Splitting performCalc into pieces

In particular, I would like to be able to just do the
"forward" loop (calculate()) and not the "backward" loop
(apply()). In this manner, when computing foreign biases
for acceptance in replica exchange, I will only call the
forward loop, which computes colvars and biases. Clearly,
we should move printing/analysis/hills-adding stuff
outside the "calculate" method, so as to avoid doing these
things in the acceptance calculation. I wait for this further
cleaning since, until replica exchange is not actually there,
there is no practical difference. Also, we may decide to change
a bit the name of methods (calculate/apply are becoming a bit
misleading?)

src/PlumedMain.cpp

@@ -401,11 +401,19 @@ void PlumedMain::shareData(){
   atoms.share();
 }
 
-
 void PlumedMain::performCalc(){
+  waitData();
+  justCalculate();
+  justApply();
+}
 
+void PlumedMain::waitData(){
   if(!active)return;
   atoms.wait();
+}
+
+
+void PlumedMain::justCalculate(){
 
 // calculate the active actions in order (assuming *backward* dependence)
   for(ActionSet::iterator p=actionSet.begin();p!=actionSet.end();++p){
@@ -424,6 +432,9 @@ void PlumedMain::performCalc(){
       else (*p)->calculate();
     }
   }
+}
+
+void PlumedMain::justApply(){
   
 // apply them in reverse order
   for(ActionSet::reverse_iterator p=actionSet.rbegin();p!=actionSet.rend();++p){

src/PlumedMain.h

@@ -107,6 +107,10 @@ public:
   void performCalc();
 /// Shortcut for prepareCalc() + performCalc()
   void calc();
+
+  void waitData();
+  void justCalculate();
+  void justApply();
 /// Reference to atoms object
   Atoms& getAtoms();
 /// Reference to the list of Action's