Interior boundary cracks for meshes

CHANGELOG.md

@@ -25,6 +25,11 @@ The format of this changelog is based on
   - Added `"MakeSimplex"` and `"MakeHexahedral"` mesh options to convert an input mesh to
     all tetrahedra or all hexahedra. Also adds `"SerialUniformLevels"` option to
     `config["Model"]["Refinement"]` for testing or debugging.
+  - Added `config["Model"]["CrackInternalBoundaryElements"]` which will separate or "crack" the mesh
+    along all internal boundaries. This improves the performance of error estimation and AMR
+    as the recovered smooth fields do not enforce additional erroneous continuity at
+    internal boundaries. This will change the default behaviour in the case of internal
+    impedance boundary conditions, and can be disabled by setting this option to false.
 
 ## [0.13.0] - 2024-05-20
 

docs/src/config/boundaries.md

@@ -58,7 +58,6 @@
     ],
     "Postprocessing":
     {
-        "Side": <string>,
         "SurfaceFlux":
         [
             ...
@@ -123,19 +122,6 @@ each terminal boundary.
 
 `"Postprocessing"` :  Top-level object for configuring boundary postprocessing.
 
-`"Side" ["SmallerRefractiveIndex"]` :  Defines the postprocessing side for internal
-boundary surfaces where the fields are in general double-valued. This is only relevant for
-output for [boundary visualization with ParaView](../guide/postprocessing.md#Visualization).
-The available options are:
-
-  - `"SmallerRefractiveIndex"` :  Take the value from the side where the material index of
-    refraction is smaller (speed of light is larger). Typically this selects the vacuum
-    side. For anisotropic materials, the index of refraction associated with the principal
-    direction with the smallest value is used.
-  - `"LargerRefractiveIndex"` :  Take the value from the side where the material index of
-    refraction is larger (speed of light is smaller). Typically this selects the non-vacuum
-    side.
-
 `"SurfaceFlux"` :  Array of objects for postprocessing surface flux.
 
 `"Dielectric"` :  Array of objects for postprocessing surface interface dielectric loss.
@@ -572,8 +558,7 @@ axis-aligned bounding box for all elements making up the postprocessing boundary
             "Type": <string>,
             "Thickness": <float>,
             "Permittivity": <float>,
-            "LossTan": <float>,
-            "Side": <string>
+            "LossTan": <float>
         },
         ...
     ]
@@ -585,8 +570,7 @@ with
 `"Index" [None]` :  Index of this dielectric interface, used in postprocessing output files.
 
 `"Attributes" [None]` :  Integer array of mesh boundary attributes for this dielectric
-interface. If the interface consists of multiple elements with different `"Side"` values,
-use the `"Elements"` array described below.
+interface.
 
 `"Type" [None]` :  Specifies the type of dielectric interface for this postprocessing
 boundary. See also [this page](../reference.md#Bulk-and-interface-dielectric-loss).
@@ -608,15 +592,3 @@ units.
 be the interface layer permittivity for the specific `"Type"` of interface specified.
 
 `"LossTan" [0.0]` :  Loss tangent for this lossy dielectric interface.
-
-`"Side" ["SmallerRefractiveIndex"]` :  Defines the postprocessing side when this dielectric
-interface is an internal boundary surface (and thus the electric field on the boundary is in
-general double-valued). The available options are:
-
-  - `"SmallerRefractiveIndex"` :  Take the value from the side where the material index of
-    refraction is smaller (speed of light is larger). Typically this selects the vacuum
-    side. For anisotropic materials, the index of refraction associated with the principal
-    direction with the smallest value is used.
-  - `"LargerRefractiveIndex"` :  Take the value from the side where the material index of
-    refraction is larger (speed of light is smaller). Typically this selects the non-vacuum
-    side.

docs/src/config/model.md

@@ -118,6 +118,9 @@ mesh length units.
   - `"MakeHexahedral" [false]`
   - `"ReorderElements" [false]`
   - `"CleanUnusedElements" [true]`
+  - `"CrackInternalBoundaryElements" [true]`
+  - `"RefineCrackElements" [true]`
+  - `"CrackDisplacementFactor" [1.0e-3]`
   - `"AddInterfaceBoundaryElements" [true]`
   - `"ReorientTetMesh" [false]`
   - `"Partitioning" [""]`

docs/src/guide/boundaries.md

@@ -104,7 +104,7 @@ reference.
 
     Unlike lumped ports, wave port boundaries cannot be defined internal to the
     computational domain and instead must exist only on the outer boundary of the domain
-    (they are to be  "one-sided" in the sense that mesh elements only exist on one side of
+    (they are to be "one-sided" in the sense that mesh elements only exist on one side of
     the boundary).
 
     Wave ports are not currently compatible with nonconformal mesh refinement.

examples/cpw/cpw_coax_adaptive.json

@@ -134,17 +134,15 @@
           "Type": "MS",
           "Thickness": 2.0e-3,  // μm
           "Permittivity": 10.0,
-          "LossTan": 1.0,
-          "Side": "LargerRefractiveIndex"
+          "LossTan": 1.0
         },
         {
           "Index": 3,
           "Attributes": [11],
           "Type": "MA",
           "Thickness": 2.0e-3,  // μm
           "Permittivity": 10.0,
-          "LossTan": 1.0,
-          "Side": "SmallerRefractiveIndex"
+          "LossTan": 1.0
         }
       ]
     }

examples/cpw/cpw_coax_uniform.json

@@ -134,17 +134,15 @@
           "Type": "MS",
           "Thickness": 2.0e-3,  // μm
           "Permittivity": 10.0,
-          "LossTan": 1.0,
-          "Side": "LargerRefractiveIndex"
+          "LossTan": 1.0
         },
         {
           "Index": 3,
           "Attributes": [11],
           "Type": "MA",
           "Thickness": 2.0e-3,  // μm
           "Permittivity": 10.0,
-          "LossTan": 1.0,
-          "Side": "SmallerRefractiveIndex"
+          "LossTan": 1.0
         }
       ]
     }

examples/cpw/cpw_lumped_adaptive.json

@@ -158,17 +158,15 @@
           "Type": "MS",
           "Thickness": 2.0e-3,  // μm
           "Permittivity": 10.0,
-          "LossTan": 1.0,
-          "Side": "LargerRefractiveIndex"
+          "LossTan": 1.0
         },
         {
           "Index": 3,
           "Attributes": [13],
           "Type": "MA",
           "Thickness": 2.0e-3,  // μm
           "Permittivity": 10.0,
-          "LossTan": 1.0,
-          "Side": "SmallerRefractiveIndex"
+          "LossTan": 1.0
         }
       ]
     }

examples/cpw/cpw_lumped_uniform.json

@@ -158,17 +158,15 @@
           "Type": "MS",
           "Thickness": 2.0e-3,  // μm
           "Permittivity": 10.0,
-          "LossTan": 1.0,
-          "Side": "LargerRefractiveIndex"
+          "LossTan": 1.0
         },
         {
           "Index": 3,
           "Attributes": [13],
           "Type": "MA",
           "Thickness": 2.0e-3,  // μm
           "Permittivity": 10.0,
-          "LossTan": 1.0,
-          "Side": "SmallerRefractiveIndex"
+          "LossTan": 1.0
         }
       ]
     }

examples/cpw/cpw_wave_adaptive.json

@@ -134,17 +134,15 @@
           "Type": "MS",
           "Thickness": 2.0e-3,  // μm
           "Permittivity": 10.0,
-          "LossTan": 1.0,
-          "Side": "LargerRefractiveIndex"
+          "LossTan": 1.0
         },
         {
           "Index": 3,
           "Attributes": [11],
           "Type": "MA",
           "Thickness": 2.0e-3,  // μm
           "Permittivity": 10.0,
-          "LossTan": 1.0,
-          "Side": "SmallerRefractiveIndex"
+          "LossTan": 1.0
         }
       ]
     }

examples/cpw/cpw_wave_uniform.json

@@ -134,17 +134,15 @@
           "Type": "MS",
           "Thickness": 2.0e-3,  // μm
           "Permittivity": 10.0,
-          "LossTan": 1.0,
-          "Side": "LargerRefractiveIndex"
+          "LossTan": 1.0
         },
         {
           "Index": 3,
           "Attributes": [11],
           "Type": "MA",
           "Thickness": 2.0e-3,  // μm
           "Permittivity": 10.0,
-          "LossTan": 1.0,
-          "Side": "SmallerRefractiveIndex"
+          "LossTan": 1.0
         }
       ]
     }

palace/drivers/basesolver.cpp

@@ -147,15 +147,13 @@ void BaseSolver::SolveEstimateMarkRefine(std::vector<std::unique_ptr<Mesh>> &mes
       Mpi::Warning("AMR is not currently supported for transient simulations!\n");
       return false;
     }
-    return refinement.max_it > 0;
+    return (refinement.max_it > 0);
   }();
   if (use_amr && mesh.size() > 1)
   {
     Mpi::Print("\nFlattening mesh sequence:\n AMR will start from the final mesh in "
                "the sequence of a priori refinements\n");
     mesh.erase(mesh.begin(), mesh.end() - 1);
-    constexpr bool refine = true, fix_orientation = true;
-    mesh.back()->Get().Finalize(refine, fix_orientation);
   }
   MPI_Comm comm = mesh.back()->GetComm();