Merge branch 'development' into add_analysis_embedded_boundary_remova…

…l_depth

.azure-pipelines.yml

@@ -77,7 +77,7 @@ jobs:
     displayName: Cache Python Libraries
 
   - bash: |
-      set -eu -o pipefail
+      set -o nounset errexit pipefail
       cat /proc/cpuinfo | grep "model name" | sort -u
       df -h
       echo 'Acquire::Retries "3";' | sudo tee /etc/apt/apt.conf.d/80-retries
@@ -146,25 +146,36 @@ jobs:
     displayName: 'Install dependencies'
 
   - bash: |
-      set -eu -o pipefail
+      # set options
+      set -o nounset errexit pipefail
+      # display disk space usage
       df -h
-
       # configure
       export AMReX_CMAKE_FLAGS="-DAMReX_ASSERTIONS=ON -DAMReX_TESTING=ON"
-      cmake -S . -B build       \
-        ${AMReX_CMAKE_FLAGS}    \
-        ${WARPX_CMAKE_FLAGS}    \
-        -DWarpX_TEST_CLEANUP=ON \
-        -DWarpX_TEST_FPETRAP=ON
-
+      export WARPX_TEST_FLAGS="-DWarpX_TEST_CLEANUP=ON -DWarpX_TEST_FPETRAP=ON -DWarpX_TEST_DEBUG=ON"
+      cmake -S . -B build    \
+        ${AMReX_CMAKE_FLAGS} \
+        ${WARPX_CMAKE_FLAGS} \
+        ${WARPX_TEST_FLAGS}
       # build
       cmake --build build -j 2
+      # display disk space usage
       df -h
     displayName: 'Build'
 
   - bash: |
-      set -eu -o pipefail
-
+      # set options
+      set -o nounset errexit pipefail
       # run tests (exclude pytest.AMReX when running Python tests)
       ctest --test-dir build --output-on-failure -E AMReX
     displayName: 'Test'
+
+  - bash: |
+      # set options
+      set -o nounset errexit pipefail
+      # find and print backtrace
+      find build/bin/ -type f -name "Backtrace*" \
+        -exec echo -e "\nBacktrace\n---------\n{}\n---------" \; \
+        -exec cat {} \;
+    displayName: 'Logs'
+    condition: always()

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,58 @@
+---
+name: Bug report
+about: Report a bug or unexpected behavior.
+labels: [bug]
+---
+
+_Please remove any sensitive information (e.g., passwords, API keys) from your submission.
+Please check the relevant boxes and fill in the specific versions or details for the relevant items.
+Thank you for taking the time to report this issue. We will respond as soon as possible._
+
+## Description
+A clear and concise description of the bug.
+
+## Expected behavior
+What did you expect to happen when you encountered the issue?
+
+## How to reproduce
+Please provide (if available):
+- WarpX inputs files
+- PICMI Python files
+- Python post-processing scripts
+
+If you are unable to provide certain files or scripts, please describe the steps you took to encounter the issue.
+
+Please minimize your inputs/scripts to be concise and focused on the issue.
+For instance, make the simulation scripts as small and fast to run as possible.
+
+## System information
+Please check all relevant boxes and provide details.
+
+- Operating system (name and version):
+  - [ ] Linux: e.g., Ubuntu 22.04 LTS
+  - [ ] macOS: e.g., macOS Monterey 12.4
+  - [ ] Windows: e.g., Windows 11 Pro
+- Version of WarpX: e.g., latest, 24.10, etc.
+- Installation method:
+  - [ ] Conda
+  - [ ] Spack
+  - [ ] PyPI
+  - [ ] Brew
+  - [ ] From source with CMake
+  - [ ] Module system on an HPC cluster
+- Other dependencies: yes/no, describe
+- Computational resources:
+  - [ ] MPI: e.g., 2 MPI processes
+  - [ ] OpenMP: e.g., 2 OpenMP threads
+  - [ ] CPU: e.g., 2 CPUs
+  - [ ] GPU: e.g., 2 GPUs (NVIDIA, AMD, etc.)
+
+If you encountered the issue on an HPC cluster, please check our [HPC documentation](https://warpx.readthedocs.io/en/latest/install/hpc.html) to see if your HPC cluster is already supported.
+
+## Steps taken so far
+What troubleshooting steps have you taken so far, and what were the results?
+
+Have you tried debugging the code, following the instructions in our [debugging documentation](https://warpx.readthedocs.io/en/latest/usage/workflows/debugging.html)?
+
+## Additional information
+If applicable, please add any additional information that may help explain the issue, such as log files (e.g., build logs, error logs, etc.), error messages (e.g., compiler errors, runtime errors, etc.), screenshots, or other relevant details.

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1 @@
+blank_issues_enabled: true

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,27 @@
+---
+name: Feature request
+about: Suggest a new feature or enhancement.
+labels: [enhancement]
+---
+
+_Please remove any sensitive information (e.g., passwords, API keys) from your submission.
+Please check the relevant boxes and fill in the specific versions or details for the relevant items.
+Thank you for taking the time to report this issue. We will respond as soon as possible._
+
+## Context and motivation
+Please provide a clear and concise description of the context that is prompting you to request a new feature. What problem are you trying to solve, and how will this feature help you achieve your goals?
+
+## Proposed feature
+Describe the feature you would like to add to WarpX in detail. Please include:
+- A clear and concise description of the feature
+- Any relevant technical requirements or specifications
+- How you envision the feature being used
+
+## Alternative solutions
+Have you considered any alternative solutions or features that could achieve the same goal? If so, please describe them and explain why you believe the proposed feature is the best solution.
+
+## Additional information
+If applicable, please provide any additional information that may be relevant to the feature request, such as:
+- Links to existing codes or implementations
+- References to relevant publications or research
+- Any specific use cases or scenarios where the feature would be particularly useful

.github/ISSUE_TEMPLATE/installation-issue.md

@@ -0,0 +1,49 @@
+---
+name: Installation issue
+about: Report an issue with installing or setting up WarpX.
+labels: [install]
+---
+
+_Please remove any sensitive information (e.g., passwords, API keys) from your submission.
+Please check the relevant boxes and fill in the specific versions or details for the relevant items.
+Thank you for taking the time to report this issue. We will respond as soon as possible._
+
+## Description
+A clear and concise description of the issue.
+
+## System information
+- Operating system (name and version):
+  - [ ] Linux: e.g., Ubuntu 22.04 LTS
+  - [ ] macOS: e.g., macOS Monterey 12.4
+  - [ ] Windows: e.g., Windows 11 Pro
+- Version of WarpX: e.g., latest, 24.10, etc.
+- Installation method:
+  - [ ] Conda
+  - [ ] Spack
+  - [ ] PyPI
+  - [ ] Brew
+  - [ ] From source with CMake
+  - [ ] Module system on an HPC cluster
+- Other dependencies: yes/no, describe
+- Computational resources:
+  - [ ] CPU
+  - [ ] GPU: e.g., NVIDIA, AMD, etc.
+
+If you encountered the issue on an HPC cluster, please check our [HPC documentation](https://warpx.readthedocs.io/en/latest/install/hpc.html) to see if your HPC cluster is already supported.
+
+If you encountered the issue installing from source with CMake, please provide the output of the following steps:
+1. buildsystem generation: output of `cmake --fresh -S . -B build` (include your specific build options, e.g., `-DWarpX_DIMS=3`)
+2. project build: output of `cmake --build build` (include your specific build options, e.g., `-j 4`)
+
+If applicable, please add any additional information about your software environment:
+- [ ] CMake: e.g., 3.24.0
+- [ ] C++ compiler: e.g., GNU 11.3 with NVCC 12.0.76
+- [ ] Python: e.g., CPython 3.12
+- [ ] MPI: e.g., OpenMPI 4.1.1
+- [ ] FFTW: e.g., 3.3.10
+- [ ] HDF5: e.g., 1.14.0
+- [ ] ADIOS2: e.g., 2.10.0
+- Other dependencies: yes/no, describe
+
+## Additional information
+If applicable, please add any additional information that may help explain the issue, such as log files (e.g., build logs, error logs, etc.), error messages (e.g., compiler errors, runtime errors, etc.), screenshots, or other relevant details.

.github/workflows/cuda.yml

@@ -137,7 +137,7 @@ jobs:
         which nvcc || echo "nvcc not in PATH!"
 
         git clone https://github.com/AMReX-Codes/amrex.git ../amrex
-        cd ../amrex && git checkout --detach 92679babfc2cc66ca06ee591a80001db57c89878 && cd -
+        cd ../amrex && git checkout --detach 24.11 && 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: v0.7.1
+  rev: v0.7.2
   hooks:
     # Run the linter
     - id: ruff

CMakeLists.txt

@@ -1,7 +1,7 @@
 # Preamble ####################################################################
 #
 cmake_minimum_required(VERSION 3.24.0)
-project(WarpX VERSION 24.10)
+project(WarpX VERSION 24.11)
 
 include(${WarpX_SOURCE_DIR}/cmake/WarpXFunctions.cmake)
 
@@ -90,6 +90,13 @@ mark_as_advanced(WarpX_TEST_CLEANUP)
 option(WarpX_TEST_FPETRAP "Run CI tests with FPE-trapping runtime parameters" OFF)
 mark_as_advanced(WarpX_TEST_FPETRAP)
 
+# Advanced option to run CI tests with the -g compile option
+option(WarpX_TEST_DEBUG "Run CI tests with the -g compile option" OFF)
+mark_as_advanced(WarpX_TEST_DEBUG)
+if(WarpX_TEST_DEBUG)
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -g1")
+endif()
+
 set(WarpX_DIMS_VALUES 1 2 3 RZ)
 set(WarpX_DIMS 3 CACHE STRING "Simulation dimensionality <1;2;3;RZ>")
 list(REMOVE_DUPLICATES WarpX_DIMS)

Docs/source/conf.py

@@ -107,9 +107,9 @@ def __init__(self, *args, **kwargs):
 # built documents.
 #
 # The short X.Y version.
-version = "24.10"
+version = "24.11"
 # The full version, including alpha/beta/rc tags.
-release = "24.10"
+release = "24.11"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

Docs/source/highlights.rst

@@ -191,6 +191,11 @@ Please see :ref:`this section <acknowledge_warpx_all_refs>`.
 Nuclear Fusion and Plasma Confinement
 *************************************
 
+#. Scheffel J. and Jäderberg J. and Bendtz K. and Holmberg R. and Lindvall K.,
+   **Axial Confinement in the Novatron Mirror Machine**.
+   arXiv 2410.20134
+   `DOI:10.48550/arXiv.2410.20134 <https://doi.org/10.48550/arXiv.2410.20134>`__
+
 #. Affolter M., Thompson R., Hepner S., Hayes E. C., Podolsky V., Borghei M., Carlsson J., Gargone A., Merthe D., McKee E., Langtry R.,
    **The Orbitron: A crossed-field device for co-confinement of high energy ions and electrons**.
    AIP Advances **14**, 085025, 2024.

Docs/source/usage/parameters.rst

@@ -493,6 +493,37 @@ 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.
 
+    * ``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.
+      The expressions are given for the low and high boundary on each axis, as listed below. The tangential fields are specified as
+      expressions that can depend on the location and time. The tangential fields are in two pairs, the electric fields and the
+      magnetic fields. In each pair, if one is specified, the other will be set to zero if not also specified.
+
+      * ``insulator.area_x_lo(y,z)``: For the lower x (or r) boundary, expression specifying the insulator location
+
+      * ``insulator.area_x_hi(y,z)``: For the upper x (or r) boundary, expression specifying the insulator location
+
+      * ``insulator.area_y_lo(x,z)``: For the lower y boundary, expression specifying the insulator location
+
+      * ``insulator.area_y_hi(x,z)``: For the upper y boundary, expression specifying the insulator location
+
+      * ``insulator.area_z_lo(x,y)``: For the lower z boundary, expression specifying the insulator location
+
+      * ``insulator.area_z_hi(x,y)``: For the upper z boundary, expression specifying the insulator location
+
+      * ``insulator.Ey_x_lo(y,z,t)``, ``insulator.Ez_x_lo(y,z,t)``, ``insulator.By_x_lo(y,z,t)``, ``insulator.Bz_x_lo(y,z,t)``: expressions of the tangential field values for the lower x (or r) boundary
+
+      * ``insulator.Ey_x_hi(y,z,t)``, ``insulator.Ez_x_hi(y,z,t)``, ``insulator.By_x_hi(y,z,t)``, ``insulator.Bz_x_hi(y,z,t)``: expressions of the tangential field values for the upper x (or r) boundary
+
+      * ``insulator.Ex_y_lo(x,z,t)``, ``insulator.Ez_y_lo(x,z,t)``, ``insulator.Bx_y_lo(x,z,t)``, ``insulator.Bz_y_lo(x,z,t)``: expressions of the tangential field values for the lower y boundary
+
+      * ``insulator.Ex_y_hi(x,z,t)``, ``insulator.Ez_y_hi(x,z,t)``, ``insulator.Bx_y_hi(x,z,t)``, ``insulator.Bz_y_hi(x,z,t)``: expressions of the tangential field values for the upper y boundary
+
+      * ``insulator.Ex_z_lo(x,y,t)``, ``insulator.Ey_z_lo(x,y,t)``, ``insulator.Bx_z_lo(x,y,t)``, ``insulator.By_z_lo(x,y,t)``: expressions of the tangential field values for the lower z boundary
+
+      * ``insulator.Ex_z_hi(x,y,t)``, ``insulator.Ey_z_hi(x,y,t)``, ``insulator.Bx_z_hi(x,y,t)``, ``insulator.By_z_hi(x,y,t)``: expressions of the tangential field values for the upper z boundary
+
     * ``none``: No boundary condition is applied to the fields with the electromagnetic solver. This option must be used for the RZ-solver at `r=0`.
 
     * ``neumann``: For the electrostatic multigrid solver, a Neumann boundary condition (with gradient of the potential equal to 0) will be applied on the specified boundary.

Examples/CMakeLists.txt

@@ -198,7 +198,7 @@ function(add_warpx_test
     if(WarpX_TEST_CLEANUP)
         add_test(
             NAME ${name}.cleanup
-            COMMAND ${CMAKE_COMMAND} -E rm -rf ${THIS_WORKING_DIR}
+            COMMAND ${CMAKE_COMMAND} -P ${CMAKE_SOURCE_DIR}/Examples/test_cleanup.cmake ${THIS_WORKING_DIR}
         )
         # test cleanup depends on test run
         set_property(TEST ${name}.cleanup APPEND PROPERTY DEPENDS "${name}.run")

Examples/Tests/flux_injection/analysis_flux_injection_from_eb.py

@@ -32,7 +32,7 @@
 fn = sys.argv[1]
 ds = yt.load(fn)
 ad = ds.all_data()
-t_max = ds.current_time.item()  # time of simulation
+t_inj = 0.5e-8  # duration for which the flux injection was active
 
 # Extract the dimensionality of the simulation
 with open("./warpx_used_inputs", "r") as f:
@@ -52,7 +52,7 @@
     emission_surface = 4 * np.pi * R**2  # in m^2
 elif dims == "2D":
     emission_surface = 2 * np.pi * R  # in m
-Ntot = flux * emission_surface * t_max
+Ntot = flux * emission_surface * t_inj
 
 # Parameters of the histogram
 hist_bins = 50

Examples/Tests/flux_injection/inputs_base_from_eb

@@ -29,6 +29,8 @@ electron.inject_from_embedded_boundary = 1
 electron.num_particles_per_cell = 100
 electron.flux_profile = parse_flux_function
 electron.flux_function(x,y,z,t) = "1."
+electron.flux_tmin = 0.25e-8
+electron.flux_tmax = 0.75e-8
 electron.momentum_distribution_type = gaussianflux
 electron.ux_th = 0.01
 electron.uy_th = 0.01

Examples/Tests/pec/CMakeLists.txt

@@ -30,3 +30,13 @@ add_warpx_test(
     diags/diag1000020  # output
     OFF  # dependency
 )
+
+add_warpx_test(
+    test_2d_pec_field_insulator  # name
+    2  # dims
+    2  # nprocs
+    inputs_test_2d_pec_field_insulator  # inputs
+    analysis_default_regression.py  # analysis
+    diags/diag1000010  # output
+    OFF  # dependency
+)

Examples/Tests/pec/inputs_test_2d_pec_field_insulator

@@ -0,0 +1,34 @@
+# Maximum number of time steps
+max_step = 10
+
+# number of grid points
+amr.n_cell = 32 32
+amr.blocking_factor = 16
+
+# Maximum level in hierarchy (for now must be 0, i.e., one level in total)
+amr.max_level = 0
+
+# Geometry
+geometry.dims = 2
+geometry.prob_lo = 0.     2.e-2 # physical domain
+geometry.prob_hi = 1.e-2  3.e-2
+
+# Boundary condition
+boundary.field_lo = neumann      periodic
+boundary.field_hi = PECInsulator periodic
+
+warpx.serialize_initial_conditions = 1
+
+# Verbosity
+warpx.verbose = 1
+
+# CFL
+warpx.cfl = 1.0
+
+insulator.area_x_hi(y,z) = (2.25e-2 <= z and z <= 2.75e-2)
+insulator.By_x_hi(y,z,t) = min(t/1.0e-12,1)*1.e1*3.3e-4
+
+# Diagnostics
+diagnostics.diags_names = diag1
+diag1.intervals = 10
+diag1.diag_type = Full

Examples/test_cleanup.cmake

@@ -0,0 +1,7 @@
+# delete all test files except backtrace
+file(GLOB test_files ${CMAKE_ARGV3}/*)
+foreach(file ${test_files})
+    if(NOT ${file} MATCHES "Backtrace*")
+        execute_process(COMMAND ${CMAKE_COMMAND} -E rm -r ${file})
+    endif()
+endforeach()