Skins the [Mesh] according to individual bins for temperature, density, and subdomain ID. More...

#include <MoabSkinner.h>

Inheritance diagram for MoabSkinner:

Classes
struct	VolData
	Encode MOAB information about volumes needed when creating surfaces. More...

Public Member Functions
	MoabSkinner (const InputParameters &parameters)

virtual void	execute () override

virtual void	initialize () override

virtual void	finalize () override

virtual void	threadJoin (const UserObject &) override

virtual moab::ErrorCode	check (const moab::ErrorCode input) const

std::string	materialName (const unsigned int &block, const unsigned int &density, const unsigned int &temp) const

virtual void	update ()
	Perform the skinning operation.

virtual void	setMaterialNames (std::vector< std::string > names)

unsigned int	nBins () const

virtual unsigned int	getTemperatureBin (const Elem *const elem) const

virtual unsigned int	getDensityBin (const Elem *const elem) const

virtual unsigned int	getSubdomainBin (const Elem *const elem) const

void	setUseDisplacedMesh (const bool &use)

virtual void	setScaling (const Real &scale)

virtual void	setVerbosity (const bool &verbose)

virtual void	makeDependentOnExternalAction ()

unsigned int	getAuxiliaryVariableNumber (const std::string &name, const std::string &param_name) const

void	reset ()
	Clear mesh data.

virtual unsigned int	getBin (const unsigned int &temp_bin, const unsigned int &density_bin, const unsigned int &subdomain_bin) const

virtual const bool &	hasGraveyard () const

void	setGraveyard (bool build)

virtual unsigned int	nDensityBins () const

virtual bool	hasDensitySkinning () const

const std::shared_ptr< moab::Interface > &	moabPtr () const

Static Public Member Functions
static InputParameters	validParams ()

Protected Types
enum class	BoundaryConditionType { Transmission , Vacuum , Reflective }
	Boundary condition types that can be assigned to DAGMC surfaces. More...

enum	Sense { BACKWARDS = -1 , FORWARDS = 1 }
	Encode the whether the surface normal faces into or out of the volume. More...

Protected Member Functions
MooseMesh &	getMooseMesh ()
	Get the MooseMesh (displaced or not, depending on _use_displaced)

MeshBase &	getDAGMCGeometryMesh ()

void	buildTetMesh ()
	If the mesh has non-tetrahedral elements, clone it into _tet_mesh and convert to all-TET4.

void	createMOABElems ()

virtual void	createTags ()
	Helper method to create MOAB tags.

void	createGroup (const unsigned int &id, const std::string &name, moab::EntityHandle &group_set)

void	createVol (const unsigned int &id, moab::EntityHandle &volume_set, moab::EntityHandle group_set)
	Helper method to create MOAB volume entity set.

void	createSurf (const unsigned int &id, moab::EntityHandle &surface_set, moab::Range &faces, const std::vector< VolData > &voldata, BoundaryConditionType bc_type=BoundaryConditionType::Transmission)
	Helper method to create MOAB surface entity set.

void	createSurfaces (moab::Range &faces, VolData &voldata, unsigned int &surf_id, BoundaryConditionType bc_type=BoundaryConditionType::Transmission)

void	createSurfaceFromBox (const BoundingBox &box, const VolData &voldata, unsigned int &surf_id, bool normalout, const Real &factor)

std::vector< moab::EntityHandle >	createNodesFromBox (const BoundingBox &box, const Real &factor) const

void	createCornerTris (const std::vector< moab::EntityHandle > &verts, unsigned int corner, unsigned int v1, unsigned int v2, unsigned int v3, bool normalout, moab::Range &surface_tris)
	Create 3 tri faces stemming from one corner of a cude (an open tetrahedron)

moab::EntityHandle	createTri (const std::vector< moab::EntityHandle > &vertices, unsigned int v1, unsigned int v2, unsigned int v3)
	Create MOAB tri surface element.

void	updateSurfData (moab::EntityHandle surface_set, const VolData &data)
	Add parent-child metadata relating a surface to its volume.

void	setTags (moab::EntityHandle ent, std::string name, std::string category, unsigned int id, int dim)
	Generic method to set the tags that DAGMC requires.

void	setTagData (moab::Tag tag, moab::EntityHandle ent, std::string data, unsigned int SIZE)
	Helper function to wrap moab::tag_set_data for a string.

void	setTagData (moab::Tag tag, moab::EntityHandle ent, void *data)
	Helper function to wrap moab::tag_set_data for a generic pointer.

const std::vector< std::vector< unsigned int > > &	getTetSets (ElemType type) const

void	buildGraveyard (unsigned int &vol_id, unsigned int &surf_id)
	Build a graveyard volume around the domain.

virtual void	findBlocks ()
	Store a mapping from [Mesh] subdomain IDs to an index, to be used for binning by block ID.

virtual void	sortElemsByResults ()
	Sort all the elements in the [Mesh] into bins for temperature, density, and subdomain.

void	findSurfaces ()
	Group the binned elems into local temperature regions and find their surfaces.

std::set< BoundaryID >	boundaryNamesToIDs (const std::vector< BoundaryName > &names, const std::string &param_name)

void	checkBoundaryConditionOverlap () const
	Error if the same sideset ID appears in both vacuum and reflective BC sets.

BoundaryConditionType	boundaryConditionType (const Elem *const elem, const unsigned int side, const libMesh::BoundaryInfo &boundary_info) const

void	splitSkinByBoundaryCondition (const moab::Range &region, const moab::Range &skin, moab::Range &transmission_tris, moab::Range &vacuum_tris, moab::Range &reflective_tris)

void	createSurfacesFromSkin (const moab::Range &region, moab::Range &skin, VolData &voldata, unsigned int &surf_id)

void	recordBoundaryConditionSurface (moab::EntityHandle surface_set, BoundaryConditionType bc_type)

BoundaryConditionType	recordedBoundaryCondition (moab::EntityHandle surface_set) const

unsigned int	firstBoundaryConditionGroupID () const

void	createBoundaryConditionGroups ()

std::string	boundaryConditionGroupName (BoundaryConditionType bc_type) const

void	groupLocalElems (std::set< dof_id_type > elems, std::vector< moab::Range > &localElems)

bool	resetMOAB ()
	Clear MOAB entity sets.

void	findSurface (const moab::Range &region, moab::EntityHandle group, unsigned int &vol_id, unsigned int &surf_id, moab::EntityHandle &volume_set)
	Find the surfaces for the provided range and add to group.

virtual void	write ()
	Write MOAB volume and/or skin meshes to file.

Protected Attributes
std::unique_ptr< NumericVector< Number > >	_serialized_solution

std::shared_ptr< moab::Interface >	_moab
	MOAB interface.

bool	_verbose
	Whether to print diagnostic information.

const std::string &	_temperature_name
	Name of the temperature variable.

const Real &	_temperature_min
	Lower bound of temperature bins.

const Real &	_temperature_max
	Upper bound of temperature bins.

const unsigned int &	_n_temperature_bins
	Number of temperature bins.

const Real	_temperature_bin_width
	Temperature bin width.

const bool	_bin_by_density
	Whether elements are binned by density (in addition to temperature and block)

std::vector< std::string >	_material_names

const Real &	_faceting_tol
	Faceting tolerence needed by DAGMC.

const Real &	_geom_tol
	Geometry tolerence needed by DAGMC.

const Real &	_graveyard_scale_inner
	Multiplier on bounding box for inner surface of graveyard.

const Real &	_graveyard_scale_outer
	Multiplier on bounding box for outer surface of graveyard.

const bool &	_output_skins
	Whether to output the MOAB mesh skins to a .h5m file.

const bool &	_output_full
	Whether to output the MOAB mesh to a .h5m file.

bool	_build_graveyard

bool	_set_implicit_complement_material = false
	Whether to assign a material to the implicit complement region.

std::string	_implicit_complement_group_name
	OpenMC material name or ID which will be assigned to the implicit complement.

bool	_use_displaced
	Whether the skinned mesh should be generated from a displaced mesh.

Real	_scaling
	Length multiplier to get from [Mesh] units into OpenMC's centimeters.

unsigned int	_n_write
	Count number of times output files have been written.

bool	_standalone
	Whether this class runs by itself, or is controlled by an external class.

bool	_tet_mesh_built
	True when buildTetMesh() is called.

std::unique_ptr< MeshBase >	_tet_mesh
	TET4 clone of the MOOSE mesh. Present only when the source mesh contains non-tetrahedral elements. Rebuilt each update() cycle.

std::unique_ptr< moab::Skinner >	skinner
	Moab skinner for finding temperature surfaces.

std::unique_ptr< moab::GeomTopoTool >	gtt
	Topology tool for setting surface sense.

std::map< dof_id_type, std::vector< moab::EntityHandle > >	_id_to_elem_handles
	Map from libmesh id to MOAB element entity handles.

std::unordered_map< dof_id_type, moab::EntityHandle >	_node_id_to_handle
	Map from libMesh id to MOAB vertex handles.

moab::EntityHandle	offset
	Save the first tet entity handle.

std::string	_density_name
	Name of the MOOSE variable containing the density.

std::set< BoundaryID >	_vacuum_bcs_surface_ids
	Resolved vacuum BC sideset IDs (from 'vacuum_bcs_surfaces' input parameter)

std::set< BoundaryID >	_reflective_bcs_surface_ids
	Resolved reflective BC sideset IDs (from 'reflective_bcs_surfaces' input parameter)

std::map< moab::EntityHandle, BoundaryConditionType >	_surface_bc_types

std::unordered_map< moab::EntityHandle, dof_id_type >	_elem_handle_to_id
	Reverse map from MOAB tet entity handle to libMesh element ID. Populated in createMOABElems()

bool	_set_bcs
	Whether to assign boundary conditions to surfaces.

Real	_density_min
	Lower bound of density bins.

Real	_density_max
	Upper bound of density bins.

Real	_density_bin_width
	Density bin width.

unsigned int	_n_density_bins
	Number of density bins.

unsigned int	_n_block_bins
	Number of block bins.

std::vector< std::set< dof_id_type > >	_elem_bins
	Mapping from total bin ID to a set of elements sorted into that bin.

std::map< SubdomainID, unsigned int >	_blocks
	Blocks in the [Mesh].

moab::EntityHandle	_all_tets
	Entity handle to represent the set of all tets.

std::map< moab::EntityHandle, std::vector< VolData > >	surfsToVols
	Save some topological data: map from surface handle to vol handle and sense.

moab::Tag	geometry_dimension_tag
	Tag for dimension for geometry.

moab::Tag	id_tag
	Tag for entitiy set ID.

moab::Tag	faceting_tol_tag
	Tag for faceting tolerance.

moab::Tag	geometry_resabs_tag
	Tag needed by DAGMC.

moab::Tag	category_tag
	Tag for type of entity set.

moab::Tag	name_tag
	Tag for name of entity set.

std::vector< Real >	_temperature_bin_bounds
	Bounds of the temperature bins.

std::vector< Real >	_density_bin_bounds
	Bounds of the density bins.

std::vector< std::vector< unsigned int > >	_tet4_nodes
	Node ordering for a TET4 MOAB element, based on libMesh node numberings.

std::vector< std::vector< unsigned int > >	_tet10_nodes

unsigned int	_temperature_var_num
	Auxiliary variable number for temperature.

unsigned int	_density_var_num
	Auxiliary variable number for density.

const unsigned int	NODES_PER_MOAB_TET = 4
	Number of nodes per MOAB tet (which are first order, so TET4)

const Real	BIN_TOLERANCE = 1e-6
	Tolerance to use for comparing values to bin bounds.

std::map< SubdomainID, std::string >	_block_id_to_material_name
	Map from mesh SubdomainID to OpenMC material name.

Detailed Description

Skins the [Mesh] according to individual bins for temperature, density, and subdomain ID.

Skins a [Mesh] according to temperature, density, and subdomain. The MOAB surfaces bounding those grouped elements are then generated, providing geometry information needed for DAGMC to then track particles on this new geometry.

Member Enumeration Documentation

◆ BoundaryConditionType

enum class MoabSkinner::BoundaryConditionType

strongprotected

Boundary condition types that can be assigned to DAGMC surfaces.

Enumerator
Transmission
Vacuum
Reflective

◆ Sense

enum MoabSkinner::Sense

protected

Encode the whether the surface normal faces into or out of the volume.

Enumerator
BACKWARDS
FORWARDS

Constructor & Destructor Documentation

◆ MoabSkinner()

MoabSkinner::MoabSkinner ( const InputParameters & parameters )

Member Function Documentation

◆ boundaryConditionGroupName()

std::string MoabSkinner::boundaryConditionGroupName ( BoundaryConditionType bc_type ) const

protected

Get the DAGMC group name used to assign a boundary condition type

Parameters

[in] bc_type boundary condition type

Returns: DAGMC group name

◆ boundaryConditionType()

BoundaryConditionType MoabSkinner::boundaryConditionType	(	const Elem *const	elem,
		const unsigned int	side,
		const libMesh::BoundaryInfo &	boundary_info
	)		const

protected

Determine which BC type, if any, applies to a side of an element based on the sidesets that side belongs to.

Parameters

[in]	elem	element (in the DAGMC geometry mesh)
[in]	side	side index on the element
[in]	boundary_info	boundary info of the DAGMC geometry mesh

Returns: boundary condition type to assign to the side

◆ boundaryNamesToIDs()

std::set< BoundaryID > MoabSkinner::boundaryNamesToIDs	(	const std::vector< BoundaryName > &	names,
		const std::string &	param_name
	)

protected

Convert sideset names or numeric IDs to mesh BoundaryIDs and validate that each is a sideset. Both string names and integer IDs are accepted.

Parameters

[in]	names	sideset names or IDs
[in]	param_name	input parameter name, for error messages

Returns: resolved boundary IDs

◆ buildGraveyard()

void MoabSkinner::buildGraveyard	(	unsigned int &	vol_id,
		unsigned int &	surf_id
	)

protected

Build a graveyard volume around the domain.

The graveyard is a containing volume which bounds the volume of interest. This is only needed if the skinned geometry is going to be input into a Monte Carlo solver. For performance reasons, a cubic shell is optimal. So, here we build two cubic surfaces, both larger than the bounding box of the "actual" geometry. We name this region "mat:Graveyard", so that when OpenMC parses the geometry it knows to assign "void" to this region, and set vacuum BCs on the outer surfaces of the cubic shell. The remaining space between the "actual" geometry and the inner graveyard surface is treated as the implicit complement of the rest of the geometry (e.g. a transmissive region).

◆ buildTetMesh()

void MoabSkinner::buildTetMesh ( )

protected

If the mesh has non-tetrahedral elements, clone it into _tet_mesh and convert to all-TET4.

◆ check()

virtual moab::ErrorCode MoabSkinner::check ( const moab::ErrorCode input ) const

virtual

Wrap the error handling in MOAB to print errors to user

Parameters

[in] input MOAB error code

Returns: error mode

◆ checkBoundaryConditionOverlap()

void MoabSkinner::checkBoundaryConditionOverlap ( ) const

protected

Error if the same sideset ID appears in both vacuum and reflective BC sets.

◆ createBoundaryConditionGroups()

void MoabSkinner::createBoundaryConditionGroups ( )

protected

Create the DAGMC BC group entity sets from the surfaces recorded during skinning and add them to the MOAB geometry

◆ createCornerTris()

void MoabSkinner::createCornerTris	(	const std::vector< moab::EntityHandle > &	verts,
		unsigned int	corner,
		unsigned int	v1,
		unsigned int	v2,
		unsigned int	v3,
		bool	normalout,
		moab::Range &	surface_tris
	)

protected

Create 3 tri faces stemming from one corner of a cude (an open tetrahedron)

◆ createGroup()

void MoabSkinner::createGroup	(	const unsigned int &	id,
		const std::string &	name,
		moab::EntityHandle &	group_set
	)

protected

Helper method to create MOAB group entity set

Parameters

[in]	id	ID for the group
[in]	name	name for the group
[in]	group_set	group of entities

◆ createMOABElems()

void MoabSkinner::createMOABElems ( )

protected

Copy the libMesh [Mesh] into a MOAB mesh. This first loops through all of the nodes, and rebuilds each as a MOAB vertex. Then, we loop over all of the elements and rebuild each as a TET4 (if the libMesh mesh has TET10 elements, they are each rebuilt into 8 TET4 elements). When the source mesh contained non-tetrahedral elements, the geometry mesh is the internally-converted all-TET4 clone rather than the MOOSE mesh

◆ createNodesFromBox()

std::vector< moab::EntityHandle > MoabSkinner::createNodesFromBox	(	const BoundingBox &	box,
		const Real &	factor
	)		const

protected

Create MOAB nodes from a bounding box

Parameters

[in]	box	bounding box
[in]	factor	multiplicative factor to resize the bounding box sides

Returns: nodes

◆ createSurf()

void MoabSkinner::createSurf	(	const unsigned int &	id,
		moab::EntityHandle &	surface_set,
		moab::Range &	faces,
		const std::vector< VolData > &	voldata,
		BoundaryConditionType	bc_type = `BoundaryConditionType::Transmission`
	)

protected

Helper method to create MOAB surface entity set.

◆ createSurfaceFromBox()

void MoabSkinner::createSurfaceFromBox	(	const BoundingBox &	box,
		const VolData &	voldata,
		unsigned int &	surf_id,
		bool	normalout,
		const Real &	factor
	)

protected

Create a MOAB surface from a bounding box

◆ createSurfaces()

void MoabSkinner::createSurfaces	(	moab::Range &	faces,
		VolData &	voldata,
		unsigned int &	surf_id,
		BoundaryConditionType	bc_type = `BoundaryConditionType::Transmission`
	)

protected

Helper method to create MOAB surfaces with no overlaps; bc_type is recorded on every surface created or matched by this call

◆ createSurfacesFromSkin()

void MoabSkinner::createSurfacesFromSkin	(	const moab::Range &	region,
		moab::Range &	skin,
		VolData &	voldata,
		unsigned int &	surf_id
	)

protected

Classify and create DAGMC surfaces from find_skin() result. Splits the skin into transmission, vacuum, and reflective subsets and calls createSurfaces() for each type.

Parameters

[in]	region	MOAB tets forming the current local region
[in]	skin	skinned triangles bounding the region
[in]	voldata	volume to associate with the created surfaces
[in,out]	surf_id	running counter of surface IDs

◆ createTags()

virtual void MoabSkinner::createTags ( )

protectedvirtual

Helper method to create MOAB tags.

◆ createTri()

moab::EntityHandle MoabSkinner::createTri	(	const std::vector< moab::EntityHandle > &	vertices,
		unsigned int	v1,
		unsigned int	v2,
		unsigned int	v3
	)

protected

Create MOAB tri surface element.

◆ createVol()

void MoabSkinner::createVol	(	const unsigned int &	id,
		moab::EntityHandle &	volume_set,
		moab::EntityHandle	group_set
	)

protected

Helper method to create MOAB volume entity set.

◆ execute()

virtual void MoabSkinner::execute ( )

overridevirtual

◆ finalize()

virtual void MoabSkinner::finalize ( )

overridevirtual

◆ findBlocks()

virtual void MoabSkinner::findBlocks ( )

protectedvirtual

Store a mapping from [Mesh] subdomain IDs to an index, to be used for binning by block ID.

◆ findSurface()

void MoabSkinner::findSurface	(	const moab::Range &	region,
		moab::EntityHandle	group,
		unsigned int &	vol_id,
		unsigned int &	surf_id,
		moab::EntityHandle &	volume_set
	)

protected

Find the surfaces for the provided range and add to group.

◆ findSurfaces()

void MoabSkinner::findSurfaces ( )

protected

Group the binned elems into local temperature regions and find their surfaces.

◆ firstBoundaryConditionGroupID()

unsigned int MoabSkinner::firstBoundaryConditionGroupID ( ) const

protected

Return the first group ID available after material, graveyard, and implicit-complement groups.

Returns: first available boundary condition group ID

◆ getAuxiliaryVariableNumber()

unsigned int MoabSkinner::getAuxiliaryVariableNumber	(	const std::string &	name,
		const std::string &	param_name
	)		const

Get variable number in the auxiliary system

Parameters

[in]	name	variable name
[in]	param_name	parameter name, for printing a helpful error message

Returns: variable number

◆ getBin()

virtual unsigned int MoabSkinner::getBin	(	const unsigned int &	temp_bin,
		const unsigned int &	density_bin,
		const unsigned int &	subdomain_bin
	)		const

virtual

Get total bin index given individual indices for the temperature, density, and subdomain bins

Parameters

[in]	temp_bin	temperature bin
[in]	density_bin	density bin
[in]	subdomain_bin	subdomain ID bin

Returns: total bin index

◆ getDAGMCGeometryMesh()

MeshBase & MoabSkinner::getDAGMCGeometryMesh ( )

protected

Return the mesh used for DAGMC geometry construction.

Returns: *_tet_mesh when the source mesh contained non-tetrahedral elements and an internal conversion was performed; otherwise returns getMooseMesh().getMesh().

◆ getDensityBin()

virtual unsigned int MoabSkinner::getDensityBin ( const Elem *const elem ) const

virtual

Get the bin index for the density

Parameters

[in] elem element

Returns: density bin index

◆ getMooseMesh()

MooseMesh & MoabSkinner::getMooseMesh ( )

protected

Get the MooseMesh (displaced or not, depending on _use_displaced)

◆ getSubdomainBin()

virtual unsigned int MoabSkinner::getSubdomainBin ( const Elem *const elem ) const

inlinevirtual

Get the bin index for the subdomain

Parameters

[in] elem element

Returns: subdomain bin index

◆ getTemperatureBin()

virtual unsigned int MoabSkinner::getTemperatureBin ( const Elem *const elem ) const

virtual

Get the bin index for the temperature

Parameters

[in] elem element

Returns: temperature bin index

◆ getTetSets()

const std::vector< std::vector< unsigned int > > & MoabSkinner::getTetSets ( ElemType type ) const

protected

Get the node numberings for the MOAB TET4 elements to build for each [Mesh] element

Parameters

[in] type element type

◆ groupLocalElems()

void MoabSkinner::groupLocalElems	(	std::set< dof_id_type >	elems,
		std::vector< moab::Range > &	localElems
	)

protected

Group a given bin into local regions NB elems in param is a copy, localElems is a reference

◆ hasDensitySkinning()

virtual bool MoabSkinner::hasDensitySkinning ( ) const

inlinevirtual

Whether density skinning is applied

Returns: using density skinning

◆ hasGraveyard()

virtual const bool & MoabSkinner::hasGraveyard ( ) const

inlinevirtual

Whether the skinner builds a graveyard

Returns: whether a graveyard is built

◆ initialize()

virtual void MoabSkinner::initialize ( )

overridevirtual

◆ makeDependentOnExternalAction()

virtual void MoabSkinner::makeDependentOnExternalAction ( )

inlinevirtual

Indicate whether this userobject is run by itself (for testing purposes) or controlled by some other class.

◆ materialName()

std::string MoabSkinner::materialName	(	const unsigned int &	block,
		const unsigned int &	density,
		const unsigned int &	temp
	)		const

◆ moabPtr()

const std::shared_ptr< moab::Interface > & MoabSkinner::moabPtr ( ) const

inline

Get pointer to underlying moab interface

Returns: pointer to moab interface

◆ nBins()

unsigned int MoabSkinner::nBins ( ) const

Get the total number of bins

Returns: total number of bins

◆ nDensityBins()

virtual unsigned int MoabSkinner::nDensityBins ( ) const

inlinevirtual

Number of density bins; if greater than 1, this means we must be re-generating OpenMC materials during the course of the simulation.

Returns: number of density bins

◆ recordBoundaryConditionSurface()

void MoabSkinner::recordBoundaryConditionSurface	(	moab::EntityHandle	surface_set,
		BoundaryConditionType	bc_type
	)

protected

Record that a DAGMC surface meshset has been assigned a BC type. Called from createSurf() and from the overlap path in createSurfaces().

Parameters

[in]	surface_set	surface meshset
[in]	bc_type	boundary condition type assigned to the surface

◆ recordedBoundaryCondition()

BoundaryConditionType MoabSkinner::recordedBoundaryCondition ( moab::EntityHandle surface_set ) const

protected

Get the boundary condition type previously recorded for a surface, if any

Parameters

[in] surface_set surface meshset

Returns: recorded boundary condition type (Transmission if the surface has no explicit BC)

◆ reset()

void MoabSkinner::reset ( )

Clear mesh data.

◆ resetMOAB()

bool MoabSkinner::resetMOAB ( )

protected

Clear MOAB entity sets.

◆ setGraveyard()

void MoabSkinner::setGraveyard ( bool build )

Set the graveyard setting

Parameters

[in] build whether to build a graveyard

◆ setMaterialNames()

virtual void MoabSkinner::setMaterialNames ( std::vector< std::string > names )

inlinevirtual

Set the names to be used for naming the subdomains in the skinned mesh. This is used when material names are supplied externally rather than through the 'material_blocks' and 'material_names' input parameters.

Parameters

[in] names names for subdomains

◆ setScaling()

virtual void MoabSkinner::setScaling ( const Real & scale )

inlinevirtual

Set the length multiplier to get from [Mesh] units into centimeters

Parameters

[in] scale multiplier

◆ setTagData() [1/2]

void MoabSkinner::setTagData	(	moab::Tag	tag,
		moab::EntityHandle	ent,
		std::string	data,
		unsigned int	SIZE
	)

protected

Helper function to wrap moab::tag_set_data for a string.

◆ setTagData() [2/2]

void MoabSkinner::setTagData	(	moab::Tag	tag,
		moab::EntityHandle	ent,
		void *	data
	)

protected

Helper function to wrap moab::tag_set_data for a generic pointer.

◆ setTags()

void MoabSkinner::setTags	(	moab::EntityHandle	ent,
		std::string	name,
		std::string	category,
		unsigned int	id,
		int	dim
	)

protected

Generic method to set the tags that DAGMC requires.

◆ setUseDisplacedMesh()

void MoabSkinner::setUseDisplacedMesh ( const bool & use )

Override the user parameter for use_displaced

Parameters

[in] use whether to use the displaced mesh

◆ setVerbosity()

virtual void MoabSkinner::setVerbosity ( const bool & verbose )

inlinevirtual

Set the verbosity level

Parameters

[in] verbose whether to print diagnostic information

◆ sortElemsByResults()

virtual void MoabSkinner::sortElemsByResults ( )

protectedvirtual

Sort all the elements in the [Mesh] into bins for temperature, density, and subdomain.

◆ splitSkinByBoundaryCondition()

void MoabSkinner::splitSkinByBoundaryCondition	(	const moab::Range &	region,
		const moab::Range &	skin,
		moab::Range &	transmission_tris,
		moab::Range &	vacuum_tris,
		moab::Range &	reflective_tris
	)

protected

Classify the skinned triangles for one region into transmission, vacuum, and reflective sets by checking each triangle against the BC sidesets.

Parameters

[in]	region	MOAB tets forming the current local region
[in]	skin	skinned triangles bounding the region
[out]	transmission_tris	triangles with no boundary condition (transmission)
[out]	vacuum_tris	triangles assigned vacuum boundary conditions
[out]	reflective_tris	triangles assigned reflective boundary conditions

◆ threadJoin()

virtual void MoabSkinner::threadJoin ( const UserObject & )

inlineoverridevirtual

◆ update()

virtual void MoabSkinner::update ( )

virtual

Perform the skinning operation.

◆ updateSurfData()

void MoabSkinner::updateSurfData	(	moab::EntityHandle	surface_set,
		const VolData &	data
	)

protected

Add parent-child metadata relating a surface to its volume.

◆ validParams()

static InputParameters MoabSkinner::validParams ( )

static

◆ write()

virtual void MoabSkinner::write ( )

protectedvirtual

Write MOAB volume and/or skin meshes to file.

Member Data Documentation

◆ _all_tets

moab::EntityHandle MoabSkinner::_all_tets

protected

Entity handle to represent the set of all tets.

◆ _bin_by_density

const bool MoabSkinner::_bin_by_density

protected

Whether elements are binned by density (in addition to temperature and block)

◆ _block_id_to_material_name

std::map<SubdomainID, std::string> MoabSkinner::_block_id_to_material_name

protected

Map from mesh SubdomainID to OpenMC material name.

◆ _blocks

std::map<SubdomainID, unsigned int> MoabSkinner::_blocks

protected

Blocks in the [Mesh].

◆ _build_graveyard

bool MoabSkinner::_build_graveyard

protected

Whether to build a graveyard as two additional cube surfaces surrounding the mesh. This is only needed if the skinned geometry is fed into a Monte Carlo code.

◆ _density_bin_bounds

std::vector<Real> MoabSkinner::_density_bin_bounds

protected

Bounds of the density bins.

◆ _density_bin_width

Real MoabSkinner::_density_bin_width

protected

Density bin width.

◆ _density_max

Real MoabSkinner::_density_max

protected

Upper bound of density bins.

◆ _density_min

Real MoabSkinner::_density_min

protected

Lower bound of density bins.

◆ _density_name

std::string MoabSkinner::_density_name

protected

Name of the MOOSE variable containing the density.

◆ _density_var_num

unsigned int MoabSkinner::_density_var_num

protected

Auxiliary variable number for density.

◆ _elem_bins

std::vector<std::set<dof_id_type> > MoabSkinner::_elem_bins

protected

Mapping from total bin ID to a set of elements sorted into that bin.

◆ _elem_handle_to_id

std::unordered_map<moab::EntityHandle, dof_id_type> MoabSkinner::_elem_handle_to_id

protected

Reverse map from MOAB tet entity handle to libMesh element ID. Populated in createMOABElems()

◆ _faceting_tol

const Real& MoabSkinner::_faceting_tol

protected

Faceting tolerence needed by DAGMC.

◆ _geom_tol

const Real& MoabSkinner::_geom_tol

protected

Geometry tolerence needed by DAGMC.

◆ _graveyard_scale_inner

const Real& MoabSkinner::_graveyard_scale_inner

protected

Multiplier on bounding box for inner surface of graveyard.

◆ _graveyard_scale_outer

const Real& MoabSkinner::_graveyard_scale_outer

protected

Multiplier on bounding box for outer surface of graveyard.

◆ _id_to_elem_handles

std::map<dof_id_type, std::vector<moab::EntityHandle> > MoabSkinner::_id_to_elem_handles

protected

Map from libmesh id to MOAB element entity handles.

◆ _implicit_complement_group_name

std::string MoabSkinner::_implicit_complement_group_name

protected

OpenMC material name or ID which will be assigned to the implicit complement.

◆ _material_names

std::vector<std::string> MoabSkinner::_material_names

protected

Material names corresponding to each subdomain. These are used to name the new skinned volumes in MOAB

◆ _moab

std::shared_ptr<moab::Interface> MoabSkinner::_moab

protected

MOAB interface.

◆ _n_block_bins

unsigned int MoabSkinner::_n_block_bins

protected

Number of block bins.

◆ _n_density_bins

unsigned int MoabSkinner::_n_density_bins

protected

Number of density bins.

◆ _n_temperature_bins

const unsigned int& MoabSkinner::_n_temperature_bins

protected

Number of temperature bins.

◆ _n_write

unsigned int MoabSkinner::_n_write

protected

Count number of times output files have been written.

◆ _node_id_to_handle

std::unordered_map<dof_id_type, moab::EntityHandle> MoabSkinner::_node_id_to_handle

protected

Map from libMesh id to MOAB vertex handles.

◆ _output_full

const bool& MoabSkinner::_output_full

protected

Whether to output the MOAB mesh to a .h5m file.

◆ _output_skins

const bool& MoabSkinner::_output_skins

protected

Whether to output the MOAB mesh skins to a .h5m file.

◆ _reflective_bcs_surface_ids

std::set<BoundaryID> MoabSkinner::_reflective_bcs_surface_ids

protected

Resolved reflective BC sideset IDs (from 'reflective_bcs_surfaces' input parameter)

◆ _scaling

Real MoabSkinner::_scaling

protected

Length multiplier to get from [Mesh] units into OpenMC's centimeters.

◆ _serialized_solution

std::unique_ptr<NumericVector<Number> > MoabSkinner::_serialized_solution

protected

◆ _set_bcs

bool MoabSkinner::_set_bcs

protected

Whether to assign boundary conditions to surfaces.

◆ _set_implicit_complement_material

bool MoabSkinner::_set_implicit_complement_material = false

protected

Whether to assign a material to the implicit complement region.

◆ _standalone

bool MoabSkinner::_standalone

protected

Whether this class runs by itself, or is controlled by an external class.

◆ _surface_bc_types

std::map<moab::EntityHandle, BoundaryConditionType> MoabSkinner::_surface_bc_types

protected

Map from DAGMC surface meshset to its assigned BC type, recorded during skinning. Transmission surfaces are not recorded (they need no DAGMC group).

◆ _temperature_bin_bounds

std::vector<Real> MoabSkinner::_temperature_bin_bounds

protected

Bounds of the temperature bins.

◆ _temperature_bin_width

const Real MoabSkinner::_temperature_bin_width

protected

Temperature bin width.

◆ _temperature_max

const Real& MoabSkinner::_temperature_max

protected

Upper bound of temperature bins.

◆ _temperature_min

const Real& MoabSkinner::_temperature_min

protected

Lower bound of temperature bins.

◆ _temperature_name

const std::string& MoabSkinner::_temperature_name

protected

Name of the temperature variable.

◆ _temperature_var_num

unsigned int MoabSkinner::_temperature_var_num

protected

Auxiliary variable number for temperature.

◆ _tet10_nodes

std::vector<std::vector<unsigned int> > MoabSkinner::_tet10_nodes

protected

Node ordering for eight TET4 MOAB elements, based on libMesh node numberings for a TET10 element. We re-build the libMesh element into first-order MOAB elements.

◆ _tet4_nodes

std::vector<std::vector<unsigned int> > MoabSkinner::_tet4_nodes

protected

Node ordering for a TET4 MOAB element, based on libMesh node numberings.

◆ _tet_mesh

std::unique_ptr<MeshBase> MoabSkinner::_tet_mesh

protected

TET4 clone of the MOOSE mesh. Present only when the source mesh contains non-tetrahedral elements. Rebuilt each update() cycle.

◆ _tet_mesh_built

bool MoabSkinner::_tet_mesh_built

protected

True when buildTetMesh() is called.

◆ _use_displaced

bool MoabSkinner::_use_displaced

protected

Whether the skinned mesh should be generated from a displaced mesh.

◆ _vacuum_bcs_surface_ids

std::set<BoundaryID> MoabSkinner::_vacuum_bcs_surface_ids

protected

Resolved vacuum BC sideset IDs (from 'vacuum_bcs_surfaces' input parameter)

◆ _verbose

bool MoabSkinner::_verbose

protected

Whether to print diagnostic information.

◆ BIN_TOLERANCE

const Real MoabSkinner::BIN_TOLERANCE = 1e-6

protected

Tolerance to use for comparing values to bin bounds.

◆ category_tag

moab::Tag MoabSkinner::category_tag

protected

Tag for type of entity set.

◆ faceting_tol_tag

moab::Tag MoabSkinner::faceting_tol_tag

protected

Tag for faceting tolerance.

◆ geometry_dimension_tag

moab::Tag MoabSkinner::geometry_dimension_tag

protected

Tag for dimension for geometry.

◆ geometry_resabs_tag

moab::Tag MoabSkinner::geometry_resabs_tag

protected

Tag needed by DAGMC.

◆ gtt

std::unique_ptr<moab::GeomTopoTool> MoabSkinner::gtt

protected

Topology tool for setting surface sense.

◆ id_tag

moab::Tag MoabSkinner::id_tag

protected

Tag for entitiy set ID.

◆ name_tag

moab::Tag MoabSkinner::name_tag

protected

Tag for name of entity set.

◆ NODES_PER_MOAB_TET

const unsigned int MoabSkinner::NODES_PER_MOAB_TET = 4

protected

Number of nodes per MOAB tet (which are first order, so TET4)

◆ offset

moab::EntityHandle MoabSkinner::offset

protected

Save the first tet entity handle.

◆ skinner

std::unique_ptr<moab::Skinner> MoabSkinner::skinner

protected

Moab skinner for finding temperature surfaces.

◆ surfsToVols

std::map<moab::EntityHandle, std::vector<VolData> > MoabSkinner::surfsToVols

protected

Save some topological data: map from surface handle to vol handle and sense.

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

include/userobjects/MoabSkinner.h

Classes

Public Member Functions

Static Public Member Functions

Protected Types

Protected Member Functions

Protected Attributes

Detailed Description

Member Enumeration Documentation

◆ BoundaryConditionType

◆ Sense

Constructor & Destructor Documentation

◆ MoabSkinner()

Member Function Documentation

◆ boundaryConditionGroupName()

◆ boundaryConditionType()

◆ boundaryNamesToIDs()

◆ buildGraveyard()

◆ buildTetMesh()

◆ check()

◆ checkBoundaryConditionOverlap()

◆ createBoundaryConditionGroups()

◆ createCornerTris()

◆ createGroup()

◆ createMOABElems()

◆ createNodesFromBox()

◆ createSurf()

◆ createSurfaceFromBox()

◆ createSurfaces()

◆ createSurfacesFromSkin()

◆ createTags()

◆ createTri()

◆ createVol()

◆ execute()

◆ finalize()

◆ findBlocks()

◆ findSurface()

◆ findSurfaces()

◆ firstBoundaryConditionGroupID()

◆ getAuxiliaryVariableNumber()

◆ getBin()

◆ getDAGMCGeometryMesh()

◆ getDensityBin()

◆ getMooseMesh()

◆ getSubdomainBin()

◆ getTemperatureBin()

◆ getTetSets()

◆ groupLocalElems()

◆ hasDensitySkinning()

◆ hasGraveyard()

◆ initialize()

◆ makeDependentOnExternalAction()

◆ materialName()

◆ moabPtr()

◆ nBins()

◆ nDensityBins()

◆ recordBoundaryConditionSurface()

◆ recordedBoundaryCondition()

◆ reset()

◆ resetMOAB()

◆ setGraveyard()

◆ setMaterialNames()

◆ setScaling()

◆ setTagData() [1/2]

◆ setTagData() [2/2]

◆ setTags()

◆ setUseDisplacedMesh()

◆ setVerbosity()

◆ sortElemsByResults()

◆ splitSkinByBoundaryCondition()

◆ threadJoin()

◆ update()

◆ updateSurfData()

◆ validParams()

◆ write()

Member Data Documentation

◆ _all_tets

◆ _bin_by_density

◆ _block_id_to_material_name

◆ _blocks

◆ _build_graveyard