--- trunk/gadget/simann.cc	2015/07/24 18:36:24	12
+++ trunk/gadget/simann.cc	2015/07/30 12:36:46	14
@@ -304,8 +304,6 @@
 ////              trialx[i] = x[i];
 ////          }
 //
-////          cout << "param:" << param[l] << "-" << trialx[param[l]] << endl;
-//
 //          //Evaluate the function with the trial point trialx and return as -trialf
 //          trialf = EcoSystem->SimulateAndUpdate(trialx);
 //          trialf = -trialf;
@@ -326,9 +324,7 @@
 //            handle.logMessage(LOGINFO, "\nSimulated Annealing finished with a likelihood score of", score);
 //            return;
 //          }
-////          cout << "f:" << trialf << endl;
 //          //Accept the new point if the new function value better
-////          cout << "mustAccept:" << trialf << "|" << funcval<< endl;
 //          if ((trialf - funcval) > verysmall) {
 //            for (i = 0; i < nvars; i++)
 //              x[i] = trialx[i];
@@ -352,7 +348,6 @@
 //              nrej++;
 //            }
 //          }
-////          cout << "goog VALUE:" << funcval << endl;
 //          // JMB added check for really silly values
 //          if (isZero(trialf)) {
 //            handle.logMessage(LOGINFO, "Error in Simulated Annealing optimisation after", iters, "function evaluations, f(x) = 0");
@@ -451,9 +446,10 @@
 
   double tmp, p, pp, ratio, nsdiv;
   double fopt, funcval, trialf;
-  int    a, i, j, k, l, offset, quit;
+  int    a, i, j, k, l, quit;
   int    rchange, rcheck, rnumber;  //Used to randomise the order of the parameters
 
+  // store the info of the different threads
   struct Storage {
   	  DoubleVector trialx;
   	  double newLikelihood;
@@ -474,8 +470,12 @@
   IntVector nacp(nvars, 0);
 
   EcoSystem->resetVariables();  //JMB need to reset variables in case they have been scaled
-  if (scale)
-    EcoSystem->scaleVariables();
+  if (scale) {
+  		EcoSystem->scaleVariables();
+  		int numThr = omp_get_max_threads ( );
+  		for(i = 0; i < numThr; i++) // scale the variables for the ecosystem of every thread
+  			EcoSystems[i]->scaleVariables();
+  	}
   EcoSystem->getOptScaledValues(x);
   EcoSystem->getOptLowerBounds(lowerb);
   EcoSystem->getOptUpperBounds(upperb);
@@ -511,7 +511,6 @@
 
   //the function is to be minimised so switch the sign of funcval (and trialf)
   funcval = -funcval;
-  offset = EcoSystem->getFuncEval();  //number of function evaluations done before loop
   nacc++;
   cs /= lratio;  //JMB save processing time
   nsdiv = 1.0 / ns;
@@ -530,15 +529,16 @@
   for (i=0; i<numThr; ++i)
 	  storage[i].trialx = trialx;
 
-  //Start the main loop.  Note that it terminates if
-  //(i) the algorithm succesfully optimises the function or
-  //(ii) there are too many function evaluations
-  int aux;
 
- DoubleVector vns(nvars, 0);
+  int aux; //store the number of evaluations that are not useful for the algorithm
+
+ DoubleVector vns(nvars, 0); //vector of ns
  int ns_ = ceil(numThr/2.);
  double res;
   aux=0;
+  //Start the main loop.  Note that it terminates if
+  //(i) the algorithm succesfully optimises the function or
+  //(ii) there are too many function evaluations
   while (1) {
     for (a = 0; a < nt; ++a) {
       //Randomize the order of the parameters once in a while, to avoid
@@ -740,12 +740,11 @@
 }
 #endif
 
+// calcule a new point
 void OptInfoSimann::newValue(int nvars, int l, IntVector& param, DoubleVector& trialx,
 		DoubleVector& x, DoubleVector& lowerb, DoubleVector& upperb, DoubleVector& vm)
 {
 	int i, k;
-//	double old = trialx[param[l]];
-//	cout << "[" << endl;
 	  for (i = 0; i < nvars; ++i) {
 		if (i == param[l]) {
 		  trialx[i] = x[i] + ((randomNumber(&seed) * 2.0) - 1.0) * vm[i];
@@ -763,12 +762,13 @@
 		  }
 		} else
 		  trialx[i] = x[i];
-//		cout <<" " << trialx[i];
 	  }
-
-//	  cout << endl<< "old[" <<param[l] << "]:" << old <<"-" << trialx[param[l]]<< " - " << vm[param[l]]<<endl;
 }
 
+/*################################################################################
+ * code use in the template (seq_optimize_template.h)
+ ################################################################################*/
+
 
 //Generate trialx, the trial value of x
 void newValue(int nvars, int l, IntVector& param, DoubleVector& trialx,
@@ -1037,7 +1037,7 @@
 		EcoSystem->scaleVariables();
 #ifndef NO_OPENMP
 		int numThr = omp_get_max_threads ( );
-		for(i = 0; i < numThr; i++)
+		for(i = 0; i < numThr; i++) // scale the variables for the ecosystem of every thread
 			EcoSystems[i]->scaleVariables();
 #endif
 	}