From 717bdc8ed6d4feea36dbe0d8e084308c8bb817fc Mon Sep 17 00:00:00 2001
From: Max Bonomi <massimiliano.bonomi@gmail.com>
Date: Mon, 11 Jul 2011 17:08:13 -0700
Subject: [PATCH] Update version of NeighborList. It should work also when you
update the NL at every step.
---
src/NeighborList.cpp | 38 +++++++++++++++++++++++---------------
src/NeighborList.h | 9 +++++----
2 files changed, 28 insertions(+), 19 deletions(-)
diff --git a/src/NeighborList.cpp b/src/NeighborList.cpp
index 0d1089148..c9043f0ea 100644
--- a/src/NeighborList.cpp
+++ b/src/NeighborList.cpp
@@ -12,15 +12,13 @@ NeighborList::NeighborList(vector<unsigned> list0, vector<unsigned> list1,
list0_(list0), list1_(list1),
distance_(distance), pbc_(pbc), stride_(stride)
{
- if(stride_<2){
- // I need to access to log here. still don't know how to do it
- // log.printf("Stride should be greater or equal to 2")
- }
// find maximum index atom
unsigned imax0= *max_element(list0_.begin(),list0_.end());
unsigned imax1= *max_element(list1_.begin(),list1_.end());
-// initialize indexes_
- indexes_.resize(max(imax0,imax1)+1);
+// initialize indexes
+ imax_=max(imax0,imax1)+1;
+ indexes_.resize(imax_);
+ newindexes_.resize(imax_);
// initialize neighbor list with all the atoms
// NB: the neighbor list contains the atomic index of the atoms
// not the index in the array of positions
@@ -32,26 +30,29 @@ NeighborList::NeighborList(vector<unsigned> list0, vector<unsigned> list1,
}
}
-// indexes_[i] is the index of the array of positions
-// (the one requested from the MD code) of an atom with atomic index i.
-// This method should be called every time the array of position is requested to change
-void NeighborList::updateIndexes(vector<unsigned> request)
+vector<unsigned> NeighborList::createIndexes(vector<unsigned> request)
{
- indexes_.clear();
+ vector<unsigned> indexes;
+ indexes.resize(imax_);
for(unsigned int i=0;i<request.size();++i){
- indexes_[request[i]]=i;
+ indexes[request[i]]=i;
}
+ return indexes;
}
+// this method should be called at the end of the step
+// before the update of the neighbor list
vector<unsigned> NeighborList::getFullList()
{
vector<unsigned> request=list0_;
request.insert(request.end(),list1_.begin(),list1_.end());
- updateIndexes(request);
+ indexes_=createIndexes(request);
return request;
}
-vector<unsigned> NeighborList::update(vector<Vector> positions)
+// this method should be called at the beginning of the step
+// when nl must be updated
+vector<unsigned> NeighborList::prepareUpdate(vector<Vector> positions)
{
vector<unsigned> request=list0_;
// clean neighbors list
@@ -78,10 +79,17 @@ vector<unsigned> NeighborList::update(vector<Vector> positions)
}
request.insert(request.end(),neighbors_[i].begin(),neighbors_[i].end());
}
- updateIndexes(request);
+ newindexes_=createIndexes(request);
return request;
}
+// this method should be called at the end of the step
+// when nl must be updated, before getFullList()
+void NeighborList::finishUpdate()
+{
+ indexes_=newindexes_;
+}
+
unsigned NeighborList::getStride() const
{
return stride_;
diff --git a/src/NeighborList.h b/src/NeighborList.h
index 0eb1cee74..2b447a875 100644
--- a/src/NeighborList.h
+++ b/src/NeighborList.h
@@ -8,17 +8,18 @@
/// NeighborList
class NeighborList
{
- std::vector<unsigned> list0_,list1_,indexes_;
+ std::vector<unsigned> list0_,list1_,indexes_,newindexes_;
std::vector< std::vector<unsigned> > neighbors_;
double distance_;
PLMD::Pbc *pbc_;
- unsigned stride_;
- void updateIndexes(std::vector<unsigned> request);
+ unsigned stride_, imax_;
+ void createIndexes(std::vector<unsigned> request);
public:
NeighborList(std::vector<unsigned> list0, std::vector<unsigned> list1,
double distance, unsigned stride, PLMD::Pbc *pbc);
std::vector<unsigned> getFullList();
- std::vector<unsigned> update(std::vector<PLMD::Vector> positions);
+ std::vector<unsigned> prepareUpdate(std::vector<PLMD::Vector> positions);
+ void finishUpdate();
std::vector<unsigned> getNeighbors(unsigned index);
unsigned getStride() const;
unsigned getNumberOfAtoms() const;
--
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