Added diagnostic check for watertight nodesets #29068

DanielYankura · 2024-11-13T18:25:50Z

-Loops through all elements and sides
-If side is external it checks if all its nodes are assigned to a nodeset

Reason

Adds new diagnostic tool for users

Design

If feature it turned on, it loops through each element, then the element's sides. If the sides are external it checks each node to ensure it's been assigned to a nodeset. If not, the node id is printed for reference.

Impact

Adds watertight nodeset check to Mesh Diagnostics

GiudGiud · 2024-11-13T18:30:54Z

framework/src/meshgenerators/MeshDiagnosticsGenerator.C

+  params.addParam<MooseEnum>(
+      "check_for_watertight_nodesets",
+      chk_option,
+      "whether to check for external nodes that are not assigned to any nodeset");
  params.addParam<MooseEnum>(


let s add a parameter for the nodesets that are supposed to englobe the entire mesh. when this parameter is in use, the nodes are only checked against those "blessed" nodesets

same for sidsets
actually now that I see that this is not an option for sidesets, let s keep it for future work

Sounds good. I'll open a new issue for adding that parameter to the sideset and nodeset checks.

GiudGiud · 2024-11-13T18:53:38Z

framework/src/meshgenerators/MeshDiagnosticsGenerator.C

+    mooseError("The nodeset check only works for 2D and 3D meshes");
+  auto & boundary_info = mesh->get_boundary_info();
+  boundary_info.build_side_list();
+  const auto nodeset_map = boundary_info.get_nodeset_map();


where is the _boundary_node_id being initialized in libmesh? is the previous call doing it?

I believe that gets initialized when the mesh is first read in or made?

let s be sure we dont need to "prepare_for_use" for this diagnostics to work

So I looked into it. The node ids get added to _boundary_node_id after execute_mesh_generators is called in ActionWarehouse.C. From what I can tell the mesh is always initialized before this test could ever be called.

after execute_mesh_generators

wouldnt that be too late then?

Sorry, it's the execute_mesh_generators task that initializes _boundary_node_id. After initialization mesh diagnostics runs. So that task runs both I believe, but it should initialize first.

GiudGiud

looks good

GiudGiud · 2024-11-13T18:54:13Z

framework/src/meshgenerators/MeshDiagnosticsGenerator.C

+
+  for (const auto elem : mesh->active_element_ptr_range())
+  {
+    for (auto i : elem->side_index_range())


Suggested change

for (auto i : elem->side_index_range())

for (const auto i : elem->side_index_range())

GiudGiud · 2024-11-13T18:54:22Z

framework/src/meshgenerators/MeshDiagnosticsGenerator.C

+      // Check if side is external
+      if (elem->neighbor_ptr(i) == nullptr)
+      {
+        // Side is externa, now check nodes


Suggested change

// Side is externa, now check nodes

// Side is external, now check nodes

GiudGiud · 2024-11-13T18:56:05Z

framework/src/meshgenerators/MeshDiagnosticsGenerator.C

+            if (num_nodes_without_nodeset < _num_outputs)
+            {
+              message = "Node " + std::to_string(node->id()) +
+                        " is external, but has not been assigned to a nodeset";


Suggested change

" is external, but has not been assigned to a nodeset";

" is on an external boundary of the mesh, but has not been assigned to a nodeset";

GiudGiud · 2024-11-13T18:56:57Z

test/tests/meshgenerators/mesh_diagnostics_generator/tests

+      cli_args = '--mesh-only'
+      mesh_mode = 'replicated'
+      expect_out = 'Number of external nodes that have not been assigned to a nodeset: 1'
+      detail = '2D meshed square missing a nodeset on one side'


Suggested change

detail = '2D meshed square missing a nodeset on one side'

detail = '2D meshed square with one external node that does not belong to a nodeset'

GiudGiud · 2024-11-13T18:57:02Z

test/tests/meshgenerators/mesh_diagnostics_generator/tests

+      cli_args = '--mesh-only'
+      mesh_mode = 'replicated'
+      expect_out = 'Number of external nodes that have not been assigned to a nodeset: 1'
+      detail = '3D meshed cube missing a nodeset on one side'


moosebuild · 2024-11-13T21:10:49Z

Job Documentation, step Docs: sync website on 6004474 wanted to post the following:

View the site here

This comment will be updated on new commits.

moosebuild · 2024-11-13T21:20:52Z

Job Coverage, step Generate coverage on 6004474 wanted to post the following:

Framework coverage

	61ed70	#29068 600447
	Total	Total	+/-	New
Rate	85.13%	85.13%	+0.00%	97.56%
Hits	107285	107322	+37	40
Misses	18743	18743	-	1

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This comment will be updated on new commits.

moosebuild · 2024-11-13T22:55:44Z

Job Precheck, step Clang format on 0c3d1cd wanted to post the following:

Your code requires style changes.

A patch was auto generated and copied here
You can directly apply the patch by running, in the top level of your repository:

curl -s https://mooseframework.inl.gov/docs/PRs/29068/clang_format/style.patch | git apply -v

Alternatively, with your repository up to date and in the top level of your repository:

git clang-format 7377410027ba9dbf48902235a0437fdf96485e29

GiudGiud · 2024-11-14T18:46:24Z

framework/src/meshgenerators/MeshDiagnosticsGenerator.C

+          {
+            // This node does not have a nodeset!!!
+            num_nodes_without_nodeset++;
+            checked_nodes.insert(*node);


this is deprecated in libmesh (this copy-construction I think?)

you should store the ids. that s enough to distinguish nodes

Thanks! I was trying to figure out why it was failing that test. I think I have the same issue in #28701 so I'll fix it in that one as well.

I didnt remember that one was still open. Do you need anything else from me for that? Are we waiting on Roy's review?

I think I'm just waiting on Roy's review. Though if this one get's merged first I might have to make some changes to the other before it can be merged.

-Loops through all elements and sides -If side is external it checks if all its nodes are assigned to a nodeset closes idaholab#28822

-Fixed spelling mistake -made iterator const -improved error messages

…h deprecation error

DanielYankura requested review from lindsayad, roystgnr and GiudGiud as code owners November 13, 2024 18:25

GiudGiud reviewed Nov 13, 2024

View reviewed changes

GiudGiud self-assigned this Nov 13, 2024

GiudGiud reviewed Nov 14, 2024

View reviewed changes

DanielYankura added 5 commits November 14, 2024 15:01

Added diagnostic check for watertight nodesets

b26277b

-Loops through all elements and sides -If side is external it checks if all its nodes are assigned to a nodeset closes idaholab#28822

Made formatting changes for Civet

ab61eb3

Made changes for PR

d7a8ed0

-Fixed spelling mistake -made iterator const -improved error messages

Style changes for Civte again

2006878

checked_nodes array now takes node id instead of node to avoid libmes…

6004474

…h deprecation error

DanielYankura force-pushed the water_tight_nodeset_check branch from 24cb4b1 to 6004474 Compare November 14, 2024 22:02

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Added diagnostic check for watertight nodesets #29068

Added diagnostic check for watertight nodesets #29068

DanielYankura commented Nov 13, 2024

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moosebuild commented Nov 13, 2024 •

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moosebuild commented Nov 13, 2024 •

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moosebuild commented Nov 13, 2024

GiudGiud Nov 14, 2024

DanielYankura Nov 14, 2024

GiudGiud Nov 14, 2024

DanielYankura Nov 14, 2024

	for (auto i : elem->side_index_range())
	for (const auto i : elem->side_index_range())

	// Side is externa, now check nodes
	// Side is external, now check nodes

	" is external, but has not been assigned to a nodeset";
	" is on an external boundary of the mesh, but has not been assigned to a nodeset";

	detail = '2D meshed square missing a nodeset on one side'
	detail = '2D meshed square with one external node that does not belong to a nodeset'

Added diagnostic check for watertight nodesets #29068

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Added diagnostic check for watertight nodesets #29068

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DanielYankura commented Nov 13, 2024

Reason

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moosebuild commented Nov 13, 2024 • edited Loading

moosebuild commented Nov 13, 2024 • edited Loading

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moosebuild commented Nov 13, 2024 •

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moosebuild commented Nov 13, 2024 •

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