Is there an easy way to include arbitrary convergence constraints to the mcsqs code? For example, I would like to test the convergence of mcsqs as a function of the simulated annealing temperature. The -itol=… does not work very well for my particular system. I would like to stop mcsqs when three different instances of the code generate the same structure.
Unfortunately, the different instances of the code do not talk to each other at all (which is actually good for efficiency reasons!), so such check would have to be done outside of the code, by reading the output files.
You could grep the string "Objective_function" in the bestcorr*.out files and look for duplicates.
(sort -u could be useful for that).