--- trunk/gadget/hooke.cc	2015/07/24 18:36:24	12
+++ trunk/gadget/hooke.cc	2015/07/30 12:36:46	14
@@ -156,17 +156,9 @@
   DoubleVector z(point);
 
   minf = prevbest;
-//  for (int k=0;k<point.Size(); k++)
-//	  cout << z[k] ;
-//  cout << endl;
   for (i = 0; i < point.Size(); i++) {
-
-//	  for (int k=0;k<point.Size(); k++)
-//	  	  cout << z[k] << " " ;
-//cout << endl;
     z[param[i]] = point[param[i]] + delta[param[i]];
     ftmp = EcoSystem->SimulateAndUpdate(z);
-//    cout << i <<"-z["<< param[i]<<"]:" <<z[param[i]] << " - " << ftmp << endl;
     if (ftmp < minf) {
       minf = ftmp;
     } else {
@@ -178,7 +170,6 @@
       else
         z[param[i]] = point[param[i]];
     }
-//    cout << i <<"-z["<< param[i]<<"]:" <<z[param[i]] << " - " << ftmp  <<" - " << prevbest << endl;
   }
 
   for (i = 0; i < point.Size(); i++)
@@ -222,8 +213,8 @@
 	  if ((i + paral_tokens -1) >= nvars)
 		  paral_tokens = nvars - i;
 	  omp_set_dynamic(0);
-	  omp_set_nested(1);
-#pragma omp parallel for num_threads(paral_tokens) private(k)
+	  omp_set_nested(1); //permit the nested parallelization
+#pragma omp parallel for num_threads(paral_tokens) private(k) //parallelize the parameters (numThr/2)
 	  for (j = 0; j < paral_tokens; ++j) {
 		  storage[j].z = z;
 		  storage[j].delta = delta;
@@ -233,7 +224,7 @@
 		  v1[k] +=  delta[k];
 		  v2[k] -=  delta[k];
 
-#pragma omp parallel sections num_threads(2)
+#pragma omp parallel sections num_threads(2) //parrallelize the +/- delta simulation for each parameter
 		  {
 	#pragma omp section
 			  {
@@ -300,7 +291,7 @@
   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
   EcoSystem->getOptScaledValues(x);
@@ -644,11 +635,9 @@
 	   IntVector trapped(nvars, 0);
 
 	   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
 	   EcoSystem->getOptScaledValues(x);
 	   EcoSystem->getOptLowerBounds(lowerb);
 	   EcoSystem->getOptUpperBounds(upperb);