Merge remote-tracking branch 'origin/par-metrics' into HEAD

Author: dschwoerer

.github/workflows/clang-tidy-review.yml

@@ -24,7 +24,6 @@ jobs:
         uses: ZedThree/clang-tidy-review@v0.23.1
         id: review
         with:
-          annotations: true
           build_dir: build
           apt_packages: "libfftw3-dev,libnetcdf-c++4-dev,libopenmpi-dev,petsc-dev,slepc-dev,liblapack-dev,libparpack2-dev,libsundials-dev,uuid-dev"
           config_file: ".clang-tidy"

include/bout/field.hxx

@@ -296,13 +296,15 @@ inline void checkPositive(const T& f, const std::string& name = "field",
 template <typename T>
 inline T toFieldAligned(const T& f, const std::string& region = "RGN_ALL") {
   static_assert(bout::utils::is_Field_v<T>, "toFieldAligned only works on Fields");
+  ASSERT3(f.getCoordinates() != nullptr);
   return f.getCoordinates()->getParallelTransform().toFieldAligned(f, region);
 }
 
 /// Convert \p f from field-aligned space in \p region (default: whole domain)
 template <typename T>
 inline T fromFieldAligned(const T& f, const std::string& region = "RGN_ALL") {
   static_assert(bout::utils::is_Field_v<T>, "fromFieldAligned only works on Fields");
+  ASSERT3(f.getCoordinates() != nullptr);
   return f.getCoordinates()->getParallelTransform().fromFieldAligned(f, region);
 }
 

include/bout/field2d.hxx

@@ -25,6 +25,7 @@
  *
  */
 #include "bout/utils.hxx"
+#include <optional>
 class Field2D;
 
 #pragma once
@@ -251,8 +252,7 @@ public:
   Field2D& operator/=(BoutReal rhs);
 
   // FieldData virtual functions
-
-  bool is3D() const override { return false; }
+  FieldType field_type() const override { return FieldType::field2d; }
 
 #if CHECK > 0
   void doneComms() override { bndry_xin = bndry_xout = bndry_yup = bndry_ydown = true; }

include/bout/field3d.hxx

@@ -497,7 +497,7 @@ public:
   Field3D& update_subtraction_inplace(BoutReal rhs);
 
   // FieldData virtual functions
-  bool is3D() const override { return true; }
+  FieldType field_type() const override { return FieldType::field3d; }
 
 #if CHECK > 0
   void doneComms() override { bndry_xin = bndry_xout = bndry_yup = bndry_ydown = true; }

include/bout/field_data.hxx

@@ -6,7 +6,7 @@
  * Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu
  *
  * Contact: Ben Dudson, bd512@york.ac.uk
- * 
+ *
  * This file is part of BOUT++.
  *
  * BOUT++ is free software: you can redistribute it and/or modify
@@ -33,6 +33,7 @@ class FieldData;
 #include "bout/bout_types.hxx"
 #include "bout/unused.hxx"
 
+#include <cstdint>
 #include <map>
 #include <memory>
 #include <string>
@@ -71,13 +72,22 @@ public:
   /// Get variable location
   virtual CELL_LOC getLocation() const;
 
+  /// Enum to distinguish the different kinds of Fields
+  enum class FieldType : std::uint8_t { field3d, field2d, fieldperp };
+  /// Is this an instance of `Field3D`, `Field2D`, or `FieldPerp`?
+  virtual FieldType field_type() const = 0;
+
   // Defines interface which must be implemented
   /// True if variable is 3D
-  virtual bool is3D() const = 0;
+  [[deprecated("Use `field_type()` instead")]]
+  bool is3D() const {
+    return field_type() == FieldType::field3d;
+  }
+
   /// Number of BoutReals in one element
   virtual int elementSize() const { return 1; }
 
-  virtual void doneComms(){}; // Notifies that communications done
+  virtual void doneComms() {}; // Notifies that communications done
 
   // Boundary conditions
   void setBoundary(const std::string& name); ///< Set the boundary conditions
@@ -86,13 +96,13 @@ public:
   copyBoundary(const FieldData& f); ///< Copy the boundary conditions from another field
 
   virtual void applyBoundary(bool UNUSED(init) = false) {}
-  virtual void applyTDerivBoundary(){};
+  virtual void applyTDerivBoundary() {};
 
-  virtual void applyParallelBoundary(){};
-  virtual void applyParallelBoundary(BoutReal UNUSED(t)){};
-  virtual void applyParallelBoundary(const std::string& UNUSED(condition)){};
+  virtual void applyParallelBoundary() {};
+  virtual void applyParallelBoundary(BoutReal UNUSED(t)) {};
+  virtual void applyParallelBoundary(const std::string& UNUSED(condition)) {};
   virtual void applyParallelBoundary(const std::string& UNUSED(region),
-                                     const std::string& UNUSED(condition)){};
+                                     const std::string& UNUSED(condition)) {};
   // JMAD
   void addBndryFunction(FuncPtr userfunc, BndryLoc location);
   void addBndryGenerator(FieldGeneratorPtr gen, BndryLoc location);

include/bout/fieldgroup.hxx

@@ -1,34 +1,33 @@
 #ifndef BOUT_FIELDGROUP_H
 #define BOUT_FIELDGROUP_H
 
-#include "bout/field_data.hxx"
-#include <bout/field3d.hxx>
-
+#include <bout/traits.hxx>
 #include <bout/vector2d.hxx>
 #include <bout/vector3d.hxx>
 
 #include <vector>
 
-#include <algorithm>
+class Field2D;
+class Field3D;
+class FieldPerp;
+class Field;
 
 /// Group together fields for easier communication
 ///
-/// Note: The FieldData class is used as a base class,
-/// which is inherited by Field2D, Field3D, Vector2D and Vector3D
-/// however Vector2D and Vector3D are stored by reference to their
-/// components (x,y,z) as Field2D or Field3D objects.
+/// Note: The `Field` class is used as a base class,
+/// which is inherited by `Field2D`, `Field3D`, `FieldPerp`;
+/// however `Vector2D` and `Vector3D` are stored by reference to their
+/// components ``(x, y, z)`` as `Field2D` or `Field3D` objects.
 class FieldGroup {
 public:
   FieldGroup() = default;
   FieldGroup(const FieldGroup& other) = default;
   FieldGroup(FieldGroup&& other) = default;
   FieldGroup& operator=(const FieldGroup& other) = default;
   FieldGroup& operator=(FieldGroup&& other) = default;
+  ~FieldGroup() = default;
 
-  /// Constructor with a single FieldData \p f
-  FieldGroup(FieldData& f) { fvec.push_back(&f); }
-
-  /// Constructor with a single Field3D \p f
+  FieldGroup(Field& f) { fvec.push_back(&f); }
   FieldGroup(Field3D& f) {
     fvec.push_back(&f);
     f3vec.push_back(&f);
@@ -56,7 +55,7 @@ public:
   }
 
   /// Variadic constructor. Allows an arbitrary number of
-  /// FieldData arguments
+  /// Field arguments
   ///
   /// The explicit keyword prevents FieldGroup being constructed with arbitrary
   /// types. In particular arguments to add() cannot be implicitly converted
@@ -78,12 +77,12 @@ public:
     return *this;
   }
 
-  /// Add a FieldData \p f to the group.
+  /// Add a Field \p f to the group.
   ///
   /// A pointer to this field will be stored internally,
   /// so the lifetime of this variable should be longer
   /// than the lifetime of this group.
-  void add(FieldData& f) { fvec.push_back(&f); }
+  void add(Field& f) { fvec.push_back(&f); }
 
   // Add a 3D field \p f, which goes into both vectors.
   //
@@ -121,12 +120,8 @@ public:
   }
 
   /// Add multiple fields to this group
-  ///
-  /// This is a variadic template which allows Field3D objects to be
-  /// treated as a special case. An arbitrary number of fields can be
-  /// added.
   template <typename... Ts>
-  void add(FieldData& t, Ts&... ts) {
+  void add(Field& t, Ts&... ts) {
     add(t);     // Add the first using functions above
     add(ts...); // Add the rest
   }
@@ -165,16 +160,14 @@ public:
   }
 
   /// Iteration over all fields
-  using iterator = std::vector<FieldData*>::iterator;
-  iterator begin() { return fvec.begin(); }
-  iterator end() { return fvec.end(); }
+  auto begin() { return fvec.begin(); }
+  auto end() { return fvec.end(); }
 
   /// Const iteration over all fields
-  using const_iterator = std::vector<FieldData*>::const_iterator;
-  const_iterator begin() const { return fvec.begin(); }
-  const_iterator end() const { return fvec.end(); }
+  auto begin() const { return fvec.cbegin(); }
+  auto end() const { return fvec.cend(); }
 
-  const std::vector<FieldData*>& get() const { return fvec; }
+  const std::vector<Field*>& get() const { return fvec; }
 
   /// Iteration over 3D fields
   const std::vector<Field3D*>& field3d() const { return f3vec; }
@@ -183,8 +176,8 @@ public:
   void makeUnique();
 
 private:
-  std::vector<FieldData*> fvec; // Vector of fields
-  std::vector<Field3D*> f3vec;  // Vector of 3D fields
+  std::vector<Field*> fvec;    // Vector of fields
+  std::vector<Field3D*> f3vec; // Vector of 3D fields
 };
 
 /// Combine two FieldGroups

include/bout/fieldperp.hxx

@@ -5,7 +5,7 @@
  * Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu
  *
  * Contact: Ben Dudson, bd512@york.ac.uk
- * 
+ *
  * This file is part of BOUT++.
  *
  * BOUT++ is free software: you can redistribute it and/or modify
@@ -23,6 +23,8 @@
  *
  **************************************************************************/
 
+#include <cstddef>
+#include <optional>
 #include <vector>
 class FieldPerp;
 
@@ -45,8 +47,8 @@ class Field3D; // #include "bout/field3d.hxx"
 
 /*!
  * Represents a 2D field perpendicular to the magnetic field
- * at a particular index in Y, which only varies in X-Z. 
- * 
+ * at a particular index in Y, which only varies in X-Z.
+ *
  * Primarily used inside field solvers
  */
 class FieldPerp : public Field {
@@ -59,7 +61,8 @@ public:
   FieldPerp(Mesh* fieldmesh = nullptr, CELL_LOC location_in = CELL_CENTRE,
             int yindex_in = -1,
             DirectionTypes directions_in = {YDirectionType::Standard,
-                                            ZDirectionType::Standard});
+                                            ZDirectionType::Standard},
+            std::optional<size_t> regionID = {});
 
   /*!
    * Copy constructor. After this the data
@@ -205,7 +208,7 @@ public:
 
   /*!
    * Access to the underlying data array at a given x,z index
-   * 
+   *
    * If CHECK > 2 then bounds checking is performed, otherwise
    * no checks are performed
    */
@@ -241,9 +244,9 @@ public:
   }
 
   /*!
-   * Access to the underlying data array. (X,Y,Z) indices for consistency with 
+   * Access to the underlying data array. (X,Y,Z) indices for consistency with
    * other field types
-   * 
+   *
    */
   BoutReal& operator()(int jx, int UNUSED(jy), int jz) { return (*this)(jx, jz); }
 
@@ -252,7 +255,7 @@ public:
   }
 
   /*!
-   * Addition, modifying in-place. 
+   * Addition, modifying in-place.
    * This loops over the entire domain, including guard/boundary cells
    */
   FieldPerp& operator+=(const FieldPerp& rhs);
@@ -261,7 +264,7 @@ public:
   FieldPerp& operator+=(BoutReal rhs);
 
   /*!
-   * Subtraction, modifying in place. 
+   * Subtraction, modifying in place.
    * This loops over the entire domain, including guard/boundary cells
    */
   FieldPerp& operator-=(const FieldPerp& rhs);
@@ -270,7 +273,7 @@ public:
   FieldPerp& operator-=(BoutReal rhs);
 
   /*!
-   * Multiplication, modifying in place. 
+   * Multiplication, modifying in place.
    * This loops over the entire domain, including guard/boundary cells
    */
   FieldPerp& operator*=(const FieldPerp& rhs);
@@ -279,7 +282,7 @@ public:
   FieldPerp& operator*=(BoutReal rhs);
 
   /*!
-   * Division, modifying in place. 
+   * Division, modifying in place.
    * This loops over the entire domain, including guard/boundary cells
    */
   FieldPerp& operator/=(const FieldPerp& rhs);
@@ -300,7 +303,7 @@ public:
    */
   int getNz() const override { return nz; };
 
-  bool is3D() const override { return false; }
+  FieldType field_type() const override { return FieldType::fieldperp; }
 
   friend void swap(FieldPerp& first, FieldPerp& second) noexcept;
 

include/bout/globalindexer.hxx

@@ -86,7 +86,7 @@ public:
 
     int localSize = size();
     MPI_Comm comm =
-        std::is_same_v<T, FieldPerp> ? fieldmesh->getXcomm() : BoutComm::get();
+        std::is_same_v<T, FieldPerp> ? fieldmesh->getXZcomm() : BoutComm::get();
     fieldmesh->getMpi().MPI_Scan(&localSize, &globalEnd, 1, MPI_INT, MPI_SUM, comm);
     globalEnd--;
     int counter = globalStart = globalEnd - size() + 1;

include/bout/hypre_interface.hxx

@@ -159,7 +159,7 @@ public:
   explicit HypreVector(IndexerPtr<T> indConverter) : indexConverter(indConverter) {
     Mesh& mesh = *indConverter->getMesh();
     const MPI_Comm comm =
-        std::is_same_v<T, FieldPerp> ? mesh.getXcomm() : BoutComm::get();
+        std::is_same_v<T, FieldPerp> ? mesh.getXZcomm() : BoutComm::get();
 
     HYPRE_BigInt jlower = indConverter->getGlobalStart();
     HYPRE_BigInt jupper = jlower + indConverter->size() - 1; // inclusive end
@@ -380,7 +380,7 @@ public:
       : hypre_matrix(new HYPRE_IJMatrix, MatrixDeleter{}), index_converter(indConverter) {
     Mesh* mesh = indConverter->getMesh();
     const MPI_Comm comm =
-        std::is_same_v<T, FieldPerp> ? mesh->getXcomm() : BoutComm::get();
+        std::is_same_v<T, FieldPerp> ? mesh->getXZcomm() : BoutComm::get();
     parallel_transform = &mesh->getCoordinates()->getParallelTransform();
 
     ilower = indConverter->getGlobalStart();
@@ -812,7 +812,7 @@ public:
                            "values are: gmres, bicgstab, pcg")
                       .withDefault(HYPRE_SOLVER_TYPE::bicgstab);
 
-    comm = std::is_same_v<T, FieldPerp> ? mesh.getXcomm() : BoutComm::get();
+    comm = std::is_same_v<T, FieldPerp> ? mesh.getXZcomm() : BoutComm::get();
 
     auto print_level =
         options["hypre_print_level"]