MOCASSIN 2.02 manual
The source files are contained in a subdirectory called
source/. MOCASSIN looks for the
input.in file from a subdirectory called
input/. The atomic data files should all be contained in a subdirectory named
data/. Most of the atomic data files should not need to be changed at all. Unless you decide to update some of them, in which case (under the GPL agreement) you should also email me with the changes so that I can include them in the public version of the code. The dust optical data library and other dust related data files are contained in a subdirectory named
The user's input files may be a combination of the following files, depending on the processes included in a given simulation.
This is the main input file where you can specify all the keywords to define your simulation. Some example input files are given for the Meudon/Lexington benchmark cases (see pure photoionisation benchmarks).
gas abundances file
This is the nebular abundances file which should have the name specified by the user in the nebComposition field of the
input.in file. Some sample files are given for the Meudon/Lexington benchmarks.
gas density file
This the nebular density structure file which should have the name specified by the user in the densityFile field of the
input.in file. The format of this file is given in densityFile.
stellar atmosphere file
This is the stellar atmosphere file which should have the name specified by the user in the contShape field of the
input.in file. The format of this file is given in contShape.
dust number density file
This should contain the dust number density distribution across the grid. Its name and path should be specified in the
input.in file by the keyword Ndust.
dust to hydrogen or dust to gas ratio
This contains the dust to hydrogen or dust to gas ratio distribution across the grid. Its name and path should be specified in the
input.in file by the keyword MdMh or MdMg, respectively.
dust species and grain size distribution files
The names of these two files must be specified in the
input.in file following the keyword dustFile. The dust species file should contain a first line specifying how many species are to be included, and then successive lines containing the names of the optical data (n,k or Qs) file and the relative abundance of the species.
e.g. for a pure silicate model (using the Draine and Lee 1984 data) :
1 'dustData/sil-dl.nk' 1.0
The grain size distribution file should contain a first line specifying how many grain sizes are to be included, the rest of the file should consist of three columns : index, radius (in um), weight. Grain size distribution files can be created using the makeGrainSizeDistribution.f90 program included in the
e.g. for a single grain size
1 size 1 0.16 1.0
Input files for multigrid simulations are described in running multiple spatialgrids.
The plot.in file is used by the mocassinPlot driver in order to create 3D grids of line emission. This file must be place (or linked to) the
input/ subdirectory. The plot.out and the grid4.out files are written out to
output/ and can then be used to create emission line maps by integration along any given line of sight.
Monochromatic grids are created using the mono keyword, and individual lines using the line keyword.
mono line 2 4861. 4861. line 93 4686. 4686. line 1529 5007. 5007. line 1540 4363. 4363. line 2407 6733. 6733. line 2408 6718. 6718. line 929 6583. 6583.
The integer following the keyword line is the line index number as given in the lineFlux.out file. NOTE that the line indices will be different for different simulations as they depend on which elements are included and on the number of ionisation stages accounted for. The 2nd and 3rd indices contain the central wavelength of the line (these are redundant for monochromatic plots, however they must be included).