Eliminated box copy

There was an extra copy of the box in ActionAtomistic,
namely ActionAtomistic::box and ActionAtomistic::pbc.

This means that one should take care of both copies when changing it,
which is error prone.

I eliminated ActionAtomistic::box

src/core/ActionAtomistic.cpp

@@ -113,6 +113,7 @@ void ActionAtomistic::calculateAtomicNumericalDerivatives( ActionWithValue* a, c
       value[j*natoms+i][k]=a->getOutputQuantity(j);
     }
   }
+ Tensor box(pbc.getBox());
  for(int i=0;i<3;i++) for(int k=0;k<3;k++){
    double arg0=box(i,k);
    for(int j=0;j<natoms;j++) positions[j]=pbc.realToScaled(positions[j]);
@@ -203,7 +204,6 @@ void ActionAtomistic::parseAtomList(const std::string&key,const int num, std::ve
 
 
 void ActionAtomistic::retrieveAtoms(){
-  box=atoms.box;
   pbc=atoms.pbc;
   Colvar*cc=dynamic_cast<Colvar*>(this);
   if(cc && cc->checkIsEnergy()) energy=atoms.getEnergy();

src/core/ActionAtomistic.h

@@ -25,6 +25,7 @@
 #include "Action.h"
 #include "tools/Tensor.h"
 #include "Atoms.h"
+#include "tools/Pbc.h"
 #include <vector>
 #include <set>
 
@@ -43,7 +44,6 @@ class ActionAtomistic :
   std::set<AtomNumber>  unique;
   std::vector<Vector>   positions;       // positions of the needed atoms
   double                energy;
-  Tensor                box;
   Pbc&                  pbc;
   Tensor                virial;
   std::vector<double>   masses;
@@ -216,7 +216,7 @@ const double & ActionAtomistic::getEnergy()const{
 
 inline
 const Tensor & ActionAtomistic::getBox()const{
-  return box;
+  return pbc.getBox();
 }
 
 inline