DOI: 10.5281/zenodo.3686329

Calculate density and temperature from observed molecular emission lines, using radiative transfer models.

Our models assume that the molecular emission lines emerge from a multi-density medium rather than from a single density alone. The density distribution is assumed to be log-normal or log-normal with a power-law tail. The parameters (density, temperature and the width of density distribution) are inferred using Bayesian statistics, i.e. Markov chain Monte Carlo (MCMC).

Given an ascii table of observed molecular intensities [K km/s], the results (mass-weighted mean density, temperature and width of the density distribution) are saved in an output ascii file. Furthermore, diagnostic plots are created to assess the quality of the fit/derived parameters.

• May 23, 2022 | Version 1.5 (minor update):

  • Update: User may now also enter/change the number of MCMC simulations to run

  • Bugfix: In cases where sampler did not converge (Tau is infinite or log-probability is neg. infinity) previous versions crashed with "ValueError: cannot convert float NaN to integer" when trying to produce corner plots. Now, the program continues execution and shows one of the following Warnings: "Warning: Tau is NaN, corner plot cannot be created!" or "Warning: MCMC did not converge, you may try to increase the number of simulations (nsims)!"

• Feb 27, 2021 | Version 1.4 (minor update):

  • Bugfix: Fixing import of CS model grid

  • Update: Code updated to remove deprecation warnings

• Feb 26, 2021 | Version 1.3 (major update):

  • New: The user may optionally infer the parameters (density, temperature, width of density distribution) via application of the MCMC method.

  • New: Diagnosis plots (corner plots) are produced when MCMC method is used.

  • Update: Code updated to Python 3.X

  • Update: Re-calculation of models, now including the following transitions: 12CO (up to J=3), 13CO (up to J=3), C18O (up to J=3), C17O (up to J=3), HCN (up to J=3), HCO+ (up to J=3), HNC (up to J=3) and CS (up to J=3)

• Mar 31, 2020 | Version 1.2 (major update):

  • New: An online version is now available at:

           http://www.densegastoolbox.com
    

  • New: The models can be explored using an interactive application at:

           http://www.densegastoolbox.com/explorer
    

  • Update: Model fit parameters are: density (mass-weighted), temperature and width of the distribution. The temperature and NOW ALSO WIDTH can be fixed.

  • Update: Re-calculation of models, now including the following transitions: 12CO (up to J=3), 13CO (up to J=3), C18O (up to J=3), C17O (up to J=3), HCN (up to J=3), HCO+ (up to J=3) and HNC (up to J=3)

  • Update: The one-zone model grids are now more extended with H_2 densities between 10^-2 and 10^8 cm^-3.

  • Update: Diagnosis plots improved: (n,T) vs. chi2 and (n,width) vs. chi2

  • See "example.py" for how to use the Dense Gas Toolbox. It's easy!

  • Still needs Python 2.7 (will be upgraded to 3.X).

• Feb 28, 2020 | Version 1.1 (minor update):

  • This release now includes the data table ("ascii_galaxy.txt") used by "example.py".

• Feb 25, 2020 | Version 1.0:

  • The initial release contains models for the following lines: 12CO (1-0), 12CO (2-1), 12CO (3-2), 13CO (1-0), HCN (1-0), HNC (1-0) and HCO+ (1-0)

  • abundances and optical depths are fixed based on observations of the EMPIRE survey

  • Two density distributions (PDFs) are available: lognorm and lognorm+power law

  • Model fit parameters are: density (mass-weighted), temperature and width of the distribution. The temperature can be fixed.

  • Emissivities per density bin are calculated using RADEX, i.e. LVG method for an expanding sphere. These one-zone model grids are limited to H_2 densities between 10 and 10^8 cm^-3.

  • The total line intensity is found from summation of the emissivities per H_2 molecule along the gas density distribution (and multiplication with column per linewidth and abundance). For some models, at the very low and very high density ends, the extent of the PDF exceeds the one-zone density grid limits (10-10^8 cm^-3). In these regimes (where emissivities are very low anyway for the molecules under consideration), the emissivities are set constant to the grid limit value.

  • See "example.py" for how to use the Dense Gas Toolbox. It's easy!

  • Needs Python 2.7 (will be upgraded to 3.X).

  • Depends on the following Python packages: numpy, matplotlib, pylab, scipy