The VTKMeshGenerator class provides a class implementation of VTK generated meshes. More...

#include <VTKMeshGenerator.hpp>

Inheritance diagram for geos::VTKMeshGenerator:

[legend]

Public Member Functions
	VTKMeshGenerator (const string &name, Group *const parent)
	Main constructor for MeshGenerator base class. More...

virtual void	fillCellBlockManager (CellBlockManager &cellBlockManager, SpatialPartition &partition) override
	Generate the mesh using the VTK library. More...

void	importFieldOnArray (Block block, string const &blockName, string const &meshFieldName, bool isMaterialField, dataRepository::WrapperBase &wrapper) const override
	import field from the mesh on the array accessible via the given wrapper. More...

virtual void	freeResources () override
	Free internal resources associated with mesh/data import. More...

Public Member Functions inherited from geos::ExternalMeshGeneratorBase
	ExternalMeshGeneratorBase (const string &name, Group *const parent)
	Constructor. More...

Public Member Functions inherited from geos::MeshGeneratorBase
	MeshGeneratorBase (string const &name, Group *const parent)
	Main constructor for MeshGenerator base class. More...

virtual void	expandObjectCatalogs () override
	This function is used to expand any catalogs in the data structure.

virtual Group *	createChild (string const &childKey, string const &childName) override
	Create a new geometric object (box, plane, etc) as a child of this group. More...

void	generateMesh (Group &parent, SpatialPartition &partition)
	Generate the mesh object the input mesh object. More...

const std::map< string, string > &	getVolumicFieldsMapping () const
	Get the name mapping between mesh volumic field names and internal GEOSX volumic field names. More...

const std::map< string, string > &	getSurfacicFieldsMapping () const
	Get the name mapping between mesh surfacic field names and internal GEOSX surfacic field names. More...

Public Member Functions inherited from geos::dataRepository::Group
virtual bool	registerCallback (void *func, const std::type_info &funcType)
	Register a callback function on the group. More...

virtual void	reinit ()
	Performs re-initialization of certain variable depending on the solver being used.

	Group (string const &name, Group *const parent)
	Constructor. More...

	Group (string const &name, conduit::Node &rootNode)
	Constructor. More...

	Group (Group &&source)=default
	Move constructor. More...

virtual	~Group ()
	Destructor, deletes all Groups and Wrappers owned by this Group.

	Group ()=delete
	Deleted default constructor.

	Group (Group const &)=delete
	Deleted copy constructor.

Group &	operator= (Group const &)=delete
	Deleted copy assignment operator. More...

Group &	operator= (Group &&)=delete
	Deleted move assignment operator. More...

void	printDataHierarchy (integer indent=0) const
	Prints the data hierarchy recursively. More...

string	dumpInputOptions () const

string	dumpSubGroupsNames () const

string	dumpWrappersNames () const

template<typename T = Group>
T &	registerGroup (string const &name, std::unique_ptr< T > newObject)
	Register a new Group as a sub-group of current Group. More...

template<typename T = Group>
T &	registerGroup (string const &name, T *newObject)
	Register a new Group as a sub-group of current Group. More...

template<typename T = Group>
T &	registerGroup (string const &name)
	Register a new Group as a sub-group of current Group. More...

template<typename T = Group>
T &	registerGroup (subGroupMap::KeyIndex const &keyIndex)
	Register a new Group as a sub-group of current Group. More...

template<typename T = Group, typename TBASE = Group>
T &	registerGroup (string const &name, string const &catalogName)
	Register a new Group as a sub-group of current Group. More...

void	deregisterGroup (string const &name)
	Removes a child group from this group. More...

template<typename T = Group, typename KEY = void>
T *	getGroupPointer (KEY const &key)
	Return a pointer to a sub-group of the current Group. More...

template<typename T = Group, typename KEY = void>
const T *	getGroupPointer (KEY const &key) const
	Return a pointer to a sub-group of the current Group. More...

template<typename T = Group, typename KEY = void>
T &	getGroup (KEY const &key)
	Return a reference to a sub-group of the current Group. More...

template<typename T = Group, typename KEY = void>
const T &	getGroup (KEY const &key) const
	Return a reference to a sub-group of the current Group. More...

template<typename T = Group>
T &	getGroupByPath (string const &path)
	Retrieve a group from the hierarchy using a path. More...

template<typename T = Group>
const T &	getGroupByPath (string const &path) const
	Retrieve a group from the hierarchy using a path. More...

subGroupMap &	getSubGroups ()
	Get the subgroups object. More...

const subGroupMap &	getSubGroups () const
	Get the subgroups object. More...

localIndex	numSubGroups () const
	return the number of sub groups in this Group More...

std::vector< string >	getSubGroupsNames () const

template<typename T = Group>
bool	hasGroup (string const &name) const
	Check whether a sub-group exists. More...

template<typename T >
bool	hasSubGroupOfType () const
	Check whether a sub-group exists by type. More...

template<typename GROUPTYPE = Group, typename ... GROUPTYPES, typename LAMBDA >
void	forSubGroups (LAMBDA &&lambda)
	Apply the given functor to subgroups that can be casted to one of specified types. More...

template<typename GROUPTYPE = Group, typename ... GROUPTYPES, typename LAMBDA >
void	forSubGroups (LAMBDA &&lambda) const
	Apply the given functor to subgroups that can be casted to one of specified types. More...

template<typename GROUPTYPE = Group, typename ... GROUPTYPES, typename LAMBDA >
void	forSubGroupsIndex (LAMBDA &&lambda)
	Apply the given functor to subgroups that can be casted to one of specified types. More...

template<typename GROUPTYPE = Group, typename ... GROUPTYPES, typename LAMBDA >
void	forSubGroupsIndex (LAMBDA &&lambda) const
	Apply the given functor to subgroups that can be casted to one of specified types. More...

template<typename GROUPTYPE = Group, typename ... GROUPTYPES, typename LOOKUP_CONTAINER , typename LAMBDA >
void	forSubGroups (LOOKUP_CONTAINER const &subGroupKeys, LAMBDA &&lambda)
	Apply the given functor to subgroups that can be casted to one of specified types. More...

template<typename GROUPTYPE = Group, typename ... GROUPTYPES, typename LOOKUP_CONTAINER , typename LAMBDA >
void	forSubGroups (LOOKUP_CONTAINER const &subGroupKeys, LAMBDA &&lambda) const
	Apply the given functor to subgroups that can be casted to one of specified types. More...

template<typename LAMBDA >
void	forWrappers (LAMBDA &&lambda)
	Apply the given functor to wrappers. More...

template<typename LAMBDA >
void	forWrappers (LAMBDA &&lambda) const
	Apply the given functor to wrappers. More...

template<typename TYPE , typename ... TYPES, typename LAMBDA >
void	forWrappers (LAMBDA &&lambda)
	Apply the given functor to wrappers that can be cast to one of specified types. More...

template<typename TYPE , typename ... TYPES, typename LAMBDA >
void	forWrappers (LAMBDA &&lambda) const
	Apply the given functor to wrappers that can be cast to one of specified types. More...

virtual void	initialize_postMeshGeneration ()
	initialization post generation of the mesh.

void	initialize ()
	Run initialization functions on this and all subgroups. More...

virtual void	initializationOrder (string_array &order)
	Sets the initialization order for sub-Groups. More...

void	initializePostInitialConditions ()
	Initialization routine to be called after calling ApplyInitialConditions(). More...

void	postRestartInitializationRecursive ()
	Initialization routine to be called after calling reading a restart file. More...

void	processInputFileRecursive (xmlWrapper::xmlDocument &xmlDocument, xmlWrapper::xmlNode &targetNode)
	Recursively read values using ProcessInputFile() from the input file and put them into the wrapped values for this group. Also add the includes content to the xmlDocument when `Include` nodes are encountered. More...

void	processInputFileRecursive (xmlWrapper::xmlDocument &xmlDocument, xmlWrapper::xmlNode &targetNode, xmlWrapper::xmlNodePos const &nodePos)
	Same as processInputFileRecursive(xmlWrapper::xmlDocument &, xmlWrapper::xmlNode &) but allow to reuse an existing xmlNodePos. More...

void	postProcessInputRecursive ()
	Recursively call postProcessInput() to apply post processing after reading input values.

template<typename T , typename TBASE = T>
Wrapper< TBASE > &	registerWrapper (string const &name, wrapperMap::KeyIndex::index_type *const rkey=nullptr)
	Create and register a Wrapper around a new object. More...

template<typename T , typename TBASE = T>
Wrapper< TBASE > &	registerWrapper (Group::wrapperMap::KeyIndex const &viewKey)
	Create and register a Wrapper around a new object. More...

template<typename T >
Wrapper< T > &	registerWrapper (string const &name, std::unique_ptr< T > newObject)
	Register a Wrapper around a given object and take ownership. More...

template<typename T >
Wrapper< T > &	registerWrapper (string const &name, T *newObject)
	Register a Wrapper around an existing object, does not take ownership of the object. More...

WrapperBase &	registerWrapper (std::unique_ptr< WrapperBase > wrapper)
	Register and take ownership of an existing Wrapper. More...

void	deregisterWrapper (string const &name)
	Removes a Wrapper from this group. More...

void	generateDataStructureSkeleton (integer const level)
	Build a complete datastructure for schema generation. More...

virtual void	setSchemaDeviations (xmlWrapper::xmlNode schemaRoot, xmlWrapper::xmlNode schemaParent, integer documentationType)
	Inform the schema generator of any deviations between the xml and GEOS data structures. More...

virtual void	registerDataOnMeshRecursive (Group &meshBodies)
	Calls RegisterDataOnMesh() recursively. More...

virtual void	registerDataOnMesh (Group &meshBodies)
	Register data on mesh entities. More...

virtual localIndex	packSize (string_array const &wrapperNames, integer const recursive, bool onDevice, parallelDeviceEvents &events) const
	Get the size required to pack a list of wrappers. More...

virtual localIndex	packSize (string_array const &wrapperNames, arrayView1d< localIndex const > const &packList, integer const recursive, bool onDevice, parallelDeviceEvents &events) const
	Get the size required to pack a list of indices within a list of wrappers. More...

localIndex	packSize (arrayView1d< localIndex const > const &packList, integer const recursive, bool onDevice, parallelDeviceEvents &events) const
	Get the size required to pack a list of indices for all registered wrappers. More...

virtual localIndex	pack (buffer_unit_type *&buffer, string_array const &wrapperNames, integer const recursive, bool onDevice, parallelDeviceEvents &events) const
	Pack a list of wrappers to a buffer. More...

virtual localIndex	pack (buffer_unit_type *&buffer, string_array const &wrapperNames, arrayView1d< localIndex const > const &packList, integer const recursive, bool onDevice, parallelDeviceEvents &events) const
	Pack a list of indices within a list of wrappers. More...

localIndex	pack (buffer_unit_type *&buffer, arrayView1d< localIndex const > const &packList, integer const recursive, bool onDevice, parallelDeviceEvents &events) const
	Pack a list of indices for all registered wrappers. More...

virtual localIndex	unpack (buffer_unit_type const *&buffer, arrayView1d< localIndex > &packList, integer const recursive, bool onDevice, parallelDeviceEvents &events, MPI_Op op=MPI_REPLACE)
	Unpack a buffer. More...

template<typename KEY >
const WrapperBase &	getWrapperBase (KEY const &key) const
	Return a reference to a WrapperBase stored in this group. More...

template<typename KEY >
WrapperBase &	getWrapperBase (KEY const &key)
	Return a reference to a WrapperBase stored in this group. More...

indexType	getWrapperIndex (string const &name) const

const wrapperMap &	wrappers () const
	Get access to the internal wrapper storage. More...

wrapperMap &	wrappers ()
	Get access to the internal wrapper storage. More...

indexType	numWrappers () const
	Return the number of wrappers. More...

std::vector< string >	getWrappersNames () const

template<typename LOOKUP_TYPE >
bool	hasWrapper (LOOKUP_TYPE const &lookup) const
	Check if a wrapper exists. More...

template<typename T , typename LOOKUP_TYPE >
const Wrapper< T > &	getWrapper (LOOKUP_TYPE const &index) const
	Retrieve a Wrapper stored in this group. More...

template<typename T , typename LOOKUP_TYPE >
Wrapper< T > &	getWrapper (LOOKUP_TYPE const &index)
	Retrieve a Wrapper stored in this group. More...

template<typename T , typename LOOKUP_TYPE >
const Wrapper< T > *	getWrapperPointer (LOOKUP_TYPE const &index) const
	Retrieve a Wrapper stored in this group. More...

template<typename T , typename LOOKUP_TYPE >
Wrapper< T > *	getWrapperPointer (LOOKUP_TYPE const &index)
	Retrieve a Wrapper stored in this group. More...

template<typename T , typename LOOKUP_TYPE >
GEOS_DECLTYPE_AUTO_RETURN	getReference (LOOKUP_TYPE const &lookup) const
	Look up a wrapper and get reference to wrapped object. More...

template<typename T , typename LOOKUP_TYPE >
T &	getReference (LOOKUP_TYPE const &lookup)
	Look up a wrapper and get reference to wrapped object. More...

virtual void	resize (localIndex const newSize)
	Resize the group and all contained wrappers that resize with parent. More...

virtual void	reserve (indexType const newsize)
	Set the new capacity and reserve it in all wrappers that resize with parent. More...

localIndex	capacity () const
	Get the "capacity" of the group, which determines the capacity of resizable wrappers. More...

localIndex	size () const
	Get the "size" of the group, which determines the number of elements in resizable wrappers. More...

const string &	getName () const
	Get group name. More...

string	getPath () const
	Return the path of this Group in the data repository. Starts with '/' followed by the hierarchy of the children of the "Problem" in which the Group is. More...

const DataContext &	getDataContext () const

template<typename KEY >
const DataContext &	getWrapperDataContext (KEY key) const

Group &	getParent ()
	Access the group's parent. More...

const Group &	getParent () const
	Access the group's parent. More...

bool	hasParent () const

localIndex	getIndexInParent () const
	Get the group's index within its parent group. More...

localIndex	getSubGroupIndex (keyType const &key) const
	Get the index of a sub-Group within this group. More...

int	sizedFromParent () const
	Check whether this Group is resized when its parent is resized. More...

Group &	setSizedFromParent (int val)
	Set whether this wrapper is resized when its parent is resized. More...

RestartFlags	getRestartFlags () const
	Get flags that control restart output of this group. More...

void	setRestartFlags (RestartFlags flags)
	Set flags that control restart output of this group. More...

InputFlags	getInputFlags () const
	Get input flags for schema generation. More...

void	setInputFlags (InputFlags flags)
	Set input flags for schema generation. More...

conduit::Node &	getConduitNode ()
	Return the Conduit node object associated with this group. More...

const conduit::Node &	getConduitNode () const
	Return the Conduit node object associated with this group. More...

void	prepareToWrite ()
	Register the group and its wrappers with Conduit.

void	finishWriting ()
	Write the group and its wrappers into Conduit.

void	loadFromConduit ()
	Read the group and its wrappers from Conduit.

void	enableLogLevelInput ()
	Enable verbosity input for object.

void	setLogLevel (integer const logLevel)
	Set verbosity level. More...

integer	getLogLevel () const

Static Public Member Functions
static string	catalogName ()
	Return the name of the VTKMeshGenerator in object Catalog. More...

Static Public Member Functions inherited from geos::MeshGeneratorBase
static string	catalogName ()
	Return the name of the MeshGenerator in object catalog. More...

static CatalogInterface::CatalogType &	getCatalog ()
	Accessor for the singleton Catalog object. More...

Static Public Member Functions inherited from geos::dataRepository::Group
template<typename T0 , typename T1 , typename ... CASTTYPES, typename CONTAINERTYPE , typename LAMBDA >
static bool	applyLambdaToContainer (CONTAINERTYPE &container, LAMBDA &&lambda)
	Apply a given functor to a container if the container can be cast to one of the specified types. More...

static CatalogInterface::CatalogType &	getCatalog ()
	Get the singleton catalog for this class. More...

Additional Inherited Members
Public Types inherited from geos::MeshGeneratorBase
enum	Block { VOLUMIC, SURFACIC, LINEIC }
	Describe which kind of block must be considered.

using	CatalogInterface = dataRepository::CatalogInterface< MeshGeneratorBase, string const &, Group *const >
	using alias for templated Catalog meshGenerator type

Public Types inherited from geos::dataRepository::Group
using	subGroupMap = MappedVector< Group, Group *, keyType, indexType >
	The template specialization of MappedVector to use for the collection of sub-Group objects.

using	wrapperMap = MappedVector< WrapperBase, WrapperBase *, keyType, indexType >
	The template specialization of MappedVector to use for the collection wrappers objects.

using	CatalogInterface = dataRepository::CatalogInterface< Group, string const &, Group *const >
	Type alias for catalog interface used by this class. See CatalogInterface.

Protected Member Functions inherited from geos::ExternalMeshGeneratorBase
void	postProcessInput () override

Protected Member Functions inherited from geos::dataRepository::Group
virtual void	initializePreSubGroups ()
	Called by Initialize() prior to initializing sub-Groups.

virtual void	initializePostSubGroups ()
	Called by Initialize() after to initializing sub-Groups.

virtual void	initializePostInitialConditionsPreSubGroups ()
	Called by InitializePostInitialConditions() prior to initializing sub-Groups.

virtual void	initializePostInitialConditionsPostSubGroups ()
	Called by InitializePostInitialConditions() after to initializing sub-Groups.

virtual void	postRestartInitialization ()
	Performs initialization required after reading from a restart file.

Protected Attributes inherited from geos::ExternalMeshGeneratorBase
Path	m_filePath
	Path to the mesh file.

R1Tensor	m_translate
	Translation vector that will be applied to the point coordinates (prior to scaling)

R1Tensor	m_scale
	Scale factor that will be applied to the point coordinates (after translation)

array1d< string >	m_volumicFieldsToImport
	Names of the fields to be copied from an external reader into GEOSX data structure.

array1d< string >	m_volumicFieldsInGEOSX
	String array of the GEOSX user declared volumic fields.

array1d< string >	m_surfacicFieldsToImport
	Names of the surfacic fields to be copied from an external reader into GEOSX data structure.

array1d< string >	m_surfacicFieldsInGEOSX
	String array of the GEOSX user declared surfacic fields.

Protected Attributes inherited from geos::MeshGeneratorBase
std::map< string, string >	m_volumicFields
	Mapping from volumic field source to GEOSX field.

std::map< string, string >	m_surfacicFields
	Mapping from surfacic field source to GEOSX field.

Detailed Description

The VTKMeshGenerator class provides a class implementation of VTK generated meshes.

Definition at line 35 of file VTKMeshGenerator.hpp.

Constructor & Destructor Documentation

◆ VTKMeshGenerator()

geos::VTKMeshGenerator::VTKMeshGenerator	(	const string &	name,
		Group *const	parent
	)

Main constructor for MeshGenerator base class.

Parameters

[in]	name	of the VTKMeshGenerator object
[in]	parent	the parent Group pointer for the MeshGenerator object

Member Function Documentation

◆ catalogName()

static string geos::VTKMeshGenerator::catalogName ( )

inlinestatic

Return the name of the VTKMeshGenerator in object Catalog.

Returns: string that contains the key name to VTKMeshGenerator in the Catalog

Definition at line 51 of file VTKMeshGenerator.hpp.

◆ fillCellBlockManager()

virtual void geos::VTKMeshGenerator::fillCellBlockManager	(	CellBlockManager &	cellBlockManager,
		SpatialPartition &	partition
	)

overridevirtual

Generate the mesh using the VTK library.

Parameters

[in,out]	cellBlockManager	the CellBlockManager that will receive the meshing information
[in]	partition	the number of domain in each direction (x,y,z) for InternalMesh only, not used here

This method leverages the VTK library to load the meshes. The supported formats are the official VTK ones dedicated to unstructured grids (.vtu, .pvtu and .vtk) and structured grids (.vts, .vti and .pvts).

Please note that this mesh generator works only with a number of MPI processes than can be decomposed into a power of 2.

If a .vtu, .vts, .vti or .vtk file is used, the root MPI process will load it. The mesh will be then redistribute among all the available MPI processes
If a .pvtu or .pvts file is used, it means that the mesh is pre-partionned in the file system. The available MPI processes will load the pre-partionned mesh. The mesh will be then redistributed among ALL the available MPI processes.

The properties on the mesh will be also and redistributed. The only compatible types are double and float. The properties can be multi-dimensional. The name of the properties has to have the right name in order to be used by GEOSX. For instance, the property that stored the input porosity in GEOSX is named "referencePorosity", so the mesh has to have a property names "referencePorosity".

The regions are defined using a property called "attribute" that can be defined in the input mesh. This property will be held by each volume elements. This method will created several CellBlocks, named using the combination of the attribute index and the type of the element. For instance, the cells of a mesh with two regions will hold the attribute "1", or "2". The CellBlocks will be instantiated according to the attribute and the type of the cells. If the region "1" has wedges, tetrahedron and hexahedron, three CellBlocks will be created names 1_tetrahedron, 1_wedges and 1_hexahedron. The ElementRegions have to be be defined in the XML file.

The node sets of surface are defined in the same way, using the same property names "attribute" defined in the input mesh. The node sets will hold a name that is just the attribute index. For instance, if a mesh has three surfaces of interest, with triangles and/or quads holding an attribute value of 1, 2 or 3, three node sets named "1", "2" and "3" will be instantiated by this method

Reimplemented from geos::MeshGeneratorBase.

◆ freeResources()

virtual void geos::VTKMeshGenerator::freeResources ( )

overridevirtual

Free internal resources associated with mesh/data import.

This is relevant for mesh generators that load external mesh files. Once this method is called, they can release any memory allocated.

Reimplemented from geos::MeshGeneratorBase.

◆ importFieldOnArray()

void geos::VTKMeshGenerator::importFieldOnArray	(	Block	block,
		string const &	blockName,
		string const &	meshFieldName,
		bool	isMaterialField,
		dataRepository::WrapperBase &	wrapper
	)		const

overridevirtual

import field from the mesh on the array accessible via the given wrapper.

Parameters

block	Type of block to import from.
blockName	name of the block to copy data from.
meshFieldName	name of the field in the meshd
isMaterialField	Indicate if we want to import material or regular fields
wrapper	Wrapper to access the array

Implements geos::MeshGeneratorBase.

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

coreComponents/mesh/generators/VTKMeshGenerator.hpp

Public Member Functions

Static Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ VTKMeshGenerator()

Member Function Documentation

◆ catalogName()

◆ fillCellBlockManager()

◆ freeResources()

◆ importFieldOnArray()