From 8ac14edb9a08cf63385c5a88afc314c8accee1fe Mon Sep 17 00:00:00 2001
From: Roy Stogner <Roy.Stogner@inl.gov>
Date: Thu, 11 Jul 2024 15:19:41 -0500
Subject: [PATCH 01/11] BoundingBox print and iostreams support

---
 include/geom/bounding_box.h | 19 +++++++++++++++++++
 src/geom/bounding_box.C     |  6 ++++++
 2 files changed, 25 insertions(+)

diff --git a/include/geom/bounding_box.h b/include/geom/bounding_box.h
index 4c8f44355d8..81af4c9cd38 100644
--- a/include/geom/bounding_box.h
+++ b/include/geom/bounding_box.h
@@ -151,6 +151,25 @@ class BoundingBox : public std::pair<Point, Point>
    * constructor and by invalidate().
    */
   void scale(const Real factor);
+
+  /**
+   * Formatted print, by default to \p libMesh::out.
+   */
+  void print(std::ostream & os = libMesh::out) const;
+
+  /**
+   * Formatted print as above but supports the syntax:
+   *
+   * \code
+   * BoundingBox b;
+   * std::cout << b << std::endl;
+   * \endcode
+   */
+  friend std::ostream & operator << (std::ostream & os, const BoundingBox & b)
+  {
+    b.print(os);
+    return os;
+  }
 };
 
 
diff --git a/src/geom/bounding_box.C b/src/geom/bounding_box.C
index f5620b4d575..c1978f9c4c4 100644
--- a/src/geom/bounding_box.C
+++ b/src/geom/bounding_box.C
@@ -150,4 +150,10 @@ void BoundingBox::scale(const Real factor)
   }
 }
 
+
+void BoundingBox::print(std::ostream & os) const
+{
+  os << "(min=" << this->min() << ", max=" << this->max() << ")";
+}
+
 } // namespace libMesh

From 5a5ba3bad3f86dbfe1042fd1cf0bb08c757a243f Mon Sep 17 00:00:00 2001
From: Roy Stogner <Roy.Stogner@inl.gov>
Date: Thu, 11 Jul 2024 15:20:31 -0500
Subject: [PATCH 02/11] Entities BoundingBox testing in GmshIO

Right now we ignore the point locations and the curve/surface/volume
bounding box extents in a GMSH $Entities section; this led to unexpected
behavior in #3899

Let's insist that those locations and bounding boxes are accurate.
False positives for these tests are an easy fix (edit the $Entities),
whereas missed true positives lead to erroneous simulations.
---
 src/mesh/gmsh_io.C | 75 ++++++++++++++++++++++++++++++++++++++++++++--
 1 file changed, 72 insertions(+), 3 deletions(-)

diff --git a/src/mesh/gmsh_io.C b/src/mesh/gmsh_io.C
index 6baa7986594..70937756ffc 100644
--- a/src/mesh/gmsh_io.C
+++ b/src/mesh/gmsh_io.C
@@ -19,6 +19,7 @@
 #include "libmesh/libmesh_config.h"
 #include "libmesh/libmesh_logging.h"
 #include "libmesh/boundary_info.h"
+#include "libmesh/bounding_box.h"
 #include "libmesh/elem.h"
 #include "libmesh/gmsh_io.h"
 #include "libmesh/mesh_base.h"
@@ -192,6 +193,9 @@ void GmshIO::read_mesh(std::istream & in)
   // the entity tag/id
   std::map<std::pair<unsigned, int>, int> entity_to_physical_id;
 
+  // Map from entities to bounding boxes.  The key is the same.
+  std::map<std::pair<unsigned, int>, BoundingBox> entity_to_bounding_box;
+
   // For reading the file line by line
   std::string s;
 
@@ -299,6 +303,9 @@ void GmshIO::read_mesh(std::istream & in)
                                      "Sorry, you cannot currently specify multiple subdomain or "
                                      "boundary ids for a given geometric entity");
 
+                entity_to_bounding_box[std::make_pair(0, point_tag)] =
+                  BoundingBox(Point(x,y,z),Point(x,y,z));
+
                 if (num_physical_tags)
                 {
                   in >> physical_tag;
@@ -316,6 +323,9 @@ void GmshIO::read_mesh(std::istream & in)
                                      "I don't believe that we can specify multiple subdomain or "
                                      "boundary ids for a given geometric entity");
 
+                entity_to_bounding_box[std::make_pair(1, curve_tag)] =
+                  BoundingBox(Point(minx,miny,minz),Point(maxx,maxy,maxz));
+
                 if (num_physical_tags)
                 {
                   in >> physical_tag;
@@ -336,6 +346,9 @@ void GmshIO::read_mesh(std::istream & in)
                                      "I don't believe that we can specify multiple subdomain or "
                                      "boundary ids for a given geometric entity");
 
+                entity_to_bounding_box[std::make_pair(2, surface_tag)] =
+                  BoundingBox(Point(minx,miny,minz),Point(maxx,maxy,maxz));
+
                 if (num_physical_tags)
                 {
                   in >> physical_tag;
@@ -356,6 +369,9 @@ void GmshIO::read_mesh(std::istream & in)
                                      "I don't believe that we can specify multiple subdomain or "
                                      "boundary ids for a given geometric entity");
 
+                entity_to_bounding_box[std::make_pair(3, volume_tag)] =
+                  BoundingBox(Point(minx,miny,minz),Point(maxx,maxy,maxz));
+
                 if (num_physical_tags)
                 {
                   in >> physical_tag;
@@ -625,19 +641,47 @@ void GmshIO::read_mesh(std::istream & in)
                     std::size_t gmsh_element_id;
                     in >> gmsh_element_id;
 
+                    // Make sure this element isn't somewhere
+                    // unexpected
+
+                    // A default bounding box is [inf,-inf] (empty);
+                    // swap that and we get [-inf,inf] (everything)
+                    BoundingBox expected_bounding_box;
+                    std::swap(expected_bounding_box.min(),
+                              expected_bounding_box.max());
+
+                    if (auto it = entity_to_bounding_box.find
+                          (std::make_pair(entity_dim, entity_tag));
+                        it != entity_to_bounding_box.end())
+                      expected_bounding_box = it->second;
+
                     // Get the remainder of the line that includes the nodes ids
                     std::getline(in, s);
                     std::istringstream is(s);
                     std::size_t local_node_counter = 0, gmsh_node_id;
                     while (is >> gmsh_node_id)
                     {
+                      Node * node = mesh.node_ptr(nodetrans[gmsh_node_id]);
+
+                      // Make sure the file is consistent about entity
+                      // placement
+                      libmesh_error_msg_if
+                        (!expected_bounding_box.contains_point(*node),
+                         "$Elements dim " << entity_dim << " element "
+                         << gmsh_element_id << " (entity " << entity_tag
+                         << ", " <<
+                         Utility::enum_to_string(eletype.type) <<
+                         ") has node at " << *static_cast<Node*>(node)
+                         << "\n outside entity physical bounding box " <<
+                         expected_bounding_box);
+
                       // Add node pointers to the elements.
                       // If there is a node translation table, use it.
                       if (eletype.nodes.size() > 0)
                           elem->set_node(eletype.nodes[local_node_counter++]) =
-                            mesh.node_ptr(nodetrans[gmsh_node_id]);
+                            node;
                       else
-                          elem->set_node(local_node_counter++) = mesh.node_ptr(nodetrans[gmsh_node_id]);
+                          elem->set_node(local_node_counter++) = node;
                     }
 
                     // Make sure that the libmesh element we added has nnodes nodes.
@@ -665,8 +709,33 @@ void GmshIO::read_mesh(std::istream & in)
                     std::size_t gmsh_element_id, gmsh_node_id;
                     in >> gmsh_element_id;
                     in >> gmsh_node_id;
+
+                    // Make sure the file is consistent about entity
+                    // placement
+
+                    // A default bounding box is [inf,-inf] (empty);
+                    // swap that and we get [-inf,inf] (everything)
+                    BoundingBox expected_bounding_box;
+                    std::swap(expected_bounding_box.min(),
+                              expected_bounding_box.max());
+
+                    if (auto it = entity_to_bounding_box.find
+                          (std::make_pair(entity_dim, entity_tag));
+                        it != entity_to_bounding_box.end())
+                      expected_bounding_box = it->second;
+
+                    Node * node = mesh.node_ptr(nodetrans[gmsh_node_id]);
+
+                    libmesh_error_msg_if
+                      (!expected_bounding_box.contains_point(*node),
+                       "$Elements dim " << entity_dim << " element "
+                       << gmsh_element_id << " (entity " << entity_tag <<
+                       ") has node at " << *static_cast<Node*>(node)
+                       << "\n outside entity physical bounding box " <<
+                       expected_bounding_box);
+
                     mesh.get_boundary_info().add_node(
-                      nodetrans[gmsh_node_id],
+                      node,
                       static_cast<boundary_id_type>(entity_to_physical_id[
                                                       std::make_pair(entity_dim, entity_tag)]));
                   } // end for (loop over elements in entity block)

From 1802440bc48775f0273a7f9eb3d7c7f09a544e83 Mon Sep 17 00:00:00 2001
From: Roy Stogner <Roy.Stogner@inl.gov>
Date: Thu, 11 Jul 2024 15:24:10 -0500
Subject: [PATCH 03/11] Unit test for new Gmsh error testing

---
 tests/Makefile.am       |   1 +
 tests/mesh/mesh_input.C |  32 ++++++
 tests/meshes/block.msh  | 215 ++++++++++++++++++++++++++++++++++++++++
 3 files changed, 248 insertions(+)
 create mode 100644 tests/meshes/block.msh

diff --git a/tests/Makefile.am b/tests/Makefile.am
index 996a2723ec6..2a0bd0985e8 100644
--- a/tests/Makefile.am
+++ b/tests/Makefile.am
@@ -153,6 +153,7 @@ data = matrices/geom_1_extraction_op.m \
        meshes/1_quad.bxt.gz \
        meshes/25_quad.bxt.gz \
        meshes/bad_64bit_elem_integers.e \
+       meshes/block.msh \
        meshes/BlockWithHole_Patch9.bxt.gz \
        meshes/constrain10to4.m \
        meshes/Cube_With_Sidesets.e \
diff --git a/tests/mesh/mesh_input.C b/tests/mesh/mesh_input.C
index b135b828605..ea934745c0d 100644
--- a/tests/mesh/mesh_input.C
+++ b/tests/mesh/mesh_input.C
@@ -13,6 +13,7 @@
 #include <libmesh/abaqus_io.h>
 #include <libmesh/dyna_io.h>
 #include <libmesh/exodusII_io.h>
+#include <libmesh/gmsh_io.h>
 #include <libmesh/nemesis_io.h>
 #include <libmesh/vtk_io.h>
 #include <libmesh/tetgen_io.h>
@@ -20,6 +21,7 @@
 #include "test_comm.h"
 #include "libmesh_cppunit.h"
 
+#include <regex>
 
 using namespace libMesh;
 
@@ -190,6 +192,10 @@ public:
   CPPUNIT_TEST( testDynaFileMappingsCyl3d);
 #endif // LIBMESH_HAVE_GZSTREAM
 #endif // LIBMESH_DIM > 1
+       //
+#if LIBMESH_DIM > 1
+  CPPUNIT_TEST( testGmsh );
+#endif
 
 #ifdef LIBMESH_HAVE_TETGEN
   CPPUNIT_TEST( testTetgenIO );
@@ -1508,6 +1514,32 @@ public:
     helperTestingDynaQuad(mesh);
   }
 
+  void testGmsh ()
+  {
+    LOG_UNIT_TEST;
+
+    Mesh mesh(*TestCommWorld);
+
+    GmshIO gmsh_io(mesh);
+
+#ifdef LIBMESH_ENABLE_EXCEPTIONS
+    std::string what = "";
+    try
+    {
+      if (mesh.processor_id() == 0)
+        gmsh_io.read("meshes/block.msh");
+    }
+    catch (libMesh::LogicError & e)
+    {
+      what = e.what();
+    }
+
+    TestCommWorld->broadcast(what);
+    std::regex msg_regex("outside entity physical bounding box");
+    CPPUNIT_ASSERT(std::regex_search(what, msg_regex));
+#endif
+  }
+
   void testTetgenIO ()
   {
 #ifdef LIBMESH_HAVE_TETGEN
diff --git a/tests/meshes/block.msh b/tests/meshes/block.msh
new file mode 100644
index 00000000000..9ad5c63b867
--- /dev/null
+++ b/tests/meshes/block.msh
@@ -0,0 +1,215 @@
+$MeshFormat
+4.1 0 8
+$EndMeshFormat
+$PhysicalNames
+18
+0 1 "PointC"
+0 2 "PointA"
+0 3 "PointB"
+1 4 "lineBeamA" lower_dimensional_block
+1 5 "lineBeamB" lower_dimensional_block
+3 6 "Base"
+2 7 "PlateA" lower_dimensional_block
+2 8 "Base_YMin_0"
+2 9 "Base_XMin_0"
+2 10 "Base_XMax_0"
+2 11 "Base_YMax_0"
+2 12 "Base_ZMin_0"
+2 13 "BoundaryXMin"
+2 14 "BoundaryXMax"
+2 15 "BoundaryYMin"
+2 16 "BoundaryYMax"
+2 17 "BoundaryZMin"
+2 18 "BoundaryZMax"
+$EndPhysicalNames
+$Entities
+3 2 12 1
+1 0 0 -14 1 1
+2 14 0 -14 1 2
+3 -14 15 -14 1 3
+1 -14 -10 -14 0 0 -14 1 4 0
+2 -14 0 -14 0 15 -14 1 5 0
+1 -14 -10 -14 0 0 -14 1 7 0
+2 -14 -10 -17 14 -10 -14 1 8 0
+3 -14 -10 -17 -14 15 -14 1 9 0
+4 14 -10 -17 14 15 -14 1 10 0
+5 -14 15 -17 14 15 -14 1 11 0
+6 -14 -10 -17 14 15 -17 1 12 0
+7 -14 -10 -17 -14 15 -14 1 13 0
+8 14 -10 -17 14 15 -14 1 14 0
+9 -14 -10 -17 14 -10 -14 1 15 0
+10 -14 15 -17 14 15 -14 1 16 0
+11 -14 -10 -17 14 15 -17 1 17 0
+12 -14 -10 -14 14 15 -14 1 18 0
+1 -14 -10 -17 14 15 -14 1 6 0
+$EndEntities
+$Nodes
+1 46 1 46
+3 1 0 46
+1
+2
+3
+4
+5
+6
+7
+8
+9
+10
+11
+12
+13
+14
+15
+16
+17
+18
+19
+20
+21
+22
+23
+24
+25
+26
+27
+28
+29
+30
+31
+32
+33
+34
+35
+36
+37
+38
+39
+40
+41
+42
+43
+44
+45
+46
+-14 0 -14
+-14 -10 -14
+0 -10 -14
+0 0 -14
+-14 15 -14
+14 15 -14
+14 0 -14
+14 -10 -14
+-14 -10 -17
+-14 15 -17
+14 15 -17
+14 -10 -17
+-14 -5 -14
+-6.99999999999998 -5.00000000000001 -14
+-7 -10 -14
+-7 0 -14
+0 -5 -14
+-14 7.5 -14
+-7 7.5 -14
+0 15 -14
+14 7.5 -14
+14 -5 -14
+7 -10 -14
+-14 -10 -15.5
+-14 15 -15.5
+-14 2.5 -17
+14 15 -15.5
+0 15 -17
+14 2.5 -17
+14 -10 -15.5
+0 -10 -17
+7 -5 -14
+7 7.5 -14
+7 0 -14
+-14 -5 -15.5
+-14 7.5 -15.5
+0 15 -15.5
+14 7.5 -15.5
+14 -5 -15.5
+-7 -10 -15.5
+7 -10 -15.5
+0 2.5 -17
+7 7.5 -15.5
+-7 7.5 -15.5
+-7 -5 -15.5
+7 -5 -15.5
+$EndNodes
+$Elements
+18 53 1 53
+0 1 15 1
+1 1
+0 2 15 1
+2 2
+0 3 15 1
+3 3
+1 1 8 1
+4 1 3 14
+1 2 8 1
+5 5 4 19
+3 1 11 13
+6 11 5 4 6 37 19 43 27 33 20
+7 11 5 10 4 37 25 28 43 44 19
+8 9 1 2 3 35 13 24 40 15 14
+9 6 7 4 11 21 34 33 27 43 38
+10 3 9 1 4 40 35 14 17 16 45
+11 10 5 1 4 25 18 36 44 16 19
+12 7 8 4 12 22 32 34 39 46 30
+13 3 4 8 12 17 32 23 41 30 46
+14 9 10 4 12 26 44 45 31 46 42
+15 11 4 10 12 43 44 28 29 42 46
+16 9 10 1 4 26 36 35 45 16 44
+17 11 7 4 12 38 34 43 29 46 39
+18 4 3 9 12 17 40 45 46 31 41
+2 1 9 2
+19 1 2 3 13 15 14
+20 1 3 4 14 17 16
+2 2 9 3
+21 3 2 9 15 24 40
+22 3 12 8 41 30 23
+23 3 9 12 40 31 41
+2 3 9 3
+24 1 9 2 35 24 13
+25 1 5 10 18 25 36
+26 1 10 9 36 26 35
+2 4 9 3
+27 11 6 7 27 21 38
+28 12 7 8 39 22 30
+29 12 11 7 29 38 39
+2 5 9 2
+30 11 5 6 37 20 27
+31 10 5 11 25 37 28
+2 6 9 2
+32 12 9 10 31 26 42
+33 11 12 10 29 42 28
+2 7 9 3
+34 1 9 2 35 24 13
+35 5 10 1 25 36 18
+36 10 9 1 26 35 36
+2 8 9 3
+37 6 7 11 21 38 27
+38 7 8 12 22 30 39
+39 11 7 12 38 39 29
+2 9 9 3
+40 9 3 2 40 15 24
+41 3 12 8 41 30 23
+42 12 3 9 41 40 31
+2 10 9 2
+43 11 5 6 37 20 27
+44 5 11 10 37 28 25
+2 11 9 2
+45 9 10 12 26 42 31
+46 11 12 10 29 42 28
+2 12 9 7
+47 6 5 4 20 19 33
+48 3 1 2 14 13 15
+49 7 6 4 21 33 34
+50 3 4 1 17 16 14
+51 4 5 1 19 18 16
+52 8 7 4 22 34 32
+53 4 3 8 17 23 32
+$EndElements

From 95d841f06dd036279d8a5158b43d79361cf0b65a Mon Sep 17 00:00:00 2001
From: Roy Stogner <Roy.Stogner@inl.gov>
Date: Thu, 11 Jul 2024 15:25:48 -0500
Subject: [PATCH 04/11] Re-bootstrap

---
 tests/Makefile.in | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tests/Makefile.in b/tests/Makefile.in
index 438f79930e5..b3dd2a8e046 100644
--- a/tests/Makefile.in
+++ b/tests/Makefile.in
@@ -2235,6 +2235,7 @@ data = matrices/geom_1_extraction_op.m \
        meshes/1_quad.bxt.gz \
        meshes/25_quad.bxt.gz \
        meshes/bad_64bit_elem_integers.e \
+       meshes/block.msh \
        meshes/BlockWithHole_Patch9.bxt.gz \
        meshes/constrain10to4.m \
        meshes/Cube_With_Sidesets.e \

From e9ab243083528410ef0d07a100f661bd2da74e35 Mon Sep 17 00:00:00 2001
From: Roy Stogner <roy@stogners.org>
Date: Fri, 12 Jul 2024 11:56:55 -0500
Subject: [PATCH 05/11] Add BoundingBox::max_size()

---
 include/geom/bounding_box.h |  9 +++++++++
 src/geom/bounding_box.C     | 15 +++++++++++++++
 2 files changed, 24 insertions(+)

diff --git a/include/geom/bounding_box.h b/include/geom/bounding_box.h
index 81af4c9cd38..38b63c70170 100644
--- a/include/geom/bounding_box.h
+++ b/include/geom/bounding_box.h
@@ -152,6 +152,15 @@ class BoundingBox : public std::pair<Point, Point>
    */
   void scale(const Real factor);
 
+  /**
+   * Returns the maximum size of a finite box extent.
+   *
+   * If the bounding box is infinite (or effectively so, e.g. using
+   * numeric_limits<Real>::max()) in some dimension, then that
+   * dimension is ignored.
+   */
+  Real max_size() const;
+
   /**
    * Formatted print, by default to \p libMesh::out.
    */
diff --git a/src/geom/bounding_box.C b/src/geom/bounding_box.C
index c1978f9c4c4..73d0ca0ef7f 100644
--- a/src/geom/bounding_box.C
+++ b/src/geom/bounding_box.C
@@ -62,6 +62,21 @@ bool BoundingBox::contains_point (const Point & p) const
 }
 
 
+
+Real BoundingBox::max_size() const
+{
+  Real size = 0;
+  for (unsigned int d = 0; d != LIBMESH_DIM; ++d)
+    {
+      Real sized = this->second(d) - this->first(d);
+      if (!libmesh_isinf(sized))
+        size = std::max(size, sized);
+    }
+  return size;
+}
+
+
+
 void BoundingBox::intersect_with (const BoundingBox & other_box)
 {
   this->first(0)  = std::max(this->first(0),  other_box.first(0));

From 8babc57d2c4b366d820bce0348de55bc8564b46a Mon Sep 17 00:00:00 2001
From: Roy Stogner <roy@stogners.org>
Date: Fri, 12 Jul 2024 11:57:23 -0500
Subject: [PATCH 06/11] Add BoundingBox::contains_point() with tolerances

---
 include/geom/bounding_box.h | 11 ++++++++++
 src/geom/bounding_box.C     | 41 +++++++++++++++++++++++++++++++++++++
 2 files changed, 52 insertions(+)

diff --git a/include/geom/bounding_box.h b/include/geom/bounding_box.h
index 38b63c70170..2feb728f85b 100644
--- a/include/geom/bounding_box.h
+++ b/include/geom/bounding_box.h
@@ -116,6 +116,17 @@ class BoundingBox : public std::pair<Point, Point>
    */
   bool contains_point (const Point &) const;
 
+  /**
+   * \returns \p true if the bounding box contains the given point,
+   * to within at least one of the given tolerance(s).  At least one
+   * tolerance should be set to greater than zero; otherwise use the
+   * other \p contains_point overload for efficiency.
+   *
+   * Relative tolerances are computed relative to the maximum finite
+   * extent of the bounding box, \p max_size()
+   */
+  bool contains_point (const Point &, Real abs_tol, Real rel_tol) const;
+
   /**
    * Sets this bounding box to be the intersection with the other
    * bounding box.
diff --git a/src/geom/bounding_box.C b/src/geom/bounding_box.C
index 73d0ca0ef7f..7e87483d3db 100644
--- a/src/geom/bounding_box.C
+++ b/src/geom/bounding_box.C
@@ -77,6 +77,47 @@ Real BoundingBox::max_size() const
 
 
 
+bool BoundingBox::contains_point
+  (const Point & p, Real abs_tol, Real rel_tol) const
+{
+  libmesh_assert_greater_equal(abs_tol, 0);
+  libmesh_assert_greater_equal(rel_tol, 0);
+
+  // Just use the other contains_point overload
+  libmesh_assert_greater(rel_tol+abs_tol, 0);
+
+  // Find absolute tolerance from relative tolerance
+  const Real tol = std::max(abs_tol, this->max_size()*rel_tol);
+
+  // Make local variables first to make things more clear in a moment
+  const Real my_min_x = this->first(0) - tol;
+  const Real my_max_x = this->second(0) + tol;
+  bool x_int = is_between(my_min_x, p(0), my_max_x);
+
+  bool intersection_true = x_int;
+
+#if LIBMESH_DIM > 1
+  const Real my_min_y = this->first(1) - tol;
+  const Real my_max_y = this->second(1) + tol;
+  bool y_int = is_between(my_min_y, p(1), my_max_y);
+
+  intersection_true = intersection_true && y_int;
+#endif
+
+
+#if LIBMESH_DIM > 2
+  const Real my_min_z = this->first(2) - tol;
+  const Real my_max_z = this->second(2) + tol;
+  bool z_int = is_between(my_min_z, p(2), my_max_z);
+
+  intersection_true = intersection_true && z_int;
+#endif
+
+  return intersection_true;
+}
+
+
+
 void BoundingBox::intersect_with (const BoundingBox & other_box)
 {
   this->first(0)  = std::max(this->first(0),  other_box.first(0));

From 3e3a033e8e256f8a33cfc54119ee47a9c7f337c0 Mon Sep 17 00:00:00 2001
From: Roy Stogner <roy@stogners.org>
Date: Fri, 12 Jul 2024 11:57:44 -0500
Subject: [PATCH 07/11] Use tolerances in Gmsh bounding box tests

If the $Entities list says the box bottoms out at 0 but we see 1e-17,
that's okay.
---
 src/mesh/gmsh_io.C | 15 +++++++++++----
 1 file changed, 11 insertions(+), 4 deletions(-)

diff --git a/src/mesh/gmsh_io.C b/src/mesh/gmsh_io.C
index 70937756ffc..d5f38ea7561 100644
--- a/src/mesh/gmsh_io.C
+++ b/src/mesh/gmsh_io.C
@@ -664,9 +664,12 @@ void GmshIO::read_mesh(std::istream & in)
                       Node * node = mesh.node_ptr(nodetrans[gmsh_node_id]);
 
                       // Make sure the file is consistent about entity
-                      // placement
+                      // placement.  Well, mostly consistent.  We have
+                      // files that claim a bounding box but still
+                      // have points epsilon outside it.
                       libmesh_error_msg_if
-                        (!expected_bounding_box.contains_point(*node),
+                        (!expected_bounding_box.contains_point
+                           (*node, 0, /* relative */ TOLERANCE),
                          "$Elements dim " << entity_dim << " element "
                          << gmsh_element_id << " (entity " << entity_tag
                          << ", " <<
@@ -711,7 +714,7 @@ void GmshIO::read_mesh(std::istream & in)
                     in >> gmsh_node_id;
 
                     // Make sure the file is consistent about entity
-                    // placement
+                    // placement.
 
                     // A default bounding box is [inf,-inf] (empty);
                     // swap that and we get [-inf,inf] (everything)
@@ -726,8 +729,12 @@ void GmshIO::read_mesh(std::istream & in)
 
                     Node * node = mesh.node_ptr(nodetrans[gmsh_node_id]);
 
+                    // We'll accept *mostly* consistent.  We have
+                    // files that claim a bounding box but still have
+                    // points epsilon outside it.
                     libmesh_error_msg_if
-                      (!expected_bounding_box.contains_point(*node),
+                      (!expected_bounding_box.contains_point
+                         (*node, 0, /* relative */ TOLERANCE),
                        "$Elements dim " << entity_dim << " element "
                        << gmsh_element_id << " (entity " << entity_tag <<
                        ") has node at " << *static_cast<Node*>(node)

From 52d29fd32bcf088f1d1569ad9a651844b64d8d3a Mon Sep 17 00:00:00 2001
From: Roy Stogner <roy@stogners.org>
Date: Tue, 16 Jul 2024 08:12:14 -0500
Subject: [PATCH 08/11] Don't let casting confuse our new assertions

---
 src/geom/bounding_box.C | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/geom/bounding_box.C b/src/geom/bounding_box.C
index 7e87483d3db..cf1c644053a 100644
--- a/src/geom/bounding_box.C
+++ b/src/geom/bounding_box.C
@@ -80,11 +80,11 @@ Real BoundingBox::max_size() const
 bool BoundingBox::contains_point
   (const Point & p, Real abs_tol, Real rel_tol) const
 {
-  libmesh_assert_greater_equal(abs_tol, 0);
-  libmesh_assert_greater_equal(rel_tol, 0);
+  libmesh_assert_greater_equal(abs_tol, Real(0));
+  libmesh_assert_greater_equal(rel_tol, Real(0));
 
   // Just use the other contains_point overload
-  libmesh_assert_greater(rel_tol+abs_tol, 0);
+  libmesh_assert_greater(rel_tol+abs_tol, Real(0));
 
   // Find absolute tolerance from relative tolerance
   const Real tol = std::max(abs_tol, this->max_size()*rel_tol);

From eaeedd306fa062d49a1ad0c6f1840151aeaba3bc Mon Sep 17 00:00:00 2001
From: Roy Stogner <roy@stogners.org>
Date: Tue, 16 Jul 2024 12:14:53 -0500
Subject: [PATCH 09/11] Add a good .msh file (swiped from MOOSE) to tests

---
 tests/Makefile.am       |   1 +
 tests/mesh/mesh_input.C |  20 ++++++-
 tests/meshes/circle.msh | 128 ++++++++++++++++++++++++++++++++++++++++
 3 files changed, 147 insertions(+), 2 deletions(-)
 create mode 100644 tests/meshes/circle.msh

diff --git a/tests/Makefile.am b/tests/Makefile.am
index 2a0bd0985e8..ad0aa10da3a 100644
--- a/tests/Makefile.am
+++ b/tests/Makefile.am
@@ -155,6 +155,7 @@ data = matrices/geom_1_extraction_op.m \
        meshes/bad_64bit_elem_integers.e \
        meshes/block.msh \
        meshes/BlockWithHole_Patch9.bxt.gz \
+       meshes/circle.msh \
        meshes/constrain10to4.m \
        meshes/Cube_With_Sidesets.e \
        meshes/exodus_elements/read_exodus_EDGE2.e \
diff --git a/tests/mesh/mesh_input.C b/tests/mesh/mesh_input.C
index ea934745c0d..f65c1ee52b9 100644
--- a/tests/mesh/mesh_input.C
+++ b/tests/mesh/mesh_input.C
@@ -194,7 +194,8 @@ public:
 #endif // LIBMESH_DIM > 1
        //
 #if LIBMESH_DIM > 1
-  CPPUNIT_TEST( testGmsh );
+  CPPUNIT_TEST( testBadGmsh );
+  CPPUNIT_TEST( testGoodGmsh );
 #endif
 
 #ifdef LIBMESH_HAVE_TETGEN
@@ -1514,7 +1515,7 @@ public:
     helperTestingDynaQuad(mesh);
   }
 
-  void testGmsh ()
+  void testBadGmsh ()
   {
     LOG_UNIT_TEST;
 
@@ -1540,6 +1541,21 @@ public:
 #endif
   }
 
+  void testGoodGmsh ()
+  {
+    LOG_UNIT_TEST;
+
+    Mesh mesh(*TestCommWorld);
+
+    GmshIO gmsh_io(mesh);
+
+    if (mesh.processor_id() == 0)
+      gmsh_io.read("meshes/circle.msh");
+    MeshCommunication().broadcast(mesh);
+
+    CPPUNIT_ASSERT_EQUAL(mesh.n_elem(), dof_id_type(14));
+  }
+
   void testTetgenIO ()
   {
 #ifdef LIBMESH_HAVE_TETGEN
diff --git a/tests/meshes/circle.msh b/tests/meshes/circle.msh
new file mode 100644
index 00000000000..be421bac10f
--- /dev/null
+++ b/tests/meshes/circle.msh
@@ -0,0 +1,128 @@
+$MeshFormat
+4.1 0 8
+$EndMeshFormat
+$PhysicalNames
+2
+1 2 "outer"
+2 1 "domain"
+$EndPhysicalNames
+$Entities
+5 4 1 0
+1 1 0 0 0 
+2 0 1 0 0 
+3 0 0 0 0 
+4 -1 0 0 0 
+5 0 -1 0 0 
+1 5.551115123125783e-17 0 0 1 1 0 1 2 2 1 -2 
+2 -1 5.551115123125783e-17 0 0 1 0 0 2 2 -4 
+3 -1 -1 0 -5.551115123125783e-17 0 0 0 2 4 -5 
+4 0 -1 0 1 -5.551115123125783e-17 0 0 2 5 -1 
+1 -1 -1 0 1 1 0 1 1 4 1 2 3 4 
+$EndEntities
+$Nodes
+9 37 1 37
+0 1 0 1
+1
+1 0 0
+0 2 0 1
+2
+0 1 0
+0 4 0 1
+3
+-1 0 0
+0 5 0 1
+4
+0 -1 0
+1 1 0 3
+5
+6
+7
+0.7071067795767627 0.7071067827963323 0
+0.9238795321515167 0.3826834332336513 0
+0.3826834311765871 0.9238795330035807 0
+1 2 0 3
+8
+9
+10
+-0.7071067827963323 0.7071067795767627 0
+-0.3826834332336513 0.9238795321515167 0
+-0.9238795330035807 0.3826834311765871 0
+1 3 0 3
+11
+12
+13
+-0.7071067795767627 -0.7071067827963323 0
+-0.9238795321515167 -0.3826834332336513 0
+-0.3826834311765871 -0.9238795330035807 0
+1 4 0 3
+14
+15
+16
+0.7071067827963323 -0.7071067795767627 0
+0.3826834332336513 -0.9238795321515167 0
+0.9238795330035807 -0.3826834311765871 0
+2 1 0 21
+17
+18
+19
+20
+21
+22
+23
+24
+25
+26
+27
+28
+29
+30
+31
+32
+33
+34
+35
+36
+37
+0.268765817223823 0.1113264469548191 0
+-0.3632776934576478 -0.1504745480222367 0
+-0.1902402587220213 0.4476830150213186 0
+0.1820395197735081 -0.4510798723262105 0
+0.6343829086119115 0.05566322347740954 0
+0.2254026684986655 -0.1698767126856957 0
+0.591019759886754 -0.2255399361631052 0
+0.4879362984002928 0.4092166148755757 0
+0.2584332604273707 0.5773948989088254 0
+0.03926277925090085 0.2795047309880688 0
+0.4445731512849203 -0.5790933259514865 0
+-0.09512012936101064 0.7238415075106593 0
+-0.5951201293610107 0.2238415075106593 0
+-0.4486735207591768 0.5773948972990407 0
+0.09101975988675405 -0.7255399361631052 0
+-0.2625336299016273 -0.5790933275612714 0
+-0.5351922365172053 -0.4287906654092845 0
+-0.09061908684206985 -0.3007772101742236 0
+-0.6816388467288239 -0.07523727401111835 0
+-0.2767589760898345 0.148604233499541 0
+-0.04725593811691242 -0.01957405053370881 0
+$EndNodes
+$Elements
+2 16 1 16
+1 1 8 2
+1 1 5 6 
+2 5 2 7 
+2 1 9 14
+3 1 17 20 21 22 23 
+4 17 5 19 24 25 26 
+5 14 1 20 16 23 27 
+6 5 2 19 7 28 25 
+7 8 3 19 10 29 30 
+8 11 4 20 13 31 32 
+9 18 11 20 33 32 34 
+10 3 18 19 35 36 29 
+11 1 5 17 6 24 21 
+12 3 11 18 12 33 35 
+13 2 8 19 9 30 28 
+14 4 14 20 15 27 31 
+15 17 18 20 37 34 22 
+16 18 17 19 37 26 36 
+$EndElements

From 8a0cc8e54b6054eed9b4bcc43b3c3df7d6229369 Mon Sep 17 00:00:00 2001
From: roystgnr <roy@stogners.org>
Date: Fri, 19 Jul 2024 15:48:11 -0500
Subject: [PATCH 10/11] Apply suggestions from code review

Co-authored-by: Alex Lindsay <alexander.lindsay@inl.gov>
---
 include/geom/bounding_box.h | 2 +-
 src/geom/bounding_box.C     | 6 +++---
 src/mesh/gmsh_io.C          | 4 ++--
 3 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/include/geom/bounding_box.h b/include/geom/bounding_box.h
index 2feb728f85b..138c3bd83ad 100644
--- a/include/geom/bounding_box.h
+++ b/include/geom/bounding_box.h
@@ -125,7 +125,7 @@ class BoundingBox : public std::pair<Point, Point>
    * Relative tolerances are computed relative to the maximum finite
    * extent of the bounding box, \p max_size()
    */
-  bool contains_point (const Point &, Real abs_tol, Real rel_tol) const;
+  bool contains_point (const Point & p, Real abs_tol, Real rel_tol) const;
 
   /**
    * Sets this bounding box to be the intersection with the other
diff --git a/src/geom/bounding_box.C b/src/geom/bounding_box.C
index cf1c644053a..12acb150467 100644
--- a/src/geom/bounding_box.C
+++ b/src/geom/bounding_box.C
@@ -92,14 +92,14 @@ bool BoundingBox::contains_point
   // Make local variables first to make things more clear in a moment
   const Real my_min_x = this->first(0) - tol;
   const Real my_max_x = this->second(0) + tol;
-  bool x_int = is_between(my_min_x, p(0), my_max_x);
+  const bool x_int = is_between(my_min_x, p(0), my_max_x);
 
   bool intersection_true = x_int;
 
 #if LIBMESH_DIM > 1
   const Real my_min_y = this->first(1) - tol;
   const Real my_max_y = this->second(1) + tol;
-  bool y_int = is_between(my_min_y, p(1), my_max_y);
+  const bool y_int = is_between(my_min_y, p(1), my_max_y);
 
   intersection_true = intersection_true && y_int;
 #endif
@@ -108,7 +108,7 @@ bool BoundingBox::contains_point
 #if LIBMESH_DIM > 2
   const Real my_min_z = this->first(2) - tol;
   const Real my_max_z = this->second(2) + tol;
-  bool z_int = is_between(my_min_z, p(2), my_max_z);
+  const bool z_int = is_between(my_min_z, p(2), my_max_z);
 
   intersection_true = intersection_true && z_int;
 #endif
diff --git a/src/mesh/gmsh_io.C b/src/mesh/gmsh_io.C
index d5f38ea7561..e294f9b1d57 100644
--- a/src/mesh/gmsh_io.C
+++ b/src/mesh/gmsh_io.C
@@ -669,7 +669,7 @@ void GmshIO::read_mesh(std::istream & in)
                       // have points epsilon outside it.
                       libmesh_error_msg_if
                         (!expected_bounding_box.contains_point
-                           (*node, 0, /* relative */ TOLERANCE),
+                           (*node, /* abs */ 0, /* relative */ TOLERANCE),
                          "$Elements dim " << entity_dim << " element "
                          << gmsh_element_id << " (entity " << entity_tag
                          << ", " <<
@@ -734,7 +734,7 @@ void GmshIO::read_mesh(std::istream & in)
                     // points epsilon outside it.
                     libmesh_error_msg_if
                       (!expected_bounding_box.contains_point
-                         (*node, 0, /* relative */ TOLERANCE),
+                         (*node, /* abs */ 0, /* relative */ TOLERANCE),
                        "$Elements dim " << entity_dim << " element "
                        << gmsh_element_id << " (entity " << entity_tag <<
                        ") has node at " << *static_cast<Node*>(node)

From cb9cbf5b80784f1cdb09c4e57807c686ea59c507 Mon Sep 17 00:00:00 2001
From: Roy Stogner <roy@stogners.org>
Date: Fri, 19 Jul 2024 16:18:48 -0500
Subject: [PATCH 11/11] Handle "basically" infinite bounding box extents

---
 src/geom/bounding_box.C | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/geom/bounding_box.C b/src/geom/bounding_box.C
index 12acb150467..f23aa22c035 100644
--- a/src/geom/bounding_box.C
+++ b/src/geom/bounding_box.C
@@ -69,7 +69,9 @@ Real BoundingBox::max_size() const
   for (unsigned int d = 0; d != LIBMESH_DIM; ++d)
     {
       Real sized = this->second(d) - this->first(d);
-      if (!libmesh_isinf(sized))
+      if (!libmesh_isinf(sized) &&
+          this->second(d) != std::numeric_limits<Real>::max() &&
+          this->first(d) != -std::numeric_limits<Real>::max())
         size = std::max(size, sized);
     }
   return size;