Merge branch 'development' into apply_constant_fields_directly

.clang-tidy

@@ -7,14 +7,17 @@ Checks: '
         -bugprone-unchecked-optional-access,
     cert-*,
         -cert-err58-cpp,
-    cppcoreguidelines-avoid-goto,
-    cppcoreguidelines-interfaces-global-init,
+    cppcoreguidelines-*,
+        -cppcoreguidelines-avoid-c-arrays,
+        -cppcoreguidelines-avoid-magic-numbers,
         -cppcoreguidelines-avoid-non-const-global-variables,
         -cppcoreguidelines-init-variables,
         -cppcoreguidelines-macro-usage,
-        -cppcoreguidelines-narrowing-conversions,
         -cppcoreguidelines-no-malloc,
+        -cppcoreguidelines-narrowing-conversions,
+        -cppcoreguidelines-non-private-member-variables-in-classes,
         -cppcoreguidelines-owning-memory,
+        -cppcoreguidelines-pro-*,
     google-build-explicit-make-pair,
     google-build-namespaces,
     google-global-names-in-headers,

.github/workflows/cuda.yml

@@ -18,10 +18,6 @@ jobs:
     env:
       CXXFLAGS: "-Werror"
       CMAKE_GENERATOR: Ninja
-      # setuptools/mp4py work-around, see
-      #   https://github.com/mpi4py/mpi4py/pull/159
-      #   https://github.com/mpi4py/mpi4py/issues/157#issuecomment-1001022274
-      SETUPTOOLS_USE_DISTUTILS: stdlib
     steps:
     - uses: actions/checkout@v3
     - uses: actions/setup-python@v4
@@ -75,7 +71,8 @@ jobs:
           -DAMReX_CUDA_ERROR_CAPTURE_THIS=ON
         cmake --build build_sp -j 2
 
-        python3 -m pip install --upgrade pip setuptools wheel
+        python3 -m pip install --upgrade pip
+        python3 -m pip install --upgrade build packaging setuptools wheel
         export WARPX_MPI=ON
         export PYWARPX_LIB_DIR=$PWD/build_sp/lib/site-packages/pywarpx/
         python3 -m pip wheel .
@@ -111,20 +108,16 @@ jobs:
         which nvcc || echo "nvcc not in PATH!"
 
         git clone https://github.com/AMReX-Codes/amrex.git ../amrex
-        cd ../amrex && git checkout --detach da79aff8053058371a78d4bf85488384242368ee && cd -
+        cd ../amrex && git checkout --detach d36463103daed09a40cdea235041a6ab79ff280c && cd -
         make COMP=gcc QED=FALSE USE_MPI=TRUE USE_GPU=TRUE USE_OMP=FALSE USE_PSATD=TRUE USE_CCACHE=TRUE -j 2
 
   build_nvhpc21-11-nvcc:
     name: [email protected] NVCC/NVC++ Release [tests]
     runs-on: ubuntu-20.04
     if: github.event.pull_request.draft == false
-    env:
-      # For NVHPC, Ninja is slower than the default:
-      #CMAKE_GENERATOR: Ninja
-      # setuptools/mp4py work-around, see
-      #   https://github.com/mpi4py/mpi4py/pull/159
-      #   https://github.com/mpi4py/mpi4py/issues/157#issuecomment-1001022274
-      SETUPTOOLS_USE_DISTUTILS: stdlib
+    #env:
+    #  # For NVHPC, Ninja is slower than the default:
+    #  CMAKE_GENERATOR: Ninja
     steps:
     - uses: actions/checkout@v3
     - name: Dependencies
@@ -175,7 +168,8 @@ jobs:
         #   https://github.com/mpi4py/mpi4py/issues/114
         #export CFLAGS="-noswitcherror"
 
-        #python3 -m pip install --upgrade pip setuptools wheel
+        #python3 -m pip install --upgrade pip
+        #python3 -m pip install --upgrade build packaging setuptools wheel
         #export WARPX_MPI=ON
         #export PYWARPX_LIB_DIR=$PWD/build/lib/site-packages/pywarpx/
         #python3 -m pip wheel .

.github/workflows/intel.yml

@@ -41,7 +41,8 @@ jobs:
         export CXX=$(which icpc)
         export CC=$(which icc)
 
-        python3 -m pip install --upgrade pip setuptools wheel
+        python3 -m pip install --upgrade pip
+        python3 -m pip install --upgrade build packaging setuptools wheel
 
         cmake -S . -B build_dp \
           -DCMAKE_VERBOSE_MAKEFILE=ON \
@@ -104,7 +105,7 @@ jobs:
         export CC=$(which icx)
 
         python3 -m pip install --upgrade pip
-        python3 -m pip install --upgrade setuptools wheel
+        python3 -m pip install --upgrade build packaging setuptools wheel
 
         cmake -S . -B build_sp         \
           -DCMAKE_CXX_FLAGS_RELEASE="-O1 -DNDEBUG" \
@@ -178,6 +179,6 @@ jobs:
 
      # Skip this as it will copy the binary artifacts and we are tight on disk space
      #   python3 -m pip install --upgrade pip
-     #   python3 -m pip install --upgrade setuptools wheel
+     #   python3 -m pip install --upgrade build packaging setuptools wheel
      #   PYWARPX_LIB_DIR=$PWD/build_sp/lib/site-packages/pywarpx/ python3 -m pip wheel .
      #   python3 -m pip install *.whl

.github/workflows/macos.yml

@@ -16,10 +16,6 @@ jobs:
       HOMEBREW_NO_INSTALLED_DEPENDENTS_CHECK: TRUE
       # For macOS, Ninja is slower than the default:
       #CMAKE_GENERATOR: Ninja
-      # setuptools/mp4py work-around, see
-      #   https://github.com/mpi4py/mpi4py/pull/159
-      #   https://github.com/mpi4py/mpi4py/issues/157#issuecomment-1001022274
-      SETUPTOOLS_USE_DISTUTILS: stdlib
     steps:
     - uses: actions/checkout@v3
     - name: Brew Cache
@@ -65,7 +61,7 @@ jobs:
     - name: build WarpX
       run: |
         python3 -m pip install --upgrade pip
-        python3 -m pip install --upgrade pip setuptools wheel
+        python3 -m pip install --upgrade build packaging setuptools wheel
 
         cmake -S . -B build_dp         \
           -DCMAKE_VERBOSE_MAKEFILE=ON  \

.github/workflows/ubuntu.yml

@@ -167,10 +167,6 @@ jobs:
       CXX: clang++
       # On CI for this test, Ninja is slower than the default:
       #CMAKE_GENERATOR: Ninja
-      # setuptools/mp4py work-around, see
-      #   https://github.com/mpi4py/mpi4py/pull/159
-      #   https://github.com/mpi4py/mpi4py/issues/157#issuecomment-1001022274
-      SETUPTOOLS_USE_DISTUTILS: stdlib
     steps:
     - uses: actions/checkout@v3
     - name: install dependencies
@@ -190,7 +186,8 @@ jobs:
           ccache-openmp-pyfull-
     - name: build WarpX
       run: |
-        python3 -m pip install --upgrade pip setuptools wheel
+        python3 -m pip install --upgrade pip
+        python3 -m pip install --upgrade build packaging setuptools wheel
 
         export CXXFLAGS="-Werror -Wno-error=pass-failed"
 

.github/workflows/windows.yml

@@ -41,7 +41,9 @@ jobs:
         cmake --build build --config Debug --parallel 2
         if(!$?) { Exit $LASTEXITCODE }
 
-        python3 -m pip install --upgrade pip setuptools wheel
+        python3 -m pip install --upgrade pip
+        if(!$?) { Exit $LASTEXITCODE }
+        python3 -m pip install --upgrade build packaging setuptools wheel
         if(!$?) { Exit $LASTEXITCODE }
         cmake --build build --config Debug --target install
         if(!$?) { Exit $LASTEXITCODE }
@@ -64,7 +66,7 @@ jobs:
     - uses: actions/checkout@v3
     - uses: actions/setup-python@v4
       with:
-        python-version: '3.x'
+        python-version: '3.8'
     - uses: seanmiddleditch/gha-setup-ninja@master
     - name: CCache Cache
       uses: actions/cache@v3
@@ -100,7 +102,9 @@ jobs:
         cmake --build build --config Release --target install
         if errorlevel 1 exit 1
 
-        python3 -m pip install --upgrade pip setuptools wheel
+        python3 -m pip install --upgrade pip
+        if errorlevel 1 exit 1
+        python3 -m pip install --upgrade build packaging setuptools wheel
         if errorlevel 1 exit 1
         python3 -m pip install --upgrade -r requirements.txt
         if errorlevel 1 exit 1

CMakeLists.txt

@@ -1,7 +1,7 @@
 # Preamble ####################################################################
 #
 cmake_minimum_required(VERSION 3.20.0)
-project(WarpX VERSION 23.10)
+project(WarpX VERSION 23.11)
 
 include(${WarpX_SOURCE_DIR}/cmake/WarpXFunctions.cmake)
 
@@ -127,7 +127,7 @@ option(WarpX_PYTHON_IPO
 )
 
 set(pyWarpX_VERSION_INFO "" CACHE STRING
-    "PEP-440 conformant version (set by distutils)")
+    "PEP-440 conformant version (set by setup.py)")
 
 # enforce consistency of dependent options
 if(WarpX_APP OR WarpX_PYTHON)

Docs/source/acknowledge_us.rst

@@ -55,9 +55,8 @@ If your project uses a specific algorithm or component, please consider citing t
 
 - Sandberg R T, Lehe R, Mitchell C E, Garten M, Qiang J, Vay J-L and Huebl A.
   **Hybrid Beamline Element ML-Training for Surrogates in the ImpactX Beam-Dynamics Code**.
-  14th International Particle Accelerator Conference (IPAC'23), WEPA101, *in print*, 2023.
-  `preprint <https://www.ipac23.org/preproc/pdf/WEPA101.pdf>`__,
-  `DOI:10.18429/JACoW-IPAC-23-WEPA101 <https://doi.org/10.18429/JACoW-IPAC-23-WEPA101>`__
+  14th International Particle Accelerator Conference (IPAC'23), WEPA101, 2023.
+  `DOI:10.18429/JACoW-IPAC2023-WEPA101 <https://doi.org/10.18429/JACoW-IPAC2023-WEPA101>`__
 
 - Huebl A, Lehe R, Zoni E, Shapoval O, Sandberg R T, Garten M, Formenti A, Jambunathan R, Kumar P, Gott K, Myers A, Zhang W, Almgren A, Mitchell C E, Qiang J, Sinn A, Diederichs S, Thevenet M, Grote D, Fedeli L, Clark T, Zaim N, Vincenti H, Vay JL.
   **From Compact Plasma Particle Sources to Advanced Accelerators with Modeling at Exascale**.
@@ -75,6 +74,11 @@ If your project uses a specific algorithm or component, please consider citing t
   *New Journal of Physics* **24** 025009, 2022.
   `DOI:10.1088/1367-2630/ac4ef1 <https://doi.org/10.1088/1367-2630/ac4ef1>`__
 
+- Lehe R, Blelly A, Giacomel L, Jambunathan R, Vay JL.
+  **Absorption of charged particles in perfectly matched layers by optimal damping of the deposited current**.
+  *Physical Review E* **106** 045306, 2022.
+  `DOI:10.1103/PhysRevE.106.045306 <https://doi.org/10.1103/PhysRevE.106.045306>`__
+
 - Zoni E, Lehe R, Shapoval O, Belkin D, Zaim N, Fedeli L, Vincenti H, Vay JL.
   **A hybrid nodal-staggered pseudo-spectral electromagnetic particle-in-cell method with finite-order centering**. *Computer Physics Communications* **279**, 2022.
   `DOI:10.1016/j.cpc.2022.108457 <https://doi.org/10.1016/j.cpc.2022.108457>`__

Docs/source/conf.py

@@ -79,9 +79,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = u'23.10'
+version = u'23.11'
 # The full version, including alpha/beta/rc tags.
-release = u'23.10'
+release = u'23.11'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

Docs/source/dataanalysis/formats.rst

@@ -19,7 +19,7 @@ When using the AMReX `plotfile` format, users can set the ``amrex.async_out=1``
 option to perform the IO in a non-blocking fashion, meaning that the simulation
 will continue to run while an IO thread controls writing the data to disk.
 This can significantly reduce the overall time spent in IO. This is primarily intended for
-large runs on supercomputers such as Summit and Cori; depending on the MPI
+large runs on supercomputers (e.g. at OLCF or NERSC); depending on the MPI
 implementation you are using, you may not see a benefit on your workstation.
 
 When writing plotfiles, each rank will write to a separate file, up to some maximum number

Docs/source/highlights.rst

@@ -24,11 +24,10 @@ Scientific works in laser-plasma and beam-plasma acceleration.
    Phys. Rev. Research **5**, 033112, 2023
    `DOI:10.1103/PhysRevResearch.5.033112 <https://doi.org/10.1103/PhysRevResearch.5.033112>`__
 
-#. Sandberg R T, Lehe R, Mitchell C E, Garten M, Qiang J, Vay J-L, Huebl A.
+#. Sandberg R T, Lehe R, Mitchell C E, Garten M, Qiang J, Vay J-L and Huebl A.
    **Hybrid Beamline Element ML-Training for Surrogates in the ImpactX Beam-Dynamics Code**.
-   14th International Particle Accelerator Conference (IPAC'23), WEPA101, *in print*, 2023.
-   `preprint <https://www.ipac23.org/preproc/pdf/WEPA101.pdf>`__,
-   `DOI:10.18429/JACoW-IPAC-23-WEPA101 <https://doi.org/10.18429/JACoW-IPAC-23-WEPA101>`__
+   14th International Particle Accelerator Conference (IPAC'23), WEPA101, 2023.
+   `DOI:10.18429/JACoW-IPAC2023-WEPA101 <https://doi.org/10.18429/JACoW-IPAC2023-WEPA101>`__
 
 #. Wang J, Zeng M, Li D, Wang X, Gao J.
    **High quality beam produced by tightly focused laser driven wakefield accelerators**.
@@ -141,3 +140,11 @@ High-Performance Computing and Numerics
 Scientific works in High-Performance Computing, applied mathematics and numerics.
 
 Please see :ref:`this section <acknowledge_warpx_all_refs>`.
+
+Nuclear Fusion - Magnetically Confined Plasmas
+**********************************************
+
+#. Nicks, B. S., Putvinski, S. and Tajima, T.
+   **Stabilization of the Alfvén-ion cyclotron instability through short plasmas: Fully kinetic simulations in a high-beta regime**.
+   Physics of Plasmas **30**, 102108, 2023.
+   `DOI:10.1063/5.0163889 <https://doi.org/10.1063/5.0163889>`__

Docs/source/install/cmake.rst

@@ -211,7 +211,8 @@ PICMI Python Bindings
 
    .. code-block:: bash
 
-      python3 -m pip install -U pip setuptools wheel
+      python3 -m pip install -U pip
+      python3 -m pip install -U build packaging setuptools wheel
       python3 -m pip install -U cmake
       python3 -m pip install -r requirements.txt
 

Docs/source/install/hpc.rst

@@ -33,7 +33,6 @@ This section documents quick-start guides for a selection of supercomputers that
    :maxdepth: 1
 
    hpc/adastra
-   hpc/cori
    hpc/crusher
    hpc/frontier
    hpc/fugaku