reporter point marker to mark mesh for refinement around points given…

… by a reporter. closes idaholab#18886 included Logan and Daniels suggestions
lynnmunday · Sep 28, 2021 · 2ff1533 · 2ff1533
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diff --git a/framework/doc/content/source/markers/ReporterPointMarker.md b/framework/doc/content/source/markers/ReporterPointMarker.md
@@ -0,0 +1,19 @@
+# ReporterPointMarker
+
+!syntax description /Adaptivity/Markers/ReporterPointMarker
+
+## Description
+
+The `ReporterPointMarker` is a stand-alone marker that marks all
+elements containing points defined by coordinates given in a `Reporter`.
+
+
+## Example Input Syntax
+
+!listing test/tests/markers/reporter_point_marker/point_marker_test.i block=Adaptivity
+
+!syntax parameters /Adaptivity/Markers/ReporterPointMarker
+
+!syntax inputs /Adaptivity/Markers/ReporterPointMarker
+
+!syntax children /Adaptivity/Markers/ReporterPointMarker
diff --git a/framework/include/markers/ReporterPointMarker.h b/framework/include/markers/ReporterPointMarker.h
@@ -0,0 +1,42 @@
+//* This file is part of the MOOSE framework
+//* https://www.mooseframework.org
+//*
+//* All rights reserved, see COPYRIGHT for full restrictions
+//* https://github.com/idaholab/moose/blob/master/COPYRIGHT
+//*
+//* Licensed under LGPL 2.1, please see LICENSE for details
+//* https://www.gnu.org/licenses/lgpl-2.1.html
+
+#pragma once
+
+#include "Marker.h"
+#include "ReporterInterface.h"
+
+/**
+ * Marks all elements near a given boundary for refinement/coarsening
+ */
+class ReporterPointMarker : public Marker, public ReporterInterface
+{
+public:
+  static InputParameters validParams();
+  ReporterPointMarker(const InputParameters & parameters);
+  virtual void markerSetup() override;
+
+protected:
+  virtual MarkerValue computeElementMarker() override;
+
+  /// marker value to give elements containing a point
+  const MarkerValue _inside;
+  /// marker for elements not containing points
+  const MarkerValue _empty;
+  /// x coordinate
+  const std::vector<Real> & _x_coord;
+  /// y coordinate
+  const std::vector<Real> & _y_coord;
+  ///z coordinate
+  const std::vector<Real> & _z_coord;
+  /// Pointer to PointLocatorBase object
+  std::unique_ptr<PointLocatorBase> _pl;
+  /// list of sort uniqued elements containing points
+  std::set<dof_id_type> _point_elems;
+};
diff --git a/framework/src/markers/ReporterPointMarker.C b/framework/src/markers/ReporterPointMarker.C
@@ -0,0 +1,71 @@
+//* This file is part of the MOOSE framework
+//* https://www.mooseframework.org
+//*
+//* All rights reserved, see COPYRIGHT for full restrictions
+//* https://github.com/idaholab/moose/blob/master/COPYRIGHT
+//*
+//* Licensed under LGPL 2.1, please see LICENSE for details
+//* https://www.gnu.org/licenses/lgpl-2.1.html
+
+#include "ReporterPointMarker.h"
+
+registerMooseObject("MooseApp", ReporterPointMarker);
+
+InputParameters
+ReporterPointMarker::validParams()
+{
+  InputParameters params = Marker::validParams();
+  params.addClassDescription("Marks the region inside or empty if it contains a reporter defined "
+                             "point for refinement or coarsening.");
+  params.addRequiredParam<ReporterName>("x_coord_name", "reporter x-coordinate name");
+  params.addRequiredParam<ReporterName>("y_coord_name", "reporter y-coordinate name");
+  params.addRequiredParam<ReporterName>("z_coord_name", "reporter z-coordinate name");
+  MooseEnum marker_states = Marker::markerStates();
+  params.addRequiredParam<MooseEnum>(
+      "inside", marker_states, "How to mark elements containing a point");
+  params.addRequiredParam<MooseEnum>(
+      "empty", marker_states, "How to mark elements not containing a point");
+  return params;
+}
+
+ReporterPointMarker::ReporterPointMarker(const InputParameters & parameters)
+  : Marker(parameters),
+    ReporterInterface(this),
+    _inside(parameters.get<MooseEnum>("inside").getEnum<MarkerValue>()),
+    _empty(parameters.get<MooseEnum>("empty").getEnum<MarkerValue>()),
+    _x_coord(getReporterValue<std::vector<Real>>("x_coord_name", REPORTER_MODE_REPLICATED)),
+    _y_coord(getReporterValue<std::vector<Real>>("y_coord_name", REPORTER_MODE_REPLICATED)),
+    _z_coord(getReporterValue<std::vector<Real>>("z_coord_name", REPORTER_MODE_REPLICATED))
+{
+}
+
+void
+ReporterPointMarker::markerSetup()
+{
+  _pl = _fe_problem.mesh().getPointLocator();
+  _pl->enable_out_of_mesh_mode();
+  const auto npoints = _x_coord.size();
+  if (npoints != _y_coord.size() || npoints != _z_coord.size())
+    mooseError("The coordinate vectors are a different size.  \n",
+               "   x_coord size = ",
+               npoints,
+               ";  y_coord size = ",
+               _y_coord.size(),
+               ";  z_coord size = ",
+               _z_coord.size());
+
+  _point_elems.clear();
+  for (std::size_t i = 0; i < npoints; ++i)
+  {
+    Point pt(_x_coord[i], _y_coord[i], _z_coord[i]);
+    const auto elem = (*_pl)(pt);
+    if (elem)
+      _point_elems.insert(elem->id());
+  }
+}
+
+Marker::MarkerValue
+ReporterPointMarker::computeElementMarker()
+{
+  return (_point_elems.count(_current_elem->id()) ? _inside : _empty);
+}
diff --git a/test/tests/markers/box_marker/gold/box_marker_test_out.e b/test/tests/markers/box_marker/gold/box_marker_test_out.e
diff --git a/test/tests/markers/reporter_point_marker/gold/point_marker_test_out.e b/test/tests/markers/reporter_point_marker/gold/point_marker_test_out.e
@@ -0,0 +1 @@
+../../box_marker/gold/box_marker_test_out.e
diff --git a/test/tests/markers/reporter_point_marker/gold/reporter_marker_adapt_test_out.csv b/test/tests/markers/reporter_point_marker/gold/reporter_marker_adapt_test_out.csv
@@ -0,0 +1,8 @@
+time,n_elements
+0,0
+0.1,25
+0.2,31
+0.3,34
+0.4,43
+0.5,46
+0.6,46
diff --git a/test/tests/markers/reporter_point_marker/point_marker_test.i b/test/tests/markers/reporter_point_marker/point_marker_test.i
@@ -0,0 +1,60 @@
+[Mesh]
+  type = GeneratedMesh
+  dim = 2
+  nx = 10
+  ny = 10
+  elem_type = QUAD4
+[]
+
+[Problem]
+  solve = false
+[]
+
+[Executioner]
+  type = Steady
+[]
+
+[Reporters]
+  [coords]
+    type=ConstantReporter
+    real_vector_names = 'x y z'
+    real_vector_values = '.31 .41 .51  .31 .41 .51 .31 .41 .51 .8;
+                          .31 .31 .31 .41  .41 .41 .51 .51 .51 .8;
+                           0   0   0  0   0   0  0  0   0  1;'
+    outputs=none
+  []
+  [bad_coords]
+    type=ConstantReporter
+    real_vector_names = 'x y z'
+    real_vector_values = '.31 .41 .51;
+                          .31 .31 .31 .41  .41 .41 .51 .51;
+                           0   0   0  0   0   0  0  0   0  1;'
+    outputs=none
+  []
+[]
+
+[Adaptivity]
+  [Markers]
+      active = 'box'
+    [box]
+      type = ReporterPointMarker
+      x_coord_name = coords/x
+      y_coord_name = coords/y
+      z_coord_name = coords/z
+      inside = refine
+      empty = do_nothing
+    []
+    [bad_coord]
+      type = ReporterPointMarker
+      x_coord_name = bad_coords/x
+      y_coord_name = bad_coords/y
+      z_coord_name = bad_coords/z
+      inside = refine
+      empty = do_nothing
+    []
+  []
+[]
+
+[Outputs]
+  exodus=true
+[]
diff --git a/test/tests/markers/reporter_point_marker/reporter_marker_adapt_test.i b/test/tests/markers/reporter_point_marker/reporter_marker_adapt_test.i
@@ -0,0 +1,76 @@
+[Mesh]
+  type = GeneratedMesh
+  dim = 2
+  nx = 5
+  ny = 5
+[]
+
+[Problem]
+  solve = false
+[]
+
+[Executioner]
+  type = Transient
+  num_steps = 6
+  dt = 0.1
+[]
+
+[Reporters]
+  [coords]
+    type=ConstantReporter
+    real_vector_names = 'y z'
+    real_vector_values = '.51 .91; 0 0;'
+    outputs=none
+  []
+[]
+[Functions]
+  [xfcn]
+    type = ParsedFunction
+    value = t+0.01 #offset so marker is not on element edge
+  []
+[]
+
+[Postprocessors]
+  [xfcn_pp]
+    type = FunctionValuePostprocessor
+    function = xfcn
+    execute_on = timestep_end
+    outputs = none
+  []
+  [x_pp]
+    type = Receiver
+    default = .91
+    outputs = none
+  []
+  [n_elements]
+    type = NumElems
+    execute_on = 'timestep_end'
+  []
+[]
+
+[VectorPostprocessors]
+  [xfcn_vpp]
+    type = VectorOfPostprocessors
+    postprocessors = 'xfcn_pp x_pp'
+    outputs = none
+  []
+[]
+
+[Adaptivity]
+  marker = x_moving
+  max_h_level = 2
+  [Markers]
+    [x_moving]
+      type = ReporterPointMarker
+      x_coord_name = xfcn_vpp/xfcn_vpp
+      y_coord_name = coords/y
+      z_coord_name = coords/z
+      inside = REFINE
+      empty = COARSEN
+    []
+  []
+[]
+
+[Outputs]
+  csv = true
+[]
diff --git a/test/tests/markers/reporter_point_marker/tests b/test/tests/markers/reporter_point_marker/tests
@@ -0,0 +1,27 @@
+[Tests]
+  group = 'Reporter Point Marker'
+  design = "/Markers/index.md /ReporterPointMarker.md"
+  issues = '#18886'
+  [mark_only]
+    type = 'Exodiff'
+    input = 'point_marker_test.i'
+    exodiff = 'point_marker_test_out.e'
+    scale_refine = 2
+    requirement = "The adaptivity system shall create an auxiliary field variable that marks "
+                  "elements containing the points from the reporter for refinement."
+  []
+  [wrong_size_error]
+    type = 'RunException'
+    input = 'point_marker_test.i'
+    cli_args = 'Adaptivity/Markers/active=bad_coord'
+    expect_err = "x_coord size = 3;  y_coord size = 8;  z_coord size = 10"
+    requirement = "The marker shall create an error if the coordinate vectors are not all the same size"
+  []
+  [adaptivity]
+    type = 'CSVDiff'
+    input = 'reporter_marker_adapt_test.i'
+    csvdiff = 'reporter_marker_adapt_test_out.csv'
+    requirement = "The marker shall be used for adaptivity for a moving point, "
+     "being able to coarsen elements the point moves out of but not coarsen elements if it contains point."
+  []
+[]