EXAMPLE_MCMC1.yaml

timing: False
debug: False
stop_at_error: False

likelihood:
  lsst_y1.lsst_cosmic_shear:
    path: ./external_modules/data/lsst_y1
    print_datavector: False
    accuracyboost: 1.0
    integration_accuracy: 0
    kmax_boltzmann: 5.0
    # 1 EE2, 2 Halofit
    non_linear_emul: 2
    IA_model: 0
    IA_redshift_evolution: 3

params:
  As_1e9:
    prior:
      min: 0.5
      max: 5
    ref:
      dist: norm
      loc: 2.1
      scale: 0.2
    proposal: 0.2
    latex: 10^9 A_\mathrm{s}
    drop: true
    renames: A
  ns:
    prior:
      min: 0.87
      max: 1.07
    ref:
      dist: norm
      loc: 0.96605
      scale: 0.015
    proposal: 0.015
    latex: n_\mathrm{s}
  H0:
    prior:
      min: 55
      max: 91
    ref:
      dist: norm
      loc: 67.32
      scale: 3
    proposal: 3
    latex: H_0
  omegab:
    prior:
      min: 0.03
      max: 0.07
    ref:
      dist: norm
      loc: 0.0495
      scale: 0.005
    proposal: 0.005
    latex: \Omega_\mathrm{b}
    drop: true
  omegam:
    prior:
      min: 0.1
      max: 0.9
    ref:
      dist: norm
      loc: 0.316
      scale: 0.015
    proposal: 0.015
    latex: \Omega_\mathrm{m}
    drop: true
  w:
    prior:
      min: -3
      max: -0.01
    ref:
      dist: norm
      loc: -0.99
      scale: 0.02
    proposal: 0.02
    latex: w_{0,\mathrm{DE}}
  mnu:
    value: 0.06
  tau:
    value: 0.0697186
    latex: \tau_\mathrm{reio}
  # ---------------------------------------------------------------------------------------
  # ------------------------------------- DERIVED PARAMETERS ------------------------------
  # ---------------------------------------------------------------------------------------
  # WARNING: DO NOT REMOVE omegabh2/omegach2/omegamh2/wa/As/ FROM DERIVED PARAMETERS
  # WARNING: DO NOT REMOVE THE DROP FLAG FROM omegab/omegam/As_1e9/w0pwa
  # SEE: github.com/CosmoLike/cocoa#warning-warning-warning-weak-lensing-yaml-files-in-cobaya-
  # --------------------------------------------------------------------------------------- 
  As:
    value: 'lambda As_1e9: 1e-9 * As_1e9'
    latex: A_\mathrm{s}
  omegabh2:
    value: 'lambda omegab, H0: omegab*(H0/100)**2'
    latex: \Omega_\mathrm{b} h^2
  omegach2:
    value: 'lambda omegam, omegab, mnu, H0: (omegam-omegab)*(H0/100)**2-(mnu*(3.046/3)**0.75)/94.0708'
    latex: \Omega_\mathrm{c} h^2
  omegal:
    latex: \Omega_\Lambda
  omegamh2:
    derived: 'lambda omegam, H0: omegam*(H0/100)**2'
    latex: \Omega_\mathrm{m} h^2
  sigma8:
    latex: \sigma_8
  s8h5:
    derived: 'lambda sigma8, H0: sigma8*(H0*1e-2)**(-0.5)'
    latex: \sigma_8/h^{0.5}
  s8omegamp5:
    derived: 'lambda sigma8, omegam: sigma8*omegam**0.5'
    latex: \sigma_8 \Omega_\mathrm{m}^{0.5}
  s8omegamp25:
    derived: 'lambda sigma8, omegam: sigma8*omegam**0.25'
    latex: \sigma_8 \Omega_\mathrm{m}^{0.25}
  age:
    latex: '{\rm{Age}}/\mathrm{Gyr}'
  rdrag:
    latex: r_\mathrm{drag}
  yheused:
    latex: Y_P^\mathrm{BBN}
  omegan2:
    latex: \Omega_\mathrm{\\nu} h^2
  omegan:
    derived: 'lambda omegan2, H0: omegan2/((H0/100)**2)'
    latex: \Omega_\mathrm{\\nu}
  LSST_BARYON_Q1:
    value: 0.0
    latex: Q1_\mathrm{LSST}^1
  LSST_BARYON_Q2:
    value: 0.0
    latex: Q2_\mathrm{LSST}^2
  # WL photo-z errors
  LSST_DZ_S1:
    prior:
      dist: norm
      loc: 0.0414632
      scale: 0.002
    ref:
      dist: norm
      loc: 0.0414632
      scale: 0.002
    proposal: 0.002
    latex: \Delta z_\mathrm{s,LSST}^1
  LSST_DZ_S2:
    prior:
      dist: norm
      loc: 0.00147332
      scale: 0.002
    ref:
      dist: norm
      loc: 0.00147332
      scale: 0.002
    proposal: 0.002
    latex: \Delta z_\mathrm{s,LSST}^2
  LSST_DZ_S3:
    prior:
      dist: norm
      loc: 0.0237035
      scale: 0.002
    ref:
      dist: norm
      loc: 0.0237035
      scale: 0.002
    proposal: 0.002
    latex: \Delta z_\mathrm{s,LSST}^3
  LSST_DZ_S4:
    prior:
      dist: norm
      loc: -0.0773436
      scale: 0.002
    ref:
      dist: norm
      loc: -0.0773436
      scale: 0.002
    proposal: 0.002
    latex: \Delta z_\mathrm{s,LSST}^4
  LSST_DZ_S5:
    prior:
      dist: norm
      loc: -8.67127e-05
      scale: 0.002
    ref:
      dist: norm
      loc: -8.67127e-05
      scale: 0.002
    proposal: 0.002
    latex: \Delta z_\mathrm{s,LSST}^5
  # Intrinsic alignment
  LSST_A1_1:
    prior:
      min: -5
      max:  5
    ref:
      dist: norm
      loc: 0.7
      scale: 0.5
    proposal: 0.5
    latex: A_\mathrm{1-IA,LSST}^1
  LSST_A1_2:
    prior:
      min: -5
      max:  5
    ref:
      dist: norm
      loc: -1.7
      scale: 0.5
    proposal: 0.5
  # Shear calibration parameters
  LSST_M1:
    prior:
      dist: norm
      loc: 0.0191832
      scale: 0.005
    ref:
      dist: norm
      loc: 0.0191832
      scale: 0.005
    proposal: 0.005
    latex: m_\mathrm{LSST}^1
  LSST_M2:
    prior:
      dist: norm
      loc: -0.0431752
      scale: 0.005
    ref:
      dist: norm
      loc: -0.0431752
      scale: 0.005
    proposal: 0.005
    latex: m_\mathrm{LSST}^2
  LSST_M3:
    prior:
      dist: norm
      loc: -0.034961
      scale: 0.005
    ref:
      dist: norm
      loc: -0.034961
      scale: 0.005
    proposal: 0.005
    latex: m_\mathrm{LSST}^3
  LSST_M4:
    prior:
      dist: norm
      loc: -0.0158096
      scale: 0.005
    ref:
      dist: norm
      loc: -0.0158096
      scale: 0.005
    proposal: 0.005
    latex: m_\mathrm{LSST}^4
  LSST_M5:
    prior:
      dist: norm
      loc: -0.0158096
      scale: 0.005
    ref:
      dist: norm
      loc: -0.0158096
      scale: 0.005
    proposal: 0.005
    latex: m_\mathrm{LSST}^5

theory:
  camb:
    path: ./external_modules/code/CAMB
    stop_at_error: False
    use_renames: True
    extra_args:
      halofit_version: takahashi
      AccuracyBoost: 1.1
      lens_potential_accuracy: 1.0
      num_massive_neutrinos: 1
      nnu: 3.046
      dark_energy_model: ppf
      accurate_massive_neutrino_transfers: false
      k_per_logint: 20

sampler:
  mcmc:
    # ---------------------------------------------------------------------
    # File (w/ path) or matrix defining a covariance matrix for the proposal:
    # - null (default): will be generated from params info (prior and proposal)
    # - matrix: remember to set `covmat_params` to the parameters in the matrix
    covmat: ./projects/lsst_y1/EXAMPLE_MCMC1.covmat
    covmat_params:
    # --------------------------------------
    # --------------------------------------
    # Proposal covariance matrix learning
    # --------------------------------------
    # --------------------------------------
    learn_proposal: True
    # Don't learn if convergence better than...
    learn_proposal_Rminus1_min: 0.035
    # Don't learn if convergence is worse than...
    learn_proposal_Rminus1_max: 150
    # (even earlier if a param is not in the given covariance matrix)
    learn_proposal_Rminus1_max_early: 300.
    # --------------------------------------
    # --------------------------------------
    # Convergence and stopping
    # --------------------------------------
    # --------------------------------------
    # Maximum number of posterior evaluations
    max_samples: .inf
    # Gelman-Rubin R-1 on means
    Rminus1_stop: 0.005
    # Gelman-Rubin R-1 on std deviations
    Rminus1_cl_stop: 0.15
    Rminus1_cl_level: 0.95
    # --------------------------------------
    # --------------------------------------
    # Exploiting speed hierarchy
    # --------------------------------------
    # --------------------------------------
    measure_speeds: False
    drag: False
    # Cosmolike Cosmic Shear without Cosmo change is ~0.1seconds (8 cores) @OCelote
    blocking:
      - [1,
          [
            As_1e9, ns, H0, omegab, omegam, w 
          ]
        ]
      - [6,
          [
            LSST_DZ_S1, LSST_DZ_S2, LSST_DZ_S3, LSST_DZ_S4, LSST_DZ_S5, LSST_A1_1, LSST_A1_2
          ]
        ]
      - [25,
          [
            LSST_M1, LSST_M2, LSST_M3, LSST_M4, LSST_M5
          ]
        ]
    oversample_power: 0.3
    oversample_thin: True
    # --------------------------------------
    # --------------------------------------
    # Avoid chain getting suck forever
    # --------------------------------------
    # --------------------------------------
    max_tries: .inf
    burn_in: 0
    # ---------------------------------------------------------------------
    # ---------------------------------------------------------------------
    # When no MPI used, number of fractions of the chain to compare
    # ---------------------------------------------------------------------
    # ---------------------------------------------------------------------
    Rminus1_single_split: 4

output: ./projects/lsst_y1/chains/EXAMPLE_MCMC1