From c74ded59b79e6f03bbf5e1585f24f541680b8e30 Mon Sep 17 00:00:00 2001
From: Max Bonomi <massimiliano.bonomi@gmail.com>
Date: Tue, 12 Jul 2011 14:12:24 -0700
Subject: [PATCH] Added initialize() methods to initialize the nl to the full
list
---
src/NeighborList.cpp | 20 ++++++++++++++++----
src/NeighborList.h | 4 ++--
2 files changed, 18 insertions(+), 6 deletions(-)
diff --git a/src/NeighborList.cpp b/src/NeighborList.cpp
index 9b0107151..c1535d88b 100644
--- a/src/NeighborList.cpp
+++ b/src/NeighborList.cpp
@@ -20,9 +20,11 @@ NeighborList::NeighborList(vector<unsigned> list0, vector<unsigned> list1, bool
if(!do_pair){
nallpairs_=nlist0_*nlist1_;
}else{
- // if(nlist0_!=nlist1_) error
+// if(nlist0_!=nlist1_) error
nallpairs_=nlist0_;
}
+// initialize neighborlist
+ initialize();
}
NeighborList::NeighborList(vector<unsigned> list0, Pbc *pbc=NULL,
@@ -34,6 +36,16 @@ NeighborList::NeighborList(vector<unsigned> list0, Pbc *pbc=NULL,
nlist0_=list0.size();
twolists_=false;
nallpairs_=nlist0_*(nlist0_-1)/2;
+ // initialize neighborlist
+ initialize();
+}
+
+void NeighborList::initialize()
+{
+ neighbors_.clear();
+ for(unsigned int i=0;i<nallpairs_;++i){
+ neighbors_.push_back(getIndexPair(i));
+ }
}
// this method should be called at the end of the step
@@ -43,8 +55,8 @@ vector<unsigned> NeighborList::getFullAtomList() const
return fullatomlist_;
}
-// this method return the pair of indexes in the array of positions
-// of a given pair "ipair" from the complete list
+// this method returns the pair of indexes of the positions array
+// of a given pair (ipair) from the list of all possible pairs
pair<unsigned,unsigned> NeighborList::getIndexPair(unsigned ipair)
{
pair<unsigned,unsigned> index;
@@ -53,7 +65,7 @@ pair<unsigned,unsigned> NeighborList::getIndexPair(unsigned ipair)
}else if (twolists_ && !do_pair_){
index=pair<unsigned,unsigned>(ipair/nlist1_,ipair%nlist1_+nlist0_);
}else if (!twolists_){
-// still to fix the map between mono and multi index
+// still to fix the map between mono and multi index here
index=pair<unsigned,unsigned>(ipair/nlist1_,ipair%nlist1_+nlist0_);
}
return index;
diff --git a/src/NeighborList.h b/src/NeighborList.h
index e2f1be338..caabcc1ef 100644
--- a/src/NeighborList.h
+++ b/src/NeighborList.h
@@ -14,6 +14,7 @@ class NeighborList
std::vector< std::pair<unsigned,unsigned> > neighbors_;
double distance_;
unsigned stride_,nlist0_,nlist1_,nallpairs_;
+ void initialize();
std::pair<unsigned,unsigned> getIndexPair(unsigned ipair);
std::vector<unsigned> createIndexes(std::vector<unsigned> request);
template<typename T>
@@ -35,5 +36,4 @@ public:
~NeighborList(){};
};
-#endif
-
+#endif
\ No newline at end of file
--
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