Merge branch 'development' into add_analysis_embedded_boundary_remova…

…l_depth

.github/workflows/clang_sanitizers.yml

@@ -15,8 +15,7 @@ concurrency:
 jobs:
   build_UB_sanitizer:
     name: Clang UB sanitizer
-    runs-on: ubuntu-22.04
-    container: ubuntu:23.10
+    runs-on: ubuntu-24.04
     if: github.event.pull_request.draft == false
     env:
       CC: clang
@@ -65,10 +64,6 @@ jobs:
     - name: run with UB sanitizer
       run: |
 
-        # We need these two lines because these tests run inside a docker container
-        export OMPI_ALLOW_RUN_AS_ROOT=1
-        export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
-
         export OMP_NUM_THREADS=2
 
         #MPI implementations often leak memory
@@ -81,9 +76,9 @@ jobs:
 
   build_thread_sanitizer:
     name: Clang thread sanitizer
-    runs-on: ubuntu-22.04
-    container: ubuntu:23.10
-    if: github.event.pull_request.draft == false
+    runs-on: ubuntu-24.04
+    # TODO Fix data race conditions and re-enable job
+    if: 0 #github.event.pull_request.draft == false
     env:
       CC: clang
       CXX: clang++
@@ -149,10 +144,6 @@ jobs:
         export TSAN_OPTIONS='ignore_noninstrumented_modules=1'
         export ARCHER_OPTIONS="verbose=1"
 
-        # We need these two lines because these tests run inside a docker container
-        export OMPI_ALLOW_RUN_AS_ROOT=1
-        export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=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

.github/workflows/cuda.yml

@@ -126,7 +126,7 @@ jobs:
         which nvcc || echo "nvcc not in PATH!"
 
         git clone https://github.com/AMReX-Codes/amrex.git ../amrex
-        cd ../amrex && git checkout --detach 456c93c7d9512f1cdffac0574973d7df41417898 && cd -
+        cd ../amrex && git checkout --detach 96db0a665ff1e6bbe638490fd02d3aafb9188f6b && 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/dependencies/clang17.sh

@@ -7,11 +7,6 @@
 
 set -eu -o pipefail
 
-# This dependency file is currently used within a docker container,
-# which does not come with sudo.
-apt-get -qqq update
-apt-get -y install sudo
-
 # `man apt.conf`:
 #   Number of retries to perform. If this is non-zero APT will retry
 #   failed files the given number of times.

.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: v0.7.3
+  rev: v0.8.2
   hooks:
     # Run the linter
     - id: ruff

CMakeLists.txt

@@ -1,7 +1,7 @@
 # Preamble ####################################################################
 #
 cmake_minimum_required(VERSION 3.24.0)
-project(WarpX VERSION 24.11)
+project(WarpX VERSION 24.12)
 
 include(${WarpX_SOURCE_DIR}/cmake/WarpXFunctions.cmake)
 

Docs/requirements.txt

@@ -13,7 +13,7 @@ openpmd-viewer  # for checksumAPI
 
 # PICMI API docs
 # note: keep in sync with version in ../requirements.txt
-picmistandard==0.31.0
+picmistandard==0.33.0
 # for development against an unreleased PICMI version, use:
 # picmistandard @ git+https://github.com/picmi-standard/picmi.git#subdirectory=PICMI_Python
 

Docs/source/conf.py

@@ -107,9 +107,9 @@ def __init__(self, *args, **kwargs):
 # built documents.
 #
 # The short X.Y version.
-version = "24.11"
+version = "24.12"
 # The full version, including alpha/beta/rc tags.
-release = "24.11"
+release = "24.12"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

Docs/source/refs.bib

@@ -480,6 +480,18 @@ @article{VayFELB2009
   url = {https://doi.org/10.1063/1.3080930},
 }
 
+@article{Barnes2021,
+  title = {Improved C1 shape functions for simplex meshes},
+  author = {D.C. Barnes},
+  journal = {Journal of Computational Physics},
+  volume = {424},
+  pages = {109852},
+  year = {2021},
+  issn = {0021-9991},
+  doi = {https://doi.org/10.1016/j.jcp.2020.109852},
+  url = {https://www.sciencedirect.com/science/article/pii/S0021999120306264},
+}
+
 @article{Rhee1987,
     author = {Rhee, M. J. and Schneider, R. F. and Weidman, D. J.},
     title = "{Simple time‐resolving Thomson spectrometer}",

Docs/source/usage/parameters.rst

@@ -236,6 +236,23 @@ Overall simulation parameters
         \boldsymbol{\nabla}^2 \phi = - \rho/\epsilon_0 \qquad \boldsymbol{E} = - \boldsymbol{\nabla}\phi \\
         \boldsymbol{\nabla}^2 \boldsymbol{A} = - \mu_0 \boldsymbol{j} \qquad \boldsymbol{B} = \boldsymbol{\nabla}\times\boldsymbol{A}
 
+    * ``labframe-effective-potential``: Poisson's equation is solved with a modified dielectric function
+      (resulting in an "effective potential") to create a semi-implicit scheme which is robust to the
+      numerical instability seen in explicit electrostatic PIC when :math:`\Delta t \omega_{pe} > 2`.
+      If this option is used the additional parameter ``warpx.effective_potential_factor`` can also be
+      specified to set the value of :math:`C_{EP}` (default 4). The method is stable for :math:`C_{EP} \geq 1`
+      regardless of :math:`\Delta t`, however, the larger :math:`C_{EP}` is set, the lower the numerical plasma
+      frequency will be and therefore care must be taken to not set it so high that the plasma mode
+      hybridizes with other modes of interest.
+      Details of the method can be found in Appendix A of :cite:t:`param-Barnes2021` (note that in that paper
+      the method is referred to as "semi-implicit electrostatic" but here it has been renamed to "effective potential"
+      to avoid confusion with the semi-implicit method of Chen et al.).
+      In short, the code solves:
+
+      .. math::
+
+        \boldsymbol{\nabla}\cdot\left(1+\frac{C_{EP}}{4}\sum_{s \in \text{species}}(\omega_{ps}\Delta t)^2 \right)\boldsymbol{\nabla} \phi = - \rho/\epsilon_0 \qquad \boldsymbol{E} = - \boldsymbol{\nabla}\phi
+
     * ``relativistic``: Poisson's equation is solved **for each species**
       in their respective rest frame. The corresponding field
       is mapped back to the simulation frame and will produce both E and B
@@ -2680,7 +2697,7 @@ WarpX has five types of diagnostics:
 ``TimeAveraged`` diagnostics only allow field data, which they output after averaging over a period of time,
 ``BackTransformed`` diagnostics are used when running a simulation in a boosted frame, to reconstruct output data to the lab frame,
 ``BoundaryScraping`` diagnostics are used to collect the particles that are absorbed at the boundary, throughout the simulation, and
-``ReducedDiags`` allow the user to compute some reduced quantity (particle temperature, max of a field) and write a small amount of data to text files.
+``ReducedDiags`` enable users to compute specific reduced quantities, such as particle temperature, energy histograms, or maximum field values, and efficiently save this in-situ analyzed data to files.
 Similar to what is done for physical species, WarpX has a class Diagnostics that allows users to initialize different diagnostics, each of them with different fields, resolution and period.
 This currently applies to standard diagnostics, but should be extended to back-transformed diagnostics and reduced diagnostics (and others) in a near future.
 
@@ -3064,23 +3081,22 @@ In addition to their usual attributes, the saved particles have
 Reduced Diagnostics
 ^^^^^^^^^^^^^^^^^^^
 
-``ReducedDiags`` allow the user to compute some reduced quantity (particle temperature, max of a field) and write a small amount of data to text files.
+``ReducedDiags`` enable users to compute specific reduced quantities, such as particle temperature, energy histograms, or maximum field values, and efficiently save this in-situ analyzed data to files.
+This shifts analysis from post-processing to runtime calculation of reduction operations (average, maximum, ...) and can greatly save disk space when "raw" particle and field outputs from `FullDiagnostics` can be avoided in favor of single values, 1D or 2D data at possibly even higher time resolution.
 
 * ``warpx.reduced_diags_names`` (`strings`, separated by spaces)
-    The names given by the user of simple reduced diagnostics.
-    Also the names of the output `.txt` files.
-    This reduced diagnostics aims to produce simple outputs
-    of the time history of some physical quantities.
+    A list of user-given names for reduced diagnostics.
+    By default, these names are also prefixing the names of output files.
     If ``warpx.reduced_diags_names`` is not provided in the input file,
-    no reduced diagnostics will be done.
+    no reduced diagnostics will be activated during the run.
     This is then used in the rest of the input deck;
     in this documentation we use ``<reduced_diags_name>`` as a placeholder.
 
 * ``<reduced_diags_name>.type`` (`string`)
     The type of reduced diagnostics associated with this ``<reduced_diags_name>``.
     For example, ``ParticleEnergy``, ``FieldEnergy``, etc.
     All available types are described below in detail.
-    For all reduced diagnostics,
+    For all reduced diagnostics that are writing tabular data into text files,
     the first and the second columns in the output file are
     the time step and the corresponding physical time in seconds, respectively.
 
@@ -3590,22 +3606,27 @@ Reduced Diagnostics
     * ``Timestep``
         This type outputs the simulation's physical timestep (in seconds) at each mesh refinement level.
 
-* ``<reduced_diags_name>.intervals`` (`string`)
+* ``reduced_diags.intervals`` (`string`)
     Using the `Intervals Parser`_ syntax, this string defines the timesteps at which reduced
-    diagnostics are written to file.
+    diagnostics are written to the file.
+    This can also be specified for the specific diagnostic by setting ``<reduced_diags_name>.intervals``.
 
-* ``<reduced_diags_name>.path`` (`string`) optional (default `./diags/reducedfiles/`)
-    The path that the output file will be stored.
+* ``reduced_diags.path`` (`string`) optional (default `./diags/reducedfiles/`)
+    The path where the output file will be stored.
+    This can also be specified for the specific diagnostic by setting ``<reduced_diags_name>.path``.
 
-* ``<reduced_diags_name>.extension`` (`string`) optional (default `txt`)
-    The extension of the output file.
+* ``reduced_diags.extension`` (`string`) optional (default `txt`)
+    The extension of the output file (the suffix).
+    This can also be specified for the specific diagnostic by setting ``<reduced_diags_name>.extension``.
 
-* ``<reduced_diags_name>.separator`` (`string`) optional (default a `whitespace`)
+* ``reduced_diags.separator`` (`string`) optional (default a `whitespace`)
     The separator between row values in the output file.
     The default separator is a whitespace.
+    This can also be specified for the specific diagnostic by setting ``<reduced_diags_name>.separator``.
 
-* ``<reduced_diags_name>.precision`` (`integer`) optional (default `14`)
+* ``reduced_diags.precision`` (`integer`) optional (default `14`)
     The precision used when writing out the data to the text files.
+    This can also be specified for the specific diagnostic by setting ``<reduced_diags_name>.precision``.
 
 Lookup tables and other settings for QED modules
 ------------------------------------------------

Docs/source/usage/python.rst

@@ -146,6 +146,10 @@ Particle distributions can be used for to initialize particles in a particle spe
 
 .. autoclass:: pywarpx.picmi.AnalyticDistribution
 
+.. autoclass:: pywarpx.picmi.UniformFluxDistribution
+
+.. autoclass:: pywarpx.picmi.AnalyticFluxDistribution
+
 .. autoclass:: pywarpx.picmi.ParticleListDistribution
 
 Particle layouts determine how to microscopically place macro particles in a grid cell.

Examples/Physics_applications/laser_ion/inputs_test_2d_laser_ion_acc_picmi.py

@@ -196,7 +196,6 @@
 histuH_rdiag = picmi.ReducedDiagnostic(
     diag_type="ParticleHistogram",
     name="histuH",
-    period=100,
     species=hydrogen,
     bin_number=1000,
     bin_min=0.0,
@@ -208,7 +207,6 @@
 histue_rdiag = picmi.ReducedDiagnostic(
     diag_type="ParticleHistogram",
     name="histue",
-    period=100,
     species=electrons,
     bin_number=1000,
     bin_min=0.0,
@@ -222,7 +220,6 @@
 histuzAll_rdiag = picmi.ReducedDiagnostic(
     diag_type="ParticleHistogram",
     name="histuzAll",
-    period=100,
     species=hydrogen,
     bin_number=1000,
     bin_min=-0.474,
@@ -233,7 +230,6 @@
 field_probe_z_rdiag = picmi.ReducedDiagnostic(
     diag_type="FieldProbe",
     name="FieldProbe_Z",
-    period=100,
     integrate=0,
     probe_geometry="Line",
     x_probe=0.0,
@@ -246,7 +242,6 @@
 field_probe_scat_point_rdiag = picmi.ReducedDiagnostic(
     diag_type="FieldProbe",
     name="FieldProbe_ScatPoint",
-    period=1,
     integrate=0,
     probe_geometry="Point",
     x_probe=0.0,
@@ -256,7 +251,6 @@
 field_probe_scat_line_rdiag = picmi.ReducedDiagnostic(
     diag_type="FieldProbe",
     name="FieldProbe_ScatLine",
-    period=100,
     integrate=1,
     probe_geometry="Line",
     x_probe=-2.5e-6,
@@ -267,7 +261,8 @@
 )
 
 load_balance_costs_rdiag = picmi.ReducedDiagnostic(
-    diag_type="LoadBalanceCosts", name="LBC", period=100
+    diag_type="LoadBalanceCosts",
+    name="LBC",
 )
 
 # Set up simulation
@@ -278,6 +273,7 @@
     particle_shape="cubic",
     warpx_numprocs=[1, 2],  # deactivate `numprocs` for dynamic load balancing
     warpx_use_filter=1,
+    warpx_reduced_diags_intervals=100,
     warpx_load_balance_intervals=100,
     warpx_load_balance_costs_update="heuristic",
 )

Examples/Tests/CMakeLists.txt

@@ -72,6 +72,7 @@ add_subdirectory(restart)
 add_subdirectory(restart_eb)
 add_subdirectory(rigid_injection)
 add_subdirectory(scraping)
+add_subdirectory(effective_potential_electrostatic)
 add_subdirectory(silver_mueller)
 add_subdirectory(single_particle)
 add_subdirectory(space_charge_initialization)

Examples/Tests/effective_potential_electrostatic/CMakeLists.txt

@@ -0,0 +1,12 @@
+# Add tests (alphabetical order) ##############################################
+#
+
+add_warpx_test(
+    test_3d_effective_potential_electrostatic_picmi  # name
+    3  # dims
+    2  # nprocs
+    inputs_test_3d_effective_potential_electrostatic_picmi.py  # inputs
+    analysis.py  # analysis
+    diags/field_diag/  # output
+    OFF  # dependency
+)