From 726dacff025c87a38ed5fef43ec8c9a3348219d0 Mon Sep 17 00:00:00 2001
From: Max Bonomi <massimiliano.bonomi@gmail.com>
Date: Mon, 11 Jul 2011 15:15:32 -0700
Subject: [PATCH] Changed int to unsigned

---
 src/NeighborList.cpp | 40 ++++++++++++++++++++--------------------
 src/NeighborList.h   | 20 ++++++++++----------
 2 files changed, 30 insertions(+), 30 deletions(-)

diff --git a/src/NeighborList.cpp b/src/NeighborList.cpp
index 043383534..0788ac09e 100644
--- a/src/NeighborList.cpp
+++ b/src/NeighborList.cpp
@@ -7,7 +7,7 @@
 using namespace PLMD;
 using namespace std;
 
-NeighborList::NeighborList(vector<int> list0, vector<int> list1,
+NeighborList::NeighborList(vector<unsigned> list0, vector<unsigned> list1,
                            double distance, unsigned stride, Pbc *pbc=NULL):  
                            list0_(list0), list1_(list1),
                            distance_(distance), pbc_(pbc), stride_(stride)
@@ -17,30 +17,30 @@ NeighborList::NeighborList(vector<int> list0, vector<int> list1,
   //log.printf("stride should be greater or equal to 2")
  }
 // find maximum index atom
- int imax0= *max_element(list0_.begin(),list0_.end());
- int imax1= *max_element(list1_.begin(),list1_.end());
+ unsigned imax0= *max_element(list0_.begin(),list0_.end());
+ unsigned imax1= *max_element(list1_.begin(),list1_.end());
  indexes_.resize(max(imax0,imax1)+1);
  neighbors_.resize(list0_.size());
 // initialize neighbor list with all the atoms
- for(int i=0;i<list0_.size();++i){
-  for(int j=0;j<list1_.size();++j){
+ for(unsigned int i=0;i<list0_.size();++i){
+  for(unsigned int j=0;j<list1_.size();++j){
     neighbors_[i].push_back(list1_[j]);
   }
  }
 }
 
-vector<int> NeighborList::getFullList()
+vector<unsigned> NeighborList::getFullList()
 {
  indexes_.clear();
- vector<int> request=list0_;
+ vector<unsigned> request=list0_;
  request.insert(request.end(),list1_.begin(),list1_.end());
- for(int i=0;i<request.size();++i) indexes_[request[i]]=i; 
+ for(unsigned i=0;i<request.size();++i) indexes_[request[i]]=i; 
  return request;
 }
 
-vector<int> NeighborList::update(vector<Vector> positions)
+vector<unsigned> NeighborList::update(vector<Vector> positions)
 {
- vector<int> request=list0_;
+ vector<unsigned> request=list0_;
  neighbors_.clear();
  neighbors_.resize(list0_.size());
 // check if positions array has the correct length
@@ -49,8 +49,8 @@ vector<int> NeighborList::update(vector<Vector> positions)
   //log.printf("ERROR you need to request all the atoms before updating NL\n"); 
  }
 // update neighbors
- for(int i=0;i<list0_.size();++i){
-  for(int j=list0_.size();j<list0_.size()+list1_.size();++j){
+ for(unsigned int i=0;i<list0_.size();++i){
+  for(unsigned int j=list0_.size();j<list0_.size()+list1_.size();++j){
    Vector distance;
    if(pbc_!=NULL){
     distance=pbc_->distance(positions[i],positions[j]);
@@ -65,31 +65,31 @@ vector<int> NeighborList::update(vector<Vector> positions)
  request.insert(request.end(),neighbors_[i].begin(),neighbors_[i].end());
  }
  indexes_.clear();
- for(int i=0;i<request.size();++i) indexes_[request[i]]=i;
+ for(unsigned int i=0;i<request.size();++i) indexes_[request[i]]=i;
  return request;
 }
 
-int NeighborList::getStride() const
+unsigned NeighborList::getStride() const
 {
  return stride_;
 }
 
-vector<int> NeighborList::getNeighbors(int index)
+vector<unsigned> NeighborList::getNeighbors(unsigned index)
 {
- vector<int> neigh;
- for(int i=0;i<getNumberOfNeighbors(index);++i){
-  int iatom=neighbors_[index][i];
+ vector<unsigned> neigh;
+ for(unsigned int i=0;i<getNumberOfNeighbors(index);++i){
+  unsigned iatom=neighbors_[index][i];
   neigh.push_back(indexes_[iatom]);
  }
  return neigh; 
 }
 
-int NeighborList::getNumberOfNeighbors(int index)
+unsigned NeighborList::getNumberOfNeighbors(unsigned index)
 {
  return neighbors_[index].size();
 }
 
-int NeighborList::getNumberOfAtoms() const
+unsigned NeighborList::getNumberOfAtoms() const
 {
  return neighbors_.size();
 }
diff --git a/src/NeighborList.h b/src/NeighborList.h
index 4815c4208..012dc63e8 100644
--- a/src/NeighborList.h
+++ b/src/NeighborList.h
@@ -8,20 +8,20 @@
 /// NeighborList 
 class NeighborList  
 {
-  std::vector<int> list0_,list1_,indexes_; 
-  std::vector< std::vector<int> > neighbors_;
+  std::vector<unsigned> list0_,list1_,indexes_; 
+  std::vector< std::vector<unsigned> > neighbors_;
   double distance_;
   PLMD::Pbc *pbc_;
-  int stride_;
+  unsigned stride_;
 public:
-  NeighborList(std::vector<int> list0, std::vector<int> list1,
+  NeighborList(std::vector<unsigned> list0, std::vector<unsigned> list1,
                double distance, unsigned stride, PLMD::Pbc *pbc);
-  std::vector<int> getFullList();
-  std::vector<int> update(std::vector<PLMD::Vector> positions);
-  std::vector<int> getNeighbors(int index);  
-  int getStride() const;
-  int getNumberOfAtoms() const;
-  int getNumberOfNeighbors(int index);
+  std::vector<unsigned> getFullList();
+  std::vector<unsigned> update(std::vector<PLMD::Vector> positions);
+  std::vector<unsigned> getNeighbors(unsigned index);  
+  unsigned getStride() const;
+  unsigned getNumberOfAtoms() const;
+  unsigned getNumberOfNeighbors(unsigned index);
   ~NeighborList(){};
 };
 
-- 
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