How to run BART_init and what to expect

2014 August 4th, Jasmina Blecic jasmina@physics.ucf.edu Original version

The BART_init folder contains source files for generating initial conditions 
for BART. Before running the code, the user is asked to make a working 
directory and copy the BART.cgf file and the tep file inside the directory. 
The location of the tepfile needs to be defined in the TEA_config.py inside 
the TEA directory, as well.
The code is executed with the simple command ../BART_init.py. The code will 
take the information from the BART.cfg file and perform the following:

1. Read the BART.cfg file and store the parameters.
2. Make a subdirectory with the current date and time to place all generated
   files.
3. Copy the BART.cfg and tep file to the current date and time directory.
4. STEP-1 => Based on the user choose of the top and bottom atmospheric pressure
   and log or lin scale, it will generate a pressure file with the desired name
   and the extension .pres, <NAME>.pres. The function makeP.py is called.
5. STEP-2 => Based on the user choice of solar, non-solar, swapped or 
   non-swapped elemental abundances, it will generate an abundances file with 
   the desired name and extension .abn, <NAME>.abn. The function makeAbun.py 
   is called.
6. STEP-3 => Based on the user choice of the initial PT parameters it will
   generate an initial PT profile. The plots will be produced and placed in 
   the current date and time subdirectory. The user can check the plots and 
   accept or decline the PT profile. The code will wait for the user to press
   return (enter) to continue, or the CtrC to break. To change the PT profile,
   the user needs to terminate the code and choose different set of initial PT
   parameters and run it again until satisfied. The code takes the tepfile, 
   read the information needed, and calls the plot_initialPT() function placed
   inside the InitialPT.py module.
7. STEP-4 ==> The code will now generate the pre atmospheric file. The user 
   chooses the name of the output, and input and output species. User must 
   choose the names that TEA code can recognize (read install_guide.txt placed 
   in the TEA/TEA_doc subdirectory).
8. STEP-5 ==> The TEA code is called to calculate thermochemical equilibrium
   abundances. The final output file is placed in the current date and time
   directory with the name user chooses and the extension .tea.

The initial conditions, pressure, temperature, radii, and abundances are stored
in the final atmospheric file <NAME>.tea. This file is to be used by BART.

The BART_init directory contains the following source files:

BARTinit.py *           # main module
makeP.py *              # pressure module
makeABun.py *           # abundances module
makeatm.py *            # TEA pre-atmospheric file generator module 
InitialPT.py *          # initial PT generator module
PT.py                   # PT module containing functions to generate PT profile
reader.py               # tep reader
abundances.txt          # elemental abundances file (Asplund et al. 2009) 
BART.cfg                # BART init configuration file
ReadMe                  # this file

* these files must be executable

The files generated by this code and placed in the current date and time
directory are:

pressure_file.pres
abundances_file.abn
pre_atm_file.atm
initialPT.png
initialPTSmoothed.png
final_TEA_output.tea

Files copied from the source directory to the current date and time directory:
BART.cfg
tepfile_name.tep