Various fixes

- Update schema to account for CoordinateSystem
- Fix bugs with config parsing and update some more config files
- Refactor point cloud calculations to reduce duplication and hide local functions

docs/src/config/boundaries.md

@@ -247,7 +247,8 @@ accounts for nonzero metal thickness.
     {
         "Index": <int>,
         "Attributes": [<int array>],
-        "Direction": <string>,
+        "Direction": <string> or <float array>,
+        "CoordinateSystem": <string>,
         "Excitation": <bool>,
         "R": <float>,
         "L": <float>,
@@ -258,8 +259,9 @@ accounts for nonzero metal thickness.
         "Elements":
         [
             {
-                "Attributes": [<int array>],
-                "Direction": <string>
+                "Attributes": <string> or <float array>,
+                "Direction": <string>,
+                "CoordinateSystem": <string>
             },
             ...
         ]
@@ -276,12 +278,20 @@ with
 boundary. If this port is to be a multielement lumped port with more than a single lumped
 element, use the `"Elements"` array described below.
 
-`"Direction" [None]` :  Direction to define the polarization direction of the port field
-mode on this lumped port boundary. Lumped ports must be axis-aligned unless the port is a
-coaxial port. The available options are: `"+X"`, `"-X"`, `"+Y"`, `"-Y"`, `"+Z"`, `"-Z"`,
-`"+R"`, `"-R"` (`"R"` is for a coaxial lumped port). If this port is to be a multielement
-lumped port with more than a single lumped element, use the `"Elements"` array described
-below.
+`"Direction" [None]` :  Direction to define the polarization direction of the
+port field mode on this lumped port boundary. Axis aligned lumped ports can be
+specified using keywords: `"+X"`, `"-X"`, `"+Y"`, `"-Y"`, `"+Z"`, `"-Z"`, while
+coaxial lumped ports can be specified using `"+R"`, `"-R"`. The direction can
+alternatively be specified as a normalized array of three values, for example
+`[0, 1, 0]`. If a vector direction is specified, the `"CoordinateSystem"` value
+specifies the coordinate system it is expressed in. If this port is to be a
+multielement lumped port with more than a single lumped element, use the
+`"Elements"` array described below.
+
+`"CoordinateSystem" ["Cartesian"]` : Coordinate system used to express the
+`"Direction"` vector, the options are `"Cartesian"` and `"Cylindrical"`. If a
+keyword argument is used for `"Direction"` this value is ignored, and the
+appropriate coordinate system is used instead.
 
 `"Excitation" [false]` :  Turns on or off port excitation for this lumped port boundary for
 driven or transient simulation types.
@@ -320,6 +330,11 @@ should not be combined with the `"Direction"` field described above. Each elemen
 multielement lumped port can be described by its own unique direction, which is specified
 here. The elements of a multielement port add in parallel.
 
+`"Elements"[]["CoordinateSystem"] [None]` :  This option is for multielement
+lumped ports and should not be combined with the `"CoordinateSystem"` field
+described above. Each element of a multielement lumped port can be described by
+its own unique direction, and corresponding coordinate system.
+
 ## `boundaries["WavePort"]`
 
 ```json
@@ -375,12 +390,14 @@ those specified under [`config["Boundaries"]["PEC"]["Attributes"]`]
     {
         "Index": <int>,
         "Attributes": [<int array>],
-        "Direction": <string>
+        "Direction": <string> or <float array>,
+        "CoordinateSystem": <string>,
         "Elements":
         [
             {
                 "Attributes": [<int array>],
-                "Direction": <string>
+                "Direction": <string> or <float array>,
+                "CoordinateSystem": <string>,
             },
             ...
         ]
@@ -404,18 +421,29 @@ boundary. The available options are the same as under
 this source is to be a multielement source which distributes the source across more than a
 single lumped element, use the `"Elements"` array described below.
 
+`"CoordinateSystem" ["Cartesian"]` :  Defines the coordinate system for the source current
+direction for this surface current boundary. The available options are the same as under
+[`config["Boundaries"]["LumpedPort"]["CoordinateSystem"]`](#boundaries%5B%22LumpedPort%22%5D). If
+this source is to be a multielement source which distributes the source across more than a
+single lumped element, use the `"Elements"` array described below.
+
 `"Elements"[]["Attributes"] [None]` :  This option is for multielement surface current
 boundaries should not be combined with the `"Attributes"` field described above. Each
 element of a multielement current source can be described by its own unique integer array of
 mesh boundary attributes, which are specified here. The elements of a multielement source
 add in parallel to give the same total current as a single-element source.
 
 `"Elements"[]["Direction"] [None]` :  This option is for multielement surface current
-boundaires and should not be combined with the `"Direction"` field described above. Each
+boundaries and should not be combined with the `"Direction"` field described above. Each
 element of a multielement current source can be described by its own unique direction,
 which is specified here. The elements of a multielement source add in parallel to give the
 same total current as a single-element source.
 
+`"Elements"[]["CoordinateSystem"] ["Cartesian"]` :  This option is for multielement surface current
+boundaries and should not be combined with the `"CoordinateSystem"` field described above. Each
+element of a multielement current source can be described by its own unique
+direction, and corresponding coordinate system.
+
 ## `boundaries["Ground"]`
 
 ```json
@@ -516,7 +544,10 @@ postprocessing boundary.
 
 `"Direction" [None]` :  Defines the global direction with which to orient the surface
 normals with computing the magnetic flux for this inductance postprocessing boundary. The
-available options are: `"+X"`, `"-X"`, `"+Y"`, `"-Y"`, `"+Z"`, `"-Z"`.
+available options are: `"+X"`, `"-X"`, `"+Y"`, `"-Y"`, `"+Z"`, `"-Z"`. The
+direction can alternatively be specified as a normalized array of three values,
+for example `[0, 1, 0]`. The true surface normal is used in the calculation,
+`"Direction"` is only used to ensure the correct choice of orientation of the normal.
 
 ## `boundaries["Postprocessing"]["Dielectric"]`
 
@@ -528,7 +559,7 @@ available options are: `"+X"`, `"-X"`, `"+Y"`, `"-Y"`, `"+Z"`, `"-Z"`.
         {
             "Index": <int>,
             "Attributes": [<int array>],
-            "Side": <string>,
+            "Side": <string> or <float array>,
             "Thickness": <float>,
             "Permittivity": <float>,
             "PermittivityMA": <float>,
@@ -539,7 +570,7 @@ available options are: `"+X"`, `"-X"`, `"+Y"`, `"-Y"`, `"+Z"`, `"-Z"`.
             [
                 {
                     "Attributes": [<int array>],
-                    "Side": <string>
+                    "Side": <string> or <float array>
                 },
                 ...
             ]

examples/coaxial/coaxial_matched.json

@@ -41,7 +41,8 @@
         "Index": 2,
         "Attributes": [4],
         "R": 50.0,  // Ω, perfect matching
-        "Direction": "+R"  // Coaxial lumped port
+        "Direction": [1,0,0],  // Coaxial lumped port
+        "CoordinateSystem": "Cylindrical"
       }
     ]
   },

examples/cpw/cpw_lumped_uniform.json

@@ -79,7 +79,8 @@
         [
           {
             "Attributes": [4],
-            "Direction": [0,1,0]
+            "Direction": [0,1,0],
+            "CoordinateSystem": "Cartesian"
           },
           {
             "Attributes": [8],
@@ -98,7 +99,8 @@
           },
           {
             "Attributes": [9],
-            "Direction": [0,-1,0]
+            "Direction": [0,-1,0],
+            "CoordinateSystem": "Cartesian"
           }
         ]
       },

examples/rings/rings.json

@@ -44,12 +44,14 @@
       {
         "Index": 1,
         "Attributes": [4],  // Inner ring
-        "Direction": [-0.5, 0.8660254037844386, 0.0] // "+Y" rotated pi/6 around (0,0,1)
+        "Direction": [-0.5, 0.8660254037844386, 0.0], // "+Y" rotated pi/6 around (0,0,1)
+        "CoordinateSystem": "Cartesian"
       },
       {
         "Index": 2,
         "Attributes": [5],  // Outer ring
-        "Direction": [-0.5, 0.8660254037844386, 0.0] // "+Y" rotated pi/6 around (0,0,1)
+        "Direction": [-0.5, 0.8660254037844386, 0.0], // "+Y" rotated pi/6 around (0,0,1)
+        "CoordinateSystem": "Cartesian"
       }
     ],
     "Postprocessing":  // Inductance from flux instead of energy

palace/fem/lumpedelement.hpp

@@ -141,9 +141,7 @@ class CoaxialElementData : public LumpedElementData
       sign(direction[0] > 0),
       bounding_ball(mesh::GetBoundingBall(*fespace.GetParMesh(), marker, true))
   {
-    MFEM_VERIFY(std::abs(bounding_ball.planar_normal[0]) == 0 &&
-                    std::abs(bounding_ball.planar_normal[1]) == 0 &&
-                    std::abs(bounding_ball.planar_normal[2]) == 0,
+    MFEM_VERIFY(bounding_ball.planar_normal.norm() > 0,
                 "Boundary elements must be coplanar to define a coaxial port.");
 
     double A = GetArea(fespace);

palace/utils/configfile.cpp

@@ -699,13 +699,13 @@ void ImpedanceBoundaryData::SetUp(json &boundaries)
   }
 }
 
-namespace
-{
-
 NLOHMANN_JSON_SERIALIZE_ENUM(CoordinateSystem,
                              {{CoordinateSystem::CARTESIAN, "Cartesian"},
                               {CoordinateSystem::CYLINDRICAL, "Cylindrical"}})
 
+namespace
+{
+
 // Helper function for extracting a DataNode from a json, if the is_port
 // value is set to true, will extract the normal vector from either the provided
 // keyword argument or from a specified 3 vector. In extracting the normal
@@ -729,7 +729,7 @@ auto ParseDataNode(json &j, const std::string &key_word, bool is_port = true)
     }
     catch (json::exception)
     {
-      MFEM_VERIFY(!is_port, "A port requires the direction be specified");
+      MFEM_VERIFY(!is_port, "A port requires " << key_word << " be specified");
       return node;
     }
   }
@@ -880,6 +880,7 @@ void LumpedPortBoundaryData::SetUp(json &boundaries)
         // Cleanup
         elem.erase("Attributes");
         elem.erase("Direction");
+        elem.erase("CoordinateSystem");
         MFEM_VERIFY(elem.empty(),
                     "Found an unsupported configuration file keyword under \"LumpedPort\" "
                     "or \"Terminal\" boundary element!\n"
@@ -913,6 +914,7 @@ void LumpedPortBoundaryData::SetUp(json &boundaries)
     p.erase("Excitation");
     p.erase("Attributes");
     p.erase("Direction");
+    p.erase("CoordinateSystem");
     p.erase("Elements");
     MFEM_VERIFY(p.empty(), "Found an unsupported configuration file keyword under "
                            "\"LumpedPort\" or \"Terminal\"!\n"
@@ -1009,6 +1011,7 @@ void SurfaceCurrentBoundaryData::SetUp(json &boundaries)
         // Cleanup
         elem.erase("Attributes");
         elem.erase("Direction");
+        elem.erase("CoordinateSystem");
         MFEM_VERIFY(elem.empty(), "Found an unsupported configuration file keyword "
                                   "under \"SurfaceCurrent\" boundary element!\n"
                                       << elem.dump(2));
@@ -1028,6 +1031,7 @@ void SurfaceCurrentBoundaryData::SetUp(json &boundaries)
     s.erase("Attributes");
     s.erase("Direction");
     s.erase("Elements");
+    s.erase("CoordinateSystem");
     MFEM_VERIFY(
         s.empty(),
         "Found an unsupported configuration file keyword under \"SurfaceCurrent\"!\n"
@@ -1095,6 +1099,7 @@ void InductancePostData::SetUp(json &postpro)
     i.erase("Index");
     i.erase("Attributes");
     i.erase("Direction");
+    i.erase("CoordinateSystem");
     MFEM_VERIFY(i.empty(),
                 "Found an unsupported configuration file keyword under \"Inductance\"!\n"
                     << i.dump(2));
@@ -1170,6 +1175,7 @@ void InterfaceDielectricPostData::SetUp(json &postpro)
         // Cleanup
         e.erase("Attributes");
         e.erase("Side");
+        e.erase("CoordinateSystem");
         MFEM_VERIFY(e.empty(), "Found an unsupported configuration file keyword "
                                "under \"Dielectric\" boundary element!\n"
                                    << e.dump(2));
@@ -1200,6 +1206,7 @@ void InterfaceDielectricPostData::SetUp(json &postpro)
     d.erase("Thickness");
     d.erase("Attributes");
     d.erase("Side");
+    d.erase("CoordinateSystem");
     MFEM_VERIFY(d.empty(),
                 "Found an unsupported configuration file keyword under \"Dielectric\"!\n"
                     << d.dump(2));