Skip to content

Running SPECIES: Output files

Jump to bottom
Maritza Soto edited this page Sep 21, 2020 · 4 revisions

Spectral files

These are the files that involve working with the spectra alone, before computing the equivalent width for the spectral lines.

  • Combined spectra: These files can be created when the -make1D option is used. They will be corrected to restframe. They will be stored in the Spectra/ directory, under the name starname_inst_res_1d.fits.

  • Restframe spectra: This is the spectra corrected to restframe, and corresponds to the input used for the equivalent width computation. The velocity correction to apply is computed by performing a cross-correlation function (CCF) between the spectra and a binary mask, consisting on all the lines between 5500 and 6050 A, for the G2 spectral type mask. The files are called starname_inst_res.fits, and are stored in the Spectra/.

  • Plot CCF: These plots show the CCF between the spectra and the binary mask, used to correct the spectra to restframe. The top panel shows three spectral lines (6021.8, 6024.06 and 6027.06 A) with its position in the original spectra (grey), and in the corrected spectra (black), along with three vertical lines representing the correct restframe position (red). The bottom panel show the corresponding CCF, with its computed velocity. They are stored in Spectra/plots_ccf/.

  • Plot lines: These plots show four spectral lines (6021.8, 6024.06, 6027.06 and 6562.8 A) in the restframe-corrected spectrum, along with red lines corresponding to their restframe position. They are stored in Spectra/plots_fit/.

Equivalent width files

These are the files produced by the EWComputation module, with the equivalent width (EW) information.

  • EW for the iron lines: File with the EWs for the iron lines (default file with the linelist is Spectra/linelist.dat, otherwise specified using the -linelist option). The files contains five columns: Wavelength, EW, EW_50, EW_84_50, EW_50_16. The last three columns are taken from the distribution of equivalent widths, and correspond to the median, 84th percentile - 50th, and 50th-16th percentile (more information can be found in Soto et al. 2020). The files are called starname_inst.txt, and are stored in EW/.

  • EW for the atomic abundances: File with the EWs for the spectral lines from the abundances linelist (default file is Spectra/lines_ab.dat, otherwise specified using the -linelist_ab option). They follow the same format as the file for the iron lines, and are stored in EW/starname_inst_ab.txt. file

  • Fit plots: Plots of the fits made to each line. Each panel will be composed of two panels, with the top one showing the continuum fit and the points used to estimate the continuum, and the bottom showing the line fit. The estimated EW, and Gaussian parameters estimated for each line are given in the text. Generated only if the -plotEW option is used, and are stored in EW/plots_EW/.

  • Error plots: Plots of the EW distribution obtained when changing the fit parameters according to their respective uncertainties. Generated only if the -plotEW option is used, and are stored in EW/plots_EW/.

Debugging files

These files describe each step of the parameters computation. They are useful for the cases when there is a problem with the code, and one wants to know in which part of the computation it happened. SPECIES is intended to be completely automatic, therefore it is possible to follow the computation for each star by studying the debugging files. These are stored in debugging_files/.

MOOG

These files correspond to the MOOG output, when assuming an atmospheric model with the correct parameters. These are:

  • output/MOOG_output_files/starname_inst_out.test
  • output/MOOG_output_files/starname_inst_ab_out.test

A plot showing the correlations between the iron abundance, excitation potential, and reduced equivalent width, and the difference between the abundances of FeI and FeII, is also generated and is stored in output/MOOG_output_files/starname_inst.pdf.

Rotational and macroturbulent velocity

These are plots created during the computation of the rotational and macroturbulent velocity. They are located in plots_broadening/.

  • starname_inst_a_vsini.pdf: Shows the change of S with the abundance (left panels) and rotational velocity (right panels). Each line represents a different line.

  • starname_inst_vsini_new.pdf: The the line fits, created with the final values for vsini and vmac. The panels with red background are the lines that were not included in the final values, due to them not representing a good fit to the observed line.

  • starname_inst_vsini_paper.pdf: Combination of the two previous files, for the purposes of including it in a publication.

For a better understanding of the quantities being plotted please refer to the project paper.

Physical parameters computation

These are files produced during the computation of the physical parameters through isochrone interpolation.

  • Chain files: These files contain the model chains obtained from the isochrone interpolation. They're usually rewritten each time SPECIES is run for a certain star, unless the -mass_from_file option is used, in which case the model is read from them. The files stored in isochrones/starname_inst_samples.h5.

  • Distribution plots: These plots show the final distribution for the parameters in the isochrone models, after doing the interpolation, along with their correlations between each other. Three plots are generated here: 1) corner_derived showing Teff, logg, age, mass, radius, distance, eep, and logL, 2) corner_physical showing mass, radius, age, Teff, logg, feh, distance, AV, and 3) corner_observed showing the distribution of the input parameters to the model. Blue lines mark the input values. All the plots are located in isochrones/plots/starname_inst_{corner_derived, corner_physical, corner_observed}.pdf.

  • H-R plot: Shows the H-R diagram obtained for each star, based on the isochrone interpolation results. The color line represents the most probable model, with the gray lines representing other models obtained from the distribution of the parameters. These plots are located in isochrones/plots/starname_inst_isochrones.pdf.

Final output

Files containing the final values (and uncertainties) for the parameters computed by SPECIES. They can be found in the output/ directory. If the ascii format is chosen (by using the -output_format={Both, ASCII}) then two files will be created: 1) summary file with only a few columns (named output_name.dat), and 2) the full output with all the columns (named output_name_full.dat).

The output parameters are (italic names refer to the columns included in the summary ascii file):

  • Starname
  • Instrument
  • RV: Radial velocity used to correct the spectrum to restframe (in km/s).
  • [Fe/H], Temperature, logg and vt: Atmospheric parameters (plus their uncertainties) estimated from the equivalent widths of FeI and FeII.
  • nFeI and nFeII: Number of iron lines (neutral and ionized) used in the atmospheric parameter computation.
  • exception: 1 or 2. Flag indicating if the atmospheric parameters were correctly estimated (1) or not convergence was reached (2). If exception is 2, the estimation of the physical parameter, and rotational and macroturbulence velocity won't be performed.
  • vsini and vmac: Rotational and macroturbulence velocity (plus their uncertainties) in km/s.
  • Mass, Age, iso_logg, Radius, logL, eep: Physical parameters, representing the median value of each distribution. For each value, the upper (err_parameter1) and lower (err_parameter2) uncertainties, obtained from the parameter distributions, are also given. For the definition of the eep parameter, please refer to Soto et al. 2020. Mass, Radius, and logL are given in solar units. Age is in Gyr units.
  • P_preMS, P_MS, P_RGB, P_HB, P_postHB: Probability of the star being in the pre-main sequence, main sequence, red giant branch, horizontal branch (or red clump), and post horizontal branch, respectively. For more details, please refer to Soto et al. 2020.
  • use_Tc, use_vt, use_iso_logg: Indicates whether the temperature from photometry, a set value for the microturbulence, or the isochrone-derived logg were used for the computation of the atmospheric parameters.
  • T_photo, err_T_photo, T_photo_relation: Temperature obtained from photometric relations, and the relation used.
  • Av: Extinction estimated for the star.
  • El, e_El, nEl: Abundances for each individual element El, and number of lines used for the computation. These columns are not generated if the -no_abundance key was used, or if no appropriate line list was given.

It is also possible to choose the columns to output using the -columns option.

Temporary files

These are files created and used by SPECIES during the computation of the parameters, but should be deleted once the final results have been found. These are:

  • MOOGFEB2017/{ab_alias, ab_alias_2, alias_synth, abfind_alias_v, abfind_alias_v_2, ab_alias_ab, ab_alias_ab_2}.par
  • atm_models/{alias, alias_ab, alias_v}.atm
  • output/{alias, alias_out, alias_ab, alias_ab_out, alias_l, alias_li, alias_s, alias_sn}.test
  • MOOG_linelist/{lines.alias, lines.alias_ab, lines.alias_v}.txt
  • Spectra/alias_n.dat

alias is a 6-character random string, used as an alias for the starname during the computation. The alias used for each star is included in the debugging file for each star. n is just an integer.

In the cases where an error occurs during the computation, SPECIES will just skip the star but the temporary files will not be deleted. You can then just manually delete them.

Clone this wiki locally