Running SPECIES: Input Files

As mentioned previously, the input files needed to run SPECIES are a high resolution echelle spectra (.fits file) and a set of auxiliary files, which are not mandatory.

Input spectra

SPECIES currently accepts spectra from several instruments, mainly HARPS, FEROS, UVES, HIRES, AAT, CORALIE, and LCO-NRES. The files have to be placed in the Spectra/ directory, and are explained as follow:

• HARPS: The HARPS spectra can be retrieved from the Phase 3 data retrieval in the ESO archive. SPECIES uses the s1d fits file, for the A fibre, and consist of the spectra from all the orders already combined. The file has to be called starname_harps.fits. It also accepts spectra reduced using the ceres pipeline. In those cases, the spectra will be divided by orders, which SPECIES will identify and treat the data accordingly (see the FEROS file handling).

• FEROS: The FEROS spectra can be retrieved from the Phase 3 data retrieval in the ESO archive, reduced by the ESO pipeline, or can be reduced data from other pipelines. The difference between both files is that, for the case of the data processed with the ESO pipeline, its format is very similar to the HARPS one, that is, all the orders are already combined. The spectra from other pipelines usually comes with each spectral order separated, in which case SPECIES will combine to create a 1D spectrum, which will be used to estimate the stellar RV and correct it to restframe. When combining the spectral orders, if two consecutive orders overlap in wavelength, then SPECIES will select the data from the red order (that is because the performance of FEROS improves in the red part of the spectrum, increasing the signal-to-noise of the data). The FEROS files has to be called starname_feros.fits.

• UVES: The UVES spectra can be retrieved from the Phase 3 data retrieval in the ESO archive. SPECIES will accept two versions of the data: the full spectrum combined (in which case the file has to be called starname_uves.fits), or with the red and blue parts separated. In the latter case, then SPECIES will take both files and combine the spectra. If there is overlap in wavelength between the red and blue parts, then SPECIES will select the data from the highest signal-to-noise (S/N) part. The files have to be called starname_uves_red.fits and starname_uves_blue.fits.

• HIRES: The HIRES spectra can be obtained from the KOA data archive. The spectra has to be already reduced, and without the iodine cell. Before downloading the files, make sure that the spectra is present in most of the spectral orders. It is not necessary to include the calibration files. SPECIES will combine the spectra from the different spectral orders, taken the data with the highest signal to noise (S/N) for the case when the orders overlap. The resulting spectra will be placed in Spectra/starname_hires.fits. The folder with the files has to be called starname_hires/, and be placed in the Spectra/ directory.

• Other instruments: Spectra from other instruments can be handled by SPECIES, as long as it has been reduced already, and has good spectral coverage within the 5000-6500 A region. Make sure the data is in .fits format, and follows at least one of the following formats: 1) file data showing the flux array in 1D format, and with the header containing the information necessary to construct the wave array, or 2) the wave and flux arrays contained within the data section of the file. In the latter case, the data can be 1D or separated by spectral orders. If there're problems when processing the spectra (usually errors arising from the Spectra.py, Instruments.py, and/or Ccf.py modules), please contact me and I'll try to find the correct format to use.

Auxiliary files

These files contain additional information for SPECIES. They are described as follows:

• file params: This file contains information about the atmospheric parameters, as well as broadening, macroturbulence and rotational velocities. You can specify initial values for the parameters, and whether you want to keep that value uncharged through the computation of not. The file must have a header with the names of the columns, and each column has to be separated by spaces or tabs. They are as follow:

  • Starname: Starname_inst, with inst is the instrument used to obtain the spectra.
  • hold: Name (or list of names) of the parameters you wish to hold to a certain value during the computation. The names have to be comma-limited and with no spaces in between. Accepted names are temperature, metallicity, pressure, and velocity.
  • T, logg, met, micro, vsini, vmac: The values can follow three different formats: 1) only value, 2) value plus uncertainty, in which case for quantities have to be comma-separated and with no spaces in between, or 3) no, in which case no initial value is given. For this last case, make sure that the quantity in not included in the hold string.

Example:

Starname	hold	T	logg	met	micro	vsini	vmac
HD55_harps	temperature,metallicity	4760.1	no	-0.72	1.123	1.38,0.44	2.33,0.54

• file with boundaries: File with the ranges accepted for the atmospheric parameters. The file must have a header with the names of the columns (Starname, temperature, metallicity, gravity, and velocity), and each column has to be separated by spaces or tabs. For each parameters, the upper and lower boundaries have to be given, separated by a comma. If no boundaries are given, replace it with no.

Example:

Starname	temperature	metallicity	gravity	velocity
NG021676	no	no	4.0,5.0	no

• file colors: File with photometric information for each star. The file must have a header with the names of the columns, and each column has to be separated by spaces or tabs. They are as follow:

  • Starname: Name of the star, without the instrument.
  • Extinction: Whether the extinction for each magnitude is computed. In that case, you must specify RA, DEC, and Parallax.
  • Apparent magnitudes: Magnitude in several bands for each star. If no magnitude is known, replace it with no. Magnitudes are: B, V, R, I, J, H, K, Bt, Vt, b, and y.
  • Parallax: value and uncertainty, in mas, separated by a comma.
  • RA and DEC: in degrees.
  • pmRA and pmDEC: Proper motion of the star, in mas/yr. With value and uncertainty, separated by a comma.

Starname	Extinction	B	V	R	I	J	H	K	Bt	Vt	b	y	Parallax	RA	DEC	pmRA	pmDEC
HIP19483	no	6.383	5.442	no	no	4.128	3.588	3.516	no	no	no	no	9.1010,0.1059	62.59383306	-6.923825	-0.091,0.135	-11.616,0.083

• file coords: File with coordinates for each star, in deg. The columns are Starname, RA, and DEC, all separated by spaces or tabs. The file header must include the name of the columns.