Particle Tracking + Refactored IO

cmake/adios2Config.cmake

@@ -13,7 +13,7 @@ set(ADIOS2_USE_Fortran
 
 # Format/compression support
 set(ADIOS2_USE_HDF5
-    ON
+    OFF
     CACHE BOOL "Use HDF5 for ADIOS2")
 
 set(ADIOS2_USE_MPI

cmake/benchmark.cmake

@@ -20,7 +20,7 @@ add_executable(${exec} ${src})
 
 set(libs ntt_global ntt_metrics ntt_kernels ntt_archetypes ntt_framework)
 if(${output})
-  list(APPEND libs ntt_output ntt_checkpoint)
+  list(APPEND libs ntt_output)
 endif()
 add_dependencies(${exec} ${libs})
 target_link_libraries(${exec} PRIVATE ${libs} stdc++fs)

cmake/tests.cmake

@@ -9,9 +9,6 @@ add_subdirectory(${SRC_DIR}/kernels ${CMAKE_CURRENT_BINARY_DIR}/kernels)
 add_subdirectory(${SRC_DIR}/archetypes ${CMAKE_CURRENT_BINARY_DIR}/archetypes)
 add_subdirectory(${SRC_DIR}/framework ${CMAKE_CURRENT_BINARY_DIR}/framework)
 add_subdirectory(${SRC_DIR}/output ${CMAKE_CURRENT_BINARY_DIR}/output)
-if(${output})
-  add_subdirectory(${SRC_DIR}/checkpoint ${CMAKE_CURRENT_BINARY_DIR}/checkpoint)
-endif()
 
 set(TEST_DIRECTORIES "")
 
@@ -27,10 +24,6 @@ endif()
 
 list(APPEND TEST_DIRECTORIES output)
 
-if(${output})
-  list(APPEND TEST_DIRECTORIES checkpoint)
-endif()
-
 foreach(test_dir IN LISTS TEST_DIRECTORIES)
   add_subdirectory(${SRC_DIR}/${test_dir}/tests
                    ${CMAKE_CURRENT_BINARY_DIR}/${test_dir}/tests)

dev/nix/adios2.nix

@@ -19,7 +19,7 @@ let
     BUILD_TESTING = "OFF";
     ADIOS2_BUILD_EXAMPLES = "OFF";
     ADIOS2_USE_MPI = if mpi then "ON" else "OFF";
-    ADIOS2_HAVE_HDF5_VOL = if mpi then "ON" else "OFF";
+    ADIOS2_HAVE_HDF5_VOL = if (mpi && hdf5) then "ON" else "OFF";
     CMAKE_BUILD_TYPE = "Release";
   };
   stdenv = pkgs.gcc13Stdenv;
@@ -40,8 +40,27 @@ stdenv.mkDerivation {
 
   propagatedBuildInputs = [
     pkgs.gcc13
-  ] ++ (if hdf5 then (if mpi then [ pkgs.hdf5-mpi ] else [ pkgs.hdf5-cpp ]) else [ ]);
-  # ++ (if mpi then [ pkgs.openmpi ] else [ ]);
+  ]
+  ++ (
+    if hdf5 then
+      (
+        if mpi then
+          [
+            pkgs.hdf5-mpi
+          ]
+        else
+          [ pkgs.hdf5-cpp ]
+      )
+    else
+      (
+        if mpi then
+          [
+            pkgs.mpi
+          ]
+        else
+          [ ]
+      )
+  );
 
   configurePhase = ''
     cmake -B build $src ${

dev/nix/kokkos.nix

@@ -7,7 +7,7 @@
 
 let
   name = "kokkos";
-  pversion = "4.6.01";
+  pversion = "4.7.01";
   compilerPkgs = {
     "HIP" = with pkgs.rocmPackages; [
       llvm.rocm-merged-llvm
@@ -56,7 +56,7 @@ pkgs.stdenv.mkDerivation rec {
   src = pkgs.fetchgit {
     url = "https://github.com/kokkos/kokkos/";
     rev = "${pversion}";
-    sha256 = "sha256-+yszUbdHqhIkJZiGLZ9Ln4DYUosuJWKhO8FkbrY0/tY=";
+    sha256 = "sha256-MgphOsKE8umgYxVQZzex+elgvDDC09JaMCoU5YXaLco=";
   };
 
   nativeBuildInputs = with pkgs; [
@@ -92,15 +92,4 @@ pkgs.stdenv.mkDerivation rec {
   installPhase = ''
     cmake --install build
   '';
-
-  # cmakeFlags = [
-  #   "-D CMAKE_CXX_STANDARD=17"
-  #   "-D CMAKE_CXX_EXTENSIONS=OFF"
-  #   "-D CMAKE_POSITION_INDEPENDENT_CODE=TRUE"
-  #   "-D Kokkos_ARCH_${getArch { }}=ON"
-  #   (if gpu != "none" then "-D Kokkos_ENABLE_${gpu}=ON" else "")
-  #   "-D CMAKE_BUILD_TYPE=Release"
-  # ] ++ (cmakeExtraFlags.${gpu} src);
-
-  # enableParallelBuilding = true;
 }

dev/nix/shell.nix

@@ -5,7 +5,7 @@
   },
   gpu ? "NONE",
   arch ? "NATIVE",
-  hdf5 ? true,
+  hdf5 ? false,
   mpi ? false,
 }:
 
@@ -62,27 +62,26 @@ pkgs.mkShell {
     pkgs.zlib
   ]);
 
-  shellHook =
-    ''
-      BLUE='\033[0;34m'
-      NC='\033[0m'
+  shellHook = ''
+    BLUE='\033[0;34m'
+    NC='\033[0m'
 
-      echo "following environment variables are set:"
-    ''
-    + pkgs.lib.concatStringsSep "" (
-      pkgs.lib.mapAttrsToList (
-        category: vars:
-        pkgs.lib.concatStringsSep "" (
-          pkgs.lib.mapAttrsToList (name: value: ''
-            export ${name}=${value}
-            echo -e "  ''\${BLUE}${name}''\${NC}=${value}"
-          '') vars.${gpuUpper}
-        )
-      ) envVars
-    )
-    + ''
-      echo ""
-      echo -e "${name} nix-shell activated"
-    '';
+    echo "following environment variables are set:"
+  ''
+  + pkgs.lib.concatStringsSep "" (
+    pkgs.lib.mapAttrsToList (
+      category: vars:
+      pkgs.lib.concatStringsSep "" (
+        pkgs.lib.mapAttrsToList (name: value: ''
+          export ${name}=${value}
+          echo -e "  ''\${BLUE}${name}''\${NC}=${value}"
+        '') vars.${gpuUpper}
+      )
+    ) envVars
+  )
+  + ''
+    echo ""
+    echo -e "${name} nix-shell activated"
+  '';
 
 }

input.example.toml

@@ -302,10 +302,19 @@
     #   @default: "Boris" [massive]; "Photon" [massless]
     #   @enum: "Boris", "Vay", "Boris,GCA", "Vay,GCA", "Photon", "None"
     pusher = ""
-    # Number of additional (payload) variables for each particle of the given species
+    # Number of additional real-valued variables (payloads) for each particle of the given species
     #   @type: ushort
     #   @default: 0
-    n_payloads = ""
+    n_payloads_real = ""
+    # Number of additional integer-valued variables (payloads) for each particle of the given species
+    #   @type: ushort
+    #   @default: 0
+    #   @note: If tracking is enabled, one or two extra integer payloads are reserved (depending on whether MPI is enabled)
+    n_payloads_int = ""
+    # Enable tracking of particles using indices for the given species
+    #   @type: bool
+    #   @default: false
+    tracking = ""
     # Radiation reaction to use for the species
     #   @type: string
     #   @default: "None"

src/CMakeLists.txt

@@ -33,10 +33,6 @@ add_subdirectory(${SRC_DIR}/framework ${CMAKE_CURRENT_BINARY_DIR}/framework)
 add_subdirectory(${SRC_DIR}/engines ${CMAKE_CURRENT_BINARY_DIR}/engines)
 add_subdirectory(${SRC_DIR}/output ${CMAKE_CURRENT_BINARY_DIR}/output)
 
-if(${output})
-  add_subdirectory(${SRC_DIR}/checkpoint ${CMAKE_CURRENT_BINARY_DIR}/checkpoint)
-endif()
-
 set(ENTITY ${PROJECT_NAME}.xc)
 set(SOURCES ${SRC_DIR}/entity.cpp)