Moved documentation in .h in doxygen format

src/NeighborList.cpp

@@ -31,14 +31,12 @@ NeighborList::NeighborList(const vector<AtomNumber>& list0, const vector<AtomNum
  initialize();
 }
 
-
 NeighborList::NeighborList(const vector<AtomNumber>& list0, const bool& do_pbc,
                            const Pbc& pbc, const double& distance,
                            const unsigned& stride):
                            do_pbc_(do_pbc), pbc_(pbc),
                            distance_(distance), stride_(stride)
 {
-// store full list of atoms needed
  fullatomlist_=list0;
  nlist0_=list0.size();
  twolists_=false;
@@ -46,7 +44,6 @@ NeighborList::NeighborList(const vector<AtomNumber>& list0, const bool& do_pbc,
  initialize();
 }
 
-// initialize neighborlist with all possible pairs
 void NeighborList::initialize()
 {
  neighbors_.clear();
@@ -55,16 +52,11 @@ void NeighborList::initialize()
  }
 }
 
-// this methods returns the list of all atoms
-// it should be called at the end of the step
-// before the update of the neighbor list or in the prep stage
 vector<AtomNumber>& NeighborList::getFullAtomList()
 {
  return fullatomlist_;
 }
 
-// this method returns the pair of indexes of the positions array
-// of pair "ipair" among the list of all possible pairs
 pair<unsigned,unsigned> NeighborList::getIndexPair(unsigned ipair)
 {
  pair<unsigned,unsigned> index;
@@ -79,18 +71,14 @@ pair<unsigned,unsigned> NeighborList::getIndexPair(unsigned ipair)
  return index;
 }
 
-// this method updates the neighbor list and prepare the new
-// list of atoms to request to the MD code
 void NeighborList::update(const vector<Vector>& positions)
 {
-// clean neighbors list
  neighbors_.clear();
 // check if positions array has the correct length
  if(positions.size()!=fullatomlist_.size()){
   // i need to access to log here. still don't know how to do it
   //log.printf("ERROR you need to request all the atoms one step before updating the NL\n"); 
  }
-// update neighbors. cycle on all possible pairs
  for(unsigned int i=0;i<nallpairs_;++i){
    pair<unsigned,unsigned> index=getIndexPair(i);
    unsigned index0=index.first;
@@ -109,7 +97,6 @@ void NeighborList::update(const vector<Vector>& positions)
  setRequestList();
 }
 
-// template to remove duplicates from a list of types <T>
 template<typename T>
 void NeighborList::removeDuplicates(std::vector<T>& vec)
 {
@@ -117,7 +104,6 @@ void NeighborList::removeDuplicates(std::vector<T>& vec)
     vec.erase(std::unique(vec.begin(), vec.end()), vec.end());
 }
 
-// extract the list of atoms from the list of close pairs
 void NeighborList::setRequestList()
 {
  requestlist_.clear();
@@ -129,10 +115,6 @@ void NeighborList::setRequestList()
  //removeDuplicates<AtomNumber>(request);
 }
 
-// this method should be called at the end of the step when nl is updated
-// it updates the indexes in the neighbor list to match the new
-// ordering in the future positions array at the next iteration
-// and returns the new list of atoms to request to the MD code
 vector<AtomNumber>& NeighborList::getReducedAtomList()
 {
  std::vector< pair<unsigned,unsigned> > newneighbors;
@@ -151,28 +133,21 @@ vector<AtomNumber>& NeighborList::getReducedAtomList()
  return requestlist_;
 }
 
-// get the update stride of the Neighbor List
 unsigned NeighborList::getStride() const
 {
  return stride_;
 }
 
-// size of the Neighbor List
 unsigned NeighborList::size() const
 {
  return neighbors_.size();
 }
 
-// this method returns the pair of indexes in the positions array of
-// the close pair "i"
 const pair<unsigned,unsigned> & NeighborList::operator[] (unsigned i) const
 {
  return neighbors_[i];
 }
 
-// this method returns the list of indexes in the positions array of the
-// neighbors of the atom "index", where "index" refers to the index in the
-// positions array
 vector<unsigned> NeighborList::getNeighbors(unsigned index)
 {
  vector<unsigned> neighbors;

src/NeighborList.h

@@ -8,7 +8,7 @@
 
 namespace PLMD{
 
-/// NeighborList 
+/// A class that implements neighbor lists from two lists or a single list of atoms
 class NeighborList  
 {
   bool do_pair_,do_pbc_,twolists_;
@@ -17,10 +17,15 @@ class NeighborList
   std::vector< std::pair<unsigned,unsigned> > neighbors_;
   double distance_;
   unsigned stride_,nlist0_,nlist1_,nallpairs_;
+/// Initialize the neighbor list with all possible pairs
   void initialize();
-  std::pair<unsigned,unsigned> getIndexPair(unsigned ipair);
+/// Return the pair of indexes in the positions array
+/// of the two atoms forming the i-th pair among all possible pairs  
+  std::pair<unsigned,unsigned> getIndexPair(unsigned i);
+/// Template to remove duplicates from a list of types <T>
   template<typename T> 
    void removeDuplicates(std::vector<T>& vec);
+/// Extract the list of atoms from the current list of close pairs
   void setRequestList();
 public:
   NeighborList(const std::vector<PLMD::AtomNumber>& list0,
@@ -30,13 +35,24 @@ public:
   NeighborList(const std::vector<PLMD::AtomNumber>& list0, const bool& do_pbc,
                const PLMD::Pbc& pbc, const double& distance=1.0e+30,
                const unsigned& stride=0);
-                             
+/// Return the list of all atoms that are needed to rebuild the neighbor list.
+/// This method should be called at the end of the step
+/// before the update of the neighbor list or in prep stage                             
   std::vector<PLMD::AtomNumber>& getFullAtomList();
+/// Update the indexes in the neighbor list to match the
+/// ordering in the new positions array
+/// and return the new list of atoms that must be requested to the main code
   std::vector<PLMD::AtomNumber>& getReducedAtomList();
+/// Update the neighbor list and prepare the new
+/// list of atoms that will be requested to the main code  
   void update(const std::vector<PLMD::Vector>& positions);
+/// Get the update stride of the neighbor list
   unsigned getStride() const;
+/// Get the size of the neighbor list
   unsigned size() const;
+/// Get the i-th pair of the neighbor list
   const std::pair<unsigned,unsigned> & operator[] (unsigned i)const;
+/// Get the list of neighbors of the i-th atom
   std::vector<unsigned> getNeighbors(unsigned i);
   ~NeighborList(){};
 };