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Installation
SPECIES is currently hosted on GitHub, and in order to install it you just need to place the corresponding folder in your preferred location.
Before installing SPECIES, make sure all the necessary files and folders are included. The files are: SPECIES.py, Atmos.py, AtmosGrid.py, AtmosInterpol.py, CalcBroadening.py, CalcErrors_new.py, CalcErrorsGiant_new.py, CalcParams.py, Ccf.py, EWComputation.py, PhotometricRelations_class.py, FindIsochrones.py, Instruments.py, and Spectra.py.
The folders, and its contents, are:
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EW/:plots_EW/ -
MOOGFEB2017/: MOOG files,abfind.par. MOOG_linelist/-
Spectra:linelist.dat,lines_ab.dat,plots_ccf/,plots_fit/. -
atm_models/:atlas9/ -
binary_masks/: G2.mas, K0.mas, K5.mas, M2.mas. debugging_files/-
isochrones/:plots/ -
output/:MOOG_output_files/,coeffs_error_files/ plots_broadening/
SPECIES uses a large number of python packages in order to optimize the calculation of the parameters. Most of them are included in your average python installation, but some of them have to be installed separately. These are:
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numpy(http://www.numpy.org) -
scipy(https://www.scipy.org) -
matplotlib(http://matplotlib.org)
For SPECIES, it is necessary that the default backend for matplotlib is Agg, in order to avoid problems with the multiprocessing package. In order to change that, first locate where your matplotlibrc file is. Do the following:
import matplotlib
matplotlib.matplotlib_fname()and in the matplotlibrc file change the backend:
backend : Agg-
astropy(http://www.astropy.org) -
astroquery(http://astroquery.readthedocs.io/en/latest/) -
PyAstronomy(http://www.hs.uni-hamburg.de/DE/Ins/Per/Czesla/PyA/PyA/index.html) -
isochrones(http://isochrones.readthedocs.io/en/latest/)
We find that with MultiNest/PyMultiNest (http://astrobetter.com/wiki/MultiNest+Installation+Notes) we obtain more accurate results for the mass and age computation than with emcee (http://dan.iel.fm/emcee/current/), therefore we recommend having MultiNest installed in your computer.
After installing isochrones, open your terminal and type:
nosetests isochrones
That should download the grid data. In case it gets interrupted, delete the ~/.isochrones directory and try again.
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uncertainties(https://pythonhosted.org/uncertainties/) -
mwdust(https://github.com/jobovy/mwdust)