Merge branch 'plasma_chamber' of github.com:ajnonaka/WarpX into plasm…

…a_chamber

.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 24.12 && 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: v0.7.4
+  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/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/usage/parameters.rst

@@ -3589,22 +3589,27 @@ This shifts analysis from post-processing to runtime calculation of reduction op
     * ``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
 ------------------------------------------------

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/implicit/inputs_test_1d_semi_implicit_picard

@@ -85,7 +85,6 @@ diag1.electrons.variables = z w ux uy uz
 diag1.protons.variables = z w ux uy uz
 
 warpx.reduced_diags_names = particle_energy field_energy
+reduced_diags.intervals = 1
 particle_energy.type = ParticleEnergy
-particle_energy.intervals = 1
 field_energy.type = FieldEnergy
-field_energy.intervals = 1

Examples/Tests/implicit/inputs_test_1d_theta_implicit_picard

@@ -85,7 +85,6 @@ diag1.electrons.variables = z w ux uy uz
 diag1.protons.variables = z w ux uy uz
 
 warpx.reduced_diags_names = particle_energy field_energy
+reduced_diags.intervals = 1
 particle_energy.type = ParticleEnergy
-particle_energy.intervals = 1
 field_energy.type = FieldEnergy
-field_energy.intervals = 1

Examples/Tests/implicit/inputs_test_2d_theta_implicit_jfnk_vandb

@@ -109,7 +109,6 @@ diag1.electrons.variables = x z w ux uy uz
 diag1.protons.variables = x z w ux uy uz
 
 warpx.reduced_diags_names = particle_energy field_energy
+reduced_diags.intervals = 1
 particle_energy.type = ParticleEnergy
-particle_energy.intervals = 1
 field_energy.type = FieldEnergy
-field_energy.intervals = 1

Examples/Tests/implicit/inputs_test_2d_theta_implicit_jfnk_vandb_filtered

@@ -109,7 +109,6 @@ diag1.electrons.variables = x z w ux uy uz
 diag1.protons.variables = x z w ux uy uz
 
 warpx.reduced_diags_names = particle_energy field_energy
+reduced_diags.intervals = 1
 particle_energy.type = ParticleEnergy
-particle_energy.intervals = 1
 field_energy.type = FieldEnergy
-field_energy.intervals = 1

Examples/Tests/implicit/inputs_test_2d_theta_implicit_strang_psatd

@@ -92,7 +92,6 @@ diag1.electrons.variables = x z w ux uy uz
 diag1.protons.variables = x z w ux uy uz
 
 warpx.reduced_diags_names = particle_energy field_energy
+reduced_diags.intervals = 1
 particle_energy.type = ParticleEnergy
-particle_energy.intervals = 1
 field_energy.type = FieldEnergy
-field_energy.intervals = 1

Python/pywarpx/picmi.py

@@ -2770,6 +2770,21 @@ class Simulation(picmistandard.PICMI_Simulation):
 
     warpx_used_inputs_file: string, optional
         The name of the text file that the used input parameters is written to,
+
+    warpx_reduced_diags_path: string, optional
+        Sets the default path for reduced diagnostic output files
+
+    warpx_reduced_diags_extension: string, optional
+        Sets the default extension for reduced diagnostic output files
+
+    warpx_reduced_diags_intervals: string, optional
+        Sets the default intervals for reduced diagnostic output files
+
+    warpx_reduced_diags_separator: string, optional
+        Sets the default separator for reduced diagnostic output files
+
+    warpx_reduced_diags_precision: integer, optional
+        Sets the default precision for reduced diagnostic output files
     """
 
     # Set the C++ WarpX interface (see _libwarpx.LibWarpX) as an extension to
@@ -2836,6 +2851,12 @@ def init(self, kw):
         self.checkpoint_signals = kw.pop("warpx_checkpoint_signals", None)
         self.numprocs = kw.pop("warpx_numprocs", None)
 
+        self.reduced_diags_path = kw.pop("warpx_reduced_diags_path", None)
+        self.reduced_diags_extension = kw.pop("warpx_reduced_diags_extension", None)
+        self.reduced_diags_intervals = kw.pop("warpx_reduced_diags_intervals", None)
+        self.reduced_diags_separator = kw.pop("warpx_reduced_diags_separator", None)
+        self.reduced_diags_precision = kw.pop("warpx_reduced_diags_precision", None)
+
         self.inputs_initialized = False
         self.warpx_initialized = False
 
@@ -2902,6 +2923,13 @@ def initialize_inputs(self):
 
         pywarpx.warpx.numprocs = self.numprocs
 
+        reduced_diags = pywarpx.warpx.get_bucket("reduced_diags")
+        reduced_diags.path = self.reduced_diags_path
+        reduced_diags.extension = self.reduced_diags_extension
+        reduced_diags.intervals = self.reduced_diags_intervals
+        reduced_diags.separator = self.reduced_diags_separator
+        reduced_diags.precision = self.reduced_diags_precision
+
         particle_shape = self.particle_shape
         for s in self.species:
             if s.particle_shape is not None:
@@ -3943,7 +3971,7 @@ def __init__(
         self,
         diag_type,
         name=None,
-        period=1,
+        period=None,
         path=None,
         extension=None,
         separator=None,

Python/setup.py

@@ -65,7 +65,7 @@
 
 setup(
     name="pywarpx",
-    version="24.11",
+    version="24.12",
     packages=["pywarpx"],
     package_dir={"pywarpx": "pywarpx"},
     description="""Wrapper of WarpX""",

Regression/Checksum/benchmarks_json/test_2d_pec_field_insulator.json

@@ -1,11 +1,11 @@
 {
   "lev=0": {
     "Bx": 0.0,
-    "By": 0.33065279639752304,
+    "By": 0.3605690508580849,
     "Bz": 0.0,
-    "Ex": 31873416.396984838,
+    "Ex": 37101418.32484252,
     "Ey": 0.0,
-    "Ez": 99285542.27022335,
+    "Ez": 108228802.9434361,
     "jx": 0.0,
     "jy": 0.0,
     "jz": 0.0

Source/BoundaryConditions/PEC_Insulator.cpp

@@ -62,8 +62,9 @@ namespace
                                   amrex::GpuArray<FieldBoundaryType, 3> const fbndry_hi)
     {
         using namespace amrex::literals;
+        amrex::IntVect ijk_next = ijk_vec;
+        amrex::IntVect ijk_nextp1 = ijk_vec;
         amrex::IntVect ijk_mirror = ijk_vec;
-        amrex::IntVect ijk_mirrorp1 = ijk_vec;
         bool OnBoundary = false;
         bool GuardCell = false;
         bool isInsulatorBoundary = false;
@@ -114,12 +115,14 @@ namespace
                     } else if (ig > 0) {
                         GuardCell = true;
 
+                        // Location of the next cells inward
+                        ijk_next[idim] = ijk_vec[idim] - ig*iside;
+                        ijk_nextp1[idim] = ijk_next[idim] - ig*iside;
+
                         // Mirror location inside the domain by "ig" number of cells
                         ijk_mirror[idim] = ( (iside == -1)
                                         ? (dom_lo[idim] + ig - (1 - is_nodal[idim]))
-                                        : (dom_hi[idim] + 1 - ig));
-                        // Location twice as far in, for extrapolation
-                        ijk_mirrorp1[idim] = 2*ijk_mirror[idim] - ijk_vec[idim];
+                                        : (dom_hi[idim] - ig + 1));
 
                         // Check for components with even symmetry.
                         // True for E_like and tangential, and B_like and normal
@@ -156,12 +159,12 @@ namespace
                 // The value on the boundary is left unmodified
                 // The values in the guard cells are extrapolated
                 if (GuardCell) {
-                    field(ijk_vec, n) = 2._rt*field(ijk_mirror, n) - field(ijk_mirrorp1, n);
+                    field(ijk_vec, n) = 2._rt*field(ijk_next, n) - field(ijk_nextp1, n);
                 }
             } else if ((OnBoundary || GuardCell) && set_field) {
                 field(ijk_vec, n) = field_value;
             } else if (GuardCell) {
-                field(ijk_vec, n) = 2._rt*field(ijk_mirror, n) - field(ijk_mirrorp1, n);
+                field(ijk_vec, n) = 2._rt*field(ijk_next, n) - field(ijk_nextp1, n);
             }
         } else {
             if (OnBoundary && (E_like ^ is_normal_to_boundary)) {