[WIP] Add test for particle boundary interaction

Examples/Tests/particle_boundary_interaction/PICMI_inputs_rz.py

@@ -0,0 +1,165 @@
+#!/usr/bin/env python3
+#
+# --- 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 mirror_reflection():
+    buffer = particle_containers.ParticleBoundaryBufferWrapper() #boundary buffer
+    scraping=(len(buffer.get_particle_boundary_buffer("electrons", 'eb', 'deltaTimeScraped', 0))>0) #bouleen saying if particles where scraped
+
+    if scraping: #otherwise np.concatenate doesnt work
+        delta_t = np.concatenate(buffer.get_particle_boundary_buffer("electrons", 'eb', 'deltaTimeScraped', 0))
+
+
+        #STEP 1: extract the different parameters of the boundary buffer (normal, time, position)
+        r = np.concatenate(buffer.get_particle_boundary_buffer("electrons", 'eb', 'x', 0))
+        theta = np.concatenate(buffer.get_particle_boundary_buffer("electrons", 'eb', 'theta', 0))
+        z = np.concatenate(buffer.get_particle_boundary_buffer("electrons", 'eb', 'z', 0))
+        x= r*np.cos(theta) #from RZ coordinates to 3D coordinates
+        y= r*np.sin(theta)
+        ux = np.concatenate(buffer.get_particle_boundary_buffer("electrons", 'eb', 'ux', 0))
+        uy = np.concatenate(buffer.get_particle_boundary_buffer("electrons", 'eb', 'uy', 0))
+        uz = np.concatenate(buffer.get_particle_boundary_buffer("electrons", 'eb', 'uz', 0))
+        w = np.concatenate(buffer.get_particle_boundary_buffer("electrons", 'eb', 'w', 0))
+        nx = np.concatenate(buffer.get_particle_boundary_buffer("electrons", 'eb', 'nx', 0))
+        ny = np.concatenate(buffer.get_particle_boundary_buffer("electrons", 'eb', 'ny', 0))
+        nz = np.concatenate(buffer.get_particle_boundary_buffer("electrons", 'eb', 'nz', 0))
+
+
+        #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 to 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

Examples/Tests/particle_boundary_interaction/analysis.py

@@ -0,0 +1,51 @@
+#!/usr/bin/env python
+
+"""
+This script tests the last coordinate after adding an electron.
+The sphere is centered on O and has a radius of 0.2 (EB)
+The electron is initially at: (0,0,-0.25) and moves with a velocity:
+(0.5e10,0,1.0e10) with a time step of 1e-11.
+An input file PICMI_inputs_rz.py is used.
+"""
+import os
+import sys
+
+import numpy as np
+from openpmd_viewer import OpenPMDTimeSeries
+import yt
+
+yt.funcs.mylog.setLevel(0)
+sys.path.insert(1, '../../../../warpx/Regression/Checksum/')
+import checksumAPI
+
+# Open plotfile specified in command line
+filename = sys.argv[1]
+test_name = os.path.split(os.getcwd())[1]
+checksumAPI.evaluate_checksum(test_name, filename, output_format='openpmd')
+
+ts = OpenPMDTimeSeries('./diags/diag1/')
+
+it=ts.iterations
+x,y,z=ts.get_particle(['x','y','z'], species='electrons', iteration=it[-1])
+
+# Analytical results calculated
+x_analytic=0.03532
+y_analytic=0.00000
+z_analytic=-0.20531
+
+print('NUMERICAL coordinates of the point of contact:')
+print('x=%5.5f, y=%5.5f, z=%5.5f' % (x[0], y[0], z[0]))
+print('\n')
+print('ANALYTICAL coordinates of the point of contact:')
+print('x=%5.5f, y=%5.5f, z=%5.5f' % (x_analytic, y_analytic, z_analytic))
+
+tolerance=1e-5
+
+diff_x=np.abs((x[0]-x_analytic)/x_analytic)
+diff_z=np.abs((z[0]-z_analytic)/z_analytic)
+
+print('\n')
+print("percentage error for x = %5.4f %%" %(diff_x *100))
+print("percentage error for z = %5.4f %%" %(diff_z *100))
+
+assert (diff_x < tolerance) and (y[0] < 1e-8) and (diff_z < tolerance), 'Test particle_boundary_interaction did not pass'

Regression/WarpX-tests.ini

@@ -4664,6 +4664,27 @@ doVis = 0
 compareParticles = 1
 analysisRoutine = Examples/Tests/energy_conserving_thermal_plasma/analysis.py
 
+[particle_boundary_interaction]
+buildDir = .
+inputFile = Examples/Tests/particle_boundary_interaction/PICMI_inputs_rz.py
+runtime_params =
+customRunCmd = python3 PICMI_inputs_rz.py
+dim = 2
+addToCompileString = USE_PYTHON_MAIN=TRUE USE_RZ=TRUE
+cmakeSetupOpts = -DWarpX_DIMS="RZ" -DWarpX_EB=ON -DWarpX_PYTHON=ON
+target = pip_install
+restartTest = 0
+useMPI = 1
+numprocs = 2
+useOMP = 1
+numthreads = 1
+compileTest = 0
+doVis = 0
+compareParticles = 1
+particleTypes = electrons
+outputFile = particle_boundary_interaction_plt
+analysisRoutine = Examples/Tests/particle_boundary_interaction/analysis.py
+
 [focusing_gaussian_beam]
 buildDir = .
 inputFile = Examples/Tests/gaussian_beam/inputs_focusing_beam