updates to cobaya interface

cobaya_interface/configs/complex_main.ini

@@ -12,7 +12,8 @@ full-shape-alpha = True
 filename = /global/homes/w/wmturner/repos/vega/vega/models/Planck18/DESI-2024_z_2.33.fits
 
 [output]
-filename = /pscratch/sd/w/wmturner/LyA-directfit/minimize/test_minimize
+filename = /pscratch/sd/w/wmturner/LyA-directfit/mcmc/sample_5/no-distortion/test
+# what is this used for?
 
 [sample]
 #bias_LYA = True

cobaya_interface/configs/lyalya_lyalya.ini

@@ -4,7 +4,10 @@ tracer1 = LYA
 tracer2 = LYA
 tracer1-type = continuous
 tracer2-type = continuous
-filename = /pscratch/sd/w/wmturner/picca_runs_v3/uncontaminated_mock/truth/full/cf_lya_x_lya_exp.fits
+filename = /pscratch/sd/w/wmturner/picca_runs_v3/uncontaminated_mock/truth/full/cf_lya_x_lya_exp_no-dist.fits
+#filename = /pscratch/sd/w/wmturner/picca_runs_v3/uncontaminated_mock/continuum_fitting/full/cf_lya_x_lya_exp.fits
+#distortion-file = /pscratch/sd/w/wmturner/picca_runs_v3/uncontaminated_mock/continuum_fitting/full/dmat_lya_x_lya.fits
+distortion = False
 
 [cuts]
 rp-min = -200.

cobaya_interface/info_full.yaml

@@ -0,0 +1,134 @@
+output: /pscratch/sd/w/wmturner/LyA-directfit/mcmc/full/mcmc_full
+likelihood:
+  likelihood.Likelihood: 
+    python_path: /global/homes/w/wmturner/repos/vega/cobaya_interface
+params:
+  As:
+    latex: A_s
+    prior:
+      max: 3e-9
+      min: 1e-9
+    ref:
+      dist: norm
+      loc: 2.1e-9
+      scale: 4e-10
+  D_H_fid:
+    latex: D_{H, fid}
+    value: 853.772277153506
+  D_M_fid:
+    latex: D_{M, fid}
+    value: 3882.64271129613
+  H0:
+    latex: H_0
+    prior:
+      max: 73
+      min: 62
+    ref:
+      dist: norm
+      loc: 67.36
+      scale: 3
+    proposal: 0.0001
+  beta_LYA:
+    latex: \beta
+    prior:
+      max: 2
+      min: 1
+    ref:
+      dist: norm
+      loc: 1.67
+      scale: 0.03
+    proposal: 0.0001
+  bias_LYA: 
+    latex: bias
+    prior:
+      max: 0
+      min: -0.2
+    proposal: 0.0001
+    ref:
+      dist: norm
+      loc: -0.1171
+      scale: 0.01
+  or_photon:
+    value: 5.44985776336301e-05
+    latex: \Omega_{r,\gamma}
+  or_neutrino:
+    value: 2.5133613689346e-05
+    latex: \Omega_{r,\nu}
+  ns:
+    latex: n_s
+    prior:
+      max: 1.1
+      min: 0.85
+    ref:
+      dist: norm
+      loc: 0.9649
+      scale: 0.03
+    proposal: 0.0001
+  ombh2:
+    latex: \Omega_\mathrm{b} h^2
+    prior:
+      max: 0.04
+      min: 0.001
+    ref:
+      dist: norm
+      loc: 0.02237
+      scale: 0.005
+    proposal: 0.0001
+  omch2:
+      latex: \Omega_\mathrm{C} h^2
+      prior:
+        max: 0.2
+        min: 0.01
+      ref:
+        dist: norm
+        loc: 0.12
+        scale: 0.01
+      proposal: 0.0001
+  omk:
+    latex: \Omega_\mathrm{k}
+    value: 0
+  omnuh2:
+    latex: \Omega_\mathrm{\nu} h^2
+    value: 0.0006
+#  omnuh2:
+#    latex: \Omega_\mathrm{\nu} h^2
+#    prior:
+#      max: 0.001
+#      min: 0.0001
+#    ref:
+#      dist: norm
+#      loc: 0.0006
+#      scale: 0.00006
+sampler:
+  mcmc:
+    Rminus1_stop: 0.01
+    max_tries: 10000
+    learn_proposal: True
+    learn_proposal_Rminus1_max: 2.
+theory:
+  camb:
+    extra_args:
+      #Accuracy.AccuratePolarization: false
+      #Accuracy.AccurateReionization: false
+      #DoLensing: false
+      #Reion.Reionization: false
+      #Reion.include_helium_fullreion: false
+      #SourceTerms.counts_ISW: false
+      #SourceTerms.counts_density: false
+      #SourceTerms.counts_potential: false
+      #SourceTerms.counts_timedelay: false
+      #SourceTerms.limber_windows: false
+      #SourceTerms.line_basic: false
+      #SourceTerms.line_distortions: false
+      #SourceTerms.use_21cm_mK: false
+      #WantCls: false
+      #WantDerivedParameters: false
+      #WantScalars: false
+      #Want_CMB: false
+      #Want_CMB_lensing: false
+      #Want_cl_2D_array: false
+      #max_eta_k_tensor: 0
+      #max_l: 2
+      #max_l_tensor: 0
+      WantDerivedParameters: True
+

cobaya_interface/info_full_future.yaml

@@ -0,0 +1,94 @@
+theory:
+   camb:
+     extra_args:
+       WantDerivedParameters: True
+output: /pscratch/sd/w/wmturner/LyA-directfit/mcmc/full/mcmc_full
+likelihood:
+  likelihood.Likelihood: 
+    python_path: /global/homes/w/wmturner/repos/vega/cobaya_interface
+params:
+  logA:
+    prior:
+      min: 0.5
+      max: 6
+    ref: 3.05
+    proposal: 0.001
+    latex: \log(10^{10} A_\mathrm{s})
+    drop: true
+  As:
+    value: 'lambda logA: 1e-10*np.exp(logA)'
+    latex: A_\mathrm{s}
+  ns: 
+    prior:
+      min: 0.8
+      max: 1.2
+    ref:
+      dist: norm
+      loc: 0.9655
+      scale: 0.05
+    proposal: 0.0001
+    #value: 0.9655
+    latex: n_\mathrm{s}
+#################################    LYA   #############################################
+  log_biasLYA:
+    prior:
+      min: -2.
+      max: 0
+    ref: -0.93
+    proposal: 0.001
+    latex: log(bias_{LYA})
+  bias_LYA:
+    derived: 'lambda log_biasLYA: -10**(log_biasLYA)'
+    latex: bias_{LYA} 
+  beta_LYA:
+    latex: \beta_{LYA}
+    prior:
+      min: 0
+      max: 5
+    ref:
+      dist: norm
+      loc: 1.67
+      scale: 0.02
+    proposal: 0.0001
+#########################################################################################
+  H0:
+    prior:
+      min: 40
+      max: 100
+    proposal: 0.0001
+    ref: 
+      dist: norm
+      loc:   70
+      scale: 3
+    latex: H_0
+  rdrag:
+    latex: r_d
+  H0_rd:
+    derived: 'lambda H0, rdrag: H0*rdrag/299792'
+    latex: H_{0}r_{d}/c
+  ombh2:
+    prior:
+      min: 0.01
+      max: 0.05
+    proposal: 0.0001
+    latex: \Omega_\mathrm{b} h^2
+  omch2:
+    value: 'lambda omegam, ombh2, mnu, H0: (omegam)*(H0/100)**2 - ombh2 -(mnu*(3.046/3)**0.75)/94.0708'
+    latex: \Omega_\mathrm{c} h^2
+  omegam:
+    prior:
+      min: 0.01
+      max: 0.99
+    ref: 0.3
+    proposal: 0.0001
+    latex: \Omega_\mathrm{m}
+  omegal:
+    latex: \Omega_\Lambda
+  mnu: 0.06
+  tau: 0.055
+sampler:
+  mcmc:
+    Rminus1_stop: 0.001
+    max_tries: 10000
+    learn_proposal: True
+    learn_proposal_Rminus1_max: 2.