FASMA 2.0

Stellar spectral analysis package.

FASMA delivers the atmospheric stellar parameters (effective temperature, surface gravity, metallicity, microturbulence, macroturbulence, and rotational velocity) based on the spectral synthesis technique. The principle of this technique relies on the comparison of synthetic spectra with observations to yield the best-fit parameters under a χ² minimization process. FASMA 2.0 is now updated to deliver also chemical abundances of 13 elements (Li, Na, Mg, Al, Si, Ca, Sc, Ti, V, Cr, Mn, and Ni).

The python code runs with python 3 and is wrapped around the spectral synthesis package in fortran: MOOG version 2019 (Sneden et al. 1973) that we plan to update with the latest releases.

The spectral synthesis technique requires model atmospheres for the calculation of the synthetic spectra by MOOG which is provided with FASMA. FASMA includes two grids of models in MOOG readable format, Kurucz and marcs that cover the parameter space for both dwarf and giant stars with metallicity limit of -5.0 dex.

Contact here for bugs: maria.tsantaki@inaf.it

Installation

Installing FASMA requires 2 simple steps.

1) Run the installation script install_fasma.sh, in the FASMA-synthesis folder, in order to unzip the model atmospheres and install MOOG (MOOG uses gfortran, f77, or g77 compilers). During this installation, a recent version of gfortran is required and the user will be asked about system requirements: 'rh64' for 64-bit linux system, 'rh' for 32-bit linux system, 'maclap' for mac laptop, 'macdesk' for mac desktop.

sh $ ./install_fasma.sh

2) Then install FASMA with pip: sh $ pip install .

Or, if you do not have sudo access, replace the pip command with: sh $ pip install --user .

A list of basic python packages will be installed automatically with pip (see requirements).

To uninstall FASMA:

sh $ pip uninstall FASMA

Usage

FASMA by the configuration file

FASMA is so easy. You can run FASMA from the terminal by configuring the options in the config.yml file and then run in the working directory:

sh $ fasma

If the configuration file is called something else (e.g. congig.yml), then run:

sh $ fasma config.yml

FASMA produces a log file, fasma.log, which catches errors in order to inform the user.

FASMA with scripts

For large lists of stars, it is preferable to use FASMA inside scripts. The configuration options are inserted from a dictionary. The main functions to use is FASMA() and the result() to obtain the output.

```python FASMA(cfgfile='config.yml', overwrite=None, **kwargs)

Input

cfgfile : str Configuration file (default: config.yml) overwrite : bool Overwrite the synthresults.dat file (default: False) **kwargs : dict Options to overwrite the default configuration options

Output

synthresults.dat : file Easy readable table with results (tab separated) ```

```python result()

Output

result : dict output parameters in dictionary ```

The expected output dictionary of result() includes the following:

python if 'element' is True: 'linelist': str 'observations': str 'teff': float 'logg': float 'feh': float 'vt': float 'vmac': float 'vsini': float 'element': str 'abund': float 'erabund': float 'chi2': str 'time': int 'model': str 'resolution': int 'snr': int 'spectrum': { 'wave' : float, 'flux' : float}

python if 'minimize' is True: 'linelist': str 'observations': str 'teff': float 'erteff': float 'logg': float 'erlogg': float 'feh': float 'erfeh': float 'vt': float 'ervt': float 'vmac': float 'ervmac': float 'vsini': float 'ervsini': float 'chi2': float 'time': int 'model': str 'resolution': int 'snr': int 'spectrum': { 'wave' : float, 'flux' : float}

The above functions can be used as in this example:

```python from FASMA import FASMA

options = {'observations': '/home/FASMA-synthesis/FASMA/spectra/Sun_HARPS.fits', 'minimize': True, 'plot':True} driver = FASMA(**options) result = driver.result() feh = result['feh'] ```

The input options are presented in the next section and have the save terminology as in the configuration file. The result is a dictionary with the final parameters which are saved to a file (synthresults.dat or synthresults_elements.dat).

Configuration file

The complete list of options of the configuration file has the following format. These are the default values:

yaml star: teff: 5777 logg: 4.44 feh: 0.0 vmac: 3.21 vsini: 1.9 vt: 1.0 MOOGv: 2019 damping: 1 element: False fix_feh: False fix_logg: False fix_teff: False fix_vmac: False fix_vsini: False fix_vt: False intervals_file: 'intervals.lst' limb: 0.6 linelist: 'linelist.lst' minimize: False model: 'apogee_kurucz' observations: False plot: False plot_res: False refine: False resolution: null save: False snr: null step_flux: 3.0 step_wave: 0.01

The configuration file (yaml format) is space sensitive and it can include only the values which are other than the defaults. The user can check if the format is correct here. This file must be in the folder where FASMA runs.

There are various configuration combinations depending on what the user wants. A mandatory requirement is to insert the complete path of the line list and the interval file. The option Number 2 below is recommended for the parameter determination.

1) This is the simplest option for FASMA where a synthetic spectrum is created with solar values and plotted. The rest options not listed are set to default.

yaml star: linelist: /home/FASMA-synthesis/FASMA/rawLinelist/linelist.lst intervals_file: /home/FASMA-synthesis/FASMA/rawLinelist/intervals.lst

The default line list is in the rawLinelist folder already provided within FASMA.

2) For a given line list select your options, e.g.:

yaml star: linelist: /home/FASMA-synthesis/FASMA/rawLinelist/linelist.lst intervals_file: /home/FASMA-synthesis/FASMA/rawLinelist/intervals.lst fix_vmac: true fix_vt: true minimize: true refine: true observations: /home/FASMA-synthesis/FASMA/spectra/Sun_HARPS.fits resolution: 115000 plot: true

This example indicates that for the observed spectrum Sun_HARPS.fits with resolution 115000, FASMA will initialize the minimization process starting from solar values, keeping the parameters vmac and vt fixed and using the refine option (see below). This option was used to derive parameters in Tsantaki et al. (2018). The spectral regions for the synthesis are defined in the intervals.lst file with the option intervals_file. The final spectrum will be plotted. For the not listed options, FASMA uses the default ones.

3) For a given line list and a set of initial values, a synthetic spectrum is creared, saved in the results folder, and plotted.

yaml star: teff: 5777 logg: 4.44 vmac: 3.21 vsini: 1.9 vt: 1.0 linelist: /home/FASMA-synthesis/FASMA/rawLinelist/linelist.lst intervals_file: /home/FASMA-synthesis/FASMA/rawLinelist/intervals.lst resolution: 115000 plot: true save: true 4) This option will deliver the chemical abundance of Ti but can be adopted for any of the provided elements (Li, Na, Mg, Al, Si, Ca, Sc, Ti, V, Cr, Mn, Ni). Note that for this option the line list and intervals are different than for the stellar parameters. The options minimize and element contradict each other.

yaml star: teff: 5777 logg: 4.44 vmac: 3.21 vsini: 1.9 vt: 1.0 element: 'Ti' linelist: /home/FASMA-synthesis/FASMA/rawLinelist/elements.lst intervals_file: /home/FASMA-synthesis/FASMA/rawLinelist/intervals_elements.lst observations: /home/FASMA-synthesis/FASMA/spectra/Sun_HARPS.fits resolution: 115000 plot: true save: true 5) For multiple stars:

yaml HD105: element: 'Ti' linelist: /home/FASMA-synthesis/FASMA/rawLinelist/elements.lst intervals_file: /home/FASMA-synthesis/FASMA/rawLinelist/intervals_elements.lst observations: /home/FASMA-synthesis/FASMA/spectra/HD105_HARPS.fits resolution: 115000 HD1156: element: 'Ti' linelist: /home/FASMA-synthesis/FASMA/rawLinelist/elements.lst intervals_file: /home/FASMA-synthesis/FASMA/rawLinelist/intervals_elements.lst observations: /home/FASMA-synthesis/FASMA/spectra/HD1156_HARPS.fits resolution: 115000

Default Options

The default options of FASMA can be changed in the configuration file config.cfg or inserted in the FASMA() function.

1) The model atmospheres included in FASMA are: apogee_kurucz, and marcs. yaml model: marcs

2) The version of MOOG currently is 2019 but can easily updated to newer versions. This is relevant only if the output files change for future updates of MOOG. yaml MOOGv: 2019

3) If save is True, the output synthetic spectrum is saved in the folder results. The output is saved in a .spec format and is read with the astropy.io fits module.

yaml save: False

4) If any of these options is set to True, then they are fixed during the minimization process. yaml teff: False logg: False feh: False vt: False vmac: False vsini: False

5) These are plotting options of the synthetic/observed spectra (plot) and of their residuals in case of minimization (plotres). ```yaml plot: False plotres: False ```

6) The damping option of MOOG to deal with the van der Waals broadening. The acceptable values are: 0, 1, 2. yaml damping: 1

7) The wavelength step for the synthetic spectrum to be created (stepwave) and the flux limit to consider opacity distributions from the neighboring lines (stepflux), both measured in Angstrom. These are the same options in MOOG. yaml step_wave: 0.01 step_flux: 3.0

8) If minimize appears in the options, the minimization process will start to find the best-fit parameters for the observed spectrum, therefore observations must be included in the options. yaml minimize: False

9) The refine option performs corrections on the derived parameters after the minimization for a more detailed analysis. After a first run, a second minimization starts with optimized microturbulence and macroturbulence values according to the parameters of the first run. Refine will also remove bad flux points and missing lines. yaml refine: False

10) The name of the spectrum is given here. The full path of the spectrum should be given. Note that the spectrum has to be in a specific format (see below). yaml observations: False

11) These files contain the lines with their atomic parameters (linelist.lst) and the intervals of the synthesis (intervals.lst). FASMA already has specific lists in the rawLinelist folder. The complete path should be given.

yaml linelist: linelist.lst intervals_file: intervals.lst

12) The signal-to-noise (SNR) value of the observed spectra can be given by the user (optional). It is used for the normalization process. Otherwise, the SNR is calculated by the PyAstronomy function within FASMA. yaml snr: null

13) The resolution of the synthetic spectrum or the resolution of the observed spectrum. This value is necessary when minimization is on. yaml resolution: null

14) The limb darkening coefficient for the vsini broadening calculations. It is set fixed to 0.6 but can have different values depending on luminosity class. yaml limb: 0.6

15) This option will start the minimization process to derive the chemical abundance of a specific element. The element has to be set from this list: Li, Na, Mg, Al, Si, Ca, Sc, Ti, V, Cr, Mn, Ni. In this case the line list and intervals are different than the standard derivation of the stellar parameters and should be changed to elements.lst and intervals_elements.lst, respectively located in the rawLinelist folder. For the derivation of the chemical abundance the minimize option should be False. yaml element: False

Inputs

Input spectra

The main input is the stellar spectrum which has to be in a specific format.

1) a text file (.dat or .txt) with 2 columns for the wavelength and flux.

2) a fits file (.fits). FASMA reads fits files from the ESO archive (ESO SDP 1D spectrum) and also 1D files which include the key words 'CRVAL1' and 'CDELT1' in their header.

3) a table fits format (.spec). This is the format FASMA saves the output synthetic spectra if requested.

FASMA assumes the wavelength is in Angstrom and that the spectrum has been corrected for radial velocity shifts. This is an example on how to correct for such RV shifts. We advice the use of the fits format as reading them is much faster than the text files.

Input line lists

1) linelist.lst -- the line list for the derivation of stellar parameters as tested in Tsantaki et al. (2018) 2) intervals.lst -- the list of the spectral regions for the spectral synthesis 3) elements.lst -- the line list for the derivation of the chemical abundances from VALD 4) intervals_elements.lst the lines of the specific elements where the intervals are calculated from Adibekyan et al. (2015) and Delgado-Mena et al. (2015)

The user can adapt the above files (tab separated), such as adding more elements to the line lists.

Outputs

The delivered stellar parameters are saved in the synthresults.dat and the chemical abundances in the synthresults_elements.dat.

For a set of parameters (Teff, logg, [M/H]), a model atmosphere is obtained by interpolating from the model grid. The model atmosphere is created in the out.atm file. It is a tabulated form of the basic physical properties (temperature, pressure, etc.) at each layer of the atmosphere.

The raw synthetic spectrum without any broadening created by MOOG is saved in summary.out.

The linelist.moog contains the line list in the format readable by MOOG and result.out is a summary of all the parameters used for the synthesis of the spectrum.

The MOOG configuration file is batch.par and its options are set from the config.yml file.

Documentation

This content is also included here as a manual for easy access. Moreover, we provide documentation on the functions at docs folder where the user can build the documentation with make html .

Testing

There are some basic tests to check if the installation is correct in FASMA/test for the solar spectrum. Run python test_FASMA.py and check the output files for the expected solar parameters.

Contributing

FASMA needs input to improve. Users are welcome to ask questions, propose a new features, or report a bugs either by opening an issue on GitHub (preferably) or contact here: maria.tsantaki@inaf.it

AUTHORS

• M. Tsantaki
• D. Andreasen
• G. Teixeira