Fixing bug in calculation of non-uniform correction

As pointed out by Haruki Seto, the non-uniform correction
terms d1_dx and d1_dy were not recalculated if dx and dy were
changed.

This fix moves the calculation of d1_dx and d1_dy into the
geometry() function, which should be called whenever metric
tensor components are changed.

src/mesh/coordinates.cxx

@@ -169,26 +169,7 @@ Coordinates::Coordinates(Mesh *mesh) {
     throw BoutException("Differential geometry failed\n");
   }
 
-  //////////////////////////////////////////////////////
-  /// Non-uniform meshes. Need to use DDX, DDY
-
-  OPTION(Options::getRoot(), non_uniform, false);
-
-  Field2D d2x, d2y; // d^2 x / d i^2
-  // Read correction for non-uniform meshes
-  if (mesh->get(d2x, "d2x")) {
-    output_warn.write("\tWARNING: differencing quantity 'd2x' not found. Calculating from dx\n");
-    d1_dx = mesh->indexDDX(1. / dx); // d/di(1/dx)
-  } else {
-    d1_dx = -d2x / (dx * dx);
-  }
 
-  if (mesh->get(d2y, "d2y")) {
-    output_warn.write("\tWARNING: differencing quantity 'd2y' not found. Calculating from dy\n");
-    d1_dy = mesh->indexDDY(1. / dy); // d/di(1/dy)
-  } else {
-    d1_dy = -d2y / (dy * dy);
-  }
 
   if (mesh->get(ShiftTorsion, "ShiftTorsion")) {
     output_warn.write("\tWARNING: No Torsion specified for zShift. Derivatives may not be correct\n");
@@ -365,6 +346,27 @@ int Coordinates::geometry() {
 
   mesh->communicate(com);
 
+  //////////////////////////////////////////////////////
+  /// Non-uniform meshes. Need to use DDX, DDY
+
+  OPTION(Options::getRoot(), non_uniform, false);
+
+  Field2D d2x, d2y; // d^2 x / d i^2
+  // Read correction for non-uniform meshes
+  if (mesh->get(d2x, "d2x")) {
+    output_warn.write("\tWARNING: differencing quantity 'd2x' not found. Calculating from dx\n");
+    d1_dx = mesh->indexDDX(1. / dx); // d/di(1/dx)
+  } else {
+    d1_dx = -d2x / (dx * dx);
+  }
+
+  if (mesh->get(d2y, "d2y")) {
+    output_warn.write("\tWARNING: differencing quantity 'd2y' not found. Calculating from dy\n");
+    d1_dy = mesh->indexDDY(1. / dy); // d/di(1/dy)
+  } else {
+    d1_dy = -d2y / (dy * dy);
+  }
+
   return 0;
 }