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86bd95a
Montepython wrapper for Hillipop and Lollipop
mtristram Dec 11, 2023
17af57c
Clean comments in the code
mtristram Dec 11, 2023
4b8001d
Param file for Planck20 Hillipop and Lollipop likelihoods
mtristram Dec 15, 2023
99b1816
Remove nonlinear requirements for Class
mtristram Dec 21, 2023
fd49541
Force marginalisation for Lollipop
mtristram Dec 21, 2023
bd981bc
Comment prior for A_planck (if already included in Hillipop)
mtristram Dec 21, 2023
fb40966
Add lite versions for Hillipop p
mtristram Dec 22, 2023
7506eec
Remove nonlinear rquirement for CLASS
mtristram Dec 22, 2023
c54e4b6
Add covmat for hlpTTTEEE+lolE+lowlT
mtristram Dec 26, 2023
5bdcb5e
Update param file
mtristram Dec 26, 2023
58d456f
rename
mtristram Dec 26, 2023
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Update README
mtristram Dec 26, 2023
4665292
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mtristram Dec 26, 2023
1964df4
Merge branch '3.6' of github.com:mtristram/montepython_public into 3.6
mtristram Dec 26, 2023
448fdab
rename README
mtristram Dec 26, 2023
e2bace3
Update README.md
mtristram Dec 26, 2023
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Update README.md
mtristram Dec 26, 2023
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rename README
mtristram Dec 26, 2023
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d33b4b1
Merge branch '3.6' of github.com:mtristram/montepython_public into 3.6
mtristram Dec 26, 2023
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Rename likelihood lollipop EE+BB+EB
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Rename lollipop EB
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Merge branch '3.6' of github.com:mtristram/montepython_public into 3.6
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28 changes: 28 additions & 0 deletions covmat/planck20_TTTEEE.covmat
Original file line number Diff line number Diff line change
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# omega_b, omega_cdm, n_s, ln10^{10}A_s, tau_reio, 100*theta_s, A_planck, cal100A, cal100B, cal143B, cal217A, cal217B, AdustT, beta_dustT, AdustP, beta_dustP, Aradio, Adusty, beta_dusty, Acib, Atsz, Aksz, xi, z_reio, Omega_Lambda, A_s, H0
1.840240e-08 -9.844223e-08 2.461074e-07 3.466029e-07 1.791125e-07 9.747048e-09 2.114019e-08 -7.859908e-08 -1.849875e-08 -9.439712e-08 -3.123796e-08 -5.127669e-08 -1.218057e-07 1.612356e-08 2.057271e-07 -4.992869e-08 9.731289e-07 9.862855e-07 4.055256e-08 3.925337e-07 3.954476e-06 -7.070384e-05 7.713336e-07 1.197509e-05 6.777182e-07 7.235976e-16 5.478000e-05
-9.844223e-08 1.453346e-06 -3.458809e-06 -1.418125e-06 -1.803109e-06 -9.490650e-08 -1.898047e-07 2.862719e-07 5.488950e-07 8.259054e-07 2.585908e-07 4.928197e-07 6.632473e-07 -2.328195e-08 -1.609441e-06 9.665055e-07 9.515673e-06 -4.229444e-06 1.817085e-07 -3.786795e-06 -3.373463e-05 2.469045e-04 -5.891204e-06 -1.335299e-04 -8.820154e-06 -2.956279e-15 -6.377312e-04
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-9.439712e-08 8.259054e-07 -2.432890e-06 -3.246388e-05 1.047667e-06 -1.026150e-07 4.407630e-07 1.925199e-05 1.781603e-05 3.700643e-05 1.916173e-05 1.756032e-05 -1.654469e-05 -5.922455e-07 -2.328865e-05 -1.186339e-07 -1.032480e-03 -2.586462e-04 -5.832466e-06 -1.270953e-05 -5.151174e-04 5.053475e-04 -1.318968e-05 1.389484e-04 -5.390549e-06 -6.781155e-14 -4.131433e-04
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-5.127669e-08 4.928197e-07 -1.615055e-06 -1.444148e-05 6.099767e-07 -4.657357e-08 4.628820e-07 9.845116e-06 7.558668e-06 1.756032e-05 -3.814880e-05 5.669923e-05 -1.949274e-05 4.645827e-07 -1.129255e-05 -7.126504e-07 -1.708754e-03 -3.966261e-05 -6.495942e-06 1.280121e-05 4.693752e-04 3.353928e-04 -1.058132e-04 8.130375e-05 -3.136340e-06 -3.016777e-14 -2.372048e-04
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1.612356e-08 -2.328195e-08 -2.799777e-07 7.041550e-07 -1.624189e-07 4.201974e-08 -1.107084e-07 -2.479901e-07 -5.723337e-07 -5.922455e-07 -1.229002e-06 4.645827e-07 4.581974e-05 9.979283e-05 1.198632e-06 -9.581335e-07 4.797010e-04 5.994743e-05 -7.095976e-06 1.712167e-05 -3.669122e-04 2.183215e-04 -4.650691e-05 -1.781926e-05 3.777093e-07 1.473960e-15 3.584764e-05
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9.731289e-07 9.515673e-06 5.673456e-04 2.764393e-03 -4.848227e-04 1.943370e-06 8.468127e-04 -4.461737e-03 3.131913e-03 -1.032480e-03 -1.279889e-03 -1.708754e-03 1.225531e-03 4.797010e-04 5.397361e-03 1.145459e-03 2.251021e+01 -8.509432e-01 2.326935e-02 3.380926e-01 -5.897223e+00 -2.219705e+00 5.642074e-01 -4.911396e-02 -4.732883e-05 5.758056e-12 -1.588059e-03
9.862855e-07 -4.229444e-06 2.354717e-04 4.339771e-04 -2.691597e-05 1.955609e-06 9.146022e-05 6.863017e-05 -3.367207e-04 -2.586462e-04 6.936332e-05 -3.966261e-05 6.226687e-03 5.994743e-05 -5.429908e-04 -1.974027e-04 -8.509432e-01 3.490880e-01 -1.409323e-02 -1.328494e-01 4.654434e-01 -4.728364e-01 -1.808381e-02 -2.976879e-03 3.654253e-05 9.071442e-13 2.991911e-03
4.055256e-08 1.817085e-07 -3.976805e-06 6.333277e-06 3.661810e-07 1.116957e-07 -9.103157e-07 -1.957729e-06 -5.261447e-06 -5.832466e-06 -3.144755e-06 -6.495942e-06 -4.098436e-05 -7.095976e-06 7.773019e-06 5.635922e-06 2.326935e-02 -1.409323e-02 2.006805e-03 -6.223253e-04 -7.418521e-03 2.562491e-03 -1.117960e-03 3.492301e-05 -5.427980e-07 1.311581e-14 1.306783e-05
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3.954476e-06 -3.373463e-05 -1.984541e-04 5.022837e-04 4.333970e-05 7.874163e-06 1.026862e-04 1.155702e-03 -1.802217e-03 -5.151174e-04 2.404845e-04 4.693752e-04 -5.877500e-03 -3.669122e-04 -1.002273e-03 -2.080866e-04 -5.897223e+00 4.654434e-01 -7.418521e-03 -8.948235e-02 2.773842e+00 -7.441553e-01 -3.626788e-01 2.712531e-03 2.347130e-04 1.060807e-12 1.808377e-02
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5.478000e-05 -6.377312e-04 1.555086e-03 9.077986e-04 8.480720e-04 6.389753e-05 9.977298e-05 -1.927229e-04 -2.266320e-04 -4.131433e-04 -1.360365e-04 -2.372048e-04 -3.115967e-04 3.584764e-05 7.944932e-04 -4.114280e-04 -1.588059e-03 2.991911e-03 1.306783e-05 1.434847e-03 1.808377e-02 -1.546286e-01 2.756848e-03 6.159178e-02 4.007586e-03 1.893555e-12 2.976239e-01
102 changes: 102 additions & 0 deletions input/Planck20_TTTEEE.param
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#------Experiments to test (separated with commas)-----
# To see all the available ones, please look in the
# montepython/likelihoods folder. Every folder there is a valid likelihood to
# test.
data.experiments=['Planck20_Hillipop_TTTEEE','Planck_lowl_TT','Planck20_Lollipop_EE']


#------ Settings for the over-sampling.
# The first element will always be set to 1, for it is the sampling of the
# cosmological parameters. The other numbers describe the over sampling of the
# nuisance parameter space. This array must have the same dimension as the
# number of blocks in your run (so, 1 for cosmological parameters, and then 1
# for each experiment with varying nuisance parameters).
# Note that when using Planck likelihoods, you definitely want to use [1, 4],
# to oversample as much as possible the 14 nuisance parameters.
# Remember to order manually the experiments from slowest to fastest (putting
# Planck as the first set of experiments should be a safe bet, except if you
# also have LSS experiments).
# If you have experiments without nuisance, you do not need to specify an
# additional entry in the over_sampling list (notice for instance that, out of
# the three Planck likelihoods used, only Planck_highl requires nuisance
# parameters, therefore over_sampling has a length of two (cosmology, plus one
# set of nuisance).
data.over_sampling=[1, 4]



#------ Parameter list -------
# data.parameters[class name] = [mean, min, max, 1-sigma, scale, role]
# - if min max irrelevant, put to -1 or None (if you want a boundary of -1, use -1.0)
# - if fixed, put 1-sigma to 0
# - if scale irrelevant, put to 1, otherwise to the appropriate factor
# - role is either 'cosmo', 'nuisance' or 'derived'


# Cosmological parameters list
data.parameters['omega_b'] = [0.0223, 0.017, 0.027, 0.0002, 1, 'cosmo']
data.parameters['omega_cdm'] = [0.1188, 0.09, 0.15, 0.002, 1, 'cosmo']
data.parameters['n_s'] = [ 0.968, 0.9, 1.1, 0.005, 1, 'cosmo']
data.parameters['ln10^{10}A_s'] = [ 3.040, 2.7, 3.4, 0.02, 1, 'cosmo']
data.parameters['tau_reio'] = [ 0.058, 0.01, 0.17, 0.008, 1, 'cosmo']
data.parameters['100*theta_s'] = [1.0410, 1.03, 1.05, 0.0003, 1, 'cosmo']

# Nuisance parameter list, same call, except the name does not have to be a class name
# Note the nuisance parameters must follow *immediately after* the cosmo parameters,
# MP expects cosmo, nuisance, derived

# Nuisance parameters
data.parameters['A_planck'] = [ 1.0, 0.9, 1.1, 0.0025, 1, 'nuisance']
data.parameters['cal100A'] = [ 1.0, 0.9, 1.1, 0.005, 1, 'nuisance']
data.parameters['cal100B'] = [ 1.0, 0.9, 1.1, 0.005, 1, 'nuisance']
data.parameters['cal143A'] = [ 1.0, 1, 1, 0, 1, 'nuisance']
data.parameters['cal143B'] = [ 1.0, 0.9, 1.1, 0.005, 1, 'nuisance']
data.parameters['cal217A'] = [ 1.0, 0.9, 1.1, 0.005, 1, 'nuisance']
data.parameters['cal217B'] = [ 1.0, 0.9, 1.1, 0.005, 1, 'nuisance']

data.parameters['AdustT'] = [ 1.0, 0.5, 1.5, 0.03, 1, 'nuisance']
data.parameters['beta_dustT'] = [ 1.51, 1.2, 1.8, 0.01, 1, 'nuisance']
data.parameters['AdustP'] = [ 1.0, 0.5, 1.5, 0.03, 1, 'nuisance']
data.parameters['beta_dustP'] = [ 1.58, 1.2, 1.8, 0.02, 1, 'nuisance']
data.parameters['Aradio'] = [ 63.3, 0, 150, 4.7, 1, 'nuisance']
data.parameters['beta_radio'] = [ -0.8, -0.8, -0.8, 0, 1, 'nuisance']
data.parameters['Adusty'] = [ 6.07, 0, 100, 0.6, 1, 'nuisance']
data.parameters['beta_dusty'] = [ 1.75, 1.6, 1.9, 0.06, 1, 'nuisance']
data.parameters['Acib'] = [ 1.0, 0., 20, 0.3, 1, 'nuisance']
data.parameters['Atsz'] = [ 5.9, 0., 50, 1.6, 1, 'nuisance']
data.parameters['Aksz'] = [ 1.0, 0., 50, 2.5, 1, 'nuisance']
data.parameters['xi'] = [ 0.4, -1., 1., 0.3, 1, 'nuisance']

# Derived parameter list
data.parameters['z_reio'] = [0, None, None, 0, 1, 'derived']
data.parameters['Omega_Lambda'] = [0, None, None, 0, 1, 'derived']
data.parameters['A_s'] = [0, None, None, 0, 1e-9, 'derived']
data.parameters['H0'] = [0, None, None, 0, 1, 'derived']
#data.parameters['sigma8'] = [0, None, None, 0, 1, 'derived']


# CLASS parameters
data.cosmo_arguments['sBBN file'] = data.path['cosmo']+'/external/bbn/sBBN_2017.dat'
data.cosmo_arguments['k_pivot'] = 0.05
data.cosmo_arguments['N_ur'] = 2.0328
data.cosmo_arguments['N_ncdm'] = 1
data.cosmo_arguments['m_ncdm'] = 0.06
data.cosmo_arguments['T_ncdm'] = 0.71611
data.cosmo_arguments['l_max_scalars'] = 2500
data.cosmo_arguments['non_linear'] = 'halofit'

# These two are required to get sigma8 as a derived parameter
# (class must compute the P(k) until sufficient k)
#data.cosmo_arguments['output'] = 'mPk'
#data.cosmo_arguments['P_k_max_h/Mpc'] = 1.


#------ Mcmc parameters ----
# Number of steps taken, by default (overwritten by the -N command)
data.N=10
# Number of accepted steps before writing to file the chain. Larger means less
# access to disc, but this is not so much time consuming.
data.write_step=5


# Note: MP will only interpret comments if the line begins with # (you cannot add comments at the end of lines!)
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Planck20_Hillipop_TT.data_directory = ''
Planck20_Hillipop_TT.file = ''

Planck20_Hillipop_TT.use_nuisance = ['A_planck','cal100A','cal100B','cal143A','cal143B','cal217A','cal217B','Aradio','Adusty','AdustT','Acib','Atsz','Aksz','Aksz','xi','beta_dustT','beta_radio','beta_dusty']

Planck20_Hillipop_TT.A_planck_prior_center = 1
Planck20_Hillipop_TT.A_planck_prior_std = 0.0025
Planck20_Hillipop_TT.AdustT_prior_center = 1.0
Planck20_Hillipop_TT.AdustT_prior_std = 0.1
Planck20_Hillipop_TT.beta_dustT_prior_center = 1.51
Planck20_Hillipop_TT.beta_dustT_prior_std = 0.01
Planck20_Hillipop_TT.beta_dusty_prior_center = 1.75
Planck20_Hillipop_TT.beta_dusty_prior_std = 0.06
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from montepython.likelihood_class import Likelihood
import numpy as np
import planck_2020_hillipop
import os
import tempfile

packages_path = os.environ.get("COBAYA_PACKAGES_PATH") or os.path.join(
tempfile.gettempdir(), "Hillipop_packages"
)

class Planck20_Hillipop_TT(Likelihood):
def __init__(self, path, data, command_line):
Likelihood.__init__(self, path, data, command_line)

#Create Cobaya likelihood
self.lik = planck_2020_hillipop.TT({"packages_path": packages_path})

self.need_cosmo_arguments(
data, {'lensing': 'yes', 'output': 'tCl pCl lCl', 'l_max_scalars': self.lik.lmax})

print( "Init Hillipop TT done !")

def loglkl(self, cosmo, data):

cls = self.get_cl(cosmo)

fac = cls['ell'] * (cls['ell']+1) / (2*np.pi)
dl = {mode:np.zeros(self.lik.lmax+1) for mode in ['TT','TE','EE']}
for mode in ['TT','TE','EE']:
dl[mode][cls['ell']] = fac*cls[mode.lower()]

data_params = {par:data.mcmc_parameters[par]['current'] for par in data.get_mcmc_parameters(['nuisance'])}

#fix beta_cib to beta_dusty
if 'beta_cib' not in data_params:
data_params['beta_cib'] = data_params['beta_dusty']

#compute log-likelihood
lkl = self.lik.loglike(dl, **data_params)
# print( lkl)

#Add priors
lkl = self.add_nuisance_prior(lkl, data)

return lkl


def add_nuisance_prior(self, lkl, data):
# Recover the current value of the nuisance parameter.
for nuisance in self.use_nuisance:
nuisance_value = float(
data.mcmc_parameters[nuisance]['current'] *
data.mcmc_parameters[nuisance]['scale'])

# add prior on nuisance parameters
if hasattr(self, "%s_prior_center" % nuisance) and getattr(self, "%s_prior_std" % nuisance) > 0:
# convenience variables
prior_center = getattr(self, "%s_prior_center" % nuisance)
prior_std = getattr(self, "%s_prior_std" % nuisance)
lkl += -0.5*((nuisance_value-prior_center)/prior_std)**2

return lkl
22 changes: 22 additions & 0 deletions montepython/likelihoods/Planck20_Hillipop_TT/README.md
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# Hillipop is a high-l polarized likelihood for Planck PR4 data.

Hillipop is a multifrequency CMB likelihood for Planck data. The likelihood is a spectrum-based Gaussian approximation for cross-correlation spectra from Planck 100, 143 and 217GHz split-frequency maps, with semi-analytic estimates of the Cl covariance matrix based on the data. The cross-spectra are debiased from the effects of the mask and the beam leakage using Xpol (a generalization to polarization of the algorithm presented in Tristram et al. 2005) before being compared to the model, which includes CMB and foreground residuals. They cover the multipoles from ℓ = 30 to 2500.

Reference:\
[Tristram et al., A&A, 2023](https://arxiv.org/abs/2309.10034)

The code is available here:\
[https://github.com/planck-npipe/hillipop](https://github.com/planck-npipe/hillipop)\
This is a wrapper for MontePython.

You need to install the code before:
```
pip install planck-2020-hillipop
```

Then get the data, untar and set the variable $COBAYA_PACKAGES_PATH to the local directory:
```
wget https://portal.nersc.gov/cfs/cmb/planck2020/likelihoods/planck_2020_hillipop_TT_v4.2.tar.gz
tar -zxvf planck_2020_hillipop_TT_v4.2.tar.gz --directory /path/to/data
export COBAYA_PACKAGES_PATH=/path/to/data
```
1 change: 1 addition & 0 deletions montepython/likelihoods/Planck20_Hillipop_TT/__init__.py
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from .Planck20_Hillipop_TT import Planck20_Hillipop_TT
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