def analysis(g):
spectrum_lamdwidth_fwhm = np.zeros_like(g.z)
spectrum_lamdwidth_std = np.zeros_like(g.z)
for zz in range(g.nZ):
spectrum_lamdwidth_fwhm[zz] = None
spectrum_lamdwidth_std[zz] = None
if np.sum(g.spec[:, zz]) != 0:
pos, width, arr = fwhm3(g.spec[:, zz])
if width != None:
if arr[0] == arr[-1]:
dlambda = abs(g.freq_lamd[pos] - g.freq_lamd[pos - 1])
else:
dlambda = abs(
(g.freq_lamd[arr[0]] - g.freq_lamd[arr[-1]]) /
(arr[0] - arr[-1]))
spectrum_lamdwidth_fwhm[
zz] = dlambda * width / g.freq_lamd[pos]
# spectrum_lamdwidth_fwhm[zz] = abs(g.freq_lamd[arr[0]] - g.freq_lamd[arr[-1]]) / g.freq_lamd[pos] # the FWHM of spectral line (error when peakpos is at the edge of lamdscale)
spectrum_lamdwidth_std[zz] = std_moment(
g.freq_lamd, g.spec[:, zz]) / n_moment(g.freq_lamd,
g.spec[:, zz], 0, 1)
######### end of section copied from genesis_plot.py
brightness = g.energy / spectrum_lamdwidth_std
for i in range(len(g.z)):
if g.z[i] < 1:
brightness[i] = 0
return g.energy, spectrum_lamdwidth_std, g.z, brightness, g.p_int, g.xrms, g.yrms, g.I, g.s
def evalBeamWithGenesis(dir, run=True, startcharge=250, genesis_file='NEW_SHORT_NOM_TD_v7.in', beam_file='CLA-FMS-APER-02.hdf5'):
# Genesis run:
data={'gen_file': genesis_file,
'file_pout': dir,
'file_beam':'beamfile.txt',
'i_scan':0,
'gen_launch':'',
'stat_run':1,
'idump':0,
'i_edist':0,
'i_beam':0,
'i_rad':0,
'i_dpa':0,
'i_dfl':0,
'i_HDF5':1,
'HDF5_file': dir+'/'+beam_file,
'i_match': 0}
if run:
data['gen_launch'] = '/opt/OpenMPI-3.1.3/bin/mpiexec --timeout 600 -np 12 /opt/Genesis/bin/genesis2 < tmp.cmd 2>&1 > /dev/null'
else:
data['gen_launch'] = ''
f = FEL_sim(data)
A_inp = f.read_GEN_input_file()
g = f.GEN_simul_preproc(A_inp, dirno=dir, startcharge=startcharge)
p = map(np.mean, zip(*g.p_int))
g.Lsat, g.Lsatindex = find_saturation(p, g.z)
# this section is copied from genesis_plot.py - to calculate bandwidth
spectrum_lamdwidth_fwhm = np.zeros_like(g.z)
spectrum_lamdwidth_std = np.zeros_like(g.z)
for zz in range(g.nZ):
spectrum_lamdwidth_fwhm[zz] = None
spectrum_lamdwidth_std[zz] = None
if np.sum(g.spec[:,zz])!=0:
pos, width, arr = fwhm3(g.spec[:, zz])
if width != None:
if arr[0] == arr[-1]:
dlambda = abs(g.freq_lamd[pos] - g.freq_lamd[pos-1])
else:
dlambda = abs( (g.freq_lamd[arr[0]] - g.freq_lamd[arr[-1]]) / (arr[0] - arr[-1]) )
spectrum_lamdwidth_fwhm[zz] = dlambda * width / g.freq_lamd[pos]
# spectrum_lamdwidth_fwhm[zz] = abs(g.freq_lamd[arr[0]] - g.freq_lamd[arr[-1]]) / g.freq_lamd[pos] # the FWHM of spectral line (error when peakpos is at the edge of lamdscale)
spectrum_lamdwidth_std[zz] = std_moment(g.freq_lamd, g.spec[:, zz]) / n_moment(g.freq_lamd, g.spec[:, zz], 0, 1)
######### end of section copied from genesis_plot.py
brightness = g.energy / spectrum_lamdwidth_std
for i in range(len(g.z)):
if g.z[i] < 5:
brightness[i] = 0
max = np.argmax(brightness)
maxe = np.argmax(g.energy)
g.spectrum_lamdwidth_std = spectrum_lamdwidth_std
return g.energy[max], g.spectrum_lamdwidth_std[max], g.z[max], g.energy[maxe], g.spectrum_lamdwidth_std[maxe], g.z[maxe], g.bunch_length, g
def evalBeamWithGenesis(dir, dirno=1):
# Genesis run:
data = {
'gen_file': 'NEW_SHORT_NOM_TD_v7.in',
'file_pout': outputdir,
'file_beam': 'beamfile.txt',
'i_scan': 0,
'gen_launch':
'/opt/OpenMPI-3.1.3/bin/mpiexec --timeout 300 -np 5 /opt/Genesis/bin/genesis2 < tmp.cmd 2>&1 > /dev/null',
'stat_run': 1,
'idump': 0,
'i_edist': 0,
'i_beam': 0,
'i_rad': 0,
'i_dpa': 0,
'i_dfl': 0,
'i_HDF5': 1,
'HDF5_file': dir + '/' + 'CLA-FMS-APER-01.hdf5',
'i_match': 0
}
f = FEL_sim(data)
A_inp = f.read_GEN_input_file()
g = f.GEN_simul_preproc(A_inp, dirno=dirno)
# this section is copied from genesis_plot.py - to calculate bandwidth
spectrum_lamdwidth_fwhm = np.zeros_like(g.z)
spectrum_lamdwidth_std = np.zeros_like(g.z)
for zz in range(g.nZ):
spectrum_lamdwidth_fwhm[zz] = None
spectrum_lamdwidth_std[zz] = None
if np.sum(g.spec[:, zz]) != 0:
pos, width, arr = fwhm3(g.spec[:, zz])
if width != None:
if arr[0] == arr[-1]:
dlambda = abs(g.freq_lamd[pos] - g.freq_lamd[pos - 1])
else:
dlambda = abs(
(g.freq_lamd[arr[0]] - g.freq_lamd[arr[-1]]) /
(arr[0] - arr[-1]))
spectrum_lamdwidth_fwhm[
zz] = dlambda * width / g.freq_lamd[pos]
# spectrum_lamdwidth_fwhm[zz] = abs(g.freq_lamd[arr[0]] - g.freq_lamd[arr[-1]]) / g.freq_lamd[pos] # the FWHM of spectral line (error when peakpos is at the edge of lamdscale)
spectrum_lamdwidth_std[zz] = std_moment(
g.freq_lamd, g.spec[:, zz]) / n_moment(g.freq_lamd,
g.spec[:, zz], 0, 1)
######### end of section copied from genesis_plot.py
return g.energy[-1], spectrum_lamdwidth_std[-1]
def evalBeamWithGenesis(ind, zpos=s):
print 'in evalBeamWithGenesis\n\n\n'
print ind
# copy file to backup location with random file name (needs better identifier...)
if os.path.exists('scan_0/ip_seed_-1/run.0.gout') == True:
os.system('cp scan_0/ip_seed_-1/run.0.gout genesis_out/run%i.out' %
random.randint(10000, 99999))
os.system('rm -R scan_0')
# normalise so that every list of rands adds to 1, then write beamfile
sum_rands = sum(ind)
norm_rands = ind / sum_rands
sum_norm_rands = sum(norm_rands)
current = norm_rands * av_current * num_slices
write_beamfile('beamfile.txt', zpos, current)
# Genesis run:
data = {
'gen_file': 'NEW_SHORT_NOM_TD_v7.in',
'file_pout': outputdir,
'file_beam': 'beamfile.txt',
'i_scan': 0,
'gen_launch': 'genesis2.0',
'stat_run': 1,
'idump': 0,
'i_edist': 0,
'i_beam': 1,
'i_rad': 0,
'i_dpa': 0,
'i_dfl': 0
}
#f = FEL_simulation_block.FEL_simulation_block(data)
f = FEL_sim(data)
A_inp = f.read_GEN_input_file()
g = f.GEN_simul_preproc(A_inp)
# this section is copied from genesis_plot.py - to calculate bandwidth
spectrum_lamdwidth_fwhm = np.zeros_like(g.z)
spectrum_lamdwidth_std = np.zeros_like(g.z)
for zz in range(g.nZ):
spectrum_lamdwidth_fwhm[zz] = None
spectrum_lamdwidth_std[zz] = None
if np.sum(g.spec[:, zz]) != 0:
pos, width, arr = fwhm3(g.spec[:, zz])
if width != None:
if arr[0] == arr[-1]:
dlambda = abs(g.freq_lamd[pos] - g.freq_lamd[pos - 1])
else:
dlambda = abs(
(g.freq_lamd[arr[0]] - g.freq_lamd[arr[-1]]) /
(arr[0] - arr[-1]))
spectrum_lamdwidth_fwhm[
zz] = dlambda * width / g.freq_lamd[pos]
# spectrum_lamdwidth_fwhm[zz] = abs(g.freq_lamd[arr[0]] - g.freq_lamd[arr[-1]]) / g.freq_lamd[pos] # the FWHM of spectral line (error when peakpos is at the edge of lamdscale)
spectrum_lamdwidth_std[zz] = std_moment(
g.freq_lamd, g.spec[:, zz]) / n_moment(g.freq_lamd,
g.spec[:, zz], 0, 1)
######### end of section copied from genesis_plot.py
#return Emax
#print spectrum_lamdwidth_fwhm[-1]
print 'bandwidth = ', spectrum_lamdwidth_std[-1]
print 'pulse energy =', g.energy[-1]
return g.energy[-1], spectrum_lamdwidth_std[-1]