def map_dbt_lightcone():
for i in range(0, len(redshifts)):
# print 'filename: setup_dirs.resultsdir()+'map_dbt_lightcone_'+str('%.3f' % redshifts[i])+'.dat'
filename = setup_dirs.resultsdir() + "map_dbt_lightcone_" + str("%.3f" % redshifts[i]) + ".dat"
temp_filename = setup_dirs.path() + "Temper3D_" + str("%.3f" % redshifts[i]) + ".bin"
xfrac_filename = setup_dirs.path() + "xfrac3d_" + str("%.3f" % redshifts[i]) + ".bin"
if i % 2 == 0:
density_filename = (
"/research/prace/244Mpc_RT/244Mpc_f2_8.2pS_250/coarser_densities/"
+ str("%.3f" % redshifts[i])
+ "n_all.dat"
)
else:
density_filename = (
"/research/prace/244Mpc_RT/244Mpc_f2_8.2pS_250/coarser_densities/"
+ str("%.3f" % redshifts[i - 1])
+ "n_all.dat"
)
tfile = c2t.TemperFile(temp_filename)
xfile = c2t.XfracFile(xfrac_filename).xi
if ss == " ":
dfile = c2t.DensityFile(density_filename).cgs_density
else:
dfile = np.ones(ss ** 3).reshape(ss, ss, ss) * 1.981e-10 * (1 + redshifts[i]) ** 3
dT_box = c2t.calc_dt_full_lightcone(xfile, tfile, dfile, redshifts[i])
IO.writemap(dT_box, filename)
print "Written map to " + filename
def scatter_contour():
for i in range(start,len(redshifts)):
print "Doing redshift " + str(redshifts[i])+"..."
xfrac_filename = setup_dirs.path()+'xfrac3d_'+str('%.3f' % redshifts[i]) + '.bin'
xfrac = c2t.XfracFile(xfrac_filename).xi.flatten()
print "Read ionized fraction"
temp_filename = setup_dirs.path() + 'Temper3D_'+str('%.3f' % redshifts[i]) + '.bin'
temperature = c2t.TemperFile(temp_filename).temper.flatten()
print "Read Temperature"
print "Generating plots..."
plot_scatter_contour(xfrac,temperature,"contour_scatter_xfrac_temperature","Temperature (K)","Ionised Fraction",i)
def xfrac_histogram():
'''plot hisograms'''
for i in range(1,len(redshifts)):#max(1,start),len(redshifts)):
print redshifts[i]
xfrac_filename = setup_dirs.path()+'xfrac3d_'+str('%.3f' % redshifts[i]) + '.bin'
xfrac_HI = c2t.XfracFile(xfrac_filename).xi
xfracHe1_filename = setup_dirs.path()+'xfrac3dHe1_'+str('%.3f' % redshifts[i]) + '.bin'
xfrac_He1 = c2t.XfracFile(xfracHe1_filename).xi
xfracHe2_filename = setup_dirs.path()+'xfrac3dHe2_'+str('%.3f' % redshifts[i]) + '.bin'
xfrac_He2 = c2t.XfracFile(xfracHe2_filename).xi
plot_3_log_histograms(xfrac_HI[len(xfrac_HI[:,0,0])/2,:,:],xfrac_He1[len(xfrac_HI[:,0,0])/2,:,:],xfrac_He2[len(xfrac_HI[:,0,0])/2,:,:],"Ionised Fraction, Redshift:" +str('%.3f' % redshifts[i]),"loghist_xfrac_"+str(i+10)+'_'+str('%.3f' % redshifts[i]),"Ionised Fraction")
def map_temp():
for i in range(start, len(redshifts)):
filename = setup_dirs.resultsdir() + "map_temper_" + str("%.3f" % redshifts[i]) + ".dat"
temp_filename = setup_dirs.path() + "Temper3D_" + str("%.3f" % redshifts[i]) + ".bin"
tfile = c2t.TemperFile(temp_filename)
IO.writemap(tfile.temper, filename)
print "Writen map to " + filename
def lightcone_xfrac(rsd=''):
filenames = ["" for x in range(len(redshifts))]
if rsd!='':
vel_files=["" for x in range(len(redshifts)/2)]#]'/research/prace/sph_smooth_cubepm_130329_10_4000_244Mpc_ext2_test/global/so/nc250'+'%.3fv_all.dat'%z for z in redshifts]
dens_files=["" for x in range(len(redshifts)/2)]#]'/research/prace/sph_smooth_cubepm_130329_10_4000_244Mpc_ext2_test/global/so/nc250'+'%.3fv_all.dat'%z for z in redshifts]
# filenames[0] = len(redshifts)
mini = -457
maxi=83
for i in range(len(filenames)):
#filenames[i] = setup_dirs.path() + 'lightcone_temp/Temper3D_'+str('%.3f' % redshifts[i]) + '.bin'
filenames[i] = filename = setup_dirs.path()+'xfrac3d_'+str('%.3f' % redshifts[i]) + '.bin'
if i%2==0 and rsd!='':
vel_files[i/2]='/research/prace/sph_smooth_cubepm_130329_10_4000_244Mpc_ext2_test/global/so/nc250/'+str('%.3f' % redshifts[i])+'v_all.dat'
dens_files[i/2]='/research/prace/sph_smooth_cubepm_130329_10_4000_244Mpc_ext2_test/global/so/nc250/%.3fn_all.dat'%redshifts[i]
noreds=10
# redshifts_many = np.zeros(len(redshifts)*noreds)
# for i in range(len(redshifts)-1):
# for j in range(noreds):
# redshifts_many[i+j]=redshifts[i]-(redshifts[i+1]-redshifts[i])*j/noreds
print filenames
im,z=c2t.make_lightcone(filenames)#,interpolation='step_cell')
if rsd!='':
vel_lightcone, z = c2t.make_velocity_lightcone(vel_files, dens_files)#,redshifts[0], redshifts[len(redshifts)-1])
rsd_xfrac = c2t.get_distorted_dt(im, vel_lightcone, z, \
num_particles=30, los_axis=2, velocity_axis=0, \
periodic=False)
im=np.asarray(rsd_xfrac)
plot_lightcone(im[125,:,::-1],i,"Ionised Fraction","lightcone_rsd_xfrac",mini,maxi,z,cmap='Blues_r')
else:
im=np.asarray(im)
plot_lightcone(im[125,:,::-1],i,"Ionised Fraction","lightconexfrac",mini,maxi,z,cmap='Blues_r')
def temp_histrogram():
for i in range(start,len(redshifts)):
temp_filename = setup_dirs.path() + 'Temper3D_'+str('%.3f' % redshifts[i]) + '.bin'
data = c2t.TemperFile(temp_filename).temper
data = data.flatten()
print len(data), 250**3
plot_log_histogram(data,"loghist_temper_shortrange_"+str(i+10)+'_'+str('%.3f' % redshifts[i]),"Temperature(K)","Redshift:" +str('%.3f' % redshifts[i]),"loghist_temper_shortrange_"+str(i+10)+'_'+str('%.3f' % redshifts[i]),"Temperature(K)")
def mean_xfrac(id):
file = open(setup_dirs.resultsdir()+'mean_xfrac'+id+'.dat', 'w')
for i in range(len(redshifts)):
xfrac_filename = setup_dirs.path()+'xfrac3d'+id+'_'+str('%.3f' % redshifts[i]) + '.bin'
xfile = c2t.XfracFile(xfrac_filename)
file.write(str(np.mean(xfile.xi)) + '\n')
file.close()
print "Written mean xfrac to "+setup_dirs.resultsdir()+'mean_xfrac'+id+'.dat'
def plotxfrac(id):
for i in range(start,len(redshifts)):
print "Doing redshift " + str(redshifts[i])+"..."
xfrac_filename = setup_dirs.path()+'xfrac3d'+id+'_'+str('%.3f' % redshifts[i]) + '.bin'
xfrac = c2t.XfracFile(xfrac_filename).xi
maxi = 1.0
mini = 0.000199999994948
plot(xfrac[mesh/2,:,:],i,id + "Ionised Fraction","xfrac"+id,mini,maxi,cmap='Blues_r',type='log')
def min_temp():
file = open(setup_dirs.resultsdir()+'min_temp.dat', 'w')
for i in range(len(redshifts)):
filename = setup_dirs.path()+'Temper3D_'+str('%.3f' % redshifts[i]) + '.bin'
data = c2t.TemperFile(filename)
file.write(str(np.amin(data.temper)) + '\n')
file.close()
print "Written mean Temperature to "+setup_dirs.resultsdir()+'min_temp.dat'
def map_xfrac(id):
# for i in range(len(redshifts)-6,len(redshifts)-4):
print len(redshifts)
for i in range(start, len(redshifts)):
filename = setup_dirs.resultsdir() + "map_xfrac" + id + "_" + str("%.3f" % redshifts[i]) + ".dat"
xfrac_filename = setup_dirs.path() + "xfrac3d" + id + "_" + str("%.3f" % redshifts[i]) + ".bin"
xfile = c2t.XfracFile(xfrac_filename)
IO.writemap(xfile.xi, filename)
print "Written map to " + filename
def plottemp():
for i in range(start,len(redshifts)):
print "Doing redshift " + str(redshifts[i])+"..."
temp_filename = setup_dirs.path() + 'Temper3D_'+str('%.3f' % redshifts[i]) + '.bin'
temperature = c2t.TemperFile(temp_filename).temper
mini=0.0
maxi = 14300.0
# if (i == (len(redshifts)-25)):
# maxi = findmax(temperature)/2.0
plot(temperature[mesh/2,:,:],i,"Temperature (K)","temp",mini,maxi)
def map_dbt():
for i in range(start, len(redshifts)):
filename = setup_dirs.resultsdir() + "map_dbt_" + str("%.3f" % redshifts[i]) + ".bin"
temp_filename = setup_dirs.path() + "Temper3D_" + str("%.3f" % redshifts[i]) + ".bin"
xfrac_filename = setup_dirs.path() + "xfrac3d_" + str("%.3f" % redshifts[i]) + ".bin"
if i % 2 == 0:
density_filename = (
"/research/prace/244Mpc_RT/244Mpc_f2_8.2pS_250/coarser_densities/"
+ str("%.3f" % redshifts[i])
+ "n_all.dat"
)
else:
density_filename = (
"/research/prace/244Mpc_RT/244Mpc_f2_8.2pS_250/coarser_densities/"
+ str("%.3f" % redshifts[i - 1])
+ "n_all.dat"
)
tfile = c2t.TemperFile(temp_filename)
xfile = c2t.XfracFile(xfrac_filename).xi
if ss != " ":
abu_he = 0.074
G_grav = 6.674e-11
pc = 3.086e16
Mpc = 1e6 * pc
H0 = 0.7 * 100.0 * 1.0e5 / Mpc
rho_crit_0 = 3.0 * H0 * H0 / (8.0 * np.pi * G_grav)
Omega_B = 0.044
mu = (1.0 - abu_he) + 4.0 * abu_he
m_p = 1.672661e-24
dfile = np.ones(ss ** 3).reshape(ss, ss, ss)
dfile = dfile * rho_crit_0 * Omega_B / (mu * m_p) * (1.0 + redshifts[i]) ** 3
dfile = dfile * 1.23581719037e-35
else:
dfile = c2t.DensityFile(density_filename).cgs_density
dT_box = c2t.calc_dt_full(xfile, tfile, dfile, redshifts[i])
# IO.writemap(dT_box,filename)
IO.writebin(dT_box, filename)
print "Written map to " + filename
def mean_dbt_hightemp():
file = open(setup_dirs.resultsdir()+'mean_dbt_hightemp.dat','w')
for i in range(len(redshifts)):
filename = setup_dirs.resultsdir()+'map_dbt_hightemp'+str('%.3f' % redshifts[i])+'.dat'
temp_filename = setup_dirs.path()+'Temper3D_'+str('%.3f' % redshifts[i]) + '.bin'
xfrac_filename = setup_dirs.path() +'xfrac3d_'+str('%.3f' % redshifts[i]) + '.bin'
if i%2==0:
density_filename='/research/prace/244Mpc_RT/244Mpc_f2_8.2pS_250/coarser_densities/' + str('%.3f' % redshifts[i]) + 'n_all.dat'
else:
density_filename='/research/prace/244Mpc_RT/244Mpc_f2_8.2pS_250/coarser_densities/' + str('%.3f' % redshifts[i-1]) + 'n_all.dat'
tfile = c2t.TemperFile(temp_filename)
xfile = c2t.XfracFile(xfrac_filename).xi
if ss!=' ':
dfile = np.ones(ss**3).reshape(ss,ss,ss)*1.981e-10*(1+redshifts[i])**3
else:
dfile = c2t.DensityFile(density_filename).cgs_density
dT_box = c2t.calc_dt(xfile, dfile, redshifts[i]) #returned in micro kelvin! update plots
file.write(str(np.mean(dT_box))+'\n')
print "Written mean dbt to " + setup_dirs.resultsdir()+'mean_dbt_hightemp.dat'
def mean_temp_igm():
file = open(setup_dirs.resultsdir()+'mean_temp_igm.dat', 'w')
file2= open(setup_dirs.resultsdir()+'fraction_ionised.dat','w')
for i in range(len(redshifts)):
filename = setup_dirs.path()+'Temper3D_'+str('%.3f' % redshifts[i]) + '.bin'
data = c2t.TemperFile(filename)
xfrac_filename = setup_dirs.path()+'xfrac3d_'+str('%.3f' % redshifts[i]) + '.bin'
xfile = c2t.XfracFile(xfrac_filename)
igm_data=[]
ionisedpoints=0
for i in range(len(data.temper[1,:,1])):
for j in range(len(data.temper[1,:,1])):
for k in range(len(data.temper[1,:,1])):
if xfile.xi[i,j,k] < 1e3:
igm_data.append(data.temper[i,j,k])
else:
ionisedpoints=ionisedpoints+1
file.write(str(np.mean(igm_data)) + '\n')
file.write(str(ionisedpoints/250**3))
file.close()
print "Written mean Temperature to "+setup_dirs.resultsdir()+'mean_temp_igm.dat'
def blurtemp():
for z in range(start,len(redshifts)):
print "Doing redshift " + str(redshifts[z])+"..."
temp_filename = setup_dirs.path() + 'Temper3D_'+str('%.3f' % redshifts[z]) + '.bin'
T = c2t.TemperFile(temp_filename).temper
Tb=np.zeros(10**3).reshape(10,10,10)
nobins=20
for i in range(len(T[:,1,1])):
for j in range(len(T[:,1,1])):
for k in range(len(T[:,1,1])):
Tb[i/20,j/20,k/20]=Tb[i/20,j/20,k/20]+T[i,j,k]
Tb=Tb/20**3
IO.writebin(Tb,"tests/blurred/temp_"+str(redshifts[z])+".bin")
print "written to tests/blurred/temp_"+str(redshifts[z])+".bin"
def equation_of_state():
print redshifts
for i in range(start,len(redshifts)):
print "Doing redshift " + str(redshifts[i])+"..."
if nosteps == 2 or i<nosteps:
density_filename='/research/prace/244Mpc_RT/244Mpc_f2_8.2pS_250/coarser_densities/' + str('%.3f' % redshifts[i-i%nosteps]) + 'n_all.dat'
print "density filename: "+ str('%.3f' % redshifts[i-(i)%nosteps]) + 'n_all.dat'
else:
density_filename='/research/prace/244Mpc_RT/244Mpc_f2_8.2pS_250/coarser_densities/' + str('%.3f' % redshifts[i-i%nosteps-1]) + 'n_all.dat'
print "density filename: "+ str('%.3f' % redshifts[i-(i)%nosteps-1]) + 'n_all.dat'
density = c2t.DensityFile(density_filename).cgs_density.flatten()
print "Read density file"
temp_filename = setup_dirs.path() + 'Temper3D_'+str('%.3f' % redshifts[i]) + '.bin'
temperature = c2t.TemperFile(temp_filename).temper.flatten()
print "Read temperature"
print "Generating plots..."
plot_scatter_contour(density,temperature,"equation_of_state","Temperature (K)","Density ($\mathrm{\Omega}$)",i)
def compare_hisograms_temperature():
for i in range(12,len(redshifts)):
temp_filename = setup_dirs.path() + 'Temper3D_'+str('%.3f' % redshifts[i]) + '.bin'
data = c2t.TemperFile(temp_filename).temper
data = data.flatten() #need to import other dataset and put in right format
def temp_power_spectrum():
for i in range(len(redshifts)):
print "Doing redshift: " + str(redshifts[i])
data=c2t.TemperFile(setup_dirs.path()+"Temper3D_"+str('%.3f' % redshifts[i])+".bin").temper
powerspec=ps.power_spectrum_1d(data,100)
IO.write2data(powerspec[0],powerspec[1],setup_dirs.resultsdir()+'/powerSpectra_temp_'+str('%.3f' % redshifts[i])+'.dat',setup_dirs.resultsdir()+'/powerSpectraFrequencies_dbt_100b_'+str('%.3f' % redshifts[i])+'.dat')
def xfrac_power_spectrum(id):
for i in range(len(redshifts)):
print "Doing redshift: " + str(redshifts[i])
data=c2t.XfracFile(setup_dirs.path()+"xfrac3d"+id+'_'+str('%.3f' % redshifts[i])+".bin").xi
powerspec=ps.power_spectrum_1d(data,100)
IO.write2data(powerspec[0],powerspec[1],setup_dirs.resultsdir()+'/powerSpectra_xfrac_'+id+'_'+str('%.3f' % redshifts[i])+'.dat',setup_dirs.resultsdir()+'/powerSpectraFrequencies_dbt_100b_'+str('%.3f' % redshifts[i])+'.dat')
