Merge branch 'dev' into fix-coarsens

.github/workflows/generate-reference-data.yml

@@ -30,7 +30,7 @@ jobs:
     - uses: ursg/gcc-problem-matcher@master
     - name: Compile vlasiator (Testpackage build)
       run: |
-        srun -M carrington --job-name CI_ref_tp_compile --interactive --nodes=1 -n 1 -c 16 --mem=40G -p short -t 0:10:0 bash -c 'module purge; module load GCC/11.2.0; module load OpenMPI/4.1.1-GCC-11.2.0 ; module load PMIx/4.1.0-GCCcore-11.2.0; module load PAPI/6.0.0.1-GCCcore-11.2.0; export VLASIATOR_ARCH=carrington_gcc_openmpi; make -j 16 testpackage; sleep 10s'
+        srun -M carrington --job-name CI_ref_tp_compile --interactive --nodes=1 -n 1 -c 16 --mem=40G -p short -t 0:10:0 bash -c 'module purge; module load GCC/13.2.0; module load OpenMPI/4.1.6-GCC-13.2.0 ; module load PMIx/4.2.6-GCCcore-13.2.0; module load PAPI/7.1.0-GCCcore-13.2.0; export VLASIATOR_ARCH=carrington_gcc_openmpi; make -j 16 testpackage; sleep 10s'
     - name: Make sure the output binary is visible in lustre
       uses: nick-fields/retry@v3
       with:
@@ -59,7 +59,7 @@ jobs:
     - name: Checkout source
       uses: actions/checkout@v4
       with:
-        submodules: true
+        submodules: false
     - name: Download testpackage binary
       uses: actions/download-artifact@v4
       with:

.github/workflows/github-ci.yml

@@ -18,7 +18,7 @@ jobs:
     # Build libraries for the current version of the docker image
     # (to be used in any subsequent compilation and run jobs on said image)
     runs-on: ubuntu-latest
-    container: ursg/vlasiator_ci:20240131_1
+    container: ursg/vlasiator_ci:20241101_1
 
     steps:
       - name: Checkout source
@@ -98,7 +98,7 @@ jobs:
   build_production:
     # Build Vlasiator with production flags
     runs-on: ubuntu-latest
-    container: ursg/vlasiator_ci:20240131_1
+    container: ursg/vlasiator_ci:20241101_1
     needs: build_libraries
 
     steps:
@@ -124,6 +124,64 @@ jobs:
         path: vlasiator
         if-no-files-found: error
 
+  build_production_1st_order_time:
+    # Build Vlasiator with production flags
+    runs-on: ubuntu-latest
+    container: ursg/vlasiator_ci:20241101_1
+    needs: build_libraries
+
+    steps:
+    - name: Checkout source
+      uses: actions/checkout@v4
+      with:
+        submodules: true
+    - name: Download libraries
+      uses: actions/download-artifact@v4
+      with:
+        name: libraries
+    - name: Unpack libraries
+      run: tar --zstd -xvf libraries.tar.zstd
+    - uses: ursg/gcc-problem-matcher@master
+    - name: Compile vlasiator (Release build)
+      run: |
+        VLASIATOR_ARCH=github_actions make clean
+        VLASIATOR_ARCH=github_actions COMPFLAGS="-DFS_1ST_ORDER_TIME " make -j 3
+    - name: Upload release binary
+      uses: actions/upload-artifact@v4
+      with:
+        name: vlasiator-1st_order_time
+        path: vlasiator
+        if-no-files-found: error
+
+  build_production_1st_order_space:
+    # Build Vlasiator with production flags
+    runs-on: ubuntu-latest
+    container: ursg/vlasiator_ci:20241101_1
+    needs: build_libraries
+
+    steps:
+    - name: Checkout source
+      uses: actions/checkout@v4
+      with:
+        submodules: true
+    - name: Download libraries
+      uses: actions/download-artifact@v4
+      with:
+        name: libraries
+    - name: Unpack libraries
+      run: tar --zstd -xvf libraries.tar.zstd
+    - uses: ursg/gcc-problem-matcher@master
+    - name: Compile vlasiator (Release build)
+      run: |
+        VLASIATOR_ARCH=github_actions make clean
+        VLASIATOR_ARCH=github_actions COMPFLAGS="-DFS_1ST_ORDER_SPACE " make -j 3
+    - name: Upload release binary
+      uses: actions/upload-artifact@v4
+      with:
+        name: vlasiator-1st_order_space
+        path: vlasiator
+        if-no-files-found: error
+
 
   build_testpackage:
     # Build Vlasiator with testpackage flags, on the carrington cluster
@@ -339,7 +397,7 @@ jobs:
   build_ionosphereTests:
     # Build IonosphereSolverTests miniApp
     runs-on: ubuntu-latest
-    container: ursg/vlasiator_ci:20240131_1
+    container: ursg/vlasiator_ci:20241101_1
     needs: build_libraries
     steps:
     - name: Checkout source
@@ -375,7 +433,7 @@ jobs:
 
   run_ionosphere_LFMtest:
     runs-on: ubuntu-latest
-    container: ursg/vlasiator_ci:20240131_1
+    container: ursg/vlasiator_ci:20241101_1
     needs: build_ionosphereTests
     steps:
     - name: Checkout source
@@ -420,7 +478,7 @@ jobs:
 
   check_cfg_files:
     runs-on: ubuntu-latest
-    container: ursg/vlasiator_ci:20240131_1
+    container: ursg/vlasiator_ci:20241101_1
     needs: [build_libraries, build_production]
     steps:
     - name: Checkout source

build_libraries.sh

@@ -57,7 +57,7 @@ if [[ $PLATFORM != "-arriesgado" && $PLATFORM != "-appleM1" ]]; then  # This fai
 fi
 
 # Build jemalloc
-wget https://github.com/jemalloc/jemalloc/releases/download/5.3.0/jemalloc-5.3.0.tar.bz2
+curl -O -L https://github.com/jemalloc/jemalloc/releases/download/5.3.0/jemalloc-5.3.0.tar.bz2
 tar xjf jemalloc-5.3.0.tar.bz2
 cd jemalloc-5.3.0
 ./configure --prefix=$WORKSPACE/libraries${PLATFORM} --with-jemalloc-prefix=je_ && make -j 4 && make install

common.h

@@ -165,15 +165,27 @@ namespace CellParams {
       P_11,     /*!< Pressure P_xx component, computed by Vlasov propagator. */
       P_22,     /*!< Pressure P_yy component, computed by Vlasov propagator. */
       P_33,     /*!< Pressure P_zz component, computed by Vlasov propagator. */
+      P_23,     /*!< Pressure P_yz component, computed by Vlasov propagator. */
+      P_13,     /*!< Pressure P_xz component, computed by Vlasov propagator. */
+      P_12,     /*!< Pressure P_xy component, computed by Vlasov propagator. */
       P_11_DT2, /*!< Intermediate step value for RK2 time stepping in field solver. Computed from P_11_R and P_11_V. */
       P_22_DT2, /*!< Intermediate step value for RK2 time stepping in field solver. Computed from P_22_R and P_22_V. */
       P_33_DT2, /*!< Intermediate step value for RK2 time stepping in field solver. Computed from P_33_R and P_33_V. */
+      P_23_DT2, /*!< Intermediate step value for RK2 time stepping in field solver. Computed from P_23_R and P_23_V. */
+      P_13_DT2, /*!< Intermediate step value for RK2 time stepping in field solver. Computed from P_13_R and P_13_V. */
+      P_12_DT2, /*!< Intermediate step value for RK2 time stepping in field solver. Computed from P_12_R and P_12_V. */
       P_11_R,   /*!< P_xx component after propagation in ordinary space */
       P_22_R,   /*!< P_yy component after propagation in ordinary space */
       P_33_R,   /*!< P_zz component after propagation in ordinary space */
+      P_23_R,   /*!< P_yz component after propagation in ordinary space */
+      P_13_R,   /*!< P_xz component after propagation in ordinary space */
+      P_12_R,   /*!< P_xy component after propagation in ordinary space */
       P_11_V,   /*!< P_xx component after propagation in velocity space */
       P_22_V,   /*!< P_yy component after propagation in velocity space */
       P_33_V,   /*!< P_zz component after propagation in velocity space */
+      P_23_V,   /*!< P_yz component after propagation in velocity space */
+      P_12_V,   /*!< P_xy component after propagation in velocity space */
+      P_13_V,   /*!< P_xz component after propagation in velocity space */
       EXVOL,    /*!< Volume electric field averaged over spatial cell, x-component.*/
       EYVOL,    /*!< Volume electric field averaged over spatial cell, y-component.*/
       EZVOL,    /*!< Volume electric field averaged over spatial cell, z-component.*/
@@ -209,11 +221,12 @@ namespace CellParams {
       AMR_DB,
       AMR_ALPHA1,
       AMR_ALPHA2,
+      P_ANISOTROPY,
+      AMR_VORTICITY,
       RECENTLY_REFINED,
       BULKV_FORCING_X, /*! Externally forced drift velocity (ex. from the ionosphere) */
       BULKV_FORCING_Y, /*! Externally forced drift velocity (ex. from the ionosphere) */
       BULKV_FORCING_Z, /*! Externally forced drift velocity (ex. from the ionosphere) */
-      FORCING_CELL_NUM, /*! Number of boundary cells that have forced a bulkv here */
       N_SPATIAL_CELL_PARAMS
    };
 }
@@ -236,6 +249,22 @@ namespace bvolderivatives {
    };
 }
 
+namespace vderivatives {
+   // Essentially a copy from dmoments
+   enum {
+      dVxdx,     /*!< Derivative of volume-averaged Vx to x-direction. */
+      dVxdy,     /*!< Derivative of volume-averaged Vx to y-direction. */
+      dVxdz,     /*!< Derivative of volume-averaged Vx to z-direction. */
+      dVydx,     /*!< Derivative of volume-averaged Vy to x-direction. */
+      dVydy,     /*!< Derivative of volume-averaged Vy to y-direction. */
+      dVydz,     /*!< Derivative of volume-averaged Vy to z-direction. */
+      dVzdx,     /*!< Derivative of volume-averaged Vz to x-direction. */
+      dVzdy,     /*!< Derivative of volume-averaged Vz to y-direction. */
+      dVzdz,     /*!< Derivative of volume-averaged Vz to z-direction. */
+      N_V_DERIVATIVES
+   };
+}
+
 // FsGrid< std::array<Real, fsgrids::bfield::N_BFIELD>, FS_STENCIL_WIDTH> & perBGrid,
 // FsGrid< std::array<Real, fsgrids::bfield::N_BFIELD>, FS_STENCIL_WIDTH> & perBDt2Grid,
 // FsGrid< std::array<Real, fsgrids::efield::N_EFIELD>, FS_STENCIL_WIDTH> & EGrid,

datareduction/datareducer.cpp

@@ -2962,7 +2962,21 @@ void initializeDataReducers(DataReducer * outputReducer, DataReducer * diagnosti
       }
       if(P::systemWriteAllDROs || lowercase == "vg_amr_alpha2") {
          outputReducer->addOperator(new DRO::DataReductionOperatorCellParams("vg_amr_alpha2",CellParams::AMR_ALPHA2,1));
-         outputReducer->addMetadata(outputReducer->size()-1,"","","$\\alpha_2","");
+         outputReducer->addMetadata(outputReducer->size()-1,"","","$\\alpha_2$","");
+         if(!P::systemWriteAllDROs) {
+            continue;
+         }
+      }
+      if(P::systemWriteAllDROs || lowercase == "vg_pressure_anisotropy") {
+         outputReducer->addOperator(new DRO::DataReductionOperatorCellParams("vg_pressure_anisotropy",CellParams::P_ANISOTROPY,1));
+         outputReducer->addMetadata(outputReducer->size()-1,"","","$P_\\perp / P_\\parallel$","");
+         if(!P::systemWriteAllDROs) {
+            continue;
+         }
+      }
+      if(P::systemWriteAllDROs || lowercase == "vg_amr_vorticity") {
+         outputReducer->addOperator(new DRO::DataReductionOperatorCellParams("vg_amr_vorticity",CellParams::AMR_VORTICITY,1));
+         outputReducer->addMetadata(outputReducer->size()-1,"","","Vorticity","");
          if(!P::systemWriteAllDROs) {
             continue;
          }