Merge pull request #140 from RevathiJambunathan/HSdevmerge_240304

HSdevmerge 240304

.github/workflows/clang_tidy.yml

@@ -8,14 +8,17 @@ concurrency:
 
 jobs:
   run_clang_tidy:
-    name: clang-tidy
+    strategy:
+      matrix:
+        dim: [1, 2, RZ, 3]
+    name: clang-tidy-${{ matrix.dim }}D
     runs-on: ubuntu-22.04
     if: github.event.pull_request.draft == false
     steps:
     - uses: actions/checkout@v4
     - name: install dependencies
       run: |
-        .github/workflows/dependencies/clang14.sh
+        .github/workflows/dependencies/clang15.sh
     - name: set up cache
       uses: actions/cache@v4
       with:
@@ -32,26 +35,26 @@ jobs:
         export CCACHE_LOGFILE=${{ github.workspace }}/ccache.log.txt
         ccache -z
 
-        export CXX=$(which clang++)
-        export CC=$(which clang)
+        export CXX=$(which clang++-15)
+        export CC=$(which clang-15)
 
-        cmake -S . -B build_clang_tidy \
-          -DCMAKE_VERBOSE_MAKEFILE=ON  \
-          -DWarpX_DIMS="1;2;RZ;3"      \
-          -DWarpX_MPI=ON               \
-          -DWarpX_COMPUTE=OMP          \
-          -DWarpX_PSATD=ON             \
-          -DWarpX_QED=ON               \
-          -DWarpX_QED_TABLE_GEN=ON     \
-          -DWarpX_OPENPMD=ON           \
-          -DWarpX_PRECISION=SINGLE     \
+        cmake -S . -B build_clang_tidy      \
+          -DCMAKE_VERBOSE_MAKEFILE=ON       \
+          -DWarpX_DIMS="${{ matrix.dim }}"  \
+          -DWarpX_MPI=ON                    \
+          -DWarpX_COMPUTE=OMP               \
+          -DWarpX_PSATD=ON                  \
+          -DWarpX_QED=ON                    \
+          -DWarpX_QED_TABLE_GEN=ON          \
+          -DWarpX_OPENPMD=ON                \
+          -DWarpX_PRECISION=SINGLE          \
           -DCMAKE_CXX_COMPILER_LAUNCHER=ccache
 
         cmake --build build_clang_tidy -j 4
 
         ${{github.workspace}}/.github/workflows/source/makeMakefileForClangTidy.py --input ${{github.workspace}}/ccache.log.txt
         make -j4 --keep-going -f clang-tidy-ccache-misses.mak \
-            CLANG_TIDY=clang-tidy \
+            CLANG_TIDY=clang-tidy-15 \
             CLANG_TIDY_ARGS="--config-file=${{github.workspace}}/.clang-tidy --warnings-as-errors=*"
 
         ccache -s

.github/workflows/cuda.yml

@@ -115,7 +115,7 @@ jobs:
         which nvcc || echo "nvcc not in PATH!"
 
         git clone https://github.com/AMReX-Codes/amrex.git ../amrex
-        cd ../amrex && git checkout --detach 2ecafcff40132f56eb2b494e1a374684ff97117a && cd -
+        cd ../amrex && git checkout --detach 24.03 && cd -
         make COMP=gcc QED=FALSE USE_MPI=TRUE USE_GPU=TRUE USE_OMP=FALSE USE_PSATD=TRUE USE_CCACHE=TRUE -j 4
 
         ccache -s

.github/workflows/dependencies/clang14.sh → .github/workflows/dependencies/clang15.sh

@@ -15,17 +15,17 @@ echo 'Acquire::Retries "3";' | sudo tee /etc/apt/apt.conf.d/80-retries
 sudo apt-get -qqq update
 sudo apt-get install -y \
     cmake               \
-    clang-14            \
-    clang-tidy-14       \
+    clang-15            \
+    clang-tidy-15       \
     libblas-dev         \
-    libc++-14-dev       \
+    libc++-15-dev       \
     libboost-math-dev   \
     libfftw3-dev        \
     libfftw3-mpi-dev    \
     libhdf5-openmpi-dev \
     liblapack-dev       \
     libopenmpi-dev      \
-    libomp-dev          \
+    libomp-15-dev          \
     ninja-build
 
 # ccache

CMakeLists.txt

@@ -1,7 +1,7 @@
 # Preamble ####################################################################
 #
 cmake_minimum_required(VERSION 3.20.0)
-project(WarpX VERSION 24.02)
+project(WarpX VERSION 24.03)
 
 include(${WarpX_SOURCE_DIR}/cmake/WarpXFunctions.cmake)
 

CONTRIBUTING.rst

@@ -10,10 +10,7 @@ Git workflow
 ------------
 
 The WarpX project uses `git <https://git-scm.com>`_ for version control.
-If you are new to git, you can follow one of these tutorials:
-
-- `Learn git with bitbucket <https://www.atlassian.com/git/tutorials/learn-git-with-bitbucket-cloud>`_
-- `git - the simple guide <http://rogerdudler.github.io/git-guide/>`_
+If you are new to git, you can follow `this tutorial <https://swcarpentry.github.io/git-novice/>`__.
 
 Configure your GitHub Account & Development Machine
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Docs/source/conf.py

@@ -103,9 +103,9 @@ def __init__(self, *args, **kwargs):
 # built documents.
 #
 # The short X.Y version.
-version = u'24.02'
+version = u'24.03'
 # The full version, including alpha/beta/rc tags.
-release = u'24.02'
+release = u'24.03'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

Docs/source/developers/testing.rst

@@ -34,6 +34,20 @@ For instance, compiling with ``clang++ -Werror`` would be:
    export CXXFLAGS="-Werror"
 
 
+Run Pre-Commit Tests Locally
+----------------------------
+
+When proposing code changes to Warpx, we perform a couple of automated stylistic and correctness checks on the code change.
+You can run those locally before you push to save some time, install them once like this:
+
+.. code-block:: sh
+
+   python -m pip install -U pre-commit
+   pre-commit install
+
+See `pre-commit.com <https://pre-commit.com>`__ and our ``.pre-commit-config.yaml`` file in the repository for more details.
+
+
 Run the test suite locally
 --------------------------
 

Docs/source/install/cmake.rst

@@ -223,11 +223,11 @@ For PICMI Python bindings, configure WarpX to produce a library and call our ``p
 .. code-block:: bash
 
    # find dependencies & configure for all WarpX dimensionalities
-   cmake -S . -B build -DWarpX_DIMS="1;2;RZ;3" -DWarpX_PYTHON=ON
+   cmake -S . -B build_py -DWarpX_DIMS="1;2;RZ;3" -DWarpX_PYTHON=ON
 
 
    # build and then call "python3 -m pip install ..."
-   cmake --build build --target pip_install -j 4
+   cmake --build build_py --target pip_install -j 4
 
 **That's it!**
 You can now :ref:`run a first 3D PICMI script <usage-picmi>` from our :ref:`examples <usage-examples>`.
@@ -324,10 +324,10 @@ This is the workflow most developers will prefer as it allows rapid re-compiles:
 .. code-block:: bash
 
    # build WarpX executables and libraries
-   cmake -S . -B build -DWarpX_DIMS="1;2;RZ;3" -DWarpX_PYTHON=ON
+   cmake -S . -B build_py -DWarpX_DIMS="1;2;RZ;3" -DWarpX_PYTHON=ON
 
    # build & install Python only
-   cmake --build build -j 4 --target pip_install
+   cmake --build build_py -j 4 --target pip_install
 
 There is also a ``--target pip_install_nodeps`` option that :ref:`skips pip-based dependency checks <developers-local-compile-pylto>`.
 

Docs/source/usage/workflows/python_extend.rst

@@ -90,6 +90,12 @@ This object is the Python equivalent to the C++ ``WarpX`` simulation class.
 
    .. py:method:: get_particle_boundary_buffer
 
+   .. py:method:: set_potential_on_domain_boundary(potential_[lo/hi]_[x/y/z]: str)
+
+      The potential on the domain boundaries can be modified when using the electrostatic solver.
+      This function updates the strings and function parsers which set the domain
+      boundary potentials during the Poisson solve.
+
    .. py:method:: set_potential_on_eb(potential: str)
 
       The embedded boundary (EB) conditions can be modified when using the electrostatic solver.

Examples/Tests/embedded_boundary_diffraction/analysis_fields.py

@@ -0,0 +1,41 @@
+#!/usr/bin/env python3
+"""
+This test checks the implementation of the embedded boundary in cylindrical geometry,
+by checking the diffraction of a laser by an embedded boundary here.
+We then check that the first minimum of the diffracted intensity pattern
+occurs along the angle given by the theoretical Airy pattern, i.e.
+theta_diffraction = 1.22 * lambda / d
+"""
+import os
+import sys
+
+import numpy as np
+from openpmd_viewer import OpenPMDTimeSeries
+from scipy.ndimage import gaussian_filter1d
+
+sys.path.insert(1, '../../../../warpx/Regression/Checksum/')
+import checksumAPI
+
+ts = OpenPMDTimeSeries('./EmbeddedBoundaryDiffraction_plt/')
+
+# Extract the intensity as a function of r and z
+Ex, info = ts.get_field('E', 'x', iteration=300)
+I = gaussian_filter1d(Ex**2, sigma=5, axis=0) # Extract intensity by averaging E^2 over wavelength
+irmax = np.argmax( I, axis=-1)
+
+# Find the radius of the first minimum, as a function of z
+def r_first_minimum(iz):
+    ir = len(info.r)//2
+    while I[iz, ir+1] < I[iz, ir]:
+        ir += 1
+    return info.r[ir]
+r = np.array([ r_first_minimum(iz) for iz in range(len(info.z)) ])
+
+# Check that this corresponds to the prediction from the Airy pattern
+theta_diffraction = np.arcsin(1.22*0.1/0.4)/2
+assert np.all( abs(r[50:] - theta_diffraction*info.z[50:]) < 0.03 )
+
+# Open the right plot file
+filename = sys.argv[1]
+test_name = os.path.split(os.getcwd())[1]
+checksumAPI.evaluate_checksum(test_name, filename, output_format='openpmd')

Examples/Tests/embedded_boundary_diffraction/inputs_rz

@@ -0,0 +1,42 @@
+# This script tests the diffraction of a laser by
+# a cylindrical object, represented by an embedded boundary here
+
+max_step = 300
+amr.n_cell = 128 256
+amr.max_grid_size = 256
+amr.max_level = 0
+
+geometry.dims = RZ
+geometry.prob_lo     =  0. -0.2
+geometry.prob_hi     =  2   1.4
+warpx.cfl = 0.99
+algo.particle_shape = 1
+
+boundary.field_lo = none absorbing_silver_mueller
+boundary.field_hi = pec absorbing_silver_mueller
+
+# Make the cylindrical object that the laser will diffract on
+my_constants.aperture_l = 0.01
+my_constants.aperture_r = 0.2
+warpx.eb_implicit_function = "if( (abs(z)<0.5*aperture_l) and (x<aperture_r), 1, -1 )"
+
+warpx.n_rz_azimuthal_modes = 2
+
+# Laser
+lasers.names        = laser1
+laser1.profile      = Gaussian
+laser1.position     = 0. 0. -0.1
+laser1.direction    = 0. 0. 1.
+laser1.polarization = 1. 0. 0.
+laser1.profile_waist = 1.
+laser1.profile_duration = 100
+laser1.profile_t_peak = 0
+laser1.profile_focal_distance = 0
+laser1.e_max        = 1.
+laser1.wavelength   = 0.1
+
+diagnostics.diags_names = diag1
+diag1.intervals = 100
+diag1.diag_type = Full
+diag1.fields_to_plot = Er Et Ez Br Bt Bz
+diag1.format = openpmd