Simplified virial calculation in GHOST

Similarly to what happens in Colvar class, I made
also for ActionWithVirtualAtom a method setBoxDerivativesNoPbc
that can be used to set the virial contribution when the Pbc have not
been used in the calculation of derivatives.

This should make the addition of new vatom actions easier

src/core/ActionWithVirtualAtom.cpp

@@ -86,6 +86,21 @@ void ActionWithVirtualAtom::setBoxDerivatives(const std::vector<Tensor> &d){
   for(unsigned i=0;i<3;i++) for(unsigned j=0;j<3;j++) boxDerivatives[j][i][j]+=pos[i];
 }
 
+void ActionWithVirtualAtom::setBoxDerivativesNoPbc(){
+  std::vector<Tensor> bd(3);
+  for(unsigned i=0;i<3;i++) for(unsigned j=0;j<3;j++) for(unsigned k=0;k<3;k++){
+// Notice that this expression is very similar to the one used in Colvar::setBoxDerivativesNoPbc().
+// Indeed, we have the negative of a sum over dependent atoms (l) of the external product between positions
+// and derivatives. Notice that this only works only when Pbc have not been used to compute
+// derivatives.
+    for(unsigned l=0;l<getNumberOfAtoms();l++){
+      bd[k][i][j]-=getPosition(l)[i]*derivatives[l][j][k];
+    }
+  }
+  setBoxDerivatives(bd);
+}
+
+
 
 void ActionWithVirtualAtom::setGradientsIfNeeded(){
   if(isOptionOn("GRADIENTS")) { 

src/core/ActionWithVirtualAtom.h

@@ -66,6 +66,13 @@ protected:
 /// On the other hand if the vatom position is a non-linear function of atomic coordinates this
 /// should be called (see vatom::Ghost).
   void setBoxDerivatives(const std::vector<Tensor> &d);
+/// Set box derivatives automatically.
+/// It should be called after the settomsDerivatives has been used for all
+/// single atoms.
+/// \warning It only works for virtual atoms NOT using PBCs!
+///          This implies that all atoms used + the new virtual atom should be
+///          in the same periodic image.
+  void setBoxDerivativesNoPbc();
 public:
   void setGradients();
   const std::map<AtomNumber,Tensor> & getGradients()const;

src/vatom/Ghost.cpp

@@ -90,11 +90,6 @@ void Ghost::calculate(){
   Vector pos;
   vector<Tensor> deriv(getNumberOfAtoms());
   vector<Vector> n;
-  Vector pp[3];
-
-  pp[0]=getPosition(0);
-  pp[1]=pp[0]+delta(getPosition(0), getPosition(1));
-  pp[2]=pp[0]+delta(getPosition(0), getPosition(2));
 
 // first versor 
   Vector n01 = delta(getPosition(0), getPosition(1));
@@ -184,17 +179,7 @@ void Ghost::calculate(){
   setAtomsDerivatives(deriv);
 
 // Virial contribution
-  std::vector<Tensor> bd(3);
-  for(unsigned i=0;i<3;i++) for(unsigned j=0;j<3;j++) for(unsigned k=0;k<3;k++){
-// Notice that this expression is very similar to the one used in Colvar::setBoxDerivativesNoPbc().
-// Indeed, we have the negative of a sum over dependent atoms (l) of the external product between positions
-// and derivatives. Notice that positions here should be computed in the same periodic image
-// as pos.
-    for(unsigned l=0;l<3;l++){
-      bd[k][i][j]-=pp[l][i]*deriv[l][j][k];
-    }
-  }
-  setBoxDerivatives(bd);
+  setBoxDerivativesNoPbc();
 }
 
 }