Welcome to Bjet_MCMC

Bjet_MCMC is a tool to automatically model multiwavelength spectral energy distributions of blazars, considering one-zone synchrotron-self-Compton (SSC) model with or without the addition of external inverse-Compton process from the thermal emission of the nucleus. It also contains manual fitting functionalities for multi-zone SSC modeling. This tool is built as an MCMC python wrapper around the C++ code Bjet.

License

The code is licensed under a BSD 3-Clause License.

Acknowledgments and citation

• If you use this code in a scientific publication or communication, please cite the paper Hervet et al. 2024 .

• For any use of the multi-zones SSC option, please also cite Hervet at al. 2015 .

• To reference a specific version, you can also use Zenodo citation:

  

Note

This project is under active development.

Contents

• Installation and running Bjet_MCMC
  • Installation
  • Running Bjet_MCMC for the first time
• Dependencies
  • emcee
  • scipy
  • invoke
  • matplotlib
  • corner
  • tqdm
  • h5py
• Configuration file
  • Example of a configuration file
• Data format
  • Example of an SED data file
• Outputs
  • backend.h5
  • Text files
  • Science plots
  • \(\chi^2\) plots
  • Corner plot
• Running Bjet manually (bjet_core)
  • run_Bjet_manual.py
  • Parameter file
  • Manual installation of bjet_core
  • Usage
    • Options for calling the executable:
    • Parameter files
    • Modes:
    • Valid values for model type:
    • Order of parameters in command line:
• Computing Optimization Advice
  • Configuration
  • Testing
  • OpenHPC - Slurm
• API
  • bjet_core
    • bj_core02 namespace
    • Functions and Variables in processes_supp_core
  • bjet_mcmc Package
    • Submodules
      • bjet_mcmc.blazar_clean module
        • clean()
      • bjet_mcmc.blazar_initialize module
        • compile_bjet()
        • initialize()
        • make_dirs()
      • bjet_mcmc.blazar_mcmc module
      • bjet_mcmc.blazar_model module
        • add_data()
        • command_line_sub_strings()
        • create_params_file()
        • file_make_SED()
        • make_SED()
        • make_model()
        • params_linear_to_log()
        • params_log_to_linear()
        • process_model()
      • bjet_mcmc.blazar_plots module
        • N_e_BknPowLaw()
        • cooling_time_Thomson()
        • corner_plot()
        • get_min_max_per_point()
        • get_params_1sigma_ranges()
        • plot_1sigma()
        • plot_1sigma_plots()
        • plot_chain()
        • plot_chi_squared()
        • plot_cooling_times()
        • plot_data()
        • plot_likelihood_profiles()
        • plot_model()
        • plot_model_and_data()
        • plot_particle_spectrum()
        • residual_plot()
        • scale_to_values()
      • bjet_mcmc.blazar_properties module
        • BlazarProperties
        • modelProperties()
      • bjet_mcmc.blazar_report module
        • get_best_log_prob_and_params()
        • get_indices_within_1sigma()
        • load_from_backend()
        • make_text_file()
        • min_max_params_1sigma()
        • parse_info_doc()
        • save()
        • save_plots_and_info()
        • show_results()
        • text_report()
      • bjet_mcmc.blazar_run_mcmc module
        • mcmc()
        • run_mcmc()
      • bjet_mcmc.blazar_utils module
        • chi_squared()
        • chi_squared_Limit_to_err()
        • chi_squared_from_model()
        • e_to_v()
        • get_random_parameters()
        • log_prior()
        • log_prob_from_model()
        • log_probability()
        • min_max_parameters()
        • random_defaults()
        • random_eic_from_std()
        • read_configs()
        • read_data()
        • v_to_e()
      • bjet_mcmc.user_SED_plot module
        • e_to_v()
        • v_to_e()