fix merge conflict

.clang-tidy

@@ -19,6 +19,7 @@ Checks: '
         -cppcoreguidelines-avoid-non-const-global-variables,
         -cppcoreguidelines-init-variables,
         -cppcoreguidelines-macro-usage,
+        -cppcoreguidelines-missing-std-forward,
         -cppcoreguidelines-narrowing-conversions,
         -cppcoreguidelines-non-private-member-variables-in-classes,
         -cppcoreguidelines-owning-memory,
@@ -29,6 +30,7 @@ Checks: '
     misc-*,
         -misc-no-recursion,
         -misc-non-private-member-variables-in-classes,
+        -misc-include-cleaner,
     modernize-*,
         -modernize-avoid-c-arrays,
         -modernize-return-braced-init-list,
@@ -44,7 +46,6 @@ Checks: '
         -readability-implicit-bool-conversion,
         -readability-isolate-declaration,
         -readability-magic-numbers,
-        -readability-misleading-indentation,
         -readability-named-parameter,
         -readability-uppercase-literal-suffix
     '
@@ -58,6 +59,7 @@ CheckOptions:
   value:        "true"
 - key:          misc-use-anonymous-namespace.HeaderFileExtensions
   value:        "H,"
-
+- key:          performance-move-const-arg.CheckTriviallyCopyableMove
+  value:        "false"
 
 HeaderFilterRegex: 'Source[a-z_A-Z0-9\/]+\.H$'

.github/workflows/clang_tidy.yml

@@ -26,7 +26,7 @@ jobs:
     - uses: actions/checkout@v4
     - name: install dependencies
       run: |
-        .github/workflows/dependencies/clang.sh 16
+        .github/workflows/dependencies/clang.sh 17
     - name: set up cache
       uses: actions/cache@v4
       with:
@@ -43,8 +43,8 @@ jobs:
         export CCACHE_LOGFILE=${{ github.workspace }}/ccache.log.txt
         ccache -z
 
-        export CXX=$(which clang++-16)
-        export CC=$(which clang-16)
+        export CXX=$(which clang++-17)
+        export CC=$(which clang-17)
 
         cmake -S . -B build_clang_tidy      \
           -DCMAKE_VERBOSE_MAKEFILE=ON       \
@@ -62,7 +62,7 @@ jobs:
 
         ${{github.workspace}}/.github/workflows/source/makeMakefileForClangTidy.py --input ${{github.workspace}}/ccache.log.txt
         make -j4 --keep-going -f clang-tidy-ccache-misses.mak \
-            CLANG_TIDY=clang-tidy-16 \
+            CLANG_TIDY=clang-tidy-17 \
             CLANG_TIDY_ARGS="--config-file=${{github.workspace}}/.clang-tidy --warnings-as-errors=*"
 
         ccache -s

.github/workflows/cuda.yml

@@ -127,7 +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 78bdf0faabc4101d5333ebb421e553efcc7ec04e && cd -
+        cd ../amrex && git checkout --detach 198da4879a63f1bc8c4e8d674bf9185525318f61 && 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

.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: v0.9.4
+  rev: v0.9.6
   hooks:
     # Run the linter
     - id: ruff

Docs/requirements.txt

@@ -27,5 +27,6 @@ sphinx-copybutton
 sphinx-design
 sphinx_rtd_theme>=1.1.1
 sphinxcontrib-bibtex
+sphinxcontrib-googleanalytics
 sphinxcontrib-napoleon
 yt  # for checksumAPI

Docs/source/conf.py

@@ -56,8 +56,13 @@
     "sphinx_design",
     "breathe",
     "sphinxcontrib.bibtex",
+    "sphinxcontrib.googleanalytics",
 ]
 
+# Google Analytics
+googleanalytics_id = "G-QZGY5060MZ"
+googleanalytics_enabled = True
+
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ["_templates"]
 

Docs/source/developers/particles.rst

@@ -141,7 +141,7 @@ Attribute name        ``int``/``real``  Description                         Wher
                                         Wheeler process                                physics is used.
 ====================  ================  ==================================  ===== ==== ======================
 
-WarpX allows extra runtime attributes to be added to particle containers (through ``NewRealComp("attrname")`` or ``NewIntComp("attrname")``).
+WarpX allows extra runtime attributes to be added to particle containers (through ``AddRealComp("attrname")`` or ``AddIntComp("attrname")``).
 The attribute name can then be used to access the values of that attribute.
 For example, using a particle iterator, ``pti``, to loop over the particles the command ``pti.GetAttribs(particle_comps["attrname"]).dataPtr();`` will return the values of the ``"attrname"`` attribute.
 

Docs/source/highlights.rst

@@ -14,7 +14,12 @@ Plasma-Based Acceleration
 
 Scientific works in laser-plasma and beam-plasma acceleration.
 
-#. Shrock JE, Rockafellow E, Miao B, Le M, Hollinger RC, Wang S, Gonsalves AJ, Picksley A, Rocca JJ, and Milchberg HM
+#. Ma M, Zeng M, Wang J, Lu G, Yan W, Chen L, and Li D.
+   **Particle-in-cell simulation of laser wakefield accelerators with oblique lasers in quasicylindrical geometry**.
+   Phys. Rev. Accel. Beams **28**, 021301, 2025
+   `DOI:10.1103/PhysRevAccelBeams.28.021301 <https://doi.org/10.1103/PhysRevAccelBeams.28.021301>`__
+
+#. Shrock JE, Rockafellow E, Miao B, Le M, Hollinger RC, Wang S, Gonsalves AJ, Picksley A, Rocca JJ, and Milchberg HM.
    **Guided Mode Evolution and Ionization Injection in Meter-Scale Multi-GeV Laser Wakefield Accelerators**.
    Phys. Rev. Lett. **133**, 045002, 2024
    `DOI:10.1103/PhysRevLett.133.045002 <https://link.aps.org/doi/10.1103/PhysRevLett.133.045002>`__
@@ -154,6 +159,16 @@ High Energy Astrophysical Plasma Physics
 
 Scientific works in astrophysical plasma modeling.
 
+#. Jambunathan R, Jones H, Corrales L, Klion H, Roward ME, Myers A, Zhang W, Vay J-L.
+   **Application of mesh refinement to relativistic magnetic reconnection**.
+   Physics of Plasmas ***32*** 1, 2025
+   `DOI:10.1063/5.0233583 <https://doi.org/10.1063/5.0233583>`__
+
+#. Ghosh S, Bhat P.
+   **Magnetic Reconnection: An Alternative Explanation of Radio Emission in Galaxy Clusters**.
+   The Astrophysical Journal Letters **979** 1, 2025.
+   `DOI:10.3847/2041-8213/ad9f2d <https://doi.org/10.3847/2041-8213/ad9f2d>`__
+
 #. Klion H, Jambunathan R, Rowan ME, Yang E, Willcox D, Vay J-L, Lehe R, Myers A, Huebl A, Zhang W.
    **Particle-in-Cell simulations of relativistic magnetic reconnection with advanced Maxwell solver algorithms**.
    The Astrophysical Journal **952** 8, 2023.

Docs/source/refs.bib

@@ -35,6 +35,17 @@ @ARTICLE{Birdsall1991
 year = {1991}
 }
 
+@misc{Janssen2016
+author = {Janssen, J. F. J. and Pitchford L. C. and Hagelaar G. J. M. and van Dijk J.},
+doi = {10.1088/0963-0252/25/5/055026},
+journal = {Plasma Sources Science and Technology},
+number = {5},
+pages = {055026},
+title = {{Evaluation of angular scattering models for electron-neutral collisions in Monte Carlo simulations}},
+volume = {25},
+year = {2016}
+}
+
 @misc{Lim2007,
 author = {Lim, Chul-Hyun},
 issn = {0419-4217},

Docs/source/theory/boundary_conditions.rst

@@ -301,3 +301,23 @@ the right boundary is reflecting.
 
 .. bibliography::
    :keyprefix: bc-
+
+.. _theory-bc-pmc:
+
+Perfect Magnetic Conductor
+----------------------------
+
+This boundary can be used to model a symmetric surface, where charges and current are
+symmetric across the boundary.
+This is equivalent to the Neumann (zero-derivative) boundary condition.
+For the electromagnetic solve, at PMC, the tangential magnetic field and the normal electric
+field are odd across the boundary and set to 0 on the boundary.
+In the guard-cell region, those fields are set equal and
+opposite to the respective field component in the mirror location across the PMC boundary.
+The other components, the normal magnetic field and tangential electric field, are even
+and set equal to the field component in the mirror location in the domain across the PMC boundary.
+
+The PMC boundary condition also impacts the deposition of charge and current density.
+The charge and current densities deposited into the guard cells are reflected back into
+the domain, adding them to the mirror cells in the domain.
+This represents the charge and current from the virtual symmetric particles in the guard cells.

Docs/source/theory/multiphysics/collisions.rst

@@ -121,13 +121,23 @@ The particle velocity in the COM frame is then isotropically scattered using the
 Back scattering
 ^^^^^^^^^^^^^^^
 
-The process is the same as for elastic scattering above expect the scattering angle is fixed at :math:`\pi`, meaning the particle velocity in the COM frame is updated to :math:`-\vec{u}_c`.
+The process is the same as for elastic scattering above except the scattering angle is fixed at :math:`\pi`, meaning the particle velocity in the COM frame is updated to :math:`-\vec{u}_c`.
 
 Excitation
 ^^^^^^^^^^
 
 The process is also the same as for elastic scattering except the excitation energy cost is subtracted from the particle energy. This is done by reducing the velocity before a scattering angle is chosen.
 
+Forward scattering
+^^^^^^^^^^^^^^^^^^
+
+This process operates in two ways:
+
+1. If an excitation energy cost is provided, the energy cost is subtracted from the particle energy and no scattering is performed.
+2. If an excitation energy cost is not provided, the particle is not scattered and the velocity is unchanged (corresponding to a scattering angle of :math:`0` in the elastic scattering process above).
+
+See :cite:t:`b-Janssen2016` for a recommended use of this process.
+
 Benchmarks
 ----------
 

Docs/source/usage/parameters.rst

@@ -533,6 +533,8 @@ Domain Boundary Conditions
 
     * ``pec``: This option can be used to set a Perfect Electric Conductor at the simulation boundary. Please see the :ref:`PEC theory section <theory-bc-pec>` for more details. Note that PEC boundary is invalid at `r=0` for the RZ solver. Please use ``none`` option. This boundary condition does not work with the spectral solver.
 
+    * ``pmc``: This option can be used to set a Perfect Magnetic Conductor at the simulation boundary. Please see the :ref:`PEC theory section <theory-bc-pmc>` for more details. This is equivalent to ``Neumann``. This boundary condition does not work with the spectral solver.
+
     * ``pec_insulator``: This option specifies a mixed perfect electric conductor and insulator boundary, where some part of the
       boundary is PEC and some is insulator. In the insulator portion, the normal fields are extrapolated and the tangential fields
       are either set to the specified value or extrapolated. The region that is insulator is specified using a spatially dependent expression with the insulator being in the area where the value of the expression is greater than zero.
@@ -2167,8 +2169,8 @@ Details about the collision models can be found in the :ref:`theory section <mul
 
 * ``<collision_name>.scattering_processes`` (`strings` separated by spaces)
     Only for ``dsmc`` and ``background_mcc``. The scattering processes that should be
-    included. Available options are ``elastic``, ``back`` & ``charge_exchange``
-    for ions and ``elastic``, ``excitationX`` & ``ionization`` for electrons.
+    included. Available options are ``elastic``, ``excitationX``, ``forward``, ``back``, and ``charge_exchange``
+    for ions and ``elastic``, ``excitationX``, ``ionization`` & ``forward`` for electrons.
     Multiple excitation events can be included for electrons corresponding to
     excitation to different levels, the ``X`` above can be changed to a unique
     identifier for each excitation process. For each scattering process specified

Examples/Tests/particle_data_python/inputs_test_2d_particle_attr_access_picmi.py

@@ -150,8 +150,8 @@ def add_particles():
 ##########################
 
 assert elec_wrapper.nps == 270 / (2 - args.unique)
-assert elec_wrapper.particle_container.get_comp_index("w") == 2
-assert elec_wrapper.particle_container.get_comp_index("newPid") == 6
+assert elec_wrapper.particle_container.get_real_comp_index("w") == 2
+assert elec_wrapper.particle_container.get_real_comp_index("newPid") == 6
 
 new_pid_vals = elec_wrapper.get_particle_real_arrays("newPid", 0)
 for vals in new_pid_vals:

Examples/Tests/particle_data_python/inputs_test_2d_prev_positions_picmi.py

@@ -111,8 +111,8 @@
 elec_count = elec_wrapper.nps
 
 # check that the runtime attributes have the right indices
-assert elec_wrapper.particle_container.get_comp_index("prev_x") == 6
-assert elec_wrapper.particle_container.get_comp_index("prev_z") == 7
+assert elec_wrapper.particle_container.get_real_comp_index("prev_x") == 6
+assert elec_wrapper.particle_container.get_real_comp_index("prev_z") == 7
 
 # sanity check that the prev_z values are reasonable and
 # that the correct number of values are returned

Examples/Tests/pec/CMakeLists.txt

@@ -41,6 +41,16 @@ add_warpx_test(
     OFF  # dependency
 )
 
+add_warpx_test(
+    test_3d_pmc_field  # name
+    3  # dims
+    2  # nprocs
+    inputs_test_3d_pmc_field  # inputs
+    "analysis_pec.py diags/diag1000134"  # analysis
+    "analysis_default_regression.py --path diags/diag1000134"  # checksum
+    OFF  # dependency
+)
+
 add_warpx_test(
     test_2d_pec_field_insulator_implicit  # name
     2  # dims

Examples/Tests/pec/inputs_test_3d_pmc_field

@@ -0,0 +1,54 @@
+# Set-up to test the PMC Boundary condition for the fields
+# Constructive interference between the incident and reflected wave result in a
+# standing wave.
+
+# max step
+max_step = 134
+
+# number of grid points
+amr.n_cell = 32 32 256
+
+# Maximum allowable size of each subdomain
+amr.max_grid_size = 1024
+amr.blocking_factor = 32
+
+amr.max_level = 0
+
+# Geometry
+geometry.dims = 3
+geometry.prob_lo     =  -8.e-6 -8.e-6 -4.e-6
+geometry.prob_hi     =   8.e-6  8.e-6  4.e-6
+
+# Boundary condition
+boundary.field_lo = periodic periodic pmc
+boundary.field_hi = periodic periodic pmc
+
+warpx.serialize_initial_conditions = 1
+
+# Verbosity
+warpx.verbose = 1
+
+# Algorithms
+algo.current_deposition = esirkepov
+# CFL
+warpx.cfl = 0.9
+
+
+my_constants.z1 = -2.e-6
+my_constants.z2 = 2.e-6
+my_constants.wavelength = 1.e-6
+warpx.E_ext_grid_init_style = parse_E_ext_grid_function
+warpx.Ez_external_grid_function(x,y,z) = "0."
+warpx.Ex_external_grid_function(x,y,z) = "0."
+warpx.Ey_external_grid_function(x,y,z) = "((1.e5*sin(2*pi*(z)/wavelength)) * (z<z2) * (z>z1))"
+
+warpx.B_ext_grid_init_style = parse_B_ext_grid_function
+warpx.Bx_external_grid_function(x,y,z)= "(((-1.e5*sin(2*pi*(z)/wavelength))/clight))*(z<z2) * (z>z1) "
+warpx.By_external_grid_function(x,y,z)= "0."
+warpx.Bz_external_grid_function(x,y,z) = "0."
+
+# Diagnostics
+diagnostics.diags_names = diag1
+diag1.intervals = 134
+diag1.diag_type = Full
+diag1.fields_to_plot = Ey Bx

Examples/Tests/restart/inputs_test_2d_runtime_components_picmi.py

@@ -107,7 +107,8 @@
 np.random.seed(30025025)
 
 electron_wrapper = particle_containers.ParticleContainerWrapper("electrons")
-electron_wrapper.add_real_comp("newPid")
+if not sim.amr_restart:
+    electron_wrapper.add_real_comp("newPid")
 
 
 def add_particles():
@@ -140,8 +141,8 @@ def add_particles():
 ##########################
 
 assert electron_wrapper.nps == 90
-assert electron_wrapper.particle_container.get_comp_index("w") == 2
-assert electron_wrapper.particle_container.get_comp_index("newPid") == 6
+assert electron_wrapper.particle_container.get_real_comp_index("w") == 2
+assert electron_wrapper.particle_container.get_real_comp_index("newPid") == 6
 
 new_pid_vals = electron_wrapper.get_particle_real_arrays("newPid", 0)
 for vals in new_pid_vals:

Python/pywarpx/particle_containers.py

@@ -170,7 +170,9 @@ def add_particles(
         # --- Note that the velocities are handled separately and not included in attr
         # --- (even though they are stored as attributes in the C++)
         for key, vals in kwargs.items():
-            attr[:, self.particle_container.get_comp_index(key) - built_in_attrs] = vals
+            attr[
+                :, self.particle_container.get_real_comp_index(key) - built_in_attrs
+            ] = vals
 
         nattr_int = 0
         attr_int = np.empty([0], dtype=np.int32)
@@ -264,7 +266,7 @@ def get_particle_real_arrays(self, comp_name, level, copy_to_host=False):
         List of arrays
             The requested particle array data
         """
-        comp_idx = self.particle_container.get_comp_index(comp_name)
+        comp_idx = self.particle_container.get_real_comp_index(comp_name)
 
         data_array = []
         for pti in libwarpx.libwarpx_so.WarpXParIter(self.particle_container, level):
@@ -309,7 +311,7 @@ def get_particle_int_arrays(self, comp_name, level, copy_to_host=False):
         List of arrays
             The requested particle array data
         """
-        comp_idx = self.particle_container.get_icomp_index(comp_name)
+        comp_idx = self.particle_container.get_int_comp_index(comp_name)
 
         data_array = []
         for pti in libwarpx.libwarpx_so.WarpXParIter(self.particle_container, level):
@@ -842,16 +844,16 @@ def get_particle_boundary_buffer(self, species_name, boundary, comp_name, level)
         )
         data_array = []
         # loop over the real attributes
-        if comp_name in part_container.real_comp_names:
-            comp_idx = part_container.real_comp_names[comp_name]
+        if comp_name in part_container.real_soa_names:
+            comp_idx = part_container.get_real_comp_index(comp_name)
             for ii, pti in enumerate(
                 libwarpx.libwarpx_so.BoundaryBufferParIter(part_container, level)
             ):
                 soa = pti.soa()
                 data_array.append(xp.array(soa.get_real_data(comp_idx), copy=False))
         # loop over the integer attributes
-        elif comp_name in part_container.int_comp_names:
-            comp_idx = part_container.int_comp_names[comp_name]
+        elif comp_name in part_container.int_soa_names:
+            comp_idx = part_container.get_int_comp_index(comp_name)
             for ii, pti in enumerate(
                 libwarpx.libwarpx_so.BoundaryBufferParIter(part_container, level)
             ):