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Only share mass and charge at first step
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@GiovanniBussi
GiovanniBussi committed Sep 17, 2013
1 parent 50ce0d0 commit 73c5c8f
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Showing 2 changed files with 52 additions and 22 deletions.
73 changes: 51 additions & 22 deletions src/core/Atoms.cpp
View file
Expand Up @@ -32,6 +32,10 @@ using namespace std;

namespace PLMD {

/// We assume that charges and masses are constant along the simulation
/// Set this to false if you want to revert to the original (expensive) behavior
static const bool shareMassAndChargeOnlyAtFirstStep=true;

class PlumedMain;

Atoms::Atoms(PlumedMain&plumed):
Expand All @@ -47,6 +51,7 @@ Atoms::Atoms(PlumedMain&plumed):
boxHasBeenSet(false),
forcesHaveBeenSet(0),
virialHasBeenSet(false),
massAndChargeOK(false),
plumed(plumed),
naturalUnits(false),
timestep(0.0),
Expand Down Expand Up @@ -121,6 +126,13 @@ void Atoms::setForces(void*p,int i){

void Atoms::share(){
std::set<AtomNumber> unique;
// At first step I scatter all the atoms so as to store their mass and charge
// Notice that this works with the assumption that charges and masses are
// not changing during the simulation!
if(!massAndChargeOK && shareMassAndChargeOnlyAtFirstStep){
shareAll();
return;
}
if(dd && int(gatindex.size())<natoms){
for(unsigned i=0;i<actions.size();i++) if(actions[i]->isActive()) {
unique.insert(actions[i]->getUnique().begin(),actions[i]->getUnique().end());
Expand All @@ -139,9 +151,14 @@ void Atoms::shareAll(){
void Atoms::share(const std::set<AtomNumber>& unique){
plumed_assert( positionsHaveBeenSet==3 && massesHaveBeenSet );
mdatoms->getBox(box);
mdatoms->getMasses(gatindex,masses);
mdatoms->getCharges(gatindex,charges);
mdatoms->getPositions(gatindex,positions);
// how many double per atom should be scattered:
int ndata=3;
if(!massAndChargeOK){
ndata=5;
mdatoms->getCharges(gatindex,charges);
mdatoms->getMasses(gatindex,masses);
}
if(dd && int(gatindex.size())<natoms){
if(dd.async){
for(unsigned i=0;i<dd.mpi_request_positions.size();i++) dd.mpi_request_positions[i].wait();
Expand All @@ -151,11 +168,13 @@ void Atoms::share(const std::set<AtomNumber>& unique){
for(std::set<AtomNumber>::const_iterator p=unique.begin();p!=unique.end();++p){
if(dd.g2l[p->index()]>=0){
dd.indexToBeSent[count]=p->index();
dd.positionsToBeSent[5*count+0]=positions[p->index()][0];
dd.positionsToBeSent[5*count+1]=positions[p->index()][1];
dd.positionsToBeSent[5*count+2]=positions[p->index()][2];
dd.positionsToBeSent[5*count+3]=masses[p->index()];
dd.positionsToBeSent[5*count+4]=charges[p->index()];
dd.positionsToBeSent[ndata*count+0]=positions[p->index()][0];
dd.positionsToBeSent[ndata*count+1]=positions[p->index()][1];
dd.positionsToBeSent[ndata*count+2]=positions[p->index()][2];
if(!massAndChargeOK){
dd.positionsToBeSent[ndata*count+3]=masses[p->index()];
dd.positionsToBeSent[ndata*count+4]=charges[p->index()];
}
count++;
}
}
Expand All @@ -164,7 +183,7 @@ void Atoms::share(const std::set<AtomNumber>& unique){
dd.mpi_request_index.resize(dd.Get_size());
for(int i=0;i<dd.Get_size();i++){
dd.mpi_request_index[i]=dd.Isend(&dd.indexToBeSent[0],count,i,666);
dd.mpi_request_positions[i]=dd.Isend(&dd.positionsToBeSent[0],5*count,i,667);
dd.mpi_request_positions[i]=dd.Isend(&dd.positionsToBeSent[0],ndata*count,i,667);
}
}else{
const int n=(dd.Get_size());
Expand All @@ -175,17 +194,19 @@ void Atoms::share(const std::set<AtomNumber>& unique){
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;
for(int i=0;i<n;++i) displ5[i]=displ[i]*5;
for(int i=0;i<n;++i) counts5[i]=counts[i]*ndata;
for(int i=0;i<n;++i) displ5[i]=displ[i]*ndata;
dd.Allgatherv(&dd.indexToBeSent[0],count,&dd.indexToBeReceived[0],&counts[0],&displ[0]);
dd.Allgatherv(&dd.positionsToBeSent[0],5*count,&dd.positionsToBeReceived[0],&counts5[0],&displ5[0]);
dd.Allgatherv(&dd.positionsToBeSent[0],ndata*count,&dd.positionsToBeReceived[0],&counts5[0],&displ5[0]);
int tot=displ[n-1]+counts[n-1];
for(int i=0;i<tot;i++){
positions[dd.indexToBeReceived[i]][0]=dd.positionsToBeReceived[5*i+0];
positions[dd.indexToBeReceived[i]][1]=dd.positionsToBeReceived[5*i+1];
positions[dd.indexToBeReceived[i]][2]=dd.positionsToBeReceived[5*i+2];
masses[dd.indexToBeReceived[i]] =dd.positionsToBeReceived[5*i+3];
charges[dd.indexToBeReceived[i]] =dd.positionsToBeReceived[5*i+4];
positions[dd.indexToBeReceived[i]][0]=dd.positionsToBeReceived[ndata*i+0];
positions[dd.indexToBeReceived[i]][1]=dd.positionsToBeReceived[ndata*i+1];
positions[dd.indexToBeReceived[i]][2]=dd.positionsToBeReceived[ndata*i+2];
if(!massAndChargeOK){
masses[dd.indexToBeReceived[i]] =dd.positionsToBeReceived[ndata*i+3];
charges[dd.indexToBeReceived[i]] =dd.positionsToBeReceived[ndata*i+4];
}
}
}
}
Expand All @@ -197,6 +218,9 @@ void Atoms::share(const std::set<AtomNumber>& unique){

void Atoms::wait(){
dataCanBeSet=false; // Everything should be set by this stage
// How many double per atom should be scattered
int ndata=3;
if(!massAndChargeOK)ndata=5;

if(dd){
dd.Bcast(box,0);
Expand All @@ -213,19 +237,24 @@ void Atoms::wait(){
for(int i=0;i<dd.Get_size();i++){
dd.Recv(&dd.indexToBeReceived[count],dd.indexToBeReceived.size()-count,i,666,status);
int c=status.Get_count<int>();
dd.Recv(&dd.positionsToBeReceived[5*count],dd.positionsToBeReceived.size()-5*count,i,667);
dd.Recv(&dd.positionsToBeReceived[ndata*count],dd.positionsToBeReceived.size()-ndata*count,i,667);
count+=c;
}
for(int i=0;i<count;i++){
positions[dd.indexToBeReceived[i]][0]=dd.positionsToBeReceived[5*i+0];
positions[dd.indexToBeReceived[i]][1]=dd.positionsToBeReceived[5*i+1];
positions[dd.indexToBeReceived[i]][2]=dd.positionsToBeReceived[5*i+2];
masses[dd.indexToBeReceived[i]] =dd.positionsToBeReceived[5*i+3];
charges[dd.indexToBeReceived[i]] =dd.positionsToBeReceived[5*i+4];
positions[dd.indexToBeReceived[i]][0]=dd.positionsToBeReceived[ndata*i+0];
positions[dd.indexToBeReceived[i]][1]=dd.positionsToBeReceived[ndata*i+1];
positions[dd.indexToBeReceived[i]][2]=dd.positionsToBeReceived[ndata*i+2];
if(!massAndChargeOK){
masses[dd.indexToBeReceived[i]] =dd.positionsToBeReceived[ndata*i+3];
charges[dd.indexToBeReceived[i]] =dd.positionsToBeReceived[ndata*i+4];
}
}
}
if(collectEnergy) dd.Sum(energy);
}
// I take note that masses and charges have been set once for all
// at the beginning of the simulation.
if(shareMassAndChargeOnlyAtFirstStep) massAndChargeOK=true;
}

void Atoms::updateForces(){
Expand Down
1 change: 1 addition & 0 deletions src/core/Atoms.h
View file
Expand Up @@ -69,6 +69,7 @@ class Atoms
bool boxHasBeenSet;
unsigned forcesHaveBeenSet;
bool virialHasBeenSet;
bool massAndChargeOK;

std::map<std::string,std::vector<AtomNumber> > groups;

Expand Down

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