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Vay Deposition: Add Cumulative Sums (#2958)
* Implement Cumulative Sum * Implement Subtraction of Average * Fix Bug, Remove Abort w/ Periodic Single Box * Enforce Consistency w/ Periodic Single Box * Cleaning * Cleaning * Fix Bugs * Cleaning * Compute Cumulative Sums Before Sync * Always Loop Over Full Boxes * MFIter without Tiling * Cleaning * Do Not Store Cumulative Sums * Add Two-Particle Test (3D) * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Set 3D Velocity in CI Test * Precompute Normalization Factors * Add Two-Particle Test (2D) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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‎Examples/Tests/VayDeposition/analysis.py‎

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#!/usr/bin/env python3
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# Copyright 2019-2022
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#
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# This file is part of WarpX.
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#
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# License: BSD-3-Clause-LBNL
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import os
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import sys
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import numpy as np
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from scipy.constants import epsilon_0
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import yt
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yt.funcs.mylog.setLevel(50)
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sys.path.insert(1, '../../../../warpx/Regression/Checksum/')
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import checksumAPI
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# Plotfile data set
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fn = sys.argv[1]
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ds = yt.load(fn)
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# Check relative L-infinity spatial norm of rho/epsilon_0 - div(E)
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data = ds.covering_grid(
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level=0,
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left_edge=ds.domain_left_edge,
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dims=ds.domain_dimensions)
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rho = data[('boxlib','rho')].to_ndarray()
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divE = data[('boxlib','divE')].to_ndarray()
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error_rel = np.amax(np.abs(divE-rho/epsilon_0))/np.amax(np.abs(rho/epsilon_0))
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tolerance = 1e-3
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print("Error on charge conservation:")
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print("error_rel = {}".format(error_rel))
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print("tolerance = {}".format(tolerance))
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assert( error_rel < tolerance )
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# Checksum analysis
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test_name = os.path.split(os.getcwd())[1]
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checksumAPI.evaluate_checksum(test_name, fn)

‎Examples/Tests/VayDeposition/inputs_2d‎

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# algo
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algo.charge_deposition = standard
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algo.current_deposition = vay
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algo.maxwell_solver = psatd
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algo.particle_pusher = vay
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algo.particle_shape = 3
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# amr
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amr.max_level = 0
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amr.n_cell = 128 128
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# boundary
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boundary.field_hi = periodic periodic
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boundary.field_lo = periodic periodic
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# diag
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diag1.diag_type = Full
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diag1.intervals = 50
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diag1.fields_to_plot = By Ex Ez jx jz rho divE
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# diagnostics
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diagnostics.diags_names = diag1
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# electron
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electron.charge = -q_e
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electron.injection_style = "SingleParticle"
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electron.mass = 9e-22
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electron.single_particle_pos = 0. 0. 0.
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electron.single_particle_vel = 0.5 0. 0.5
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electron.single_particle_weight = 1.
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# geometry
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geometry.coord_sys = 0
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geometry.dims = 2
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geometry.prob_hi = 45. 45.
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geometry.prob_lo = -45. -45.
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# ion
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ion.charge = q_e
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ion.injection_style = "SingleParticle"
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ion.mass = 9e-22
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ion.single_particle_pos = 0. 0. 0.
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ion.single_particle_vel = -0.5 0. -0.5
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ion.single_particle_weight = 1.
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# max_step
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max_step = 50
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# particles
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particles.species_names = electron ion
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# psatd
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psatd.nox = 4
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psatd.noz = 4
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psatd.nx_guard = 20
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psatd.nz_guard = 20
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psatd.periodic_single_box_fft = 0
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psatd.update_with_rho = 0
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# warpx
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warpx.cfl = 0.9999
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warpx.do_nodal = 1
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warpx.serialize_initial_conditions = 1
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warpx.use_filter = 1
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warpx.verbose = 1

‎Examples/Tests/VayDeposition/inputs_3d‎

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# algo
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algo.charge_deposition = standard
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algo.current_deposition = vay
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algo.maxwell_solver = psatd
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algo.particle_pusher = vay
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algo.particle_shape = 3
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# amr
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amr.max_level = 0
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amr.n_cell = 64 64 64
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# boundary
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boundary.field_hi = periodic periodic periodic
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boundary.field_lo = periodic periodic periodic
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# diag
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diag1.diag_type = Full
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diag1.intervals = 25
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diag1.fields_to_plot = Bx By Bz Ex Ey Ez jx jy jz rho divE
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# diagnostics
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diagnostics.diags_names = diag1
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# electron
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electron.charge = -q_e
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electron.injection_style = "SingleParticle"
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electron.mass = 9e-22
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electron.single_particle_pos = 0. 0. 0.
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electron.single_particle_vel = 0.5 0.5 0.5
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electron.single_particle_weight = 1.
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# geometry
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geometry.coord_sys = 0
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geometry.dims = 3
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geometry.prob_hi = 45. 45. 45.
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geometry.prob_lo = -45. -45. -45.
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# ion
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ion.charge = q_e
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ion.injection_style = "SingleParticle"
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ion.mass = 9e-22
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ion.single_particle_pos = 0. 0. 0.
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ion.single_particle_vel = -0.5 -0.5 -0.5
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ion.single_particle_weight = 1.
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# max_step
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max_step = 25
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# particles
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particles.species_names = electron ion
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# psatd
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psatd.nox = 4
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psatd.noy = 4
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psatd.noz = 4
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psatd.nx_guard = 20
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psatd.ny_guard = 20
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psatd.nz_guard = 20
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psatd.periodic_single_box_fft = 0
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psatd.update_with_rho = 0
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# warpx
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warpx.cfl = 0.9999
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warpx.do_nodal = 1
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warpx.serialize_initial_conditions = 1
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warpx.use_filter = 1
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warpx.verbose = 1

‎Regression/Checksum/benchmarks_json/VayDeposition2D.json‎

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{
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"electron": {
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"particle_cpu": 0.0,
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"particle_id": 1.0,
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"particle_momentum_x": 1.349066061e-13,
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"particle_momentum_y": 0.0,
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"particle_momentum_z": 1.349066061e-13,
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"particle_position_x": 14.351043713724023,
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"particle_position_y": 14.351043713724023,
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"particle_weight": 1.0
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},
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"ion": {
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"particle_cpu": 0.0,
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"particle_id": 2.0,
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"particle_momentum_x": 1.349066061e-13,
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"particle_momentum_y": 0.0,
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"particle_momentum_z": 1.349066061e-13,
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"particle_position_x": 14.351043713724023,
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"particle_position_y": 14.351043713724023,
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"particle_weight": 1.0
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},
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"lev=0": {
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"By": 4.8850423335524976e-15,
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"Ex": 1.5748554237210878e-06,
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"Ez": 1.5745640654762762e-06,
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"divE": 7.364434433257197e-08,
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"jx": 7.96477185276095e-11,
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"jz": 7.971109000864354e-11,
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"rho": 6.481496783075554e-19
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}
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}

‎Regression/Checksum/benchmarks_json/VayDeposition3D.json‎

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{
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"electron": {
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"particle_cpu": 0.0,
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"particle_id": 1.0,
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"particle_momentum_x": 1.349066061e-13,
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"particle_momentum_y": 1.349066061e-13,
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"particle_momentum_z": 1.349066061e-13,
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"particle_position_x": 13.286484722880228,
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"particle_position_y": 13.286484722880228,
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"particle_position_z": 13.286484722880228,
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"particle_weight": 1.0
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},
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"ion": {
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"particle_cpu": 0.0,
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"particle_id": 2.0,
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"particle_momentum_x": 1.349066061e-13,
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"particle_momentum_y": 1.349066061e-13,
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"particle_momentum_z": 1.349066061e-13,
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"particle_position_x": 13.286484722880228,
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"particle_position_y": 13.286484722880228,
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"particle_position_z": 13.286484722880228,
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"particle_weight": 1.0
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},
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"lev=0": {
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"Bx": 8.481813081143231e-16,
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"By": 8.481813081143229e-16,
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"Bz": 8.481813081143229e-16,
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"Ex": 3.0819459288113856e-07,
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"Ey": 3.0819459288113856e-07,
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"Ez": 3.0819459288113856e-07,
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"divE": 1.317737929174611e-08,
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"jx": 1.3111027684847054e-11,
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"jy": 1.311102768484716e-11,
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"jz": 1.3111027684847218e-11,
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"rho": 1.1522660947689872e-19
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}
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}

‎Regression/WarpX-tests.ini‎

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doVis = 0
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compareParticles = 1
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analysisRoutine = Examples/Tests/ion_stopping/analysis_ion_stopping.py
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[VayDeposition2D]
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buildDir = .
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inputFile = Examples/Tests/VayDeposition/inputs_2d
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runtime_params =
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dim = 2
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addToCompileString = USE_PSATD=TRUE
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cmakeSetupOpts = -DWarpX_DIMS=2 -DWarpX_PSATD=ON
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restartTest = 0
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useMPI = 1
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numprocs = 2
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useOMP = 1
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numthreads = 1
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compileTest = 0
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doVis = 0
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compareParticles = 1
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particleTypes = electron ion
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analysisRoutine = Examples/Tests/VayDeposition/analysis.py
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[VayDeposition3D]
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buildDir = .
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inputFile = Examples/Tests/VayDeposition/inputs_3d
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runtime_params =
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dim = 3
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addToCompileString = USE_PSATD=TRUE
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cmakeSetupOpts = -DWarpX_DIMS=3 -DWarpX_PSATD=ON
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restartTest = 0
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useMPI = 1
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numprocs = 2
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useOMP = 1
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numthreads = 1
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compileTest = 0
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doVis = 0
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compareParticles = 1
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particleTypes = electron ion
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analysisRoutine = Examples/Tests/VayDeposition/analysis.py

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