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Diffstat (limited to 'Examples/Tests/langmuir/analysis_3d.py')
-rwxr-xr-x | Examples/Tests/langmuir/analysis_3d.py | 198 |
1 files changed, 198 insertions, 0 deletions
diff --git a/Examples/Tests/langmuir/analysis_3d.py b/Examples/Tests/langmuir/analysis_3d.py new file mode 100755 index 000000000..2e56e64d6 --- /dev/null +++ b/Examples/Tests/langmuir/analysis_3d.py @@ -0,0 +1,198 @@ +#!/usr/bin/env python3 + +# Copyright 2019-2022 Jean-Luc Vay, Maxence Thevenet, Remi Lehe, Axel Huebl +# +# +# This file is part of WarpX. +# +# License: BSD-3-Clause-LBNL +# +# This is a script that analyses the simulation results from +# the script `inputs.multi.rt`. This simulates a 3D periodic plasma wave. +# The electric field in the simulation is given (in theory) by: +# $$ E_x = \epsilon \,\frac{m_e c^2 k_x}{q_e}\sin(k_x x)\cos(k_y y)\cos(k_z z)\sin( \omega_p t)$$ +# $$ E_y = \epsilon \,\frac{m_e c^2 k_y}{q_e}\cos(k_x x)\sin(k_y y)\cos(k_z z)\sin( \omega_p t)$$ +# $$ E_z = \epsilon \,\frac{m_e c^2 k_z}{q_e}\cos(k_x x)\cos(k_y y)\sin(k_z z)\sin( \omega_p t)$$ +import os +import re +import sys + +import matplotlib.pyplot as plt +from mpl_toolkits.axes_grid1.axes_divider import make_axes_locatable +import yt + +yt.funcs.mylog.setLevel(50) + +import numpy as np +from scipy.constants import c, e, epsilon_0, m_e + +sys.path.insert(1, '../../../../warpx/Regression/Checksum/') +import checksumAPI + +# this will be the name of the plot file +fn = sys.argv[1] + +# Parse test name and check if current correction (psatd.current_correction=1) is applied +current_correction = True if re.search( 'current_correction', fn ) else False + +# Parse test name and check if Vay current deposition (algo.current_deposition=vay) is used +vay_deposition = True if re.search( 'Vay_deposition', fn ) else False + +# Parse test name and check if div(E)/div(B) cleaning (warpx.do_div<e,b>_cleaning=1) is used +div_cleaning = True if re.search('div_cleaning', fn) else False + +# Parameters (these parameters must match the parameters in `inputs.multi.rt`) +epsilon = 0.01 +n = 4.e24 +n_osc_x = 2 +n_osc_y = 2 +n_osc_z = 2 +lo = [-20.e-6, -20.e-6, -20.e-6] +hi = [ 20.e-6, 20.e-6, 20.e-6] +Ncell = [64, 64, 64] + +# Wave vector of the wave +kx = 2.*np.pi*n_osc_x/(hi[0]-lo[0]) +ky = 2.*np.pi*n_osc_y/(hi[1]-lo[1]) +kz = 2.*np.pi*n_osc_z/(hi[2]-lo[2]) +# Plasma frequency +wp = np.sqrt((n*e**2)/(m_e*epsilon_0)) + +k = {'Ex':kx, 'Ey':ky, 'Ez':kz} +cos = {'Ex': (0,1,1), 'Ey':(1,0,1), 'Ez':(1,1,0)} + +def get_contribution( is_cos, k, idim ): + du = (hi[idim]-lo[idim])/Ncell[idim] + u = lo[idim] + du*( 0.5 + np.arange(Ncell[idim]) ) + if is_cos[idim] == 1: + return( np.cos(k*u) ) + else: + return( np.sin(k*u) ) + +def get_theoretical_field( field, t ): + amplitude = epsilon * (m_e*c**2*k[field])/e * np.sin(wp*t) + cos_flag = cos[field] + x_contribution = get_contribution( cos_flag, kx, 0 ) + y_contribution = get_contribution( cos_flag, ky, 1 ) + z_contribution = get_contribution( cos_flag, kz, 2 ) + + E = amplitude * x_contribution[:, np.newaxis, np.newaxis] \ + * y_contribution[np.newaxis, :, np.newaxis] \ + * z_contribution[np.newaxis, np.newaxis, :] + + return( E ) + +# Read the file +ds = yt.load(fn) + +# Check that the particle selective output worked: +species = 'electrons' +print('ds.field_list', ds.field_list) +for field in ['particle_weight', + 'particle_momentum_x']: + print('assert that this is in ds.field_list', (species, field)) + assert (species, field) in ds.field_list +for field in ['particle_momentum_y', + 'particle_momentum_z']: + print('assert that this is NOT in ds.field_list', (species, field)) + assert (species, field) not in ds.field_list +species = 'positrons' +for field in ['particle_momentum_x', + 'particle_momentum_y']: + print('assert that this is NOT in ds.field_list', (species, field)) + assert (species, field) not in ds.field_list + +t0 = ds.current_time.to_value() +data = ds.covering_grid(level = 0, left_edge = ds.domain_left_edge, dims = ds.domain_dimensions) +edge = np.array([(ds.domain_left_edge[2]).item(), (ds.domain_right_edge[2]).item(), \ + (ds.domain_left_edge[0]).item(), (ds.domain_right_edge[0]).item()]) + +# Check the validity of the fields +error_rel = 0 +for field in ['Ex', 'Ey', 'Ez']: + E_sim = data[('mesh',field)].to_ndarray() + E_th = get_theoretical_field(field, t0) + max_error = abs(E_sim-E_th).max()/abs(E_th).max() + print('%s: Max error: %.2e' %(field,max_error)) + error_rel = max( error_rel, max_error ) + +# Plot the last field from the loop (Ez at iteration 40) +fig, (ax1, ax2) = plt.subplots(1, 2, dpi = 100) +# First plot (slice at y=0) +E_plot = E_sim[:,Ncell[1]//2+1,:] +vmin = E_plot.min() +vmax = E_plot.max() +cax1 = make_axes_locatable(ax1).append_axes('right', size = '5%', pad = '5%') +im1 = ax1.imshow(E_plot, origin = 'lower', extent = edge, vmin = vmin, vmax = vmax) +cb1 = fig.colorbar(im1, cax = cax1) +ax1.set_xlabel(r'$z$') +ax1.set_ylabel(r'$x$') +ax1.set_title(r'$E_z$ (sim)') +# Second plot (slice at y=0) +E_plot = E_th[:,Ncell[1]//2+1,:] +vmin = E_plot.min() +vmax = E_plot.max() +cax2 = make_axes_locatable(ax2).append_axes('right', size = '5%', pad = '5%') +im2 = ax2.imshow(E_plot, origin = 'lower', extent = edge, vmin = vmin, vmax = vmax) +cb2 = fig.colorbar(im2, cax = cax2) +ax2.set_xlabel(r'$z$') +ax2.set_ylabel(r'$x$') +ax2.set_title(r'$E_z$ (theory)') +# Save figure +fig.tight_layout() +fig.savefig('Langmuir_multi_analysis.png', dpi = 200) + +tolerance_rel = 5e-2 + +print("error_rel : " + str(error_rel)) +print("tolerance_rel: " + str(tolerance_rel)) + +assert( error_rel < tolerance_rel ) + +# Check relative L-infinity spatial norm of rho/epsilon_0 - div(E) +# with current correction (and periodic single box option) or with Vay current deposition +if current_correction: + tolerance = 1e-9 +elif vay_deposition: + tolerance = 1e-3 +if current_correction or vay_deposition: + rho = data[('boxlib','rho')].to_ndarray() + divE = data[('boxlib','divE')].to_ndarray() + error_rel = np.amax( np.abs( divE - rho/epsilon_0 ) ) / np.amax( np.abs( rho/epsilon_0 ) ) + print("Check charge conservation:") + print("error_rel = {}".format(error_rel)) + print("tolerance = {}".format(tolerance)) + assert( error_rel < tolerance ) + +if div_cleaning: + ds_old = yt.load('Langmuir_multi_psatd_div_cleaning_plt000038') + ds_mid = yt.load('Langmuir_multi_psatd_div_cleaning_plt000039') + ds_new = yt.load(fn) # this is the last plotfile + + ad_old = ds_old.covering_grid(level = 0, left_edge = ds_old.domain_left_edge, dims = ds_old.domain_dimensions) + ad_mid = ds_mid.covering_grid(level = 0, left_edge = ds_mid.domain_left_edge, dims = ds_mid.domain_dimensions) + ad_new = ds_new.covering_grid(level = 0, left_edge = ds_new.domain_left_edge, dims = ds_new.domain_dimensions) + + rho = ad_mid['rho'].v.squeeze() + divE = ad_mid['divE'].v.squeeze() + F_old = ad_old['F'].v.squeeze() + F_new = ad_new['F'].v.squeeze() + + # Check max norm of error on dF/dt = div(E) - rho/epsilon_0 + # (the time interval between the old and new data is 2*dt) + dt = 1.203645751e-15 + x = F_new - F_old + y = (divE - rho/epsilon_0) * 2 * dt + error_rel = np.amax(np.abs(x - y)) / np.amax(np.abs(y)) + tolerance = 1e-2 + print("Check div(E) cleaning:") + print("error_rel = {}".format(error_rel)) + print("tolerance = {}".format(tolerance)) + assert(error_rel < tolerance) + +test_name = os.path.split(os.getcwd())[1] + +if re.search( 'single_precision', fn ): + checksumAPI.evaluate_checksum(test_name, fn, rtol=1.e-3) +else: + checksumAPI.evaluate_checksum(test_name, fn) |