Added preparation step for Actions

New virtual method for Actions which is called at steps when action is
active just before atoms sharing. This is the right place where Actions
can change their atom requirements. E.g., you can do

class ColvarSomething{
...
void prepare();
}

void ColvarSomething::prepare(){
// take here your decision and eventually change the requested atoms
}

src/Action.cpp

@@ -109,6 +109,11 @@ void Action::calculateNumericalDerivatives(){
   assert(0);
 }
 
+void Action::prepare(){
+  return;
+}
+
+
 
 
 

src/Action.h

@@ -107,6 +107,13 @@ public:
 
   PlumedCommunicator& comm;
 
+/// Prepare an Action for calculation
+/// This can be used by Action if they need some special preparation
+/// before calculation. Typical case is for collective variables
+/// which would like to change their list of requested atoms.
+/// By default (if not overridden) does nothing.
+  virtual void prepare();
+
 /// Calculate an Action.
 /// This method is called one or more times per step.
 /// The set of all Actions is calculated in forward order.
@@ -114,7 +121,7 @@ public:
 
 /// Apply an Action.
 /// This method is called one time per step.
-/// The set of all Actions is applied in backword order.
+/// The set of all Actions is applied in backward order.
   virtual void apply()=0;
 
 /// Tell to the Action to flush open files

src/PlumedMain.cpp

@@ -373,8 +373,6 @@ void PlumedMain::prepareDependencies(){
 
   atoms.setCollectEnergy(false);
 
-// activate all the actions which are on step
-// activation is recursive and enables also the dependencies
   for(ActionSet::iterator p=actionSet.begin();p!=actionSet.end();p++){
     (*p)->deactivate();
     if(Colvar *c=dynamic_cast<Colvar*>(*p)) {
@@ -382,13 +380,19 @@ void PlumedMain::prepareDependencies(){
     }
   }
 
+// activate all the actions which are on step
+// activation is recursive and enables also the dependencies
   for(unsigned i=0;i<pilots.size();++i){
     if(pilots[i]->onStep()){
       pilots[i]->activate();
       active=true;
      }
   };
-}
+
+// allow actions to update their request list before atoms are shared
+  for(ActionSet::iterator p=actionSet.begin();p!=actionSet.end();p++)
+    if((*p)->isActive()) (*p)->prepare();
+  }
 
 void PlumedMain::shareData(){
   if(active)atoms.share();