def plot_rb(self):
fig = plt.figure()
plt.plot(self.zeta_array, self.rb)
plt.plot(self.zeta_array, self.rb_maxrho)
ax = plt.gca()
ax.set_ylabel(r'$k_p r_b$', fontsize=14)
ax.set_xlabel(r'$k_p \zeta$', fontsize=14)
ax.legend([r'$r_b$ from zero crossing', r'$r_b$ from global maximum'])
filesuffix = '_t_%06.f' % (np.floor(self.g3d.get_time()))
fileprefix = 'plasma_charge_rb'
saveformat = 'eps'
savepath = self.args.savepath
mkdirs_if_nexist(savepath)
savename = fileprefix + filesuffix + '.' + saveformat
fig.savefig(savepath + '/' + savename, format=saveformat)
if self.args.h5plot:
h5lp = H5Plot()
h5lp.inherit_matplotlib_line_plots(ax)
h5lp.write(savepath + '/' + fileprefix + filesuffix + '.h5')
if self.args.verbose:
print('Saved "' + savename + '" at: ' + self.args.savepath)
plt.close(fig)
def plot_r_lines(self):
if not hasattr(self, 'r_z_slice_model'):
self.gen_model_sheath()
z_inds = np.int16(np.linspace(0, self.Nzeta - 1, 10))
fig = plt.figure()
for z_ind in z_inds:
p = plt.plot(self.r_array, self.r_z_slice[:, z_ind])
plt.plot(self.r_array,
self.r_z_slice_model[:, z_ind],
color=p[0].get_color(),
linestyle='--')
plt.plot(self.r_array,
self.r_z_slice_model_flocmax[:, z_ind],
color=p[0].get_color(),
linestyle='-.')
ax = plt.gca()
ax.set_ylabel(r'$\rho$', fontsize=14)
ax.set_xlabel(r'$k_p r$', fontsize=14)
filesuffix = '_t_%06.f' % (np.floor(self.g3d.get_time()))
fileprefix = 'plasma_charge_r'
saveformat = 'eps'
savepath = self.args.savepath
mkdirs_if_nexist(savepath)
savename = fileprefix + filesuffix + '.' + saveformat
fig.savefig(savepath + '/' + savename, format=saveformat)
plt.close(fig)
if self.args.h5plot:
h5lp = H5Plot()
h5lp.inherit_matplotlib_line_plots(ax)
h5lp.write(savepath + '/' + fileprefix + filesuffix + '.h5')
if self.args.verbose:
print('Saved "' + savename + '" at: ' + self.args.savepath)
def saveas_eps_pdf(fig,
savepath,
savename,
h5plot=True,
verbose=True,
fformat='pdf',
transparent=True):
fformat_list = ['eps', 'pdf']
if fformat not in fformat_list:
print("Error: fformat must be one of: " + fformat_list)
if savepath != None:
if savepath == '':
savepath = '.'
else:
mkdirs_if_nexist(savepath)
fig.savefig(savepath + '/' + savename + '.' + fformat,
format=fformat,
transparent=transparent)
if verbose:
sys.stdout.write('Saved "%s.%s" at: %s/\n' %
(savename, fformat, savepath))
sys.stdout.flush()
if h5plot:
h5lp = H5Plot()
h5lp.inherit_matplotlib_line_plots(plt.gca())
h5lp.write(savepath + '/' + savename + '.h5')
if verbose:
sys.stdout.write('Saved "%s.h5" at: %s/\n' %
(savename, savepath))
sys.stdout.flush()
def calc_transversal_probability_density(r_max, nx, nb, ni, rbunch, lbunch):
ELECTRON_CHARGE_IN_COUL = 1.60217657e-19
ELECTRON_MASS_IN_KG = 9.10938291e-31
VAC_PERMIT_FARAD_PER_M = 8.854187817e-12
SPEED_OF_LIGHT_IN_M_PER_S = 299792458
omega_alpha = 4.13e16
# [s^-1]
E_alpha = 5.1e11
# [V/m]
elec_density = 1e+23 # [1/m^3]
omega_p = np.sqrt(4 * np.pi * elec_density * (ELECTRON_CHARGE_IN_COUL**2) /
(VAC_PERMIT_FARAD_PER_M * ELECTRON_MASS_IN_KG))
E_0 = omega_p * ELECTRON_MASS_IN_KG * SPEED_OF_LIGHT_IN_M_PER_S / ELECTRON_CHARGE_IN_COUL
#Use zeta array in order to calculate delta t
savepath = './plots/g3d-line/'
mkdirs_if_nexist(savepath)
bunch_array = np.arange(0, lbunch + lbunch / 10, lbunch / 10)
bunch_array_sum = np.cumsum(bunch_array)
deltat = np.abs(bunch_array_sum) / omega_p
vcalc_ion_rate = np.vectorize(calc_ion_rate)
r_array = np.arange(0, r_max + r_max / nx, r_max / nx)
c1prime = -1 / 2 * nb
c3prime = -1 / 2 * rbunch**2 * (nb)
savename = 'Ex_analytic'
E = np.zeros(shape=np.shape(r_array))
for i in range(len(r_array)):
if (r_array[i] <= rbunch):
E[i] = np.real(c1prime) * r_array[i]
else:
E[i] = np.real(c3prime) / r_array[i]
fig = plt.figure()
ax = fig.add_subplot(111)
ax.plot(np.append(-r_array[::-1], r_array), np.append(-(E[::-1]), E[:]))
x, Ex = plot_hipace_Ex(-0.2) # input = zeta pos
ax.plot(x, Ex)
h5lp = H5Plot()
h5lp.inherit_matplotlib_line_plots(ax)
h5lp.write(savepath + '/' + savename + '.h5')
plt.show()
#use zeta array for shaping the elctric field to get the same spacing etc.
#print(Earray)
ionization_rate = np.zeros(shape=np.shape(r_array))
ionization_rate[:] = vcalc_ion_rate(E * E_0, 1, 13.659843449, 13.659843449,
0, 0) # complete formulae for hydrogen
#print(ionization_rate[1])
fig = plt.figure()
ax = fig.add_subplot(111)
#print('Deltat is %0.3e' %deltat)
#computing the ionization probability
savename = 'ion_probability_test'
ion_probability = np.zeros(shape=(len(bunch_array) - 1,
len(ionization_rate)))
for i in range(1, 2): #len(bunch_array)):
ion_probability[i -
1, :] = 1.0 - np.exp(-ionization_rate[:] * deltat[i])
ax.plot(np.append(-r_array[::-1], r_array),
np.append((ion_probability[i - 1, ::-1]),
ion_probability[i - 1, :]),
label=('prob at lb: ' +
str(np.around(bunch_array[i], decimals=1))))
#ax.legend()
h5lp = H5Plot()
h5lp.inherit_matplotlib_line_plots(ax)
h5lp.write(savepath + '/' + savename + '.h5')
plt.show()
def plot_deltarho_rhomax_sheathcharge(self):
if not hasattr(self, 'rb'):
self.calc_rb()
if not hasattr(self, 'rho_max'):
self.calc_deltarho_rhomax_sheathcharge()
fig_charge = plt.figure()
plt.plot(self.zeta_array, self.charge)
ax_charge = plt.gca()
ax_charge.set_ylabel(r'$\lambda=\int_{r_b}^\infty r \rho(r) dr$',
fontsize=14)
ax_charge.set_xlabel(r'$k_p \zeta$', fontsize=14)
charge_fileprefix = 'charge'
fig_rhomax = plt.figure()
plt.plot(self.zeta_array, self.rho_max)
plt.plot(self.zeta_array, self.rho_flocmax)
ax_rhomax = plt.gca()
ax_rhomax.legend(
[r'using global maximum', r'using first local maximum'])
ax_rhomax.set_ylabel(r'$\rho_\mathrm{max}$', fontsize=14)
ax_rhomax.set_xlabel(r'$k_p \zeta$', fontsize=14)
rhomax_fileprefix = 'rho_max'
fig_deltarho = plt.figure()
plt.plot(self.zeta_array, self.delta_rho)
plt.plot(self.zeta_array, self.delta_rho_flocmax)
ax_deltarho = plt.gca()
ax_deltarho.legend(
[r'using global maximum', r'using first local maximum'])
ax_deltarho.set_ylabel(r'$\Delta_\rho$', fontsize=14)
ax_deltarho.set_xlabel(r'$k_p \zeta$', fontsize=14)
deltarho_fileprefix = 'delta_rho'
filesuffix = '_t_%06.f' % (np.floor(self.g3d.get_time()))
saveformat = 'eps'
savepath = self.args.savepath
mkdirs_if_nexist(savepath)
charge_savename = charge_fileprefix + filesuffix + '.' + saveformat
rhomax_savename = rhomax_fileprefix + filesuffix + '.' + saveformat
deltarho_savename = deltarho_fileprefix + filesuffix + '.' + saveformat
fig_charge.savefig(savepath + '/' + charge_savename, format=saveformat)
if self.args.verbose:
print('Saved "' + charge_savename + '" at: ' + self.args.savepath)
fig_rhomax.savefig(savepath + '/' + rhomax_savename, format=saveformat)
if self.args.verbose:
print('Saved "' + rhomax_savename + '" at: ' + self.args.savepath)
fig_deltarho.savefig(savepath + '/' + deltarho_savename,
format=saveformat)
if self.args.verbose:
print('Saved "' + deltarho_savename + '" at: ' +
self.args.savepath)
if self.args.h5plot:
h5lp = H5Plot()
h5lp.inherit_matplotlib_line_plots(ax_charge)
h5lp.write(savepath + '/' + charge_fileprefix + filesuffix + '.h5')
h5lp = H5Plot()
h5lp.inherit_matplotlib_line_plots(ax_rhomax)
h5lp.write(savepath + '/' + rhomax_fileprefix + filesuffix + '.h5')
h5lp = H5Plot()
h5lp.inherit_matplotlib_line_plots(ax_deltarho)
h5lp.write(savepath + '/' + deltarho_fileprefix + filesuffix +
'.h5')
plt.show()
def main():
parser = h5plot_parser()
args = parser.parse_args()
if len(sys.argv) == 1:
parser.print_help()
sys.exit(1)
fig = plt.figure(figsize=(6, 5))
if (args.line_no != None) and (len(args.line_no) != len(args.paths)):
print(
'ERROR: number of selected lines must be equal to the number of provided hdf5 files!'
)
sys.exit(1)
if (args.labels != None) and (len(args.labels) != len(args.paths)):
print(
'ERROR: number of prepend labels must be equal to the number of provided hdf5 files!'
)
sys.exit(1)
h5lp = []
linestyles = ['-', '--', '-.', ':']
save_append_str = ''
type_str = 'comp'
if not args.latexoff:
plt.rc('text', usetex=True)
plt.rc('font', family='serif')
j = 0
if args.diff:
h5firstlp = H5Plot()
h5firstlp.read(args.paths[0])
type_str = 'diff'
for (x, y, label, linestyle, color) in h5firstlp.get_line_plots():
if j == 0:
x0 = x
y0 = y
j += 1
h5firstlp = H5Plot()
h5firstlp.read(args.paths[0])
for (x, y, label, linestyle, color) in h5firstlp.get_line_plots():
if not args.extrue:
if (any(y < 0) and any(y > 0)):
for i in range(1, len(x)):
if y[i] > 0 and y[i - 1] < 0:
y_strich = -(y[i + 5] - y[i - 6]) / abs(x[i + 5] -
x[i - 6])
print('slope around root: from %f to %f is : %f' %
((x[i + 5]), x[i - 6], y_strich))
else:
print('there are not roots')
else:
for i in range(1, len(x)):
if x[i - 1] * x[i] < 0:
y_strich = (y[i] - y[i - 1]) / abs(x[i] - x[i - 1])
print('slope at x = %f is : %f' %
((x[i] + x[i - 1]) / 2, y_strich))
i = 0
for path in args.paths:
if not os.path.isfile(path):
print('ERROR: File %s does not exist!' % path)
sys.exit(1)
h5lp.append(H5Plot())
h5lp[i].read(path)
if args.cno == None:
argcolor = plt.cm.Dark2(i)
else:
argcolor = plt.cm.Dark2(args.cno[i])
j = 0
for (x, y, label, linestyle, color) in h5lp[i].get_line_plots():
if args.labels != None:
save_append_str += '_' + args.labels[i]
label = args.labels[i]
if label == '_line0':
label = path
if not args.latexoff:
if label[0] != '$' or label[-1] != '$':
label = r'$\textrm{' + label + '}$'
if args.diff:
if (j == 0 and i == 0):
continue
else:
y -= np.interp(x, x0, y0)
if args.lstyle == None:
linestyle_code = linestyles[i % len(linestyles)]
else:
linestyle_code = linestyles[args.lstyle[i]]
if (args.line_no != None):
if args.line_no[i] == j:
if args.absylog:
plt.semilogy(x,
y,
label=label,
linestyle=linestyle_code,
color=argcolor)
else:
plt.plot(x,
y,
label=label,
linestyle=linestyle_code,
color=argcolor)
else:
if args.absylog:
plt.semilogy(x,
y,
label=label,
linestyle=linestyle_code,
color=argcolor)
else:
#plt.plot(x, y, label=label, linestyle=linestyle, color=color)
plt.plot(x,
y,
label=label,
linestyle=linestyle_code,
color=argcolor)
j += 1
i += 1
ax = plt.gca()
ax.set_xlabel(h5lp[0].get_xlab(), fontsize=14)
ax.set_ylabel(h5lp[0].get_ylab(), fontsize=14)
handles, labels = ax.get_legend_handles_labels()
#plt.legend(flip(handles, 2), flip(labels, 2), ncol=2)
plt.legend(frameon=False)
plt.gcf().subplots_adjust(left=0.15, bottom=0.15)
if not (-3.0 < math.log(np.max(abs(y)), 10) < 3.0):
ax.yaxis.set_major_formatter(FormatStrFormatter('%.1e'))
plt.gcf().subplots_adjust(left=0.18)
plt.show()
fname, fext = os.path.splitext(args.paths[0])
save_path_name = fname + save_append_str + '_' + type_str + '.' + args.file_format
fig.savefig(save_path_name, format=args.file_format)
plt.close(fig)
if args.verbose:
sys.stdout.write('Saved: %s\n' % save_path_name)
sys.stdout.flush()
def main():
parser = h5plot_parser()
args = parser.parse_args()
if len(sys.argv) == 1:
parser.print_help()
sys.exit(1)
fig = plt.figure(figsize=(6, 5))
if (args.line_no != None) and (len(args.line_no) != len(args.paths)):
print(
'ERROR: number of selected lines must be equal to the number of provided hdf5 files!'
)
sys.exit(1)
if (args.labels != None) and (len(args.labels) != len(args.paths)):
print(
'ERROR: number of prepend labels must be equal to the number of provided hdf5 files!'
)
sys.exit(1)
h5lp = []
linestyles = ['-', '--', '-.', ':']
save_append_str = ''
type_str = 'comp'
if not args.latexoff:
plt.rc('text', usetex=True)
plt.rc('font', family='serif')
j = 0
if args.diff:
h5firstlp = H5Plot()
h5firstlp.read(args.paths[0])
type_str = 'diff'
for (x, y, label, linestyle, color) in h5firstlp.get_line_plots():
if j == 0:
x0 = x
y0 = y
j += 1
h5firstlp = H5Plot()
h5firstlp.read(args.paths[0])
for (x, y, label, linestyle, color) in h5firstlp.get_line_plots():
x_p = x[int(np.floor(len(x) / 2)):]
y_p = y[int(np.floor(len(y) / 2)):]
n = len(x_p) #the number of data
mean = sum(x_p * y_p) / n #note this correction
sigma = sum(y_p * (x_p - mean)**2) / n
def gaus(x, a, x0, sigma):
return a * exp(-(x - x0)**2 / (2 * sigma**2))
popt, pcov = curve_fit(gaus, x_p, y_p, p0=[max(y_p), mean, sigma])
i = 0
for path in args.paths:
if not os.path.isfile(path):
print('ERROR: File %s does not exist!' % path)
sys.exit(1)
h5lp.append(H5Plot())
h5lp[i].read(path)
if args.cno == None:
argcolor = plt.cm.Dark2(i)
else:
argcolor = plt.cm.Dark2(args.cno[i])
j = 0
for (x, y, label, linestyle, color) in h5lp[i].get_line_plots():
if args.labels != None:
save_append_str += '_' + args.labels[i]
label = args.labels[i]
if label == '_line0':
label = path
if not args.latexoff:
if label[0] != '$' or label[-1] != '$':
label = r'$\textrm{' + label + '}$'
if args.diff:
if (j == 0 and i == 0):
continue
else:
y -= np.interp(x, x0, y0)
if args.lstyle == None:
linestyle_code = linestyles[i % len(linestyles)]
else:
linestyle_code = linestyles[args.lstyle[i]]
if (args.line_no != None):
if args.line_no[i] == j:
if args.absylog:
plt.semilogy(x,
y,
label=label,
linestyle=linestyle_code,
color=argcolor)
else:
plt.plot(x,
y,
label=label,
linestyle=linestyle_code,
color=argcolor)
plt.plot(x_p, gaus(x_p, *popt), 'r--', label='fit')
else:
if args.absylog:
plt.semilogy(x,
y,
label=label,
linestyle=linestyle_code,
color=argcolor)
else:
#plt.plot(x, y, label=label, linestyle=linestyle, color=color)
plt.plot(x,
y,
label=label,
linestyle=linestyle_code,
color=argcolor)
plt.plot(x_p, gaus(x_p, *popt), 'r--', label='fit')
j += 1
i += 1
ax = plt.gca()
ax.set_xlabel(h5lp[0].get_xlab(), fontsize=14)
ax.set_ylabel(h5lp[0].get_ylab(), fontsize=14)
handles, labels = ax.get_legend_handles_labels()
#plt.legend(flip(handles, 2), flip(labels, 2), ncol=2)
plt.legend(frameon=False)
plt.gcf().subplots_adjust(left=0.15, bottom=0.15)
if not (-3.0 < math.log(np.max(abs(y)), 10) < 3.0):
ax.yaxis.set_major_formatter(FormatStrFormatter('%.1e'))
plt.gcf().subplots_adjust(left=0.18)
plt.show()
fname, fext = os.path.splitext(args.paths[0])
save_path_name = fname + save_append_str + '_' + type_str + '.' + args.file_format
fig.savefig(save_path_name, format=args.file_format)
plt.close(fig)
if args.verbose:
sys.stdout.write('Saved: %s\n' % save_path_name)
sys.stdout.flush()
def main():
parser = h5plot_parser()
args = parser.parse_args()
if args.maketitle:
''' Calculating plasma frequency for length '''
ELECTRON_CHARGE_IN_COUL = 1.60217657e-19
ELECTRON_MASS_IN_KG = 9.10938291e-31
VAC_PERMIT_FARAD_PER_M = 8.854187817e-12
SPEED_OF_LIGHT_IN_M_PER_S = 299792458.0
omega_p = np.sqrt( args.n0 * (ELECTRON_CHARGE_IN_COUL**2)/ (VAC_PERMIT_FARAD_PER_M * ELECTRON_MASS_IN_KG));
skin_depth = SPEED_OF_LIGHT_IN_M_PER_S/omega_p
if len(sys.argv)==1:
parser.print_help()
sys.exit(1)
saveformat = args.file_format
h5lp = []
linestyles = ['-', '--', '-.', ':']
save_append_str = ''
type_str = 'comp'
if args.latexon:
plt.rc('text', usetex=True)
plt.rc('font', family='serif')
j = 0
i = 0
for path in args.paths:
fig = plt.figure(figsize=(7,5))
if not os.path.isfile(path):
print('ERROR: File %s does not exist!' % path)
sys.exit(1)
h5lp.append(H5Plot())
h5lp[i].read(path)
timestamp = path.split("_")[-1].split(".h5")[0]
if args.data2:
for files in args.data2:
if timestamp in files or args.manual:
print('Reading second data set...')
h5secondlp = H5Plot()
h5secondlp.read(files)
if args.cno == None:
argcolor = plt.cm.tab20(6)
else:
argcolor = plt.cm.tab20(args.cno[0])
j = 0
for (x, y, label, linestyle, color) in h5lp[i].get_line_plots():
if args.labels != None:
save_append_str += '_' + args.labels[i]
label = args.labels[i]
if label == '_line0':
label = path
if args.latexon:
if label[0] != '$' or label[-1] != '$':
label = r'$\textrm{' + label + '}$'
if args.abs:
y = np.abs(y)
if args.lstyle == None:
linestyle_code = linestyles[0]
else:
linestyle_code = linestyles[args.lstyle[0]]
if args.absylog:
plt.semilogy( x, y, label=label, linestyle=linestyle_code, color=argcolor, zorder=20)
else:
#plt.plot(x, y, label=label, linestyle=linestyle, color=color)
plt.plot(x, y, label=label, linestyle=linestyle_code, color=argcolor, zorder=20)
ax = plt.gca()
ax.tick_params('y', colors=argcolor)
plt.gcf().subplots_adjust(left=0.15, bottom=0.15, right=1-0.15)
if not (-3.0 < math.log(np.max(abs(y)),10) < 3.0):
ax.yaxis.set_major_formatter(FormatStrFormatter('%.1e'))
plt.gcf().subplots_adjust(left=0.18)
ax2 = ax.twinx()
''' PLOTTING THE SECOND PLOT '''
if args.cno == None:
argcolor = plt.cm.tab20(1)
else:
argcolor = plt.cm.tab20(args.cno[1])
ax2.tick_params('y', colors=argcolor)
j = 0
for (x2, y2, label, linestyle, color) in h5secondlp.get_line_plots():
if args.labels != None:
save_append_str += '_' + args.labels[i]
label = args.labels[i]
if label == '_line0':
label = path
if args.latexon:
if label[0] != '$' or label[-1] != '$':
label = r'$\textrm{' + label + '}$'
if args.abs:
y2 = np.abs(y2)
if args.lstyle == None:
linestyle_code = linestyles[0]
else:
linestyle_code = linestyles[args.lstyle[1]]
if args.absy2log:
plt.semilogy( x2, y2, label=label, linestyle=linestyle_code, color=argcolor, zorder=0)
else:
#plt.plot(x, y, label=label, linestyle=linestyle, color=color)
plt.plot(x2, y2, label=label, linestyle=linestyle_code, color=argcolor, zorder=0)
if args.xlim != None:
ax.set_xlim(args.xlim[0],args.xlim[1])
if args.ylim != None:
ax.set_ylim(args.ylim[0],args.ylim[1])
if args.y2lim != None:
ax2.set_ylim(args.y2lim[0],args.y2lim[1])
if args.xlab != None:
xlab = args.xlab
else:
xlab = h5lp[0].get_xlab()
if args.ylab != None:
ylab = args.ylab
else:
ylab = []
ylab.append(h5lp[0].get_ylab())
ylab.append(h5secondlp.get_ylab())
if args.latexon:
if xlab[0] != '$' or xlab[-1] != '$':
xlab = r'$' + xlab + '$'
if args.latexon:
if ylab[0,0] != '$' or ylab[0,-1] != '$':
ylab[0] = r'$' + ylab[0] + '$'
ylab[1] = r'$' + ylab[1] + '$'
ax.set_xlabel(xlab, fontsize=14)
ax.set_ylabel(ylab[0], fontsize=14)
ax2.set_ylabel(ylab[1], fontsize=14)
ax.set_zorder(ax2.get_zorder()+1) # put ax in front of ax2
ax.patch.set_visible(False) # hide the 'canvas'
# handles, labels = ax.get_legend_handles_labels()
# #plt.legend(flip(handles, 2), flip(labels, 2), ncol=2)
# plt.legend(frameon=False)
#plt.gcf().subplots_adjust(left=0.15, bottom=0.15, right=0.15)
if not (-3.0 < math.log(np.max(abs(y2)),10) < 3.0):
ax2.yaxis.set_major_formatter(FormatStrFormatter('%.1e'))
plt.gcf().subplots_adjust(right=1-0.18)
#plt.show()
''' make the title '''
if args.maketitle:
time = np.around(float(timestamp))
distance = time*skin_depth*1e2
title = 'Time: ' + str(time) + r'$\,\omega_p^{-1}$ ' + ' Distance: ' + str(np.around(distance,2)) + r'$\,$cm'
plt.title(title)
if args.show:
plt.show()
spath, fname = os.path.split(args.paths[0])
if args.savepath != None:
spath = args.savepath
if not args.manual:
save_name = type_str + '_' + fname + save_append_str + '_' + timestamp
else:
save_name = type_str + '_' + fname + save_append_str
if saveformat==args.file_format:
saveas_png(fig, spath, save_name, args.dpi)
else:
saveas_eps_pdf(fig, savepath=spath, savename=save_name)
plt.close(fig)