From eafefd2637c352883158f055f94cc0fa780fc8c4 Mon Sep 17 00:00:00 2001
From: Gareth Tribello <gt@eider.phy.qub.ac.uk>
Date: Wed, 22 Apr 2015 08:10:25 +0100
Subject: [PATCH] Fixed potential bug in Atoms
If you had your atoms distributed among the domains such that one
node had on all the Atoms there could be a problem in running plumed.
This change fixes this problem. Also deleted rogue check in
AdjacencyMatrixAction
---
src/core/Atoms.cpp | 23 +++++++++++++----------
src/core/Atoms.h | 2 +-
src/multicolvar/AdjacencyMatrixAction.cpp | 1 -
3 files changed, 14 insertions(+), 12 deletions(-)
diff --git a/src/core/Atoms.cpp b/src/core/Atoms.cpp
index 9f713ebf3..636f526fa 100644
--- a/src/core/Atoms.cpp
+++ b/src/core/Atoms.cpp
@@ -52,7 +52,7 @@ Atoms::Atoms(PlumedMain&plumed):
forcesHaveBeenSet(0),
virialHasBeenSet(false),
massAndChargeOK(false),
- shuffledAtoms(false),
+ shuffledAtoms(0),
plumed(plumed),
naturalUnits(false),
timestep(0.0),
@@ -141,7 +141,7 @@ void Atoms::share(){
shareAll();
return;
}
- if(dd && shuffledAtoms){
+ if(dd && shuffledAtoms>0){
for(unsigned i=0;i<actions.size();i++) if(actions[i]->isActive()) {
unique.insert(actions[i]->getUnique().begin(),actions[i]->getUnique().end());
}
@@ -151,7 +151,7 @@ void Atoms::share(){
void Atoms::shareAll(){
std::set<AtomNumber> unique;
- if(dd && shuffledAtoms)
+ if(dd && shuffledAtoms>0)
for(int i=0;i<natoms;i++) unique.insert(AtomNumber::index(i));
share(unique);
}
@@ -167,7 +167,7 @@ void Atoms::share(const std::set<AtomNumber>& unique){
mdatoms->getCharges(gatindex,charges);
mdatoms->getMasses(gatindex,masses);
}
- if(dd && shuffledAtoms){
+ if(dd && shuffledAtoms>0){
if(dd.async){
for(unsigned i=0;i<dd.mpi_request_positions.size();i++) dd.mpi_request_positions[i].wait();
for(unsigned i=0;i<dd.mpi_request_index.size();i++) dd.mpi_request_index[i].wait();
@@ -237,7 +237,7 @@ void Atoms::wait(){
if(collectEnergy) energy=md_energy;
- if(dd && shuffledAtoms){
+ if(dd && shuffledAtoms>0){
// receive toBeReceived
Communicator::Status status;
if(dd.async){
@@ -322,21 +322,24 @@ void Atoms::setAtomsGatindex(int*g){
for(unsigned i=0;i<gatindex.size();i++) gatindex[i]=g[i];
for(unsigned i=0;i<dd.g2l.size();i++) dd.g2l[i]=-1;
if( gatindex.size()==natoms ){
- shuffledAtoms=false;
+ shuffledAtoms=0;
for(unsigned i=0;i<gatindex.size();i++){
- if( gatindex[i]!=i ){ shuffledAtoms=true; break; }
+ if( gatindex[i]!=i ){ shuffledAtoms=1; break; }
}
} else {
- shuffledAtoms=true;
+ shuffledAtoms=1;
+ }
+ if(dd){
+ dd.Sum(shuffledAtoms);
+ for(unsigned i=0;i<gatindex.size();i++) dd.g2l[gatindex[i]]=i;
}
- if(dd) for(unsigned i=0;i<gatindex.size();i++) dd.g2l[gatindex[i]]=i;
}
void Atoms::setAtomsContiguous(int start){
for(unsigned i=0;i<gatindex.size();i++) gatindex[i]=start+i;
for(unsigned i=0;i<dd.g2l.size();i++) dd.g2l[i]=-1;
if(dd) for(unsigned i=0;i<gatindex.size();i++) dd.g2l[gatindex[i]]=i;
- if(gatindex.size()<natoms) shuffledAtoms=true;
+ if(gatindex.size()<natoms) shuffledAtoms=1;
}
void Atoms::setRealPrecision(int p){
diff --git a/src/core/Atoms.h b/src/core/Atoms.h
index 74f523d3b..6673a51e8 100644
--- a/src/core/Atoms.h
+++ b/src/core/Atoms.h
@@ -70,7 +70,7 @@ class Atoms
unsigned forcesHaveBeenSet;
bool virialHasBeenSet;
bool massAndChargeOK;
- bool shuffledAtoms;
+ unsigned shuffledAtoms;
std::map<std::string,std::vector<AtomNumber> > groups;
diff --git a/src/multicolvar/AdjacencyMatrixAction.cpp b/src/multicolvar/AdjacencyMatrixAction.cpp
index 968d32c5d..92ef381f4 100644
--- a/src/multicolvar/AdjacencyMatrixAction.cpp
+++ b/src/multicolvar/AdjacencyMatrixAction.cpp
@@ -60,7 +60,6 @@ tmpdf(1)
}
for(unsigned j=i;j<nfunc;++j){
- plumed_assert( j*(i+1)<0.5*(nfunc*nfunc+nfunc) );
std::string sw, errors; parseNumbered("SWITCH",ibase+j+1,sw);
if(sw.length()==0){
std::string num; Tools::convert(ibase+j+1,num);
--
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