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Running SPECIES

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Maritza Soto edited this page Sep 21, 2020 · 7 revisions

In order to execute SPECIES, you need a high resolution echelle spectra, plus other auxiliary files, which will be better explained in the next page.

The Spectra has to be placed in the Spectra/ directory, with the following name format: starname_inst.fits, where inst is the name of the instrument used to obtain the spectra, in non-capital letters.

Once that is ready, along with the auxiliary files (if needed), then execute SPECIES by typing

python SPECIES.py

You can also add or modify some options for SPECIES, by adding them on the command line. These are:

  • -starlist: Name of the stars to use, separated by commas. If the list is too long, retrieve it from inside the code, in the part that says
# List of stars for which to compute the parameters

  • -inst: Names of the instruments you want to use, separated by commas and in non-capital letters. Choices are (all, harps, feros, hires, aat, coralie, uves, lconres). If "all" is included, spectra from all accepted instruments will be used. Default is "all".

  • -ncores: Number of cores to use. Default is 3.

  • -output_format: Format of the output file. Choices are ['Both', 'ASCII', 'FITS']. Default is 'Both'.

  • -output: Name of the output file, without extension. Default is 'summary_output'.

  • -hold_params: Option to set the atmospheric parameters to a certain value. When used, no argument has to be given.

  • -file_params: Name of the file with the values for the parameters to hold. Will be used only if -hold_params was activated.

  • -set_boundaries: Option to change the boundaries of the atmospheric parameters. When used, no argument has to be given.

  • -file_with_boundaries: Name of the file with the boundaries for the atmospheric parameters. Will only be used if -set_boundaries was activated.

  • -no_abundance: Option to avoid the computation of atomic abundances. When used, no argument has to be given.

  • -no_error: Option to avoid the computation of uncertainties to the atmospheric parameters. When used, no argument has to be given.

  • -no_debug: Option to avoid the creation of a debug file for each star, where the details of the computation will be stored. When used, no argument has to be given.

  • -no_check_t: Option to avoid checking the temperature from SPECIES with the one obtained from photometric relations. The temperature from photometry will still be computed, but it won't be compared with the one obtained from SPECIES. When used, no argument has to be given.

  • -file_colors: Name of the file with photometric colors. If they are not given, the colors will be retrieved from Vizier.

  • -use_coords: Option to use the coordinates of the star, instead of its name, to look for the star colors. When used, no other arguments has to be given.

  • -file_coords: Name of the file with the coordinates of the stars (in deg). Used only if -use_coords was activated.

  • -mass_from_file: Option to load the chains created during a previous mass calculation, stored in isochrones/*.h5

  • -no_vt_hold: Do not try to run the computation with vt = 1.2 km/s in the case it does not converge. Default is False.

  • -no_r_iso_logg: Do not use the logg from isochrones interpolation to recompute the atmospheric parameters when there is disagreement with the spectroscopic one. Default is False.

  • -age_limits: Set limits to the parameters space for the stellar age. It has to be in the format log(age), with age in years (not Gyr). Default is None.

  • -path_spectra: Path to the directory containing the spectra. It has to be relative to the path of SPECIES, or the absolute path. Default is ./Spectra/.

  • -columns: Columns to include in the output. The name of the star, instrument and exception will always be included. Default is "All".

  • -giant: If the star, or list of stars, are considered to be giants. Default is False. Not using this option does not mean SPECIES won't work with giant stars, it will still treat a star to be giant if the photometric indices classify it as one or the surface gravity is within the giant star regime. This option just ensures that the star will be treated as a giant from the star.

  • -path_iso: Path to the directory where all the files related to the mass computation will be stored. It has to be relative to the path of SPECIES, or the absolute path. Default is ./isochrones/.

  • -path_ew: Path to the directory where the plots of the equivalent width for all the lines will be stored. It has to be relative to the path of SPECIES, or the absolute path. Default is ./EW/plots_EW/.

  • -skip_mass: Skip the mass, radius, age, photometric logg, and luminosity computation. Usually done to reduce computation time. Default is False.

  • -no_rv: Disable restframe correction. Default is False (restframe correction is performed).

  • -skip_vsini: Skip the vsini and vmac computation. Default is False.

  • -only_EW: Compute only the equivalent widths, skipping the derivation of the stellar parameters. Default is False.

  • -linelist: Name of the file with the FeI and FeII linelist. Default is linelist.dat. The file has to be inside the ./Spectra/ directory, or specified relative to the './Spectra/' directory. If a linelist different from the default one is used, the EWs will be recomputed, unless the -no_EW_recomp option is used.

  • -no_EW_recomp: Do not recompute the EWs when the linelist is different from the default one. Default is False.

  • -linelist_ab: Name of the file with the element abundances linelist. Default is lines_ab.dat. The file has to be inside the ./Spectra/ directory, or specified relative to the './Spectra/' directory. If a linelist different from the default one is used, the EWs will be recomputed, unless the -no_EW_recomp_ab option is used.

  • -no_EW_recomp_ab: Do not recompute the EWs when the element abundances linelist is different from the default one. Default is False.

  • -refit: Recompute the equivalent widths. Default is False.

  • -plot_mass: Generate the plots from the isochrone interpolation (see Running SPECIES: Output files). Default is False.

  • -minimization: Minimization method used for the estimation for the atmospheric parameters. Choices are downhill_simplex or per_parameter. Default is downhill_simplex. It is recommended you do not change this. This option will be removed in future releases of SPECIES, leaving just the downhill_simplex option.

  • -other_instrument: Allow for spectra from other instruments different from the ones listed in the -inst option description.

  • -redo_restframe: Redo the restframe correction. If this option is used, the equivalent widths will be recomputed as well.

  • -read_mode: Mode used to estimate the correlation between the FeI abundance and the line excitation potential and reduced EW, during the atmospheric parameter computation. Choices are linearregression, odr, moog. Default is linearregression. It is recommended you do not change this parameter.

  • -make_1d: Generate the 1D spectrum used to estimate the restframe correction. Has to be used during the first run of a star through SPECIES (before the _res.fits file is created), or in conjunction with the -redo_restframe option.

  • -plotEW: Create the equivalent width plots, showing the continuum normalization and Gaussian fits for each accepted line, plus the uncertainty distribution plots.

For example, if I want to run SPECIES for the star HD10700, using only the HARPS spectra available, the coordinates listed in the fits header, and the output file to be called 'summary_HD10700', then I'd type:

python SPECIES.py -output summary_HD10700 -use_coords -starlist HD10700 -inst harps

If I only want to redo the restframe correction for two stars, generate the 1D spectrum, and compute and plot the EWs using the Spectra/lines_mod.dat linelist for the iron lines:

python SPECIES.py -starlist star1,star2 -redo_restframe -make_1D -linelist lines_mod.dat -only_EW -plotEW
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