From 3c33d42d3bdac47a5f765b7fcdf331385c153101 Mon Sep 17 00:00:00 2001
From: Giovanni Bussi <giovanni.bussi@gmail.com>
Date: Tue, 7 May 2013 17:06:44 +0200
Subject: [PATCH] Modified use of neighbor list in COORDINATION
It solves a known problem with the calculation
of acceptance in replica exchange with COORDINATION
and NLIST.
Notice that it changes the behavior of neighbor list
in the first two steps of a simulation. Previously,
during those steps full pair list was used. Now,
first step is equivalent to any other step
multiple of NL_STRIDE. Because of this, I updated
a couple of regtests.
---
regtest/multicolvar/rt20-mpi/colvar.reference | 4 ++--
regtest/multicolvar/rt20/colvar.reference | 4 ++--
src/colvar/CoordinationBase.cpp | 22 +++++++++----------
src/colvar/CoordinationBase.h | 3 ++-
4 files changed, 16 insertions(+), 17 deletions(-)
diff --git a/regtest/multicolvar/rt20-mpi/colvar.reference b/regtest/multicolvar/rt20-mpi/colvar.reference
index 514344336..93677d871 100644
--- a/regtest/multicolvar/rt20-mpi/colvar.reference
+++ b/regtest/multicolvar/rt20-mpi/colvar.reference
@@ -1,6 +1,6 @@
#! FIELDS time d1.less_than d2.less_than c1
- 0.000000 3.71160 3.70528 3.71160
- 0.050000 3.65204 3.64568 3.65204
+ 0.000000 3.71160 3.70528 3.63725
+ 0.050000 3.65204 3.64568 3.57396
0.100000 3.68479 3.67845 3.61408
0.150000 3.74173 3.73336 3.66938
0.200000 3.80672 3.79754 3.73794
diff --git a/regtest/multicolvar/rt20/colvar.reference b/regtest/multicolvar/rt20/colvar.reference
index 514344336..93677d871 100644
--- a/regtest/multicolvar/rt20/colvar.reference
+++ b/regtest/multicolvar/rt20/colvar.reference
@@ -1,6 +1,6 @@
#! FIELDS time d1.less_than d2.less_than c1
- 0.000000 3.71160 3.70528 3.71160
- 0.050000 3.65204 3.64568 3.65204
+ 0.000000 3.71160 3.70528 3.63725
+ 0.050000 3.65204 3.64568 3.57396
0.100000 3.68479 3.67845 3.61408
0.150000 3.74173 3.73336 3.66938
0.200000 3.80672 3.79754 3.73794
diff --git a/src/colvar/CoordinationBase.cpp b/src/colvar/CoordinationBase.cpp
index 5806073c2..dbef34b52 100644
--- a/src/colvar/CoordinationBase.cpp
+++ b/src/colvar/CoordinationBase.cpp
@@ -45,7 +45,8 @@ CoordinationBase::CoordinationBase(const ActionOptions&ao):
PLUMED_COLVAR_INIT(ao),
pbc(true),
serial(false),
-reduceListAtNextStep(false)
+invalidateList(true),
+firsttime(true)
{
parseFlag("SERIAL",serial);
@@ -106,12 +107,14 @@ CoordinationBase::~CoordinationBase(){
}
void CoordinationBase::prepare(){
- if(reduceListAtNextStep){
+ if(nl->getStride()>0)
+ if(firsttime || (getStep()%nl->getStride()==0)){
+ requestAtoms(nl->getFullAtomList());
+ invalidateList=true;
+ firsttime=false;
+ }else{
requestAtoms(nl->getReducedAtomList());
- reduceListAtNextStep=false;
- }
- if(nl->getStride()>0 && (getStep()-nl->getLastUpdate())>=nl->getStride()){
- requestAtoms(nl->getFullAtomList());
+ invalidateList=false;
}
}
@@ -124,7 +127,7 @@ void CoordinationBase::calculate()
vector<Vector> deriv(getNumberOfAtoms());
// deriv.resize(getPositions().size());
- if(nl->getStride()>0 && (getStep()-nl->getLastUpdate())>=nl->getStride()){
+ if(nl->getStride()>0 && invalidateList){
nl->update(getPositions());
}
@@ -167,11 +170,6 @@ void CoordinationBase::calculate()
setValue (ncoord);
setBoxDerivatives (virial);
- if(nl->getStride()>0 && (getStep()-nl->getLastUpdate())>=nl->getStride()){
- reduceListAtNextStep=true;
- nl->setLastUpdate(getStep());
- }
-
}
}
}
diff --git a/src/colvar/CoordinationBase.h b/src/colvar/CoordinationBase.h
index 6bf546f35..bc32f934a 100644
--- a/src/colvar/CoordinationBase.h
+++ b/src/colvar/CoordinationBase.h
@@ -33,7 +33,8 @@ class CoordinationBase : public Colvar {
bool pbc;
bool serial;
NeighborList *nl;
- bool reduceListAtNextStep;
+ bool invalidateList;
+ bool firsttime;
public:
CoordinationBase(const ActionOptions&);
--
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