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< 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	isDataOnly () const

virtual bool	enabled () const

std::shared_ptr< MooseObject >	getSharedPtr ()

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

MooseApp &	getMooseApp () const

const std::string &	type () const

virtual const std::string &	name () const

std::string	typeAndName () const

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

void	callMooseError (std::string msg, const bool with_prefix) const

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

const InputParameters &	parameters () const

MooseObjectName	uniqueName () 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 &nm) const

void	paramError (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

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

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

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

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

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

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

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

void	mooseInfo (Args &&... args) 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 void	setHasGenerateData (InputParameters &params)

Public Attributes
const ConsoleStream	_console

Static Public Attributes
static const std::string	data_only_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. More...

virtual void	generateData ()

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)

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)

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? More...

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

Geometry	_geometry
	EBSD data file mesh information. More...

const unsigned int	_pre_refine

std::unique_ptr< MeshBase > &	_base

MooseMesh *const	_mesh

const bool &	_enabled

MooseApp &	_app

const std::string	_type

const std::string	_name

const InputParameters &	_pars

Factory &	_factory

ActionFactory &	_action_factory

const Parallel::Communicator &	_communicator

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.

Referenced by EBSDReader::readFile().

42 { return _filename; }

EBSDMeshGenerator::_filename

const FileName & _filename

Name of the file containing the EBSD data.

Definition: EBSDMeshGenerator.h:54

◆ getEBSDGeometry()

const Geometry& EBSDMeshGenerator::getEBSDGeometry ( ) const

inline

Definition at line 41 of file EBSDMeshGenerator.h.

Referenced by EBSDReader::readFile().

41 { return _geometry; }

EBSDMeshGenerator::_geometry

Geometry _geometry

EBSD data file mesh information.

Definition: EBSDMeshGenerator.h:57

◆ readEBSDHeader()

void EBSDMeshGenerator::readEBSDHeader ( )

protected

Read the EBSD data file header.

Definition at line 111 of file EBSDMeshGenerator.C.

Referenced by buildMeshSubgenerator().

 {
   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;
 }

◆ validParams()

InputParameters EBSDMeshGenerator::validParams ( )

static

Definition at line 22 of file EBSDMeshGenerator.C.

Referenced by EBSDMeshErrorTest::testParam().

 {
   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;
 }

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

Detailed Description

Constructor & Destructor Documentation

◆ EBSDMeshGenerator()

Member Function Documentation

◆ buildMeshSubgenerator()

◆ generate()

◆ getEBSDFilename()

◆ getEBSDGeometry()

◆ readEBSDHeader()

◆ validParams()

Member Data Documentation

◆ _base

◆ _distributed

◆ _filename

◆ _geometry

◆ _pre_refine