From 32de30f7c45158d8a3413d5e8a6a872bcfe15b16 Mon Sep 17 00:00:00 2001
From: Giovanni Bussi <giovanni.bussi@gmail.com>
Date: Wed, 21 Aug 2013 12:11:41 +0200
Subject: [PATCH] Replacements with enhanced Communicator class
I replaced everywhere it made sense the new Communicator class
syntax. This commit is not strictly necessary, but provides
examples of the simpler syntax so I think should be merged
---
src/bias/MetaD.cpp | 8 +++----
src/cltools/Driver.cpp | 10 ++++-----
src/colvar/CoordinationBase.cpp | 4 ++--
src/colvar/PathMSDBase.cpp | 4 ++--
src/core/Atoms.cpp | 6 +++---
src/core/GREX.cpp | 24 ++++++++++-----------
src/multicolvar/StoreCentralAtomsVessel.cpp | 2 +-
src/multicolvar/StoreColvarVessel.cpp | 2 +-
src/tools/BiasRepresentation.cpp | 4 ++--
src/tools/OFile.cpp | 2 +-
src/vesselbase/ActionWithVessel.cpp | 2 +-
11 files changed, 34 insertions(+), 34 deletions(-)
diff --git a/src/bias/MetaD.cpp b/src/bias/MetaD.cpp
index b241afa03..4e4602fce 100644
--- a/src/bias/MetaD.cpp
+++ b/src/bias/MetaD.cpp
@@ -651,8 +651,8 @@ void MetaD::addGaussian(const Gaussian& hill)
BiasGrid_->getPoint(ineigh,xx);
allbias[i]=evaluateGaussian(xx,hill,&allder[ncv*i]);
}
- comm.Sum(&allbias[0],allbias.size());
- comm.Sum(&allder[0],allder.size());
+ comm.Sum(allbias);
+ comm.Sum(allder);
for(unsigned i=0;i<neighbors.size();++i){
unsigned ineigh=neighbors[i];
for(unsigned j=0;j<ncv;++j){der[j]=allder[ncv*i+j];}
@@ -719,8 +719,8 @@ double MetaD::getBiasAndDerivatives(const vector<double>& cv, double* der)
//finite difference test
//finiteDifferenceGaussian(cv,hills_[i]);
}
- comm.Sum(&bias,1);
- if(der) comm.Sum(&der[0],getNumberOfArguments());
+ comm.Sum(bias);
+ if(der) comm.Sum(der,getNumberOfArguments());
}else{
if(der){
vector<double> vder(getNumberOfArguments());
diff --git a/src/cltools/Driver.cpp b/src/cltools/Driver.cpp
index e23712919..9d586582a 100644
--- a/src/cltools/Driver.cpp
+++ b/src/cltools/Driver.cpp
@@ -380,8 +380,8 @@ int Driver<real>::main(FILE* in,FILE*out,Communicator& pc){
start[i+1]=start[i]+loc[i];
}
loc[npe-1]=natoms-start[npe-1];
- intracomm.Bcast(&loc[0],npe,0);
- intracomm.Bcast(&start[0],npe,0);
+ intracomm.Bcast(loc,0);
+ intracomm.Bcast(start,0);
pd_nlocal=loc[intracomm.Get_rank()];
pd_start=start[intracomm.Get_rank()];
if(intracomm.Get_rank()==0){
@@ -516,8 +516,8 @@ int Driver<real>::main(FILE* in,FILE*out,Communicator& pc){
p.cmd("calc");
// this is necessary as only processor zero is adding to the virial:
- intracomm.Bcast(&virial[0],9,0);
- if(debug_pd) intracomm.Sum(&forces[0],natoms*3);
+ intracomm.Bcast(virial,0);
+ if(debug_pd) intracomm.Sum(forces);
if(debug_dd){
for(int i=0;i<dd_nlocal;i++){
forces[3*dd_gatindex[i]+0]=dd_forces[3*i+0];
@@ -525,7 +525,7 @@ int Driver<real>::main(FILE* in,FILE*out,Communicator& pc){
forces[3*dd_gatindex[i]+2]=dd_forces[3*i+2];
}
dd_forces.assign(3*natoms,0.0);
- intracomm.Sum(&forces[0],natoms*3);
+ intracomm.Sum(forces);
}
if(debug_grex &&step%grex_stride==0){
p.cmd("GREX savePositions");
diff --git a/src/colvar/CoordinationBase.cpp b/src/colvar/CoordinationBase.cpp
index 3da9a230b..680e112c2 100644
--- a/src/colvar/CoordinationBase.cpp
+++ b/src/colvar/CoordinationBase.cpp
@@ -163,9 +163,9 @@ void CoordinationBase::calculate()
}
if(!serial){
- comm.Sum(&ncoord,1);
+ comm.Sum(ncoord);
if(!deriv.empty()) comm.Sum(&deriv[0][0],3*deriv.size());
- comm.Sum(&virial[0][0],9);
+ comm.Sum(virial);
}
for(unsigned i=0;i<deriv.size();++i) setAtomsDerivatives(i,deriv[i]);
diff --git a/src/colvar/PathMSDBase.cpp b/src/colvar/PathMSDBase.cpp
index e741bc582..7913eddda 100644
--- a/src/colvar/PathMSDBase.cpp
+++ b/src/colvar/PathMSDBase.cpp
@@ -137,8 +137,8 @@ void PathMSDBase::calculate(){
for(unsigned j=0;j<nat;j++) tmp_derivs2[i*nat+j]=tmp_derivs[j];
}
// reduce over all processors
- comm.Sum(&tmp_distances[0],imgVec.size());
- comm.Sum(&tmp_derivs2[0][0],3*imgVec.size()*nat);
+ comm.Sum(tmp_distances);
+ comm.Sum(tmp_derivs2);
// assign imgVec[i].distance and imgVec[i].distder
for(unsigned i=0;i<imgVec.size();i++){
imgVec[i].distance=tmp_distances[i];
diff --git a/src/core/Atoms.cpp b/src/core/Atoms.cpp
index ce3ec1455..4fc70c706 100644
--- a/src/core/Atoms.cpp
+++ b/src/core/Atoms.cpp
@@ -172,7 +172,7 @@ void Atoms::share(const std::set<AtomNumber>& unique){
vector<int> displ(n);
vector<int> counts5(n);
vector<int> displ5(n);
- dd.Allgather(&count,1,&counts[0],1);
+ dd.Allgather(count,counts);
displ[0]=0;
for(int i=1;i<n;++i) displ[i]=displ[i-1]+counts[i-1];
for(int i=0;i<n;++i) counts5[i]=counts[i]*5;
@@ -199,7 +199,7 @@ void Atoms::wait(){
dataCanBeSet=false; // Everything should be set by this stage
if(dd){
- dd.Bcast(&box[0][0],9,0);
+ dd.Bcast(box,0);
}
pbc.setBox(box);
@@ -224,7 +224,7 @@ void Atoms::wait(){
charges[dd.indexToBeReceived[i]] =dd.positionsToBeReceived[5*i+4];
}
}
- if(collectEnergy) dd.Sum(&energy,1);
+ if(collectEnergy) dd.Sum(energy);
}
}
diff --git a/src/core/GREX.cpp b/src/core/GREX.cpp
index 081f5ddce..1e0250e13 100644
--- a/src/core/GREX.cpp
+++ b/src/core/GREX.cpp
@@ -72,13 +72,13 @@ void GREX::cmd(const string&key,void*val){
std::string s;
// note that for PEs!=root this is automatically 0 (comm defaults to MPI_COMM_SELF)
myreplica=intercomm.Get_rank();
- intracomm.Sum(&myreplica,1);
+ intracomm.Sum(myreplica);
Tools::convert(myreplica,s);
plumedMain.setSuffix("."+s);
}else if(key=="prepare"){
CHECK_INIT(initialized,key);
if(intracomm.Get_rank()==0) return;
- intracomm.Bcast(&partner,1,0);
+ intracomm.Bcast(partner,0);
calculate();
}else if(key=="setPartner"){
CHECK_INIT(initialized,key);
@@ -89,7 +89,7 @@ void GREX::cmd(const string&key,void*val){
}else if(key=="calculate"){
CHECK_INIT(initialized,key);
if(intracomm.Get_rank()!=0) return;
- intracomm.Bcast(&partner,1,0);
+ intracomm.Bcast(partner,0);
calculate();
}else if(key=="getLocalDeltaBias"){
CHECK_INIT(initialized,key);
@@ -102,14 +102,14 @@ void GREX::cmd(const string&key,void*val){
double x;
atoms.MD2double(val,x);
localUNow=x*(atoms.getMDUnits().getEnergy()/atoms.getUnits().getEnergy());
- intracomm.Sum(&localUNow,1);
+ intracomm.Sum(localUNow);
}else if(key=="cacheLocalUSwap"){
CHECK_INIT(initialized,key);
CHECK_NULL(val,key);
double x;
atoms.MD2double(val,x);
localUSwap=x*(atoms.getMDUnits().getEnergy()/atoms.getUnits().getEnergy());
- intracomm.Sum(&localUSwap,1);
+ intracomm.Sum(localUSwap);
}else if(key=="getForeignDeltaBias"){
CHECK_INIT(initialized,key);
CHECK_NULL(val,key);
@@ -120,7 +120,7 @@ void GREX::cmd(const string&key,void*val){
if(intracomm.Get_rank()!=0) return;
allDeltaBias.assign(intercomm.Get_size(),0.0);
allDeltaBias[intercomm.Get_rank()]=localDeltaBias;
- intercomm.Sum(&allDeltaBias[0],intercomm.Get_size());
+ intercomm.Sum(allDeltaBias);
}else{
// multi word commands
std::vector<std::string> words=Tools::getWords(key);
@@ -158,11 +158,11 @@ void GREX::calculate(){
vector<char> rbuf(nn);
localDeltaBias=-plumedMain.getBias();
if(intracomm.Get_rank()==0){
- Communicator::Request req=intercomm.Isend(&buffer.c_str()[0],nn,partner,1066);
- intercomm.Recv(&rbuf[0],rbuf.size(),partner,1066);
+ Communicator::Request req=intercomm.Isend(buffer,partner,1066);
+ intercomm.Recv(rbuf,partner,1066);
req.wait();
}
- intracomm.Bcast(&rbuf[0],nn,0);
+ intracomm.Bcast(rbuf,0);
istringstream i(string(&rbuf[0],rbuf.size()));
atoms.readBinary(i);
plumedMain.setExchangeStep(true);
@@ -172,12 +172,12 @@ void GREX::calculate(){
localDeltaBias+=plumedMain.getBias();
localDeltaBias+=localUSwap-localUNow;
if(intracomm.Get_rank()==0){
- Communicator::Request req=intercomm.Isend(&localDeltaBias,1,partner,1067);
- intercomm.Recv(&foreignDeltaBias,1,partner,1067);
+ Communicator::Request req=intercomm.Isend(localDeltaBias,partner,1067);
+ intercomm.Recv(foreignDeltaBias,partner,1067);
req.wait();
//fprintf(stderr,">>> %d %d %20.12f %20.12f %20.12f %20.12f\n",intercomm.Get_rank(),partner,localDeltaBias,foreignDeltaBias,localUSwap,localUNow);
}
- intracomm.Bcast(&foreignDeltaBias,1,0);
+ intracomm.Bcast(foreignDeltaBias,0);
}
}
diff --git a/src/multicolvar/StoreCentralAtomsVessel.cpp b/src/multicolvar/StoreCentralAtomsVessel.cpp
index d34f14cd8..833d008f0 100644
--- a/src/multicolvar/StoreCentralAtomsVessel.cpp
+++ b/src/multicolvar/StoreCentralAtomsVessel.cpp
@@ -79,7 +79,7 @@ bool StoreCentralAtomsVessel::calculate(){
}
void StoreCentralAtomsVessel::finish(){
- comm.Sum( &active_atoms[0], active_atoms.size() );
+ comm.Sum(active_atoms);
}
Vector StoreCentralAtomsVessel::getPosition( const unsigned& ivec ) const {
diff --git a/src/multicolvar/StoreColvarVessel.cpp b/src/multicolvar/StoreColvarVessel.cpp
index 4ea5301c2..893252a2c 100644
--- a/src/multicolvar/StoreColvarVessel.cpp
+++ b/src/multicolvar/StoreColvarVessel.cpp
@@ -98,7 +98,7 @@ bool StoreColvarVessel::calculate(){
}
void StoreColvarVessel::finish(){
- comm.Sum( &active_atoms[0], active_atoms.size() );
+ comm.Sum(active_atoms);
performCalculationUsingAllValues();
}
diff --git a/src/tools/BiasRepresentation.cpp b/src/tools/BiasRepresentation.cpp
index 66c3033cb..25d35ee9b 100644
--- a/src/tools/BiasRepresentation.cpp
+++ b/src/tools/BiasRepresentation.cpp
@@ -189,8 +189,8 @@ void BiasRepresentation::pushKernel( IFile *ifile ){
// a pointer of double as it was in old gaussian
for(int j=0;j<ndim;++j){ allder[ndim*i+j]=tmpder[j];tmpder[j]=0.;}
}
- mycomm.Sum(&allbias[0],allbias.size());
- mycomm.Sum(&allder[0],allder.size());
+ mycomm.Sum(allbias);
+ mycomm.Sum(allder);
for(unsigned i=0;i<neighbors.size();++i){
unsigned ineigh=neighbors[i];
for(unsigned j=0;j<ndim;++j){der[j]=allder[ndim*i+j];}
diff --git a/src/tools/OFile.cpp b/src/tools/OFile.cpp
index 7820ee202..f61d89d3a 100644
--- a/src/tools/OFile.cpp
+++ b/src/tools/OFile.cpp
@@ -42,7 +42,7 @@ size_t OFile::llwrite(const char*ptr,size_t s){
if(!fp) plumed_merror("writing on uninitilized File");
r=fwrite(ptr,1,s,fp);
}
- if(comm) comm->Bcast(&r,1,0);
+ if(comm) comm->Bcast(r,0);
return r;
}
diff --git a/src/vesselbase/ActionWithVessel.cpp b/src/vesselbase/ActionWithVessel.cpp
index b9b3436f3..6ed5e7a2a 100644
--- a/src/vesselbase/ActionWithVessel.cpp
+++ b/src/vesselbase/ActionWithVessel.cpp
@@ -227,7 +227,7 @@ bool ActionWithVessel::calculateAllVessels(){
void ActionWithVessel::finishComputations(){
// MPI Gather everything
- if(!serial && buffer.size()>0) comm.Sum( &buffer[0],buffer.size() );
+ if(!serial && buffer.size()>0) comm.Sum( buffer);
// Set the final value of the function
for(unsigned j=0;j<functions.size();++j) functions[j]->finish();
--
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