Merge branch 'fixing-nlist' into v2.0

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

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_;
 }
 

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_;