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Mol3D: 3D line and dust continuum radiative transfer code
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author:         Florian Ober  
version:        Jan 2016 
email:          [email protected]  

You are free to use and extend this code, 
but if you do so please cite:

'Ober et al. 2015, Astronomy and Astrophysics, Volume 579, A105'

and write me an E-Mail.

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Parts of this code are based on MC3D (Wolf et al. 1999/2003)

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[A]  Preparations

--  cfitsio library --

This code needs cfitsio. Therefore, download it either from  
http://heasarc.gsfc.nasa.gov/fitsio/fitsio.html  
or have a look into your favored linux distribution software archive.
  
The easiest way is to install cfitsio via your software repository,  
for example:

    Arch linux:
>pacman -S cfitsio

    Ubuntu (14.04):
>apt-get install libcfitsio3

    openSUSE (13.1)
>zypper install cfitsio


If you do so you can skip this section and go directly to the next  
section (-- compiler --)  
  
The second possibility is to install cfitsio into the directory   
above this Mol3D installation (e.g., './../cfitsio'). Please note, it works  
best if you install cfitsio with shared libraries:  

>cd ../cfitsio/

>./configure

>./make shared

Don't forget to update your LD_LIBRARY_PATH:
  
>export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/path/to/cfitsio/directory"

The best way is adding this command to your local ~/.bashrc
  
-- compiler --
  
Intel Fortran compiler should give the best performence, but Gfortran
should also work.
  
  
-- optional --
Python3 (matplotlib, numpy, astropy) is required for visualisation.  
  
This code uses OpenMP for parallelisation
  
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[B] 
You have to (re-)compile the code:
  
>make new

The default compiler is Intel Fortran compiler.
You can change the compiler in the make process by

>make FC=gfortran new

For better performance we recommend to use:

>make CO=fast new

To use OpenMP:

>make CO=para new

For more options on the make process check out
>make help

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[C]

Run the code:

>./mol3d

All input parameters are stored in the ./input/input.dat file.
Also it is possible to use another input file:

>./mol3d "/path/to/input-file"

The disk model can be changed by editing the ./src/model_mod.f90 file.
Please do not forget to recompile the code afterwards.

In addition, all input settings can be adjusted by editing the
./src/initiate.f90 file

Please note: The code is still in development and bugs may exist! If
you find one, please report to [email protected]

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[D]

Visualisation scripts are found in the 'visualize' folder. 
Python3 (matplotlib, numpy, astropy) is required.

There are 3 main routines to visualize your results:

>cd visualize

>./show_model.py "project_name"         # shows density, temperature and velocity maps

>./make_spectrum.py "project_name"      # shows spectra

>./visual_mol3d.py "project_name"       # shows everything (calls the routines above)

If you changed the result path in the input file, you also need to adjust
the file "path_results" in the visualize directory, otherwise you can provide the path:

>./visual_mol3d.py "project_name" "results_path"


If you have further problems in running the code, please do not hesitate
to ask me.