Scafacos

here is what I've done:
1 - I moved the initialization for scafacos to where tcl command has been defined from where the integration is about to begin. here the initial value for params and solver initials will be set and params will tune.
2- since params need to be broadcast only once, I've create a new function called update params to separate bcast from setting box_l and periodicity, and to to the correction for these (and re-tuning if necessary) values before integration.  

p.s.: I tried to remember what we have discussed, if I'm doing a wrong thing please correct me.