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runradex - NEMO frontend to run the RADEX program
runradex mol=
outdir= [parameter=value]
RADEX is a statistical equilibrium
radiative transfer code. This particular version is a one-dimensional non-LTE
radiative transfer code, that uses the escape probability formulation assuming
an isothermal and homogeneous medium without large-scale velocity fields.
RADEX is comparable to the LVG method and provides a useful tool in rapidly
analyzing a large set of observational data providing constraints on physical
conditions, such as density and kinetic temperature.
RADEX provides an alternative
to the widely used rotation diagram method which relies upon the availability
of many optically thin emission lines and is useful only in roughly constraining
the excitation temperature in addition to the column density. RADEX makes
no extrapolation of collisional rate coefficients outside the temperature
range specified in the molecular data file used as input. Instead they are
kept constant.
In addition to this frontend to the original fortran program,
there is also an online version available (see below).
The following
parameters are recognized in any order if the keyword is also given:
- mol=
- Input molecular data file e.g. hco+.dat, from $RADEXDAT. If the filename starts
with . or /, it will be taken as an absolute or relative address, else a
predefined location (such as $RADEXDAT) will be used. No default.
- outdir=
- Run directory within which all files will be created. No default.
- out=
- Output
filename [output.txt]
- fmin=
- The statistical equilibrium calculation
takes all spectral lines of the molecular model into account, but the output
only lists lines at frequencies between the given minimum and maximum frequency
given here. Allowed range is 0.1 - 1e7 GHz. [50]
- fmax=
- Maximum frequency
in GHz. [500]
- tkin=
- Kinetic temperature of the medium in K. Allowed
range is 0.1 - 10,000. [20]
- partner=
- Collision partner name(s). Pick (m)any
from: H2,p-H2,o-H2,e,H,He. [H2]
- density=
- Number density (cm^-3) of collision
partners (usually just H2). By default, collisions with He are not taken
into account. To approximate their effect, multiply the H2 density by 1.2
for an He/H2=0.2 abundance. The effects of mass and geometrical cross section
between He and H2 cancel out to first order. One number required for each
partner. [1e4]
- tbg=
- Rayleigh-Jeans equivalent temperature of the background
radiation field, assumed to be of black body shape. Default is the cosmic
microwave background. Units are K. [2.73]
- cdmol=
- Column density of the
molecule to calculate line strengths for, in cm^-2. [1e13]
- deltav=
- Thermal
+ turbulent width (FWHM) of the lines, in km/s. Allowed range is 1e-3 to
1e3. [1.0]
This frontend is particularly useful to run a large
number of models, optionally followed by some more analysis. For example,
here is a set of models run at a grid of temperature and densities:
foreach tkin (15 20 25 30 35)
foreach cdmol (1e12 3e12 1e13 3e13 1e14)
runradex hco+.dat run_${tkin}_$cdmol tkin=$tkin cdmol=$cdmol
end
end
this will create a series of run directories (run_15_1e12,run_15_1e13,
... run_35_3e13) with a local file called output.txt containing the output
from RADEX. There are also two python scripts in the distribution of RADEX
with examples how to run over a grid of models and extract or fit data.
http://www.sron.rug.nl/~vdtak/radex/index.shtml
http://www.strw.leidenuniv.nl/~moldata/
- molecular data (and their format description)
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.
$NEMO/usr/radex/runradex.c - source code
$RADEXDAT/hco+.dat - default example molecular data file
$rundir/input.txt - input text file for radex itself, generated by runradex
$rundir/radex.log - logfile , created by radex
Peter Teuben
07-Jan-12 V0.1 Created PJT
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