Fix axis regularisation

src/fluid/boundary/axis.cpp

@@ -28,39 +28,31 @@ void Axis::SymmetrizeEx1Side(int jref) {
   IdefixArray3D<real> Ex1 = this->ex;
   IdefixArray1D<real> Ex1Avg = this->Ex1Avg;
 
-  if(isTwoPi) {
-    idefix_for("Ex1_ini",0,data->np_tot[IDIR],
-        KOKKOS_LAMBDA(int i) {
-          Ex1Avg(i) = ZERO_F;
-        });
-
-    idefix_for("Ex1_Symmetrize",data->beg[KDIR],data->end[KDIR],0,data->np_tot[IDIR],
-      KOKKOS_LAMBDA(int k,int i) {
-        Kokkos::atomic_add(&Ex1Avg(i),  Ex1(k,jref,i));
+  idefix_for("Ex1_ini",0,data->np_tot[IDIR],
+      KOKKOS_LAMBDA(int i) {
+        Ex1Avg(i) = ZERO_F;
       });
-    if(needMPIExchange) {
-      #ifdef WITH_MPI
-        Kokkos::fence();
-        // sum along all of the processes on the same r
-        MPI_Allreduce(MPI_IN_PLACE, Ex1Avg.data(), data->np_tot[IDIR], realMPI,
-                      MPI_SUM, data->mygrid->AxisComm);
-      #endif
-    }
 
-    int ncells=data->mygrid->np_int[KDIR];
-
-    idefix_for("Ex1_Store",0,data->np_tot[KDIR],0,data->np_tot[IDIR],
-    KOKKOS_LAMBDA(int k,int i) {
-      Ex1(k,jref,i) = Ex1Avg(i)/((real) ncells);
-    });
-  } else {
-    // if we're not doing full two pi, the flow is symmetric with respect to the axis, and the axis
-    // EMF is simply zero
-    idefix_for("Ex1_Store",0,data->np_tot[KDIR],0,data->np_tot[IDIR],
+  idefix_for("Ex1_Symmetrize",data->beg[KDIR],data->end[KDIR],0,data->np_tot[IDIR],
     KOKKOS_LAMBDA(int k,int i) {
-      Ex1(k,jref,i) = ZERO_F;
+      Kokkos::atomic_add(&Ex1Avg(i),  Ex1(k,jref,i));
     });
+  if(needMPIExchange) {
+    #ifdef WITH_MPI
+      Kokkos::fence();
+      // sum along all of the processes on the same r
+      MPI_Allreduce(MPI_IN_PLACE, Ex1Avg.data(), data->np_tot[IDIR], realMPI,
+                    MPI_SUM, data->mygrid->AxisComm);
+    #endif
   }
+
+  int ncells=data->mygrid->np_int[KDIR];
+
+  idefix_for("Ex1_Store",0,data->np_tot[KDIR],0,data->np_tot[IDIR],
+  KOKKOS_LAMBDA(int k,int i) {
+    Ex1(k,jref,i) = Ex1Avg(i)/((real) ncells);
+  });
+
 #endif
 }
 
@@ -100,9 +92,9 @@ void Axis::RegularizeCurrentSide(int side) {
       sign = -1;
     }
     IdefixArray1D<real> BAvg = this->Ex1Avg;
-    IdefixArray1D<real> x2 = data->x[JDIR];
     IdefixArray1D<real> x1 = data->x[IDIR];
     IdefixArray1D<real> dx3 = data->dx[KDIR];
+    IdefixArray1D<real> dx2 = data->dx[JDIR];
 
     idefix_for("B_ini",0,data->np_tot[IDIR],
           KOKKOS_LAMBDA(int i) {
@@ -132,8 +124,7 @@ void Axis::RegularizeCurrentSide(int side) {
 
     idefix_for("fixJ",0,data->np_tot[KDIR],0,data->np_tot[IDIR],
         KOKKOS_LAMBDA(int k,int i) {
-          real th = x2(jc);
-          real fact = 2*sign/(deltaPhi*x1(i)*sin(th));
+          real fact = 2*sign/(deltaPhi*x1(i)*dx2(jc));
           J(IDIR, k,js,i) = BAvg(i)*fact;
         });
 

src/fluid/calcRightHandSide.hpp

@@ -363,7 +363,7 @@ struct Fluid_CalcRHSFunctor {
         #if (GEOMETRY == SPHERICAL) && (COMPONENTS == 3)
           rhs[iMPHI] /= FABS(sinx2(j));
           if constexpr(Phys::mhd) {
-            rhs[iBPHI] = -dt / (rt(i)*dx(j)) * (Flux(iBPHI, k, j+1, i) - Flux(iBPHI, k, j, i));
+            rhs[iBPHI] = -dt / (x1(i)*dx(j)) * (Flux(iBPHI, k, j+1, i) - Flux(iBPHI, k, j, i));
           } // MHD
         #endif // GEOMETRY
       }

test/IO/pydefix/README.md

@@ -42,3 +42,10 @@ export pybind11_DIR=env/lib/python3.10/site-packages/pybind11
 ```
 
 you can then run cmake which should be able to find pybind11, and compile the code.
+
+If while running the code using a python interpreter in an environment, you run into errors stating that some module
+installed in your environement is not present. This is because pybind11 does not always capture your venv. You need to force the following environement variables (replace XX by your python version)
+
+```bash
+export PYTHONPATH=$VIRTUAL_ENV/lib/python3.XX/site-packages:$PYTHONPATH
+```