Merge pull request #766 from baagaard-usgs/add-orphan-vertices-check

Add check for orphan vertices in check of mesh topology

Author: baagaard-usgs

libsrc/pylith/meshio/MeshIOPetsc.cc

@@ -144,7 +144,7 @@ pylith::meshio::MeshIOPetsc::_read(void) {
             err = PetscObjectSetOptionsPrefix((PetscObject) dmMesh, _prefix.c_str());PYLITH_CHECK_ERROR(err);
         } // if
         err = DMPlexDistributeSetDefault(dmMesh, PETSC_FALSE);PYLITH_CHECK_ERROR(err);
-        err = DMSetFromOptions(dmMesh);PYLITH_CHECK_ERROR(err);
+        err = DMSetFromOptions(dmMesh);PYLITH_CHECK_ERROR_MSG(err, "Error creating mesh with MeshIOPetsc.");
 
         _MeshIOPetsc::fixMaterialLabel(&dmMesh);
         _MeshIOPetsc::fixBoundaryLabels(&dmMesh);

libsrc/pylith/topology/MeshOps.cc

@@ -376,6 +376,7 @@ pylith::topology::MeshOps::checkTopology(const Mesh& mesh) {
 
     _MeshOps::Events::logger.eventBegin(_MeshOps::Events::checkTopologySkeleton);
     err = DMPlexCheckSkeleton(dmMesh, cellHeight);PYLITH_CHECK_ERROR_MSG(err, "Error in topology of mesh cells.");
+    err = DMPlexCheckOrphanVertices(dmMesh);PYLITH_CHECK_ERROR_MSG(err, "Mesh contains vertices not connected to cells.");
     _MeshOps::Events::logger.eventEnd(_MeshOps::Events::checkTopologySkeleton);
 
     /* Other check functions that we are not using:

tests/libtests/meshio/TestMeshIOAscii.cc

@@ -94,7 +94,23 @@ pylith::meshio::TestMeshIOAscii::testRead(void) {
     _checkVals();
 
     PYLITH_METHOD_END;
-} // testRead3DIndexOne
+} // testRead
+
+
+// ----------------------------------------------------------------------
+// Test read() with error.
+void
+pylith::meshio::TestMeshIOAscii::testReadError(void) {
+    PYLITH_METHOD_BEGIN;
+    assert(_io);
+
+    // Read mesh
+    delete _mesh;_mesh = new pylith::topology::Mesh;
+    _io->setFilename(_data->filename.c_str());
+    CHECK_THROWS_AS(_io->read(_mesh), std::runtime_error);
+
+    PYLITH_METHOD_END;
+} // testRead
 
 
 // End of file

tests/libtests/meshio/TestMeshIOAscii.hh

@@ -37,6 +37,9 @@ public:
     /// Test read().
     void testRead(void);
 
+    /// Test read() with known errors.
+    void testReadError(void);
+
     // PROTECTED METHODS ////////////////////////////////////////////////
 protected:
 

tests/libtests/meshio/TestMeshIOAscii_Cases.cc

@@ -35,6 +35,10 @@ class pylith::meshio::TestMeshIOAscii_Cases {
 
     static TestMeshIO_Data* Hex3D_Index1(void);
 
+    static TestMeshIO_Data* Tri_OrphanVertex(void);
+
+    static TestMeshIO_Data* Hex_OrphanVertex(void);
+
 }; // TestMeshIOAscii_Cases
 
 // ------------------------------------------------------------------------------------------------
@@ -55,10 +59,17 @@ TEST_CASE("TestMeshIOAscii::Hex3D::testWriteRead", "[TestMeshIOAscii][testWriteR
 TEST_CASE("TestMeshIOAscii::Quad2D_Comments::testRead", "[TestMeshIOAscii][testRead]") {
     pylith::meshio::TestMeshIOAscii(pylith::meshio::TestMeshIOAscii_Cases::Quad2D_Comments()).testRead();
 }
-TEST_CASE("TestMeshIOAscii::Hex3D_Index1::testReas", "[TestMeshIOAscii][testRead]") {
+TEST_CASE("TestMeshIOAscii::Hex3D_Index1::testRead", "[TestMeshIOAscii][testRead]") {
     pylith::meshio::TestMeshIOAscii(pylith::meshio::TestMeshIOAscii_Cases::Hex3D_Index1()).testRead();
 }
 
+TEST_CASE("TestMeshIOAscii::Tri_OrphanVertex::testReadError", "[TestMeshIOAscii][testReadError]") {
+    pylith::meshio::TestMeshIOAscii(pylith::meshio::TestMeshIOAscii_Cases::Tri_OrphanVertex()).testReadError();
+}
+TEST_CASE("TestMeshIOAscii::Hex_OrphanVertex::testReadError", "[TestMeshIOAscii][testReadError]") {
+    pylith::meshio::TestMeshIOAscii(pylith::meshio::TestMeshIOAscii_Cases::Hex_OrphanVertex()).testReadError();
+}
+
 // ------------------------------------------------------------------------------------------------
 pylith::meshio::TestMeshIO_Data*
 pylith::meshio::TestMeshIOAscii_Cases::Quad2D(void) {
@@ -368,4 +379,26 @@ pylith::meshio::TestMeshIOAscii_Cases::Hex3D_Index1(void) {
 } // Hex3D_Index1
 
 
+// ------------------------------------------------------------------------------------------------
+pylith::meshio::TestMeshIO_Data*
+pylith::meshio::TestMeshIOAscii_Cases::Tri_OrphanVertex(void) {
+    TestMeshIO_Data* data = new TestMeshIO_Data();assert(data);
+
+    data->filename = "data/tri_orphan_vertex.mesh";
+
+    return data;
+} // Hex3D_Index1
+
+
+// ------------------------------------------------------------------------------------------------
+pylith::meshio::TestMeshIO_Data*
+pylith::meshio::TestMeshIOAscii_Cases::Hex_OrphanVertex(void) {
+    TestMeshIO_Data* data = new TestMeshIO_Data();assert(data);
+
+    data->filename = "data/hex_orphan_vertex.mesh";
+
+    return data;
+} // Hex3D_Index1
+
+
 // End of file

tests/libtests/meshio/data/Makefile.am

@@ -61,6 +61,7 @@ dist_noinst_DATA = \
 	noembed_tet.msh \
 	nosplit_tri.msh \
 	tri3.mesh \
+	tri_orphan_vertex.mesh \
 	tri3_vertex_t10.vtk \
 	tri3_cell_t10.vtk \
 	quad4.mesh \
@@ -70,6 +71,7 @@ dist_noinst_DATA = \
 	tet4_vertex_t10.vtk \
 	tet4_cell_t10.vtk \
 	hex8.mesh \
+	hex_orphan_vertex.mesh \
 	hex8_vertex_t10.vtk \
 	hex8_cell_t10.vtk \
 	tri3_mat_vertex_t10.vtk \

tests/libtests/meshio/data/hex_orphan_vertex.mesh

@@ -0,0 +1,57 @@
+// Mesh with an orphan vertex (verify topology check fails).
+mesh = {
+  dimension = 3
+  use-index-zero = true
+  vertices = {
+    dimension = 3
+    count = 12
+    coordinates = {
+             0     -1.0 -1.0 -1.0
+             1     -1.0  1.0 -1.0
+             2      0.0 -1.0 -1.0
+             3      0.0  1.0 -1.0
+             4      1.0 -1.0 -1.0
+             5      1.0  1.0 -1.0
+             6     -1.0 -1.0  1.0
+             7     -1.0  1.0  1.0
+             8      0.0 -1.0  1.0
+             9      0.0  1.0  1.0
+            10      1.0 -1.0  1.0
+            11      1.0  1.0  1.0
+    }
+  }
+  cells = {
+    count = 1
+    num-corners = 8
+    simplices = {
+             0       0  2  3  1  6  8  9  7
+    }
+    material-ids = {
+             0   1
+    }
+  }
+  group = {
+    name = fault
+    type = vertices
+    count = 4
+    indices = {
+      2  3  8  9
+    }
+  }
+  group = {
+    name = front
+    type = vertices
+    count = 4
+    indices = {
+      0  1  6  7
+    }
+  }
+  group = {
+    name = top
+    type = vertices
+    count = 6
+    indices = {
+      6  7  8  9  10 11
+    }
+  }
+}

tests/libtests/meshio/data/tri_orphan_vertex.mesh

@@ -0,0 +1,26 @@
+// Mesh with an orphan vertex (verify topology check fails).
+mesh = {
+  dimension = 2
+  use-index-zero = true
+  vertices = {
+    dimension = 2
+    count = 4
+    coordinates = {
+             0     -1.0  0.0
+             1      0.0 -1.0
+             2      0.0  1.0
+             3      1.0  0.0
+    }
+  }
+  cells = {
+    count = 1
+    num-corners = 3
+    simplices = {
+             0       0  1  2
+    }
+    material-ids = {
+             0   1
+             1   0
+    }
+  }
+}