Reference

This section contains a more complete description of the PFANT pipeline and the files and file types involved.

Spectral synthesis pipeline

Figure 9 – Spectral synthesis pipeline - Fortran programs (boxes) and their input/output files.

Input/output data files

The different file types in the pipeline will be explained in the next subsections.

Stellar data and running settings

Table 2 – stellar and running settings data files. The “–options” column shows the command-line options that can be used to change the name for a particular file, e.g., run4.py --fn_main main-other.dat.

Default name	–option	Description
main.dat	–fn_main	main configuration file containing all stellar parameters except abundances
abonds.dat	–fn_abonds	chemical abundances
dissoc.dat	–fn_dissoc	dissociation equilibrium data. This file is optional, and can be created using abed.py if needed

Common data files

Table 3 – Common data files.

Default name	–option	Description
absoru2.dat	–fn_absoru2	absorption info for continuum calculation.
atoms.dat	–fn_atoms	atomic line list
molecules.dat	–fn_molecules	molecular line list
mollist.dat	–fn_mollist	list of molecular line list files
hmap.dat	–fn_hmap	hydrogen line list
partit.dat	–fn_partit	partition functions
grid.mod or	–fn_modgrid	MARCS atmospheric model grid (models only)
grid.moo	–fn_moo	MARCS atmospheric model grid (models with opacities) (Figure 10)

Molecular line lists can be provided as a single file (default molecules.dat) or through a “list of molecular line lists files” (LOMLLF) (default mollist.dat). If the latter is found, single linelist file will be ignored and all files listed in the LOMLLF file will be loaded instead.

Figure 10 – 3D grid of atmospheric models. The scatterplot in the figure shows the (teff, glog, [Fe/H]) values for all existing atmospheric models in the grid (this is the file “grid.moo” provided). The uppermost point represents the Sun.

Files created by the Fortran programs

Files created by innewmarcs

Table 4 – Files created by innewmarcs

Default name	command-line option	Description
modeles.mod	–fn_modeles	atmospheric model (binary file) (Figure 8A)
modeles.opa	–fn_opa	atmospheric model: opacities (MARCS “.opa” format) (Figure 8B,8C)

Figure 11 – Atmospheric model information (Sun). (A) data in file modeles.mod; (B), (C) data in modeles.opa

innewmarcs creates two separate files (Table 4). They are created separately for historical reasons. “modeles.opa” follows the same structure of “.opa” files downloaded from the MARCS website. “modeles.mod” does not follow the same structure of MARCS “.mod” files. Figure 8 illustrates the information contained in these files.

Files created by hydro2

hydro2 creates a series of files named “thalha” (Figure 12), “thbeta”, “thgamma”, “thdelta”, “thepsilon” etc. (the series of hydrogen lines is given in file “hmap.dat”).

Figure 12 – Example of H-alpha line profile calculated by hydro2.

Files created by pfant

Table 5 - Files created by pfant

Default name	Description
flux.spec	un-normalized flux (erg/cm**2/s/Hz multiplied by 10**5)
flux.cont	continuum flux (erg/cm**2/s/Hz multiplied by 10**5)
flux.norm	normalized flux (un-normalized flux)/(continuum flux)

Figure 13 – plots showing three pfant output files for the [4000, 7000] angstrom region: calculated spectrum; continuum; normalized spectrum. The common prefix “flux” can be changed in file “main.dat” to give a set of files with different names.

Files created by nulbad

nulbad creates a file whose name by default is the full input file name with the FWHM added with three decimal places. For example,

nulbad --fwhm 1.2

creates a file named “flux.norm.nulbad.1.200”.

To change this, use option “–fn_cv”, for example,

nulbad --fwhm 1.2 --fn_cv another-name

Todo

Another page containing the visual maps of the text files, such as main.dat