The molfra.out file lists each molecular fragment present every time the coordinates are saved.

The frequency that coordinates are saved is set by the iout2 keyword in the control file.
The bond-order cutoff is set by the cutof3 keyword in the control file. The default value is 0.3 meaning that atoms are considered "connected" if they have at least a bond order of 0.3.

After the simulation is run, the molfra.out file is written based on the bond-order cutoff. It is important to note that if you want to choose a different cutoff, you must do it before running the simulation. There is also currently no way to post-process a run with a different cutoff from the one set during the simulation.

To plot out this data, the script molfraanal (found in ~jkua/bin/ ) will write out two files that you can read into GNUplot (one by mass, one by # of each of molecular fragment). To use the script, copy it to the appropriate directory containing your molfra.out file and type ./molfraanal

You will be prompted for two inputs. The first is the filename which is molfra.out (obviously, unless you renamed the file). For the second, just type 1. for the major structures. (If you put a number less than 1 you'll get some of the minor fragments too.) There will be two output files, fr1.dat and mass1.dat. You can delete the mass1.dat file. I suggest you rename the file and then you can use GNUplot to plot x-y data to see which fragments are present during the simulation.