Apply clang-format changes

Author: dschwoerer

include/bout/field.hxx

@@ -531,18 +531,18 @@ T pow(BoutReal lhs, const T& rhs, const std::string& rgn = "RGN_ALL") {
 #ifdef FIELD_FUNC
 #error This macro has already been defined
 #else
-#define FIELD_FUNC(_name, func)                                     \
-  template <typename T, typename = bout::utils::EnableIfField<T>>  \
-  inline T _name(const T& f, const std::string& rgn = "RGN_ALL") {  \
-    AUTO_TRACE();                                                  \
-    /* Check if the input is allocated */                          \
-    checkData(f);                                                  \
-    /* Define and allocate the output result */                    \
-    T result{emptyFrom(f)};                                        \
-    BOUT_FOR(d, result.getRegion(rgn)) { result[d] = func(f[d]); } \
-    result.name = std::string(#_name  "(") + f.name + std::string(")");	\
-    checkData(result);                                             \
-    return result;                                                 \
+#define FIELD_FUNC(_name, func)                                        \
+  template <typename T, typename = bout::utils::EnableIfField<T>>      \
+  inline T _name(const T& f, const std::string& rgn = "RGN_ALL") {     \
+    AUTO_TRACE();                                                      \
+    /* Check if the input is allocated */                              \
+    checkData(f);                                                      \
+    /* Define and allocate the output result */                        \
+    T result{emptyFrom(f)};                                            \
+    BOUT_FOR(d, result.getRegion(rgn)) { result[d] = func(f[d]); }     \
+    result.name = std::string(#_name "(") + f.name + std::string(")"); \
+    checkData(result);                                                 \
+    return result;                                                     \
   }
 #endif
 
@@ -685,16 +685,16 @@ inline T floor(const T& var, BoutReal f, const std::string& rgn = "RGN_ALL") {
   }
 #if BOUT_USE_FCI_AUTOMAGIC
   if (var.isFci()) {
-    for (size_t i=0; i < result.numberParallelSlices(); ++i) {
+    for (size_t i = 0; i < result.numberParallelSlices(); ++i) {
       BOUT_FOR(d, result.yup(i).getRegion(rgn)) {
- 	if (result.yup(i)[d] < f) {
- 	  result.yup(i)[d] = f;
- 	}
+        if (result.yup(i)[d] < f) {
+          result.yup(i)[d] = f;
+        }
       }
       BOUT_FOR(d, result.ydown(i).getRegion(rgn)) {
-	if (result.ydown(i)[d] < f) {
-	  result.ydown(i)[d] = f;
-	}
+        if (result.ydown(i)[d] < f) {
+          result.ydown(i)[d] = f;
+        }
       }
     }
   } else

include/bout/field3d.hxx

@@ -488,7 +488,7 @@ public:
   friend class Vector2D;
 
   Field3D& calcParallelSlices();
-  void allowParallelSlices([[maybe_unused]] bool allow){
+  void allowParallelSlices([[maybe_unused]] bool allow) {
 #if CHECK > 0
     allowCalcParallelSlices = allow;
 #endif

include/bout/fv_ops.hxx

@@ -10,8 +10,8 @@
 #include "bout/vector2d.hxx"
 
 #include "bout/utils.hxx"
-#include <bout/mesh.hxx>
 #include <bout/difops.hxx>
+#include <bout/mesh.hxx>
 
 namespace FV {
 /*!

include/bout/index_derivs_interface.hxx

@@ -203,11 +203,13 @@ T DDY(const T& f, CELL_LOC outloc = CELL_DEFAULT, const std::string& method = "D
   if (f.isFci()) {
     ASSERT1(f.getDirectionY() == YDirectionType::Standard);
     T f_tmp = f;
-    if (!f.hasParallelSlices()){
+    if (!f.hasParallelSlices()) {
 #if BOUT_USE_FCI_AUTOMAGIC
       f_tmp.calcParallelSlices();
 #else
-      throw BoutException("parallel slices needed for parallel derivatives. Make sure to communicate and apply parallel boundary conditions before calling derivative");
+      throw BoutException(
+          "parallel slices needed for parallel derivatives. Make sure to communicate and "
+          "apply parallel boundary conditions before calling derivative");
 #endif
     }
     return standardDerivative<T, DIRECTION::YOrthogonal, DERIV::Standard>(f_tmp, outloc,

include/bout/interpolation_xz.hxx

@@ -134,7 +134,6 @@ public:
   }
 };
 
-
 template <bool monotonic>
 class XZHermiteSplineBase : public XZInterpolation {
 protected:
@@ -282,19 +281,15 @@ public:
                       const std::string& region = "RGN_NOBNDRY") override;
 };
 
-
-class XZMonotonicHermiteSplineLegacy: public XZHermiteSplineBase<false> {
+class XZMonotonicHermiteSplineLegacy : public XZHermiteSplineBase<false> {
 public:
   using XZHermiteSplineBase<false>::interpolate;
   virtual Field3D interpolate(const Field3D& f,
                               const std::string& region = "RGN_NOBNDRY") const override;
-  template<class... Ts>
-  XZMonotonicHermiteSplineLegacy(Ts... args) :
-    XZHermiteSplineBase<false>(args...)
-  {}
+  template <class... Ts>
+  XZMonotonicHermiteSplineLegacy(Ts... args) : XZHermiteSplineBase<false>(args...) {}
 };
 
-
 class XZInterpolationFactory
     : public Factory<XZInterpolation, XZInterpolationFactory, Mesh*> {
 public:

include/bout/mesh.hxx

@@ -842,7 +842,6 @@ public:
     return not coords->getParallelTransform().canToFromFieldAligned();
   }
 
-
 private:
   /// Allocates default Coordinates objects
   /// By default attempts to read staggered Coordinates from grid data source,

include/bout/petsclib.hxx

@@ -156,7 +156,7 @@ private:
 
 #endif // PETSC_VERSION_GE
 
-#if ! PETSC_VERSION_GE(3, 19, 0)
+#if !PETSC_VERSION_GE(3, 19, 0)
 #define PETSC_SUCCESS ((PetscErrorCode)0)
 #endif
 

include/bout/physicsmodel.hxx

@@ -275,6 +275,7 @@ protected:
 public:
   /// Output additional variables other than the evolving variables
   virtual void outputVars(Options& options);
+
 protected:
   /// Add additional variables other than the evolving variables to the restart files
   virtual void restartVars(Options& options);

src/field/field3d.cxx

@@ -96,7 +96,7 @@ Field3D::Field3D(const BoutReal val, Mesh* localmesh) : Field3D(localmesh) {
 #if BOUT_USE_FCI_AUTOMAGIC
   if (this->isFci()) {
     splitParallelSlices();
-    for (size_t i=0; i<numberParallelSlices(); ++i){
+    for (size_t i = 0; i < numberParallelSlices(); ++i) {
       yup(i) = val;
       ydown(i) = val;
     }
@@ -363,7 +363,7 @@ Field3D& Field3D::operator=(const BoutReal val) {
 
 #if BOUT_USE_FCI_AUTOMAGIC
   if (isFci() && hasParallelSlices()) {
-    for (size_t i=0; i<numberParallelSlices(); ++i){
+    for (size_t i = 0; i < numberParallelSlices(); ++i) {
       yup(i) = val;
       ydown(i) = val;
     }
@@ -902,15 +902,9 @@ void Field3D::setRegion(const std::string& region_name) {
   regionID = fieldmesh->getRegionID(region_name);
 }
 
-void Field3D::resetRegion() {
-  regionID.reset();
-};
-void Field3D::setRegion(size_t id) {
-  regionID = id;
-};
-void Field3D::setRegion(std::optional<size_t> id) {
-  regionID = id;
-};
+void Field3D::resetRegion() { regionID.reset(); };
+void Field3D::setRegion(size_t id) { regionID = id; };
+void Field3D::setRegion(std::optional<size_t> id) { regionID = id; };
 
 Field3D& Field3D::enableTracking(const std::string& name, Options& _tracking) {
   tracking = &_tracking;
@@ -929,9 +923,9 @@ Options* Field3D::track(const T& change, std::string operation) {
     const std::string changename = change.name;
 #endif
     (*tracking)[outname].setAttributes({
-      {"operation", operation},
+        {"operation", operation},
 #if BOUT_USE_TRACK
-          {"rhs.name", changename},
+        {"rhs.name", changename},
 #endif
     });
     return &(*tracking)[outname];