Running SPECIES

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:

Command	Default	Description
-starlist	any_star	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	all	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.
-ncores	3	Number of cores to use.
-output_format	Both	Format of the output file. Choices are [Both, ASCII, FITS].
-output	summary_output	Name of the output file, without extension.
-hold_params		Option to set the atmospheric parameters to a certain value.
-file_params	any_file.txt	Name of the file with the values for the parameters to hold, relative to the current directory. Will be used only if -hold_params was activated.
-set_boundaries		Option to change the boundaries of the atmospheric parameters.
-file_with_boundaries	any_file.txt	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.
-no_error		Option to avoid the computation of uncertainties to the atmospheric parameters.
-no_debug		Option to avoid the creation of a debug file for each star, where the details of the computation will be stored.
-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.
-file_colors	any_file.txt	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. The coordinates will be taken from the fits header, or can be stored in a file and given by the user using the -file_coords option.
-file_coords	any_file.txt	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.
-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.
-age_limits	None	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), and with both limits separated by a comma.
-path_spectra	./Spectra/	Path to the directory containing the spectra. It has to be relative to the path of SPECIES, or the absolute path.
-columns	All	Columns to include in the output. The name of the star, instrument and exception will always be included.
-giant		If the star, or list of stars, are considered to be giants. 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	./isochrones/	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.
-path_ew	./EW/plots_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.
-skip_mass		Skip the mass, radius, age, photometric logg, and luminosity computation. Usually done to reduce computation time.
-no_rv		Disable restframe correction.
-skip_vsini		Skip the vsini and vmac computation.
-only_EW		Compute only the equivalent widths, skipping the derivation of the stellar parameters.
-linelist	linelist.dat	Name of the file with the FeI and FeII linelist. 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.
-linelist_ab	lines_ab.dat	Name of the file with the element abundances linelist. 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.
-refit		Recompute the equivalent widths.
-plot_mass		Generate the plots from the isochrone interpolation (see Running SPECIES: Output files).
-minimization	downhill_simplex	Minimization method used for the estimation for the atmospheric parameters. Choices are downhill_simplex or per_parameter. 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	linearregression	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. 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