shbhuk / steparsyn

SteParSyn is an automatic code used to infer stellar atmospheric parameters using the spectral synthesis method.

You need to install the following python packages to run SteParSyn (e.g. using pip):

numpy scipy matplotlib astropy extinction emcee tqdm celerite george pygtc

The repository contains the following programs:

- SteParSyn.py:  the main code
- convsyn.py:    convolution code
- readstats.py:  reads the Markov chains
- runone.sh:  it calls SteParSyn.py
- runall.sh:  it calls runone.sh 
- readone.sh: it calls readstats.py 
- readall.sh: it calls readone.sh 

To install the code: clone the repo, install the dependencies, create missing dirs ... :

$  git clone https://github.com/hmtabernero/SteParSyn 
$  pip3 install --user numpy scipy matplotlib astropy extinction emcee tqdm celerite george pygtc
$  cd SteParSyn
$  mkdir eSPECTRA BINOUT PLOTS GRIDS

Download the synthetic grid (Fe_MARCS.bin) from https://drive.google.com/file/d/1pkHVbj5rNvONJSqlMO4IvhW0UBN3Jvxf/view?usp=sharing

You should put it in the folder GRIDS

Give permissions to programs:

$ chmod +x *sh

Relevant directories:

- GRIDS: here you should put the grid of synthetic spectra 
- MASKS: line masks files
- RANGES: your range files
- CONFIG: here you can control the priors and which parameters to fix, priors, etc
- OPT:   option files (iterations, number of chains, ...)
- SPECTRA: input spectra 
- eSPECTRA: best fit spectra (in ascii)
- BINOUT: pickle files containing the MCMC sampling
- PLOTS: corner plots 

The repo contains an example to compute the stellar atmospheric parameters of a solar spectrum. To run the example:

$ ./runall.sh

To get the results:

$ ./readall.sh

If you want to analyse your own data you need to do as follows (I am assuming that the name of your star is "sun_vesta")

- Provide a txt file containing: wavelengths, fluxes, and its uncertainities (same as SPECTRA/sun_vesta.txt)
- Create a mask file with: line names, line centre, mask centre, and mask width (same format as MASKS/sun_vesta_masks.txt)
- Generate an option file with your parameter options: limits, priors, etc. (You can use CONFIG/sun_vesta.conf as is)

Add the following line to runall.sh:

./runone.sh sun_vesta hermes MCMC

Add also this line to readall.sh

./readone.sh sun_vesta 

I will write a more complete manual in the near future.

Finally, please cite the SteParSyn paper if you use it in your reasearch, you can find it here: https://ui.adsabs.harvard.edu/abs/2022A%26A...657A..66T/abstract

If you have any doubts please do not hesitate to e-mail me.