Merge branch 'development' of github.com:ECP-WarpX/WarpX into 2d_lumi…

…nosity

.azure-pipelines.yml

@@ -13,6 +13,7 @@ pr:
   paths:
     exclude:
     - Docs
+    - '**/*.rst'
 
 jobs:
 - job:

.github/workflows/clang_sanitizers.yml

@@ -7,6 +7,7 @@ on:
   pull_request:
     paths-ignore:
       - "Docs/**"
+      - "**.rst"
 
 concurrency:
   group: ${{ github.ref }}-${{ github.head_ref }}-clangsanitizers

.github/workflows/clang_tidy.yml

@@ -7,6 +7,7 @@ on:
   pull_request:
     paths-ignore:
       - "Docs/**"
+      - "**.rst"
 
 concurrency:
   group: ${{ github.ref }}-${{ github.head_ref }}-clangtidy

.github/workflows/cuda.yml

@@ -7,6 +7,7 @@ on:
   pull_request:
     paths-ignore:
       - "Docs/**"
+      - "**.rst"
 
 concurrency:
   group: ${{ github.ref }}-${{ github.head_ref }}-cuda
@@ -126,7 +127,7 @@ jobs:
         which nvcc || echo "nvcc not in PATH!"
 
         git clone https://github.com/AMReX-Codes/amrex.git ../amrex
-        cd ../amrex && git checkout --detach b3f67385e62f387b548389222840486c0fffca57 && cd -
+        cd ../amrex && git checkout --detach 25.01 && cd -
         make COMP=gcc QED=FALSE USE_MPI=TRUE USE_GPU=TRUE USE_OMP=FALSE USE_FFT=TRUE USE_CCACHE=TRUE -j 4
 
         ccache -s

.github/workflows/hip.yml

@@ -7,6 +7,7 @@ on:
   pull_request:
     paths-ignore:
       - "Docs/**"
+      - "**.rst"
 
 concurrency:
   group: ${{ github.ref }}-${{ github.head_ref }}-hip

.github/workflows/insitu.yml

@@ -7,6 +7,7 @@ on:
   pull_request:
     paths-ignore:
       - "Docs/**"
+      - "**.rst"
 
 concurrency:
   group: ${{ github.ref }}-${{ github.head_ref }}-insituvis

.github/workflows/intel.yml

@@ -7,6 +7,7 @@ on:
   pull_request:
     paths-ignore:
       - "Docs/**"
+      - "**.rst"
 
 concurrency:
   group: ${{ github.ref }}-${{ github.head_ref }}-intel

.github/workflows/macos.yml

@@ -7,6 +7,7 @@ on:
   pull_request:
     paths-ignore:
       - "Docs/**"
+      - "**.rst"
 
 concurrency:
   group: ${{ github.ref }}-${{ github.head_ref }}-macos

.github/workflows/ubuntu.yml

@@ -7,6 +7,7 @@ on:
   pull_request:
     paths-ignore:
       - "Docs/**"
+      - "**.rst"
 
 concurrency:
   group: ${{ github.ref }}-${{ github.head_ref }}-ubuntu

.github/workflows/windows.yml

@@ -7,6 +7,7 @@ on:
   pull_request:
     paths-ignore:
       - "Docs/**"
+      - "**.rst"
 
 concurrency:
   group: ${{ github.ref }}-${{ github.head_ref }}-windows

.pre-commit-config.yaml

@@ -69,7 +69,7 @@ repos:
 # Python: Ruff linter & formatter
 #   https://docs.astral.sh/ruff/
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.8.4
+  rev: v0.9.1
   hooks:
     # Run the linter
     - id: ruff

CMakeLists.txt

@@ -1,7 +1,7 @@
 # Preamble ####################################################################
 #
 cmake_minimum_required(VERSION 3.24.0)
-project(WarpX VERSION 24.12)
+project(WarpX VERSION 25.01)
 
 include(${WarpX_SOURCE_DIR}/cmake/WarpXFunctions.cmake)
 
@@ -480,7 +480,7 @@ foreach(D IN LISTS WarpX_DIMS)
                 warpx_enable_IPO(pyWarpX_${SD})
             else()
                 # conditionally defined target in pybind11
-                # https://github.com/pybind/pybind11/blob/v2.12.0/tools/pybind11Common.cmake#L397-L403
+                # https://github.com/pybind/pybind11/blob/v2.13.0/tools/pybind11Common.cmake#L407-L413
                 target_link_libraries(pyWarpX_${SD} PRIVATE pybind11::lto)
             endif()
         endif()

Docs/source/conf.py

@@ -107,9 +107,9 @@ def __init__(self, *args, **kwargs):
 # built documents.
 #
 # The short X.Y version.
-version = "24.12"
+version = "25.01"
 # The full version, including alpha/beta/rc tags.
-release = "24.12"
+release = "25.01"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

Docs/source/developers/checksum.rst

@@ -22,11 +22,6 @@ This relies on the function ``evaluate_checksum``:
 
 .. autofunction:: checksumAPI.evaluate_checksum
 
-Here's an example:
-
-.. literalinclude:: ../../../Examples/Tests/embedded_circle/analysis.py
-   :language: python
-
 This can also be included as part of an existing analysis script.
 
 How to evaluate checksums from the command line

Docs/source/developers/fields.rst

@@ -119,9 +119,9 @@ Bilinear filter
 
 The multi-pass bilinear filter (applied on the current density) is implemented in ``Source/Filter/``, and class ``WarpX`` holds an instance of this class in member variable ``WarpX::bilinear_filter``. For performance reasons (to avoid creating too many guard cells), this filter is directly applied in communication routines, see ``WarpX::AddCurrentFromFineLevelandSumBoundary`` above and
 
-.. doxygenfunction:: WarpX::ApplyFilterMF(const amrex::Vector<std::array<std::unique_ptr<amrex::MultiFab>, 3>> &mfvec, int lev, int idim)
+.. doxygenfunction:: WarpX::ApplyFilterMF(const ablastr::fields::MultiLevelVectorField &mfvec, int lev, int idim)
 
-.. doxygenfunction:: WarpX::SumBoundaryJ(const amrex::Vector<std::array<std::unique_ptr<amrex::MultiFab>, 3>> &current, int lev, int idim, const amrex::Periodicity &period)
+.. doxygenfunction:: WarpX::SumBoundaryJ(const ablastr::fields::MultiLevelVectorField &current, int lev, int idim, const amrex::Periodicity &period)
 
 Godfrey's anti-NCI filter for FDTD simulations
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Docs/source/developers/gnumake/python.rst

@@ -3,7 +3,7 @@
 Installing WarpX as a Python package
 ====================================
 
-A full Python installation of WarpX can be done, which includes a build of all of the C++ code, or a pure Python version can be made which only installs the Python scripts. WarpX requires Python version 3.8 or newer.
+A full Python installation of WarpX can be done, which includes a build of all of the C++ code, or a pure Python version can be made which only installs the Python scripts. WarpX requires Python version 3.9 or newer.
 
 For a full Python installation of WarpX
 ---------------------------------------

Docs/source/developers/particles.rst

@@ -83,7 +83,7 @@ Main functions
 
 .. doxygenfunction:: PhysicalParticleContainer::PushPX
 
-.. doxygenfunction:: WarpXParticleContainer::DepositCurrent(amrex::Vector<std::array<std::unique_ptr<amrex::MultiFab>, 3>> &J, amrex::Real dt, amrex::Real relative_time)
+.. doxygenfunction:: WarpXParticleContainer::DepositCurrent(ablastr::fields::MultiLevelVectorField const &J, amrex::Real dt, amrex::Real relative_time)
 
 .. note::
    The current deposition is used both by ``PhysicalParticleContainer`` and ``LaserParticleContainer``, so it is in the parent class ``WarpXParticleContainer``.

Docs/source/install/dependencies.rst

@@ -37,7 +37,7 @@ Optional dependencies include:
 - `SENSEI 4.0.0+ <https://sensei-insitu.org>`__: for in situ analysis and visualization
 - `CCache <https://ccache.dev>`__: to speed up rebuilds (For CUDA support, needs version 3.7.9+ and 4.2+ is recommended)
 - `Ninja <https://ninja-build.org>`__: for faster parallel compiles
-- `Python 3.8+ <https://www.python.org>`__
+- `Python 3.9+ <https://www.python.org>`__
 
   - `mpi4py <https://mpi4py.readthedocs.io>`__
   - `numpy <https://numpy.org>`__

Docs/source/install/hpc/dane.rst

@@ -3,17 +3,17 @@
 Dane (LLNL)
 =============
 
-The `Dane Intel CPU cluster <https://hpc.llnl.gov/hardware/compute-platforms/dane>`_ is located at LLNL.
+The `Dane Intel CPU cluster <https://hpc.llnl.gov/hardware/compute-platforms/dane>`__ is located at LLNL.
 
 
 Introduction
 ------------
 
 If you are new to this system, **please see the following resources**:
 
-* `LLNL user account <https://lc.llnl.gov`__ (login required)
+* `LLNL user account <https://lc.llnl.gov>`__ (login required)
 * `Jupyter service <https://lc.llnl.gov/jupyter>`__ (`documentation <https://lc.llnl.gov/confluence/display/LC/JupyterHub+and+Jupyter+Notebook>`__, login required)
-* `Production directories <https://hpc.llnl.gov/hardware/file-systems>`_:
+* `Production directories <https://hpc.llnl.gov/hardware/file-systems>`__:
 
   * ``/p/lustre1/$(whoami)`` and ``/p/lustre2/$(whoami)``: personal directory on the parallel filesystem
   * Note that the ``$HOME`` directory and the ``/usr/workspace/$(whoami)`` space are NFS mounted and *not* suitable for production quality data generation.

Docs/source/install/hpc/lawrencium.rst

@@ -69,7 +69,7 @@ And since Lawrencium does not yet provide a module for them, install ADIOS2, BLA
    cmake -S src/lapackpp -B src/lapackpp-v100-build -DCMAKE_CXX_STANDARD=17 -Dgpu_backend=cuda -Dbuild_tests=OFF -DCMAKE_INSTALL_RPATH_USE_LINK_PATH=ON -DCMAKE_INSTALL_PREFIX=$HOME/sw/v100/lapackpp-master -Duse_cmake_find_lapack=ON -DBLAS_LIBRARIES=${LAPACK_DIR}/lib/libblas.a -DLAPACK_LIBRARIES=${LAPACK_DIR}/lib/liblapack.a
    cmake --build src/lapackpp-v100-build --target install --parallel 12
 
-Optionally, download and install Python packages for :ref:`PICMI <usage-picmi>` or dynamic ensemble optimizations (:ref:`libEnsemble <libensemble>`):
+Optionally, download and install Python packages for :ref:`PICMI <usage-picmi>` or dynamic ensemble optimizations (`libEnsemble <https://libensemble.readthedocs.io/en/main/>`__):
 
 .. code-block:: bash
 

Docs/source/maintenance/release.rst

@@ -28,7 +28,7 @@ In order to create a GitHub release, you need to:
  1. Create a new branch from ``development`` and update the version number in all source files.
     We usually wait for the AMReX release to be tagged first, then we also point to its tag.
 
-    There is a script for updating core dependencies of WarpX and the WarpX version:
+    There are scripts for updating core dependencies of WarpX and the WarpX version:
 
     .. code-block:: sh
 
@@ -42,6 +42,9 @@ In order to create a GitHub release, you need to:
 
     Then open a PR, wait for tests to pass and then merge.
 
+    The maintainer script ``Tools/Release/releasePR.py`` automates the steps above.
+    Please read through the instructions in the script before running.
+
  2. **Local Commit** (Optional): at the moment, ``@ax3l`` is managing releases and signs tags (naming: ``YY.MM``) locally with his GPG key before uploading them to GitHub.
 
     **Publish**: On the `GitHub Release page <https://github.com/ECP-WarpX/WarpX/releases>`__, create a new release via ``Draft a new release``.

Docs/source/refs.bib

@@ -458,6 +458,7 @@ @misc{Fallahi2020
 @article{VayFELA2009,
   title = {FULL ELECTROMAGNETIC SIMULATION OF FREE-ELECTRON LASER AMPLIFIER PHYSICS VIA THE LORENTZ-BOOSTED FRAME APPROACH},
   author = {Fawley, William M and Vay, Jean-Luc},
+  journal = {},
   abstractNote = {Numerical simulation of some systems containing charged particles with highly relativistic directed motion can by speeded up by orders of magnitude by choice of the proper Lorentz-boosted frame[1]. A particularly good example is that of short wavelength free-electron lasers (FELs) in which a high energy electron beam interacts with a static magnetic undulator. In the optimal boost frame with Lorentz factor gamma_F , the red-shifted FEL radiation and blue shifted undulator have identical wavelengths and the number of required time-steps (presuming the Courant condition applies) decreases by a factor of 2(gamma_F)**2 for fully electromagnetic simulation. We have adapted the WARP code [2]to apply this method to several FEL problems involving coherent spontaneous emission (CSE) from pre-bunched ebeams, including that in a biharmonic undulator.},
   url = {https://www.osti.gov/biblio/964405},
   place = {United States},

Docs/source/theory/multiphysics/collisions.rst

@@ -131,7 +131,7 @@ The process is also the same as for elastic scattering except the excitation ene
 Benchmarks
 ----------
 
-See the :ref:`MCC example <examples-mcc-turner>` for a benchmark of the MCC
+See the :ref:`MCC example <examples-capacitive-discharge>` for a benchmark of the MCC
 implementation against literature results.
 
 Particle cooling due to elastic collisions

Docs/source/usage/examples.rst

@@ -65,14 +65,6 @@ Microelectronics
 * `ARTEMIS manual <https://artemis-em.readthedocs.io>`__
 
 
-Nuclear Fusion
---------------
-
-.. note::
-
-   TODO
-
-
 Fundamental Plasma Physics
 --------------------------
 

Docs/source/usage/examples/thomson_parabola_spectrometer

@@ -0,0 +1 @@
+../../../../Examples/Physics_applications/thomson_parabola_spectrometer

Docs/source/usage/workflows/ml_materials/run_warpx_training.py

@@ -260,7 +260,7 @@ def get_laser(antenna_z, profile_t_peak, fill_in=True):
 diag_particle_list = ["weighting", "position", "momentum"]
 coarse_btd_end = int((L_plasma_bulk + 0.001 + stage_spacing * (N_stage - 1)) * 100000)
 stage_end_snapshots = [
-    f"{int((L_plasma_bulk+stage_spacing*ii)*100000)}:{int((L_plasma_bulk+stage_spacing*ii)*100000+50)}:5"
+    f"{int((L_plasma_bulk + stage_spacing * ii) * 100000)}:{int((L_plasma_bulk + stage_spacing * ii) * 100000 + 50)}:5"
     for ii in range(1)
 ]
 btd_particle_diag = picmi.LabFrameParticleDiagnostic(

Docs/source/usage/workflows/ml_materials/train.py

@@ -180,7 +180,7 @@ def test_dataset(model, test_source, test_target, loss_fun):
         )
 # Manual: Training loop END
 t4 = time.time()
-print(f"total training time: {t4-t3:.3f}s")
+print(f"total training time: {t4 - t3:.3f}s")
 
 ######### save model #########
 

Examples/Physics_applications/capacitive_discharge/inputs_base_1d_picmi.py

@@ -423,7 +423,7 @@ def run_sim(self):
             assert hasattr(self.solver, "phi")
 
         if libwarpx.amr.ParallelDescriptor.MyProc() == 0:
-            np.save(f"ion_density_case_{self.n+1}.npy", self.ion_density_array)
+            np.save(f"ion_density_case_{self.n + 1}.npy", self.ion_density_array)
 
         # query the particle z-coordinates if this is run during CI testing
         # to cover that functionality

Examples/Physics_applications/laser_acceleration/analysis_openpmd_rz.py

@@ -20,15 +20,15 @@
 # this is in C (Python) order; r is the fastest varying index
 (Nm, Nz, Nr) = jt.shape
 
-assert (
-    Nm == 3
-), "Wrong number of angular modes stored or possible incorrect ordering when flushed"
-assert (
-    Nr == 64
-), "Wrong number of radial points stored or possible incorrect ordering when flushed"
-assert (
-    Nz == 512
-), "Wrong number of z points stored or possible incorrect ordering when flushed"
+assert Nm == 3, (
+    "Wrong number of angular modes stored or possible incorrect ordering when flushed"
+)
+assert Nr == 64, (
+    "Wrong number of radial points stored or possible incorrect ordering when flushed"
+)
+assert Nz == 512, (
+    "Wrong number of z points stored or possible incorrect ordering when flushed"
+)
 
 assert ii.meshes["part_per_grid"][io.Mesh_Record_Component.SCALAR].shape == [
     512,
@@ -60,6 +60,6 @@
 electron_meanz = np.sum(np.dot(zlist, rhoe0)) / np.sum(rhoe0)
 beam_meanz = np.sum(np.dot(zlist, rhob0)) / np.sum(rhob0)
 
-assert (
-    (electron_meanz > 0) and (beam_meanz < 0)
-), "problem with openPMD+RZ.  Maybe openPMD+RZ mixed up the order of rho_<species> diagnostics?"
+assert (electron_meanz > 0) and (beam_meanz < 0), (
+    "problem with openPMD+RZ.  Maybe openPMD+RZ mixed up the order of rho_<species> diagnostics?"
+)

Examples/Physics_applications/laser_ion/plot_2d.py

@@ -120,7 +120,7 @@ def visualize_density_iteration(ts, iteration, out_dir):
     for ax in axs[:-1]:
         ax.set_xticklabels([])
     axs[2].set_xlabel(r"$z$ ($\mu$m)")
-    fig.suptitle(f"Iteration: {it}, Time: {time/1e-15:.1f} fs")
+    fig.suptitle(f"Iteration: {it}, Time: {time / 1e-15:.1f} fs")
 
     plt.tight_layout()
 
@@ -190,7 +190,7 @@ def visualize_field_iteration(ts, iteration, out_dir):
     for ax in axs[:-1]:
         ax.set_xticklabels([])
     axs[2].set_xlabel(r"$z$ ($\mu$m)")
-    fig.suptitle(f"Iteration: {it}, Time: {time/1e-15:.1f} fs")
+    fig.suptitle(f"Iteration: {it}, Time: {time / 1e-15:.1f} fs")
 
     plt.tight_layout()
 

Examples/Physics_applications/spacecraft_charging/analysis.py

@@ -68,6 +68,6 @@ def func(x, v0, tau):
 print("percentage error for v0 = " + str(diff_v0 * 100) + "%")
 print("percentage error for tau = " + str(diff_tau * 100) + "%")
 
-assert (diff_v0 < tolerance_v0) and (
-    diff_tau < tolerance_tau
-), "Test spacecraft_charging did not pass"
+assert (diff_v0 < tolerance_v0) and (diff_tau < tolerance_tau), (
+    "Test spacecraft_charging did not pass"
+)

Examples/Physics_applications/thomson_parabola_spectrometer/README.rst

@@ -28,7 +28,7 @@ The PICMI input file is not available for this example yet.
 
 For `MPI-parallel <https://www.mpi-forum.org>`__ runs, prefix these lines with ``mpiexec -n 4 ...`` or ``srun -n 4 ...``, depending on the system.
 
-.. literalinclude:: inputs
+.. literalinclude:: inputs_test_3d_thomson_parabola_spectrometer
    :language: ini
    :caption: You can copy this file from ``Examples/Physics_applications/thomson_parabola_spectrometer/inputs_test_3d_thomson_parabola_spectrometer``.
 

Examples/Tests/accelerator_lattice/analysis.py

@@ -118,9 +118,11 @@ def applylens(x0, vx0, vz0, gamma, lens_length, lens_strength):
 xx = xx + dt * vx
 
 # Compare the analytic to the simulated final values
-print(f"Error in x position is {abs(np.abs((xx - xx_sim)/xx))}, which should be < 0.01")
 print(
-    f"Error in x velocity is {abs(np.abs((ux - ux_sim)/ux))}, which should be < 0.002"
+    f"Error in x position is {abs(np.abs((xx - xx_sim) / xx))}, which should be < 0.01"
+)
+print(
+    f"Error in x velocity is {abs(np.abs((ux - ux_sim) / ux))}, which should be < 0.002"
 )
 
 assert abs(np.abs((xx - xx_sim) / xx)) < 0.01, Exception("error in x particle position")

Examples/Tests/boundaries/analysis.py

@@ -101,9 +101,9 @@ def do_periodic(x):
 assert len(a_id) == 1, "Absorbing particles not absorbed"
 assert np.all(vx == -vx0), "Reflecting particle velocity not correct"
 assert np.all(vz == +vz0), "Periodic particle velocity not correct"
-assert np.all(
-    np.abs((xx - xxa) / xx) < 1.0e-15
-), "Reflecting particle position not correct"
-assert np.all(
-    np.abs((zz - zza) / zz) < 1.0e-15
-), "Periodic particle position not correct"
+assert np.all(np.abs((xx - xxa) / xx) < 1.0e-15), (
+    "Reflecting particle position not correct"
+)
+assert np.all(np.abs((zz - zza) / zz) < 1.0e-15), (
+    "Periodic particle position not correct"
+)