fix merge with master

add changelog
fix test suite for -noplot

CHANGELOG.md

@@ -27,10 +27,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - fixed a bug that led to race condition when using GPU offloading, axis boundary condition and domain decomposition along X3 (!309)
 - fixed a bug that led to inconsistent results with MPI and UCT_HLLx EMF reconstruction schemes (!310)
 - fixed a bug that could result in .dmp file duplication on restart (!354)
+- Moving developement onto github.com. Some references to merge requests will likely be lost.
 - fixed a bug in v2.0 developement branch that resulted in broekn dump files when MHD was enabled with DIMENSIONS<3 (#174)
 - IDEFIX_Debug now automatically introduce Kokkos::fence at the end of each idefix_for, enforcing synchronisation between host and device when debugging (#188)
-- Moving developement onto github.com. Some references to merge requests will likely be lost.
 - Do not use git lfs anymore due to bandwidth restrictions imposed by github (#183)
+- use proper cell centroid PLM reconstruction when using non-cartesian coordinates (#196)
+- fixed a bug that could lead to low (O(1e-10)) leakage of conserved quantities along the axis (#196)
+- changed radial pressure curvature term so that machine precision balance is achieved for constant pressure flows in every geometry (#196)
 
 ### Added
 - Self-gravity (!186)

pytools/idfx_test.py

@@ -28,7 +28,7 @@ def __init__ (self):
     idefix_dir_env = os.getenv("IDEFIX_DIR")
 
     parser.add_argument("-noplot",
-                        dest="plot",
+                        dest="noplot",
                         help="disable plotting in standard tests",
                         action="store_false")
 

src/fluid/fluid.hpp

@@ -15,12 +15,15 @@
 #include "idefix.hpp"
 #include "grid.hpp"
 #include "fluid_defs.hpp"
+#include "eos.hpp"
 #include "thermalDiffusion.hpp"
 #include "bragThermalDiffusion.hpp"
 #include "selfGravity.hpp"
 #include "vtk.hpp"
 #include "dump.hpp"
-#include "eos.hpp"
+#ifdef WITH_HDF5
+#include "xdmf.hpp"
+#endif
 
 // forward class declaration
 class DataBlock;

src/output/output.cpp

@@ -11,7 +11,6 @@
 #include "fluid.hpp"
 #include "slice.hpp"
 
-
 Output::Output(Input &input, DataBlock &data) {
   idfx::pushRegion("Output::Output");
   // initialise the output objects for each format
@@ -66,24 +65,6 @@ Output::Output(Input &input, DataBlock &data) {
     }
   }
 
-
-  // Initialise xdmf outputs
-  if(input.CheckEntry("Output","xdmf")>0) {
-    xdmfPeriod = input.Get<real>("Output","xdmf",0);
-    if(xdmfPeriod>=0.0) {  // backward compatibility (negative value means no file)
-      xdmfLast = data.t - xdmfPeriod; // write something in the next CheckForWrite()
-      #ifdef WITH_HDF5
-      xdmfEnabled = true;
-      #else
-      xdmfEnabled = false;
-      IDEFIX_ERROR("Attention: HDF5 library not linked when building Idefix!");
-      #endif
-    }
-  }
-  #ifdef WITH_HDF5
-  xdmf.Init(input,data); // Always initialised in case of emergency xdmf output
-  #endif
-
   // intialise dump outputs
   if(input.CheckEntry("Output","dmp")>0) {
     dumpPeriod = input.Get<real>("Output","dmp",0);
@@ -120,6 +101,9 @@ Output::Output(Input &input, DataBlock &data) {
   data.dump->RegisterVariable(&dumpLast, "dumpLast");
   data.dump->RegisterVariable(&analysisLast, "analysisLast");
   data.dump->RegisterVariable(&vtkLast, "vtkLast");
+  #ifdef WITH_HDF5
+  data.dump->RegisterVariable(&xdmfLast, "xdmfLast");
+  #endif
 
   idfx::popRegion();
 }
@@ -312,29 +296,6 @@ void Output::ForceWriteXdmf(DataBlock &data) {
 }
 #endif
 
-#ifdef WITH_HDF5
-void Output::ForceWriteXdmf(DataBlock &data) {
-  idfx::pushRegion("Output::ForceWriteXdmf");
-
-  if(!forceNoWrite) {
-    if(userDefVariablesEnabled) {
-        if(haveUserDefVariablesFunc) {
-          // Call user-def function to fill the userdefined variable arrays
-          idfx::pushRegion("UserDef::User-defined variables function");
-          userDefVariablesFunc(data, userDefVariables);
-          idfx::popRegion();
-        } else {
-          IDEFIX_ERROR("Cannot output user-defined variables without "
-                        "enrollment of your user-defined variables function");
-        }
-      }
-      xdmfLast += xdmfPeriod;
-      xdmf.Write(data, *this);
-  }
-  idfx::popRegion();
-}
-#endif
-
 void Output::EnrollAnalysis(AnalysisFunc myFunc) {
   idfx::pushRegion("Output::EnrollAnalysis");
   if(!analysisEnabled) {

src/output/xdmf.cpp

@@ -185,7 +185,6 @@ Xdmf::Xdmf(Input &input, DataBlock *datain) {
           D_EXPAND( x1_cell = grid.x[IDIR](i + data->gbeg[IDIR]);  ,
                     x2_cell = grid.x[JDIR](j + data->gbeg[JDIR]);  ,
                     x3_cell = grid.x[KDIR](k + data->gbeg[KDIR]);  )
-
         }
         #if (GEOMETRY == CARTESIAN) || (GEOMETRY == CYLINDRICAL)
         node_coord(0,k,j,i) = x1;
@@ -251,7 +250,6 @@ Xdmf::Xdmf(Input &input, DataBlock *datain) {
     this->mpi_data_start[dir] = data->gbeg[2-dir]-grid.nghost[2-dir];
     this->mpi_data_size[dir] = grid.np_int[2-dir];
     this->mpi_data_subsize[dir] = data->np_int[2-dir];
-
   }
   #elif (DIMENSIONS == 2)
   for(int dir = 0; dir < DIMENSIONS ; dir++) {

src/output/xdmf.hpp

@@ -8,7 +8,6 @@
 #ifndef OUTPUT_XDMF_HPP_
 #define OUTPUT_XDMF_HPP_
 #include <string>
-
 #include <filesystem>
 #include <map>
 #include "idefix.hpp"
@@ -30,7 +29,6 @@
 class Output;
 class DataBlock;
 
-
 class Xdmf {
   friend class Dump;
 
@@ -123,5 +121,4 @@ void Xdmf::RegisterVariable(T& in, std::string name, int var) {
     xdmfScalarMap.emplace(name, ScalarField(in, var));
   }
 }
-
 #endif // OUTPUT_XDMF_HPP_