I am trying to run montepython to get the best-fit parameters for a new model with two extra parameters from 'scf_parameters' in addition to the six Lambda CDM parameters. Even though my class (modified for the above model) runs and gives the output well within the Lambda CDM range for a range of different values of the two scf_parametrs, the Gelman-Rubin convergence criteria R-1 gives zero for all the parameters. As a result, the covariance matrix is not being computed, and I cannot get any decent output of the posterior.
I also used the values given in the first column of Table 2 in the Planck paper: arXiv:1807.06209 to check whether my class is showing the correct output and for the input of 'H0 = 66.88', 'z_reio = 7.5', 'omega_b = 0.02212', 'omega_dm = 0.1206' (acting as CDM in my model), 'Omega_fld = 0',' Omega_scf = -1',' Omega_Lambda = 0', and 'scf_parameters = 0.0, 1e-4, 1.0, 0.0, 1e-4, 0.1, 0.0', I got the outputs within the valid range given paper except for recombination redshift which is coming around 1089.10 which is a bit outside the range, but I don't believe just for that I am getting the zero R-1 value for all the parameters. I tried all possible values of the two scf_paramters, attempted to increase their width, and tried to reduce sigma, but nothing worked.
The nuisance parameters are the same as in the input/base2018TTTEEE.param
# Derived parameters
data.parameters['tau_reio'] = [1, None, None, 0, 1, 'derived']
data.parameters['Omega0_scf'] = [1, None, None, 0, 1, 'derived']
data.parameters['YHe'] = [1, None, None, 0, 1, 'derived']
#data.parameters['H0'] = [0, None, None, 0, 1, 'derived']
data.parameters['A_s'] = [0, None, None, 0, 1e-9, 'derived']
data.parameters['sigma8'] = [0, None, None, 0, 1, 'derived']
data.parameters['100*theta_s'] = [1, None, None, 0, 1, 'derived']
# Other cosmo parameters (fixed parameters, precision parameters, etc.)
data.cosmo_arguments['sBBN file'] = data.path['cosmo']+'/external/bbn/sBBN.dat'
# BBN file path is automatically set to match CLASS version if 'sBBN file' is requested
# You can force the code to use the exact BBN file passed above with flag
#data.custom_bbn_file = True
data.cosmo_arguments['k_pivot'] = 0.05
# The base model features two massless
# and one massive neutrino with m=0.06eV.
# The settings below ensures that Neff=3.046
# and m/omega = 93.14 eV
data.cosmo_arguments['N_ur'] = 3.044
data.cosmo_arguments['N_ncdm'] = 1
data.cosmo_arguments['m_ncdm'] = 0.06
data.cosmo_arguments['T_ncdm'] = 0.71611
data.cosmo_arguments['omega_cdm'] = 1.e-9
data.cosmo_arguments['Omega_Lambda'] = 0
data.cosmo_arguments['Omega_dcdmdr'] = 0
data.cosmo_arguments['Omega_k'] = 0
data.cosmo_arguments['T_cmb'] = 2.7255
data.cosmo_arguments['Omega_idm'] = 0
data.cosmo_arguments['Omega_fld'] = 0
data.cosmo_arguments['Omega_scf'] = -1e-5
data.cosmo_arguments['attractor_ic_scf'] = 'no'
# 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 ----
data.N=10
data.write_step=5
I am getting no errors while running this file and yet in the output file I am getting the R-1 values like this
Computing mean values
--> Computing variance
--> Computing convergence criterium (Gelman-Rubin)
-> R-1 is 0.000000 for omega_b
0.000000 for omega_dm
0.000000 for H0
0.000000 for ln10^{10}A_s
0.000000 for n_s
0.000000 for z_reio
0.000000 for scf_parameters__2
0.000000 for scf_parameters__5
0.000000 for A_cib_217
0.000000 for xi_sz_cib
0.000000 for A_sz
0.000000 for ps_A_100_100
0.000000 for ps_A_143_143
0.000000 for ps_A_143_217
0.000000 for ps_A_217_217
0.000000 for ksz_norm
0.000000 for gal545_A_100
0.000000 for gal545_A_143
0.000000 for gal545_A_143_217
0.000000 for gal545_A_217
0.000000 for galf_TE_A_100
0.000000 for galf_TE_A_100_143
0.000000 for galf_TE_A_100_217
0.000000 for galf_TE_A_143
0.000000 for galf_TE_A_143_217
0.000000 for galf_TE_A_217
0.000000 for calib_100T
0.000000 for calib_217T
0.000000 for A_planck
0.000000 for tau_reio
0.000000 for Omega0_scf
0.000000 for YHe
0.000000 for A_s
0.000000 for sigma8
0.000000 for 100*theta_s
--> Not computing covariance matrix
I tried many different values of 'scf_parameters__2' and 'scf_parameters__5' with different permutations and combination and still I didn't get any valid output.
The .log file after the run look like this:
2023-02-08_200000__1.txt Number of steps:200004 Steps accepted:810 acc = 0.004 min(-loglike) = 5850.91
2023-02-08_200000__2.txt Number of steps:200000 Steps accepted:1119 acc = 0.0056 min(-loglike) = 5676.15
2023-02-08_200000__3.txt Number of steps:200000 Steps accepted:1407 acc = 0.007 min(-loglike) = 5880.92
2023-02-08_200000__4.txt Number of steps:200000 Steps accepted:1547 acc = 0.0077 min(-loglike) = 5941.33
2023-02-08_200000__5.txt Number of steps:200000 Steps accepted:1181 acc = 0.0059 min(-loglike) = 5822.86
2023-02-08_200000__6.txt Number of steps:200000 Steps accepted:1029 acc = 0.0051 min(-loglike) = 5510.55
2023-02-08_200000__7.txt Number of steps:200000 Steps accepted:1579 acc = 0.0079 min(-loglike) = 5756.84
2023-02-08_200000__8.txt Number of steps:200000 Steps accepted:1127 acc = 0.0056 min(-loglike) = 5667.24
2023-02-08_200000__9.txt Number of steps:199998 Steps accepted:907 acc = 0.0045 min(-loglike) = 5517.73
2023-02-08_200000__10.txt Number of steps:200000 Steps accepted:1583 acc = 0.0079 min(-loglike) = 5541.03
2023-02-08_200000__11.txt Number of steps:200000 Steps accepted:1256 acc = 0.0063 min(-loglike) = 5630.97
2023-02-08_200000__12.txt Number of steps:200000 Steps accepted:1189 acc = 0.0059 min(-loglike) = 5724.26
2023-02-08_200000__13.txt Number of steps:196812 Steps accepted:1380 acc = 0.007 min(-loglike) = 5899.69
2023-02-08_200000__14.txt Number of steps:200000 Steps accepted:927 acc = 0.0046 min(-loglike) = 5585.83
2023-02-08_200000__15.txt Number of steps:200000 Steps accepted:1241 acc = 0.0062 min(-loglike) = 6442.02
2023-02-08_200000__16.txt Number of steps:200000 Steps accepted:1617 acc = 0.0081 min(-loglike) = 6283.99
--> Total number of steps: 3196815
--> Total number of accepted steps: 19900
--> Minimum of -logLike : 5510.55
I have no clue how to solve the problem. It will be great if anyone can help me out on this.
Hi,
I am trying to run montepython to get the best-fit parameters for a new model with two extra parameters from 'scf_parameters' in addition to the six Lambda CDM parameters. Even though my class (modified for the above model) runs and gives the output well within the Lambda CDM range for a range of different values of the two scf_parametrs, the Gelman-Rubin convergence criteria R-1 gives zero for all the parameters. As a result, the covariance matrix is not being computed, and I cannot get any decent output of the posterior.
I also used the values given in the first column of Table 2 in the Planck paper: arXiv:1807.06209 to check whether my class is showing the correct output and for the input of 'H0 = 66.88', 'z_reio = 7.5', 'omega_b = 0.02212', 'omega_dm = 0.1206' (acting as CDM in my model), 'Omega_fld = 0',' Omega_scf = -1',' Omega_Lambda = 0', and 'scf_parameters = 0.0, 1e-4, 1.0, 0.0, 1e-4, 0.1, 0.0', I got the outputs within the valid range given paper except for recombination redshift which is coming around 1089.10 which is a bit outside the range, but I don't believe just for that I am getting the zero R-1 value for all the parameters. I tried all possible values of the two scf_paramters, attempted to increase their width, and tried to reduce sigma, but nothing worked.
Here is the glimpse of the .param file :
The nuisance parameters are the same as in the input/base2018TTTEEE.param
I am getting no errors while running this file and yet in the output file I am getting the R-1 values like this
I tried many different values of 'scf_parameters__2' and 'scf_parameters__5' with different permutations and combination and still I didn't get any valid output.
The .log file after the run look like this:
I have no clue how to solve the problem. It will be great if anyone can help me out on this.
Best, Amlan