TLI Tutorial

This mode formats the line-by-line (LBL) opacity data into a transition-line information (TLI) file, the format used by Pyrat Bay to compute opacities.

Available Databases

The following table lists the available LBL opacity databases that are compatible with Pyrat Bay:

Source	Species	References
HITRAN/HITEMP	H₂O, CO, CO₂, CH₄ (+others)	[Rothman2010] [Rothman2013] [Li2015] [Gordon2017] [Hargreaves2019]
ExoMol	H₂O, CO, CO₂, CH₄, TiO (+others)	[Tennyson2016]
Partridge & Schwenke	H₂O	[PS1997]
Schwenke	TiO	[Schwenke1998]
Plez	VO	[Plez1998]

Pyrat Bay is also compatible with the repack code to compress ExoMol or HITEMP databases (see more details in [Cubillos2017b]).

Note

Note that besides these LBL opacities, there are also collision-induced absorption (CIA) opacities that vary smoothly with wavelength. These opacities are processed as tabulated cross-section (CS) files as a function of temperature and wavelength.

Sample Configuration File

Here is an example of a TLI configuration file (tli_hitran_H2O.cfg):

[pyrat]

# Pyrat Bay run mode, select from: [tli atmosphere spectrum opacity mcmc]
runmode = tli

# List of line-transtion databases:
dblist = ./01_hit12.par

# Type of line-transition database, select from:
# [hitran exomol repack pands tioschwenke voplez]
dbtype = hitran

# List of partition functions for each database:
pflist = tips

# Initial and final wavelength:
wllow  = 0.3 um
wlhigh = 5.0 um

# Output TLI file:
tlifile = ./HITRAN_H2O_0.3-5.0um.tli

# Verbosity level (<0:errors, 0:warnings, 1:headlines, 2:details, 3:debug):
verb = 2

Databases

The dblist key specifies the opacity database to read (e.g., the ‘.par’ HITRAN files, or the ‘.trans’ ExoMol files). A TLI configuration file can contain as many dblist values as desired; this is particularly useful for molecules whose LBL data is split into multiple files (e.g., ExoMol or HITEMP data).

The dbtype key indicates of what type are the databases listed in dblist. There must be either one dbtype value for each dblist value, or a single dbtype value that applies to all dblist values. The following table lists the dbtype values for each database type:

Database	dbtype
HITRAN/HITEMP	hitran
ExoMol	exomol
repack	repack
Partridge & Schwenke (H₂O)	pands
Schwenke (TiO)	tioschwenke
Plez (VO)	voplez

Partition Functions

The partition function is a temperature-dependent property of each isotope that is required to compute line intensities. There must be either one pflist value for each dblist value, or a single pflist value that applies to all dblist values.

For the hitran databases, Pyrat Bay provides the Total Internal Partition Sums (TIPS) data (see [Laraia2011] and [Gamache2017]). In this case the user can set the pflist value to ‘tips’.

The exomol, pands, and tioschwenke databases provide the partition function as ascii tables. In this case, the user must download the partition-function files, and format them into the Pyrat Bay format. For example (from the command line):

# Download NH3 ExoMol partition-function data to current dictory:
wget http://www.exomol.com/db/NH3/14N-1H3/BYTe/14N-1H3__BYTe.pf
wget http://www.exomol.com/db/NH3/15N-1H3/BYTe-15/15N-1H3__BYTe-15.pf

# Re-format to pyratbay format:
pbay -pf exomol 14N-1H3__BYTe.pf 15N-1H3__BYTe-15.pf

The user can also generate TIPS partition-function files from the command line:

# pbay -pf tips
pbay -pf tips H2O

# Use the 'as_exomol' flag to generate a TIPS partition-function file
# to be used for exomol database (note the output isotope naming differs):
pbay -pf tips H2O as_exomol

Wavelength Boundaries

The user can specify any desired wavelength boundaries for a TLI run, by setting the wllow and wlhigh keys. The values for these keys must specify the units, along with the numeric value (see Units for a list of available units).

TLI Example

The tlifile key (a required key) must specify the name of the output TLI file. The output TLI file will include only the lines within the specified wavelength ranges (wllow and wlhigh).

When running, Pyrat Bay will also create a log file containing the screen output. The log file name can be set explicitly through the logfile key; otherwise, it will be created from the tlifile name, changing the extension to ‘.log’.

Note

Before running the tli tutorial, download the HITRAN H₂O file as in the Quick Example, and download the configuration file shown above, for example, with these shell commands:

tutorial_path=https://raw.githubusercontent.com/pcubillos/pyratbay/master/examples/tutorial
wget $tutorial_path/tli_hitran_H2O.cfg

To create the TLI file with this Sample Configuration File, run from the command line:

# Make a TLI file with opacity line-transition info:
pbay -c tli_hitran_H2O.cfg