load_skewer=True)
cosmology = data['cosmology']
box = data['box']
skewer = data['lya_statistics']['skewer']
# skewer['HI_density'] *= 1e-5
HI_density = skewer['HI_density']
tau_cholla = skewer['optical_depth']
vel_Hubble_cholla = skewer['vel_Hubble']
temperature = skewer['temperature']
velocity = skewer['velocity']
F_cholla = skewer['transmitted_flux']
tau_data = compute_optical_depth(cosmology,
box,
skewer,
space='redshift',
method='error_function')
tau = tau_data['tau']
vel_Hubble = tau_data['vel_Hubble']
F = np.exp(-tau)
diff = (tau_cholla - tau) / tau
print(f" Diff: min:{diff.min()} max:{diff.max()}")
nrows = 5
ncols = 1
fig, ax_l = plt.subplots(nrows=nrows,
ncols=ncols,
figsize=(10 * ncols, 2.5 * nrows))
los_density = skewer_dataset['density']
los_HI_density = skewer_dataset['HI_density']
los_HeII_density = skewer_dataset['HeII_density']
los_velocity = skewer_dataset['velocity']
los_temperature = skewer_dataset['temperature']
skewer_id = 0
skewer_data = {}
skewer_data['HI_density'] = los_HI_density[skewer_id]
skewer_data['temperature'] = los_temperature[skewer_id]
skewer_data['velocity'] = los_velocity[skewer_id]
skewer_data['HeII_density'] = los_HeII_density[skewer_id]
tau_los_data = compute_optical_depth(cosmology,
box,
skewer_data,
space='redshift',
method='error_function',
chem_type='HI')
vel_hubble_HI = tau_los_data['vel_Hubble']
tau_HI = tau_los_data['tau']
tau_los_data = compute_optical_depth(cosmology,
box,
skewer_data,
space='redshift',
method='error_function',
chem_type='HeII')
vel_hubble_HeII = tau_los_data['vel_Hubble']
tau_HeII = tau_los_data['tau']
dens_HI = skewer_data['HI_density']
los_data = compute_los_properties(Lbox, n_skewer_pixels, axis, pos_i,
pos_j, tree, hsml_max, pos, mass, rho, u,
mu, vel_los, hsml, HI_rho, mass_HI)
skewer_temp = los_data['temperature']
skewer_vel = los_data['velocity']
skewer_HI_density = los_data['HI_density']
skewer_density_H = los_data['density'] * X
skewer_nHI = skewer_HI_density * cgs.Msun / cgs.kpc**3 * cosmo_h**2 / cgs.M_p
x_comov, vel_Hubble, n_HI_los, skewer_tau = compute_optical_depth(
H0,
cosmo_h,
Omega_M,
Omega_L,
Lbox,
current_z,
skewer_HI_density,
skewer_temp,
skewer_vel,
space='redshift',
method='error_function',
turbulence_boost=0.0)
skewer_F = np.exp(-skewer_tau)
F_mean = skewer_F.mean()
tau_eff = -np.log(F_mean)
skewer_density_H_ewald = los_rho_H_ewald[skewer_id]
skewer_temp_ewald = los_temp_ewald[skewer_id]
skewer_vel_ewald = los_vel_ewald[skewer_id]
skewer_nHI_frac_ewald = los_nHI_frac_ewald[skewer_id]
skewer_tau_ewald = los_tau_ewald[skewer_id]