Add bulk velocity as moments to output

.github/workflows/actions.yml

@@ -1,27 +1,39 @@
 name: Unit tests
 
 on:
-  pull_request:
-    branches:
-      - '**rc'
-      - 'master'
+  push:
 
 jobs:
+  check-commit:
+    runs-on: ubuntu-latest
+    outputs:
+      run_tests: ${{ steps.check_message.outputs.run_tests }}
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+      - name: Check commit message
+        id: check_message
+        run: |
+          if git log -1 --pretty=%B | grep -q "RUNTEST"; then
+            echo "run_tests=true" >> "$GITHUB_OUTPUT"
+          else
+            echo "run_tests=false" >> "$GITHUB_OUTPUT"
+          fi
   tests:
+    needs: check-commit
+    if: needs.check-commit.outputs.run_tests == 'true'
     strategy:
       fail-fast: false
       matrix:
-        device: [amd-gpu, nvidia-gpu]
+        device: [cpu, amd-gpu, nvidia-gpu]
         precision: [double, single]
-        exclude: 
+        exclude: # my AMD GPU doesn't support fp64 atomics : (
         - device: amd-gpu 
           precision: double
-        # my AMD GPU doesn't support fp64 atomics : (
     runs-on: [self-hosted, "${{ matrix.device }}"]
-    if: contains(github.event.head_commit.message, 'totest')
     steps:
       - name: Checkout
-        uses: actions/checkout@v3.3.0
+        uses: actions/checkout@v4
       - name: Configure
         run: |
           if [ "${{ matrix.device }}" = "nvidia-gpu" ]; then
@@ -35,6 +47,8 @@ jobs:
             fi
           elif [ "${{ matrix.device }}" = "amd-gpu" ]; then
             FLAGS="-D Kokkos_ENABLE_HIP=ON -D Kokkos_ARCH_AMD_GFX1100=ON"
+          elif [ "${{ matrix.device }}" = "cpu" ]; then
+            FLAGS="-D mpi=ON"
           fi
           cmake -B build -D TESTS=ON -D output=ON -D precision=${{ matrix.precision }} $FLAGS
       - name: Compile

.gitignore

@@ -51,6 +51,8 @@ venv/
 # CMake testing files
 Testing/
 
+tags
+.clangd
 .schema.json
 *_old/
 action-token

.taplo.toml

@@ -0,0 +1,6 @@
+[formatting]
+  align_entries    = true
+  indent_tables    = true
+  indent_entries   = true
+  trailing_newline = true
+  align_comments   = true

CMakeLists.txt

@@ -8,12 +8,13 @@ project(
   VERSION 1.2.0
   LANGUAGES CXX C)
 add_compile_options("-D ENTITY_VERSION=\"${PROJECT_VERSION}\"")
-execute_process(COMMAND
-  bash -c "git diff --quiet src/ && echo $(git rev-parse HEAD) || echo $(git rev-parse HEAD)-mod"
+execute_process(
+  COMMAND
+    bash -c
+    "git diff --quiet src/ && echo $(git rev-parse HEAD) || echo $(git rev-parse HEAD)-mod"
   WORKING_DIRECTORY "${CMAKE_SOURCE_DIR}"
   OUTPUT_VARIABLE GIT_HASH
-  ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE
-)
+  ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE)
 message(STATUS "Git hash: ${GIT_HASH}")
 add_compile_options("-D ENTITY_GIT_HASH=\"${GIT_HASH}\"")
 
@@ -25,56 +26,57 @@ include(${CMAKE_CURRENT_SOURCE_DIR}/cmake/defaults.cmake)
 
 # defaults
 set(DEBUG
-  ${default_debug}
-  CACHE BOOL "Debug mode")
+    ${default_debug}
+    CACHE BOOL "Debug mode")
 
 set(precision
-  ${default_precision}
-  CACHE STRING "Precision")
+    ${default_precision}
+    CACHE STRING "Precision")
 set(pgen
-  ${default_pgen}
-  CACHE STRING "Problem generator")
+    ${default_pgen}
+    CACHE STRING "Problem generator")
 
 set(gui
-  ${default_gui}
-  CACHE BOOL "Use GUI [nttiny]")
+    ${default_gui}
+    CACHE BOOL "Use GUI [nttiny]")
 set(output
-  ${default_output}
-  CACHE BOOL "Enable output")
+    ${default_output}
+    CACHE BOOL "Enable output")
 set(mpi
-  ${default_mpi}
-  CACHE BOOL "Use MPI")
+    ${default_mpi}
+    CACHE BOOL "Use MPI")
 
 # -------------------------- Compilation settings -------------------------- #
 set(CMAKE_CXX_STANDARD 17)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
+set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
 
 if(${DEBUG} STREQUAL "OFF")
   set(CMAKE_BUILD_TYPE
-    Release
-    CACHE STRING "CMake build type")
-  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DNDEBUG")
+      Release
+      CACHE STRING "CMake build type")
+  set(CMAKE_CXX_FLAGS
+      "${CMAKE_CXX_FLAGS} -DNDEBUG -Wno-unused-local-typedefs -Wno-unknown-cuda-version"
+  )
 else()
   set(CMAKE_BUILD_TYPE
-    Debug
-    CACHE STRING "CMake build type")
+      Debug
+      CACHE STRING "CMake build type")
   set(CMAKE_CXX_FLAGS
-    "${CMAKE_CXX_FLAGS} -DDEBUG -Wall -Wextra -Wno-unknown-pragmas")
+      "${CMAKE_CXX_FLAGS} -DDEBUG -Wall -Wextra -Wno-unknown-pragmas")
 endif()
 
-set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-unused-local-typedefs")
-
 # options
 set(precisions
-  "single" "double"
-  CACHE STRING "Precisions")
+    "single" "double"
+    CACHE STRING "Precisions")
 
 include(${CMAKE_CURRENT_SOURCE_DIR}/cmake/config.cmake)
 
 # ------------------------- Third-Party Tests ------------------------------ #
 set(BUILD_TESTING
-  OFF
-  CACHE BOOL "Build tests")
+    OFF
+    CACHE BOOL "Build tests")
 
 # ------------------------ Third-party dependencies ------------------------ #
 include(${CMAKE_CURRENT_SOURCE_DIR}/cmake/kokkosConfig.cmake)
@@ -98,21 +100,13 @@ endif()
 if(${output})
   include(${CMAKE_CURRENT_SOURCE_DIR}/cmake/adios2Config.cmake)
   find_or_fetch_dependency(adios2 FALSE)
-  if (NOT DEFINED ENV{HDF5_ROOT})
-    set(USE_CUSTOM_HDF5 OFF)
-    if (DEFINED ENV{CONDA_PREFIX})
+  if(NOT DEFINED ENV{HDF5_ROOT})
+    if(DEFINED ENV{CONDA_PREFIX})
       execute_process(COMMAND bash -c "conda list | grep \"hdf5\" -q"
-        RESULT_VARIABLE HDF5_INSTALLED)
-      if (HDF5_INSTALLED EQUAL 0)
+                      RESULT_VARIABLE HDF5_INSTALLED)
+      if(HDF5_INSTALLED EQUAL 0)
         set(HDF5_ROOT $ENV{CONDA_PREFIX})
-      else()
-        set(USE_CUSTOM_HDF5 ON)
       endif()
-    else()
-      set(USE_CUSTOM_HDF5 ON)
-    endif()
-    if (USE_CUSTOM_HDF5)
-      message(FATAL_ERROR "HDF5_ROOT is not set. Please set it to the root of the HDF5 installation")
     endif()
   endif()
   find_package(HDF5 REQUIRED)
@@ -129,6 +123,9 @@ link_libraries(${DEPENDENCIES})
 if(TESTS)
   # ---------------------------------- Tests --------------------------------- #
   include(${CMAKE_CURRENT_SOURCE_DIR}/cmake/tests.cmake)
+elseif(BENCHMARK)
+  # ------------------------------ Benchmark --------------------------------- #
+  include(${CMAKE_CURRENT_SOURCE_DIR}/cmake/benchmark.cmake)
 else()
   # ----------------------------------- GUI ---------------------------------- #
   if(${gui})

README.md

@@ -10,21 +10,29 @@ Our [detailed documentation](https://entity-toolkit.github.io/) includes everyth
 
 [![License](https://img.shields.io/badge/License-BSD%203--Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause)
 
-## Core developers (alphabetical)
+## Lead developers
 
-👀 __Yangyang Cai__ {[@StaticObserver](https://github.com/StaticObserver): GRPIC}
+☕ __Hayk Hakobyan__ {[@haykh](https://github.com/haykh)}
 
-💁‍♂️ __Alexander Chernoglazov__ {[@SChernoglazov](https://github.com/SChernoglazov): PIC}
+🥔 __Jens Mahlmann__ {[@jmahlmann](https://github.com/jmahlmann)}
 
-🍵 __Benjamin Crinquand__ {[@bcrinquand](https://github.com/bcrinquand): GRPIC, cubed-sphere}
+💁‍♂️ __Alexander Chernoglazov__ {[@SChernoglazov](https://github.com/SChernoglazov)}
+
+🧋 __Alisa Galishnikova__ {[@alisagk](https://github.com/alisagk)}
+
+🐬 __Sasha Philippov__ {[@sashaph](https://github.com/sashaph)}
 
-🧋 __Alisa Galishnikova__ {[@alisagk](https://github.com/alisagk): GRPIC}
+## Contributors (alphabetical)
 
-☕ __Hayk Hakobyan__ {[@haykh](https://github.com/haykh): framework, PIC, GRPIC, cubed-sphere}
+🎸 __Ludwig Böss__ {[@LudwigBoess](https://github.com/LudwigBoess): PIC, framework}
+
+👀 __Yangyang Cai__ {[@StaticObserver](https://github.com/StaticObserver): GRPIC}
+
+🍵 __Benjamin Crinquand__ {[@bcrinquand](https://github.com/bcrinquand): GRPIC, cubed-sphere}
 
-🥔 __Jens Mahlmann__ {[@jmahlmann](https://github.com/jmahlmann): framework, MPI, cubed-sphere}
+🚂 __Evgeny Gorbunov__ {[@Alcauchy](https://github.com/Alcauchy): PIC, framework}
 
-🐬 __Sasha Philippov__ {[@sashaph](https://github.com/sashaph): all-around}
+:radio: __Siddhant Solanki__ {[@sidruns30](https://github.com/sidruns30): framework}
 
 🤷 __Arno Vanthieghem__ {[@vanthieg](https://github.com/vanthieg): framework, PIC}
 

benchmark/benchmark.cpp

@@ -0,0 +1,17 @@
+#include "global.h"
+
+#include <iostream>
+#include <stdexcept>
+
+auto main(int argc, char* argv[]) -> int {
+  ntt::GlobalInitialize(argc, argv);
+  try {
+    // ...
+  } catch (const std::exception& e) {
+    std::cerr << "Error: " << e.what() << std::endl;
+    GlobalFinalize();
+    return 1;
+  }
+  GlobalFinalize();
+  return 0;
+}

cmake/MPIConfig.cmake

@@ -1,3 +1,4 @@
 find_package(MPI REQUIRED)
 include_directories(${MPI_CXX_INCLUDE_PATH})
-add_compile_options("-D MPI_ENABLED")
+add_compile_options("-D MPI_ENABLED")
+

cmake/adios2Config.cmake

@@ -1,15 +1,27 @@
 # ----------------------------- Adios2 settings ---------------------------- #
-set(ADIOS2_BUILD_EXAMPLES OFF CACHE BOOL "Build ADIOS2 examples")
+set(ADIOS2_BUILD_EXAMPLES
+    OFF
+    CACHE BOOL "Build ADIOS2 examples")
 
 # Language support
-set(ADIOS2_USE_Python OFF CACHE BOOL "Use Python for ADIOS2")
-set(ADIOS2_USE_Fortran OFF CACHE BOOL "Use Fortran for ADIOS2")
+set(ADIOS2_USE_Python
+    OFF
+    CACHE BOOL "Use Python for ADIOS2")
+set(ADIOS2_USE_Fortran
+    OFF
+    CACHE BOOL "Use Fortran for ADIOS2")
 
 # Format/compression support
-set(ADIOS2_USE_ZeroMQ OFF CACHE BOOL "Use ZeroMQ for ADIOS2")
+set(ADIOS2_USE_ZeroMQ
+    OFF
+    CACHE BOOL "Use ZeroMQ for ADIOS2")
 
-set(ADIOS2_USE_MPI ${mpi} CACHE BOOL "Use MPI for ADIOS2")
+set(ADIOS2_USE_MPI
+    ${mpi}
+    CACHE BOOL "Use MPI for ADIOS2")
 
-set(ADIOS2_USE_CUDA OFF CACHE BOOL "Use CUDA for ADIOS2")
+set(ADIOS2_USE_CUDA
+    OFF
+    CACHE BOOL "Use CUDA for ADIOS2")
 
 add_compile_options("-D OUTPUT_ENABLED")

cmake/benchmark.cmake

@@ -0,0 +1,24 @@
+set(SRC_DIR ${CMAKE_CURRENT_SOURCE_DIR}/src)
+
+add_subdirectory(${SRC_DIR}/global ${CMAKE_CURRENT_BINARY_DIR}/global)
+add_subdirectory(${SRC_DIR}/metrics ${CMAKE_CURRENT_BINARY_DIR}/metrics)
+add_subdirectory(${SRC_DIR}/kernels ${CMAKE_CURRENT_BINARY_DIR}/kernels)
+add_subdirectory(${SRC_DIR}/archetypes ${CMAKE_CURRENT_BINARY_DIR}/archetypes)
+add_subdirectory(${SRC_DIR}/framework ${CMAKE_CURRENT_BINARY_DIR}/framework)
+
+if(${output})
+  add_subdirectory(${SRC_DIR}/output ${CMAKE_CURRENT_BINARY_DIR}/output)
+  add_subdirectory(${SRC_DIR}/checkpoint ${CMAKE_CURRENT_BINARY_DIR}/checkpoint)
+endif()
+
+set(exec benchmark.xc)
+set(src ${CMAKE_CURRENT_SOURCE_DIR}/benchmark/benchmark.cpp)
+
+add_executable(${exec} ${src})
+
+set(libs ntt_global ntt_metrics ntt_kernels ntt_archetypes ntt_framework)
+if(${output})
+  list(APPEND libs ntt_output ntt_checkpoint)
+endif()
+add_dependencies(${exec} ${libs})
+target_link_libraries(${exec} PRIVATE ${libs} stdc++fs)

cmake/config.cmake

@@ -3,7 +3,10 @@ function(set_precision precision_name)
   list(FIND precisions ${precision_name} PRECISION_FOUND)
 
   if(${PRECISION_FOUND} EQUAL -1)
-    message(FATAL_ERROR "Invalid precision: ${precision_name}\nValid options are: ${precisions}")
+    message(
+      FATAL_ERROR
+        "Invalid precision: ${precision_name}\nValid options are: ${precisions}"
+    )
   endif()
 
   if(${precision_name} STREQUAL "single")
@@ -13,19 +16,31 @@ endfunction()
 
 # ---------------------------- Problem generator --------------------------- #
 function(set_problem_generator pgen_name)
-  file(GLOB_RECURSE PGENS "${CMAKE_CURRENT_SOURCE_DIR}/setups/**/pgen.hpp" "${CMAKE_CURRENT_SOURCE_DIR}/setups/pgen.hpp")
+  file(GLOB_RECURSE PGENS "${CMAKE_CURRENT_SOURCE_DIR}/setups/**/pgen.hpp"
+       "${CMAKE_CURRENT_SOURCE_DIR}/setups/pgen.hpp")
   foreach(PGEN ${PGENS})
     get_filename_component(PGEN_NAME ${PGEN} DIRECTORY)
-    string(REPLACE "${CMAKE_CURRENT_SOURCE_DIR}/setups/" "" PGEN_NAME ${PGEN_NAME})
-    string(REPLACE "${CMAKE_CURRENT_SOURCE_DIR}/setups" "" PGEN_NAME ${PGEN_NAME})
+    string(REPLACE "${CMAKE_CURRENT_SOURCE_DIR}/setups/" "" PGEN_NAME
+                   ${PGEN_NAME})
+    string(REPLACE "${CMAKE_CURRENT_SOURCE_DIR}/setups" "" PGEN_NAME
+                   ${PGEN_NAME})
     list(APPEND PGEN_NAMES ${PGEN_NAME})
   endforeach()
   list(FIND PGEN_NAMES ${pgen_name} PGEN_FOUND)
   if(NOT ${pgen_name} STREQUAL "." AND ${PGEN_FOUND} EQUAL -1)
-    message(FATAL_ERROR "Invalid problem generator: ${pgen_name}\nValid options are: ${PGEN_NAMES}")
+    message(
+      FATAL_ERROR
+        "Invalid problem generator: ${pgen_name}\nValid options are: ${PGEN_NAMES}"
+    )
   endif()
-  set(PGEN ${pgen_name} PARENT_SCOPE)
+  set(PGEN
+      ${pgen_name}
+      PARENT_SCOPE)
   include_directories(${CMAKE_CURRENT_SOURCE_DIR}/setups/${pgen_name})
-  set(PGEN_FOUND TRUE PARENT_SCOPE)
-  set(problem_generators ${PGEN_NAMES} PARENT_SCOPE)
+  set(PGEN_FOUND
+      TRUE
+      PARENT_SCOPE)
+  set(problem_generators
+      ${PGEN_NAMES}
+      PARENT_SCOPE)
 endfunction()