Merge BLAST-WarpX:development into EZoni:ci_docs_skip_checks

Author: EZoni

.azure-pipelines.yml

@@ -1,7 +1,7 @@
 # -*- mode: yaml -*-
 
 pool:
-  vmImage: 'ubuntu-20.04'
+  vmImage: 'ubuntu-24.04'
 
 trigger:
   branches:
@@ -52,9 +52,12 @@ jobs:
   timeoutInMinutes: 240
 
   steps:
-  # set up caches:
+  # Ccache caching:
   # - once stored under a key, they become immutable (even if cache content changes)
   # - for a refresh the key has to change, e.g., hash of a tracked file in the key
+  - bash: |
+      mkdir -p /home/vsts/.ccache
+    displayName: 'Create Ccache Directory'
   - task: Cache@2
     continueOnError: true
     inputs:
@@ -64,7 +67,7 @@ jobs:
          Ccache | "$(System.JobName)" | .azure-pipelines.yml
       path: /home/vsts/.ccache
       cacheHitVar: CCACHE_CACHE_RESTORED
-    displayName: Cache Ccache Objects
+    displayName: 'Cache Ccache Objects'
 
   - bash: |
       set -o nounset errexit pipefail
@@ -111,6 +114,10 @@ jobs:
           -DCMAKE_CXX_STANDARD=17                         \
           -Duse_cmake_find_lapack=ON -Dbuild_tests=OFF -DCMAKE_VERBOSE_MAKEFILE=ON
       fi
+      # Remove system copy of Matplotlib to avoid conflict
+      # with version set in the requirements file - see, e.g.,
+      # https://github.com/matplotlib/matplotlib/issues/28768.
+      sudo apt remove python3-matplotlib
       # Python modules required for test analysis
       python3 -m pip install --upgrade -r Regression/requirements.txt
       python3 -m pip cache purge

.github/workflows/clang_sanitizers.yml

@@ -27,6 +27,7 @@ jobs:
             ${{ github.event.pull_request.head.repo.clone_url }}
     outputs:
       skip: ${{ env.SKIP_CHECKS }}
+
   build_UB_sanitizer:
     name: Clang UB sanitizer
     runs-on: ubuntu-24.04
@@ -82,12 +83,13 @@ jobs:
         mpirun -n 2 ./build/bin/warpx.1d Examples/Physics_applications/laser_acceleration/inputs_base_1d
         mpirun -n 2 ./build/bin/warpx.2d Examples/Physics_applications/laser_acceleration/inputs_base_2d
         mpirun -n 2 ./build/bin/warpx.3d Examples/Physics_applications/laser_acceleration/inputs_base_3d
+        mpirun -n 2 ./build/bin/warpx.2d Examples/Tests/implicit/inputs_test_2d_theta_implicit_jfnk_vandb
+
   build_thread_sanitizer:
     name: Clang thread sanitizer
     runs-on: ubuntu-24.04
-    # TODO Fix data race conditions and re-enable job
     needs: skip_checks
-    if: 0 #${{ github.event.pull_request.draft == false && needs.skip_checks.outputs.skip == 'false' }}
+    if: ${{ github.event.pull_request.draft == false && needs.skip_checks.outputs.skip == 'false' }}
     env:
       CC: clang
       CXX: clang++
@@ -124,30 +126,28 @@ jobs:
           -DWarpX_QED=ON                    \
           -DWarpX_QED_TABLE_GEN=ON          \
           -DWarpX_OPENPMD=ON                \
-          -DWarpX_EB=OFF                    \
           -DWarpX_PRECISION=DOUBLE          \
           -DWarpX_PARTICLE_PRECISION=DOUBLE
         cmake --build build -j 4
-        cmake -S . -B build_EB              \
-          -GNinja                           \
-          -DCMAKE_VERBOSE_MAKEFILE=ON       \
-          -DCMAKE_BUILD_TYPE=RelWithDebInfo \
-          -DWarpX_DIMS="2"                  \
-          -DWarpX_FFT=ON                    \
-          -DWarpX_QED=ON                    \
-          -DWarpX_QED_TABLE_GEN=ON          \
-          -DWarpX_OPENPMD=ON                \
-          -DWarpX_EB=ON                     \
-          -DWarpX_PRECISION=DOUBLE          \
-          -DWarpX_PARTICLE_PRECISION=DOUBLE
-        cmake --build build_EB -j 4
         ccache -s
         du -hs ~/.cache/ccache
     - name: Run with thread sanitizer
       run: |
+        # Disabling the gds/shmem component by using gds/hash instead
+        # is required to avoid issues with shared memory.
         export PMIX_MCA_gds=hash
-        export TSAN_OPTIONS='ignore_noninstrumented_modules=1'
+        # Archer is a data race detector for OpenMP programs.
+        # It is required to avoid false positives with OpenMP and it is
+        # included in llvm. However with many Linux it is necessary
+        # to define this environment variable to make sure that the
+        # Archer library is actually used.
+        # When the Archer library is used and ARCHER_OPTIONS="verbose=1",
+        # the following message should be displayed:
+        # Archer detected OpenMP application with TSan, supplying OpenMP synchronization semantics
+        export OMP_TOOL_LIBRARIES=/usr/lib/llvm-17/lib/libarcher.so
         export ARCHER_OPTIONS="verbose=1"
+        # This option is required to avoid false positive reports from the OpenMP runtime
+        export TSAN_OPTIONS='ignore_noninstrumented_modules=1'
         export OMP_NUM_THREADS=2
         mpirun -n 2 ./build/bin/warpx.rz Examples/Physics_applications/laser_acceleration/inputs_base_rz warpx.serialize_initial_conditions = 0
         mpirun -n 2 ./build/bin/warpx.1d Examples/Physics_applications/laser_acceleration/inputs_base_1d warpx.serialize_initial_conditions = 0
@@ -156,4 +156,4 @@ jobs:
         git clone https://github.com/BLAST-WarpX/warpx-data ../warpx-data
         cd Examples/Tests/embedded_circle
         ulimit -c unlimited
-        mpirun -n 2 ../../../build_EB/bin/warpx.2d inputs_test_2d_embedded_circle warpx.serialize_initial_conditions = 0
+        mpirun -n 2 ../../../build/bin/warpx.2d inputs_test_2d_embedded_circle warpx.serialize_initial_conditions = 0

.github/workflows/cuda.yml

@@ -134,7 +134,7 @@ jobs:
         export LD_LIBRARY_PATH=/usr/local/nvidia/lib:/usr/local/nvidia/lib64:/usr/local/cuda/lib64:${LD_LIBRARY_PATH}
         which nvcc || echo "nvcc not in PATH!"
         git clone https://github.com/AMReX-Codes/amrex.git ../amrex
-        cd ../amrex && git checkout --detach 25.03 && cd -
+        cd ../amrex && git checkout --detach e24e4a8c4df84ed71f961efe7637f86ba1c2ce62 && 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
         du -hs ~/.cache/ccache

.pre-commit-config.yaml

@@ -73,7 +73,7 @@ repos:
 # Python: Ruff linter & formatter
 #   https://docs.astral.sh/ruff/
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.11.2
+  rev: v0.11.4
   hooks:
     # Run the linter
     - id: ruff

CMakeLists.txt

@@ -1,7 +1,7 @@
 # Preamble ####################################################################
 #
 cmake_minimum_required(VERSION 3.24.0)
-project(WarpX VERSION 25.03)
+project(WarpX VERSION 25.04)
 
 include(${WarpX_SOURCE_DIR}/cmake/WarpXFunctions.cmake)
 

Docs/source/conf.py

@@ -112,9 +112,9 @@ def __init__(self, *args, **kwargs):
 # built documents.
 #
 # The short X.Y version.
-version = "25.03"
+version = "25.04"
 # The full version, including alpha/beta/rc tags.
-release = "25.03"
+release = "25.04"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

Docs/source/highlights.rst

@@ -219,6 +219,11 @@ Related works using WarpX:
 Nuclear Fusion and Plasma Confinement
 *************************************
 
+#. Tyushev M., Smolyakov A., Sabo A., Groenewald R., Necas A., and Yushmanov P.
+   **Drift-kinetic PIC simulations of plasma flow and energy transport in the magnetic mirror configuration**.
+   Physics of Plasmas **32**, 032514, 2025.
+   `DOI:10.1063/5.0227040 <https://doi.org/10.1063/5.0227040>`__
+
 #. Tyushev M., Papahn Zadeh M., Chopra N. S., Raitses Y., Romadanov I., Likhanskii A., Fubiani G., Garrigues L., Groenewald R. and Smolyakov A.
    **Mode transitions and spoke structures in  E×B Penning discharge**.
    Physics of Plasmas **32**, 013511, 2025.

Docs/source/usage/parameters.rst

@@ -126,6 +126,10 @@ Overall simulation parameters
     , this sets the relative tolerance for the iterative method used to obtain a self-consistent update of the particles at
     each iteration in the JFNK process.
 
+* ``implicit_evolve.use_mass_matrices`` (`bool`, default: false)
+    When `algo.evolve_scheme` is either `theta_implicit_em`, `strang_implicit_spectral_em`, or `semi_implicit_em` and `implicit_evolve.nonlinear_solver = newton` and a preconditioner is being used
+    , the diagonal components of the diagonal mass matrices are used to capture the plasma response in the preconditioner.
+
 * ``picard.verbose`` (`bool`, default: 1)
     When `implicit_evolve.nonlinear_solver = picard`, this sets the verbosity of the Picard solver. If true, then information
     on the nonlinear error are printed to screen at each nonlinear iteration.

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

@@ -107,7 +107,6 @@ def get_species_of_accelerator_stage(
         density_expression=f"n0*(1.+4.*(x**2+y**2)/(kp**2*Rc**4))*(0.5*(1.-cos(pi*(z-{stage_zmin})/Lplus)))*((z-{stage_zmin})<Lplus)"
         + f"+n0*(1.+4.*(x**2+y**2)/(kp**2*Rc**4))*((z-{stage_zmin})>=Lplus)*((z-{stage_zmin})<(Lplus+Lp))"
         + f"+n0*(1.+4.*(x**2+y**2)/(kp**2*Rc**4))*(0.5*(1.+cos(pi*((z-{stage_zmin})-Lplus-Lp)/Lminus)))*((z-{stage_zmin})>=(Lplus+Lp))*((z-{stage_zmin})<(Lplus+Lp+Lminus))",
-        pi=3.141592653589793,
         n0=n0,
         kp=q_e / c * math.sqrt(n0 / (m_e * ep0)),
         Rc=Rc,

Examples/Tests/collision/analysis_collision_1d.py

@@ -19,7 +19,7 @@
 
 import numpy as np
 import yt
-from scipy.constants import e
+from scipy.constants import e, m_e, m_u
 
 # this will be the name of the plot file
 last_fn = sys.argv[1]
@@ -29,7 +29,7 @@
 )
 
 # carbon 12 ion (mass = 12*amu - 6*me)
-mass = 1.992100316897910e-26
+mass = 12.0 * m_u - 6.0 * m_e
 
 # Separate macroparticles from group A (low weight) and group B (high weight)
 # by sorting based on weight

Examples/Tests/collision/analysis_collision_2d.py

@@ -31,6 +31,7 @@
 import numpy
 import post_processing_utils
 import yt
+from scipy.constants import c, m_e
 
 test_name = os.path.split(os.getcwd())[1]
 
@@ -41,9 +42,7 @@
 ni = ng * 200
 np = ne + ni
 
-c = 299792458.0
-me = 9.10938356e-31
-mi = me * 5.0
+mi = m_e * 5.0
 
 ## In the first part of the test we verify that the output data is consistent with the exponential
 ## fit.
@@ -76,7 +75,7 @@
     # get time index j
     j = int(fn[-5:])
     # compute error
-    vxe = numpy.mean(px[0:ne]) / me / c
+    vxe = numpy.mean(px[0:ne]) / m_e / c
     vxi = numpy.mean(px[ne:np]) / mi / c
     vxd = vxe - vxi
     fit = a * math.exp(b * j)

Examples/Tests/collision/analysis_collision_3d.py

@@ -30,6 +30,7 @@
 import numpy
 import post_processing_utils
 import yt
+from scipy.constants import c, m_e
 
 tolerance = 0.001
 
@@ -38,9 +39,7 @@
 ni = ng * 200
 np = ne + ni
 
-c = 299792458.0
-me = 9.10938356e-31
-mi = me * 5.0
+mi = m_e * 5.0
 
 ## In the first part of the test we verify that the output data is consistent with the exponential
 ## fit.
@@ -69,7 +68,7 @@
     # get time index j
     j = int(fn[-5:])
     # compute error
-    vxe = numpy.mean(pxe) / me / c
+    vxe = numpy.mean(pxe) / m_e / c
     vxi = numpy.mean(pxi) / mi / c
     vxd = vxe - vxi
     fit = a * math.exp(b * j)

Examples/Tests/collision/inputs_test_2d_collision_xz

@@ -47,7 +47,7 @@ electron.uz_th = 0.044237441120300
 electron.ux_m  = 0.044237441120300
 
 ion.charge = q_e
-ion.mass = 4.554691780000000e-30
+ion.mass = 5*m_e
 ion.injection_style = "NRandomPerCell"
 ion.num_particles_per_cell = 200
 ion.profile = constant

Examples/Tests/electrostatic_sphere/analysis_electrostatic_sphere.py

@@ -25,7 +25,7 @@
 import numpy as np
 import yt
 from openpmd_viewer import OpenPMDTimeSeries
-from scipy.constants import c
+from scipy.constants import c, e, epsilon_0, m_e
 from scipy.optimize import fsolve
 
 yt.funcs.mylog.setLevel(0)
@@ -41,10 +41,10 @@
 
 if emass_10:
     l2_tolerance = 0.096
-    m_e = 10
+    e_mass = 10
 else:
     l2_tolerance = 0.05
-    m_e = 9.10938356e-31  # Electron mass in kg
+    e_mass = m_e  # Electron mass in kg
 ndims = np.count_nonzero(ds.domain_dimensions > 1)
 
 if ndims == 2:
@@ -68,8 +68,7 @@
 iz0 = round((0.0 - zmin) / dz)
 
 # Constants
-eps_0 = 8.8541878128e-12  # Vacuum Permittivity in C/(V*m)
-q_e = -1.60217662e-19  # Electron charge in C
+q_e = -e  # Electron charge in C
 pi = np.pi  # Circular constant of the universe
 r_0 = 0.1  # Initial radius of sphere
 q_tot = -1e-15  # Total charge of sphere in C
@@ -81,15 +80,15 @@
 # v(r) and t(r) can be solved analytically.
 #
 # The solution r(t) solves the ODE: r''(t) = a/(r(t)**2) with initial conditions
-# r(0) = r_0, r'(0) = 0, and a = q_e*q_tot/(4*pi*eps_0*m_e)
+# r(0) = r_0, r'(0) = 0, and a = q_e*q_tot/(4*pi*epsilon_0*e_mass)
 #
 # The E was calculated at the end of the last time step
 def v_exact(r):
-    return np.sqrt(q_e * q_tot / (2 * pi * m_e * eps_0) * (1 / r_0 - 1 / r))
+    return np.sqrt(q_e * q_tot / (2 * pi * e_mass * epsilon_0) * (1 / r_0 - 1 / r))
 
 
 def t_exact(r):
-    return np.sqrt(r_0**3 * 2 * pi * m_e * eps_0 / (q_e * q_tot)) * (
+    return np.sqrt(r_0**3 * 2 * pi * e_mass * epsilon_0 / (q_e * q_tot)) * (
         np.sqrt(r / r_0 - 1) * np.sqrt(r / r_0)
         + np.log(np.sqrt(r / r_0 - 1) + np.sqrt(r / r_0))
     )
@@ -104,8 +103,8 @@ def func(rho):
 
 def E_exact(r):
     return np.sign(r) * (
-        q_tot / (4 * pi * eps_0 * r**2) * (abs(r) >= r_end)
-        + q_tot * abs(r) / (4 * pi * eps_0 * r_end**3) * (abs(r) < r_end)
+        q_tot / (4 * pi * epsilon_0 * r**2) * (abs(r) >= r_end)
+        + q_tot * abs(r) / (4 * pi * epsilon_0 * r_end**3) * (abs(r) < r_end)
     )
 
 

Examples/Tests/embedded_boundary_cube/inputs_test_3d_embedded_boundary_cube_macroscopic

@@ -3,6 +3,6 @@ FILE = inputs_base_3d
 
 # test input parameters
 algo.em_solver_medium = macroscopic
-macroscopic.epsilon = 1.5*8.8541878128e-12
-macroscopic.mu = 1.25663706212e-06
+macroscopic.epsilon = 1.5*epsilon0
+macroscopic.mu = mu0
 macroscopic.sigma = 0

Examples/Tests/embedded_boundary_rotated_cube/inputs_test_2d_embedded_boundary_rotated_cube

@@ -18,7 +18,6 @@ my_constants.xmin = -0.53
 my_constants.zmin = -0.53
 my_constants.xmax = 0.53
 my_constants.zmax = 0.53
-my_constants.pi = 3.141592653589793
 my_constants.theta = pi/8
 
 warpx.eb_implicit_function = "xr=x*cos(-theta)+z*sin(-theta); zr=-x*sin(-theta)+z*cos(-theta); max(max(xr+xmin,-(xr+xmax)), max(zr+zmin,-(zr+zmax)))"
@@ -29,12 +28,11 @@ my_constants.Lx = 1.06
 my_constants.Lz = 1.06
 my_constants.x_cent = 0.
 my_constants.z_cent = 0.
-my_constants.mu_0 = 1.25663706212e-06
 
 warpx.B_ext_grid_init_style = parse_B_ext_grid_function
 
 warpx.Bx_external_grid_function(x,y,z) = 0
-warpx.By_external_grid_function(x,y,z) = "mu_0 *
+warpx.By_external_grid_function(x,y,z) = "mu0 *
                                           cos(m * pi / Lx * (x*cos(-theta)+z*sin(-theta) - Lx / 2 - x_cent)) *
                                           cos(p * pi / Lz * (-x*sin(-theta)+z*cos(-theta) - Lz / 2 - z_cent))"
 warpx.Bz_external_grid_function(x,y,z) = 0