Merge branch 'development' of https://github.com/ECP-WarpX/WarpX into…

… HSdevmerge_240304

.github/workflows/clang_tidy.yml

@@ -15,7 +15,7 @@ jobs:
     - 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:
@@ -32,8 +32,8 @@ 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  \
@@ -51,7 +51,7 @@ jobs:
 
         ${{github.workspace}}/.github/workflows/source/makeMakefileForClangTidy.py --input ${{github.workspace}}/ccache.log.txt
         make -j4 --keep-going -f clang-tidy-ccache-misses.mak \
-            CLANG_TIDY=clang-tidy \
+            CLANG_TIDY=clang-tidy-15 \
             CLANG_TIDY_ARGS="--config-file=${{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 3525b4a3f27eb64f746dd69b6613f71bb02d6e63 && 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

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>`.
 

Examples/Tests/particles_in_pml/analysis_particles_in_pml.py

@@ -30,8 +30,16 @@
 filename = sys.argv[1]
 ds = yt.load( filename )
 
+# When extracting the fields, choose the right dimensions
+dimensions = [ n_pts for n_pts in ds.domain_dimensions ]
+if ds.max_level == 1:
+    dimensions[0] *= 2
+    dimensions[1] *= 2
+    if ds.dimensionality == 3:
+        dimensions[2] *= 2
+
 # Check that the field is low enough
-ad0 = ds.covering_grid(level=0, left_edge=ds.domain_left_edge, dims=ds.domain_dimensions)
+ad0 = ds.covering_grid(level=ds.max_level, left_edge=ds.domain_left_edge, dims=dimensions)
 Ex_array = ad0[('mesh','Ex')].to_ndarray()
 Ey_array = ad0[('mesh','Ey')].to_ndarray()
 Ez_array = ad0[('mesh','Ez')].to_ndarray()

Python/pywarpx/__init__.py

@@ -19,8 +19,9 @@
     # add anything in PATH
     paths = os.environ.get("PATH", "")
     for p in paths.split(";"):
-        if os.path.exists(p):
-            os.add_dll_directory(p)
+        p_abs = os.path.abspath(os.path.expanduser(os.path.expandvars(p)))
+        if os.path.exists(p_abs):
+            os.add_dll_directory(p_abs)
 
 from .Algo import algo
 from .Amr import amr

Regression/WarpX-GPU-tests.ini

@@ -60,7 +60,7 @@ emailBody = Check https://ccse.lbl.gov/pub/GpuRegressionTesting/WarpX/ for more
 
 [AMReX]
 dir = /home/regtester/git/amrex/
-branch = 2ecafcff40132f56eb2b494e1a374684ff97117a
+branch = 3525b4a3f27eb64f746dd69b6613f71bb02d6e63
 
 [source]
 dir = /home/regtester/git/WarpX

Regression/WarpX-tests.ini

@@ -59,7 +59,7 @@ emailBody = Check https://ccse.lbl.gov/pub/RegressionTesting/WarpX/ for more det
 
 [AMReX]
 dir = /home/regtester/AMReX_RegTesting/amrex/
-branch = 2ecafcff40132f56eb2b494e1a374684ff97117a
+branch = 3525b4a3f27eb64f746dd69b6613f71bb02d6e63
 
 [source]
 dir = /home/regtester/AMReX_RegTesting/warpx
@@ -2525,7 +2525,7 @@ numthreads = 1
 compileTest = 0
 doVis = 0
 compareParticles = 0
-analysisRoutine = Examples/Tests/particles_in_pml/analysis_particles_in_pml_2dmr.py
+analysisRoutine = Examples/Tests/particles_in_pml/analysis_particles_in_pml.py
 
 [particles_in_pml_3d_MR]
 buildDir = .

Source/AcceleratorLattice/AcceleratorLattice.cpp

@@ -102,6 +102,6 @@ AcceleratorLattice::UpdateElementFinder (int const lev) // NOLINT(readability-ma
 LatticeElementFinderDevice
 AcceleratorLattice::GetFinderDeviceInstance (WarpXParIter const& a_pti, int const a_offset) const
 {
-    LatticeElementFinder & finder = (*m_element_finder)[a_pti];
+    const LatticeElementFinder & finder = (*m_element_finder)[a_pti];
     return finder.GetFinderDeviceInstance(a_pti, a_offset, *this);
 }

Source/BoundaryConditions/WarpX_PEC.cpp

@@ -500,7 +500,7 @@ PEC::ApplyPECtoElectronPressure (amrex::MultiFab* Pefield, const int lev,
 
     amrex::Box domain_box = warpx.Geom(lev).Domain();
     if (patch_type == PatchType::coarse) {
-        amrex::IntVect ref_ratio = ( (lev > 0) ? WarpX::RefRatio(lev-1) : amrex::IntVect(1) );
+        const amrex::IntVect ref_ratio = ( (lev > 0) ? WarpX::RefRatio(lev-1) : amrex::IntVect(1) );
         domain_box.coarsen(ref_ratio);
     }
     domain_box.convert(Pefield->ixType());
@@ -552,7 +552,7 @@ PEC::ApplyPECtoElectronPressure (amrex::MultiFab* Pefield, const int lev,
             amrex::ignore_unused(j,k);
 #endif
             // Store the array index
-            amrex::IntVect iv(AMREX_D_DECL(i,j,k));
+            const amrex::IntVect iv(AMREX_D_DECL(i,j,k));
 
             PEC::SetNeumannOnPEC(n, iv, Pe_array, mirrorfac, is_pec, fabbox);
         });

Source/Diagnostics/BTDiagnostics.cpp

@@ -901,7 +901,7 @@ BTDiagnostics::DefineFieldBufferMultiFab (const int i_buffer, const int lev)
     const int hi_k_lab = m_buffer_k_index_hi[i_buffer];
     m_buffer_box[i_buffer].setSmall( m_moving_window_dir, hi_k_lab - m_buffer_size + 1);
     m_buffer_box[i_buffer].setBig( m_moving_window_dir, hi_k_lab );
-    amrex::BoxArray buffer_ba( m_buffer_box[i_buffer] );
+    const amrex::BoxArray buffer_ba( m_buffer_box[i_buffer] );
     // Generate a new distribution map for the back-transformed buffer multifab
     const amrex::DistributionMapping buffer_dmap(buffer_ba);
     // Number of guard cells for the output buffer is zero.
@@ -1040,7 +1040,7 @@ BTDiagnostics::Flush (int i_buffer, bool force_flush)
         m_buffer_box[i_buffer].setSmall(m_moving_window_dir, (m_buffer_box[i_buffer].smallEnd(m_moving_window_dir) - 1) );
         m_buffer_box[i_buffer].setBig(m_moving_window_dir, (m_buffer_box[i_buffer].bigEnd(m_moving_window_dir) + 1) );
         const amrex::Box particle_buffer_box = m_buffer_box[i_buffer];
-        amrex::BoxArray buffer_ba( particle_buffer_box );
+        const amrex::BoxArray buffer_ba( particle_buffer_box );
         m_particles_buffer[i_buffer][0]->SetParticleBoxArray(0, buffer_ba);
         for (int isp = 0; isp < m_particles_buffer.at(i_buffer).size(); ++isp) {
             // BTD output is single level. Setting particle geometry, dmap, boxarray to level0
@@ -1467,7 +1467,7 @@ BTDiagnostics::PrepareParticleDataForOutput()
                             DefineFieldBufferMultiFab(i_buffer, lev);
                         }
                         const amrex::Box particle_buffer_box = m_buffer_box[i_buffer];
-                        amrex::BoxArray buffer_ba( particle_buffer_box );
+                        const amrex::BoxArray buffer_ba( particle_buffer_box );
                         const amrex::DistributionMapping buffer_dmap(buffer_ba);
                         m_particles_buffer[i_buffer][i]->SetParticleBoxArray(lev, buffer_ba);
                         m_particles_buffer[i_buffer][i]->SetParticleDistributionMap(lev, buffer_dmap);

Source/Diagnostics/ComputeDiagFunctors/BackTransformFunctor.cpp

@@ -81,7 +81,7 @@ BackTransformFunctor::operator ()(amrex::MultiFab& mf_dst, int /*dcomp*/, const
         slice_box.setBig(moving_window_dir, i_boost);
 
         // Make it a BoxArray
-        amrex::BoxArray slice_ba(slice_box);
+        const amrex::BoxArray slice_ba(slice_box);
         // Define MultiFab with the distribution map of the destination multifab and
         // containing all ten components that were in the slice generated from m_mf_src.
         std::unique_ptr< amrex::MultiFab > tmp_slice_ptr = nullptr;

Source/Diagnostics/FlushFormats/FlushFormatPlotfile.cpp

@@ -303,7 +303,7 @@ FlushFormatPlotfile::WriteWarpXHeader(
 
         warpx.GetPartContainer().WriteHeader(HeaderFile);
 
-        MultiParticleContainer& mypc = warpx.GetPartContainer();
+        const MultiParticleContainer& mypc = warpx.GetPartContainer();
         const int n_species = mypc.nSpecies();
         for (int i=0; i<n_species; i++)
         {

Source/Diagnostics/FullDiagnostics.cpp

@@ -43,8 +43,8 @@ using namespace amrex::literals;
 FullDiagnostics::FullDiagnostics (int i, std::string name):
     Diagnostics{i, name},
     m_solver_deposits_current{
-        !(WarpX::electromagnetic_solver_id == ElectromagneticSolverAlgo::None &&
-        WarpX::electrostatic_solver_id != ElectrostaticSolverAlgo::LabFrameElectroMagnetostatic)}
+        (WarpX::electromagnetic_solver_id != ElectromagneticSolverAlgo::None) ||
+        (WarpX::electrostatic_solver_id == ElectrostaticSolverAlgo::LabFrameElectroMagnetostatic)}
 {
     ReadParameters();
     BackwardCompatibility();

Source/Diagnostics/ReducedDiags/ColliderRelevant.cpp

@@ -63,7 +63,7 @@ ColliderRelevant::ColliderRelevant (std::string rd_name)
 : ReducedDiags{std::move(rd_name)}
 {
     // read colliding species names - must be 2
-    amrex::ParmParse pp_rd_name(m_rd_name);
+    const amrex::ParmParse pp_rd_name(m_rd_name);
     pp_rd_name.getarr("species", m_beam_name);
 
     WARPX_ALWAYS_ASSERT_WITH_MESSAGE(
@@ -203,7 +203,7 @@ void ColliderRelevant::ComputeDiags (int step)
 
     // get cell volume
     amrex::Geometry const & geom = warpx.Geom(0);
-    amrex::Real dV = AMREX_D_TERM(geom.CellSize(0), *geom.CellSize(1), *geom.CellSize(2));
+    const amrex::Real dV = AMREX_D_TERM(geom.CellSize(0), *geom.CellSize(1), *geom.CellSize(2));
 
     const auto get_idx = [&](const std::string& name){
         return m_headers_indices.at(name).idx;
@@ -544,7 +544,7 @@ void ColliderRelevant::ComputeDiags (int step)
 
     // make density MultiFabs from nodal to cell centered
     amrex::BoxArray ba = warpx.boxArray(0);
-    amrex::DistributionMapping dmap = warpx.DistributionMap(0);
+    const amrex::DistributionMapping dmap = warpx.DistributionMap(0);
     constexpr int ncomp = 1;
     constexpr int ngrow = 0;
     amrex::MultiFab mf_dst1(ba.convert(amrex::IntVect::TheCellVector()), dmap, ncomp, ngrow);

Source/Diagnostics/ReducedDiags/FieldReduction.cpp

@@ -89,7 +89,7 @@ FieldReduction::FieldReduction (std::string rd_name)
 
 void FieldReduction::BackwardCompatibility ()
 {
-    amrex::ParmParse pp_rd_name(m_rd_name);
+    const amrex::ParmParse pp_rd_name(m_rd_name);
     std::vector<std::string> backward_strings;
     WARPX_ALWAYS_ASSERT_WITH_MESSAGE(
         !pp_rd_name.queryarr("reduced_function(x,y,z,Ex,Ey,Ez,Bx,By,Bz)", backward_strings),

Source/Diagnostics/ReducedDiags/ParticleHistogram2D.cpp

@@ -267,10 +267,12 @@ void ParticleHistogram2D::WriteToFile (int step) const
     const std::string fileSuffix = std::string("_%0") + std::to_string(m_file_min_digits) + std::string("T");
     filename = filename.append(fileSuffix).append(".").append(m_openpmd_backend);
 
-    std::string filepath = m_path + m_rd_name + "/" + filename;
     // transform paths for Windows
     #ifdef _WIN32
-        filepath = openPMD::auxiliary::replace_all(filepath, "/", "\\");
+        const std::string filepath = openPMD::auxiliary::replace_all(
+            m_path + m_rd_name + "/" + filename, "/", "\\");
+    #else
+        const std::string filepath = m_path + m_rd_name + "/" + filename;
     #endif
 
     // Create the OpenPMD series

Source/Diagnostics/ReducedDiags/ReducedDiags.cpp

@@ -40,7 +40,7 @@ ReducedDiags::ReducedDiags (std::string rd_name)
     std::string restart_chkfile;
     const ParmParse pp_amr("amr");
     pp_amr.query("restart", restart_chkfile);
-    bool IsNotRestart = restart_chkfile.empty();
+    const bool IsNotRestart = restart_chkfile.empty();
 
     if (ParallelDescriptor::IOProcessor())
     {
@@ -50,7 +50,7 @@ ReducedDiags::ReducedDiags (std::string rd_name)
         { amrex::CreateDirectoryFailed(m_path); }
 
         // replace / create output file
-        std::string rd_full_file_name = m_path + m_rd_name + "." + m_extension;
+        const std::string rd_full_file_name = m_path + m_rd_name + "." + m_extension;
         m_write_header = IsNotRestart || !amrex::FileExists(rd_full_file_name); // not a restart or file doesn't exist
         if (m_write_header)
         {

Source/Diagnostics/WarpXOpenPMD.cpp

@@ -675,7 +675,7 @@ WarpXOpenPMDPlot::DumpToFile (ParticleContainer* pc,
     openPMD::ParticleSpecies currSpecies = currIteration.particles[name];
 
     // only BTD writes multiple times into the same step, zero for other methods
-    unsigned long ParticleFlushOffset = isBTD ? num_already_flushed(currSpecies) : 0;
+    const unsigned long ParticleFlushOffset = isBTD ? num_already_flushed(currSpecies) : 0;
 
     // prepare data structures the first time BTD has non-zero particles
     //   we set some of them to zero extent, so we need to time that well