[clang-format-command] fixes

include/bout/fv_ops.hxx

@@ -514,5 +514,5 @@ namespace FV {
    */
   Field3D Div_Perp_Lap(const Field3D& a, const Field3D& f,
                        CELL_LOC outloc = CELL_DEFAULT);
-}
+  }    // namespace FV
 #endif // __FV_OPS_H__

src/fileio/datafile.cxx

@@ -1202,9 +1202,9 @@ bool Datafile::write() {
     }
 
 #ifdef COORDINATES_USE_3D
-    write_f3d(name+"x", &(v.x), var.save_repeat);
-    write_f3d(name+"y", &(v.y), var.save_repeat);
-    write_f3d(name+"z", &(v.z), var.save_repeat);
+    write_f3d(name + "x", &(v.x), var.save_repeat);
+    write_f3d(name + "y", &(v.y), var.save_repeat);
+    write_f3d(name + "z", &(v.z), var.save_repeat);
 #else
     write_f2d(name+"x", &(v.x), var.save_repeat);
     write_f2d(name+"y", &(v.y), var.save_repeat);

src/invert/laplace/impls/multigrid/multigrid_laplace.cxx

@@ -592,7 +592,7 @@ BOUT_OMP(for collapse(2))
           D(i2, yindex, k2) * 2. * coords->g13(i2, yindex) / coords->dx(i2, yindex) / dz;
       // coefficient of mixed derivative stencil (could assume zero, at least initially,
       // if easier; then check this is true in constructor)
-      
+
       BoutReal dxd = (D(i2, yindex, k2)*coords->G1(i2, yindex)
         + coords->g11(i2, yindex)*ddx_C
         + coords->g13(i2, yindex)*ddz_C // (could assume zero, at least initially, if easier; then check this is true in constructor)

src/invert/laplace/impls/petsc/petsc_laplace.cxx

@@ -691,19 +691,26 @@ FieldPerp LaplacePetsc::solve(const FieldPerp& b, const FieldPerp& x0) {
                               MatA);
                     }
                   else {
-                    // // Second Order Accuracy on Boundary
-                    // Element(i,x,z,  0, 0,  3.0 / (2.0*coords->dx(x,y)), MatA );
-                    // Element(i,x,z, -1, 0, -2.0 / coords->dx(x,y), MatA );
-                    // Element(i,x,z, -2, 0,  1.0 / (2.0*coords->dx(x,y)), MatA );
-                    // Element(i,x,z, -3, 0,  0.0, MatA );  // Reset these elements to 0 in case 4th order flag was used previously: not allowed now
-                    // Element(i,x,z, -4, 0,  0.0, MatA );
-                    // Second Order Accuracy on Boundary, set half-way between grid points
-                    Element(i, x, z, 0, 0, 1.0 / coords->dx(x, y, z) / sqrt(coords->g_11(x, y, z)), MatA);
-                    Element(i, x, z, -1, 0, -1.0 / coords->dx(x, y, z) / sqrt(coords->g_11(x, y, z)), MatA);
-                    Element(i, x, z, -2, 0, 0.0, MatA);
-                    // Element(i,x,z, -3, 0,  0.0, MatA );  // Reset these elements to 0 in case 4th order flag was used previously: not allowed now
-                    // Element(i,x,z, -4, 0,  0.0, MatA );
-                  }
+                      // // Second Order Accuracy on Boundary
+                      // Element(i,x,z,  0, 0,  3.0 / (2.0*coords->dx(x,y)), MatA );
+                      // Element(i,x,z, -1, 0, -2.0 / coords->dx(x,y), MatA );
+                      // Element(i,x,z, -2, 0,  1.0 / (2.0*coords->dx(x,y)), MatA );
+                      // Element(i,x,z, -3, 0,  0.0, MatA );  // Reset these elements to 0
+                      // in case 4th order flag was used previously: not allowed now
+                      // Element(i,x,z, -4, 0,  0.0, MatA );
+                      // Second Order Accuracy on Boundary, set half-way between grid
+                      // points
+                      Element(i, x, z, 0, 0,
+                              1.0 / coords->dx(x, y, z) / sqrt(coords->g_11(x, y, z)),
+                              MatA);
+                      Element(i, x, z, -1, 0,
+                              -1.0 / coords->dx(x, y, z) / sqrt(coords->g_11(x, y, z)),
+                              MatA);
+                      Element(i, x, z, -2, 0, 0.0, MatA);
+                      // Element(i,x,z, -3, 0,  0.0, MatA );  // Reset these elements to 0
+                      // in case 4th order flag was used previously: not allowed now
+                      // Element(i,x,z, -4, 0,  0.0, MatA );
+                    }
                 }
               else {
                 if (fourth_order) {

src/mesh/boundary_standard.cxx

@@ -1887,8 +1887,8 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
       }
     }
 #else
-  throw BoutException(
-      "Applying boundary to Field2D not compatible with 3D metrics in all cases.");
+    throw BoutException(
+        "Applying boundary to Field2D not compatible with 3D metrics in all cases.");
 #endif
   }
 
@@ -2126,9 +2126,9 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
           BoutReal delta = bndry->bx * metric->dx(bndry->x, bndry->y, zk)
                            + bndry->by * metric->dy(bndry->x, bndry->y, zk);
 #else
-      BoutReal delta = bndry->bx * metric->dx(bndry->x, bndry->y)
-                       + bndry->by * metric->dy(bndry->x, bndry->y);
-      for (int zk = 0; zk < mesh->LocalNz; zk++) {
+        BoutReal delta = bndry->bx * metric->dx(bndry->x, bndry->y)
+                         + bndry->by * metric->dy(bndry->x, bndry->y);
+        for (int zk = 0; zk < mesh->LocalNz; zk++) {
 #endif
           if (fg) {
             val = fg->generate(Context(bndry, zk, loc, t, mesh));
@@ -2223,8 +2223,8 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
       }
     }
 #else
-  throw BoutException(
-      "Applying boundary to Field2D not compatible with 3D metrics in all cases.");
+    throw BoutException(
+        "Applying boundary to Field2D not compatible with 3D metrics in all cases.");
 #endif
   }
 
@@ -2328,8 +2328,8 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
                                     // cell
     }
 #else
-  throw BoutException(
-      "void BoundaryNeumann_4thOrder::apply(Field2D& f) not implemented with 3D metrics");
+    throw BoutException("void BoundaryNeumann_4thOrder::apply(Field2D& f) not "
+                        "implemented with 3D metrics");
 #endif
   }
 
@@ -2397,8 +2397,8 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
           * sqrt(metric->g_22(bndry->x, bndry->y)
                  / metric->g_22(bndry->x - bndry->bx, bndry->y - bndry->by));
 #else
-  throw BoutException(
-      "Applying boundary to Field2D not compatible with 3D metrics in all cases.");
+    throw BoutException(
+        "Applying boundary to Field2D not compatible with 3D metrics in all cases.");
 #endif
   }
 
@@ -2549,8 +2549,8 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
       } while (!bndry->isDone());
     }
 #else
-  throw BoutException(
-      "Applying boundary to Field2D not compatible with 3D metrics in all cases.");
+    throw BoutException(
+        "Applying boundary to Field2D not compatible with 3D metrics in all cases.");
 #endif
   }
 
@@ -2610,8 +2610,8 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
       } while (!bndry->isDone());
     }
 #else
-  throw BoutException(
-      "Applying boundary to Field3D not compatible with 3D metrics in ZeroLaplace case.");
+    throw BoutException("Applying boundary to Field3D not compatible with 3D metrics in "
+                        "ZeroLaplace case.");
 #endif
   }
 
@@ -2652,8 +2652,8 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
       } while (!bndry->isDone());
     }
 #else
-  throw BoutException(
-      "Applying boundary to Field2D not compatible with 3D metrics in all cases.");
+    throw BoutException(
+        "Applying boundary to Field2D not compatible with 3D metrics in all cases.");
 #endif
   }
 
@@ -2710,8 +2710,8 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
       } while (!bndry->isDone());
     }
 #else
-  throw BoutException("Applying boundary to Field3D not compatible with 3D metrics in "
-                      "ZeroLaplace2 case.");
+    throw BoutException("Applying boundary to Field3D not compatible with 3D metrics in "
+                        "ZeroLaplace2 case.");
 #endif
   }
 
@@ -2825,8 +2825,8 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
       } while (!bndry->isDone());
     }
 #else
-  throw BoutException("Applying boundary to Field3D not compatible with 3D metrics in "
-                      "ConstLaplace case.");
+    throw BoutException("Applying boundary to Field3D not compatible with 3D metrics in "
+                        "ConstLaplace case.");
 #endif
   }
 
@@ -2937,8 +2937,8 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
       }
     }
 #else
-  throw BoutException(
-      "Applying boundary to Vector3D not compatible with 3D metrics in DivCurl.");
+    throw BoutException(
+        "Applying boundary to Vector3D not compatible with 3D metrics in DivCurl.");
 #endif
   }
 

src/mesh/coordinates.cxx

@@ -895,8 +895,10 @@ Coordinates::Coordinates(Mesh* mesh, Options* options, const CELL_LOC loc,
     // Attempt to read Bxy from the grid file
     auto Bcalc = Bxy;
     if (getAtLoc(mesh, Bxy, "Bxy", suffix, location)) {
-      output_warn.write("\tWARNING: Magnitude of B field 'Bxy_{:s}' not found. Calculating "
-                        " from metric tensor\n", suffix);
+      output_warn.write(
+          "\tWARNING: Magnitude of B field 'Bxy_{:s}' not found. Calculating "
+          " from metric tensor\n",
+          suffix);
       Bxy = Bcalc;
     } else {
       Bxy = interpolateAndExtrapolate(Bxy, location, extrapolate_x, extrapolate_y, false,

src/mesh/difops.cxx

@@ -782,11 +782,11 @@ Field3D bracket(const Field3D& f, const Field2D& g, BRACKET_METHOD method,
           result(jx,jy,jz) = (Jpp + Jpx + Jxp) * spacingFactor;
         }
       }
-      }
+    }
 #else
     throw BoutException("BRACKET_ARAKAWA_OLD not valid with 3D metrics yet.");
 #endif
-      break;
+    break;
   }
   case BRACKET_SIMPLE: {
     // Use a subset of terms for comparison to BOUT-06