LIME (Line Modeling Engine)

Niels Bohr institutet, University of Copenhagen

About LIME

LIME is a 3D molecular excitation and radiation transfer code for far-infrared and (sub-)millimeter wavelength. LIME will calculate spectra of rotational transitions of atoms and molecules, given a user-supplied physical model. Details on the method can be found in C. Brinch and M. R. Hogerheijde, A&A 553, A25 (2010)

Any scientific publication making use of the LIME code should also reference this publication.

A comprehensive user manual is available online at the LIME website.

Installation notes

The LIME code needs three library packages in order to compile: qhull, gsl, and cfitsio.

Mac OS X

The easiest way is to install MacPorts. After MacPorts has been installed, type in a terminal (as root or sudo)

$ port install qhull
$ port install cfitsio
$ port install gsl

Alternatively, the library packages may be installed with Fink. After Fink has been installed, type:

$ fink install qhull6.3.1-dev cfitsio gsl

Linux / Unix / Mac OS X (alternative)

Download the sources from the following locations. Make sure to get the latest versions.

The GNU scientific library (GSL), is present on most modern Unix and Linux systems. Check for availability with gsl-config --libs. If this command returns a library path, there is no need to download and install it.

All three library packages are installed using the following

 $ configure --prefix=/path/to/LimePackage
 $ make
 $ make install

In some cases the qhull library will produce a segmentation fault unless it is compiled with the -fno-strict-aliasing flag. The example here does not require root. Some modifications to the Makefile may be required if another location is set for the installation.

Note for qhull2011.1 and later: This version of qhull will sometimes not compile unless the -Wno-sign-conversion flag is removed from the qhull Makefile. The naming of the qhull library has changed between version 2010.1 and 2011.1. Make sure to edit the qhull flag near the top of the LIME Makefile accordingly. Also, the newest versions of qhull does not include a configure script.

LIME is automatically compiled at runtime so there is no installation required and also no configure script. Do not try to make or make install LIME as this will produce an error.

Running the code

Source the file called source.me using the following commands.

For bash:

 $ . sourceme.bash

For csh:

$ source sourceme.csh

To find out whether you use bash or csh, do

$ echo $SHELL

The source command needs to be executed for each new session. The content of the file source.me can be placed in .bashrc or .cshrc for convenience in which case there is no need to source the source.me file before each session.

The code runs simply by typing

$ cd example/
$ lime model.c

The model file can have any name. The model file need not be written in C. Subroutines can also be written in Fortran (or other languages that can be linked with C, e.g., python) as long as the names comply with the standards of linking C and Fortran. See this page for information on how to link C and Fortran. If Fortran subroutines are used, the linking of LIME needs to be done with the Fortran compiler. Modify the Makefile accordingly.

Changelog

1.31: Bug was found and fixed in getJbar()
1.3: LIME can now run multiple instances in the same directory. Grid data structure has changed. A memory leak in qhull call has been closed. model.c no longer has to contain functions that are not needed. LIME can be restarted from previously calculated populations. gas- to-dust ratio has been implemented as a function rather than a constant.
1.23: Includes a tcp client so that LIME can automatically download LAMDA files. Makefile and lime script improved. Semantic updates.
1.22: Fixed a bug in the vtk output. Fixed a bug in the randomization of photon directions. vtk file now contains the normalized velocities.
1.21: A few memory leaks fixed. Output screen updated with more information. LIME now always calculates molecular density with respect to total H2 A catch for negative optically depth has been implemented.
1.2: Minor bug fix in ray-tracer (Thanks to Ruud Visser). FITS header tweaked for CASA compatability. Photon transport slightly optimized. The photons nitial directions are now randomized. Multiple lines no longer get mirrored. LIME should run faster now.
1.1: Raytracer has been rewritten and optimized and now includes an anti- aliasing filter. The FITS header has been corrected. LIME images can now be read directly by CASA. Continuum polarization implemented.
1.03: Bug fixes
1.02: Minor bug fixes and some clean-up of the code. The VTK file now contains density, temperature, molecular density and the velocity field. Faster evaluation of line-of-sight velocities
1.01: First full public release