(rz_coord_axis);
}
const ConstElemRange &
FEProblemBase::getEvaluableElementRange()
{
if (!_evaluable_local_elem_range)
{
std::vector<const DofMap *> dof_maps(es().n_systems());
for (const auto i : make_range(es().n_systems()))
{
const auto & sys = es().get_system(i);
dof_maps[i] = &sys.get_dof_map();
}
_evaluable_local_elem_range =
std::make_unique<ConstElemRange>(_mesh.getMesh().multi_evaluable_elements_begin(dof_maps),
_mesh.getMesh().multi_evaluable_elements_end(dof_maps));
}
return *_evaluable_local_elem_range;
}
const ConstElemRange &
FEProblemBase::getNonlinearEvaluableElementRange()
{
if (!_nl_evaluable_local_elem_range)
{
std::vector<const DofMap *> dof_maps(_nl.size());
for (const auto i : index_range(dof_maps))
dof_maps[i] = &_nl[i]->dofMap();
_nl_evaluable_local_elem_range =
std::make_unique<ConstElemRange>(_mesh.getMesh().multi_evaluable_elements_begin(dof_maps),
_mesh.getMesh().multi_evaluable_elements_end(dof_maps));
}
return *_nl_evaluable_local_elem_range;
}
void
FEProblemBase::initialSetup()
{
TIME_SECTION("initialSetup", 2, "Performing Initial Setup");
SubProblem::initialSetup();
if (_app.isRecovering() + _app.isRestarting() + bool(_app.getExReaderForRestart()) > 1)
mooseError("Checkpoint recovery and restart and exodus restart are all mutually exclusive.");
if (_skip_exception_check)
mooseWarning("MOOSE may fail to catch an exception when the \"skip_exception_check\" parameter "
"is used. If you receive a terse MPI error during execution, remove this "
"parameter and rerun your simulation");
// set state flag indicating that we are in or beyond initialSetup.
// This can be used to throw errors in methods that _must_ be called at construction time.
_started_initial_setup = true;
setCurrentExecuteOnFlag(EXEC_INITIAL);
// Setup the solution states (current, old, etc) in each system based on
// its default and the states requested of each of its variables
for (const auto i : index_range(_nl))
{
_nl[i]->initSolutionState();
if (getDisplacedProblem())
getDisplacedProblem()->nlSys(i).initSolutionState();
}
_aux->initSolutionState();
if (getDisplacedProblem())
getDisplacedProblem()->auxSys().initSolutionState();
// always execute to get the max number of DoF per element and node needed to initialize phi_zero
// variables
dof_id_type global_max_var_n_dofs_per_elem = 0;
for (const auto i : index_range(_nl))
{
auto & nl = *_nl[i];
dof_id_type max_var_n_dofs_per_elem;
dof_id_type max_var_n_dofs_per_node;
{
TIME_SECTION("computingMaxDofs", 3, "Computing Max Dofs Per Element");
MaxVarNDofsPerElem mvndpe(*this, nl);
Threads::parallel_reduce(*_mesh.getActiveLocalElementRange(), mvndpe);
max_var_n_dofs_per_elem = mvndpe.max();
_communicator.max(max_var_n_dofs_per_elem);
MaxVarNDofsPerNode mvndpn(*this, nl);
Threads::parallel_reduce(*_mesh.getLocalNodeRange(), mvndpn);
max_var_n_dofs_per_node = mvndpn.max();
_communicator.max(max_var_n_dofs_per_node);
global_max_var_n_dofs_per_elem =
std::max(global_max_var_n_dofs_per_elem, max_var_n_dofs_per_elem);
}
{
TIME_SECTION("assignMaxDofs", 5, "Assigning Maximum Dofs Per Elem");
nl.assignMaxVarNDofsPerElem(max_var_n_dofs_per_elem);
auto displaced_problem = getDisplacedProblem();
if (displaced_problem)
displaced_problem->nlSys(i).assignMaxVarNDofsPerElem(max_var_n_dofs_per_elem);
nl.assignMaxVarNDofsPerNode(max_var_n_dofs_per_node);
if (displaced_problem)
displaced_problem->nlSys(i).assignMaxVarNDofsPerNode(max_var_n_dofs_per_node);
}
}
{
TIME_SECTION("resizingVarValues", 5, "Resizing Variable Values");
for (unsigned int tid = 0; tid < libMesh::n_threads(); ++tid)
{
_phi_zero[tid].resize(global_max_var_n_dofs_per_elem, std::vector<Real>(getMaxQps(), 0.));
_grad_phi_zero[tid].resize(global_max_var_n_dofs_per_elem,
std::vector<RealGradient>(getMaxQps(), RealGradient(0.)));
_second_phi_zero[tid].resize(global_max_var_n_dofs_per_elem,
std::vector<RealTensor>(getMaxQps(), RealTensor(0.)));
}
}
// Set up stateful material property redistribution, if we suspect
// it may be necessary later.
addAnyRedistributers();
if (_app.isRestarting() || _app.isRecovering() || _force_restart)
{
// Only load all of the vectors if we're recovering
_req.set().setLoadAllVectors(_app.isRecovering());
TIME_SECTION("restore", 3, "Restoring from backup");
// We could have a cached backup when this app is a sub-app and has been given a Backup
if (!_app.hasInitialBackup())
_app.restore(_app.restartFolderBase(_app.getRestartRecoverFileBase()), _app.isRestarting());
else
_app.restoreFromInitialBackup(_app.isRestarting());
if (_material_props.hasStatefulProperties() || _bnd_material_props.hasStatefulProperties() ||
_neighbor_material_props.hasStatefulProperties())
_has_initialized_stateful = true;
}
else
{
ExodusII_IO * reader = _app.getExReaderForRestart();
if (reader)
{
TIME_SECTION("copyingFromExodus", 3, "Copying Variables From Exodus");
for (auto & nl : _nl)
nl->copyVars(*reader);
_aux->copyVars(*reader);
}
else
{
if (_nl[0]->hasVarCopy() || _aux->hasVarCopy())
mooseError("Need Exodus reader to restart variables but the reader is not available\n"
"Use either FileMesh with an Exodus mesh file or FileMeshGenerator with an "
"Exodus mesh file and with use_for_exodus_restart equal to true");
}
}
// Perform output related setups
_app.getOutputWarehouse().initialSetup();
// Flush all output to _console that occur during construction and initialization of objects
_app.getOutputWarehouse().mooseConsole();
// Build Refinement and Coarsening maps for stateful material projections if necessary
if ((_adaptivity.isOn() || _num_grid_steps) &&
(_material_props.hasStatefulProperties() || _bnd_material_props.hasStatefulProperties() ||
_neighbor_material_props.hasStatefulProperties()))
{
if (_has_internal_edge_residual_objects)
mooseError("Stateful neighbor material properties do not work with mesh adaptivity");
_mesh.buildRefinementAndCoarseningMaps(_assembly[0][0].get());
}
if (!_app.isRecovering())
{
/**
* If we are not recovering but we are doing restart (_app.getExodusFileRestart() == true) with
* additional uniform refinements. We have to delay the refinement until this point
* in time so that the equation systems are initialized and projections can be performed.
*/
if (_mesh.uniformRefineLevel() > 0 && _app.getExodusFileRestart())
{
if (!_app.isUltimateMaster())
mooseError(
"Doing extra refinements when restarting is NOT supported for sub-apps of a MultiApp");
adaptivity().uniformRefineWithProjection();
}
}
unsigned int n_threads = libMesh::n_threads();
// UserObject initialSetup
std::set<std::string> depend_objects_ic = _ics.getDependObjects();
std::set<std::string> depend_objects_aux = _aux->getDependObjects();
// This replaces all prior updateDependObjects calls on the old user object warehouses.
TheWarehouse::Query uo_query = theWarehouse().query().condition<AttribSystem>("UserObject");
std::vector<UserObject *> userobjs;
uo_query.queryInto(userobjs);
groupUserObjects(
theWarehouse(), getAuxiliarySystem(), _app.getExecuteOnEnum(), userobjs, depend_objects_ic);
for (auto obj : userobjs)
obj->initialSetup();
// check if jacobian calculation is done in userobject
for (THREAD_ID tid = 0; tid < n_threads; ++tid)
checkUserObjectJacobianRequirement(tid);
// Check whether nonlocal couling is required or not
checkNonlocalCoupling();
if (_requires_nonlocal_coupling)
setVariableAllDoFMap(_uo_jacobian_moose_vars[0]);
{
TIME_SECTION("initializingFunctions", 5, "Initializing Functions");
// Call the initialSetup methods for functions
for (THREAD_ID tid = 0; tid < n_threads; tid++)
{
reinitScalars(tid); // initialize scalars so they are properly sized for use as input into
// ParsedFunctions
_functions.initialSetup(tid);
}
}
{
TIME_SECTION("initializingRandomObjects", 5, "Initializing Random Objects");
// Random interface objects
for (const auto & it : _random_data_objects)
it.second->updateSeeds(EXEC_INITIAL);
}
if (!_app.isRecovering())
{
computeUserObjects(EXEC_INITIAL, Moose::PRE_IC);
{
TIME_SECTION("ICiniitalSetup", 5, "Setting Up Initial Conditions");
for (THREAD_ID tid = 0; tid < n_threads; tid++)
_ics.initialSetup(tid);
_scalar_ics.initialSetup();
}
projectSolution();
}
// Materials
if (_all_materials.hasActiveObjects(0))
{
TIME_SECTION("materialInitialSetup", 3, "Setting Up Materials");
for (THREAD_ID tid = 0; tid < n_threads; tid++)
{
// Sort the Material objects, these will be actually computed by MOOSE in reinit methods.
_materials.sort(tid);
_interface_materials.sort(tid);
// Call initialSetup on all material objects
_all_materials.initialSetup(tid);
// Discrete materials may insert additional dependencies on materials during the initial
// setup. Therefore we resolve the dependencies once more, now with the additional
// dependencies due to discrete materials.
if (_discrete_materials.hasActiveObjects())
{
_materials.sort(tid);
_interface_materials.sort(tid);
}
}
if (!_has_initialized_stateful)
{
TIME_SECTION("computingInitialStatefulProps", 3, "Computing Initial Material Values");
initElementStatefulProps(*_mesh.getActiveLocalElementRange(), true);
if (_material_props.hasStatefulProperties() || _bnd_material_props.hasStatefulProperties() ||
_neighbor_material_props.hasStatefulProperties())
_has_initialized_stateful = true;
}
}
for (THREAD_ID tid = 0; tid < n_threads; tid++)
{
_internal_side_indicators.initialSetup(tid);
_indicators.initialSetup(tid);
_markers.sort(tid);
_markers.initialSetup(tid);
}
#ifdef LIBMESH_ENABLE_AMR
if (!_app.isRecovering())
{
unsigned int n = adaptivity().getInitialSteps();
if (n && !_app.isUltimateMaster() && _app.isRestarting())
mooseError("Cannot perform initial adaptivity during restart on sub-apps of a MultiApp!");
initialAdaptMesh();
}
#endif // LIBMESH_ENABLE_AMR
if (!_app.isRecovering() && !_app.isRestarting())
{
// During initial setup the solution is copied to the older solution states (old, older, etc)
copySolutionsBackwards();
}
if (!_app.isRecovering())
{
if (haveXFEM())
updateMeshXFEM();
}
// Call initialSetup on the nonlinear system
for (auto & nl : _nl)
nl->initialSetup();
// Auxilary variable initialSetup calls
_aux->initialSetup();
if (_displaced_problem)
// initialSetup for displaced systems
_displaced_problem->initialSetup();
for (auto & nl : _nl)
nl->setSolution(*(nl->system().current_local_solution.get()));
// Update the nearest node searches (has to be called after the problem is all set up)
// We do this here because this sets up the Element's DoFs to ghost
updateGeomSearch(GeometricSearchData::NEAREST_NODE);
_mesh.updateActiveSemiLocalNodeRange(_ghosted_elems);
if (_displaced_mesh)
_displaced_mesh->updateActiveSemiLocalNodeRange(_ghosted_elems);
// We need to move the mesh in order to build a map between mortar secondary and primary