Small cleanup

Pbc are now stored in ActionAtomistic only, and not in Atoms.
This is more consistent: equivalently to atom positions,
Pbc are local to the Action.

src/ActionAtomistic.cpp

@@ -35,7 +35,7 @@ void ActionAtomistic::requestAtoms(const vector<AtomNumber> & a){
 }
 
 Vector ActionAtomistic::pbcDistance(const Vector &v1,const Vector &v2)const{
-  return plumed.getAtoms().getPbc().distance(v1,v2);
+  return pbc.distance(v1,v2);
 }
 
 void ActionAtomistic::calculateNumericalDerivatives(){
@@ -59,13 +59,13 @@ void ActionAtomistic::calculateNumericalDerivatives(){
   }
  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]=plumed.getAtoms().getPbc().realToScaled(positions[j]);
+   for(int j=0;j<natoms;j++) positions[j]=pbc.realToScaled(positions[j]);
    box(i,k)=box(i,k)+delta;
-   plumed.getAtoms().getPbc().setBox(box);
-   for(int j=0;j<natoms;j++) positions[j]=plumed.getAtoms().getPbc().scaledToReal(positions[j]);
+   pbc.setBox(box);
+   for(int j=0;j<natoms;j++) positions[j]=pbc.scaledToReal(positions[j]);
    calculate();
    box(i,k)=arg0;
-   plumed.getAtoms().getPbc().setBox(box);
+   pbc.setBox(box);
    for(int j=0;j<natoms;j++) positions[j]=savedPositions[j];
    for(int j=0;j<nval;j++) valuebox[j](i,k)=a->getValue(j)->get();
  }
@@ -101,6 +101,7 @@ void ActionAtomistic::parseAtomList(const std::string&key,std::vector<AtomNumber
 
 void ActionAtomistic::retrieveAtoms(){
   box=plumed.getAtoms().box;
+  pbc.setBox(box);
   const vector<Vector> & p(plumed.getAtoms().positions);
   const vector<double> & c(plumed.getAtoms().charges);
   const vector<double> & m(plumed.getAtoms().masses);

src/ActionAtomistic.h

@@ -6,6 +6,7 @@
 #include "PlumedMain.h"
 #include <vector>
 #include <set>
+#include "Pbc.h"
 
 namespace PLMD {
 
@@ -20,6 +21,7 @@ class ActionAtomistic :
   std::set<int>         unique;
   std::vector<Vector>   positions;       // positions of the needed atoms
   Tensor                box;
+  Pbc                   pbc;
   Tensor                virial;
   std::vector<Vector>   forces;          // forces on the needed atoms
   std::vector<double>   masses;
@@ -127,7 +129,7 @@ void ActionAtomistic::clearOutputForces(){
 
 inline
 const Pbc & ActionAtomistic::getPbc() const{
- return plumed.getAtoms().getPbc();
+ return pbc;
 }
 
 }

src/Atoms.cpp

@@ -38,7 +38,6 @@ Atoms::~Atoms(){
 void Atoms::setBox(void*p){
   mdatoms->setBox(p);
   Tensor b; mdatoms->getBox(b);
-  pbc.setBox(b);
 }
 
 void Atoms::setPositions(void*p){

src/Atoms.h

@@ -3,7 +3,6 @@
 
 #include "PlumedCommunicator.h"
 #include "Tensor.h"
-#include "Pbc.h"
 #include <vector>
 #include <set>
 #include <cassert>
@@ -32,7 +31,6 @@ class Atoms
   std::vector<int> fullList;
   
   MDAtomsBase* mdatoms;
-  Pbc     pbc;
 
   PlumedMain & plumed;
 
@@ -65,9 +63,6 @@ public:
   void setTimeStep(void*);
   double getTimeStep()const;
 
-  const Pbc& getPbc()const{return pbc;};
-  Pbc& getPbc(){return pbc;};
-
 private:
   std::vector<const ActionAtomistic*> actions;
   std::vector<int>    gatindex;