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+#!/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)