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In order to run the code two files are needed a) *.rxn file b) *.cfg file. The rxn file is where the code is written and needs to be compiled with ssc compiler. The cfg file is where all the parameters of the model (rate constants and reactant numbers) are defined.

Stimulation steps

Step 1: Download ssc compiler and install it following the instruction manual.
Step2: Compile *.rxn file by issuing the command ssc filename.rxn. This command should create an executable file
Step3: Run the model my issuing a command ./filename Ðc param_file.cfg Ðt 1.0 Ðe 300 | tail Ðn+2 > outputfile.txt. The parameter after Ðt specifies the time points at which the code will write the output while the parameter after Ðe specifies the end-time of the simulation. Edit the param_file.cfg file if you want to change the value of the rate constants and reactants. 

Changing Cluster size in the rxn file

Below we show a part of the code that needs to be edited if you want to alter the cluster size.

region periphery
 diff
  box width 100 height 100 depth 1
  box width 30 height 30 depth 1
region cluster
  box width 30 height 30 depth 1
subvolume edge 1

Change the numbers in the highlighted lines.