def check_massfunc(cosmo):
"""
Check that mass function and supporting functions can be run.
"""
z = 0.
z_arr = np.linspace(0., 2., 10)
a = 1.
a_arr = 1. / (1. + z_arr)
mhalo_scl = 1e13
mhalo_lst = [1e11, 1e12, 1e13, 1e14, 1e15, 1e16]
mhalo_arr = np.array([1e11, 1e12, 1e13, 1e14, 1e15, 1e16])
odelta = 200.
# massfunc
assert_(all_finite(ccl.massfunc(cosmo, mhalo_scl, a, odelta)))
assert_(all_finite(ccl.massfunc(cosmo, mhalo_lst, a, odelta)))
assert_(all_finite(ccl.massfunc(cosmo, mhalo_arr, a, odelta)))
assert_raises(TypeError, ccl.massfunc, cosmo, mhalo_scl, a_arr, odelta)
assert_raises(TypeError, ccl.massfunc, cosmo, mhalo_lst, a_arr, odelta)
assert_raises(TypeError, ccl.massfunc, cosmo, mhalo_arr, a_arr, odelta)
# Check whether odelta out of bounds
assert_raises(CCLError, ccl.massfunc, cosmo, mhalo_scl, a, 199.)
assert_raises(CCLError, ccl.massfunc, cosmo, mhalo_scl, a, 5000.)
# massfunc_m2r
assert_(all_finite(ccl.massfunc_m2r(cosmo, mhalo_scl)))
assert_(all_finite(ccl.massfunc_m2r(cosmo, mhalo_lst)))
assert_(all_finite(ccl.massfunc_m2r(cosmo, mhalo_arr)))
# sigmaM
assert_(all_finite(ccl.sigmaM(cosmo, mhalo_scl, a)))
assert_(all_finite(ccl.sigmaM(cosmo, mhalo_lst, a)))
assert_(all_finite(ccl.sigmaM(cosmo, mhalo_arr, a)))
assert_raises(TypeError, ccl.sigmaM, cosmo, mhalo_scl, a_arr)
assert_raises(TypeError, ccl.sigmaM, cosmo, mhalo_lst, a_arr)
assert_raises(TypeError, ccl.sigmaM, cosmo, mhalo_arr, a_arr)
# halo_bias
assert_(all_finite(ccl.halo_bias(cosmo, mhalo_scl, a)))
assert_(all_finite(ccl.halo_bias(cosmo, mhalo_lst, a)))
assert_(all_finite(ccl.halo_bias(cosmo, mhalo_arr, a)))
def get_bpe(z, n_r, delta, nmass=256):
a = 1./(1+z)
lmarr = np.linspace(8.,16.,nmass)
marr = 10.**lmarr
Dm = delta/ccl.omega_x(cosmo, a, "matter") # CCL uses Delta_m
mfunc = ccl.massfunc(cosmo, marr, a, Dm)
bh = ccl.halo_bias(cosmo, marr, a, Dm)
et = np.array([integrated_profile(get_battaglia(m,z,delta),n_r) for m in marr])
return itg.simps(et*bh*mfunc,x=lmarr)
def pk(self, k, a, lmmin=6., lmmax=17., nlm=256, return_decomposed=False):
"""
Returns power spectrum at redshift `z` sampled at all values of k in `k`.
k : array of wavenumbers in CCL units
a : scale factor
lmmin, lmmax, nlm : mass edges and sampling rate for mass integral.
return_decomposed : if True, returns 1-halo, 2-halo, bias, shot noise and total (see below for order).
"""
z = 1. / a - 1.
marr = np.logspace(lmmin, lmmax, nlm)
dlm = np.log10(marr[1] / marr[0])
u_s = self.u_sat(z, marr, k)
hmf = ccl.massfunc(self.cosmo, marr, a)
hbf = ccl.halo_bias(self.cosmo, marr, a)
rhoM = ccl.rho_x(self.cosmo, a, "matter", is_comoving=True)
n0_1h = (rhoM - np.sum(hmf * marr) * dlm) / marr[0]
n0_2h = (rhoM - np.sum(hmf * hbf * marr) * dlm) / marr[0]
#Number of galaxies
fc = self.fc_f(z)
ngm = self.n_tot(z, marr)
ncm = self.n_cent(z, marr)
nsm = self.n_sat(z, marr)
#Number density
ng = np.sum(hmf * ngm) * dlm + n0_1h * ngm[0]
if ng <= 1E-16: #Make sure we won't divide by 0
return None
#Bias
b_hod = np.sum(
(hmf * hbf * ncm)[None, :] * (fc + nsm[None, :] * u_s[:, :]),
axis=1) * dlm + n0_2h * ncm[0] * (fc + nsm[0] * u_s[:, 0])
b_hod /= ng
#1-halo
#p1h=np.sum((hmf*ncm**2)[None,:]*(fc+nsm[None,:]*u_s[:,:])**2,axis=1)*dlm+n0_1h*(ncm[0]*(fc+nsm[0]*u_s[:,0]))**2
p1h = np.sum(
(hmf * ncm)[None, :] * (2 * fc * nsm[None, :] * u_s[:, :] +
(nsm[None, :] * u_s[:, :])**2),
axis=1) * dlm + n0_1h * ncm[0] * (2 * fc * nsm[0] * u_s[:, 0] +
(nsm[0] * u_s[:, 0])**2)
p1h /= ng**2
#2-halo
p2h = b_hod**2 * ccl.linear_matter_power(self.cosmo, k, a)
if return_decomposed:
return p1h + p2h, p1h, p2h, np.ones_like(k) / ng, b_hod
else:
return p1h + p2h
def test_halo_bias_models_smoke(mf_type):
cosmo = ccl.Cosmology(Omega_c=0.27,
Omega_b=0.045,
h=0.67,
sigma8=0.8,
n_s=0.96,
transfer_function='bbks',
matter_power_spectrum='linear',
mass_function=mf_type)
hbf_cls = ccl.halos.halo_bias_from_name(MF_EQUIV[mf_type])
hbf = hbf_cls(cosmo)
for m in MS:
bm_old = ccl.halo_bias(cosmo, m, 1.)
bm_new = hbf.get_halo_bias(cosmo, m, 1.)
assert np.all(np.isfinite(bm_old))
assert np.shape(bm_old) == np.shape(m)
assert np.all(np.array(bm_old) == np.array(bm_new))
def construct_bins(self, z):
"""
Construct a binned halo mass function and bias function. This function
sets the ``self.dndlog10M`` and ``self.bias`` arrays.
Parameters:
z (float): Redshift at which to construct the mass function and bias.
"""
a = 1./(1.+z)
# Define mass bins
Mh_edges = np.logspace(np.log10(self.Mmin),
np.log10(self.Mmax),
int(self.mass_bins)+1)
Mh_centres = 0.5 * (Mh_edges[1:] + Mh_edges[:-1])
# Get mass function and bias at mass bin centres
self.dndlog10M = ccl.massfunction.massfunc(self.box.cosmo, Mh_centres,
a, overdensity=200)
self.bias = ccl.halo_bias(cosmo, Mh_centres, a, overdensity=200)
def hm_bias(cosmo,
a,
profile,
logMrange=(6, 17),
mpoints=128,
selection=None,
**kwargs):
"""Computes the halo model prediction for the bias of a given
tracer.
Args:
cosmo (:obj:`ccl.Cosmology`): cosmology.
a (array): array of scale factor values
profile (`Profile`): a profile. Only Arnaud and HOD are
implemented.
logMrange (tuple): limits of integration in log10(M/Msun)
mpoints (int): number of mass samples
selection (function): selection function in (M,z) to include
in the calculation. Pass None if you don't want to select
a subset of the M-z plane.
**kwargs: parameter used internally by the profiles.
"""
# Input handling
a = np.atleast_1d(a)
# Profile normalisations
Unorm = profile.profnorm(cosmo, a, squeeze=False, **kwargs)
Unorm = Unorm[..., None]
# Set up integration boundaries
logMmin, logMmax = logMrange # log of min and max halo mass [Msun]
mpoints = int(mpoints) # number of integration points
M = np.logspace(logMmin, logMmax, mpoints) # masses sampled
# Out-of-loop optimisations
Dm = profile.Delta / ccl.omega_x(cosmo, a, "matter") # CCL uses Delta_m
with warnings.catch_warnings():
warnings.simplefilter("ignore")
mfunc = np.array(
[ccl.massfunc(cosmo, M, A1, A2) for A1, A2 in zip(a, Dm)])
bh = np.array(
[ccl.halo_bias(cosmo, M, A1, A2) for A1, A2 in zip(a, Dm)])
# shape transformations
mfunc, bh = mfunc.T[..., None], bh.T[..., None]
if selection is not None:
select = np.array([selection(M, 1. / aa - 1) for aa in a])
select = select.T[..., None]
else:
select = 1
U, _ = profile.fourier_profiles(cosmo,
np.array([0.001]),
M,
a,
squeeze=False,
**kwargs)
# Tinker mass function is given in dn/dlog10M, so integrate over d(log10M)
b2h = simps(bh * mfunc * select * U, x=np.log10(M), axis=0).squeeze()
# Contribution from small masses (added in the beginning)
rhoM = ccl.rho_x(cosmo, a, "matter", is_comoving=True)
dlM = (logMmax - logMmin) / (mpoints - 1)
mfunc, bh = mfunc.squeeze(), bh.squeeze() # squeeze extra dimensions
n0_2h = np.array((rhoM - np.dot(M, mfunc * bh) * dlM) / M[0])[None, ...,
None]
b2h += (n0_2h * U[0]).squeeze()
b2h /= Unorm.squeeze()
return b2h.squeeze()
def hm_power_spectrum(cosmo,
k,
a,
profiles,
logMrange=(6, 17),
mpoints=128,
include_1h=True,
include_2h=True,
squeeze=True,
hm_correction=None,
selection=None,
**kwargs):
"""Computes the halo model prediction for the 3D cross-power
spectrum of two quantities.
Args:
cosmo (:obj:`ccl.Cosmology`): cosmology.
k (array): array of wavenumbers in units of Mpc^-1
a (array): array of scale factor values
profiles (tuple): tuple of two profile objects (currently
only Arnaud and HOD are implemented) corresponding to
the two quantities being correlated.
logMrange (tuple): limits of integration in log10(M/Msun)
mpoints (int): number of mass samples
include_1h (bool): whether to include the 1-halo term.
include_2h (bool): whether to include the 2-halo term.
hm_correction (:obj:`HalomodCorrection` or None):
Correction to the halo model in the transition regime.
If `None`, no correction is applied.
selection (function): selection function in (M,z) to include
in the calculation. Pass None if you don't want to select
a subset of the M-z plane.
**kwargs: parameter used internally by the profiles.
"""
# Input handling
a, k = np.atleast_1d(a), np.atleast_2d(k)
# Profile normalisations
p1, p2 = profiles
Unorm = p1.profnorm(cosmo, a, squeeze=False, **kwargs)
if p1.name == p2.name:
Vnorm = Unorm
else:
Vnorm = p2.profnorm(cosmo, a, squeeze=False, **kwargs)
if (Vnorm < 1e-16).any() or (Unorm < 1e-16).any():
return None # zero division
Unorm, Vnorm = Unorm[..., None], Vnorm[..., None] # transform axes
# Set up integration boundaries
logMmin, logMmax = logMrange # log of min and max halo mass [Msun]
mpoints = int(mpoints) # number of integration points
M = np.logspace(logMmin, logMmax, mpoints) # masses sampled
# Out-of-loop optimisations
Pl = np.array(
[ccl.linear_matter_power(cosmo, k[i], a) for i, a in enumerate(a)])
Dm = p1.Delta / ccl.omega_x(cosmo, a, "matter") # CCL uses Delta_m
with warnings.catch_warnings():
warnings.simplefilter("ignore")
mfunc = np.array(
[ccl.massfunc(cosmo, M, A1, A2) for A1, A2 in zip(a, Dm)])
if selection is not None:
select = np.array([selection(M, 1. / aa - 1) for aa in a])
mfunc *= select
# tinker10 halo bias
csm = ccl.Cosmology(Omega_c=cosmo["Omega_c"],
Omega_b=cosmo["Omega_b"],
h=cosmo["h"],
sigma8=cosmo["sigma8"],
n_s=cosmo["n_s"],
mass_function="tinker10")
with warnings.catch_warnings():
warnings.simplefilter("ignore")
bh = np.array([ccl.halo_bias(csm, M, A1, A2) for A1, A2 in zip(a, Dm)])
# shape transformations
mfunc, bh = mfunc.T[..., None], bh.T[..., None]
if selection is not None:
select = np.array([selection(M, 1. / aa - 1) for aa in a])
select = select.T[..., None]
else:
select = 1
U, UU = p1.fourier_profiles(cosmo, k, M, a, squeeze=False, **kwargs)
# optimise for autocorrelation (no need to recompute)
if p1.name == p2.name:
V = U
UV = UU
else:
V, VV = p2.fourier_profiles(cosmo, k, M, a, squeeze=False, **kwargs)
r = kwargs["r_corr"] if "r_corr" in kwargs else 0
UV = U * V * (1 + r)
# Tinker mass function is given in dn/dlog10M, so integrate over d(log10M)
P1h = simps(mfunc * select * UV, x=np.log10(M), axis=0)
b2h_1 = simps(bh * mfunc * select * U, x=np.log10(M), axis=0)
b2h_2 = simps(bh * mfunc * select * V, x=np.log10(M), axis=0)
# Contribution from small masses (added in the beginning)
rhoM = ccl.rho_x(cosmo, a, "matter", is_comoving=True)
dlM = (logMmax - logMmin) / (mpoints - 1)
mfunc, bh = mfunc.squeeze(), bh.squeeze() # squeeze extra dimensions
n0_1h = np.array((rhoM - np.dot(M, mfunc) * dlM) / M[0])[None, ..., None]
n0_2h = np.array((rhoM - np.dot(M, mfunc * bh) * dlM) / M[0])[None, ...,
None]
P1h += (n0_1h * U[0] * V[0]).squeeze()
b2h_1 += (n0_2h * U[0]).squeeze()
b2h_2 += (n0_2h * V[0]).squeeze()
F = (include_1h * P1h + include_2h *
(Pl * b2h_1 * b2h_2)) / (Unorm * Vnorm)
if hm_correction is not None:
for ia, (aa, kk) in enumerate(zip(a, k)):
R = hm_correction.rk_interp(kk, aa)
F[ia, :] *= R
return F.squeeze() if squeeze else F
pass
# Specify cosmology
cosmo = ccl.Cosmology(h=0.67,
Omega_c=0.25,
Omega_b=0.045,
n_s=0.965,
sigma8=0.834)
z = 0.
# Halo mass function
Mh = np.logspace(np.log10(MH_MIN), np.log10(MH_MAX), MH_BINS)
dndlog10m = ccl.massfunc(cosmo, Mh, 1. / (1. + z))
bh = ccl.halo_bias(cosmo, Mh, a)
# Cumulative integral of halo mass function
nm = integrate.cumtrapz(dndlog10m[::-1], -np.log10(Mh)[::-1], initial=0.)[::-1]
# Rescale nm to get cdf
cdf = nm / np.max(nm)
# Build interpolator
Mh_interp = interpolate.interp1d(cdf, np.log10(Mh), kind='linear')
np.random.seed(10)
u = np.random.uniform(size=int(1e6))
# Realise halo mass distribution
mh_real = 10.**(Mh_interp(u))
def test_halo_bias_smoke(m):
a = 0.8
b = ccl.halo_bias(COSMO, m, a)
assert np.all(np.isfinite(b))
assert np.shape(b) == np.shape(m)
def pk_gm(self,
k,
a,
lmmin=6.,
lmmax=17.,
nlm=256,
return_decomposed=False):
"""
Returns galaxy-matter power spectrum at a single scale-factor a for array of wave vectors k.
:param k: wave vector array
:param a: single scale factor value
:param lmmin: Mmin for HOD integrals
:param lmmax: Mmax for HOD integrals
:param nlm: sampling rate for mass integral
:param return_decomposed: boolean tag, if True return 1h, 2h power spectrum separately
:return:
"""
z = 1. / a - 1.
marr = np.logspace(lmmin, lmmax, nlm)
dlm = np.log10(marr[1] / marr[0])
u_nfw = self.u_sat(z, marr, k)
hmf = ccl.massfunc(self.cosmo, marr, a)
hbf = ccl.halo_bias(self.cosmo, marr, a)
rhoM = ccl.rho_x(self.cosmo, a, "matter", is_comoving=True)
n0_1h = (rhoM - np.sum(hmf * marr) * dlm) / marr[0]
n0_2h = (rhoM - np.sum(hmf * hbf * marr) * dlm) / marr[0]
# n0_2h = (rhoM - np.sum(hmf*hbf*marr)*dlm)
#Number of galaxies
fc = self.fc_f(z)
ngm = self.n_tot(z, marr)
ncm = self.n_cent(z, marr)
nsm = self.n_sat(z, marr)
#Number density
ng = np.sum(hmf * ngm) * dlm + n0_1h * ngm[0]
if ng <= 1E-16: #Make sure we won't divide by 0
return None
#Bias
b_hod=np.sum((hmf*hbf*ncm)[None,:]*(fc+nsm[None,:]*u_nfw[:,:]),axis=1)*dlm \
+ n0_2h*ncm[0]*(fc+nsm[0]*u_nfw[:,0])
b_m = np.sum((hmf * hbf)[None, :] * marr[None, :] * u_nfw[:, :],
axis=1) * dlm + n0_2h * u_nfw[:, 0]
b_hod /= ng
b_m /= rhoM
#1-halo
#p1h=np.sum((hmf*ncm**2)[None,:]*(fc+nsm[None,:]*u_s[:,:])**2,axis=1)*dlm+n0_1h*(ncm[0]*(fc+nsm[0]*u_s[:,0]))**2
p1h=np.sum((hmf*ncm)[None,:]*(fc+nsm[None,:]*u_nfw[:,:])*marr*u_nfw[:,:],axis=1)*dlm \
+ n0_1h*ncm[0]*(fc + nsm[0]*u_nfw[:,0])*u_nfw[:,0]
p1h /= ng * rhoM
#2-halo
p2h = b_hod * b_m * ccl.linear_matter_power(self.cosmo, k, a)
if return_decomposed:
return p1h + p2h, p1h, p2h, np.ones_like(k) / ng, b_hod
else:
return p1h + p2h