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Running SPECIES

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Maritza Soto edited this page Sep 18, 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. 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

  • -vt_hold: Option to set the microturbulence = 1.2 km/s when there is no convergence in the atmospheric parameters. It is only done when a set value for the microturbulence wasn't given previously, or the number of Fe I lines detected for the spectrum is larger than 10.

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
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