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https://github.com/exosports/BART

Bayesian Atmospheric Radiative Transfer fitting code
https://github.com/exosports/BART

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Bayesian Atmospheric Radiative Transfer fitting code

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README 

        
### BART

> Bayesian Atmospheric Radiative Transfer fitting code



This code implements a Bayesian, Monte Carlo-driven,

radiative-transfer scheme for extracting parameters from spectra of

planetary atmospheres.  



### Table of Contents:

* [Team Members](#team-members)

* [Getting Started](#getting-started)

* [Install and Compile](#install-and-compile)

* [Quick Example](#quick-example)

* [Be Kind](#be-kind)

* [License](#license)



### Team Members:

* [Patricio Cubillos](https://github.com/pcubillos/) (UCF, IWF) 

* Jasmina Blecic (UCF)

* Joseph Harrington (UCF)

* Patricio Rojo (U. de Chile)

* Nate Lust (UCF)

* Oliver Bowman (UCF)

* Madison Stemm (UCF)

* Andrew Foster (UCF)

* Ryan Challener (UCF)

* Michael D. Himes (UCF)



With support from:

* Thomas J. Loredo (Cornell)

* Jonathan Fortney (UCSC)

* Nikku Madhusudhan (Yale)



### Getting Started:

You can find the BART User Manual [here](https://exosports.github.io/BART/doc/BART_User_Manual.html). If you run into trouble while using BART, please feel free to use our [BART User Mailing List](https://physics.ucf.edu/mailman/listinfo/bart-user). You'll have to sign up to post (for spam reasons), but we encourage you to join. If you're a developer interested in contributing to BART, you may also be interested in our [BART Developer Mailing List](https://physics.ucf.edu/mailman/listinfo/bart-devel) (see CONTRIBUTING for more information).



### Install and Compile:

Download the latest stable version from the BART

[releases](https://github.com/exosports/BART/releases) page

(TBD).  Alternatively, clone the repository to your local

machine with the following terminal commands.

First create a working directory to place the code:

```shell

mkdir BART_demo/

cd BART_demo/

topdir=`pwd`

```



Clone the repository with all its submodules:

```shell

git clone --recursive https://github.com/exosports/BART $topdir/BART/

```



Enter the BART directory and build the conda environment:

```shell

cd $topdir/BART/

conda env create -f environment.yml

conda activate bart

```



Compile the transit module programs:

```shell

cd $topdir/BART/modules/transit/

make

```



Compile the MCcubed routines:

```shell

cd $topdir/BART/modules/MCcubed/

make

```



To remove the program binaries, execute (in the respective

directories):

```shell

make clean

```



### Quick Example:



The following script lets you quickly fit a methane emission spectrum model to a set of 10 filters between 2 and 4 um.  These instructions are meant to be executed from the shell terminal.  To begin, follow the instructions in the previous Section to install and compile the code.  Now, create a working directory in your top directory to place the files and execute the programs:

```shell

cd $topdir

mkdir run/

cd run/

```



Download the HITRAN 2012 methane line-transition database at https://hitran.org/lbl/. Extract it:

```shell

unzip 06_hit12.zip

```



Copy the pylineread configuration file and run pylineread to make the transition-line-information (TLI) file:

```shell

cp $topdir/BART/examples/demo/pyline_demo.cfg .  

$topdir/BART/modules/transit/pylineread/src/pylineread.py -c pyline_demo.cfg

```



Copy the transit configuration file and run it to make a table of opacities:

```shell

cp $topdir/BART/examples/demo/transit_demo.cfg .  

$topdir/BART/modules/transit/transit/transit -c transit_demo.cfg --justOpacity

```



Copy and run the BART configuration file for eclipse geometry:

```shell

cp $topdir/BART/examples/demo/BART_eclipse.cfg .

$topdir/BART/BART.py -c BART_eclipse.cfg

```



Copy and run the BART configuration file for transit geometry:

```shell

cp $topdir/BART/examples/demo/BART_transit.cfg .

$topdir/BART/BART.py -c BART_transit.cfg

```



### Be Kind:



A number of graduate and undergraduate-student dreams and hopes have been sacrificed on the making of this project.  Please, be kind and aknowledge their effort by citing the articles asociated to this project:



  [Harrington et al. 2022. An Open-source Bayesian Atmospheric Radiative Transfer (BART) Code. I. Design, Tests, and Application to Exoplanet HD 189733b. Planet. Sci. J. 3 80.](https://iopscience.iop.org/article/10.3847/PSJ/ac3513)



  [Cubillos et al. 2022. An Open-source Bayesian Atmospheric Radiative Transfer (BART) Code. II. The Transit Radiative Transfer Module and Retrieval of HAT-P-11b. Planet. Sci. J. 3 81.](https://iopscience.iop.org/article/10.3847/PSJ/ac348b)



  [Blecic et al. 2022. An Open-source Bayesian Atmospheric Radiative Transfer (BART) Code. III. Initialization, Atmospheric Profile Generator, Post-processing Routines. Planet. Sci. J. 3 82.](https://iopscience.iop.org/article/10.3847/PSJ/ac3515)



Thanks!



### License:



Bayesian Atmospheric Radiative Transfer (BART), a code to infer

properties of planetary atmospheres based on observed spectroscopic

information.  



This project was completed with the support of the NASA Planetary

Atmospheres Program, grant NNX12AI69G, held by Principal Investigator

Joseph Harrington. Principal developers included graduate students

Patricio E. Cubillos and Jasmina Blecic, programmer Madison Stemm, and

undergraduates M. Oliver Bowman and Andrew S. D. Foster.  The included

'transit' radiative transfer code is based on an earlier program of

the same name written by Patricio Rojo (Univ. de Chile, Santiago) when

he was a graduate student at Cornell University under Joseph

Harrington.  Statistical advice came from Thomas J. Loredo and Nate

B. Lust.  



Copyright (C) 2015-2016 University of Central Florida.

All rights reserved.  



This is a test version only, and may not be redistributed to any third

party.  Please refer such requests to us.  This program is distributed

in the hope that it will be useful, but WITHOUT ANY WARRANTY; without

even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR

PURPOSE.  



Our intent is to release this software under an open-source,

reproducible-research license, once the code is mature and the first

research paper describing the code has been accepted for publication

in a peer-reviewed journal.  We are committed to development in the

open, and have posted this code on github.com so that others can test

it and give us feedback.  However, until its first publication and

first stable release, we do not permit others to redistribute the code

in either original or modified form, nor to publish work based in

whole or in part on the output of this code.  By downloading, running,

or modifying this code, you agree to these conditions.  We do

encourage sharing any modifications with us and discussing them

openly.  



We welcome your feedback, but do not guarantee support.  Please send

feedback or inquiries to:  

Patricio Cubillos   

Jasmina Blecic   

Joseph Harrington   



or alternatively,  

Joseph Harrington, Patricio Cubillos, and Jasmina Blecic  

UCF PSB 441  

4111 Libra Drive  

Orlando, FL 32816-2385  

USA  



Thank you for testing BART!  



### BART Development Plan



0. Fully understand Pato's code (all, esp. Patricio, Jasmina) (DONE!)

1. Split transit code into initialization and loop (Patricio, Andrew) (DONE!)

2. Drive loop with arbitrary parameters (Patricio)

3. Interface transit code with MC driver (Jasmina, Patricio) (READY for testing)

4. First test: H2O-only, transit, constant abundances, constant T(p)

   (good enough for NESSF!  15 Jan)

5. Upgrades required to publish (do in any order):

   many molecules' line lists (Patricio)

   eclipse geometry (Jasmina) (READY for tests)

   CEA initial conditions/constant scaling (Jasmina) (READY for tests)

   Madhu T(p) (Jasmina)

6. Validation vs. Madhu

   (can do science now)

7. Performance upgrades:

   correlated-k

   multiple chains from one node driving single RT code

   multiple chains from one node driving multiple RT codes

   multiple chains from multiple nodes driving multiple RT codes

8. Science upgrades:

   flux-balanced layers (a la Burrows)

   constant abundances/T(p) throughout atmosphere

   line-list-difference tests

   dayside map

   phase curve

   dayside map + phase curve



Test after each upgrade, record output, compare output of next upgrade

with upgrade turned off to previous output to make sure we didn't

wreck anything.