def make_plot(rundir, file_no):
my_path = os.getcwd()
working_dir = my_path + '/' + rundir
efield_dir = working_dir + '/MS/FLD/e1/'
laser_dir = working_dir + '/MS/FLD/e2/'
eden_dir = working_dir + '/MS/DENSITY/electrons/charge/'
phase_space_dir = working_dir + '/MS/PHA/p1x1/electrons/'
p2x1_dir = working_dir + '/MS/PHA/p2x1/electrons/'
efield_prefix = 'e1-'
laser_prefix = 'e2-'
phase_prefix = 'p1x1-electrons-'
p2x1_prefix = 'p2x1-electrons-'
eden_prefix = 'charge-electrons-'
filename1 = phase_space_dir + phase_prefix + repr(file_no).zfill(
6) + '.h5'
fig = plt.figure(figsize=(12, 5))
phase_space = np.abs(osh5io.read_h5(filename1))
time = phase_space.run_attrs['TIME'][0]
fig.suptitle('Time = ' + repr(time) + '$\omega_p^{-1}$', fontsize=18)
filename2 = eden_dir + eden_prefix + repr(file_no).zfill(6) + '.h5'
filename3 = efield_dir + efield_prefix + repr(file_no).zfill(6) + '.h5'
eden = osh5io.read_h5(filename2)
ex = osh5io.read_h5(filename3)
psi = osh5io.read_h5(filename3)
den_plot = plt.subplot(121)
osh5vis.osplot(eden, title='Electron Density')
ex_plot = plt.subplot(122)
for i in range(psi.shape[0] - 2, -1, -1):
psi[i] = psi[i + 1] + psi.axes[0].increment * psi[i]
osh5vis.osplot(psi, title='Wake $\psi$ ', ylabel='$\psi [m_e c^2/e]$')
second_x = plt.twinx()
second_x.plot(ex.axes[0], ex, 'g', linestyle='-.')
second_x.set_ylabel('$E_{z}$', color='g')
second_x.tick_params(axis='y', labelcolor='g')
def make_plot(rundir, file_no):
my_path = os.getcwd()
#print(my_path)
working_dir = my_path + '/' + rundir
#print(working_dir)
efield_dir = working_dir + '/MS/FLD/e1/'
laser_dir = working_dir + '/MS/FLD/e2/'
eden_dir = working_dir + '/MS/DENSITY/electrons/charge/'
phase_space_dir = working_dir + '/MS/PHA/p1x1/electrons/'
p2x1_dir = working_dir + '/MS/PHA/p2x1/electrons/'
efield_prefix = 'e1-'
laser_prefix = 'e2-'
phase_prefix = 'p1x1-electrons-'
p2x1_prefix = 'p2x1-electrons-'
eden_prefix = 'charge-electrons-'
filename1 = phase_space_dir + phase_prefix + repr(file_no).zfill(
6) + '.h5'
fig = plt.figure(figsize=(12, 5))
phase_space = np.abs(osh5io.read_h5(filename1))
time = phase_space.run_attrs['TIME'][0]
fig.suptitle('Time = ' + repr(time) + '$\omega_p^{-1}$', fontsize=18)
filename4 = laser_dir + laser_prefix + repr(file_no).zfill(6) + '.h5'
ey = osh5io.read_h5(filename4)
ey_plot = plt.subplot(121)
osh5vis.osplot(ey, title='Laser Electric Field')
ey_plot_k = plt.subplot(122)
osh5vis.osplot(np.abs(osh5utils.fft(ey)),
xlim=[0, 20],
linestyle='-',
title='k spectrum')
def make_plot(rundir, file_no):
my_path = os.getcwd()
working_dir = my_path + '/' + rundir
efield_dir = working_dir + '/MS/FLD/e1/'
laser_dir = working_dir + '/MS/FLD/e2/'
eden_dir = working_dir + '/MS/DENSITY/electrons/charge/'
phase_space_dir = working_dir + '/MS/PHA/p1x1/electrons/'
p2x1_dir = working_dir + '/MS/PHA/p2x1/electrons/'
efield_prefix = 'e1-'
laser_prefix = 'e2-'
phase_prefix = 'p1x1-electrons-'
p2x1_prefix = 'p2x1-electrons-'
eden_prefix = 'charge-electrons-'
filename1 = phase_space_dir + phase_prefix + repr(file_no).zfill(
6) + '.h5'
fig = plt.figure(figsize=(12, 5))
phase_space = np.abs(osh5io.read_h5(filename1))
time = phase_space.run_attrs['TIME'][0]
fig.suptitle('Time = ' + repr(time) + '$\omega_p^{-1}$', fontsize=18)
filename2 = eden_dir + eden_prefix + repr(file_no).zfill(6) + '.h5'
filename3 = efield_dir + efield_prefix + repr(file_no).zfill(6) + '.h5'
eden = osh5io.read_h5(filename2)
ex = osh5io.read_h5(filename3)
den_plot = plt.subplot(121)
osh5vis.osplot(eden, title='Electron Density')
for i in range(ex.shape[0] - 2, -1, -1):
ex[i] = ex[i + 1] + ex.axes[0].increment * ex[i]
ex_plot = plt.subplot(122)
osh5vis.osplot(ex, title='Wake $\psi$ ', ylabel='$\psi [m_e c^2/e]$')
def something(rundir, file_no):
my_path = os.getcwd()
#print(my_path)
working_dir = my_path + '/' + rundir
#print(working_dir)
efield_dir = working_dir + '/MS/FLD/e1/'
laser_dir = working_dir + '/MS/FLD/e2/'
eden_dir = working_dir + '/MS/DENSITY/electrons/charge/'
iden_dir = working_dir + '/MS/DENSITY/ions/charge/'
phase_space_dir = working_dir + '/MS/PHA/p1x1/ions/'
p1x1_dir = working_dir + '/MS/PHA/p1x1/electrons/'
efield_prefix = 'e1-'
laser_prefix = 'e2-'
phase_prefix = 'p1x1-ions-'
p1x1_prefix = 'p1x1-electrons-'
eden_prefix = 'charge-electrons-'
iden_prefix = 'charge-ions-'
fig = plt.figure(figsize=(12, 16))
# filename1=phase_space_dir+phase_prefix+repr(file_no).zfill(6)+'.h5'
filename2 = eden_dir + eden_prefix + repr(file_no).zfill(6) + '.h5'
filename3 = efield_dir + efield_prefix + repr(file_no).zfill(6) + '.h5'
filename4 = laser_dir + laser_prefix + repr(file_no).zfill(6) + '.h5'
filename5 = p1x1_dir + p1x1_prefix + repr(file_no).zfill(6) + '.h5'
# filename6=iden_dir+iden_prefix+repr(file_no).zfill(6)+'.h5'
#print(filename1)
#print(filename2)
phase_space = np.abs(osh5io.read_h5(filename5))
# print(repr(phase_space))
eden = osh5io.read_h5(filename2)
ex = osh5io.read_h5(filename3)
ey = osh5io.read_h5(filename4)
# p1x1=np.abs(osh5io.read_h5(filename5))
# iden = osh5io.read_h5(filename6)
phase_plot = plt.subplot(224)
#print(repr(phase_space.axes[0].min))
#print(repr(phase_space.axes[1].min))
title = phase_space.data_attrs['LONG_NAME']
time = phase_space.run_attrs['TIME'][0]
fig.suptitle('Time = ' + repr(time) + '$\omega_p^{-1}$', fontsize=24)
ext_stuff = [
phase_space.axes[1].min, phase_space.axes[1].max,
phase_space.axes[0].min, phase_space.axes[0].max
]
data_max = max(np.abs(np.amax(phase_space)), 100)
#print(repr(data_max))
phase_contour = plt.contourf(
np.abs(phase_space + 0.000000001),
levels=[
0.000001 * data_max, 0.00001 * data_max, 0.0001 * data_max,
0.001 * data_max, 0.005 * data_max, 0.01 * data_max,
0.02 * data_max, 0.05 * data_max
],
extent=ext_stuff,
cmap='Spectral',
vmin=1e-6 * data_max,
vmax=1.5 * data_max,
norm=colors.LogNorm(vmin=0.000001 * data_max, vmax=1.5 * data_max))
phase_plot.set_title('Ion P1X1 Phase Space')
phase_plot.set_xlabel('Position [$c / \omega_{p}$]')
phase_plot.set_ylabel('Proper Velocity $\gamma v_1$ [ c ]')
# second_x = plt.twinx()
# second_x.plot(ex.axes[0],ex,'g',linestyle='-.')
#plt.colorbar()
#osh5vis.oscontour(phase_space,levels=[10**-5,10**-3,10**-1,1,10,100],colors='black',linestyles='dashed',vmin=1e-5,vmax=1000)
# plt.contour(np.abs(phase_space+0.000001),levels=[0.0001,0.001,0.01,0.05,0.1,0.2,0.5,1],extent=ext_stuff,colors='black',linestyles='dashed')
plt.colorbar(phase_contour)
den_plot = plt.subplot(223)
osh5vis.osplot(np.log(np.sum(np.abs(phase_space), axis=1) + 0.001),
title='f(v)')
ex_plot = plt.subplot(222)
osh5vis.osplot(ex, title='Wake E-field ', ylabel='$E_1 [m_e c^2/e]$')
ey_plot = plt.subplot(221)
osh5vis.osplot(ey, title='Laser Electric Field')
def something_2(rundir, file_no):
my_path = os.getcwd()
#print(my_path)
working_dir = my_path + '/' + rundir
#print(working_dir)
dir_0 = rundir + '/Vx_x/'
dir_1 = rundir + '/Ex/'
output_dir = rundir + '/movies/'
try:
os.mkdir(output_dir)
except OSError as exc:
if exc.errno != errno.EEXIST:
raise
pass
quan_0_prefix = 'vx_x_'
quan_1_prefix = 'Ex-0_'
output_prefix = 'frame_'
fig = plt.figure(figsize=(10, 8))
phase_space_filename = dir_0 + quan_0_prefix + repr(file_no).zfill(
6) + '.h5'
e1_filename = dir_1 + quan_1_prefix + repr(file_no).zfill(6) + '.h5'
output_filename = output_dir + '/' + output_prefix + repr(file_no).zfill(
6) + '.png'
phase_space_data = osh5io.read_h5(phase_space_filename)
e1_data = np.average(osh5io.read_h5(e1_filename), axis=0)
p1_x1_plot = plt.subplot(221)
osh5vis.osplot(np.log(np.abs(phase_space_data) + 1e-10),
title='Phase Space',
vmax=10,
vmin=-2,
cmap='Blues')
e1_plot = plt.subplot(222)
osh5vis.osplot(e1_data, title='Electric Field')
e1_plot.set_ylim([-0.1, 0.1])
plt.tight_layout()
fv_plot = plt.subplot(223)
# print(hdf5_data)
xmin = phase_space_data.axes[0].min
xmax = phase_space_data.axes[0].max
ymin = phase_space_data.axes[1].min
ymax = phase_space_data.axes[1].max
# dx=(xmax-xmin)/float(nx[0]-1)
# dy=(ymax-ymin)/float(nx[1]-1)
# print(dx)
# print(dy)
# xmax=xmax-dx
# ymax=ymax-dy
# xmin=xmin+10.0*dx
# ymin=ymin-10.0*dy
# print(repr(xmin)+' '+repr(xmax)+' '+repr(ymin)+' '+repr(ymax))
nx = phase_space_data.shape
xaxis = np.linspace(xmin, xmax, num=nx[0])
yaxis = np.linspace(ymin, ymax, num=nx[1])
plt.plot(xaxis, np.average(phase_space_data, axis=1))
plt.xlabel('$v/v_{th}$')
plt.ylabel('f(v) [a.u]')
fv_plot.set_ylim([0, 1500])
fv_slices = plt.subplot(224)
# print(hdf5_data)
xmin = phase_space_data.axes[0].min
xmax = phase_space_data.axes[0].max
ymin = phase_space_data.axes[1].min
ymax = phase_space_data.axes[1].max
# dx=(xmax-xmin)/float(nx[0]-1)
# dy=(ymax-ymin)/float(nx[1]-1)
# print(dx)
# print(dy)
# xmax=xmax-dx
# ymax=ymax-dy
# xmin=xmin+10.0*dx
# ymin=ymin-10.0*dy
# print(repr(xmin)+' '+repr(xmax)+' '+repr(ymin)+' '+repr(ymax))
nx = phase_space_data.shape
xaxis = np.linspace(xmin, xmax, num=nx[0])
yaxis = np.linspace(ymin, ymax, num=nx[1])
plt.plot(xaxis, np.average(phase_space_data[:, 492:532], axis=1))
plt.plot(xaxis, np.average(phase_space_data[:, 352:372], axis=1), 'r')
plt.plot(xaxis, np.average(phase_space_data[:, 652:672], axis=1), 'g')
plt.xlabel('$v/v_{th}$')
plt.ylabel('f(v) [a.u]')
fv_slices.set_ylim([0, 1500])
plt.savefig(output_filename)
def something_2(rundir,file_no):
v_phase = 1/.3
v_group = 3/v_phase
my_path=os.getcwd()
#print(my_path)
working_dir=my_path+'/'+rundir
#print(working_dir)
dir_0=rundir+'/Vx_x/'
dir_1=rundir+'/Ex/'
quan_0_prefix='vx_x_'
quan_1_prefix='Ex-0_'
fig = plt.figure(figsize=(10,8) )
phase_space_filename=dir_0+quan_0_prefix+repr(file_no).zfill(6)+'.h5'
e1_filename=dir_1+quan_1_prefix+repr(file_no).zfill(6)+'.h5'
phase_space_data = osh5io.read_h5(phase_space_filename)
e1_data = np.average(osh5io.read_h5(e1_filename),axis=0)
fig.suptitle('Landau Boundary Problem, time = '+repr(phase_space_data.run_attrs['TIME'][0])+' $\omega_p^{-1}$ \n \n')
p1_x1_plot = plt.subplot(221)
osh5vis.osplot(np.log(np.abs(phase_space_data)+1e-10),title='Phase Space',vmax=10,vmin=-2,cmap='Blues')
# =====================================================================
# =====================================================================
# the following lines draw vertical axis indicating the group velocity
# p1_x1_plot.axvline(x=512-v_group*phase_space_data.run_attrs['TIME'][0])
# p1_x1_plot.axvline(x=512+v_group*phase_space_data.run_attrs['TIME'][0])
# =====================================================================
# =====================================================================
e1_plot = plt.subplot(222)
osh5vis.osplot(e1_data,title='Electric Field')
# plt.tight_layout()
fig.subplots_adjust(top=0.82)
fv_plot = plt.subplot(223)
# print(hdf5_data)
xmin=phase_space_data.axes[0].min
xmax=phase_space_data.axes[0].max
ymin=phase_space_data.axes[1].min
ymax=phase_space_data.axes[1].max
# dx=(xmax-xmin)/float(nx[0]-1)
# dy=(ymax-ymin)/float(nx[1]-1)
# print(dx)
# print(dy)
# xmax=xmax-dx
# ymax=ymax-dy
# xmin=xmin+10.0*dx
# ymin=ymin-10.0*dy
# print(repr(xmin)+' '+repr(xmax)+' '+repr(ymin)+' '+repr(ymax))
nx=phase_space_data.shape
xaxis=np.linspace(xmin,xmax,num=nx[0])
yaxis=np.linspace(ymin,ymax,num=nx[1])
plt.plot(xaxis,np.average(phase_space_data,axis=1))
plt.xlabel('$v/v_{th}$')
plt.ylabel('f(v) [a.u]')
fv_plot.set_ylim([0, 1500])
fig.subplots_adjust(top=0.82)
fv_slices = plt.subplot(224)
# print(hdf5_data)
xmin=phase_space_data.axes[0].min
xmax=phase_space_data.axes[0].max
ymin=phase_space_data.axes[1].min
ymax=phase_space_data.axes[1].max
# dx=(xmax-xmin)/float(nx[0]-1)
# dy=(ymax-ymin)/float(nx[1]-1)
# print(dx)
# print(dy)
# xmax=xmax-dx
# ymax=ymax-dy
# xmin=xmin+10.0*dx
# ymin=ymin-10.0*dy
# print(repr(xmin)+' '+repr(xmax)+' '+repr(ymin)+' '+repr(ymax))
nx=phase_space_data.shape
xaxis=np.linspace(xmin,xmax,num=nx[0])
yaxis=np.linspace(ymin,ymax,num=nx[1])
plt.plot(xaxis,np.average(phase_space_data[:,492:532],axis=1))
plt.plot(xaxis,np.average(phase_space_data[:,352:372],axis=1),'r')
plt.plot(xaxis,np.average(phase_space_data[:,652:672],axis=1),'g')
plt.xlabel('$v/v_{th}$')
plt.ylabel('f(v) [a.u]')
fv_slices.set_ylim([0, 1500])
plt.tight_layout()
plt.show()
def srs_quick_look(path,fileno):
path_e1=path_main+'/MS/FLD/e1/'
file_prefix_e1='e1-'
path_e2=path_main+'/MS/FLD/e2/'
file_prefix_e2='e2-'
path_e3=path_main+'/MS/FLD/e3/'
file_prefix_e3='e3-'
path_b1=path_main+'/MS/FLD/b1/'
file_prefix_b1='b1-'
path_b2=path_main+'/MS/FLD/b2/'
file_prefix_b2='b2-'
path_b3=path_main+'/MS/FLD/b3/'
file_prefix_b3='b3-'
path_p1x1_e = path_main+'/MS/PHA/p1x1/species_1/'
file_prefix_p1x1_e = 'p1x1-species_1-'
# fileno = 22500
interval = 30
nfiles=10
path_p1p2_e = path_main+'/MS/PHA/p1p2/species_1/'
file_prefix_p1p2_e = 'p1p2-species_1-'
from scipy import signal
filename_e1=path_e1+file_prefix_e1+repr(fileno).zfill(6)+'.h5'
filename_e2=path_e2+file_prefix_e2+repr(fileno).zfill(6)+'.h5'
filename_e3=path_e3+file_prefix_e3+repr(fileno).zfill(6)+'.h5'
filename_b1=path_b1+file_prefix_b1+repr(fileno).zfill(6)+'.h5'
filename_b2=path_b2+file_prefix_b2+repr(fileno).zfill(6)+'.h5'
filename_b3=path_b3+file_prefix_b3+repr(fileno).zfill(6)+'.h5'
filename_p1x1_e = path_p1x1_e+file_prefix_p1x1_e+repr(fileno).zfill(6)+'.h5'
filename_p1p2_e = path_p1p2_e+file_prefix_p1p2_e+repr(fileno).zfill(6)+'.h5'
# print(filename)
e1 = osh5io.read_h5(filename_e1)
e2 = osh5io.read_h5(filename_e2)
e3 = osh5io.read_h5(filename_e3)
b1 = osh5io.read_h5(filename_b1)
b2 = osh5io.read_h5(filename_b2)
b3 = osh5io.read_h5(filename_b3)
# print(e1.axes[0].attrs)
# Method 1: Just read files
# p1x1_e = osh5io.read_h5(filename_p1x1_e)
# p1p2_e = osh5io.read_h5(filename_p1p2_e)
# Method 2: Average over N steps
interval=30
nfiles = 20
p1x1_e = phase_space_average_new(path_p1x1_e,file_prefix_p1x1_e,fileno,interval,nfiles)
p1p2_e = phase_space_average_new(path_p1p2_e,file_prefix_p1p2_e,fileno,interval,nfiles)
SMALL_SIZE = 12
MEDIUM_SIZE = 14
BIGGER_SIZE = 18
plt.rc('font', size=SMALL_SIZE) # controls default text sizes
plt.rc('axes', titlesize=SMALL_SIZE) # fontsize of the axes title
plt.rc('axes', labelsize=MEDIUM_SIZE) # fontsize of the x and y labels
plt.rc('xtick', labelsize=SMALL_SIZE) # fontsize of the tick labels
plt.rc('ytick', labelsize=SMALL_SIZE) # fontsize of the tick labels
plt.rc('legend', fontsize=SMALL_SIZE) # legend fontsize
plt.rc('figure', titlesize=BIGGER_SIZE) # fontsize of the figure title
s1 = e2*b3 - e3 * b2
s1.data_attrs['NAME']='S1'
s1.data_attrs['LONG_NAME']='S_1'
n_smooth=200
smoothing=np.ones((1,n_smooth))/n_smooth
n_avg = 200
smooth_array=np.ones((1,n_avg))/n_avg
temp=signal.convolve2d(s1,smooth_array,mode='same',boundary='wrap')
s1[:,:]=temp[:,:]
s1 = np.average(s1,axis=0)
plt.figure(figsize=(10,7.0))
plt.subplot(222)
temp=signal.convolve2d(e1,smoothing,mode='same',boundary='wrap')
osh5vis.osplot(np.average(e1,axis=0))
plt.ylim(-0.02,0.02)
# plt.subplot(222)
# osh5vis.osplot(e2,cmap='seismic',vmin=-0.02,vmax=0.02)
# plt.subplot(223)
# osh5vis.osplot(s1,cmap='PuBu',vmin=0,vmax=0.000025)
plt.subplot(221)
p1x1_e = numpy.abs(p1x1_e)
data_max= numpy.amax(p1x1_e)
p1x1_e=p1x1_e/data_max
osh5vis.oscontourf(p1x1_e,levels=[10**-5,3.0*10**-3,5*10**-3,1*10**-2,10**-1,3*10**-1,5*10**1],norm=LogNorm(),cmap='terrain',vmin=1e-3,vmax=100)
osh5vis.oscontour(p1x1_e,levels=[10**-5,3.0*10**-3,5*10**-3,1*10**-2,10**-1,3*10**-1,5*10**1],norm=LogNorm(),colors='black',linestyles='dashed',vmin=1e-5,vmax=500,colorbar=False)
plt.subplot(223)
# osh5vis.osplot(np.log(np.abs(p1p2_e)+1e-5),cmap='hsv')
p1p2_e = numpy.abs(p1p2_e)
data_max= numpy.amax(p1p2_e)
p1p2_e=p1p2_e/data_max
osh5vis.oscontourf(p1p2_e,levels=[10**-6,3.0*10**-3,5*10**-3,1*10**-2,10**-1,3*10**-1,5*10**1],norm=LogNorm(),cmap='terrain',vmin=1e-3,vmax=100)
osh5vis.oscontour(p1p2_e,levels=[10**-6,3.0*10**-3,5*10**-3,1*10**-2,10**-1,3*10**-1,5*10**1],norm=LogNorm(),colors='black',linestyles='dashed',vmin=1e-5,vmax=500,colorbar=False)
# plt.xlim(-0.8,0.8)
plt.xlim(-0.35,0.35)
plt.subplot(224)
osh5vis.osplot(s1, title='Axial <Poynting Flux>')
plt.ylim(0,0.00009)
plt.tight_layout()
plt.show()