RADEX

Radex is a computer program to calculate the strengths of atomic and molecular lines from interstellar clouds which are assumed to be homogeneous. Everyone is free to use the program, provided that publications make a reference to our paper: Van der Tak, F.F.S., Black, J.H., Schöier, F.L., Jansen, D.J., van Dishoeck, E.F., 2007, A&A 468, 627-635. This web page describes the off-line version of RADEX; click here to go to the on-line version.

Jump to: introduction    installation   running Radex  molecular data input   output files   scripting Radex  revision history
 

Installation

1. Download the distribution file by following this link.
2. Unzip and untar the distribution file:

   > gunzip radex_public.tar.gz
   > tar xf radex_public.tar
   This creates a directory Radex with subdirectories src, bin, and data.

3. Customize your setup:

   -- go to the src subdirectory
   -- edit the file Makefile to select a Fortran compiler (g77 / gfortran / ifort / ...)
   -- edit the file radex.inc to locate the molecular data area, to customize the name of the log file, and to select a geometry for the escape probability

4. Create the executable from the source code:

   > cd Radex/src
   > make
   > cd

5. Include the directory Radex/bin to your path by adding the following line to your .cshrc (or equivalent) file:

   > set path = ( $path $HOME/Radex/bin )
   (To proceed within the same shell, follow this command by "rehash".)

6. Verify that the program runs and produces correct output:
   

   > cd ..
   > radex < example.inp
   > diff example.out standard.out
   The only difference between the two files should be the Radex version.
   

7. Try it yourself:

   > cd ..
   > radex
   
   

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Running Radex

Details:

Collision partners: A maximum of seven collision partners may be defined: H₂, p-H₂, o-H₂, electrons, H (atoms), He, and H⁺. Make sure that the data file contains collisional rate coefficients for all partners for which densities are given here. In most cases, using H₂ as only partner is a good default. When H₂ is given as collision partner for CO, a thermal average of ortho and para H₂ is taken.

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Molecular data

Files with molecular data (term energies, statistical weights, Einstein coefficients, and rate coefficients for collisional deexcitation) must be placed in the subdirectory Radex/data. For many molecules of astrophysical interest, the LAMDA database provides data files in the required format. For molecules for which no collisional data exist, users need to make their own files. The databases at NASA-JPL and in Cologne provide spectroscopic data for many molecules. For collisional rate coefficients, consult NASA-GISS for the calculations of Sheldon Green, or the literature in the BASECOL and CASSIS databases for other work. Unfortunately, collisional data do not exist for all molecules of (potential) astrophysical interest. If you know about calculations that are not in the LAMDA database, please let us know!

The public distribution of Radex contains one example file (hco+.dat) in the data directory. If you need to make your own file, here is a detailed description of the required file format. Note that the same files are used by the Monte Carlo radiative transfer program Ratran. The format can be used for all molecules, whether linear (HCO⁺) or not (H₂O). The lines that start with an exclamation mark (!) are not read by the program.

% Lines 1 - 2: molecule name
% Lines 3 - 4: molecular weight (a.m.u.)
% Lines 5 - 6: number of energy levels (NLEV)
% Lines 7 - (7+NLEV): level number, level energy (cm^-1), statistical weight. These numbers may be followed by additional info such as the quantum numbers, which are however not used by the program. The levels must be listed in order of increasing energy.
% Lines (8+NLEV) - (9+NLEV): number of radiative transitions (NLIN)
% Lines (10+NLEV - (10+NLEV+NLIN): transition number, upper level, lower level, spontaneous decay rate (s^-1). These numbers may be followed by additional info such as the line frequency and upper state energy, which is however not used by the program.
% Lines (11+NLEV+NLIN) - (12+NLEV+NLIN): number of collision partners
% Lines (13+NLEV+NLIN) - (14+NLEV+NLIN): collision partner ID and reference. Valid identifications are: 1=H2, 2=para-H2, 3=ortho-H2, 4=electrons, 5=H, 6=He, 7=H+.
% Lines (15+NLEV+NLIN) - (16+NLEV+NLIN): number of transitions for which collisional data exist (NCOL)
% Lines (17+NLEV+NLIN) - (18+NLEV+NLIN): number of temperatures for which collisional data exist
% Lines (19+NLEV+NLIN) - (20+NLEV+NLIN): values of temperatures for which collisional data exist
% Lines (21+NLEV+NLIN) - (21+NLEV+NLIN+NCOL): transition number, upper level, lower level; rate coefficients (cm³s^-1) at each temperature. RADEX interpolates between rate coefficients in the specified temperature range. Outside this range, it assumes the collisional de-excitation rate coefficients are constant with T, i.e., it uses rate coefficients specified at the highest T (400 K in this case) also for higher temperatures, and similarly at temperatures below the lowest value (10 K in this case) for which rate coefficients were specified.

Example molecular data file: HCO⁺

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Radex output

The output files from Radex start with a summary of the input parameters, followed by a line-by-line listing of upper state energy (K), frequency (GHz), wavelength (micron), excitation temperature (K), optical depth, peak intensity (K), and line flux (both in K km/s and in erg/s/cm² units). Here is an example for HCO⁺ between 50 and 300 GHz.

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Scripting Radex

To use Radex to fit model parameters to observational data, or explore parameter space, the best strategy is probably to write a script that makes repeated calls to Radex. The directory Radex/bin contains two examples, written in the Python scripting language:

1. radex_column.py models the observed strength of a molecular line, The input parameters (temperature, density, and observed line strength and width) are specified at the top of the file. The program returns the best-fit value of the column density to the screen.
2. radex_grid.py calculates the ratio of (sets of) two molecular lines as a function of temperature and density. The column density and background temperature are kept constant. The result is written to file and may be plotted using any standard plotting program.

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Revision history