Mesher¶

class pyccx.mesh.Mesher(modelName)¶

Bases: object

The Mesher class provides the base interface built upon the GMSH-SDK API operations. It provides the capability to mesh multiple objects

Attributes Summary

`EPSILON`	Minimum tolerance used for truncating nodal coordinate values
`ElementOrder`
`Initialised`
`NumThreads`
`OptimiseNetgen`
`Units`
`edges`	The ids for all edge geometry in the model
`meshAssignments`
`name`	The name of the GMSH model
`physicalGroups`	The physical groups tags available in the model
`points`	The ids for all point geometry in the model
`surfaces`	The geometric entity ids for all surface geometry in the model
`version`	Version of the GMSH SDK available
`volumes`	The geometric elementary ids for all volume geometry in the model

Methods Summary

`addGeometry`(filename, name[, meshFactor])	Adds CAD geometry into the GMSH kernel.
`boundingBox`()	Returns the bounding box of the model
`clearMesh`()	Clears any meshes previously generated by GMSH
`clearMeshAssignments`([elType])	Clears the mesh assignments for the model
`clearPhysicalGroups`([dimension])	Clears all physical groups in the model :type dimension: `Optional`[`int`] :param dimension: Integer is the dimension of the physical group to clear.
`finalize`()
`generateMesh`([generate3DMesh])	Initialises the GMSH Meshing Procedure
`getAllPhysicalGroupElements`()
`getChildrenFromEntities`(id)	From a Entity, obtain all children associated with this volume - note may include shared entities.
`getElementIds`([entityId, merge])	Returns the elements for the entire model or optionally a specific entity.
`getElementTypes`()
`getElements`([entityId])	Returns the elements for the entire model or optionally a specific entity.
`getElementsByPhysicalGroups`(physicalGroup)	Returns all elements associated with a physical group
`getElementsByType`(elType[, elTag, returnElIds])	Returns all elements of type (elType) from the GMSH model, within class ElementTypes.
`getEntityName`(id)	Returns the name of an entity given an id (if assigned) :type id: `Tuple`[`int`, `int`] :param id: Dimension, Entity Id
`getFacesFromId`(surfIds)
`getGeomBoundingBoxById`(tagId)	Returns the bounding box of the geometry (volume) by id
`getGeomBoundingBoxByName`(volumeName)
`getIdByEdgeName`(edgeName)	Obtains the ID for the edge name
`getIdByEntityName`(entityName)	Obtains the ID for volume name
`getIdBySurfaceName`(surfaceName)	Obtains the elemental id for the surface name
`getIdByVolumeName`(volumeName)	Obtains the ID for volume name
`getNodeIds`()	Returns the nodal ids from the entire GMSH model :rtype: `array` :return:
`getNodes`()	Returns the nodal coordinates from the entire GMSH model.
`getNodesByEntityName`(entityName)	Returns all nodes for a selected surface region
`getNodesFromEdgeByName`(edgeName)	Returns all nodes from a geometric edge
`getNodesFromEntity`(entityId)	Returns all node ids from a selected entity in the GMSH model.
`getNodesFromSurfaceByName`(surfaceRegionName)	Returns all nodes for a selected surface region
`getNodesFromVolumeByName`(volumeName)	Returns all node ids from a selected volume domain in the GMSH model.
`getNodesInBoundingBox`(minX, minY, minZ, ...)	Returns all nodes within a bounding box
`getNumThreads`()	Gets the number of threads used for parallel processing by GMSH
`getNumberElements`([physicalGroupsOnly])	The number of elements in the mesh
`getPointsFromEntity`(id)	From an Id, obtain all Point Ids associated with this volume - note may include shared points.
`getPointsFromVolume`(id)	From a Volume Id, obtain all Point Ids associated with this volume - note may include shared points.
`getPointsFromVolumeByName`(volumeName)	Returns all geometric points from a given volume domain by its name (if assigned) :type volumeName: `str` :param volumeName: volumeName :return:
`getSurfaceFacesFromRegion`(regionName)
`getSurfaceFacesFromSurfId`(surfTagId)
`getSurfacesFromVolume`(id)	From a Volume Id, obtain all Surface Ids associated with this volume - note may include shared boundary surfaces.
`getVolumeName`(volId)	Gets the volume name (if assigned)
`identifyUnassignedElements`()	Returns the list of elements that have not been assigned element types
`initialise`()	Initialises the GMSH runtime and sets default options.
`interpTri`(triInd)
`isDirty`()	Has the model been successfully generated and no pending modifications exist.
`isMeshGenerated`()	Returns 'True' if the mesh has been successfully internally generated by GMSH
`maxPhysicalGroupId`(dim)	Returns the highest physical group id in the GMSH model
`mergeGeometry`()	Geometry is merged/fused together.
`open`(filename)	Opens a GMSH file and loads the geometry into the current modelling instance
`recombineMesh`()	Recombines the surface mesh - between triangles and quadrilaterals using the specified recombination algorithm.
`removeEdgeMeshes`()	Removes edges (1D mesh entities) from the GMSH model
`removeSurfaceMeshes`()	Removes surface meshes (2D mesh entities) from the GMSH model
`renumberElements`()	Renumbers the elements of the entire GMSH Model
`renumberNodes`()	Renumbers the nodes of the entire GMSH Model
`set2DMeshingAlgorithm`(meshingAlgorithm)	Sets the 2D meshing algorithm to use by GMSH for the model
`set3DMeshingAlgorithm`(meshingAlgorithm)	Sets the 3D meshing algorithm to use by GMSH for the model
`setAsCurrentModel`()	Sets the current model to that specified in the class instance because Only one instance of GMSH sdk is available so this must be dynamically switched between models for multiple instances of a Mesher.
`setEdgePhysicalName`(edgeId, name)	Sets the Physcal Group Name of the Curve(s)
`setEdgeSet`(grpTag, edgeName)
`setElementOrder`(elOrder)	Sets the element order globally for the entire model.
`setEntityName`(id, name)	Set the geometrical entity name - useful only as reference when viewing in the GMSH GUI
`setEntityPhysicalName`(id, name)	Sets the geometric name of the volume id
`setMeshAssignmentsById`(elIds, elType)	Set the element type and concatenate elements to this
`setMeshAssignmentsByType`(elIds, elType)	Set the element type and concatenate elements to this
`setMeshSize`(pnts, size)	Sets the mesh element size along an entity, however, this can only currently be performed by the assignment of the sizes onto point ids.
`setMeshSizeFactor`(meshSizeFactor)	The mesh factor size provides an estimate length for the initial element sizes based on proportion of the maximum bounding box length.
`setModelChanged`([state])	Any changes to GMSH model should call this to prevent inconsistency in a generated model
`setNumThreads`(numThreads)	Sets the number of threads to be used for parallel processing by GMSH
`setOptimiseNetgen`(state)	Sets an option for GMSH to internally use Netgen to optimise the element quality of the generated mesh.
`setRecombinationAlgorithm`(recombinationAlgorithm)	Sets the recombination algorithm to use by GMSH for the model
`setRecombineSurfaces`(surfId[, angle])	Set a constraints on the surface mesh (triangles) to be recombined to quadrilaterals based on the angle
`setSurfacePhysicalName`(surfId, name)	Sets the Physical Group Name of the Surfaces(s)
`setSurfaceSet`(grpTag, surfName)	Generates a surface set based on the geometric surface name.
`setUnits`(unitVal)
`setVolumePhysicalName`(volId, name)	Sets the Physical Group Name of the Volumes(s)
`showGui`()	Opens up the native GMSH Gui to inspect the geometry in the model and the mesh.
`writeMesh`(filename)	Writes the generated mesh to the file
`writeMeshInput`()	Generates the current mesh format as an abaqus (Calculix) .inp representation format

Attributes Documentation

EPSILON: float = 1e-10¶: Minimum tolerance used for truncating nodal coordinate values

ElementOrder: int = 1¶

Initialised: bool = False¶

NumThreads: int = 4¶

OptimiseNetgen: bool = True¶

Units: str = ''¶

edges¶: The ids for all edge geometry in the model

meshAssignments¶

name¶: The name of the GMSH model

physicalGroups¶: The physical groups tags available in the model

points¶: The ids for all point geometry in the model

surfaces¶: The geometric entity ids for all surface geometry in the model

version¶: Version of the GMSH SDK available

volumes¶: The geometric elementary ids for all volume geometry in the model

Methods Documentation

addGeometry(filename, name, meshFactor=0.03)¶

Adds CAD geometry into the GMSH kernel. The filename of compatible model files along with the mesh factor should be used to specify a target mesh size.

Parameters:

filename (str)
name (str) – Name to assign to the geometries imported
meshFactor (Optional[float]) – Initialise the target element size to a proportion of the average bounding box dimensions

boundingBox()¶

Returns the bounding box of the model

Return type:: ndarray
Returns:: The bounding box of the GMSH Model

clearMesh()¶

Clears any meshes previously generated by GMSH

Return type:: None

clearMeshAssignments(elType=None)¶

Clears the mesh assignments for the model

Parameters:: elType – The element type to clear the assignments
Return type:: None

clearPhysicalGroups(dimension=None)¶: Clears all physical groups in the model :type dimension: Optional[int] :param dimension: Integer is the dimension of the physical group to clear. Default is None.

classmethod finalize()¶

Return type:: None

generateMesh(generate3DMesh=True)¶

Initialises the GMSH Meshing Procedure

Parameters:: generate3DMesh – Generates the 3D Mesh -
Return type:: None

getAllPhysicalGroupElements()¶

getChildrenFromEntities(id)¶

From a Entity, obtain all children associated with this volume - note may include shared entities.

Parameters:: id (Tuple[int, int]) – Dimension, Entity Id
Return type:: List[int]
Returns:: List of Ids

getElementIds(entityId=None, merge=True)¶

Returns the elements for the entire model or optionally a specific entity.

Parameters:

entityId (Optional[Tuple[int, int]]) – The entity id to obtain elements for
merge (Optional[bool]) – Merge the element ids into a single array

Returns:

A Tuple of element types, element ids and corresponding node ids

getElementTypes()¶

getElements(entityId=None)¶

Returns the elements for the entire model or optionally a specific entity.

Parameters:: entityId (Optional[Tuple[int, int]]) – The entity id to obtain elements for
Returns:: A Tuple of element types, element ids and corresponding node ids

getElementsByPhysicalGroups(physicalGroup)¶

Returns all elements associated with a physical group

Parameters:: physicalGroup – The physical group id
Return type:: ndarray
Returns:: The element ids associated with the physical groups

getElementsByType(elType, elTag=None, returnElIds=False)¶

Returns all elements of type (elType) from the GMSH model, within class ElementTypes. Note: the element ids are returned with an index starting from 1 - internally GMSH uses an index starting from 1, like most FEA pre-processors

Parameters:

elType (BaseElementType) – Element type
elTag (Optional[Tuple[int, int]]) – Optional list of element tags to filter the element types from
returnElIds (Optional[bool]) – ‘True’ returns the element ids along with the elements

Return type:

Union[Tuple[ndarray, ndarray], ndarray]

Returns:

List of element Ids

Raises:

Exception – If the mesh is not generated

getEntityName(id)¶

Returns the name of an entity given an id (if assigned) :type id: Tuple[int, int] :param id: Dimension, Entity Id

Return type:: str

getFacesFromId(surfIds)¶

getGeomBoundingBoxById(tagId)¶

Returns the bounding box of the geometry (volume) by id

Parameters:: tagId (int) – The geometry id
Return type:: ndarray
Returns:: The bounding box of the GMSH Model

getGeomBoundingBoxByName(volumeName)¶

getIdByEdgeName(edgeName)¶

Obtains the ID for the edge name

Parameters:: edgeName (str) – Geometric edge name
Return type:: int
Returns:: Edge ID

getIdByEntityName(entityName)¶

Obtains the ID for volume name

Parameters:: entityName (str) – str
Return type:: int
Returns:: int: Volume ID

getIdBySurfaceName(surfaceName)¶

Obtains the elemental id for the surface name

Parameters:: surfaceName (str) – Geometric surface name
Return type:: int
Returns:: Surface Ids

getIdByVolumeName(volumeName)¶

Obtains the ID for volume name

Parameters:: volumeName (str) – str
Return type:: int
Returns:: int: Volume ID

getNodeIds()¶: Returns the nodal ids from the entire GMSH model :rtype: array :return:

getNodes()¶

Returns the nodal coordinates from the entire GMSH model. These are sorted automatically by the node-id

Return type:: ndarray
Returns:: The nodal coordinates to the corresponding node ids
Raises:: Exception – If the mesh is not generated

getNodesByEntityName(entityName)¶

Returns all nodes for a selected surface region

Parameters:: entityName (str) – The geometric surface name
Return type:: array
Returns:: The list of node ids associated with the selected entity id

getNodesFromEdgeByName(edgeName)¶

Returns all nodes from a geometric edge

Parameters:: edgeName (str) – The geometric edge name
Returns:: The list of node ids associated with the selected entity id

getNodesFromEntity(entityId)¶

Returns all node ids from a selected entity in the GMSH model.

Parameters:: entityId (Tuple[int, int]) – The selected geometric entity id
Return type:: array
Returns:: The node ids for the selected entity

getNodesFromSurfaceByName(surfaceRegionName)¶

Returns all nodes for a selected surface region

Parameters:: surfaceRegionName (str) – The geometric surface name
Returns:: The list of node ids associated with the selected entity id

getNodesFromVolumeByName(volumeName)¶

Returns all node ids from a selected volume domain in the GMSH model.

Parameters:: volumeName (str) – Volume name
Return type:: array
Returns:: The list of node ids associated with the selected entity id

getNodesInBoundingBox(minX, minY, minZ, maxX, maxY, maxZ)¶

Returns all nodes within a bounding box

Parameters:

minX (int) – Minimum X
minY (int) – Minimum Y
minZ (int) – Minimum Z
maxX (int) – Maximum X
maxY (int) – Maximum Y
maxZ (int) – Maximum Z

Return type:

array

Returns:

The node ids within the bounding box

classmethod getNumThreads()¶

Gets the number of threads used for parallel processing by GMSH

Return type:: int

getNumberElements(physicalGroupsOnly=True)¶

The number of elements in the mesh

Parameters:: physicalGroupsOnly – If True` mesh number consists only physical grups - default is True
Returns:

getPointsFromEntity(id)¶

From an Id, obtain all Point Ids associated with this volume - note may include shared points.

Parameters:: id (Tuple[int, int]) – Dimension and Entity ID
Return type:: List[int]
Returns:: List of Point Ids

getPointsFromVolume(id)¶

From a Volume Id, obtain all Point Ids associated with this volume - note may include shared points.

Parameters:: id (int) – Volume ID
Return type:: List[int]
Returns:: list(int) - List of Point Ids

getPointsFromVolumeByName(volumeName)¶: Returns all geometric points from a given volume domain by its name (if assigned) :type volumeName: str :param volumeName: volumeName :return:

getSurfaceFacesFromRegion(regionName)¶

getSurfaceFacesFromSurfId(surfTagId)¶

getSurfacesFromVolume(id)¶

From a Volume Id, obtain all Surface Ids associated with this volume - note may include shared boundary surfaces.

Parameters:: id (int) – Volume Id
Return type:: List[int]
Returns:: List of surface Ids

getVolumeName(volId)¶

Gets the volume name (if assigned)

Parameters:: volId (int) – int: Volume id of a region
Return type:: str

identifyUnassignedElements()¶

Returns the list of elements that have not been assigned element types

Return type:: array
Returns:: List of elements that have no element type designated

classmethod initialise()¶

Initialises the GMSH runtime and sets default options. This is called automatically once.

Return type:: None

interpTri(triInd)¶

isDirty()¶

Has the model been successfully generated and no pending modifications exist.

Return type:: bool

isMeshGenerated()¶

Returns ‘True’ if the mesh has been successfully internally generated by GMSH

Return type:: bool

maxPhysicalGroupId(dim)¶

Returns the highest physical group id in the GMSH model

Parameters:: dim (int) – int: The chosen dimension
Return type:: int
Returns:: int: The highest group id used for the chosen dimension

mergeGeometry()¶

Geometry is merged/fused together. Coincident surfaces and points are automatically merged together, which enables a coherent mesh to be generated when these align exactly.

Return type:: None

open(filename)¶

Opens a GMSH file and loads the geometry into the current modelling instance

Parameters:: filename (str) – The filename of the GMSH file
Return type:: None

recombineMesh()¶: Recombines the surface mesh - between triangles and quadrilaterals using the specified recombination algorithm.

removeEdgeMeshes()¶

Removes edges (1D mesh entities) from the GMSH model

Return type:: None

removeSurfaceMeshes()¶: Removes surface meshes (2D mesh entities) from the GMSH model

renumberElements()¶

Renumbers the elements of the entire GMSH Model

Return type:: None

renumberNodes()¶

Renumbers the nodes of the entire GMSH Model

Return type:: None

set2DMeshingAlgorithm(meshingAlgorithm)¶

Sets the 2D meshing algorithm to use by GMSH for the model

Parameters:: meshingAlgorithm (MeshingAlgorithm2D) – The selected 2D Meshing Algorithm used
Return type:: None

set3DMeshingAlgorithm(meshingAlgorithm)¶

Sets the 3D meshing algorithm to use by GMSH for the model

Parameters:: meshingAlgorithm (MeshingAlgorithm3D) – The selected 3D Meshing Algorithm used
Return type:: None

setAsCurrentModel()¶

Sets the current model to that specified in the class instance because Only one instance of GMSH sdk is available so this must be dynamically switched between models for multiple instances of a Mesher.

Return type:: None

setEdgePhysicalName(edgeId, name)¶

Sets the Physcal Group Name of the Curve(s)

Parameters:

surfId – The set of curve ids
name (str) – Name assigned to volume

Return type:

int

setEdgeSet(grpTag, edgeName)¶

Return type:: None

classmethod setElementOrder(elOrder)¶

Sets the element order globally for the entire model. Note that different element orders cannot be used within the same GMSH model during generation

Parameters:: elOrder (int) – The element order
Return type:: None

setEntityName(id, name)¶

Set the geometrical entity name - useful only as reference when viewing in the GMSH GUI

Parameters:

id (Tuple[int, int]) – Entity Dimension and Entity Id
name (str) – The entity name

Return type:

None

setEntityPhysicalName(id, name)¶

Sets the geometric name of the volume id

Parameters:

id (Tuple[int, int]) – Dimension, Entity id tuple(int, int):
name (str) – str: Name assigned to entity

Return type:

int

setMeshAssignmentsById(elIds, elType)¶

Set the element type and concatenate elements to this

Parameters:

elType (BaseElementType)
el

Return type:

None

Returns:

setMeshAssignmentsByType(elIds, elType)¶

Set the element type and concatenate elements to this

Parameters:

elType (BaseElementType)
el

Return type:

None

Returns:

setMeshSize(pnts, size)¶

Sets the mesh element size along an entity, however, this can only currently be performed by the assignment of the sizes onto point ids.

Parameters:

pnts (List[int]) – Point ids to set the mesh size
size (float) – Set the desired mesh length size at this point

Return type:

None

classmethod setMeshSizeFactor(meshSizeFactor)¶

The mesh factor size provides an estimate length for the initial element sizes based on proportion of the maximum bounding box length.

Parameters:: meshSizeFactor (float) – The mesh factor size between [0.,1.0]
Return type:: None

setModelChanged(state=False)¶

Any changes to GMSH model should call this to prevent inconsistency in a generated model

Parameters:: state (Optional[bool]) – Force the model to be shown as generated
Return type:: None

classmethod setNumThreads(numThreads)¶

Sets the number of threads to be used for parallel processing by GMSH

Parameters:: numThreads (int)
Return type:: None

classmethod setOptimiseNetgen(state)¶

Sets an option for GMSH to internally use Netgen to optimise the element quality of the generated mesh. Enabled by default.

Parameters:: state (bool) – Toggles the option
Return type:: None

setRecombinationAlgorithm(recombinationAlgorithm)¶

Sets the recombination algorithm to use by GMSH for the model

Parameters:: recombinationAlgorithm (RecombinationAlgorithm) – The selected recombination algorithm for use
Return type:: None

setRecombineSurfaces(surfId, angle=45)¶

Set a constraints on the surface mesh (triangles) to be recombined to quadrilaterals based on the angle

Parameters:

surfId – The surface identity
angle – The angle in degrees for recombination

setSurfacePhysicalName(surfId, name)¶

Sets the Physical Group Name of the Surfaces(s)

Parameters:

surfId (Any) – The set of surface ids
name (str) – Name assigned to volume

Return type:

int

setSurfaceSet(grpTag, surfName)¶

Generates a surface set based on the geometric surface name. GMSH creates an associative surface mesh, which will later be automatically removed.

Parameters:

grpTag (int) – int: A unique Geometric Id used to associate the surface set as a physical group
surfName (str) – str: The surface name for the set

Return type:

None

Returns:

classmethod setUnits(unitVal)¶

Return type:: None

setVolumePhysicalName(volId, name)¶

Sets the Physical Group Name of the Volumes(s)

Parameters:

volId (Any) – The set of volume ids
name (str) – The name assigned to volume group

Return type:

int

classmethod showGui()¶: Opens up the native GMSH Gui to inspect the geometry in the model and the mesh. This will block the Python script until the GUI is exited.

writeMesh(filename)¶

Writes the generated mesh to the file

Parameters:: filename (str) – str - Filename (including the type) to save to.
Return type:: None

writeMeshInput()¶

Generates the current mesh format as an abaqus (Calculix) .inp representation format

Returns:: The mesh string format

Mesher¶

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