def test_cosmology_repr():
"""Check that we can make a Cosmology object from its repr."""
import pyccl # noqa: F401
cosmo = ccl.Cosmology(
Omega_c=0.25, Omega_b=0.05, h=0.7, A_s=2.1e-9, n_s=0.96,
m_nu=[0.02, 0.1, 0.05], m_nu_type='list',
z_mg=[0.0, 1.0], df_mg=[0.01, 0.0])
cosmo2 = eval(str(cosmo))
assert_(
ccl.comoving_radial_distance(cosmo, 0.5) ==
ccl.comoving_radial_distance(cosmo2, 0.5))
cosmo3 = eval(repr(cosmo))
assert_(
ccl.comoving_radial_distance(cosmo, 0.5) ==
ccl.comoving_radial_distance(cosmo3, 0.5))
# same test with arrays to be sure
cosmo = ccl.Cosmology(
Omega_c=0.25, Omega_b=0.05, h=0.7, A_s=2.1e-9, n_s=0.96,
m_nu=np.array([0.02, 0.1, 0.05]), m_nu_type='list',
z_mg=np.array([0.0, 1.0]), df_mg=np.array([0.01, 0.0]))
cosmo2 = eval(str(cosmo))
assert_(
ccl.comoving_radial_distance(cosmo, 0.5) ==
ccl.comoving_radial_distance(cosmo2, 0.5))
cosmo3 = eval(repr(cosmo))
assert_(
ccl.comoving_radial_distance(cosmo, 0.5) ==
ccl.comoving_radial_distance(cosmo3, 0.5))
def test_power_mu_sigma_sigma8norm(tf):
cosmo = ccl.Cosmology(
Omega_c=0.27, Omega_b=0.045, h=0.67, sigma8=0.8, n_s=0.96,
transfer_function=tf)
cosmo_musig = ccl.Cosmology(
Omega_c=0.27, Omega_b=0.045, h=0.67, sigma8=0.8, n_s=0.96,
transfer_function=tf, mu_0=0.1, sigma_0=0.2)
# make sure sigma8 is correct
assert np.allclose(ccl.sigma8(cosmo_musig), 0.8)
if tf != 'boltzmann_isitgr':
# make sure P(k) ratio is right
a = 0.8
gfac = (
ccl.growth_factor(cosmo, a) / ccl.growth_factor(cosmo_musig, a))**2
pk_rat = (
ccl.linear_matter_power(cosmo, 1e-4, a) /
ccl.linear_matter_power(cosmo_musig, 1e-4, a))
assert np.allclose(pk_rat, gfac)
with mock.patch.dict(sys.modules, {'isitgr': None}):
with assert_raises(ImportError):
get_isitgr_pk_lin(cosmo)
# Importing ccl without isitgr is fine. No ImportError triggered.
with mock.patch.dict(sys.modules, {'isitgr': None}):
reload(ccl.boltzmann)
def test_input_nonlin_power_spectrum():
cosmo = ccl.Cosmology(Omega_c=0.27, Omega_b=0.05, h=0.7, n_s=0.965,
A_s=2e-9)
a_arr = np.linspace(0.1, 1.0, 50)
k_arr = np.logspace(np.log10(2e-4), np.log10(1), 1000)
pk_arr = np.empty(shape=(len(a_arr), len(k_arr)))
for i, a in enumerate(a_arr):
pk_arr[i] = ccl.power.nonlin_matter_power(cosmo, k_arr, a)
chi_from_ccl = ccl.background.comoving_radial_distance(cosmo, a_arr)
hoh0_from_ccl = ccl.background.h_over_h0(cosmo, a_arr)
growth_from_ccl = ccl.background.growth_factor(cosmo, a_arr)
fgrowth_from_ccl = ccl.background.growth_rate(cosmo, a_arr)
cosmo_input = ccl.Cosmology(Omega_c=0.27, Omega_b=0.05, h=0.7, n_s=0.965,
A_s=2e-9,)
cosmo_input._set_background_from_arrays(a_array=a_arr,
chi_array=chi_from_ccl,
hoh0_array=hoh0_from_ccl,
growth_array=growth_from_ccl,
fgrowth_array=fgrowth_from_ccl)
cosmo_input._set_nonlin_power_from_arrays(a_arr, k_arr, pk_arr)
pk_CCL_input = ccl.power.nonlin_matter_power(cosmo_input, k_arr, 0.5)
pk_CCL = ccl.power.nonlin_matter_power(cosmo, k_arr, 0.5)
assert np.allclose(pk_CCL_input, pk_CCL, atol=0., rtol=1e-5)
def test_power_sigma8norm_norms_consistent(tf):
# make a cosmo with A_s
cosmo = ccl.Cosmology(Omega_c=0.27,
Omega_b=0.045,
h=0.67,
A_s=2e-9,
n_s=0.96,
transfer_function=tf)
sigma8 = ccl.sigma8(cosmo)
# remake same but now give sigma8
cosmo_s8 = ccl.Cosmology(Omega_c=0.27,
Omega_b=0.045,
h=0.67,
sigma8=sigma8,
n_s=0.96,
transfer_function=tf)
# make sure they come out the same-ish
assert np.allclose(ccl.sigma8(cosmo), ccl.sigma8(cosmo_s8))
# and that the power spectra look right
a = 0.8
gfac = (ccl.growth_factor(cosmo, a) / ccl.growth_factor(cosmo_s8, a))**2
pk_rat = (ccl.linear_matter_power(cosmo, 1e-4, a) /
ccl.linear_matter_power(cosmo_s8, 1e-4, a))
assert np.allclose(pk_rat, gfac)
def test_pk2d_from_model_emu():
pars = [0.3643, 0.071075, 0.55, 0.8333, 0.9167, -0.7667, 0.1944]
cosmo_fixed = ccl.Cosmology(Omega_c=pars[0],
Omega_b=pars[1],
h=pars[2],
sigma8=pars[3],
n_s=pars[4],
w0=pars[5],
wa=pars[6],
Neff=3.04,
Omega_g=0,
Omega_k=0,
transfer_function='bbks')
cosmo = ccl.Cosmology(Omega_c=pars[0],
Omega_b=pars[1],
h=pars[2],
sigma8=pars[3],
n_s=pars[4],
w0=pars[5],
wa=pars[6],
Neff=3.04,
Omega_g=0,
Omega_k=0,
transfer_function='bbks',
matter_power_spectrum='emu')
pk = ccl.Pk2D.pk_from_model(cosmo_fixed, model='emu')
ks = np.geomspace(1E-3, 1E1, 128)
for z in [0., 0.5, 2.]:
a = 1. / (1 + z)
pk1 = pk.eval(ks, a, cosmo)
pk2 = ccl.nonlin_matter_power(cosmo, ks, a)
maxdiff = np.amax(np.fabs(pk1 / pk2 - 1))
assert maxdiff < 1E-10
def test_camb_class_consistent_smoke(kwargs=None, pkerr=1e-3):
kwargs = kwargs or {}
print('kwargs:', kwargs)
c_camb = ccl.Cosmology(Omega_c=0.25,
Omega_b=0.05,
h=0.7,
n_s=0.95,
A_s=2e-9,
transfer_function='boltzmann_camb',
**kwargs)
c_class = ccl.Cosmology(Omega_c=0.25,
Omega_b=0.05,
h=0.7,
n_s=0.95,
A_s=2e-9,
transfer_function='boltzmann_class',
**kwargs)
rel_sigma8 = np.abs(ccl.sigma8(c_camb) / ccl.sigma8(c_class) - 1)
a = 0.845
k = np.logspace(-3, 1, 100)
pk_camb = ccl.linear_matter_power(c_camb, k, a)
pk_class = ccl.linear_matter_power(c_class, k, a)
rel_pk = np.max(np.abs(pk_camb / pk_class - 1))
print('rel err pk:', rel_pk)
print('rel err sigma8:', rel_sigma8)
assert rel_sigma8 < 3e-3
assert rel_pk < pkerr
def test_mgrowth():
"""
Compare the modified growth function computed by CCL against the exact
result for a particular modification of the growth rate.
"""
# Define differential growth rate arrays
nz_mg = 128
z_mg = np.zeros(nz_mg)
df_mg = np.zeros(nz_mg)
for i in range(0, nz_mg):
z_mg[i] = 4. * (i + 0.0) / (nz_mg - 1.)
df_mg[i] = 0.1 / (1. + z_mg[i])
# Define two test cosmologies, without and with modified growth respectively
p1 = ccl.Parameters(Omega_c=0.25,
Omega_b=0.05,
Omega_k=0.,
N_nu_rel=0.,
N_nu_mass=0.,
m_nu=0.,
w0=-1.,
wa=0.,
h=0.7,
A_s=2.1e-9,
n_s=0.96)
p2 = ccl.Parameters(Omega_c=0.25,
Omega_b=0.05,
Omega_k=0.,
N_nu_rel=0.,
N_nu_mass=0.,
m_nu=0.,
w0=-1.,
wa=0.,
h=0.7,
A_s=2.1e-9,
n_s=0.96,
z_mg=z_mg,
df_mg=df_mg)
cosmo1 = ccl.Cosmology(p1)
cosmo2 = ccl.Cosmology(p2)
# We have included a growth modification \delta f = K*a, with K==0.1
# (arbitrarily). This case has an analytic solution, given by
# D(a) = D_0(a)*exp(K*(a-1)). Here we compare the growth computed by CCL
# with the analytic solution.
a = 1. / (1. + z_mg)
d1 = ccl.growth_factor(cosmo1, a)
d2 = ccl.growth_factor(cosmo2, a)
f1 = ccl.growth_rate(cosmo1, a)
f2 = ccl.growth_rate(cosmo2, a)
f2r = f1 + 0.1 * a
d2r = d1 * np.exp(0.1 * (a - 1.))
# Check that ratio of calculated and analytic results is within tolerance
assert_allclose(d2r / d2, np.ones(d2.size), rtol=GROWTH_TOLERANCE)
assert_allclose(f2r / f2, np.ones(f2.size), rtol=GROWTH_TOLERANCE)
def test_input_nonlin_raises():
cosmo_input = ccl.Cosmology(Omega_c=0.27, Omega_b=0.05, h=0.7, n_s=0.965,
A_s=2e-9)
with pytest.raises(ValueError):
cosmo_input._set_nonlin_power_from_arrays()
with pytest.raises(ValueError):
cosmo_input.compute_nonlin_power()
cosmo_input._set_nonlin_power_from_arrays()
cosmo_input = ccl.Cosmology(Omega_c=0.27, Omega_b=0.05, h=0.7, n_s=0.965,
A_s=2e-9)
with pytest.raises(ValueError):
cosmo_input._compute_nonlin_power_from_arrays()
def test_pk2d_from_model(model):
cosmo_fixed = ccl.Cosmology(
Omega_c=0.27, Omega_b=0.045, h=0.67, sigma8=0.8, n_s=0.96)
cosmo = ccl.Cosmology(
Omega_c=0.27, Omega_b=0.045, h=0.67, sigma8=0.8, n_s=0.96,
transfer_function=model)
pk = ccl.Pk2D.pk_from_model(cosmo_fixed, model=model)
ks = np.geomspace(1E-3, 1E1, 128)
for z in [0., 0.5, 2.]:
a = 1./(1+z)
pk1 = pk.eval(ks, a, cosmo)
pk2 = ccl.linear_matter_power(cosmo, ks, a)
maxdiff = np.amax(np.fabs(pk1/pk2-1))
assert maxdiff < 1E-10
def reference_models():
"""
Create a set of reference Cosmology() objects.
"""
# Standard LCDM model
p1 = ccl.Parameters(Omega_c=0.27,
Omega_b=0.045,
h=0.67,
A_s=1e-10,
n_s=0.96)
cosmo1 = ccl.Cosmology(p1)
# LCDM model with curvature
p2 = ccl.Parameters(Omega_c=0.27,
Omega_b=0.045,
h=0.67,
A_s=1e-10,
n_s=0.96,
Omega_k=0.05)
cosmo2 = ccl.Cosmology(p2)
# wCDM model
p3 = ccl.Parameters(Omega_c=0.27,
Omega_b=0.045,
h=0.67,
A_s=1e-10,
n_s=0.96,
w0=-0.95,
wa=0.05)
cosmo3 = ccl.Cosmology(p3)
# BBKS Pk
p4 = ccl.Parameters(Omega_c=0.27,
Omega_b=0.045,
h=0.67,
sigma8=0.8,
n_s=0.96)
cosmo4 = ccl.Cosmology(p4, transfer_function='bbks')
# E&H Pk
p5 = ccl.Parameters(Omega_c=0.27,
Omega_b=0.045,
h=0.67,
sigma8=0.8,
n_s=0.96)
cosmo5 = ccl.Cosmology(p5, transfer_function='eisenstein_hu')
# Return (only do one cosmology for now, for speed reasons)
return [cosmo1, cosmo4, cosmo5] # cosmo2, cosmo3
def compare_distances_mnu_hiz(z, chi_bench, dm_bench, Omega_v, w0, wa,
Neff_mnu, mnu):
"""
Compare distances calculated by pyccl with the distances in the benchmark
file.
"""
# Set Omega_K in a consistent way
Omega_k = 1.0 - Omega_c - Omega_b - Omega_v
cosmo = ccl.Cosmology(Omega_c=Omega_c,
Omega_b=Omega_b,
Neff=Neff,
h=h,
A_s=A_s,
n_s=n_s,
Omega_k=Omega_k,
w0=w0,
wa=wa,
m_nu=mnu)
# Calculate distance using pyccl
a = 1. / (1. + z)
chi = ccl.comoving_radial_distance(cosmo, a)
# Compare to benchmark data
assert_allclose(chi, chi_bench, atol=1e-12, rtol=DISTANCES_TOLERANCE_MNU)
# compare distance moudli where a!=1
a_not_one = (a != 1).nonzero()
dm = ccl.distance_modulus(cosmo, a[a_not_one])
assert_allclose(dm,
dm_bench[a_not_one],
atol=1e-3,
rtol=DISTANCES_TOLERANCE_MNU)
def compare_distances_hiz(z, chi_bench, Omega_v, w0, wa):
"""
Compare distances calculated by pyccl with the distances in the benchmark
file.
This test is only valid when radiation is explicitly set to 0.
"""
# Set Omega_K in a consistent way
Omega_k = 1.0 - Omega_c - Omega_b - Omega_v
cosmo = ccl.Cosmology(Omega_c=Omega_c,
Omega_b=Omega_b,
Neff=Neff,
h=h,
A_s=A_s,
n_s=n_s,
Omega_k=Omega_k,
w0=w0,
wa=wa,
Omega_g=0)
# Calculate distance using pyccl
a = 1. / (1. + z)
chi = ccl.comoving_radial_distance(cosmo, a) * h
# Compare to benchmark data
assert_allclose(chi, chi_bench, atol=1e-12, rtol=DISTANCES_TOLERANCE)
def compare_distances(z, chi_bench, dm_bench, Omega_v, w0, wa):
"""
Compare distances calculated by pyccl with the distances in the benchmark
file.
This test is only valid when radiation is explicitly set to 0.
"""
# Set Omega_K in a consistent way
Omega_k = 1.0 - Omega_c - Omega_b - Omega_v
cosmo = ccl.Cosmology(Omega_c=Omega_c,
Omega_b=Omega_b,
Neff=Neff,
h=h,
A_s=A_s,
n_s=n_s,
Omega_k=Omega_k,
w0=w0,
wa=wa,
Omega_g=0)
# Calculate distance using pyccl
a = 1. / (1. + z)
chi = ccl.comoving_radial_distance(cosmo, a) * h
# Compare to benchmark data
assert_allclose(chi, chi_bench, atol=1e-12, rtol=DISTANCES_TOLERANCE)
# compare distance moudli where a!=1
a_not_one = (a != 1).nonzero()
dm = ccl.distance_modulus(cosmo, a[a_not_one])
assert_allclose(dm,
dm_bench[a_not_one],
atol=1e-3,
rtol=DISTANCES_TOLERANCE * 10)
def test_power_mg(model):
mu_0 = [0., 0.1, -0.1, 0.1, -0.1]
sigma_0 = [0., 0.1, -0.1, -0.1, 0.1]
cosmo = ccl.Cosmology(
Omega_c=0.25,
Omega_b=0.05,
h=0.7,
A_s=2.1e-9,
n_s=0.96,
Neff=3.046,
mu_0=mu_0[model],
sigma_0=sigma_0[model],
Omega_k=0,
matter_power_spectrum='linear',
transfer_function='boltzmann_class')
data = np.loadtxt("./benchmarks/data/model%d_pk_MG.dat" % model)
a = 1
k = data[:, 0] * cosmo['h']
pk = data[:, 1] / (cosmo['h']**3)
pk_ccl = ccl.linear_matter_power(cosmo, k, a)
err = np.abs(pk_ccl/pk - 1)
if model == 0:
assert np.allclose(err, 0, rtol=0, atol=POWER_MG_TOL)
else:
msk = data[:, 0] > 5e-3
assert np.allclose(err[msk], 0, rtol=0, atol=POWER_MG_TOL)
def compare_distances(z, chi_bench, Omega_v, w0, wa):
"""
Compare distances calculated by pyccl with the distances in the benchmark
file.
"""
# Set Omega_K in a consistent way
Omega_k = 1.0 - Omega_c - Omega_b - Omega_n - Omega_v
# Create new Parameters and Cosmology objects
p = ccl.Parameters(Omega_c=Omega_c,
Omega_b=Omega_b,
Omega_n=Omega_n,
h=h,
A_s=A_s,
n_s=n_s,
Omega_k=Omega_k,
w0=w0,
wa=wa)
p.parameters.Omega_g = 0. # Hack to set to same value used for benchmarks
cosmo = ccl.Cosmology(p)
# Calculate distance using pyccl
a = 1. / (1. + z)
chi = ccl.comoving_radial_distance(cosmo, a) * h
# Compare to benchmark data
assert_allclose(chi, chi_bench, atol=1e-12, rtol=DISTANCES_TOLERANCE)
def test_pk2d_init():
"""
Test initialization of Pk2D objects
"""
cosmo = ccl.Cosmology(Omega_c=0.27,
Omega_b=0.045,
h=0.67,
A_s=1e-10,
n_s=0.96)
# If no input
assert_raises(ValueError, ccl.Pk2D)
# Input function has incorrect signature
assert_raises(ValueError, ccl.Pk2D, pkfunc=pk1d)
ccl.Pk2D(pkfunc=lpk2d, cosmo=cosmo)
# Input function but no cosmo
assert_raises(ValueError, ccl.Pk2D, pkfunc=lpk2d)
# Input arrays have incorrect sizes
lkarr = -4. + 6 * np.arange(100) / 99.
aarr = 0.05 + 0.95 * np.arange(100) / 99.
pkarr = np.zeros([len(aarr), len(lkarr)])
assert_raises(ValueError,
ccl.Pk2D,
a_arr=aarr,
lk_arr=lkarr,
pk_arr=pkarr[1:])
def S8z(mcmc, a, MG=False, size=None):
p = mcmc.getParams()
if size is None:
size = p.A_s.size
S8_ar = np.zeros((size, a.size))
for i in range(size):
cosmo = ccl.Cosmology(h=p.h[i],
Omega_c=p.Omega_c[i],
Omega_b=p.Omega_b[i],
A_s=1e-9 * p.A_s[i],
n_s=p.n_s[i],
w0=-1,
wa=0,
transfer_function='boltzmann_class')
# Compute everything
sigma8 = ccl.sigma8(cosmo)
Dz = ccl.background.growth_factor(cosmo, a)
Om = ccl.background.omega_x(cosmo, 1, 'matter')
if MG:
d1 = p.dpk1[i]
else:
d1 = 0
S8_ar[i] = (1 + d1 * (1 - a)) * Dz * sigma8 * (Om / 0.3)**0.5
return S8_ar
def test_power_mg(model):
mu_0 = [0., 0.1, -0.1, 0.1, -0.1]
sigma_0 = [0., 0.1, -0.1, -0.1, 0.1]
h0 = 0.7
cosmo = ccl.Cosmology(Omega_c=0.112 / h0**2,
Omega_b=0.0226 / h0**2,
h=h0,
A_s=2.1e-9,
n_s=0.96,
Neff=3.046,
mu_0=mu_0[model],
sigma_0=sigma_0[model],
Omega_k=0,
m_nu=0,
T_CMB=2.7255,
matter_power_spectrum='linear',
transfer_function='boltzmann_isitgr')
data = np.loadtxt("./benchmarks/data/model%d_pk_MG_matterpower.dat" %
model)
a = 1
k = data[:, 0] * cosmo['h']
pk = data[:, 1] / (cosmo['h']**3)
pk_ccl = ccl.linear_matter_power(cosmo, k, a)
err = np.abs(pk_ccl / pk - 1)
# cut two points due to cosmic variance
cut = data[:, 0] > 1e-04
assert np.allclose(err[cut], 0, rtol=0, atol=POWER_MG_TOL)
def test_cosmology_output():
"""
Check that status messages and other output from Cosmology() object works
correctly.
"""
# Create test cosmology object
cosmo = ccl.Cosmology(Omega_c=0.25, Omega_b=0.05, h=0.7, A_s=2.1e-9,
n_s=0.96)
# Return and print status messages
assert_no_warnings(cosmo.status)
assert_no_warnings(print, cosmo)
# Test status methods for different precomputable quantities
assert_(cosmo.has_distances is False)
assert_(cosmo.has_growth is False)
assert_(cosmo.has_linear_power is False)
assert_(cosmo.has_nonlin_power is False)
assert_(cosmo.has_sigma is False)
# Check that quantities can be precomputed
assert_no_warnings(cosmo.compute_distances)
assert_no_warnings(cosmo.compute_growth)
assert_no_warnings(cosmo.compute_linear_power)
assert_no_warnings(cosmo.compute_nonlin_power)
assert_no_warnings(cosmo.compute_sigma)
assert_(cosmo.has_distances is True)
assert_(cosmo.has_growth is True)
assert_(cosmo.has_linear_power is True)
assert_(cosmo.has_nonlin_power is True)
assert_(cosmo.has_sigma is True)
def test_parameters_set():
"""
Check that a Cosmology object doesn't let parameters be set.
"""
params = ccl.Cosmology(Omega_c=0.25,
Omega_b=0.05,
h=0.7,
A_s=2.1e-9,
n_s=0.96)
# Check that values of sigma8 and A_s won't be misinterpreted by the C code
assert_raises(ValueError,
ccl.Cosmology,
Omega_c=0.25,
Omega_b=0.05,
h=0.7,
A_s=2e-5,
n_s=0.96)
assert_raises(ValueError,
ccl.Cosmology,
Omega_c=0.25,
Omega_b=0.05,
h=0.7,
sigma8=9e-6,
n_s=0.96)
# Check that error is raised when unrecognized parameter requested
assert_raises(KeyError, lambda: params['wibble'])
def compare_growth(z, gfac_bench, Omega_v, w0, wa):
"""
Compare growth factor calculated by pyccl with the values in the benchmark
file. This test only works if radiation is explicitly set to 0.
"""
# Set Omega_K in a consistent way
Omega_k = 1.0 - Omega_c - Omega_b - Omega_v
# Create new Parameters and Cosmology objects
p = ccl.Parameters(Omega_c=Omega_c,
Omega_b=Omega_b,
Neff=Neff,
m_nu=m_nu,
h=h,
A_s=A_s,
n_s=n_s,
Omega_k=Omega_k,
w0=w0,
wa=wa)
p.parameters.Omega_g = 0. # Hack to set to same value used for benchmarks
cosmo = ccl.Cosmology(p)
# Calculate distance using pyccl
a = 1. / (1. + z)
gfac = ccl.growth_factor_unnorm(cosmo, a)
# Compare to benchmark data
assert_allclose(gfac, gfac_bench, atol=1e-12, rtol=GROWTH_TOLERANCE)
def execute(block, data):
# Calculate the firecrown likelihood as a module
# This function, which isn't designed for end users,
# is the main connection between cosmosis and firecrown.
# CosmoSIS builds the block, and passes it to us here.
# The block contains all the sample parameters.
# Create CCL cosmology
ccl_params = ['Omega_k', 'Omega_b', 'Omega_c',
'h', 'n_s', 'A_s', 'w0', 'wa']
ccl_values = {p: block['params', p] for p in ccl_params}
cosmo = pyccl.Cosmology(**ccl_values)
# Put all the parameters in the data dictionary,
# both CCL-related and others, like nuisance params.
all_params = data['parameters'].keys()
for p in all_params:
data['parameters'][p] = block['params', p]
# Call out to the log likelihood
loglike, stats = firecrown.compute_loglike(cosmo=cosmo, data=data)
# Send result back to cosmosis
block['likelihoods', 'firecrown_like'] = loglike
# Unless in quiet mode, print out what we have done
if not data['cosmosis'].get("quiet", True):
print("params = {}".format(data['parameters']))
print(f"loglike = {loglike}\n", flush=True)
# Signal success. An exception anywhere above will
# be converted to a -inf likelihood by default.
return 0
def compare_class_distances(z,
chi_bench,
dm_bench,
Neff=3.0,
m_nu=0.0,
Omega_k=0.0,
w0=-1.0,
wa=0.0):
"""
Compare distances calculated by pyccl with the distances in the CLASS
benchmark file.
"""
cosmo = ccl.Cosmology(Omega_c=Omega_c,
Omega_b=Omega_b,
Neff=Neff,
h=h,
A_s=A_s,
n_s=n_s,
Omega_k=Omega_k,
m_nu=m_nu,
w0=w0,
wa=wa)
# Calculate distance using pyccl
a = 1. / (1. + z)
chi = ccl.comoving_radial_distance(cosmo, a)
# Compare to benchmark data
assert_allclose(chi, chi_bench, rtol=DISTANCES_TOLERANCE_CLASS)
# Compare distance moudli where a!=1
a_not_one = a != 1
dm = ccl.distance_modulus(cosmo, a[a_not_one])
assert_allclose(dm, dm_bench[a_not_one], rtol=DISTANCES_TOLERANCE_CLASS)
def compute_cls(oc,ob,h,s8,ns,w,fname_out=False) :
#Fiducial cosmological parameters
cosmo=ccl.Cosmology(Omega_c=oc,Omega_b=ob,h=h,sigma8=s8,n_s=ns,w0=w,
transfer_function='eisenstein_hu')
print ccl.sigma8(cosmo)
#Tracers
tracers=[]
for i in np.arange(nbins) :
print i
# tracers.append(ccl.ClTracer(cosmo,tracer_type='nc',z=zarr,n=nz_bins[i],bias=bzarr))
tracers.append(ccl.ClTracer(cosmo,tracer_type='wl',z=zarr,n=nz_bins[i]))#,bias=bzarr))
#Power spectra
c_ij=np.zeros([LMAX+1,nbins,nbins])
for i1 in np.arange(nbins) :
for i2 in np.arange(i1,nbins) :
print i1,i2
if xcorr[i1,i2]<-1:#1E-6 :
c_ij[:,i1,i2]=0
else :
c_ij[:,i1,i2]=ccl.angular_cl(cosmo,tracers[i1],tracers[i2],np.arange(LMAX+1))#,l_limber=100)
if i1!=i2 :
c_ij[:,i2,i1]=c_ij[:,i1,i2]
if fname_out!=False :
np.save(fname_out,c_ij)
return c_ij
def compare_distances_hiz_muSig(z, chi_bench, Omega_v, w0, wa):
"""
Compare distances calculated by pyccl with the distances in the benchmark
file, for a ccl cosmology with mu / Sigma parameterisation of gravity.
Nonzero mu / Sigma should NOT affect distances so we compare to the same
benchmarks as the mu = Sigma = 0 case deliberately.
"""
# Set Omega_K in a consistent way
Omega_k = 1.0 - Omega_c - Omega_b - Omega_v
# Create new Parameters and Cosmology objects
cosmo = ccl.Cosmology(Omega_c=Omega_c,
Omega_b=Omega_b,
Neff=Neff,
h=h,
A_s=A_s,
n_s=n_s,
Omega_k=Omega_k,
w0=w0,
wa=wa,
mu_0=mu_0,
sigma_0=sigma_0,
Omega_g=0.)
# Calculate distance using pyccl
a = 1. / (1. + z)
chi = ccl.comoving_radial_distance(cosmo, a) * h
# Compare to benchmark data
assert_allclose(chi, chi_bench, atol=1e-12, rtol=DISTANCES_TOLERANCE)
def theory_corr(self, n_z2, xvals, lmax2, chi_max, zlo2, zhi2, cosmo_cat):
'''compute the correlation function from limber integration over the CAMB power spectrum'''
nz_int = self.compute_nz(n_z2)
z_vals = np.linspace(zlo2, zhi2, 1000)
n_vals = nz_int(z_vals)
ns = getattr(cosmo_cat, 'n_s', 0.963)
s8 = getattr(cosmo_cat, 'sigma8', 0.8)
Omega_c = (cosmo_cat.Om0 - cosmo_cat.Ob0)
Omega_b = cosmo_cat.Ob0
h = cosmo_cat.H0.value / 100.
cosmo_ccl = ccl.Cosmology(
Omega_c=Omega_c, Omega_b=Omega_b, h=h, sigma8=s8, n_s=ns
) #, transfer_function='boltzmann_class', matter_power_spectrum='emu')
ll = np.arange(0, 15000)
lens1 = ccl.WeakLensingTracer(cosmo_ccl, dndz=(z_vals, n_vals))
pp = ccl.angular_cl(cosmo_ccl, lens1, lens1, ll)
pp3_2 = np.zeros((lmax2, 4))
pp3_2[:, 1] = pp[:] * (ll * (ll + 1.)) / (2. * np.pi)
cxvals = np.cos(xvals / (60.) / (180. / np.pi))
vals = camb.correlations.cl2corr(pp3_2, cxvals)
return xvals, vals[:, 1], vals[:, 2]
def test_parameters_nu(m_nu_type):
cosmo = ccl.Cosmology(Omega_c=0.25,
Omega_b=0.05,
h=0.7,
A_s=2.1e-9,
n_s=0.96,
wa=0.01,
w0=-1,
Neff=3.046,
Omega_k=0.0,
m_nu=0.15,
m_nu_type=m_nu_type)
if m_nu_type == 'inverted':
assert np.allclose(cosmo['m_nu'][1]**2 - cosmo['m_nu'][0]**2,
ccl.physical_constants.DELTAM12_sq,
atol=1e-4,
rtol=0)
assert np.allclose(cosmo['m_nu'][2]**2 - cosmo['m_nu'][0]**2,
ccl.physical_constants.DELTAM13_sq_neg,
atol=1e-4,
rtol=0)
elif m_nu_type == 'normal':
assert np.allclose(cosmo['m_nu'][1]**2 - cosmo['m_nu'][0]**2,
ccl.physical_constants.DELTAM12_sq,
atol=1e-4,
rtol=0)
assert np.allclose(cosmo['m_nu'][2]**2 - cosmo['m_nu'][0]**2,
ccl.physical_constants.DELTAM13_sq_pos,
atol=1e-4,
rtol=0)
elif m_nu_type == 'single':
assert np.allclose(cosmo['m_nu'][0], 0.15, atol=1e-4, rtol=0)
assert np.allclose(cosmo['m_nu'][1], 0., atol=1e-4, rtol=0)
assert np.allclose(cosmo['m_nu'][2], 0., atol=1e-4, rtol=0)
def test_pk2d_cls():
"""
Test interplay between Pk2D and the Limber integrator
"""
cosmo = ccl.Cosmology(Omega_c=0.27,
Omega_b=0.045,
h=0.67,
A_s=1e-10,
n_s=0.96)
z = np.linspace(0., 1., 200)
n = np.exp(-((z - 0.5) / 0.1)**2)
lens1 = ccl.WeakLensingTracer(cosmo, (z, n))
ells = np.arange(2, 10)
# Check that passing no power spectrum is fine
cells = ccl.angular_cl(cosmo, lens1, lens1, ells)
assert all_finite(cells)
# Check that passing a bogus power spectrum fails as expected
assert_raises(ValueError,
ccl.angular_cl,
cosmo,
lens1,
lens1,
ells,
p_of_k_a=1)
# Check that passing a correct power spectrum runs as expected
psp = ccl.Pk2D(pkfunc=lpk2d, cosmo=cosmo)
cells = ccl.angular_cl(cosmo, lens1, lens1, ells, p_of_k_a=psp)
assert all_finite(cells)
def reference_models_nu():
"""
Create a set of reference cosmological models with massive neutrinos.
This is separate because certain functionality is not yes implemented
for massive neutrino cosmologies so will throw errors.
"""
# Emulator Pk w/neutrinos list
cosmo1 = ccl.Cosmology(Omega_c=0.27,
Omega_b=0.022 / 0.67**2,
h=0.67,
sigma8=0.8,
n_s=0.96,
Neff=3.04,
m_nu=[0.02, 0.02, 0.02],
transfer_function='boltzmann_class',
matter_power_spectrum='emu')
# Emulator Pk with neutrinos, force equalize
#p2 = ccl.Parameters(Omega_c=0.27, Omega_b=0.022/0.67**2, h=0.67, sigma8=0.8,
# n_s=0.96, Neff=3.04, m_nu=0.11)
#cosmo2 = ccl.Cosmology(p1, transfer_function='emulator',
# matter_power_spectrum='emu', emulator_neutrinos='equalize')
return [cosmo1]
def test_parameters_read_write():
"""Check that Cosmology objects can be read and written"""
params = ccl.Cosmology(Omega_c=0.25,
Omega_b=0.05,
h=0.7,
A_s=2.1e-9,
n_s=0.96,
m_nu=[0.02, 0.1, 0.05],
m_nu_type='list',
z_mg=[0.0, 1.0],
df_mg=[0.01, 0.0])
# Make a temporary file name
with tempfile.NamedTemporaryFile(delete=False) as tmpfile:
temp_file_name = tmpfile.name
# Write out and then eead in the parameters from that file
params.write_yaml(temp_file_name)
params2 = ccl.Cosmology.read_yaml(temp_file_name)
# Check the read-in params are equal to the written out ones
assert_almost_equal(params['Omega_c'], params2['Omega_c'])
assert_almost_equal(params['Neff'], params2['Neff'])
assert_almost_equal(params['sum_nu_masses'], params2['sum_nu_masses'])
# Now make a file that will be deleted so it does not exist
# and check the right error is raise
with tempfile.NamedTemporaryFile(delete=True) as tmpfile:
temp_file_name = tmpfile.name
assert_raises(IOError, ccl.Cosmology.read_yaml, filename=temp_file_name)
assert_raises(IOError,
params.read_yaml,
filename=temp_file_name +
"/nonexistent_directory/params.yml")
