Mesh generated from parameters read from a DREAM3D EBSD file. More...

#include <EBSDMeshGenerator.h>

Inheritance diagram for EBSDMeshGenerator:

Classes
struct	Geometry

Public Types
typedef DataFileName	DataFileParameterType

Public Member Functions
	EBSDMeshGenerator (const InputParameters &parameters)

std::unique_ptr< MeshBase >	generate () override

const Geometry &	getEBSDGeometry () const

const std::string &	getEBSDFilename () const

std::unique_ptr< CSG::CSGBase >	generateInternalCSG ()

std::unique_ptr< MeshBase >	generateInternal ()

const std::set< MeshGeneratorName > &	getRequestedMeshGenerators () const

const std::set< MeshGeneratorName > &	getRequestedMeshGeneratorsForSub () const

void	addParentMeshGenerator (const MeshGenerator &mg, const AddParentChildKey)

void	addChildMeshGenerator (const MeshGenerator &mg, const AddParentChildKey)

const std::set< const MeshGenerator *, Comparator > &	getParentMeshGenerators () const

const std::set< const MeshGenerator *, Comparator > &	getChildMeshGenerators () const

const std::set< const MeshGenerator *, Comparator > &	getSubMeshGenerators () const

bool	isParentMeshGenerator (const MeshGeneratorName &name, const bool direct=true) const

bool	isChildMeshGenerator (const MeshGeneratorName &name, const bool direct=true) const

bool	isNullMeshName (const MeshGeneratorName &name) const

bool	hasSaveMesh () const

bool	hasOutput () const

const std::string &	getSavedMeshName () const

bool	hasGenerateData () const

bool	hasGenerateCSG () const

bool	isDataOnly () const

virtual bool	enabled () const

std::shared_ptr< MooseObject >	getSharedPtr ()

std::shared_ptr< const MooseObject >	getSharedPtr () const

bool	isKokkosObject () const

MooseApp &	getMooseApp () const

const std::string &	type () const

const std::string &	name () const

std::string	typeAndName () const

MooseObjectParameterName	uniqueParameterName (const std::string &parameter_name) const

MooseObjectName	uniqueName () const

const InputParameters &	parameters () const

const hit::Node *	getHitNode () const

bool	hasBase () const

const std::string &	getBase () const

const T &	getParam (const std::string &name) const

std::vector< std::pair< T1, T2 > >	getParam (const std::string &param1, const std::string &param2) const

const T *	queryParam (const std::string &name) const

const T &	getRenamedParam (const std::string &old_name, const std::string &new_name) const

T	getCheckedPointerParam (const std::string &name, const std::string &error_string="") const

bool	isParamValid (const std::string &name) const

bool	isParamSetByUser (const std::string &name) const

void	connectControllableParams (const std::string &parameter, const std::string &object_type, const std::string &object_name, const std::string &object_parameter) const

void	paramError (const std::string &param, Args... args) const

void	paramWarning (const std::string &param, Args... args) const

void	paramWarning (const std::string &param, Args... args) const

void	paramInfo (const std::string &param, Args... args) const

std::string	messagePrefix (const bool hit_prefix=true) const

std::string	errorPrefix (const std::string &) const

void	mooseError (Args &&... args) const

void	mooseDocumentedError (const std::string &repo_name, const unsigned int issue_num, Args &&... args) const

void	mooseErrorNonPrefixed (Args &&... args) const

void	mooseWarning (Args &&... args) const

void	mooseWarning (Args &&... args) const

void	mooseWarningNonPrefixed (Args &&... args) const

void	mooseWarningNonPrefixed (Args &&... args) const

void	mooseDeprecated (Args &&... args) const

void	mooseDeprecated (Args &&... args) const

void	mooseDeprecatedNoTrace (Args &&... args) const

void	mooseInfo (Args &&... args) const

void	callMooseError (std::string msg, const bool with_prefix, const hit::Node *node=nullptr, const bool show_trace=true) const

std::string	getDataFileName (const std::string &param) const

std::string	getDataFileNameByName (const std::string &relative_path) const

std::string	getDataFilePath (const std::string &relative_path) const

const Parallel::Communicator &	comm () const

processor_id_type	n_processors () const

processor_id_type	processor_id () const

Static Public Member Functions
static InputParameters	validParams ()

static bool	hasGenerateData (const InputParameters &params)

static bool	hasGenerateCSG (const InputParameters &params)

static void	callMooseError (MooseApp const app, const InputParameters &params, std::string msg, const bool with_prefix, const hit::Node node, const bool show_trace=true)

static void	setHasGenerateData (InputParameters &params)

static void	setHasGenerateCSG (InputParameters &params)

Public Attributes
	usingCombinedWarningSolutionWarnings

const ConsoleStream	_console

Static Public Attributes
static const std::string	data_only_param

static const std::string	type_param

static const std::string	name_param

static const std::string	unique_name_param

static const std::string	app_param

static const std::string	moose_base_param

static const std::string	kokkos_object_param

static constexpr auto	SYSTEM

static constexpr auto	NAME

Protected Member Functions
std::unique_ptr< MeshBase > &	buildMeshSubgenerator ()

void	readEBSDHeader ()
	Read the EBSD data file header.

virtual void	generateData ()

virtual std::unique_ptr< CSG::CSGBase >	generateCSG ()

T &	copyMeshProperty (const std::string &target_data_name, const std::string &source_data_name, const std::string &source_mesh)

T &	copyMeshProperty (const std::string &source_data_name, const std::string &source_mesh)

std::unique_ptr< MeshBase > &	getMesh (const std::string &param_name, const bool allow_invalid=false)

std::vector< std::unique_ptr< MeshBase > * >	getMeshes (const std::string &param_name)

std::unique_ptr< MeshBase > &	getMeshByName (const MeshGeneratorName &mesh_generator_name)

std::vector< std::unique_ptr< MeshBase > * >	getMeshesByName (const std::vector< MeshGeneratorName > &mesh_generator_names)

std::unique_ptr< CSG::CSGBase > &	getCSGBase (const std::string &param_name)

std::unique_ptr< CSG::CSGBase > &	getCSGBaseByName (const MeshGeneratorName &mesh_generator_name)

std::vector< std::unique_ptr< CSG::CSGBase > * >	getCSGBases (const std::string &param_name)

std::vector< std::unique_ptr< CSG::CSGBase > * >	getCSGBasesByName (const std::vector< MeshGeneratorName > &mesh_generator_names)

void	declareMeshForSub (const std::string &param_name)

void	declareMeshesForSub (const std::string &param_name)

void	declareMeshForSubByName (const MeshGeneratorName &mesh_generator_name)

void	declareMeshesForSubByName (const std::vector< MeshGeneratorName > &mesh_generator_names)

std::unique_ptr< MeshBase >	buildMeshBaseObject (unsigned int dim=libMesh::invalid_uint)

std::unique_ptr< ReplicatedMesh >	buildReplicatedMesh (unsigned int dim=libMesh::invalid_uint)

std::unique_ptr< DistributedMesh >	buildDistributedMesh (unsigned int dim=libMesh::invalid_uint)

void	addMeshSubgenerator (const std::string &type, const std::string &name, Ts... extra_input_parameters)

void	addMeshSubgenerator (const std::string &type, const std::string &name, InputParameters params)

void	declareNullMeshName (const MeshGeneratorName &name)

void	flagInvalidSolutionInternal (const InvalidSolutionID invalid_solution_id) const

InvalidSolutionID	registerInvalidSolutionInternal (const std::string &message, const bool warning) const

const T &	getMeshProperty (const std::string &data_name, const std::string &prefix)

const T &	getMeshProperty (const std::string &data_name)

bool	hasMeshProperty (const std::string &data_name, const std::string &prefix) const

bool	hasMeshProperty (const std::string &data_name, const std::string &prefix) const

bool	hasMeshProperty (const std::string &data_name) const

bool	hasMeshProperty (const std::string &data_name) const

std::string	meshPropertyName (const std::string &data_name) const

T &	declareMeshProperty (const std::string &data_name, Args &&... args)

T &	declareMeshProperty (const std::string &data_name, const T &data_value)

T &	declareMeshProperty (const std::string &data_name, Args &&... args)

T &	declareMeshProperty (const std::string &data_name, const T &data_value)

T &	setMeshProperty (const std::string &data_name, Args &&... args)

T &	setMeshProperty (const std::string &data_name, const T &data_value)

T &	setMeshProperty (const std::string &data_name, Args &&... args)

T &	setMeshProperty (const std::string &data_name, const T &data_value)

Static Protected Member Functions
static std::string	meshPropertyName (const std::string &data_name, const std::string &prefix)

Protected Attributes
const bool	_distributed
	are we working on a distributed mesh?

const FileName &	_filename
	Name of the file containing the EBSD data.

Geometry	_geometry
	EBSD data file mesh information.

const unsigned int	_pre_refine

std::unique_ptr< MeshBase > &	_base

MooseMesh *const	_mesh

const bool &	_enabled

MooseApp &	_app

Factory &	_factory

ActionFactory &	_action_factory

const std::string &	_type

const std::string &	_name

const InputParameters &	_pars

const Parallel::Communicator &	_communicator

Private Member Functions
virtual std::string	meshPropertyPrefix (const std::string &) const override final

void	checkGetMesh (const MeshGeneratorName &mesh_generator_name, const std::string &param_name) const

const MeshGeneratorName *	getMeshGeneratorNameFromParam (const std::string &param_name, const bool allow_invalid) const

const std::vector< MeshGeneratorName > &	getMeshGeneratorNamesFromParam (const std::string &param_name) const

RestartableDataValue &	setMeshPropertyHelper (const std::string &data_name)

const RestartableDataValue &	getMeshPropertyInternal (const std::string &data_name, const std::string &prefix) const

void	mooseErrorInternal (Args &&... args) const

Static Private Member Functions
static const hit::Node *	getHitNode (const InputParameters &params)

static std::string	messagePrefix (const InputParameters &params, const bool hit_prefix)

Private Attributes
std::set< MeshGeneratorName >	_requested_mesh_generators

std::set< MeshGeneratorName >	_requested_mesh_generators_for_sub

std::vector< std::pair< std::string, std::unique_ptr< MeshBase > * > >	_requested_meshes

std::vector< std::pair< std::string, std::unique_ptr< CSG::CSGBase > * > >	_requested_csg_bases

std::unique_ptr< MeshBase >	_null_mesh

std::unique_ptr< CSG::CSGBase >	_null_csg_base

std::set< const MeshGenerator *, Comparator >	_parent_mesh_generators

std::set< const MeshGenerator *, Comparator >	_child_mesh_generators

std::set< const MeshGenerator *, Comparator >	_sub_mesh_generators

std::set< std::string >	_null_mesh_names

const std::string &	_save_with_name

const bool	_data_only

const ParallelParamObject &	_parent

const MooseBase &	_si_moose_base

const FEProblemBase *	_si_problem

MooseApp &	_meta_data_app

const MooseObject *const	_meta_data_object

Detailed Description

Mesh generated from parameters read from a DREAM3D EBSD file.

Definition at line 19 of file EBSDMeshGenerator.h.

Constructor & Destructor Documentation

◆ EBSDMeshGenerator()

EBSDMeshGenerator::EBSDMeshGenerator ( const InputParameters & parameters )

Definition at line 45 of file EBSDMeshGenerator.C.

  : MeshGenerator(parameters),
    _distributed(_mesh->isDistributedMesh()),
    _filename(getParam<FileName>("filename")),
    _pre_refine(isParamValid("pre_refine") ? getParam<unsigned int>("pre_refine")
                                           : getParam<unsigned int>("uniform_refine")),
    _base(buildMeshSubgenerator())
{
}

Member Function Documentation

◆ buildMeshSubgenerator()

std::unique_ptr< MeshBase > & EBSDMeshGenerator::buildMeshSubgenerator ( )

protected

Definition at line 56 of file EBSDMeshGenerator.C.

{
  readEBSDHeader();
 
  const auto generator_type =
      _distributed ? "DistributedRectilinearMeshGenerator" : "GeneratedMeshGenerator";
  auto params = _app.getFactory().getValidParams(generator_type);
 
  params.set<MooseEnum>("dim") = (_geometry.dim == 1 ? "1" : (_geometry.dim == 2 ? "2" : "3"));
 
  std::array<unsigned int, 3> nr;
  nr[0] = _geometry.n[0];
  nr[1] = _geometry.n[1];
  nr[2] = _geometry.n[2];
 
  // set min/max box length
  params.set<Real>("xmin") = _geometry.min[0];
  params.set<Real>("xmax") = nr[0] * _geometry.d[0] + _geometry.min[0];
  params.set<Real>("ymin") = _geometry.min[1];
  params.set<Real>("ymax") = nr[1] * _geometry.d[1] + _geometry.min[1];
  params.set<Real>("zmin") = _geometry.min[2];
  params.set<Real>("zmax") = nr[2] * _geometry.d[2] + _geometry.min[2];
 
  // check if the requested uniform refine level is possible and determine initial grid size
  for (auto i : make_range(_geometry.dim))
  {
    auto factor = MathUtils::pow(2, _pre_refine);
    if (nr[i] % factor != 0)
      paramError("pre_refine",
                 "EBSDMeshGenerator error. Requested levels of pre refinement not possible.");
    nr[i] /= factor;
  }
 
  if (_distributed)
  {
    params.set<dof_id_type>("nx") = nr[0];
    params.set<dof_id_type>("ny") = nr[1];
    params.set<dof_id_type>("nz") = nr[2];
    params.set<processor_id_type>("num_cores_for_partition") =
        isParamValid("num_cores_for_partition")
            ? getParam<processor_id_type>("num_cores_for_partition")
            : 0;
  }
  else
  {
    params.set<unsigned int>("nx") = nr[0];
    params.set<unsigned int>("ny") = nr[1];
    params.set<unsigned int>("nz") = nr[2];
  }
 
  addMeshSubgenerator(generator_type, name() + "_base_mesh", params);
  return getMeshByName(name() + "_base_mesh");
}

◆ generate()

std::unique_ptr< MeshBase > EBSDMeshGenerator::generate ( )

overridevirtual

Implements MeshGenerator.

Definition at line 191 of file EBSDMeshGenerator.C.

{
  if (_pre_refine)
  {
    libMesh::MeshRefinement mesh_refinement(*_base);
    mesh_refinement.uniformly_refine(_pre_refine);
  }
  return std::move(_base);
}

◆ getEBSDFilename()

const std::string & EBSDMeshGenerator::getEBSDFilename ( ) const

inline

Definition at line 42 of file EBSDMeshGenerator.h.

42{ return _filename; }

Referenced by EBSDReader::readFile().

◆ getEBSDGeometry()

const Geometry & EBSDMeshGenerator::getEBSDGeometry ( ) const

inline

Definition at line 41 of file EBSDMeshGenerator.h.

41{ return _geometry; }

Referenced by EBSDReader::readFile().

◆ readEBSDHeader()

void EBSDMeshGenerator::readEBSDHeader ( )

protected

Read the EBSD data file header.

Definition at line 111 of file EBSDMeshGenerator.C.

{
  std::ifstream stream_in(_filename.c_str());
 
  if (!stream_in)
    paramError("filename", "Can't open EBSD file: ", _filename);
 
  // Labels to look for in the header
  const std::vector<std::string> labels = {
      "x_step", "x_dim", "y_step", "y_dim", "z_step", "z_dim", "x_min", "y_min", "z_min"};
 
  // Dimension variables to store once they are found in the header
  // X_step, X_Dim, Y_step, Y_Dim, Z_step, Z_Dim
  // We use Reals even though the Dim values should all be integers...
  std::vector<Real> label_vals(labels.size(), 0.0);
 
  std::string line;
  while (std::getline(stream_in, line))
  {
    // We need to process the comment lines that have:
    // X_step, X_Dim
    // Y_step, Y_Dim
    // Z_step, Z_Dim
    // in them. The labels are case insensitive.
    if (line.find("#") == 0)
    {
      // Process lines that start with a comment character (comments and meta data)
      std::transform(line.begin(), line.end(), line.begin(), ::tolower);
 
      for (unsigned i = 0; i < labels.size(); ++i)
        if (line.find(labels[i]) != std::string::npos)
        {
          std::string dummy;
          std::istringstream iss(line);
          iss >> dummy >> dummy >> label_vals[i];
 
          // One label per line, break out of for loop over labels
          break;
        }
    }
    else
      // first non comment line marks the end of the header
      break;
  }
 
  // Copy stuff out of the label_vars array into class variables
  _geometry.d[0] = label_vals[0];
  _geometry.n[0] = label_vals[1];
  _geometry.min[0] = label_vals[6];
 
  _geometry.d[1] = label_vals[2];
  _geometry.n[1] = label_vals[3];
  _geometry.min[1] = label_vals[7];
 
  _geometry.d[2] = label_vals[4];
  _geometry.n[2] = label_vals[5];
  _geometry.min[2] = label_vals[8];
 
  unsigned int dim;
 
  // determine mesh dimension
  for (dim = 3; dim > 0 && _geometry.n[dim - 1] == 0; --dim)
    ;
 
  // check if the data has nonzero stepsizes
  for (unsigned i = 0; i < dim; ++i)
  {
    if (_geometry.n[i] == 0)
      mooseError("Error reading header, EBSD grid size is zero.");
    if (_geometry.d[i] == 0.0)
      mooseError("Error reading header, EBSD data step size is zero.");
  }
 
  if (dim == 0)
    mooseError("Error reading header, EBSD data is zero dimensional.");
 
  _geometry.dim = dim;
}

Referenced by buildMeshSubgenerator().

◆ validParams()

InputParameters EBSDMeshGenerator::validParams ( )

static

Definition at line 22 of file EBSDMeshGenerator.C.

{
  InputParameters params = MeshGenerator::validParams();
  params.addClassDescription("Mesh generated from a specified DREAM.3D EBSD data file.");
  params.addRequiredParam<FileName>("filename", "The name of the file containing the EBSD data");
 
  params.addDeprecatedParam<unsigned int>("uniform_refine",
                                          "Deprecated. Use `pre_refine` instead.",
                                          "Deprecated. Use `pre_refine` instead.");
  params.addParam<unsigned int>(
      "pre_refine",
      0,
      "Number of coarsening levels available in adaptive mesh refinement. The resulting mesh will "
      "have one mesh element per EBSD data cell, but will be based on a refined coarser mesh with "
      "'pre_refine' levels of refinement. This requires all dimension of the EBSD data to be "
      "divisible by 2^pre_refine.(this parameter was formerly called 'uniform_refine')");
 
  params.addParam<processor_id_type>(
      "num_cores_for_partition",
      "Number of cores for partitioning the graph (dafaults to the number of MPI ranks)");
  return params;
}

Referenced by EBSDMeshErrorTest::testParam().

Member Data Documentation

◆ _base

std::unique_ptr<MeshBase>& EBSDMeshGenerator::_base

protected

Definition at line 63 of file EBSDMeshGenerator.h.

Referenced by generate().

◆ _distributed

const bool EBSDMeshGenerator::_distributed

protected

are we working on a distributed mesh?

Definition at line 51 of file EBSDMeshGenerator.h.

Referenced by buildMeshSubgenerator().

◆ _filename

const FileName& EBSDMeshGenerator::_filename

protected

Name of the file containing the EBSD data.

Definition at line 54 of file EBSDMeshGenerator.h.

Referenced by getEBSDFilename(), and readEBSDHeader().

◆ _geometry

Geometry EBSDMeshGenerator::_geometry

protected

EBSD data file mesh information.

Definition at line 57 of file EBSDMeshGenerator.h.

Referenced by buildMeshSubgenerator(), getEBSDGeometry(), and readEBSDHeader().

◆ _pre_refine

const unsigned int EBSDMeshGenerator::_pre_refine

protected

Definition at line 60 of file EBSDMeshGenerator.h.

Referenced by buildMeshSubgenerator(), and generate().

The documentation for this class was generated from the following files:

phase_field/include/meshgenerators/EBSDMeshGenerator.h
phase_field/src/meshgenerators/EBSDMeshGenerator.C

Classes

Public Types

Public Member Functions

Static Public Member Functions

Public Attributes

Static Public Attributes

Protected Member Functions

Static Protected Member Functions

Protected Attributes

Private Member Functions

Static Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ EBSDMeshGenerator()

Member Function Documentation

◆ buildMeshSubgenerator()

◆ generate()

◆ getEBSDFilename()

◆ getEBSDGeometry()

◆ readEBSDHeader()

◆ validParams()

Member Data Documentation

◆ _base

◆ _distributed

◆ _filename

◆ _geometry

◆ _pre_refine