def half_light_r(sim, band='v'):
'''Calculate half light radius
Calculates entire luminosity of simulation, finds half that, sorts
stars by distance from halo center, and finds out inside which radius
the half luminosity is reached.
'''
import pynbody
import pynbody.filt as f
half_l = halo_lum(sim, band=band) * 0.5
max_high_r = np.max(sim.star['r'])
test_r = 0.5 * max_high_r
testrf = f.LowPass('r', test_r)
min_low_r = 0.0
test_l = halo_lum(sim[testrf], band=band)
it = 0
while ((np.abs(test_l - half_l) / half_l) > 0.01):
it = it + 1
if (it > 20):
break
if (test_l > half_l):
test_r = 0.5 * (min_low_r + test_r)
else:
test_r = (test_r + max_high_r) * 0.5
testrf = f.LowPass('r', test_r)
test_l = halo_lum(sim[testrf], band=band)
if (test_l > half_l):
max_high_r = test_r
else:
min_low_r = test_r
return test_r * sim.star['r'].units
def getOxygenAbundance(halo, smallify=False):
'''
According to Tremonti et al 2004.
Set smallify to false if the halo is already cut.
'''
temp = 1.5e4
coolgasf = filt.And(filt.LowPass('temp', temp),
filt.HighPass('rho', '0.03 m_p cm^-3'))
# Tremonti
if smallify:
try:
halo = half_stellar_radius(halo)
except Exception as e:
print(e)
try:
coolgash = np.sum(halo.g[coolgasf]['hydrogen'])
if coolgash == 0:
oxh = 0
print("No cool gas for halo with stellar radius " +
str(np.max(halo.star['r'].in_units('kpc'))))
else:
oxh = np.log10(
np.sum(halo.g[coolgasf]['OxMassFrac']) / (16 * coolgash)) + 12
return oxh
except Exception as e:
print(e)
print("Unable to obtain oxh")
return None
def getColdGas(halo, temp):
"""
Based on Peeples 2014
Set smallify to False if the halo being passed is already cut according to radius.
Temperature sets the lowpass limit.
"""
coolgasf = filt.And(filt.LowPass('temp', temp),
filt.HighPass('rho', '0.03 m_p cm^-3'))
mgascool = np.sum(halo.gas[coolgasf]['mass'].in_units('Msol'))
return mgascool
def half_light_r(sim, band='v', cylindrical=False):
'''Calculate half light radius
Calculates entire luminosity of simulation, finds half that, sorts
stars by distance from halo center, and finds out inside which radius
the half luminosity is reached.
If cylindrical is True compute the half light radius as seen from the z-axis.
'''
import pynbody
import pynbody.filt as f
half_l = halo_lum(sim, band=band) * 0.5
if cylindrical:
coord = 'rxy'
else:
coord = 'r'
max_high_r = np.max(sim.star[coord])
test_r = 0.5 * max_high_r
testrf = f.LowPass(coord, test_r)
min_low_r = 0.0
test_l = halo_lum(sim[testrf], band=band)
it = 0
while ((np.abs(test_l - half_l) / half_l) > 0.01):
it = it + 1
if (it > 20):
break
if (test_l > half_l):
test_r = 0.5 * (min_low_r + test_r)
else:
test_r = (test_r + max_high_r) * 0.5
testrf = f.LowPass(coord, test_r)
test_l = halo_lum(sim[testrf], band=band)
if (test_l > half_l):
max_high_r = test_r
else:
min_low_r = test_r
return test_r
def half_stellar_radius(halo):
half_sm = np.sum(halo.star['mass'].in_units('Msol'))* 0.5
max_high_r = np.max(halo.star['r'].in_units('kpc'))
#print(max_high_r)
test_r = 0.5 * max_high_r
testrf = filt.LowPass('r', test_r)
min_low_r = 0.0
test_sm = np.sum(halo[testrf].star['mass'].in_units('Msol'))
it = 0
while ((np.abs(test_sm - half_sm) / half_sm) > 0.01):
it = it + 1
if (it > 20):
break
if (test_sm > half_sm):
test_r = 0.5 * (min_low_r + test_r)
else:
test_r = (test_r + max_high_r) * 0.5
testrf = filt.LowPass('r', test_r)
test_sm = np.sum(halo[testrf].star['mass'].in_units('Msol'))
if (test_sm > half_sm):
max_high_r = test_r
else:
min_low_r = test_r
#print("Half stellar radius found as: {}".format(test_r))
diskf = filt.Sphere(str(test_r) +' kpc')
return halo[diskf]
# Clean sample: put a cut on 100 stellar particles and hallo mass max based on Moster
# Add more observations
# Stick with the clean sample 10^9 and make plots for isolated galaxies and whole population
# Select all galaxies that do not have any halo similar or larger within 3 virial - flag galaxies as isolated or non-isolated. There should be no other galaxy
# Salam isolated - still plot them as single plots
def bulk_processing(tfile, halo_nums):
ZSOLAR = 0.0130215
XSOLO = 0.84E-2 #What pynbody uses
XSOLH = 0.706
s = pynbody.load(tfile)
s.physical_units()
h = s.halos()
(s.star[filt.LowPass('OxMassFrac', 1e-7)])['OxMassFrac'] = 1e-7
(s.star[filt.LowPass('FeMassFrac', 1e-8)])['FeMassFrac'] = 1e-8
(s.star[filt.LowPass('metals', 1e-7 * ZSOLAR)])['metals'] = 1e-7 * ZSOLAR
maxHI = np.amax(s.gas['HI'])
f = open(tfile + '.data', 'wb')
for halo_num in halo_nums:
print(halo_num)
halo_ahf = h[int(halo_num)] #h.load_copy(int(halo_num))
halo_ahf = halo_ahf[pynbody.filt.Sphere(
5 * np.std(
np.sqrt(halo_ahf['x'].in_units('kpc')**2 +
halo_ahf['y'].in_units('kpc')**2 +
halo_ahf['z'].in_units('kpc')**2)),
(np.mean(halo_ahf['x'].in_units('kpc')),
np.mean(halo_ahf['y'].in_units('kpc')),
np.mean(halo_ahf['z'].in_units('kpc')))
)] #Filter out outlying particles. This was happening with Sonia. A massive dark matter particle was being included in the halos
pynbody.analysis.halo.center(halo_ahf, vel=False)
rvir = pynbody.array.SimArray(
np.max(
np.sqrt(halo_ahf['x'].in_units('kpc')**2 +
halo_ahf['y'].in_units('kpc')**2 +
halo_ahf['z'].in_units('kpc')**2)), 'kpc')
halo = halo_ahf
#halo = s[pynbody.filt.Sphere(rvir, (0,0,0))] #This code can be used to select all material within a virial radius, whether AHF considers it part of the halo or not. It presents problems for satellites as then the host halo material is included.
stars = halo.star
stars.physical_units()
#For calculating HI and halo mass
currenttime = halo.properties['time'].in_units('Gyr')
#For stellar half-mass raidus
profile_stellar = pynbody.analysis.profile.Profile(
stars,
ndin=2,
min=0,
max=np.ceil(rvir),
nbins=int(np.ceil(rvir) / 0.01))
index = np.argmin(
np.abs(profile_stellar['mass_enc'] /
max(profile_stellar['mass_enc']) - 0.5))
r_half = profile_stellar['rbins'].in_units('kpc')[index]
pickle.dump(
{
'haloid': halo_num,
'z': s.properties['z'],
'time': currenttime,
'mvir': np.sum(halo['mass'].in_units('Msol')),
'rvir': rvir,
'mgas': np.sum(halo.gas['mass'].in_units('Msol')),
'mstar': np.sum(halo.star['mass'].in_units('Msol')),
}, f, pickle.HIGHEST_PROTOCOL)
f.close()
bins = 0.5*(binedges[:-1]+binedges[1:])
return hist,bins
def write(s,filename='dumbfile.out'):
f = pynbody.util.open_(filename,'wb')
f.write(struct.pack(">i", len(s)))
s.tofile(f)
f.close()
simname = sys.argv[1]
#pp.plt.ion()
s = pynbody.load(simname)
h = s.halos()
diskf = filt.Disc('40 kpc','3 kpc')
fifmyrf = filt.LowPass('age','15 Myr')
fhmyrf = filt.LowPass('age','500 Myr')
twokpcf = filt.Sphere('2 kpc')
i=1
if (len(sys.argv) > 2):
photiords = np.genfromtxt(sys.argv[2],dtype='i8')
frac = np.float(len(np.where(np.in1d(photiords,h[i]['iord']))[0]))/len(photiords)
print 'i: %d frac: %.2f'%(i,frac)
while(((frac) < 0.5) & (i<100)):
i=i+1
frac = np.float(len(np.where(np.in1d(photiords,h[i]['iord']))[0]))/len(photiords)
print 'i: %d frac: %.2f'%(i,frac)
else:
while len(h[i].star) <2: i=i+1
if (i==100): sys.exit()
def getSFR(halo, Myr):
fifmyrf = filt.LowPass('age', str(Myr) + ' Myr')
return np.sum(halo.star[fifmyrf]['mass'].in_units('Msol')) / (Myr * 10**6)
def write(s, filename='dumbfile.out'):
f = pynbody.util.open_(filename, 'wb')
f.write(struct.pack(">i", len(s)))
s.tofile(f)
f.close()
simname = sys.argv[1]
#pp.plt.ion()
s = pynbody.load(simname)
h = s.halos()
diskf = filt.Disc('40 kpc', '3 kpc')
fifmyrf = filt.LowPass('age', '15 Myr')
twokpcf = filt.Sphere('2 kpc')
i = 1
if (len(sys.argv) > 2):
photiords = np.genfromtxt(sys.argv[2], dtype='i8')
frac = np.float(len(np.where(np.in1d(photiords,
h[i]['iord']))[0])) / len(photiords)
print 'i: %d frac: %.2f' % (i, frac)
while (((frac) < 0.5) & (i < 100)):
i = i + 1
frac = np.float(len(np.where(np.in1d(
photiords, h[i]['iord']))[0])) / len(photiords)
print 'i: %d frac: %.2f' % (i, frac)
else:
while len(h[i].star) < 2:
i = i + 1