Clean up examples folders (#3545)

* Clean up examples folders

* Use `snake_case` names

* Rename `nci_corrector` as `nci_fdtd_stability`

1 files changed, 0 insertions, 229 deletions

diff --git a/Examples/Modules/laser_injection_from_file/analysis.py b/Examples/Modules/laser_injection_from_file/analysis.py
deleted file mode 100755
index 642cb60ae..000000000
--- a/Examples/Modules/laser_injection_from_file/analysis.py
+++ /dev/null
@@ -1,229 +0,0 @@
-#!/usr/bin/env python3
-
-# Copyright 2020 Andrew Myers, Axel Huebl, Luca Fedeli
-# Remi Lehe
-#
-# This file is part of WarpX.
-#
-# License: BSD-3-Clause-LBNL
-
-
-# This file is part of the WarpX automated test suite. It is used to test the
-# injection of a laser pulse from an external binary file.
-#
-# - Generate an input binary file with a gaussian laser pulse.
-# - Run the WarpX simulation for time T, when the pulse is fully injected
-# - Compute the theory for laser envelope at time T
-# - Compare theory and simulation, for both envelope and central frequency
-
-import glob
-import os
-
-import matplotlib
-
-matplotlib.use('Agg')
-import matplotlib.pyplot as plt
-import numpy as np
-from scipy.signal import hilbert
-
-import yt ; yt.funcs.mylog.setLevel(50)
-
-#Maximum acceptable error for this test
-relative_error_threshold = 0.065
-
-#Physical parameters
-um = 1.e-6
-fs = 1.e-15
-c = 299792458
-
-#Parameters of the gaussian beam
-wavelength = 1.*um
-w0 = 6.*um
-tt = 10.*fs
-x_c = 0.*um
-t_c = 20.*fs
-foc_dist = 10*um
-E_max = 1e12
-rot_angle = -np.pi/4.0
-
-#Parameters of the tx grid
-x_l = -12.0*um
-x_r = 12.0*um
-x_points = 480
-t_l = 0.0*fs
-t_r = 40.0*fs
-t_points = 400
-tcoords = np.linspace(t_l, t_r, t_points)
-xcoords = np.linspace(x_l, x_r, x_points)
-
-def gauss(T,X,Y,opt):
-    """Compute the electric field for a Gaussian laser pulse.
-       This is used to write the binary input file.
-    """
-
-    k0 = 2.0*np.pi/wavelength
-    inv_tau2 = 1./tt/tt
-    osc_phase = k0*c*(T-t_c)
-
-    diff_factor = 1.0 + 1.0j* foc_dist * 2/(k0*w0*w0)
-    inv_w_2 = 1.0/(w0*w0*diff_factor)
-
-    pre_fact = np.exp(1.0j * osc_phase)
-
-    if opt == '3d':
-        pre_fact = pre_fact/diff_factor
-    else:
-        pre_fact = pre_fact/np.sqrt(diff_factor)
-
-    exp_arg = - (X*X + Y*Y)*inv_w_2 - inv_tau2 * (T-t_c)*(T-t_c)
-
-    return np.real(pre_fact * np.exp(exp_arg))
-
-# Function for the envelope
-def gauss_env(T,XX,ZZ):
-    '''Function to compute the theory for the envelope
-    '''
-
-    X = np.cos(rot_angle)*XX + np.sin(rot_angle)*ZZ
-    Z = -np.sin(rot_angle)*XX + np.cos(rot_angle)*ZZ
-
-    inv_tau2 = 1./tt/tt
-    inv_w_2 = 1.0/(w0*w0)
-    exp_arg = - (X*X)*inv_w_2 - inv_tau2 / c/c * (Z-T*c)*(Z-T*c)
-    return E_max * np.real(np.exp(exp_arg))
-
-def write_file(fname, x, y, t, E):
-    """ For a given filename fname, space coordinates x and y, time coordinate t
-    and field E, write a WarpX-compatible input binary file containing the
-    profile of the laser pulse
-    """
-
-    with open(fname, 'wb') as file:
-        flag_unif = 0
-        file.write(flag_unif.to_bytes(1, byteorder='little'))
-        file.write((len(t)).to_bytes(4, byteorder='little', signed=False))
-        file.write((len(x)).to_bytes(4, byteorder='little', signed=False))
-        file.write((len(y)).to_bytes(4, byteorder='little', signed=False))
-        file.write(t.tobytes())
-        file.write(x.tobytes())
-        file.write(y.tobytes())
-        file.write(E.tobytes())
-
-
-def write_file_unf(fname, x, y, t, E):
-    """ For a given filename fname, space coordinates x and y, time coordinate t
-    and field E, write a WarpX-compatible input binary file containing the
-    profile of the laser pulse. This function should be used in the case
-    of a uniform spatio-temporal mesh
-    """
-
-    with open(fname, 'wb') as file:
-        flag_unif = 1
-        file.write(flag_unif.to_bytes(1, byteorder='little'))
-        file.write((len(t)).to_bytes(4, byteorder='little', signed=False))
-        file.write((len(x)).to_bytes(4, byteorder='little', signed=False))
-        file.write((len(y)).to_bytes(4, byteorder='little', signed=False))
-        file.write(t[0].tobytes())
-        file.write(t[-1].tobytes())
-        file.write(x[0].tobytes())
-        file.write(x[-1].tobytes())
-        if len(y) == 1 :
-            file.write(y[0].tobytes())
-        else :
-            file.write(y[0].tobytes())
-            file.write(y[-1].tobytes())
-        file.write(E.tobytes())
-
-def create_gaussian_2d():
-   T, X, Y = np.meshgrid(tcoords, xcoords, np.array([0.0]), indexing='ij')
-   E_t = gauss(T,X,Y,'2d')
-   write_file("gauss_2d.txye", xcoords, np.array([0.0]), tcoords, E_t)
-   write_file_unf("gauss_2d_unf.txye", xcoords, np.array([0.0]), tcoords, E_t)
-
-
-def do_analysis(fname, compname, steps):
-    ds = yt.load(fname)
-
-    dt = ds.current_time.to_value()/steps
-
-    # Define 2D meshes
-    x = np.linspace(
-        ds.domain_left_edge[0],
-        ds.domain_right_edge[0],
-        ds.domain_dimensions[0]).v
-    z = np.linspace(
-        ds.domain_left_edge[ds.dimensionality-1],
-        ds.domain_right_edge[ds.dimensionality-1],
-        ds.domain_dimensions[ds.dimensionality-1]).v
-    X, Z = np.meshgrid(x, z, sparse=False, indexing='ij')
-
-    # Compute the theory for envelope
-    env_theory = gauss_env(+t_c-ds.current_time.to_value(), X,Z)+gauss_env(-t_c+ds.current_time.to_value(), X,Z)
-
-    # Read laser field in PIC simulation, and compute envelope
-    all_data_level_0 = ds.covering_grid(level=0,left_edge=ds.domain_left_edge, dims=ds.domain_dimensions)
-    F_laser = all_data_level_0['boxlib', 'Ey'].v.squeeze()
-    env = abs(hilbert(F_laser))
-    extent = [ds.domain_left_edge[ds.dimensionality-1], ds.domain_right_edge[ds.dimensionality-1],
-          ds.domain_left_edge[0], ds.domain_right_edge[0] ]
-
-    # Plot results
-    plt.figure(figsize=(8,6))
-    plt.subplot(221)
-    plt.title('PIC field')
-    plt.imshow(F_laser, extent=extent)
-    plt.colorbar()
-    plt.subplot(222)
-    plt.title('PIC envelope')
-    plt.imshow(env, extent=extent)
-    plt.colorbar()
-    plt.subplot(223)
-    plt.title('Theory envelope')
-    plt.imshow(env_theory, extent=extent)
-    plt.colorbar()
-    plt.subplot(224)
-    plt.title('Difference')
-    plt.imshow(env-env_theory, extent=extent)
-    plt.colorbar()
-    plt.tight_layout()
-    plt.savefig(compname, bbox_inches='tight')
-
-    relative_error_env = np.sum(np.abs(env-env_theory)) / np.sum(np.abs(env))
-    print("Relative error envelope: ", relative_error_env)
-    assert(relative_error_env < relative_error_threshold)
-
-    fft_F_laser = np.fft.fft2(F_laser)
-
-    freq_rows = np.fft.fftfreq(F_laser.shape[0],dt)
-    freq_cols = np.fft.fftfreq(F_laser.shape[1],dt)
-
-    pos_max = np.unravel_index(np.abs(fft_F_laser).argmax(), fft_F_laser.shape)
-
-    freq = np.sqrt((freq_rows[pos_max[0]])**2 +  (freq_cols[pos_max[1]]**2))
-    exp_freq = c/wavelength
-
-    relative_error_freq = np.abs(freq-exp_freq)/exp_freq
-    print("Relative error frequency: ", relative_error_freq)
-    assert(relative_error_freq < relative_error_threshold)
-
-
-
-def launch_analysis(executable):
-    create_gaussian_2d()
-    os.system("./" + executable + " inputs.2d_test_txye diag1.file_prefix=diags/plotfiles/plt")
-    do_analysis("diags/plotfiles/plt000250/", "comp_unf.pdf", 250)
-    os.system("sed 's/gauss_2d_unf.txye/gauss_2d.txye/g' inputs.2d_test_txye > inputs.2d_test_txye_non_unf")
-    os.system("./" + executable + " inputs.2d_test_txye_non_unf diag1.file_prefix=diags/plotfiles/plt")
-    do_analysis("diags/plotfiles/plt000250/", "comp_non_unf.pdf", 250)
-
-
-def main() :
-    executables = glob.glob("*.ex")
-    if len(executables) == 1 :
-        launch_analysis(executables[0])
-    else :
-        assert(False)
-    print('Passed')
-
-if __name__ == "__main__":
-    main()