🦴 fossyl 🦴

1. Download Python: Visit here to install Python
2. Download pip: Visit here to install pip
3. Run Install Command: Run the command in terminal:

   pip install fossyl
   

1. Download Python: Visit here to install Python
2. Download pip: Visit here to install pip
3. Downloading fossyl: Download the latest version of fossyl in the "Releases" tab of the Github page
4. pip Packages: Go into the directory of fossyl and run the command:

   pip install -r requirements.txt
   

1. After fossyl is installed, verify the installation by running the following command: from fossyl.h5grid import *. If you encounter any issues during installation, please reach out to Hunter Brooks for assistance.
2. Ensure that model spectra are assigned as: column 1 (wavelength) and column 2 (flux)
3. Assign the relavent variables as described below.
4. To compile code, execute the command: h5grid(model_directory, model_parm, output_h5). These are the minimum required parameters for fossyl to run. You can include optional variables if needed.

• Required Variables:

  • model_directory: File path/name to your model spectra: string:

    • example: /Desktop/spectra/test.csv

  • model_parameters: Model parameter names: list: (must be in order that the paramters are in the file name)

    • example: ['Teff', 'log(g)', '[M/H]', 'C/O', 'log(Kzz)']

  • output_file: File path/name of output file: string:

    • example: /models/test

• Optional Variables:

  • wavelength_region: The wavelength region saved for each spectrum: list
    • example: [0, 10], default=[0, np.inf]

1. Ensure that your model is compiled into a h5 file using h5grid
2. Ensure that the observed spectra are assigned as: column 1 (wavelength), column 2 (flux), and column 3 (uncertainty)
3. Once fossyl is successfully imported, define the relevant variables as shown below. Ensure that all required variables are formatted correctly.
4. To run the Markov-Chain Monte-Carlo simulation, execute the command: mcmcfit(input_file, output_file, h5_directory, model_parm). These are the minimum required parameters for fossyl to run. You can include optional variables if needed.

• Required Variables:

  • input_file: File path/name to your input spectrum: string:

    • example: /Desktop/spectra/test.csv

  • output_file: File path/name of output file: string: (do not include file type)

    • example: /Output/test

  • h5_directory: Directory name to model spectra h5 file: string: (ensure no numbers are included in path name outside of numbers in model file name)

    • example: /Desktop/model/LOWZ.h5

  • model_parm: Model parameter names: list: (must be the exact name used in h5 file)

  • example code: ['Teff', 'log(g)', '[M/H]', 'C/O', 'log(Kzz)']

• Optional Variables:

  • grid_scale: Number of grid points around best grid point in each dimension: int

    • example: 50, default=10

  • unit_wave: Astropy units of the observed and model wavelength units: list: (first index is observed, second index is model)

    • example: [u.um, u.um], default=[u.um, u.um]

  • unit_flux: Astropy units of the observed and model flux units: list: (first index is observed, second index is model)

    • example: [u.Jy, (u.erg / (u.cm**2 * u.s * u.um))], default=[(u.erg / (u.cm**2 * u.s * u.um)), (u.erg / (u.cm**2 * u.s * u.um))]

  • walkers: Number of walkers for emcee calculation: int

    • example: 25, default=15

  • steps: Number of max steps for emcee calculation: int: May be cutoff before this as a result of auto-correlation

    • example: 15000, default=1000

  • rv_fit: Whether a radial velocity is fit: boolean

    • example: True, default=False

  • monitor: Whether a monitoring step figure is displayed every 1000 steps: boolean

    • example: True, default=False

  • save_output: Whether the output tables and figures are saved: boolean

    • example: True, default=True

• Mr. Hunter Brooks
  • Email: hcb98@nau.edu

1. If you intend to publish any calculations done by fossyl, please reference Brooks et al. (in prep.).

2. Please reference the relavent model citation.