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:

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

#. Run one of the options below:

Without MARCS opacities:

.. code-block:: shell

    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:

.. code:: shell

    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)

.. code:: shell

    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**

.. code:: shell

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

or

::

    run4.py --absoru T --opa F

**MARCS opacities (absorption and scattering) only**

.. code:: shell

    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``):

.. code-block:: none

    --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.

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

    b. download it from
       `this location <https://docs.google.com/uc?export=download&confirm=4o6l&id=0B8m8GNLFiaewejd6dmJ6MW1pX2c>`__
       (or `this location <https://drive.google.com/file/d/0B8m8GNLFiaewejd6dmJ6MW1pX2c/view>`__)
       and save it as "PFANT/data/common/grid.moo"

Conversion of molecular lines from other formats to PFANT format
----------------------------------------------------------------

See :doc:`convmol`.