Running SPECIES: Output files

\section{Spectral files}

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

\begin{enumerate} \item Combined spectra: These are the files created when it is necessary for SPECIES to combine spectral orders into only one spectrum. This is done for the feros, uves, and hires data. For the case of FEROS, the combined spectra will still be called \verb+starname_feros_orders.fits+, and the original file will adopt the name\ \verb+starname_feros_orders_original.fits+. For UVES and HIRES, the combined spectra will be called \verb+starname_uves.fits+ and \verb+starname_hires.fits+, respectively. These files will be stored in the \verb+Spectra/+ directory.

\item Restframe spectra: This is the spectra corrected to restframe, and corresponds to the input given to ARES. 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\AA, for the G2 spectral type mask. The files are called \verb+starname_inst_res.fits+, and are stored in the \verb+Spectra/+ directory.

\item 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 \AA) 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 \verb+Spectra/plots_ccf/+

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

\end{enumerate}

\section{Equivalent width files}

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

\begin{enumerate} \item EW for the iron lines: File with the fit parameters and EW for the iron lines from the file \verb+linelist.dat+. They are called \verb+starname_inst.ares+, and are stored in \verb+EW/+.

\item EW for the atomic abundances: File with the fit parameters and EW for the spectral lines from the file \verb+lines_ab.dat+, which are used to compute the abundance of several elements. They are called \verb+starname_inst_ab.ares+, and are stored in \verb+EW/+.

\item Plot spectra: Plots of the 1D spectra for each star, with red lines showing the position of the lines used to obtain the EW. The inset shows the position of the H-alpha line. They are stored in the directory \verb+EW/plots_spectra/+

\end{enumerate}

\section{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 \verb+debugging_files/+

\section{MOOG} These files correspond to the MOOG output, when assuming an atmospheric model with the correct parameters. They correspond to:

\begin{enumerate} \item \verb+output/MOOG_output_files/starname_inst_out.test+ \item \verb+output/MOOG_output_files/starname_inst.test+ \item \verb+output/MOOG_output_files/starname_inst_ab_out.test+ \item \verb+output/MOOG_output_files/starname_inst_ab.test+ \end{enumerate}

\section{Rotational and macroturbulent velocity}

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

\begin{enumerate} \item \verb+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.

\item \verb+starname_inst_vsini_new.pdf+: The the line fits, created with the final values for $v\sin i$ and $v_{mac}$. 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.

\item \verb+starname_inst_vsini_paper.pdf+: Combination of the two previous files, for the purposes of including it in a publication. \end{enumerate}

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

\iffalse These files correspond to plots created during the computation of the broadening velocity, along with the macroturbulence and rotational velocities. They are all stored in \verb+output/plots_broadening/+

\begin{enumerate} \item Plots broadening: This plot consist of three panels. The top one showns the CCF between our restframe spectra and a binary mask, which is selected using the computed temperature. The middle panel is the Fourier Transform performed on the CCF, and the vertical blue line represents the frequency in which the first minimum is reached. The bottom panel shows an histogram the broadening velocity computed for each line of the spectra, after applying a Fourier Transform to the line. The red line shows the Gaussian fit found to the distribution, with its parameters ($\mu$, $\sigma$) listed.

\item Plots macroturbulence and rotational velocities: These plots show the probable values of the rotational and macroturbulence velocities, given the broadening velocity found previously. The colormap represents $1/dif$, with $dif$ the difference between $v_{mac}^2$ + $v\sin i^2$ and $v_{broad}^2$ for each set of $v_{mac}$ and $v\sin i$ in the grid. The white point is the final estimate for the velocities. These files are stored in\ \verb+output/plots_broadening/starname_inst_vsini.pdf+ \end{enumerate} \fi

\section{Mass and age calculation}

These are files produced during the computation of the mass, age, and photometric logg.

\begin{enumerate} \item Chain files: These files contain the chains performed to obtain the mass, age and photometric logg. Before performing new chains, SPECIES looks for these files and uses the already computed information. The files are in\ \verb+dotter_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}

\section{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}

\section{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}