forked from idaholab/moose
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FEProblemBase.C
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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 "RestartableDataIO.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 "ComputeBoundaryInitialConditionThread.h"
#include "MaxQpsThread.h"
#include "ActionWarehouse.h"
#include "Conversion.h"
#include "Material.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 "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 "Indicator.h"
#include "Marker.h"
#include "MultiApp.h"
#include "MultiAppTransfer.h"
#include "TransientMultiApp.h"
#include "ElementUserObject.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 "TimedPrint.h"
#include "MaxVarNDofsPerElem.h"
#include "MaxVarNDofsPerNode.h"
#include "FVKernel.h"
#include "FVTimeKernel.h"
#include "MooseVariableFV.h"
#include "FVBoundaryCondition.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 "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;
defineLegacyParams(FEProblemBase);
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",
false,
"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.addParam<bool>("skip_additional_restart_data",
false,
"True to skip additional data in equation system for restart. It is useful "
"for starting a transient calculation with a steady-state solution");
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).");
/// 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.addParam<std::vector<SubdomainName>>("block", "Block IDs for the coordinate systems");
MultiMooseEnum coord_types("XYZ RZ RSPHERICAL", "XYZ");
MooseEnum rz_coord_axis("X=0 Y=1", "Y");
params.addParam<MultiMooseEnum>(
"coord_type", coord_types, "Type of the coordinate system per block param");
params.addParam<MooseEnum>(
"rz_coord_axis", rz_coord_axis, "The rotation axis (X | Y) for axisymetric coordinates");
params.addParam<bool>(
"kernel_coverage_check", true, "Set to false to disable kernel->subdomain coverage check");
params.addParam<bool>("material_coverage_check",
true,
"Set to false to disable material->subdomain coverage check");
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<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<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.");
params.addParam<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.");
params.addPrivateParam<MooseMesh *>("mesh");
params.declareControllable("solve");
return params;
}
FEProblemBase::FEProblemBase(const InputParameters & parameters)
: SubProblem(parameters),
Restartable(this, "FEProblemBase"),
_mesh(*getCheckedPointerParam<MooseMesh *>("mesh")),
_eq(_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(nullptr),
_aux(nullptr),
_coupling(Moose::COUPLING_DIAG),
_material_props(
declareRestartableDataWithContext<MaterialPropertyStorage>("material_props", &_mesh)),
_bnd_material_props(
declareRestartableDataWithContext<MaterialPropertyStorage>("bnd_material_props", &_mesh)),
_neighbor_material_props(declareRestartableDataWithContext<MaterialPropertyStorage>(
"neighbor_material_props", &_mesh)),
_pps_data(*this),
_vpps_data(*this),
// 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),
#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),
_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")),
_material_coverage_check(getParam<bool>("material_coverage_check")),
_material_dependency_check(getParam<bool>("material_dependency_check")),
_max_qps(std::numeric_limits<unsigned int>::max()),
_max_shape_funcs(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")),
_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(
getParam<bool>("error_on_jacobian_nonzero_reallocation")),
_ignore_zeros_in_jacobian(getParam<bool>("ignore_zeros_in_jacobian")),
_force_restart(getParam<bool>("force_restart")),
_skip_additional_restart_data(getParam<bool>("skip_additional_restart_data")),
_skip_nl_system_check(getParam<bool>("skip_nl_system_check")),
_fail_next_linear_convergence_check(false),
_started_initial_setup(false),
_has_internal_edge_residual_objects(false),
_initial_setup_timer(registerTimedSection("initialSetup", 2, "Performing Initial Setup")),
_project_solution_timer(registerTimedSection("projectSolution", 2, "Projecting Initial Solutions")),
_compute_indicators_timer(registerTimedSection("computeIndicators", 1, "Computing Indicators")),
_compute_markers_timer(registerTimedSection("computeMarkers", 1, "Computing Markers")),
_compute_user_objects_timer(registerTimedSection("computeUserObjects", 1, "Computing User Objects")),
_execute_controls_timer(registerTimedSection("executeControls", 1, "Executing Controls")),
_execute_samplers_timer(registerTimedSection("executeSamplers", 1, "Executing Samplers")),
_update_active_objects_timer(registerTimedSection("updateActiveObjects", 5, "Updating Active Objects")),
_reinit_because_of_ghosting_or_new_geom_objects_timer(
registerTimedSection("reinitBecauseOfGhostingOrNewGeomObjects", 3, "Reinitializing Because of Geometric Search Objects")),
_exec_multi_app_transfers_timer(registerTimedSection("execMultiAppTransfers", 1, "Executing Transfers")),
_init_timer(registerTimedSection("init", 2, "Initializing")),
_eq_init_timer(registerTimedSection("EquationSystems::Init", 2, "Initializing Equation Systems")),
_solve_timer(registerTimedSection("solve", 1, "Solving", false)),
_check_exception_and_stop_solve_timer(registerTimedSection("checkExceptionAndStopSolve", 5)),
_advance_state_timer(registerTimedSection("advanceState", 5)),
_restore_solutions_timer(registerTimedSection("restoreSolutions", 5)),
_save_old_solutions_timer(registerTimedSection("saveOldSolutions", 5)),
_restore_old_solutions_timer(registerTimedSection("restoreOldSolutions", 5)),
_output_step_timer(registerTimedSection("outputStep", 1, "Outputting", false)),
_on_timestep_begin_timer(registerTimedSection("onTimestepBegin", 2)),
_compute_residual_l2_norm_timer(registerTimedSection("computeResidualL2Norm", 2)),
_compute_residual_sys_timer(registerTimedSection("computeResidualSys", 5)),
_compute_residual_internal_timer(registerTimedSection("computeResidualInternal", 1)),
_compute_residual_type_timer(registerTimedSection("computeResidualType", 5)),
_compute_transient_implicit_residual_timer(
registerTimedSection("computeTransientImplicitResidual", 2)),
_compute_residual_tags_timer(registerTimedSection("computeResidualTags", 5)),
_compute_jacobian_internal_timer(registerTimedSection("computeJacobianInternal", 1)),
_compute_jacobian_tags_timer(registerTimedSection("computeJacobianTags", 5)),
_compute_jacobian_blocks_timer(registerTimedSection("computeTransientImplicitJacobian", 2)),
_compute_bounds_timer(registerTimedSection("computeBounds", 1)),
_compute_post_check_timer(registerTimedSection("computePostCheck", 2)),
_compute_damping_timer(registerTimedSection("computeDamping", 1)),
_possibly_rebuild_geom_search_patches_timer(
registerTimedSection("possiblyRebuildGeomSearchPatches", 5)),
_initial_adapt_mesh_timer(registerTimedSection("initialAdaptMesh", 2, "Performing Initial Adaptivity")),
_adapt_mesh_timer(registerTimedSection("adaptMesh", 3, "Adapting Mesh")),
_update_mesh_xfem_timer(registerTimedSection("updateMeshXFEM", 5, "Updating XFEM")),
_mesh_changed_timer(registerTimedSection("meshChanged", 3, "Handling Mesh Changes")),
_mesh_changed_helper_timer(registerTimedSection("meshChangedHelper", 5)),
_check_problem_integrity_timer(registerTimedSection("notifyWhenMeshChanges", 5)),
_serialize_solution_timer(registerTimedSection("serializeSolution", 3, "Serializing Solution")),
_check_nonlinear_convergence_timer(registerTimedSection("checkNonlinearConvergence", 5, "Checking Nonlinear Convergence")),
_check_linear_convergence_timer(registerTimedSection("checkLinearConvergence", 5, "Checking Linear Convergence")),
_update_geometric_search_timer(registerTimedSection("updateGeometricSearch", 3, "Updating Geometric Search")),
_exec_multi_apps_timer(registerTimedSection("execMultiApps", 1, "Executing MultiApps", false)),
_backup_multi_apps_timer(registerTimedSection("backupMultiApps", 5, "Backing Up MultiApp")),
_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),
_displaced_neighbor_ref_pts("invert_elem_phys use_undisplaced_ref unset", "unset")
{
// 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;
_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);
_material_data.resize(n_threads);
_bnd_material_data.resize(n_threads);
_neighbor_material_data.resize(n_threads);
for (unsigned int i = 0; i < n_threads; i++)
{
_material_data[i] = std::make_shared<MaterialData>(_material_props);
_bnd_material_data[i] = std::make_shared<MaterialData>(_bnd_material_props);
_neighbor_material_data[i] = std::make_shared<MaterialData>(_neighbor_material_props);
}
_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);
_restart_io = libmesh_make_unique<RestartableDataIO>(*this);
_eq.parameters.set<FEProblemBase *>("_fe_problem_base") = this;
setCoordSystem(getParam<std::vector<SubdomainName>>("block"),
getParam<MultiMooseEnum>("coord_type"));
setAxisymmetricCoordAxis(getParam<MooseEnum>("rz_coord_axis"));
if (isParamValid("restart_file_base"))
{
std::string restart_file_base = getParam<FileNameNoExtension>("restart_file_base");
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 FEProblemBase is 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)
// Master app should hold the default database to handle system petsc options
if (!_app.isUltimateMaster())
PetscOptionsCreate(&_petsc_option_data_base);
#endif
}
void
FEProblemBase::createTagVectors()
{
// add vectors and their tags to system
auto & vectors = getParam<std::vector<TagName>>("extra_tag_vectors");
for (auto & vector : vectors)
{
auto tag = addVectorTag(vector);
_nl->addVector(tag, false, GHOSTED);
}
// add matrices and their tags
auto & matrices = getParam<std::vector<TagName>>("extra_tag_matrices");
for (auto & matrix : matrices)
{
auto tag = addMatrixTag(matrix);
_nl->addMatrix(tag);
}
}
void
FEProblemBase::newAssemblyArray(NonlinearSystemBase & nl)
{
unsigned int n_threads = libMesh::n_threads();
_assembly.resize(n_threads);
for (unsigned int i = 0; i < n_threads; ++i)
_assembly[i] = libmesh_make_unique<Assembly>(nl, i);
}
void
FEProblemBase::initNullSpaceVectors(const InputParameters & parameters, NonlinearSystemBase & nl)
{
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
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
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
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
}
Moose::CoordinateSystemType
FEProblemBase::getCoordSystem(SubdomainID sid)
{
std::map<SubdomainID, Moose::CoordinateSystemType>::iterator it = _coord_sys.find(sid);
if (it != _coord_sys.end())
return (*it).second;
else
mooseError("Requested subdomain ", sid, " does not exist.");
}
void
FEProblemBase::setCoordSystem(const std::vector<SubdomainName> & blocks,
const MultiMooseEnum & coord_sys)
{
const std::set<SubdomainID> & subdomains = _mesh.meshSubdomains();
if (blocks.size() == 0)
{
// no blocks specified -> assume the whole domain
Moose::CoordinateSystemType coord_type = Moose::COORD_XYZ; // all is going to be XYZ by default
if (coord_sys.size() == 0)
; // relax, do nothing
else if (coord_sys.size() == 1)
coord_type = Moose::stringToEnum<Moose::CoordinateSystemType>(
coord_sys[0]); // one system specified, the whole domain is going to have that system
else
mooseError("Multiple coordinate systems specified, but no blocks given.");
for (const auto & sbd : subdomains)
_coord_sys[sbd] = coord_type;
}
else
{
// user specified 'blocks' but not coordinate systems
if (coord_sys.size() == 0)
{
// set all blocks to cartesian coordinate system
for (const auto & block : blocks)
{
SubdomainID sid = _mesh.getSubdomainID(block);
_coord_sys[sid] = Moose::COORD_XYZ;
}
}
else if (coord_sys.size() == 1)
{
// set all blocks to the coordinate system specified by `coord_sys[0]`
Moose::CoordinateSystemType coord_type =
Moose::stringToEnum<Moose::CoordinateSystemType>(coord_sys[0]);
for (const auto & block : blocks)
{
SubdomainID sid = _mesh.getSubdomainID(block);
_coord_sys[sid] = coord_type;
}
}
else
{
if (blocks.size() != coord_sys.size())
mooseError("Number of blocks and coordinate systems does not match.");
for (unsigned int i = 0; i < blocks.size(); i++)
{
SubdomainID sid = _mesh.getSubdomainID(blocks[i]);
Moose::CoordinateSystemType coord_type =
Moose::stringToEnum<Moose::CoordinateSystemType>(coord_sys[i]);
_coord_sys[sid] = coord_type;
}
for (const auto & sid : subdomains)
if (_coord_sys.find(sid) == _coord_sys.end())
mooseError("Subdomain '" + Moose::stringify(sid) +
"' does not have a coordinate system specified.");
}
}
}
void
FEProblemBase::setAxisymmetricCoordAxis(const MooseEnum & rz_coord_axis)
{
_rz_coord_axis = rz_coord_axis;
}
void
FEProblemBase::addExtraVectors()
{
_nl->addExtraVectors();
_aux->addExtraVectors();
}
const ConstElemRange &
FEProblemBase::getEvaluableElementRange()
{
if (!_evaluable_local_elem_range)
{
_evaluable_local_elem_range =
libmesh_make_unique<ConstElemRange>(_mesh.getMesh().evaluable_elements_begin(_nl->dofMap()),
_mesh.getMesh().evaluable_elements_end(_nl->dofMap()));
}
return *_evaluable_local_elem_range;
}
void
FEProblemBase::initialSetup()
{
TIME_SECTION(_initial_setup_timer);
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);
addExtraVectors();
// always execute to get the max number of DoF per element and node needed to initialize phi_zero
// variables
dof_id_type max_var_n_dofs_per_elem;
dof_id_type max_var_n_dofs_per_node;
{
CONSOLE_TIMED_PRINT("Computing max dofs per elem/node");
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);
}
_nl->assignMaxVarNDofsPerElem(max_var_n_dofs_per_elem);
auto displaced_problem = getDisplacedProblem();
if (displaced_problem)
displaced_problem->nlSys().assignMaxVarNDofsPerElem(max_var_n_dofs_per_elem);
_nl->assignMaxVarNDofsPerNode(max_var_n_dofs_per_node);
if (displaced_problem)
displaced_problem->nlSys().assignMaxVarNDofsPerNode(max_var_n_dofs_per_node);
#ifndef MOOSE_SPARSE_AD
auto size_required = max_var_n_dofs_per_elem * _nl->nVariables();
if (hasMortarCoupling())
size_required *= 3;
else if (hasNeighborCoupling())
size_required *= 2;
_nl->setRequiredDerivativeSize(size_required);
#endif
for (unsigned int tid = 0; tid < libMesh::n_threads(); ++tid)
{
_phi_zero[tid].resize(_nl->getMaxVarNDofsPerElem(), std::vector<Real>(getMaxQps(), 0.));
_grad_phi_zero[tid].resize(_nl->getMaxVarNDofsPerElem(),
std::vector<RealGradient>(getMaxQps(), RealGradient(0.)));
_second_phi_zero[tid].resize(_nl->getMaxVarNDofsPerElem(),
std::vector<RealTensor>(getMaxQps(), RealTensor(0.)));
}
if (_app.isRecovering() && (_app.isUltimateMaster() || _force_restart))
{
if (_app.getRestartRecoverFileSuffix() == "cpa")
_restart_io->useAsciiExtension();
}
if ((_app.isRestarting() || _app.isRecovering()) && (_app.isUltimateMaster() || _force_restart))
{
CONSOLE_TIMED_PRINT("Restarting from file");
_restart_io->readRestartableDataHeader(true);
_restart_io->restartEquationSystemsObject();
/**
* TODO: Move the RestartableDataIO call to reload data here. Only a few tests fail when doing
* this now. Material Properties aren't sized properly at this point and fail across the board,
* there are a few other misc tests that fail too.
*
* _restart_io->readRestartableData();
*/
}
else
{
ExodusII_IO * reader = _mesh.exReader();
if (reader)
{
CONSOLE_TIMED_PRINT("Copying variables from Exodus");
_nl->copyVars(*reader);
_aux->copyVars(*reader);
}
}
// 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].get());
}
if (!_app.isRecovering())
{
/**
* If we are not recovering but we are doing restart (_app_setFileRestart() == 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.setFileRestart())
{
if (!_app.isUltimateMaster())
mooseError(
"Doing extra refinements when restarting is NOT supported for sub-apps of a MultiApp");
adaptivity().uniformRefineWithProjection();
}
}
// Do this just in case things have been done to the mesh
{
CONSOLE_TIMED_PRINT("Ghosting ghosted boundaries");
ghostGhostedBoundaries();
}
_mesh.meshChanged();
if (_displaced_problem)
{
CONSOLE_TIMED_PRINT("Updating displaced mesh");
_displaced_mesh->meshChanged();
}
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.
std::vector<UserObject *> userobjs;
theWarehouse().query().condition<AttribSystem>("UserObject").queryInto(userobjs);
groupUserObjects(theWarehouse(), userobjs, depend_objects_ic, depend_objects_aux);
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]);
// 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);
}
// Random interface objects
for (const auto & it : _random_data_objects)
it.second->updateSeeds(EXEC_INITIAL);
if (!_app.isRecovering())
{
computeUserObjects(EXEC_INITIAL, Moose::PRE_IC);
for (THREAD_ID tid = 0; tid < n_threads; tid++)
_ics.initialSetup(tid);
_scalar_ics.initialSetup();
CONSOLE_TIMED_PRINT("Projecting initial condition");
projectSolution();
}
// Materials
if (_all_materials.hasActiveObjects(0))
{
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);
// Call initialSetup on both Material and Material objects
_all_materials.initialSetup(tid);
}
CONSOLE_TIMED_PRINT("Computing initial stateful property values");
ConstElemRange & elem_range = *_mesh.getActiveLocalElementRange();
ComputeMaterialsObjectThread cmt(*this,
_material_data,
_bnd_material_data,
_neighbor_material_data,
_material_props,
_bnd_material_props,
_neighbor_material_props,
_assembly);
/**
* The ComputeMaterialObjectThread object now allocates memory as needed for the material
* storage system.
* This cannot be done with threads. The first call to this object bypasses threading by calling
* the object
* directly. The subsequent call can be called with threads.
*/
cmt(elem_range, 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)
CONSOLE_TIMED_PRINT("Copying soultions back");
copySolutionsBackwards();
}
if (!_app.isRecovering())
{
if (haveXFEM())
{
CONSOLE_TIMED_PRINT("Updating XFEM");
updateMeshXFEM();
}
}
// Call initialSetup on the nonlinear system
_nl->initialSetup();
// Auxilary variable initialSetup calls
_aux->initialSetup();
_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 slave and master
// interfaces. This map will then be used by the AgumentSparsityOnInterface ghosting functor to
// know which dofs we need ghosted when we call EquationSystems::reinit
if (_displaced_problem && _mortar_data.hasDisplacedObjects())
_displaced_problem->updateMesh();
// Build the mortar segment meshes for a couple reasons:
// 1) Get the ghosting correct for both static and dynamic meshes
// 2) Make sure the mortar mesh is built for mortar constraints that live on the static mesh
//
// It is worth-while to note that mortar meshes that live on a dynamic mesh will be built
// during residual and Jacobian evaluation because when displacements are solution variables
// the mortar mesh will move and change during the course of a non-linear solve. We DO NOT
// redo ghosting during non-linear solve, so for purpose 1) the below call has to be made
updateMortarMesh();
// Possibly reinit one more time to get ghosting correct
reinitBecauseOfGhostingOrNewGeomObjects();
if (_displaced_mesh)
_displaced_problem->updateMesh();
updateGeomSearch(); // Call all of the rest of the geometric searches
auto ti = _nl->getTimeIntegrator();
if (ti)
ti->initialSetup();
if (_app.isRestarting() || _app.isRecovering())
{
if (_app.hasCachedBackup()) // This happens when this app is a sub-app and has been given a
// Backup
{
CONSOLE_TIMED_PRINT("Restoring cached backup");
_app.restoreCachedBackup();
}
else
{
CONSOLE_TIMED_PRINT("Restoring restart data");
_restart_io->readRestartableData(_app.getRestartableData(), _app.getRecoverableData());
}
// We may have just clobbered initial conditions that were explicitly set
// In a _restart_ scenario it is completely valid to specify new initial conditions
// for some of the variables which should override what's coming from the restart file
if (!_app.isRecovering())
{
CONSOLE_TIMED_PRINT("Reprojecting initial conditions after restoring restart data");
for (THREAD_ID tid = 0; tid < n_threads; tid++)
_ics.initialSetup(tid);
_scalar_ics.sort();
projectSolution();
}
}
// HUGE NOTE: MultiApp initialSetup() MUST... I repeat MUST be _after_ restartable data has been
// restored
// Call initialSetup on the MultiApps
if (_multi_apps.hasObjects())
{
_console << COLOR_CYAN << "Initializing All MultiApps" << COLOR_DEFAULT << std::endl;
_multi_apps.initialSetup();
_console << COLOR_CYAN << "Finished Initializing All MultiApps" << COLOR_DEFAULT << std::endl;
}
// Call initialSetup on the transfers
_transfers.initialSetup();
// Call initialSetup on the MultiAppTransfers to be executed on TO_MULTIAPP
const auto & to_multi_app_objects = _to_multi_app_transfers.getActiveObjects();
for (const auto & transfer : to_multi_app_objects)
{
transfer->setCurrentDirection(Transfer::DIRECTION::TO_MULTIAPP);
transfer->initialSetup();
}
// Call initialSetup on the MultiAppTransfers to be executed on FROM_MULTIAPP
const auto & from_multi_app_objects = _from_multi_app_transfers.getActiveObjects();
for (const auto & transfer : from_multi_app_objects)
{
transfer->setCurrentDirection(Transfer::DIRECTION::FROM_MULTIAPP);
transfer->initialSetup();
}
if (!_app.isRecovering())
{
execTransfers(EXEC_INITIAL);
bool converged = execMultiApps(EXEC_INITIAL);
if (!converged)
mooseError("failed to converge initial MultiApp");
// We'll backup the Multiapp here
backupMultiApps(EXEC_INITIAL);
for (THREAD_ID tid = 0; tid < n_threads; tid++)
reinitScalars(tid);