- inputThe mesh we want to diagnose
C++ Type:MeshGeneratorName
Unit:(no unit assumed)
Controllable:No
Description:The mesh we want to diagnose
MeshDiagnosticsGenerator
Runs a series of diagnostics on the mesh to detect potential issues such as unsupported features
commentnote
This mesh generator currently will only accept serialized meshes. This is most easily accomplished by leaving the mesh type set to replicated. Some of the diagnostics would work as well for distributed meshes, contributions are welcome.
The diagnostics implemented are presented below. The filters and visualization capabilities in Paraview or other visualization software may be leveraged for further diagnostics of mesh issues.
Element volume check
Turn this check on with the "examine_element_volumes" parameter.
A minimum and a maximum element volume can be specified to the MeshDiagnosticsGenerator using the "minimum_element_volumes" and the "maximum_element_volumes" parameters. These diagnostics are mostly used to detect zero or negative volume elements, from distorted meshes.
commentnote:How to fix large elements
Large elements may be sub-divided using the RefineBlockGenerator with for example a "max_element_volume".
commentnote:How to fix negative volume elements
Negative volume elements can be flipped using a MeshRepairGenerator with the "fix_elements_orientation" parameter. This will flip them, making the volume positive, though it may not fix the Jacobian everywhere.
Side planarity check
Turn this check on with the "examine_nonplanar_sides" parameter.
Non-planar elements are generally supported in MOOSE. However, the ray-tracing capabilities treat them approximately at the moment, so it may be useful to examine the mesh before use.
Subdomain element types check
Turn this check on with the "examine_element_types" parameter.
The Exodus output format only supports a single element type (TRI3, QUAD4, HEX8, HEX20, etc) per subdomain. Rather than erroring at the time of output, this diagnostic outputs which subdomains present multiple element types.
commentnote:How to fix subdomains with mixed element types
Subdomains with mixed element types can be split by element type using a MeshRepairGenerator with the "separate_blocks_by_element_types" parameter.
Sideset orientation check
Turn this check on with the "examine_sidesets_orientation" parameter.
Sidesets are oriented. They are represented in MOOSE by a list of elements and sides. Along the boundary, the orientation of these sides should in general be consistent. If it is not, the normal of the sideset is essentially reversed from one side to the next in the sideset.
The sideset orientation check is a heuristic for a common error case. The sideset orientation is only checked for sides that are delimiting two different subdomains. The check makes sure that the order of the subdomains, e.g. which one owns the element and which one owns the element on the other side of the side (the neighbor), does not change throughout the sideset.
Element overlap checks
Turn this check on with the "examine_element_overlap" parameter.
Overlap between elements are generally undesirable. Overlapping elements can be associated with non-conformality and/or breaks in the mesh, which generally are not supported without special numerical treatments, such as using interface kernels or mortar methods. Beyond having disconnected elements, the overlap means the volume of the mesh does not match the physical space volume, raising concerns about accuracy.
We support two heuristics to detect these overlaps:
detecting when the centroid of an element is inside another element
detecting when a node of an element is inside another element
commentnote
These two checks are heuristics. They can have false negatives if elements overlap but in a way that the centroids and nodes remain outside of other elements. This can happen for example with curved side elements overlapping on a side.
Non-conformality check
Turn this check on with the "examine_non_conformality" parameter.
Non-conformality in MOOSE is generally only supported if it is arising from adaptive mesh refinement created by the underlying mesh library. Additional information about the parent/child relationship between coarse and fine elements is stored at the element level. However, numerous external meshes, especially arising from simulations using adaptive mesh refinement, will present non-conformality. To support them, we usually resort to special numerical treatments, such as mortar methods.
Non-conformality is detected by this diagnostic by looking for nodes that are near an element within a tolerance but not part of this element's nodes.
commentnote
If the non-conformality is extremely minor, and the non-conformal nodes are very close to other nodes, they can be merged together using a MeshRepairGenerator.
Non-conformality arising from Adaptive Mesh Refinement
Turn this check on with the "search_for_adaptivity_nonconformality" parameter.
In the special case of meshes where isotropic adaptive h-refinement was performed, the MeshDiagnosticsGenerator can detect at the interface between coarse and fine elements that the fine elements could be combined into a coarse element. The coarse element, if it were refined with MOOSE h-adaptivity, would be refined into the same fine elements as originally present in the mesh.
This check will only detect mesh refinement for triangle and quadrilateral 2D elements and, tetrahedral and hexahedral 3D elements. For tetrahedra, because the refinement pattern depends on the selection of a diagonal inside the coarse element, the check only considers the tip fine elements on the four vertex of the coarse element.
commentnote
This check is a heuristic. It will only detect adaptive uniform mesh refinement and it will only detect it near interfaces between coarse and fine elements. If the entire mesh is refined the same number of times for each element, it will not be detected.
commentnote
This check may report false positives on some immersed meshes and slit meshes because it will detect non-conformal nodes and will try to examine if the elements next to these nodes can be grouped to form coarser elements.
Elements and sides local Jacobian check
The local Jacobian is checked for positivity for every element and sides. Negative Jacobians are a common issue with a poor, usually externally generated, mesh.
commentnote
A fifth-order Gauss quadrature is used for this check. If you intend to use another quadrature, for example a higher order to integrate more accurately high order finite element variables, feel free to modify the generator for your needs.
Example input syntax: all diagnostics turned on
In this example, we examine a very basic mesh with all the diagnostics offered by the MeshDiagnosticsGenerator. This simple mesh presents no issue.
[Mesh]
[base]
type = GeneratedMeshGenerator
dim = 2
nx = 2
ny = 2
[]
[diag]
type = MeshDiagnosticsGenerator
input = base
examine_element_overlap = WARNING
examine_element_types = WARNING
examine_element_volumes = WARNING
examine_non_conformality = WARNING
examine_nonplanar_sides = INFO
examine_sidesets_orientation = WARNING
check_for_watertight_sidesets = WARNING
check_for_watertight_nodesets = WARNING
search_for_adaptivity_nonconformality = WARNING
check_local_jacobian = WARNING
[]
[]
[Outputs]
exodus = true
[]
Input Parameters
- check_for_watertight_nodesetsNO_CHECKwhether to check for external nodes that are not assigned to any nodeset
Default:NO_CHECK
C++ Type:MooseEnum
Unit:(no unit assumed)
Controllable:No
Description:whether to check for external nodes that are not assigned to any nodeset
- check_for_watertight_sidesetsNO_CHECKwhether to check for external sides that are not assigned to any sidesets
Default:NO_CHECK
C++ Type:MooseEnum
Unit:(no unit assumed)
Controllable:No
Description:whether to check for external sides that are not assigned to any sidesets
- check_local_jacobianNO_CHECKwhether to check the local Jacobian for negative values
Default:NO_CHECK
C++ Type:MooseEnum
Unit:(no unit assumed)
Controllable:No
Description:whether to check the local Jacobian for negative values
- examine_element_overlapNO_CHECKwhether to find overlapping elements
Default:NO_CHECK
C++ Type:MooseEnum
Unit:(no unit assumed)
Controllable:No
Description:whether to find overlapping elements
- examine_element_typesNO_CHECKwhether to look for multiple element types in the same sub-domain
Default:NO_CHECK
C++ Type:MooseEnum
Unit:(no unit assumed)
Controllable:No
Description:whether to look for multiple element types in the same sub-domain
- examine_element_volumesNO_CHECKwhether to examine volume of the elements
Default:NO_CHECK
C++ Type:MooseEnum
Unit:(no unit assumed)
Controllable:No
Description:whether to examine volume of the elements
- examine_non_conformalityNO_CHECKwhether to examine the conformality of elements in the mesh
Default:NO_CHECK
C++ Type:MooseEnum
Unit:(no unit assumed)
Controllable:No
Description:whether to examine the conformality of elements in the mesh
- examine_nonplanar_sidesNO_CHECKwhether to check element sides are planar
Default:NO_CHECK
C++ Type:MooseEnum
Unit:(no unit assumed)
Controllable:No
Description:whether to check element sides are planar
- examine_sidesets_orientationNO_CHECKwhether to check that sidesets are consistently oriented using neighbor subdomains. If a sideset is inconsistently oriented within a subdomain, this will not be detected
Default:NO_CHECK
C++ Type:MooseEnum
Unit:(no unit assumed)
Controllable:No
Description:whether to check that sidesets are consistently oriented using neighbor subdomains. If a sideset is inconsistently oriented within a subdomain, this will not be detected
- log_length_limit10How many problematic element/nodes/sides/etc are explicitly reported on by each check
Default:10
C++ Type:unsigned int
Unit:(no unit assumed)
Controllable:No
Description:How many problematic element/nodes/sides/etc are explicitly reported on by each check
- maximum_element_volumes1e+16Maximum size for element volume
Default:1e+16
C++ Type:double
Unit:(no unit assumed)
Controllable:No
Description:Maximum size for element volume
- minimum_element_volumes1e-16minimum size for element volume
Default:1e-16
C++ Type:double
Unit:(no unit assumed)
Controllable:No
Description:minimum size for element volume
- nonconformal_tol1e-06tolerance for element non-conformality
Default:1e-06
C++ Type:double
Unit:(no unit assumed)
Controllable:No
Description:tolerance for element non-conformality
- search_for_adaptivity_nonconformalityNO_CHECKwhether to check for non-conformality arising from adaptive mesh refinement
Default:NO_CHECK
C++ Type:MooseEnum
Unit:(no unit assumed)
Controllable:No
Description:whether to check for non-conformality arising from adaptive mesh refinement
Optional Parameters
- control_tagsAdds user-defined labels for accessing object parameters via control logic.
C++ Type:std::vector<std::string>
Unit:(no unit assumed)
Controllable:No
Description:Adds user-defined labels for accessing object parameters via control logic.
- enableTrueSet the enabled status of the MooseObject.
Default:True
C++ Type:bool
Unit:(no unit assumed)
Controllable:No
Description:Set the enabled status of the MooseObject.
- save_with_nameKeep the mesh from this mesh generator in memory with the name specified
C++ Type:std::string
Unit:(no unit assumed)
Controllable:No
Description:Keep the mesh from this mesh generator in memory with the name specified
Advanced Parameters
- nemesisFalseWhether or not to output the mesh file in the nemesisformat (only if output = true)
Default:False
C++ Type:bool
Unit:(no unit assumed)
Controllable:No
Description:Whether or not to output the mesh file in the nemesisformat (only if output = true)
- outputFalseWhether or not to output the mesh file after generating the mesh
Default:False
C++ Type:bool
Unit:(no unit assumed)
Controllable:No
Description:Whether or not to output the mesh file after generating the mesh
- show_infoFalseWhether or not to show mesh info after generating the mesh (bounding box, element types, sidesets, nodesets, subdomains, etc)
Default:False
C++ Type:bool
Unit:(no unit assumed)
Controllable:No
Description:Whether or not to show mesh info after generating the mesh (bounding box, element types, sidesets, nodesets, subdomains, etc)