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

… HSdevmerge_240303

.github/workflows/clang_tidy.yml

@@ -8,7 +8,10 @@ concurrency:
 
 jobs:
   run_clang_tidy:
-    name: clang-tidy
+    strategy:
+      matrix:
+        dim: [1, 2, RZ, 3]
+    name: clang-tidy-${{ matrix.dim }}D
     runs-on: ubuntu-22.04
     if: github.event.pull_request.draft == false
     steps:
@@ -35,16 +38,16 @@ jobs:
         export CXX=$(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/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 3525b4a3f27eb64f746dd69b6613f71bb02d6e63 && 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

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/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

Examples/Tests/particle_boundary_interaction/PICMI_inputs_rz.py

@@ -0,0 +1,169 @@
+#!/usr/bin/env python3
+# @Eya Dammak supervised by @Remi Lehe, 2024
+# --- Input file for particle-boundary interaction testing in RZ.
+# --- This input is a simple case of reflection
+# --- of one electron on the surface of a sphere.
+import numpy as np
+
+from pywarpx import callbacks, particle_containers, picmi
+
+##########################
+# numerics parameters
+##########################
+
+dt = 1.0e-11
+
+# --- Nb time steps
+
+max_steps = 23
+diagnostic_interval = 1
+
+# --- grid
+
+nr = 64
+nz= 64
+
+rmin = 0.0
+rmax = 2
+zmin = -2
+zmax = 2
+
+##########################
+# numerics components
+##########################
+
+grid = picmi.CylindricalGrid(
+    number_of_cells = [nr, nz],
+    n_azimuthal_modes = 1,
+    lower_bound = [rmin, zmin],
+    upper_bound = [rmax, zmax],
+    lower_boundary_conditions = ['none', 'dirichlet'],
+    upper_boundary_conditions =  ['dirichlet', 'dirichlet'],
+    lower_boundary_conditions_particles = ['absorbing', 'reflecting'],
+    upper_boundary_conditions_particles =  ['absorbing', 'reflecting']
+)
+
+
+solver = picmi.ElectrostaticSolver(
+    grid=grid, method='Multigrid',
+    warpx_absolute_tolerance=1e-7
+)
+
+embedded_boundary = picmi.EmbeddedBoundary(
+    implicit_function="-(x**2+y**2+z**2-radius**2)",
+    radius = 0.2
+)
+
+##########################
+# physics components
+##########################
+
+#one particle
+e_dist=picmi.ParticleListDistribution(x=0.0, y=0.0, z=-0.25, ux=0.5e10, uy=0.0, uz=1.0e10, weight=1)
+
+electrons = picmi.Species(
+    particle_type='electron', name='electrons', initial_distribution=e_dist, warpx_save_particles_at_eb=1
+)
+
+##########################
+# diagnostics
+##########################
+
+field_diag = picmi.FieldDiagnostic(
+    name = 'diag1',
+    grid = grid,
+    period = diagnostic_interval,
+    data_list = ['Er', 'Ez', 'phi', 'rho','rho_electrons'],
+    warpx_format = 'openpmd',
+    write_dir = '.',
+    warpx_file_prefix = 'particle_boundary_interaction_plt'
+)
+
+part_diag = picmi.ParticleDiagnostic(name = 'diag1',
+    period = diagnostic_interval,
+    species = [electrons],
+    warpx_format = 'openpmd',
+    write_dir = '.',
+    warpx_file_prefix = 'particle_boundary_interaction_plt'
+)
+
+##########################
+# simulation setup
+##########################
+
+sim = picmi.Simulation(
+    solver=solver,
+    time_step_size = dt,
+    max_steps = max_steps,
+    warpx_embedded_boundary=embedded_boundary,
+    warpx_amrex_the_arena_is_managed=1,
+)
+
+sim.add_species(
+    electrons,
+    layout = picmi.GriddedLayout(
+        n_macroparticle_per_cell=[10, 1, 1], grid=grid
+    )
+)
+sim.add_diagnostic(part_diag)
+sim.add_diagnostic(field_diag)
+
+sim.initialize_inputs()
+sim.initialize_warpx()
+
+##########################
+# python particle data access
+##########################
+
+def concat( list_of_arrays ):
+    if len(list_of_arrays) == 0:
+        # Return a 1d array of size 0
+        return np.empty(0)
+    else:
+        return np.concatenate( list_of_arrays )
+
+
+def mirror_reflection():
+    buffer = particle_containers.ParticleBoundaryBufferWrapper() #boundary buffer
+
+    #STEP 1: extract the different parameters of the boundary buffer (normal, time, position)
+    lev = 0 # level 0 (no mesh refinement here)
+    delta_t = concat(buffer.get_particle_boundary_buffer("electrons", 'eb', 'deltaTimeScraped', lev))
+    r = concat(buffer.get_particle_boundary_buffer("electrons", 'eb', 'x', lev))
+    theta = concat(buffer.get_particle_boundary_buffer("electrons", 'eb', 'theta', lev))
+    z = concat(buffer.get_particle_boundary_buffer("electrons", 'eb', 'z', lev))
+    x= r*np.cos(theta) #from RZ coordinates to 3D coordinates
+    y= r*np.sin(theta)
+    ux = concat(buffer.get_particle_boundary_buffer("electrons", 'eb', 'ux', lev))
+    uy = concat(buffer.get_particle_boundary_buffer("electrons", 'eb', 'uy', lev))
+    uz = concat(buffer.get_particle_boundary_buffer("electrons", 'eb', 'uz', lev))
+    w = concat(buffer.get_particle_boundary_buffer("electrons", 'eb', 'w', lev))
+    nx = concat(buffer.get_particle_boundary_buffer("electrons", 'eb', 'nx', lev))
+    ny = concat(buffer.get_particle_boundary_buffer("electrons", 'eb', 'ny', lev))
+    nz = concat(buffer.get_particle_boundary_buffer("electrons", 'eb', 'nz', lev))
+
+    #STEP 2: use these parameters to inject particle from the same position in the plasma
+    elect_pc = particle_containers.ParticleContainerWrapper('electrons') #general particle container
+
+    ####this part is specific to the case of simple reflection.
+    un=ux*nx+uy*ny+uz*nz
+    ux_reflect=-2*un*nx+ux #for a "mirror reflection" u(sym)=-2(u.n)n+u
+    uy_reflect=-2*un*ny+uy
+    uz_reflect=-2*un*nz+uz
+    elect_pc.add_particles(
+        x=x + (dt-delta_t)*ux_reflect, y=y + (dt-delta_t)*uy_reflect, z=z + (dt-delta_t)*uz_reflect,
+        ux=ux_reflect, uy=uy_reflect, uz=uz_reflect,
+        w=w
+        ) #adds the particle in the general particle container at the next step
+        #### Can be modified depending on the model of interaction.
+
+    buffer.clear_buffer() #reinitialise the boundary buffer
+
+callbacks.installafterstep(mirror_reflection) #mirror_reflection is called at the next step
+                                              # using the new particle container modified at the last step
+
+##########################
+# simulation run
+##########################
+
+sim.step(max_steps) #the whole process is done "max_steps" times