Miscellanea how-to

Create grid of atmospheric models

For spectral synthesis, PFANT uses model atmospheres encoded in its own binary “.mod” format. Such “.mod” files are generated by the Fortran binary innewmarcs, which interpolates within a grid of model atmospheres. This grid is also encoded in “.mod” format and can be generated using the script create-grid.py.

To create a grid of atmospheric models:

  1. Download atmospheric models of interest from MARCS website (http://marcs.astro.uu.se/) and put all files in a single directory

  2. Run one of the options below:

Without MARCS opacities:

create-grid.py --mode modbin

With MARCS opacities:

create-grid.py –mode opa

Converting “VALD3 extended” format atomic lines to PFANT format

The Vienna Atomic Line Database (VALD) is “a collection of atomic and molecular transition parameters of astronomical interest” (http://vald.astro.uu.se/).

To convert from the “VALD3 extended” to a “PFANT atomic lines” file:

vald3-to-atoms.py <vald3-extended-filename>
tune-zinf <output-from-previous-command>

This is done in two steps. The first step, vald3-to-atoms.py does the actual conversion (which is quick) and saves a file, e.g., “atoms-untuned-xxxxx.dat”

The second step (which is time-consuming) is performed by tune-zinf.py and aims to tune an important parameter used by the pfant Fortran binary.

For more information, see help for vald3-to-atoms.py, tune-zinf.py, cut-atoms.py (call these scripts with --help option).

Continuous opacities: selecting between PFANT and MARCS coefficients

By default, PFANT internally calculates the continuum absorption coefficients, then adds MARCS scattering coefficients.

PFANT-calculated continuum absorption + MARCS scattering (default)

innewmarcs --absoru T --opa T --sca T --abs F
pfant --absoru T --opa T --sca T --abs F

or

run4.py --opa T --sca T --abs F

PFANT-calculated continuum only

innewmarcs --absoru T --opa F
pfant --absoru T --opa F

or

run4.py --absoru T --opa F

MARCS opacities (absorption and scattering) only

innewmarcs --absoru F --opa T --sca T --abs T
pfant --absoru F --opa T --sca T --abs T

or

run4.py --absoru F --opa T --sca T --abs T

Note

For innewmarcs, “–opa T” causes the creation of an additional file modeles.opa besides modeles.mod.

Related command-line options (also accessible in x.py):

--opa T ...... switches on MARCS opacities
               (may be of two types: absorption and scattering)
--abs T ...... switches on MARCS absorption
--sca T ...... switches on MARCS scattering
--absoru F ... switches off PFANT internal calculation

Note

In order to use continuum opacities calculated by MARCS code (http://marcs.astro.uu.se/), you will need to create your own atmospheric model grid (using create-grid.py), or download file “grid.moo” as explained below (this file is too big to be stored on GitHub (241 MB > 100 MB)). File “grid.moo” contains a 3D grid of MARCS (http://marcs.astro.uu.se/) atmospheric models with opacities included.

  1. go to directory PFANT/data/common and run get-grid.moo.sh, or

  2. download it from this location (or this location) and save it as “PFANT/data/common/grid.moo”

Conversion of molecular lines from other formats to PFANT format

See Conversion of molecular lines lists.