print 'The critical baryon density of the universe is: ', c2t.rho_crit_0*c2t.OmegaB, ' g/cm^3' #You can also access the density in simulation units print 'The raw density at point (0,0,0) is ', dfile.raw_density[0,0,0] #Read an ionized fractions file and store it as an XfracFile object xfile = c2t.XfracFile(xfrac_filename) #The most important property of an XfracFile object is xi, which #is a numpy array containing the ionized fraction print 'The ionized fraction in point (10,223,45) is: ', xfile.xi[10,223,45] print 'The volume-averaged mean ionized fraction is: ', xfile.xi.mean() #c2raytools has several methods to calculate useful statistics, such as #mass-weighted mean ionized fraction print 'The mass-averaged mean ionized fraction is:', c2t.mass_weighted_mean_xi(xfile.xi, dfile.raw_density) #Read a velocity data file and store it as a VelocityFile object vfile = c2t.VelocityFile(velocity_filename) #Since the velocity data is actually momentum, we need the density to convert it to km/s kms = vfile.get_kms_from_density(dfile) print 'Gas velocity at cell (100,100,100) is ', kms[:,100,100,100], 'km/s' #Calculate neutral hydrogen number density n_hi = dfile.cgs_density*xfile.xi/c2t.m_p #Calculate differential brightness temperature #The calc_dt method can also take names of files so you don't have to load the #files yourself in advance. dT = c2t.calc_dt(xfile, dfile, z=xfile.z)
density_file = ''.join(glob.glob(density_path+'%.3fn_all.dat'%(z_arr[i-1])))
print 'Desnity file = %s' % density_file
dfile = c2t.DensityFile(density_file)
#Delta = dfile.raw_density/np.mean(dfile.raw_density.astype('float64'))
xfrac_file = ''.join(glob.glob(xfrac_path+'xfrac3d_%.3f.bin' % (z_arr[i])))
print 'Ionized fraction file = %s' % xfrac_file
xfile = c2t.XfracFile(xfrac_file)
irate_file = ''.join(glob.glob(xfrac_path+'IonRates3_%.3f.bin'%(z_arr[i])))
print 'Ionization rate file = %s' % irate_file
ifile = c2t.IonRateFile(irate_file)
avg_vG = ifile.irate.mean()
avg_mG = c2t.mass_weighted_mean_xi(ifile.irate,dfile.raw_density)
avg_xIIG = c2t.mass_weighted_mean_xi(ifile.irate,xfile.xi)
median_vG = np.median(ifile.irate)
ilist = np.reshape(ifile.irate,(ifile.mesh_x*ifile.mesh_y*ifile.mesh_z,1))
Dlist = np.reshape(dfile.raw_density/np.mean(dfile.raw_density.astype('float64')),(ifile.mesh_x*ifile.mesh_y*ifile.mesh_z,1))
avg_dG = 0.
count = 0
for index,Delta in enumerate(Dlist):
if (Delta < 1. - thresh): continue
elif (Delta > 1. + thresh): continue
else:
#print 'index = ',index, 'and Delta = ',Delta
avg_dG += ilist[index]
count += 1
#We are using the 114/h Mpc simulation box, so set all the proper conversion factors
c2t.set_sim_constants(boxsize_cMpc=114.)
#Read a density file and print some statistics
dfile = c2t.DensityFile(density_filename)
print 'The redshift is ', dfile.z
print 'The size of the mesh is (', dfile.mesh_x, dfile.mesh_y, dfile.mesh_z, ')'
print 'The mean baryon density is ', dfile.cgs_density.mean(), ' g/cm^3'
#Read an ionized fractions file
xfile = c2t.XfracFile(xfrac_filename)
print 'The volume-averaged mean ionized fraction is: ', xfile.xi.mean()
print 'The mass-averaged mean ionized fraction is:', c2t.mass_weighted_mean_xi(
xfile.xi, dfile.raw_density)
#Read a velocity data file
vfile = c2t.VelocityFile(velocity_filename)
#Since the velocity data is actually momentum, we need the density to convert it to km/s
kms = vfile.get_kms_from_density(dfile)
print 'Gas velocity at cell (100,100,100) is ', kms[:, 100, 100, 100], 'km/s'
#Calculate neutral hydrogen number density
n_hi = dfile.cgs_density * xfile.xi / c2t.m_p
#Calculate differential brightness temperature
dT = c2t.calc_dt(xfile, dfile)
#Get a slice through the center
z_filename = "../reds_full.dat"
# Read in z file to get snap and redshift and set mesh
z_arr = np.loadtxt(z_filename)
z_min = 10
out = open(output_filename, "w")
# Loop over z
for i in range(z_min, len(z_arr)):
print "z = %.3f" % (z_arr[i])
density_file = "".join(glob.glob(density_path + "%.3fn_all.dat" % (z_arr[i])))
if not density_file:
density_file = "".join(glob.glob(density_path + "%.3fn_all.dat" % (z_arr[i - 1])))
print "Density file = %s" % density_file
dfile = c2t.DensityFile(density_file)
# dens_arr = np.reshape(dfile.raw_density,box_vol)
xfrac_file = "".join(glob.glob(xfrac_path + "xfrac3d_%.3f.bin" % (z_arr[i])))
print "Ionized fraction file = %s" % xfrac_file
xfile = c2t.XfracFile(xfrac_file)
# xfrac_arr = np.reshape(xfile.xi,box_vol)
avg_nHII = xfile.xi.mean()
avg_mHII = c2t.mass_weighted_mean_xi(xfile.xi, dfile.raw_density)
print "z, avg_nHII, avg_mHII = %.3f %.4e %.4e" % (z_arr[i], avg_nHII, avg_mHII)
out.write("%.3f %.4e %.4e \n" % (z_arr[i], avg_nHII, avg_mHII))
out.close()
