mcsqs

Monte Carlo generator of Special Quasirandom Structures 3.48, by Axel van de Walle
   -n=[int]      nb of atom/unit cell (Default: 0)
If -n is not specified, generate clusters of the following sizes:
   -2=[real]      Maximum distance between two points within a pair (Default: 0)
   -3=[real]      Maximum distance between two points within a triplet (Default: 0)
   -4=[real]      Maximum distance between two points within a quadruplet (Default: 0)
   -5=[real]      Maximum distance between two points within a quintuplet (Default: 0)
   -6=[real]      Maximum distance between two points within a sextuplet (Default: 0)
   -l=[string]   Input file defining the random structure (default: rndstr.in)
  -cf=[string]   Input file defining the clusters (default: clusters.out)
 -tcf=[string]   Input file defining the target multibody correlations (default: internally 
                     calculated values for fully disordered state)
 -tol=[real]     Tolerance for matching correlations (default: 1e-3)
  -wr=[real]     Weight assigned to range of perfect correlation match in objective function 
                     (default 1)
  -wn=[real]     Multiplicative decrease in weight per additional point in cluster (default 1)
  -wd=[real]     Exponent of decay in weight as function of cluster diameter (default 0)
   -T=[real]     Temperature (default 1)
  -pf=[string]   Input file defining the optimization parameters (default: sqsparam.in)
  -rc            Read supercells from file sqscell.out (default: generate internally and write to 
                     sqscell.out) (Default: Off)
  -ip=[int]      Index of current process (for parallel operation) (Default: -1)
-best            Collect best SQS among the outputs of prior parallel runs (Default: Off)
 -crf=[string]   Select correlation functions (default: trigo)
  -sd=[int]      Seed for random number generation (default: use clock)
  -rt=[int]      Read parameter file every (rt) step (default:10000)
  -2d            Generate only supercells in the plane of a,b axes (Default: Off)
 -sig=[int]      Number of significant digits to print in output files (default: 6)
   -h            Display more help (Default: Off)

Perhaps missing -n=[nb of atom/cell] option?