Update documentation and code format

.clang-format

@@ -2,9 +2,9 @@
 ---
 Language:        Cpp
 AccessModifierOffset: -2
-AlignAfterOpenBracket: AlwaysBreak
-AlignConsecutiveAssignments: false
-AlignConsecutiveDeclarations: false
+AlignAfterOpenBracket: Align
+AlignConsecutiveAssignments: true
+AlignConsecutiveDeclarations: true
 AlignEscapedNewlinesLeft: false
 AlignEscapedNewlines: Left
 AlignOperands:   true
@@ -15,11 +15,10 @@ AllowShortCaseLabelsOnASingleLine: false
 AllowShortFunctionsOnASingleLine: All
 AllowShortIfStatementsOnASingleLine: false
 AllowShortLoopsOnASingleLine: false
-AlwaysBreakAfterDefinitionReturnType: TopLevel
 AlwaysBreakAfterReturnType: All
 AlwaysBreakBeforeMultilineStrings: false
 AlwaysBreakTemplateDeclarations: true
-BinPackArguments: true
+BinPackArguments: false
 BinPackParameters: false
 BraceWrapping:   
   AfterClass:      true
@@ -31,14 +30,15 @@ BraceWrapping:
   AfterStruct:     true
   AfterUnion:      false
   BeforeCatch:     false
-  BeforeElse:      false
+  BeforeElse:      true
   IndentBraces:    false
+  SplitEmptyFunction: false
 BreakBeforeBinaryOperators: None
 BreakBeforeBraces: Custom
 BreakBeforeTernaryOperators: true
-BreakConstructorInitializersBeforeComma: false
+BreakConstructorInitializers: BeforeColon
 BreakAfterJavaFieldAnnotations: false
-BreakStringLiterals: true
+BreakStringLiterals: false
 ColumnLimit:     120
 CommentPragmas:  '^ IWYU pragma:'
 ConstructorInitializerAllOnOneLineOrOnePerLine: true
@@ -65,7 +65,7 @@ KeepEmptyLinesAtTheStartOfBlocks: true
 MacroBlockBegin: ''
 MacroBlockEnd:   ''
 MaxEmptyLinesToKeep: 1
-NamespaceIndentation: None
+NamespaceIndentation: All
 ObjCBlockIndentWidth: 2
 ObjCSpaceAfterProperty: false
 ObjCSpaceBeforeProtocolList: true
@@ -76,7 +76,7 @@ PenaltyBreakString: 1000
 PenaltyExcessCharacter: 1000000
 PenaltyReturnTypeOnItsOwnLine: 60
 PointerAlignment: Left
-ReflowComments:  true
+ReflowComments:  false
 SortIncludes: false
 SpaceAfterCStyleCast: false
 SpaceBeforeAssignmentOperators: true

Examples/AMReX_DCEL/main.cpp

@@ -16,105 +16,105 @@
 using namespace amrex;
 
 namespace amrex {
-namespace EB2 {
-
-/*!
-  @brief This is an AMReX-capable version of the EBGeometry BVH accelerator. It
-  is templated as T, BV, K which indicate the EBGeometry precision, bounding
-  volume, and tree degree.
-*/
-template <class T, class BV, int K>
-class SignedDistanceBVH
-{
-public:
-  /*!
-@brief Alias for builder node, for encapsulating a "standard" BVH node
-  */
-  using BuilderNode = EBGeometry::BVH::NodeT<T, EBGeometry::DCEL::FaceT<T>, BV, K>;
-
-  /*!
-@brief Alias for linearized BVH node
-  */
-  using LinearNode = EBGeometry::BVH::LinearBVH<T, EBGeometry::DCEL::FaceT<T>, BV, K>;
-
-  /*!
-@brief Alias for always-3D vector
-  */
-  using Vec3 = EBGeometry::Vec3T<T>;
-
-  /*!
-@brief Full constructor.
-@param[in] a_filename File name. Must be a PLY file and will be parser by the
-PLY parser.
-@param[in] a_flipSign Hook for swapping inside/outside.
-  */
-  SignedDistanceBVH(const std::string a_filename, const bool a_flipSign)
-  {
-
-    // 1. Read mesh from file.
-    auto mesh = EBGeometry::Parser::PLY<T>::readIntoDCEL(a_filename);
-
-    // 2. Create a standard BVH hierarchy. This is not a compact ree.
-    auto root = std::make_shared<BuilderNode>(mesh->getFaces());
-    root->topDownSortAndPartitionPrimitives(
-      EBGeometry::DCEL::defaultBVConstructor<T, BV>, EBGeometry::DCEL::defaultPartitioner<T, BV, K>,
-      EBGeometry::DCEL::defaultStopFunction<T, BV, K>);
-
-    // 3. Flatten the tree onto a tighter memory representation.
-    m_rootNode = root->flattenTree();
-  }
-
-  /*!
-@brief Copy constructor.
-@param[in] a_other Other SDF.
-  */
-  SignedDistanceBVH(const SignedDistanceBVH& a_other)
-  {
-    this->m_rootNode = a_other.m_rootNode;
-    this->m_flipSign = a_other.m_flipSign;
-  }
-
-  /*!
-@brief AMReX's implicit function definition.
-  */
-  Real operator()(AMREX_D_DECL(Real x, Real y, Real z)) const noexcept
-  {
-    const Real sign = (m_flipSign) ? -1.0 : 1.0;
-
-    return sign * m_rootNode->signedDistance(Vec3(x, y, z));
-  };
-
-  /*!
-@brief Also an AMReX implicit function implementation
-  */
-  inline Real
-  operator()(const RealArray& p) const noexcept
-  {
-    return this->operator()(AMREX_D_DECL(p[0], p[1], p[2]));
-  }
-
-protected:
-  /*!
-@brief Root node of the linearized BVH hierarchy.
-  */
-  std::shared_ptr<LinearNode> m_rootNode;
-
-  /*!
-@brief Hook for flipping the sign
-  */
-  bool m_flipSign;
-};
-} // namespace EB2
+  namespace EB2 {
+
+    /*!
+      @brief This is an AMReX-capable version of the EBGeometry BVH accelerator. It
+      is templated as T, BV, K which indicate the EBGeometry precision, bounding
+      volume, and tree degree.
+    */
+    template <class T, class BV, int K>
+    class SignedDistanceBVH
+    {
+    public:
+      /*!
+	@brief Alias for builder node, for encapsulating a "standard" BVH node
+      */
+      using BuilderNode = EBGeometry::BVH::NodeT<T, EBGeometry::DCEL::FaceT<T>, BV, K>;
+
+      /*!
+	@brief Alias for linearized BVH node
+      */
+      using LinearNode = EBGeometry::BVH::LinearBVH<T, EBGeometry::DCEL::FaceT<T>, BV, K>;
+
+      /*!
+	@brief Alias for always-3D vector
+      */
+      using Vec3 = EBGeometry::Vec3T<T>;
+
+      /*!
+	@brief Full constructor.
+	@param[in] a_filename File name. Must be a PLY file and will be parser by the
+	PLY parser.
+	@param[in] a_flipSign Hook for swapping inside/outside.
+      */
+      SignedDistanceBVH(const std::string a_filename, const bool a_flipSign)
+      {
+
+        // 1. Read mesh from file.
+        auto mesh = EBGeometry::Parser::PLY<T>::readIntoDCEL(a_filename);
+
+        // 2. Create a standard BVH hierarchy. This is not a compact ree.
+        auto root = std::make_shared<BuilderNode>(mesh->getFaces());
+        root->topDownSortAndPartitionPrimitives(EBGeometry::DCEL::defaultBVConstructor<T, BV>,
+                                                EBGeometry::DCEL::defaultPartitioner<T, BV, K>,
+                                                EBGeometry::DCEL::defaultStopFunction<T, BV, K>);
+
+        // 3. Flatten the tree onto a tighter memory representation.
+        m_rootNode = root->flattenTree();
+      }
+
+      /*!
+	@brief Copy constructor.
+	@param[in] a_other Other SDF.
+      */
+      SignedDistanceBVH(const SignedDistanceBVH& a_other)
+      {
+        this->m_rootNode = a_other.m_rootNode;
+        this->m_flipSign = a_other.m_flipSign;
+      }
+
+      /*!
+	@brief AMReX's implicit function definition.
+      */
+      Real operator()(AMREX_D_DECL(Real x, Real y, Real z)) const noexcept
+      {
+        const Real sign = (m_flipSign) ? -1.0 : 1.0;
+
+        return sign * m_rootNode->signedDistance(Vec3(x, y, z));
+      };
+
+      /*!
+	@brief Also an AMReX implicit function implementation
+      */
+      inline Real
+      operator()(const RealArray& p) const noexcept
+      {
+        return this->operator()(AMREX_D_DECL(p[0], p[1], p[2]));
+      }
+
+    protected:
+      /*!
+	@brief Root node of the linearized BVH hierarchy.
+      */
+      std::shared_ptr<LinearNode> m_rootNode;
+
+      /*!
+	@brief Hook for flipping the sign
+      */
+      bool m_flipSign;
+    };
+  } // namespace EB2
 } // namespace amrex
 
 int
 main(int argc, char* argv[])
 {
   amrex::Initialize(argc, argv);
 
-  int n_cell = 128;
+  int n_cell        = 128;
   int max_grid_size = 32;
-  int which_geom = 0;
+  int which_geom    = 0;
 
   std::string filename;
 
@@ -129,26 +129,32 @@ main(int argc, char* argv[])
     RealBox rb;
 
     if (which_geom == 0) { // Airfoil case
-      rb = RealBox({-100, -100, -75}, {400, 100, 125});
+      rb       = RealBox({-100, -100, -75}, {400, 100, 125});
       filename = "../PLY/airfoil.ply";
-    } else if (which_geom == 1) { // Sphere case
-      rb = RealBox({-400, -400, -400}, {400, 400, 400});
+    }
+    else if (which_geom == 1) { // Sphere case
+      rb       = RealBox({-400, -400, -400}, {400, 400, 400});
       filename = "../PLY/sphere.ply";
-    } else if (which_geom == 2) { // Dodecahedron
-      rb = RealBox({-2., -2., -2.}, {2., 2., 2.});
+    }
+    else if (which_geom == 2) { // Dodecahedron
+      rb       = RealBox({-2., -2., -2.}, {2., 2., 2.});
       filename = "../PLY/dodecahedron.ply";
-    } else if (which_geom == 3) { // Horse
-      rb = RealBox({-0.12, -0.12, -0.12}, {0.12, 0.12, 0.12});
+    }
+    else if (which_geom == 3) { // Horse
+      rb       = RealBox({-0.12, -0.12, -0.12}, {0.12, 0.12, 0.12});
       filename = "../PLY/horse.ply";
-    } else if (which_geom == 4) { // Car
+    }
+    else if (which_geom == 4) { // Car
       //	    rb = RealBox({-20,-20,-20}, {20,20,20}); // Doesn't work.
-      rb = RealBox({-10, -5, -5}, {10, 5, 5}); // Works.
+      rb       = RealBox({-10, -5, -5}, {10, 5, 5}); // Works.
       filename = "../PLY/porsche.ply";
-    } else if (which_geom == 5) { // Orion
-      rb = RealBox({-10, -5, -10}, {10, 10, 10});
+    }
+    else if (which_geom == 5) { // Orion
+      rb       = RealBox({-10, -5, -10}, {10, 10, 10});
       filename = "../PLY/orion.ply";
-    } else if (which_geom == 6) { // Armadillo
-      rb = RealBox({-100, -75, -100}, {100, 125, 100});
+    }
+    else if (which_geom == 6) { // Armadillo
+      rb       = RealBox({-100, -75, -100}, {100, 125, 100});
       filename = "../PLY/armadillo.ply";
     }
 
@@ -162,9 +168,9 @@ main(int argc, char* argv[])
   // EBGeometry precision.
   constexpr int K = 4;
 
-  using T = float;
+  using T    = float;
   using Vec3 = EBGeometry::Vec3T<T>;
-  using BV = EBGeometry::BoundingVolumes::AABBT<T>;
+  using BV   = EBGeometry::BoundingVolumes::AABBT<T>;
 
   EB2::SignedDistanceBVH<T, BV, K> sdf(filename, false);