Awesome

The project of fitting SLED with PyRADEX+emcee

Why use RADEX+emcee rather than using RADEX grids?

• This code combines emcee and RADEX, performing MCMC sampling in the RADEX-parameters space WITHOUT predefined grids, which leads to faster a convergence time and a better sampling of the parameter space.
• This code directly samples the parameter space with the Affine Invariant Markov chain Monte Carlo (MCMC) Ensemble sampler. This allows a much better sampling of the parameter space.

How do you know the code is doing the right calculations?

This is a very valid concern. Nevertheless, it is always the first practice to test your code on well-studied sources (and you can also test the code yourself by comparing with literatures). That's what has been done:

• This code has been tested against a few well-studied sources. For example:
  • APM08279+5255, Weiss et al. 2007: our results are entirely consistent with the results in this paper. Their values, log(n_H2/cm⁻³) = 4.2 and log(T_K/K) = 2.4, are within the +/-1 sigma values and close to the maximum likelihood values from the calculations based on this code.
  • The Circinus Galaxy, Zhang et al. 2014: similar to APM08279+5255, the results from our code are fully consistent with the results in the reference.

Installation & usage:

Dependence:

• PyRadex: https://github.com/keflavich/pyradex
• emcee: https://github.com/dfm/emcee
• corner: https://github.com/dfm/corner.py
• other common packages: numpy, scipy, astropy, astroquery
• note that if you would like to directly use the compiled radex in this repo, you need to run the x86_64 version of python

How to produce resulting plots:

• The results are stored in the .pickle files
• Just run replot(“source_name”) after executing the python script in IPython.
• You can always check the .pickle files without the need to rerun the whole code again.
• A note on a possible decoding error for the Pickle file (Python 2 --> Python 3)
  • When you encounter an error using old Pickle file generated using Python 2: UnicodeDecodeError: 'ascii' codec can't decode byte 0xfa in position 0: ordinal not in range(128)
  • You can add , encoding='latin1' behind the line = pickle.load(pkl_file), so as = pickle.load(pkl_file, encoding='latin1'). This should solve the issue.
• Update: added a function to plot 100 MCMC examples within the 1-sigma range for posteriors (See the last figure).

Change number of walkers and iterations:

• In emcee_radex.py, change the numbers between line 404-406.
• In emcee_radex_2comp.py, change the numbers between line 540-543.

Change the solver of the radiation transfer

To use myradex (which may be more stable as mentioned in Ginsberg et al. 2016) instead of RADEX, please uncomment the following line:

import pyradex.fjdu

You may also need to change pyradex.Radex to pyradex.fjdu.Fjdu , and remove validate_colliders=False.

Directory structure:

• README.md: this file;
• emcee
  • radex_moldata: the molecular data;
  • results: the pickle files storing the MCMC results;
    • single: results of one-component fittings;
    • double: results of two-component fittings;
  • emcee_radex.py: one-component fitting code;
  • emcee_radex_2comp.py: warm + cold components, in prior Tcold < Twarm; SizeCold>SizeWarm;
• data
  • flux.note: explaining the data in Yang+2017;
  • flux.dat: this is the flux data file read by emcee_radex.py;
  • flux_for2p.dat: flux data used in emcee_radex_2comp.py;

Fitting example:

A full example of a two-component fitting, the SLED plot and the corner plots:

Here gives an example of the updated plot style (see notes on How to produce resulting plots):

Citation

Please cite our paper if you find this code useful. The paper also includes CO SLED data for 16 high-redshift submillimeter galaxies: C. Yang, A. Omont, A. Beelen et al. 2017, A&A, 608, A144.

Bibtex:

@ARTICLE{2017A&A...608A.144Y,
       author = {{Yang}, C. and {Omont}, A. and {Beelen}, A. and {Gao}, Y. and
         {van der Werf}, P. and {Gavazzi}, R. and {Zhang}, Z. -Y. and
         {Ivison}, R. and {Lehnert}, M. and {Liu}, D. and {Oteo}, I. and
         {Gonz{\'a}lez-Alfonso}, E. and {Dannerbauer}, H. and {Cox}, P. and
         {Krips}, M. and {Neri}, R. and {Riechers}, D. and {Baker}, A.~J. and
         {Micha{\l}owski}, M.~J. and {Cooray}, A. and {Smail}, I.},
        title = "{Molecular gas in the Herschel-selected strongly lensed submillimeter galaxies at z   2-4 as probed by multi-J CO lines}",
      journal = {\aap},
     keywords = {galaxies: high-redshift, galaxies: ISM, infrared: galaxies, submillimeter: galaxies, radio lines: ISM, ISM: molecules, Astrophysics - Astrophysics of Galaxies},
         year = 2017,
        month = dec,
       volume = {608},
          eid = {A144},
        pages = {A144},
          doi = {10.1051/0004-6361/201731391},
archivePrefix = {arXiv},
       eprint = {1709.04740},
 primaryClass = {astro-ph.GA},
       adsurl = {https://ui.adsabs.harvard.edu/abs/2017A&A...608A.144Y},
      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}

Authors of the code

Alexandre Beelen (ORCID: 0000-0003-3201-0185); Chentao Yang (ORCID: 0000-0002-8117-9991).