AbstractMesh

AbstractMesh_ datatype handles the finite element mesh. The structure of this data type is given here.

Summary of methods

Constructor Methods

Method Name	Purpose
Initiate	Read the mesh by reading a hdf5 file.
DEALLOCATE	Deallocate memory occupied by the mesh instance.
isEmpty	Returns true if the mesh is empty.
DeallocateKdTree	Deallocate the kdtree.
InitiateDynamicDataStructure	Initiate Kdtree related data

IOMethods

Method Name	Purpose
Import	Read mesh from hdf5 file.
Export	Export mesh to an hdf5 file.
ExportToVTK	Export mesh to a VTKfile.
Display	Display the mesh.
DisplayNodeData	Display node data.
DisplayElementData	Display element data.
DisplayFacetData	Display facet data.
DisplayInternalFacetData	Display internal facet data.
DisplayBoundaryFacetData	Display boundary facet data.
DisplayFacetElements	Display facet element shape data.
DisplayMeshInfo	Display mesh information.

Constructor methods for connectivity

Method Name	Purpose
InitiateKdTree	Initiate Kdtree.
InitiateNodeToElements	Initiate node to element data (mapping).
InitiateNodeToNodes	Initiate Node to nodes data.
InitiateExtraNodeToNodes	Initiate Node to nodes mapping (used in jump based FEM).
InitiateElementToElements	Initiate element to elements mapping.
InitiateBoundaryData	Initiate the boundary data.
InitiateEdgeConnectivity	Initiate Edge connectivity data.
InitiateFaceConnectivity	Initiate Face connectivity data.
InitiateFacetElements	Initiate boundary data.

Element information methods

Method Name	Purpose
GetElemType	Get the element name
GetElemData	Get the element data
GetElemDataPointer	Get pointer to an element data
GetNNE	Get number of nodes in an element
GetMaxNNE	Get maximum number of nodes in an element
Size	Returns the size of the mesh (total number of elements)
GetElemNum	Generic method to get list of local or global element number in mesh
GetOrientation	Get the orientation of the element
GetTotalCells	Returns the total number of cells in the mesh (obj%tElements)
GetTotalElements	Generic method for getting the total number of elements
GetGlobalElemNumber	Returns the global element number for a local element number
GetLocalElemNumber	Returns the local element number of a global element number
GetOrder	Returns the order of the element of mesh
GetMinElemNumber	Get minimum element number
GetMaxElemNumber	Get maximum element number

Topology Methods

Method Name	Purpose
GetElemTopology	Generic method to get the element topology name
GetElemTopologyIndx	Get the index of element topology
GetTotalElementsTopologyWise	Get total elements topology wise
GetTotalTopology	Get total topology
GetTotalEntities	Generic method for getting total entities in mesh and an element
GetBoundingEntity	Returns the nodal coordinates

Node Information Methods

Method Name	Purpose
GetNptrs	Get node number of mesh
GetNptrs_	Get node number of mesh
GetNptrsInBox	Get node number in a box
GetNptrsInBox_	Get node number in a box without allocation
GetInternalNptrs	Returns a vector of internal node numbers
GetInternalNptrs_	Returns a vector of internal node numbers (subroutine version, no allocation)
GetBoundaryNptrs	Returns a vector of boundary node numbers
GetTotalNodes	Get total nodes
GetTotalInternalNodes	Returns the total number of internal nodes
GetTotalBoundaryNodes	Returns the total number of boundary nodes
GetLocalNodeNumber	Returns the local node number of a global node number
GetLocalNodeNumber_	Get local node number without allocation
GetGlobalNodeNumber	Returns the global node number of a local node number
GetNodeCoord	Get node coordinates
GetNearestNode	Get nearest node
GetMinNodeNumber	Get minimum element number
GetMaxNodeNumber	Get maximum node number
GetNodeMask	Returns the mask for the presence of node

Connectivity Methods

Method Name	Purpose
GetConnectivity	Returns node numbers in an element (this is vertex connectivity)
GetConnectivity_	Generic method for getting the connectivity of an element
GetNodeConnectivity	Returns all the node connectivity of the mesh elements
GetNodeToElements	Generic method to get elements around node or nodes
GetNodeToNodes	Returns nodes connected to a given node number
GetNodeToNodes_	Returns nodes connected to a given node number
GetElementToElements	Returns elements connected to a given element number
GetElementToElements_	Get element to elements mapping
GetMaxNodeToElements	Get maximum number of node to elements
GetMaxElementToElements	Get maximum number of element to elements
GetMaxNodeToNodes	Get maximum number of node to nodes

Geometry methods

Method Name	Purpose
FindEdge	Find a edge in a cell (only for 3D)
FindFace	Find a face in a cell
GetBoundaryElementData	Returns boundary element data
GetBoundingBox	Return the bounding box
GetCellNumber	Returns the master and slave cell number of a facet element
GetFacetConnectivity	Generic method to Get the connectivity of a facet element
GetFacetElementType	Returns the facet element type of a given cell element number
GetFacetParam	Get the parameters of facet elements
GetGlobalEdgeNumber	Get global Edge number from global element and localEdgenumber
GetGlobalFaceNumber	Get global face number from global element and localFacenumber
GetLocalFacetID	Return the local facet id, so that we can Get reference element of the facet element
GetMasterCellNumber	Returns the master cell number of a facet element
GetNSD	Return the NSD
GetSlaveCellNumber	Returns the slave cell number of a facet element
GetTotalBoundaryElements	Returns the total number of boundary elements
GetTotalBoundaryFacetElements	Returns the total number of boundary facet elements
GetTotalEdges	Returns the total number of edges in the mesh (obj%tEdges)
GetTotalFaces	Returns the total number of faces in the mesh (obj%tFaces)
GetTotalFacetElements	Returns the total number of facet elements in the mesh
GetTotalInternalFacetElements	Returns the total number of internal facet elements
GetXidimension	Return the NSD

Status Check Methods

Method Name	Purpose
isInit	Returns obj%isInitiated
isNodeToElements	Check if node to elements mapping is available
isNodeToNodes	Check if node to nodes mapping is available
isExtraNodeToNodes	Check if extra node to nodes mapping is available
isElementToElements	Check if element to elements mapping is available
isEdgeConnectivity	Check if edge connectivity is available
isFaceConnectivity	Check if face connectivity is available
isBoundaryData	Check if boundary data is available
isFacetData	Check if facet data is available
isBoundaryElement	Returns true if a given global element number is a boundary element
isDomainBoundaryElement	Returns true if a given global element number is a boundary element
isDomainFacetElement	Returns true if a given global element number is a boundary element
isAnyNodePresent	Returns true if any of the node number is present
isAllNodePresent	Returns true if all of the node numbers are present
isBoundaryNode	Returns true if a given global node number is a boundary node
isNodePresent	Returns true if a node number is present
isElementPresent	Returns true if a given element number is present
isElementActive	Check if element is active

Set methods

Method Name	Purpose
SetShowTime	Set showTime option
SetBoundingBox	Set the bounding box
SetSparsity	Generic method for Setting the sparsity
SetTotalMaterial	Generic method
SetMaterial	Set material to an element
SetFacetElementType	Set the facet element type of a given cell number
SetQuality	Set mesh quality
SetParam	Set parameters of mesh
SetFacetParam	Set the parameters of facet element

Get Methods

Method Name	Purpose
GetMaterial	Returns the material id of a given medium
GetTotalMaterial	Returns the total materials in an element
GetParam	Get parameter of mesh

All methods

📄️ Structure

AbstractMesh_ datatype is simply a collection of finite elements and nodes.

📄️ ElemData

It is a data type for storing the element-data information.

📄️ NodeData

It is a data type for storing the information of node data in mesh.

📄️ InternalFacetData

Data storage for internal facet of mesh.

📄️ BoundaryFacetData

Data storage for boundary elements (i.e., facets which coincides with the boundary of mesh)

📄️ Initiate

Initiate an instance of Mesh.

📄️ Deallocate

Deallocate data stored in the mesh object.

📄️ DeallocateKdTree

Deallocate data related to the kd-tree.

📄️ Display

Displays comprehensive information about the AbstractMesh_ object including its properties, status flags, and data structures.

📄️ DisplayBoundaryFacetData

Displays information about boundary facet data in the mesh.

📄️ DisplayElementData

Displays detailed information about element data in the mesh, either for a specific element or all elements.

📄️ DisplayFacetData

Displays information about all facet data in the mesh.

📄️ DisplayFacetElemSD

Interface

📄️ DisplayFacetElements

Displays information about facet elements in the mesh.

📄️ DisplayInternalFacetData

Displays information specifically about internal facet data in the mesh.

📄️ DisplayMeshInfo

Displays concise summary information about the mesh.

📄️ DisplayNodeData

Displays detailed information about all node data in the mesh.

📄️ Export

This method exports the mesh to a hdf5 file format.

📄️ ExportToVTK

Exports an AbstractMesh_ object to a VTK file format, which can be visualized in applications like ParaView or VisIt.

📄️ Find Edge

Find an edge in a cell (only for 3D meshes).

📄️ FindFace

Find a face in a cell.

📄️ GetBoundaryElementData

Returns boundary element data for a given element.

📄️ GetBoundaryNptrs

The GetBoundaryNptrs method returns the global node numbers of all boundary nodes in the mesh. Boundary nodes are nodes that lie on the boundary of the domain.

📄️ GetBoundingBox

Return the bounding box of the mesh.

📄️ GetBoundingEntity

The GetBoundingEntity method retrieves the bounding entity numbers of the mesh. Bounding entities are higher-dimensional geometric entities that contain or bound the current mesh.

📄️ GetCellNumber

Returns the master and slave cell numbers of a facet element.

📄️ GetConnectivity

This function returns the global node numbers that define the connectivity of a given element. By default, it returns the vertex connectivity, but you can use the opt parameter to request different types of connectivity (edge, face, cell, or all).

📄️ GetConnectivity_

A more memory-efficient version of GetConnectivity that allows reusing existing arrays.

📄️ GetElemData

The GetElemData method retrieves a complete copy of the element data for a specific element in the mesh. The element data contains all information about the element including its nodes, connectivity, and properties.

📄️ GetElemDataPointer

The GetElemDataPointer method returns a pointer to the element data for a specific element in the mesh. This provides direct access to the element data without creating a copy.

📄️ GetElemNum

The GetElemNum method retrieves the element numbers (global or local) present in the mesh. It can return either all element numbers or those belonging to a specific mesh ID.

📄️ GetElemTopology

The GetElemTopology method retrieves the topology information for elements in the mesh. It can return either all element topologies present in the mesh or the topology of a specific element. Element topology refers to the geometric arrangement of nodes that defines the element shape (e.g., triangle, quadrilateral, tetrahedron, hexahedron).

📄️ GetElemTopologyIndx

The GetElemTopologyIndx method returns the topology index of a specific element in the mesh. The topology index is a numerical identifier for the element shape (1 for point, 2 for line, 3 for triangle, etc.).

📄️ GetElemType

The GetElemType method retrieves the type (name) of a specific element in the mesh. Element types define the geometric and interpolation properties of mesh elements.

📄️ GetElementToElements

Retrieves information about elements that are connected to a specified element.

📄️ GetElementToElements_

A memory-efficient version of GetElementToElements that allows reusing existing arrays.

📄️ GetFacetConnectivity

Generic method to get the connectivity of a facet element.

📄️ GetFacetElementType

Returns the facet element type of a given cell element number.

📄️ GetFacetParam

Get the parameters of facet elements.

📄️ GetGlobalEdgeNumber

Get global Edge number from global element and localEdgenumber.

📄️ GetGlobalElemNumber

The GetGlobalElemNumber method converts local element numbers to global element numbers in the mesh.

📄️ GetGlobalFaceNumber

Get global face number from global element and localFacenumber.

📄️ GetGlobalNodeNumber

The GetGlobalNodeNumber method converts local node numbers to global node numbers in the mesh. Global node numbers are used for cross-mesh references and for output/visualization.

📄️ GetInternalNptrs

The GetInternalNptrs method returns the global node numbers of all internal nodes in the mesh. Internal nodes are nodes that are not on the boundary of the domain.

📄️ GetInternalNptrs_

The GetInternalNptrs_ method retrieves the global node numbers of internal nodes without allocating new memory. The caller provides a pre-allocated array to store the results.

📄️ GetLocalElemNumber

The GetLocalElemNumber method converts global element numbers to local element numbers in the mesh.

📄️ GetLocalFacetID

Return the local facet id, so that we can get reference element of the facet element.

📄️ GetLocalNodeNumber

The GetLocalNodeNumber method converts global node numbers to local node numbers in the mesh. Local node numbers are used for internal mesh operations and array indexing.

📄️ GetLocalNodeNumber_

The GetLocalNodeNumber_ method converts global node numbers to local node numbers without allocating new memory. The caller provides a pre-allocated array to store the results.

📄️ GetMasterCellNumber

Returns the master cell number of a facet element.

📄️ GetMaterial

The GetMaterial method retrieves the material ID assigned to a specific element and medium within the mesh.

📄️ GetMaxElemNumber

The GetMaxElemNumber method returns the maximum global element number present in the mesh. This is useful for determining the range of element numbers and for array sizing.

📄️ GetMaxElementToElements

Retrieves the maximum number of elements connected to any element in the mesh.

📄️ GetMaxNNE

The GetMaxNNE method returns the maximum number of nodes in any element of the mesh. This is useful for allocating arrays that need to accommodate any element in the mesh.

📄️ GetMaxNodeNumber

The GetMaxNodeNumber method returns the maximum global node number present in the mesh. This is useful for determining the range of node numbers and for array sizing.

📄️ GetMaxNodeToElements

Retrieves the maximum number of elements connected to any node in the mesh.

📄️ GetMaxNodeToNodes

Retrieves the maximum number of nodes connected to any node in the mesh.

📄️ GetMinElemNumber

The GetMinElemNumber method returns the minimum global element number present in the mesh. This is useful for determining the range of element numbers and for array indexing.

📄️ GetMinNodeNumber

The GetMinNodeNumber method returns the minimum global node number present in the mesh. This is useful for determining the range of node numbers and for array indexing.

📄️ GetNNE

The GetNNE method returns the number of nodes in a specific element of the mesh. This is useful for determining the size of arrays needed for element-based operations.

📄️ GetNSD

Return the NSD (Number of Spatial Dimensions).

📄️ GetNearestNode

The GetNearestNode method finds the node(s) in the mesh that are closest to a given query point in space. It uses a k-d tree for efficient spatial searching.

📄️ GetNodeConnectivity

GetNodeConnectivity

📄️ GetNodeCoord

The GetNodeCoord method retrieves the coordinates of nodes in the mesh. It has multiple versions for different use cases, including getting coordinates from files, for all nodes, for specific elements, or for individual nodes.

📄️ GetNodeMask

The GetNodeMask method creates a logical mask array indicating which global node numbers are present in the mesh. This is useful for quickly checking if nodes exist and for filtering operations.

📄️ GetNodeToElements

Retrieves the global element numbers that are connected to a specified node or nodes.

📄️ GetNodeToNodes

Retrieves the global node numbers that are connected to a specified node or nodes.

📄️ GetNodeToNodes_

A memory-efficient version of GetNodeToNodes that allows reusing existing arrays.

📄️ GetNptrs

The GetNptrs method retrieves the global node numbers present in the mesh. It can return either all node numbers or those belonging to a specific mesh ID.

📄️ GetNptrsInBox

The GetNptrsInBox method retrieves the global node numbers of all nodes located within a specified bounding box in 3D space.

📄️ GetNptrsInBox_

The GetNptrsInBox_ method retrieves the global node numbers of nodes within a specified bounding box without allocating new memory. The caller provides a pre-allocated array to store the results.

📄️ GetNptrs_

The GetNptrs_ method is a subroutine version of GetNptrs that retrieves node numbers without allocation. It can return all node numbers, those for a specific mesh ID, or those for specified elements.

📄️ GetOrder

The GetOrder method retrieves the polynomial order of elements in the mesh or of a specific element. The element order determines the degree of interpolation functions used in finite element analysis.

📄️ GetOrientation

The GetOrientation method retrieves orientation flags for the cells, faces, and edges of a specific element. Orientation flags indicate how local entities are oriented with respect to the global reference frame.

📄️ GetParam

The GetParam method retrieves various parameters and properties of the mesh. It provides a comprehensive way to access mesh attributes in a single call.

📄️ GetRefElemPointer

Interface

📄️ GetSlaveCellNumber

Returns the slave cell number of a facet element.

📄️ GetTotalBoundaryElements

Returns the total number of boundary elements.

📄️ GetTotalBoundaryFacetElements

Returns the total number of boundary facet elements.

📄️ GetTotalBoundaryNodes

The GetTotalBoundaryNodes method returns the total number of boundary nodes in the mesh. Boundary nodes are nodes that lie on the boundary of the domain.

📄️ GetTotalCells

The GetTotalCells method returns the total number of cells (elements) in the mesh. It is an alias for the Size method.

📄️ GetTotalEdges

Returns the total number of edges in the mesh (obj%tEdges).

📄️ GetTotalElements

The GetTotalElements method returns the total number of elements in the mesh, with options to filter by mesh ID.

📄️ GetTotalElementsTopologyWise

The GetTotalElementsTopologyWise method returns the count of elements for each topology type in the mesh. This provides a breakdown of how many elements of each shape (point, line, triangle, etc.) are present.

📄️ GetTotalEntities

The GetTotalEntities method retrieves the total count of different entity types (vertices, edges, faces, cells) either for a specific element or for the entire mesh. This information is crucial for many mesh operations and finite element calculations.

📄️ GetTotalFaces

Returns the total number of faces in the mesh (obj%tFaces).

📄️ GetTotalFacetElements

Returns the total number of facet elements in the mesh.

📄️ GetTotalInternalFacetElements

Returns the total number of internal facet elements.

📄️ GetTotalInternalNodes

The GetTotalInternalNodes method returns the total number of internal nodes in the mesh. Internal nodes are nodes that are not on the boundary of the domain.

📄️ GetTotalMaterial

The GetTotalMaterial method returns the total number of materials defined for a specific element in the mesh.

📄️ GetTotalNodes

The GetTotalNodes method returns the total number of nodes in the mesh, with options to count nodes for specific mesh IDs or element selections.

📄️ GetTotalTopology

The GetTotalTopology method returns the total number of different element topology types present in the mesh. This indicates how many different element shapes are used in the mesh construction.

📄️ GetXiDimension

Return the xidimension of the mesh.

📄️ Import

This method reads mesh data from an HDF5 file and initializes the AbstractMesh_

📄️ InitiateBoundaryData

The InitiateBoundaryData method identifies and marks boundary elements and nodes within an AbstractMesh object.

📄️ InitiateDynamicDataStructure

This method is used to initiate the dynamic data structure of the mesh object. It is typically called during the initialization phase of the mesh object to set up any necessary data structures that will be used for dynamic operations on the mesh.

📄️ InitiateEdgeConnectivity

The InitiateEdgeConnectivity method initializes edge connectivity information in an AbstractMesh object. This method identifies all unique edges in the mesh, assigns them global edge numbers, and establishes the mapping between local element edges and these global edges.

📄️ InitiateElemSD

📄️ InitiateElementToElements

The InitiateElementToElements method establishes the element-to-element connectivity mapping in an AbstractMesh object. This connectivity represents how elements in the mesh are topologically connected to each other through shared faces, edges, or nodes, depending on the mesh dimension.

📄️ InitiateExtraNodetoNodes

The InitiateExtraNodetoNodes method builds an extended node-to-node connectivity mapping in an AbstractMesh object. Unlike the standard node-to-node connectivity, this extended mapping includes "second-degree" connections that are not directly connected through a shared element but are neighbors of neighbors.

📄️ InitiateFaceConnectivity

The InitiateFaceConnectivity method initializes the face connectivity data for elements in an AbstractMesh_ object.

📄️ InitiateFacetElements

The InitiateFacetElements method initializes facet element data for an AbstractMesh_ object.

📄️ InitiateKdTree

The InitiateKdtree method initializes a k-d tree data structure within an AbstractMesh object. This tree enables efficient spatial queries for tasks such as nearest neighbor searches, which are essential for many mesh-based operations.

📄️ InitiateNodeToElements

The InitiateNodeToElements method establishes the node-to-element connectivity mapping in an AbstractMesh object. This mapping is essential for numerous mesh operations as it allows quick identification of all elements connected to any given node.

📄️ InitiateNodeToNodes

The obj_InitiateNodetoNodes method builds the node-to-node connectivity mapping in an AbstractMesh object. This mapping represents the topological relationship between nodes in the mesh, creating a graph structure where each node knows which other nodes it's connected to through mesh elements.

📄️ IsAllNodePresent

The IsAllNodePresent method checks if all of the specified nodes exist in the mesh.

📄️ IsAnyNodePresent

The IsAnyNodePresent method checks if any of the specified nodes exist in the mesh.

📄️ IsBoundaryData

The IsBoundaryData method checks if the boundary data has been initialized in the mesh.

📄️ IsBoundaryElement

The IsBoundaryElement method checks if a specific element is a boundary element in the mesh.

📄️ IsBoundaryNode

The IsBoundaryNode method checks if a specific node is a boundary node in the mesh.

📄️ IsDomainBoundaryElement

The IsDomainBoundaryElement method checks if a specific element is a domain boundary element in the mesh.

📄️ IsDomainFacetElement

The IsDomainFacetElement method checks if a specific facet element is a domain boundary facet element in the mesh.

📄️ IsEdgeConnectivity

The IsEdgeConnectivity method checks if the edge connectivity information has been initialized in the mesh.

📄️ IsElementActive

The IsElementActive method checks if a specific element is active in the mesh.

📄️ IsElementPresent

The IsElementPresent method checks if a specific element number exists in the mesh.

📄️ IsElementToElements

The IsElementToElements method checks if the element-to-elements mapping has been initialized in the mesh.

📄️ IsEmpty

This method checks it the mesh is empty or not.

📄️ IsExtraNodeToNodes

The IsExtraNodeToNodes method checks if the extra node-to-nodes mapping has been initialized in the mesh.

📄️ IsFaceConnectivity

The IsFaceConnectivity method checks if the face connectivity information has been initialized in the mesh.

📄️ IsFacetData

The IsFacetData method checks if the facet data has been initialized in the mesh.

📄️ IsInit

The IsInit method checks if the mesh object has been properly initialized.

📄️ IsNodePresent

The IsNodePresent method checks if specific node numbers exist in the mesh. It has two versions: one for checking a single node, and another for checking multiple nodes simultaneously.

📄️ IsNodeToElements

The IsNodeToElements method checks if the node-to-elements mapping has been initialized in the mesh.

📄️ IsNodeToNodes

The IsNodeToNodes method checks if the node-to-nodes mapping has been initialized in the mesh.

📄️ SetBoundingBox

Interface

📄️ SetFacetElementType

The SetFacetElementType method sets the element type for a specific facet of a cell in the mesh. This is important for defining boundary conditions and inter-element connectivity.

📄️ SetFacetParam

The SetFacetParam method sets parameters for a facet element in the mesh.

📄️ SetMaterial

The SetMaterial method assigns material properties to elements in the mesh. It has three versions for different use cases.

📄️ SetParam

The SetParam method sets various parameters and flags in the mesh object.

📄️ SetQuality

The SetQuality method calculates and sets quality measures for mesh elements. Currently, this method is under development.

📄️ SetShowTime

By using this method you can measure the time required in each subroutine of AbstractMesh.

📄️ SetSparsity

The SetSparsity method sets the sparsity pattern of a CSR matrix based on mesh connectivity. It has four versions for different use cases.

📄️ SetTotalMaterial

The SetTotalMaterial method sets the total number of materials for elements in the mesh. It has two versions: one for a specific element, and another for all elements in the mesh.

📄️ Size

The Size method returns the total number of elements in the mesh. This is equivalent to GetTotalElements() and is provided as an alternative naming for the same functionality.