Renamed getPosition(AtomNumber) to getGlobalPosition(AtomNumber)

See #357.

The whole code, including optional modules, correctly compiles
indicating that this function was used in a single place.

In case some foreign code uses getPosition(AtomNumber), after this
update the compilation will fail (and will not just produce incorrect results).
So I think this change can be merged safely.

src/core/ActionAtomistic.h

@@ -77,8 +77,10 @@ public:
 /// Get position of i-th atom (access by relative index)
   const Vector & getPosition(int)const;
 /// Get position of i-th atom (access by absolute AtomNumber).
-/// With direct access to the global atom array
-  const Vector & getPosition(AtomNumber)const;
+/// With direct access to the global atom array.
+/// \warning Should be only used by actions that need to read the shared position array.
+///          This array is insensitive to local changes such as makeWhole(), numerical derivatives, etc.
+  const Vector & getGlobalPosition(AtomNumber)const;
 /// Get modifiable position of i-th atom (access by absolute AtomNumber).
 /// Should be used by action that need to modify the stored atomic coordinates
   Vector & modifyPosition(AtomNumber);
@@ -188,7 +190,7 @@ const Vector & ActionAtomistic::getPosition(int i)const {
 }
 
 inline
-const Vector & ActionAtomistic::getPosition(AtomNumber i)const {
+const Vector & ActionAtomistic::getGlobalPosition(AtomNumber i)const {
   return atoms.positions[i.index()];
 }
 

src/generic/WholeMolecules.cpp

@@ -178,7 +178,7 @@ WholeMolecules::WholeMolecules(const ActionOptions&ao):
 void WholeMolecules::calculate() {
   for(unsigned i=0; i<groups.size(); ++i) {
     for(unsigned j=0; j<groups[i].size()-1; ++j) {
-      const Vector & first (getPosition(groups[i][j]));
+      const Vector & first (getGlobalPosition(groups[i][j]));
       Vector & second (modifyPosition(groups[i][j+1]));
       second=first+pbcDistance(first,second);
     }