From bdb1394e9cb2619810af246c6656bb364cf9f7a0 Mon Sep 17 00:00:00 2001
From: Giovanni Bussi <giovanni.bussi@gmail.com>
Date: Mon, 30 Apr 2018 11:03:09 +0200
Subject: [PATCH] Fix on NAMD-like interface.
- when using NAMD-like interface, also update the unique list of atoms.
- moved g2l out of dd, since it is also needed when not using MPI
(in NAMD-like interface)
Partly implemented by @hanatok, see #359
---
src/core/ActionAtomistic.cpp | 2 +-
src/core/Atoms.cpp | 51 ++++++++++++++++++++++--------------
src/core/Atoms.h | 2 +-
3 files changed, 34 insertions(+), 21 deletions(-)
diff --git a/src/core/ActionAtomistic.cpp b/src/core/ActionAtomistic.cpp
index 177a979bf..a848da353 100644
--- a/src/core/ActionAtomistic.cpp
+++ b/src/core/ActionAtomistic.cpp
@@ -287,7 +287,7 @@ void ActionAtomistic::updateUniqueLocal() {
unique_local.clear();
if(atoms.dd && atoms.shuffledAtoms>0) {
for(auto pp=unique.begin(); pp!=unique.end(); ++pp) {
- if(atoms.dd.g2l[pp->index()]>=0) unique_local.insert(*pp);
+ if(atoms.g2l[pp->index()]>=0) unique_local.insert(*pp);
}
} else {
unique_local.insert(unique.begin(),unique.end());
diff --git a/src/core/Atoms.cpp b/src/core/Atoms.cpp
index 10f15e88b..13eefd36a 100644
--- a/src/core/Atoms.cpp
+++ b/src/core/Atoms.cpp
@@ -175,7 +175,7 @@ void Atoms::shareAll() {
unique.clear();
// keep in unique only those atoms that are local
if(dd && shuffledAtoms>0) {
- for(int i=0; i<natoms; i++) if(dd.g2l[i]>=0) unique.insert(AtomNumber::index(i));
+ for(int i=0; i<natoms; i++) if(g2l[i]>=0) unique.insert(AtomNumber::index(i));
} else {
for(int i=0; i<natoms; i++) unique.insert(AtomNumber::index(i));
}
@@ -205,10 +205,8 @@ void Atoms::share(const std::set<AtomNumber>& unique) {
} else {
uniq_index.clear();
uniq_index.reserve(unique.size());
- if(dd && shuffledAtoms>0) {
- for(const auto & p : unique) uniq_index.push_back(dd.g2l[p.index()]);
- } else {
- for(const auto & p : unique) uniq_index.push_back(p.index());
+ if(shuffledAtoms>0) {
+ for(const auto & p : unique) uniq_index.push_back(g2l[p.index()]);
}
mdatoms->getPositions(unique,uniq_index,positions);
}
@@ -370,8 +368,8 @@ void Atoms::DomainDecomposition::enable(Communicator& c) {
void Atoms::setAtomsNlocal(int n) {
gatindex.resize(n);
+ g2l.resize(natoms,-1);
if(dd) {
- dd.g2l.resize(natoms,-1);
// Since these vectors are sent with MPI by using e.g.
// &dd.positionsToBeSent[0]
// we make sure they are non-zero-sized so as to
@@ -381,7 +379,7 @@ void Atoms::setAtomsNlocal(int n) {
dd.positionsToBeReceived.resize(natoms*5,0.0);
dd.indexToBeSent.resize(n,0);
dd.indexToBeReceived.resize(natoms,0);
- };
+ }
}
void Atoms::setAtomsGatindex(int*g,bool fortran) {
@@ -392,7 +390,7 @@ void Atoms::setAtomsGatindex(int*g,bool fortran) {
} else {
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;
+ for(unsigned i=0; i<g2l.size(); i++) g2l[i]=-1;
if( gatindex.size()==natoms ) {
shuffledAtoms=0;
for(unsigned i=0; i<gatindex.size(); i++) {
@@ -403,8 +401,8 @@ void Atoms::setAtomsGatindex(int*g,bool fortran) {
}
if(dd) {
dd.Sum(shuffledAtoms);
- for(unsigned i=0; i<gatindex.size(); i++) dd.g2l[gatindex[i]]=i;
}
+ for(unsigned i=0; i<gatindex.size(); i++) g2l[gatindex[i]]=i;
for(unsigned i=0; i<actions.size(); i++) {
// keep in unique only those atoms that are local
@@ -416,8 +414,8 @@ void Atoms::setAtomsGatindex(int*g,bool fortran) {
void Atoms::setAtomsContiguous(int start) {
ddStep=plumed.getStep();
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;
+ for(unsigned i=0; i<g2l.size(); i++) g2l[i]=-1;
+ for(unsigned i=0; i<gatindex.size(); i++) g2l[gatindex[i]]=i;
if(gatindex.size()<natoms) shuffledAtoms=1;
for(unsigned i=0; i<actions.size(); i++) {
// keep in unique only those atoms that are local
@@ -465,14 +463,29 @@ double Atoms::getKbT()const {
void Atoms::createFullList(int*n) {
- vector<AtomNumber> fullListTmp;
- for(unsigned i=0; i<actions.size(); i++) if(actions[i]->isActive())
- fullListTmp.insert(fullListTmp.end(),actions[i]->getUnique().begin(),actions[i]->getUnique().end());
- std::sort(fullListTmp.begin(),fullListTmp.end());
- int nn=std::unique(fullListTmp.begin(),fullListTmp.end())-fullListTmp.begin();
- fullList.resize(nn);
- for(int i=0; i<nn; ++i) fullList[i]=fullListTmp[i].index();
- *n=nn;
+ if(!massAndChargeOK && shareMassAndChargeOnlyAtFirstStep) {
+ *n=natoms;
+ fullList.resize(natoms);
+ for(unsigned i=0; i<natoms; i++) fullList[i]=i;
+ } else {
+// We update here the unique list defined at Atoms::unique.
+// This is not very clear, and probably should be coded differently.
+// Hopefully this fix the longstanding issue with NAMD.
+ unique.clear();
+ for(unsigned i=0; i<actions.size(); i++) {
+ if(actions[i]->isActive()) {
+ if(!actions[i]->getUnique().empty()) {
+ atomsNeeded=true;
+ // unique are the local atoms
+ unique.insert(actions[i]->getUnique().begin(),actions[i]->getUnique().end());
+ }
+ }
+ }
+ fullList.resize(0);
+ fullList.reserve(unique.size());
+ for(const auto & p : unique) fullList.push_back(p.index());
+ *n=fullList.size();
+ }
}
void Atoms::getFullList(int**x) {
diff --git a/src/core/Atoms.h b/src/core/Atoms.h
index db5fe381d..65af02105 100644
--- a/src/core/Atoms.h
+++ b/src/core/Atoms.h
@@ -49,6 +49,7 @@ class Atoms
int natoms;
std::set<AtomNumber> unique;
std::vector<unsigned> uniq_index;
+ std::vector<int> g2l;
std::vector<Vector> positions;
std::vector<Vector> forces;
std::vector<double> masses;
@@ -112,7 +113,6 @@ class Atoms
public:
bool on;
bool async;
- std::vector<int> g2l;
std::vector<Communicator::Request> mpi_request_positions;
std::vector<Communicator::Request> mpi_request_index;
--
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