Py4CAtS --- Python scripts for Computational ATmospheric Spectroscopy

Main Scripts: From Hitran/Geisa to Optical Depths

extract: extract (select) lines of a certain molecule (and isotope) and/or wavenumber range from line parameter database
(in contrast to the "low-level" hitran and geisa scripts below molecule (and isotope) can be specified by their chemical names!)
lbl2od: computation of line-by-line optical depth due to molecular absorption (combines lbl2xs, xs2ac, ac2od)

Further Scripts (stand-alone, executable!)

hitran: extract lines of a certain molecule (and isotope) and/or wavenumber range from the HITRAN database
geisa: extract lines of a certain molecule (and isotope) and/or wavenumber range from the GEISA databank
lines: Read molecular spectroscopic line parameters (Hitran, Geisa, ... extract) and convert to new pressure/temperature
plot_atlas: plot line data, i.e., line position vs strength in 'atlas' style.
(Note:This version utilizes the xmgr plotting tool (a.k.a. ACE/gr, further developed into the GRACE tool)
lbl2xs: lbl cross sections for one molecule and several p, T
cross_section: Read and write / plot molecular cross sections (e.g., to reformat or interpolate)
(Note:This version utilizes the matplotlib python 2D plotting library)
atmos: Read atmospheric data file(s) in xy tabular ascii format: extract profiles, interpolate to new altitude grid, save in xy or namelist format.
molecules: A dictionary of dictionaries containing molecular data (id numbers, mass, ....) along with some convenience functions.
cgsUnits: Conversion of (scalar or array) physical values to different units

Supplementary Modules

xs2ac2od: the main computational functions besides the lbl functions
lineShapes: defines the Lorentz, Gauss, and Voigt line profiles (normalized to one) along with two computational routines for the complex error function
command_parser: Command line interpreter, esp. options, written ontop of Python's getopt module
(since Python2.3 optparse is available, but ....)
IO: input/output related routines
ir: constants for infrared spectroscopy and radiative transfer
pairTypes: three classes for PairOfInts, PairOfFloats, Intervals

General Remarks

Some options are used by (almost) all scripts:
-h to request help (usage description)
-c to override the default character # used to indicate comment lines in data files
-o to specify an output file (default: standard out)
-v to request more informative output messages (verbose)

Many options require one or several argument(s) (except for the boolean ones such as -h). The type of argument(s) is indicated in the help documentation:

`char`	a single character (usually a letter or digit)
`string`	a string (if there are blanks, enclose the string in quotes)
`file`	essentially a string specifying a valid file name
`int`	an integer
`float`	a real number (e.g. 3.14 or 1.23e45)
	(the "d" or "D" for the exponent of 10 is not allowed)
`interval`	two (usually real) numbers separated by comma (no blanks!)

Some scripts allow to specify a list of integers, floats, strings etc as an option (e.g. a sequence of pressures).
Use commas as separator, but do not use blanks between the list elements, i.e. say lbl2xs -p 1013,800,500
(or enclose everything in quotes: lbl2xs -p '1013, 800, 500')
Some scripts such as lbl2xs produce an output file for each input file. In these cases the -o option is used to specify the extension of the output file(s)
(Typically the input files will have the same extension, and there will be a list of output files with the common extension replaced by the string given in the -o option)

DATA

To run these scripts, you need molecular spectroscopic line parameters (essentially line positions and strengths) and atmospheric data comprising pressure, temperature, and molecular concentrations as a function of altitude.

py4cats @ libradtran

The executable scripts are in ../bin (relative to this doc directory!)
To add this directory to your search path, append the following statement to your .tcshrc (or .cshrc) file:
setenv PATH ${PATH}:${libradtranHome}/py4cats/bin
(or equivalently for the bash or korn shell)

Ideally the py4cats scripts should run on any computer. Well, almost any, of course you should have Python along with numpy (and scipy and matplotlib occasionally ....). In order to save the optical depth data using netcdf format, you also need an appropriate module such as Scientific.IO.NetCDF (from K. Hinsen's ScientificPython; Alternatively pynetcdf might help ....). In order to plot the lines (line position vs strength) with plot_atlas you also need ACE/gr = xmgr.

Documentation and Some Questions

For a detailed review of line-by-line modeling for infrared radiative transfer see this lbl2od.pdf

Known Problems

extract options:
-o (output filename (extension)) – -d (output directory) – -f (output file format)
(Possibly this is a bit confusing now?)
Two-, three grid algorithm currently implemented only for Voigt line shape
No continuum correction
Weak line rejection: presently this can be done only with extract using the -S option.