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Running SPECIES: Output files

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Maritza Soto edited this page Sep 18, 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.

\item plots CMD + distribution: These plots show the position of the star in the logg vs $T_{eff}$ diagram, using the values already computed by SPECIES. The lines represent isochrones with the same metallicity as our star, but with different masses. The black line is the isochrone corresponding to the mass obtained in SPECIES. The other panels show the distribution of mass, age, and photometric logg obtained. These plots are found in \verb+dotter_isochrones/plots/starname_inst_CMD_dist.pdf+

\item plots distribution: These plots show the distribution of mass, age and photometric logg found by SPECIES. The blue lines are the median for each distribution. The correlation between each quantity is also shown. These plots are found in \verb+dotter_isochrones/plots/starname_inst_mass_age.pdf+

\end{enumerate}

Final output

This file contains the final values for the parameters computed by SPECIES. It can be found in the \verb+output/+ directory, under the name and extension provided by the user. It has the following columns:

\begin{enumerate} \item \verb+Starname+ \item \verb+Instrument+ \item \verb+[Fe/H]+ \item \verb+err_[Fe/H]+ \item \verb+Temperature+ \item \verb+err_T+ \item \verb+logg+ \item \verb+err_logg+ \item \verb+vt+ \item \verb+err_vt+ \item \verb+nFeI+ \item \verb+nFeII+ \item \verb+exception+ \item \verb+vsini+ \item \verb+err_vsini+ \item \verb+vmac+ \item \verb+err_vmac+ \item[18-51.] \verb+[M/H]+, \verb+e_[M/H]+, \verb+nM+ \item[52.] \verb+exception_Fe+ \item[53.] \verb+exception_Ti+ \item[54.] \verb+[FeI/H]+ \item[55.] \verb+[FeII/H]+ \item[56.] \verb+Mass+ \item[57.] \verb+err_mass+ \item[58.] \verb+Age+ \item[59.] \verb+err_age+ \item[60.] \verb+Photo_logg+ \item[61.] \verb+err_photo_logg+ \item[62.] \verb+Radius+ \item[63.] \verb+err_radius+ \item[64.] \verb+use_Tc+ \item[65.] \verb+use_vt+ \item[66.] \verb+err_vt2+ \item[67.] \verb+err_T2+ \end{enumerate}

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:

\begin{enumerate} \item \verb+MOOG/abfind_starname_inst.par+ \item \verb+MOOG/abfind_starname_inst_2.par+ \item \verb+atm_models/starname_inst_n.atm+ \item \verb+output/starname_inst_out.test+ \item \verb+output/starname_inst.test+ \item \verb+MOOG_linelist/lines.starname_inst.ares+ \item \verb+MOOG/abfind_starname_inst_ab.par+ \item \verb+MOOG/abfind_starname_inst_ab_2.par+ \item \verb+atm_models/starname_inst_ab.atm+ \item \verb+output/starname_inst_ab_out.test+ \item \verb+output/starname_inst_ab.test+ \item \verb+MOOG_linelist/lines.starname_inst_ab.ares+ \end{enumerate}

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