Merge pull request #24646 from dschwen/boundary_geometry_24645

Fix Geometry UOs and Boundary Marker
idaholab · Jun 21, 2023 · d2a66a5 · d2a66a5
2 parents dd3ae2a + 38e9f82
commit d2a66a5
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Showing 13 changed files with 176 additions and 56 deletions.
diff --git a/framework/include/markers/BoundaryMarker.h b/framework/include/markers/BoundaryMarker.h
@@ -34,5 +34,5 @@ class BoundaryMarker : public Marker
   const MarkerValue _mark;
 
   /// boundary near which to mark elements
-  const BoundaryID _boundary;
+  const std::vector<BoundaryID> _boundary_ids;
 };
diff --git a/framework/include/userobjects/GeometryBase.h b/framework/include/userobjects/GeometryBase.h
@@ -41,4 +41,7 @@ class GeometryBase : public GeneralUserObject
 
   /// List of boundaries (or node sets) that will be snapped to a geometry
   const std::vector<BoundaryID> _boundary_ids;
+
+  /// List of blocks (likely lower D blocks) that will be snapped to a geometry
+  const std::vector<SubdomainID> _subdomain_ids;
 };
diff --git a/framework/src/markers/BoundaryMarker.C b/framework/src/markers/BoundaryMarker.C
@@ -21,7 +21,8 @@ BoundaryMarker::validParams()
 
   params.addRequiredParam<MooseEnum>(
       "mark", marker_states, "How to mark elements adjacent to the boundary.");
-  params.addRequiredParam<BoundaryName>("next_to", "Boundary to refine elements along");
+  params.addRequiredParam<std::vector<BoundaryName>>("next_to",
+                                                     "Boundaries to refine elements along");
   params.addParam<Real>("distance", 0.0, "Distance from the boundary to refine within");
   return params;
 }
@@ -31,7 +32,7 @@ BoundaryMarker::BoundaryMarker(const InputParameters & parameters)
     _distance(getParam<Real>("distance")),
     _bnd_elem_ids(_mesh.getBoundariesToActiveSemiLocalElemIds()),
     _mark(parameters.get<MooseEnum>("mark").getEnum<MarkerValue>()),
-    _boundary(_mesh.getBoundaryID(getParam<BoundaryName>("next_to")))
+    _boundary_ids(_mesh.getBoundaryIDs(getParam<std::vector<BoundaryName>>("next_to")))
 {
   if (_mesh.isDistributedMesh() && _distance > 0)
     mooseWarning("Elements with in `distance ` of a boundary segment on a different processor "
@@ -43,23 +44,32 @@ BoundaryMarker::computeElementMarker()
 {
   if (_distance == 0.0)
   {
-    if (_mesh.isBoundaryElem(_current_elem->id(), _boundary))
-      return _mark;
+    // is the current element member of any selected boundary element set?
+    for (const auto boundary : _boundary_ids)
+      if (_mesh.isBoundaryElem(_current_elem->id(), boundary))
+        return _mark;
 
     return DONT_MARK;
   }
   else
   {
-    const auto it = _bnd_elem_ids.find(_boundary);
-    if (it != _bnd_elem_ids.end())
-      for (const auto id : it->second)
-      {
-        const auto elem = _mesh.elemPtr(id);
-        const auto r = _current_elem->vertex_average() - elem->vertex_average();
-        if (r.norm() < _distance)
-          return _mark;
-      }
+    for (const auto boundary : _boundary_ids)
+    {
+      const auto it = _bnd_elem_ids.find(boundary);
+      if (it != _bnd_elem_ids.end())
+        for (const auto id : it->second)
+        {
+          // shortcut if we are checing the current element itself
+          if (id == _current_elem->id())
+            return _mark;
 
+          // otherwise compute distance to the boundary elements
+          const auto elem = _mesh.elemPtr(id);
+          const auto r = _current_elem->vertex_average() - elem->vertex_average();
+          if (r.norm() < _distance)
+            return _mark;
+        }
+    }
     return DONT_MARK;
   }
 }
diff --git a/framework/src/userobjects/GeometryBase.C b/framework/src/userobjects/GeometryBase.C
@@ -15,16 +15,20 @@ InputParameters
 GeometryBase::validParams()
 {
   InputParameters params = GeneralUserObject::validParams();
-  params.addClassDescription("Snap refined nodes on a given boundary to a given geometry");
+  params.addClassDescription(
+      "Snap refined nodes on a given boundary or block to a given geometry.");
   params.addParam<std::vector<BoundaryName>>(
       "boundary", "List of boundaries whose nodes are snapped to a given geometry");
+  params.addParam<std::vector<SubdomainName>>(
+      "block", "List of blocks whose nodes are snapped to a given geometry");
   return params;
 }
 
 GeometryBase::GeometryBase(const InputParameters & parameters)
   : GeneralUserObject(parameters),
     _mesh(_subproblem.mesh()),
-    _boundary_ids(_mesh.getBoundaryIDs(getParam<std::vector<BoundaryName>>("boundary")))
+    _boundary_ids(_mesh.getBoundaryIDs(getParam<std::vector<BoundaryName>>("boundary"))),
+    _subdomain_ids(_mesh.getSubdomainIDs(getParam<std::vector<SubdomainName>>("block")))
 {
 }
 
@@ -48,6 +52,7 @@ GeometryBase::meshChanged()
 {
   auto & mesh = _mesh.getMesh();
 
+  // go over boundaries
   for (auto & boundary_id : _boundary_ids)
   {
     auto node_ids = _mesh.getNodeList(boundary_id);
@@ -58,4 +63,19 @@ GeometryBase::meshChanged()
       snapNode(node);
     }
   }
+
+  // go over blocks
+  MeshBase::node_iterator node = mesh.active_nodes_begin();
+  MeshBase::node_iterator node_end = mesh.active_nodes_end();
+  for (; node != node_end; ++node)
+  {
+    // check if node is part of any of the selected blocks
+    const auto & node_blocks = _mesh.getNodeBlockIds(**node);
+    for (const auto subdomain_id : _subdomain_ids)
+      if (node_blocks.count(subdomain_id))
+      {
+        snapNode(**node);
+        break;
+      }
+  }
 }
diff --git a/test/tests/markers/boundary_marker/adjacent.i b/test/tests/markers/boundary_marker/adjacent.i
@@ -1,12 +1,3 @@
-###########################################################
-# This is a test of the Mesh Marker System. It marks
-# elements with flags indicating whether they should be
-# refined, coarsened, or left alone. This system
-# has the ability to use the Mesh Indicator System.
-#
-# @Requirement F2.50
-###########################################################
-
 [Mesh]
   type = GeneratedMesh
   dim = 2

diff --git a/test/tests/markers/boundary_marker/distance.i b/test/tests/markers/boundary_marker/distance.i
@@ -1,12 +1,3 @@
-###########################################################
-# This is a test of the Mesh Marker System. It marks
-# elements with flags indicating whether they should be
-# refined, coarsened, or left alone. This system
-# has the ability to use the Mesh Indicator System.
-#
-# @Requirement F2.50
-###########################################################
-
 [Mesh]
   type = GeneratedMesh
   dim = 2

diff --git a/test/tests/markers/boundary_marker/gold/multiple_out.e b/test/tests/markers/boundary_marker/gold/multiple_out.e
diff --git a/test/tests/markers/boundary_marker/multiple.i b/test/tests/markers/boundary_marker/multiple.i
@@ -0,0 +1,35 @@
+[Mesh]
+  type = GeneratedMesh
+  dim = 2
+[]
+
+[Variables]
+  [u]
+  []
+[]
+
+[Problem]
+  kernel_coverage_check = false
+  solve = false
+[]
+
+[Executioner]
+  type = Steady
+[]
+
+# Mesh Marker System
+[Adaptivity]
+  [Markers]
+    [boundary]
+      type = BoundaryMarker
+      next_to = 'right bottom'
+      mark = refine
+    []
+  []
+  initial_marker = boundary
+  initial_steps = 3
+[]
+
+[Outputs]
+  exodus = true
+[]
diff --git a/test/tests/markers/boundary_marker/tests b/test/tests/markers/boundary_marker/tests
@@ -1,21 +1,28 @@
 [Tests] # NOTE: This file is used for testing by the python/moosesqa package
   group = 'Boundary Marker'
   design = "/Markers/index.md /BoundaryMarker.md"
-  issues = '#1275'
+  issues = '#1275 #24645'
 
-  [./adjacent]
+  [adjacent]
     type = 'Exodiff'
     input = 'adjacent.i'
     exodiff = 'adjacent_out.e'
     requirement = "The adaptivity system shall create an auxiliary field variable that marks "
                   "elements for refinement adjacent to a boundary."
-  [../]
-  [./distance]
+  []
+  [distance]
     type = 'Exodiff'
     input = 'distance.i'
     exodiff = 'distance_out.e'
     requirement = "The adaptivity system shall create an auxiliary field variable that marks "
                   "elements for refinement within a given distance of a boundary."
     mesh_mode = REPLICATED
-  [../]
+  []
+  [multiple]
+    type = 'Exodiff'
+    input = 'multiple.i'
+    exodiff = 'multiple_out.e'
+    requirement = "The adaptivity system shall create an auxiliary field variable that marks "
+                  "elements for refinement adjacent to any of a given set of boundaries."
+  []
 []
diff --git a/test/tests/userobjects/geometry_snap/block.i b/test/tests/userobjects/geometry_snap/block.i
@@ -0,0 +1,51 @@
+[Mesh]
+  [gen]
+    type = PolyLineMeshGenerator
+    points = "0 0 0
+              0 1 0
+              1 1 0
+              1 0 0"
+    loop = true
+  []
+[]
+
+[Variables]
+  [u]
+    initial_condition = 1
+  []
+[]
+
+[Problem]
+  kernel_coverage_check = false
+  solve = false
+[]
+
+[Executioner]
+  type = Steady
+[]
+
+[UserObjects]
+  [sphere]
+    type = GeometrySphere
+    center = '0.5 0.5 0'
+    radius = 0.7071
+    block = 0
+  []
+[]
+
+[Adaptivity]
+  [Markers]
+    [const]
+      type = UniformMarker
+      mark = REFINE
+    []
+  []
+  marker = const
+  steps = 3
+[]
+
+[Outputs]
+  [out]
+    type = Exodus
+  []
+[]
diff --git a/test/tests/userobjects/geometry_snap/geometrysphere.i b/test/tests/userobjects/geometry_snap/geometrysphere.i
@@ -1,12 +1,14 @@
 [Mesh]
-  type = GeneratedMesh
-  dim = 2
+  [gen]
+    type = GeneratedMeshGenerator
+    dim = 2
+  []
 []
 
 [Variables]
-  [./u]
+  [u]
     initial_condition = 1
-  [../]
+  []
 []
 
 [Problem]
@@ -19,27 +21,27 @@
 []
 
 [UserObjects]
-  [./sphere]
+  [sphere]
     type = GeometrySphere
     boundary = 'left right top bottom'
     center = '0.5 0.5 0'
     radius = 0.7071
-  [../]
+  []
 []
 
 [Adaptivity]
-  [./Markers]
-    [./const]
+  [Markers]
+    [const]
       type = UniformMarker
       mark = REFINE
-    [../]
-  [../]
+    []
+  []
   marker = const
   steps = 3
 []
 
 [Outputs]
-  [./out]
+  [out]
     type = Exodus
-  [../]
+  []
 []
diff --git a/test/tests/userobjects/geometry_snap/gold/block_out.e-s004 b/test/tests/userobjects/geometry_snap/gold/block_out.e-s004
diff --git a/test/tests/userobjects/geometry_snap/tests b/test/tests/userobjects/geometry_snap/tests
@@ -1,11 +1,21 @@
 [Tests]
-  [./geometrysphere]
+  design = 'GeometrySphere.md'
+  [geometrysphere]
     type = 'Exodiff'
     input = 'geometrysphere.i'
     exodiff = 'geometrysphere_out.e-s004'
-
-    design = 'GeometrySphere.md'
     issues = '#9578'
-    requirement = 'The system shall support "snapping" or moving new nodes and sides created by mesh adaptivity to the surface of a geometric sphere to capture high fidelity features on curved geometries.'
-  [../]
+    requirement = "The system shall support 'snapping' or moving new nodes in sidesets created by "
+                  "mesh adaptivity to the surface of a geometric sphere to capture high fidelity "
+                  "features on curved geometries."
+  []
+  [block]
+    type = 'Exodiff'
+    input = 'block.i'
+    exodiff = 'block_out.e-s004'
+    issues = '#24645'
+    requirement = "The system shall support 'snapping' or moving new nodes in lower dimensional "
+                  "subdomains created by mesh adaptivity to the surface of a geometric sphere to "
+                  "capture high fidelity features on curved geometries."
+  []
 []