From 2bf30f5daf7c5f42911716ee019a661f106af08d Mon Sep 17 00:00:00 2001
From: Giovanni Bussi <giovanni.bussi@gmail.com>
Date: Tue, 18 Jun 2013 10:06:34 +0200
Subject: [PATCH] Fixed neighborlist
Now getReducedList can be called more than once returning the same list
I also updated a regtest.
The previous test was only testing stride=2 (or, equivalently,
stride=20 into a trajectory with stride 10).
---
regtest/multicolvar/rt20/plumed.dat | 5 +++++
src/tools/NeighborList.cpp | 8 +++++---
src/tools/NeighborList.h | 1 +
3 files changed, 11 insertions(+), 3 deletions(-)
diff --git a/regtest/multicolvar/rt20/plumed.dat b/regtest/multicolvar/rt20/plumed.dat
index af25f7458..de57ea5c6 100644
--- a/regtest/multicolvar/rt20/plumed.dat
+++ b/regtest/multicolvar/rt20/plumed.dat
@@ -4,7 +4,12 @@ c1: ...
COORDINATION GROUPA=1 GROUPB=2-100 NLIST NL_CUTOFF=2.5 NL_STRIDE=20
SWITCH={RATIONAL NN=6 MM=12 R_0=1.0}
...
+c1x: ...
+ COORDINATION GROUPA=1 GROUPB=2-100 NLIST NL_CUTOFF=2.5 NL_STRIDE=30
+ SWITCH={RATIONAL NN=6 MM=12 R_0=1.0}
+...
PRINT ARG=d1.*,d2.*,c1 FILE=colvar FMT=%8.5f STRIDE=1
+PRINT ARG=c1x FILE=colvarx
COORDINATIONNUMBER SPECIES=1-5 SWITCH={RATIONAL R_0=0.5} MORE_THAN={EXP R_0=4.0} LABEL=c2
COORDINATIONNUMBER SPECIES=1-5 SWITCH={RATIONAL R_0=0.5} MORE_THAN={EXP R_0=4.0} NUMERICAL_DERIVATIVES LABEL=c2n
DUMPDERIVATIVES ARG=c2.*,c2n.* FILE=derivatives FMT=%8.4f
diff --git a/src/tools/NeighborList.cpp b/src/tools/NeighborList.cpp
index 318e980ce..d34681a67 100644
--- a/src/tools/NeighborList.cpp
+++ b/src/tools/NeighborList.cpp
@@ -32,7 +32,7 @@ using namespace std;
NeighborList::NeighborList(const vector<AtomNumber>& list0, const vector<AtomNumber>& list1,
const bool& do_pair, const bool& do_pbc, const Pbc& pbc,
- const double& distance, const unsigned& stride):
+ const double& distance, const unsigned& stride): reduced(false),
do_pair_(do_pair), do_pbc_(do_pbc), pbc_(&pbc),
distance_(distance), stride_(stride)
{
@@ -54,7 +54,7 @@ NeighborList::NeighborList(const vector<AtomNumber>& list0, const vector<AtomNum
NeighborList::NeighborList(const vector<AtomNumber>& list0, const bool& do_pbc,
const Pbc& pbc, const double& distance,
- const unsigned& stride):
+ const unsigned& stride): reduced(false),
do_pbc_(do_pbc), pbc_(&pbc),
distance_(distance), stride_(stride){
fullatomlist_=list0;
@@ -119,10 +119,11 @@ void NeighborList::setRequestList() {
requestlist_.push_back(fullatomlist_[neighbors_[i].second]);
}
Tools::removeDuplicates(requestlist_);
+ reduced=false;
}
vector<AtomNumber>& NeighborList::getReducedAtomList() {
- for(unsigned int i=0;i<size();++i){
+ if(!reduced)for(unsigned int i=0;i<size();++i){
unsigned newindex0=0,newindex1=0;
AtomNumber index0=fullatomlist_[neighbors_[i].first];
AtomNumber index1=fullatomlist_[neighbors_[i].second];
@@ -132,6 +133,7 @@ vector<AtomNumber>& NeighborList::getReducedAtomList() {
p = std::find(requestlist_.begin(), requestlist_.end(), index1); plumed_assert(p!=requestlist_.end()); newindex1=p-requestlist_.begin();
neighbors_[i]=pair<unsigned,unsigned>(newindex0,newindex1);
}
+ reduced=true;
return requestlist_;
}
diff --git a/src/tools/NeighborList.h b/src/tools/NeighborList.h
index 4b15457a2..7a26cd4c2 100644
--- a/src/tools/NeighborList.h
+++ b/src/tools/NeighborList.h
@@ -35,6 +35,7 @@ class Pbc;
/// A class that implements neighbor lists from two lists or a single list of atoms
class NeighborList
{
+ bool reduced;
bool do_pair_,do_pbc_,twolists_;
const PLMD::Pbc* pbc_;
std::vector<PLMD::AtomNumber> fullatomlist_,requestlist_;
--
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