void DFSClusterDiameter::calculate(){
// Do the clustring
performClustering();
// Retrieve the atoms in the largest cluster
std::vector<unsigned> myatoms; retrieveAtomsInCluster( clustr, myatoms );
// Activate the relevant tasks
deactivateAllTasks(); std::vector<unsigned> active_tasks( getFullNumberOfTasks(), 0 );
for(unsigned i=1;i<myatoms.size();++i){
for(unsigned j=0;j<i;++j) active_tasks[ myatoms[i]*getNumberOfNodes() + myatoms[j] ] = 1;
}
activateTheseTasks( active_tasks );
// Now do the calculation
runAllTasks();
}
void MultiColvarBase::setupLinkCells(){
if( !linkcells.enabled() ) return ;
unsigned iblock, jblock;
if( usespecies ){
iblock=0;
} else if( current_atoms.size()<4 ){
iblock=1;
} else {
plumed_error();
}
// Count number of currently active atoms
unsigned nactive_atoms=0;
for(unsigned i=0;i<ablocks[iblock].size();++i){
if( isCurrentlyActive( ablocks[iblock][i] ) ) nactive_atoms++;
}
std::vector<Vector> ltmp_pos( nactive_atoms );
std::vector<unsigned> ltmp_ind( nactive_atoms );
nactive_atoms=0;
if( usespecies ){
ltmp_pos.resize( ablocks[0].size() ); ltmp_ind.resize( ablocks[0].size() );
for(unsigned i=0;i<ablocks[0].size();++i){
if( !isCurrentlyActive( ablocks[0][i] ) ) continue;
ltmp_ind[nactive_atoms]=ablocks[0][i];
ltmp_pos[nactive_atoms]=getPositionOfAtomForLinkCells( ltmp_ind[nactive_atoms] );
nactive_atoms++;
}
} else {
ltmp_pos.resize( ablocks[1].size() ); ltmp_ind.resize( ablocks[1].size() );
for(unsigned i=0;i<ablocks[1].size();++i){
if( !isCurrentlyActive( ablocks[1][i] ) ) continue;
ltmp_ind[nactive_atoms]=i;
ltmp_pos[nactive_atoms]=getPositionOfAtomForLinkCells( ablocks[1][i] );
nactive_atoms++;
}
}
// Build the lists for the link cells
linkcells.buildCellLists( ltmp_pos, ltmp_ind, getPbc() );
if( !usespecies ){
// Get some parallel info
unsigned stride=comm.Get_size();
unsigned rank=comm.Get_rank();
if( serialCalculation() ){ stride=1; rank=0; }
// Ensure we only do tasks where atoms are in appropriate link cells
std::vector<unsigned> linked_atoms( 1+ablocks[1].size() );
std::vector<unsigned> active_tasks( getFullNumberOfTasks(), 0 );
for(unsigned i=rank;i<ablocks[0].size();i+=stride){
if( !isCurrentlyActive( ablocks[0][i] ) ) continue;
natomsper=1; linked_atoms[0]=ltmp_ind[0]; // Note we always check atom 0 because it is simpler than changing LinkCells.cpp
linkcells.retrieveNeighboringAtoms( getPositionOfAtomForLinkCells( ablocks[0][i] ), natomsper, linked_atoms );
for(unsigned j=0;j<natomsper;++j){
for(unsigned k=bookeeping(i,linked_atoms[j]).first;k<bookeeping(i,linked_atoms[j]).second;++k) active_tasks[k]=1;
}
}
if( !serialCalculation() ) comm.Sum( active_tasks );
deactivateAllTasks();
activateTheseTasks( active_tasks );
contributorsAreUnlocked=false;
}
}
void MultiColvarBase::setupLinkCells(){
if( !linkcells.enabled() ) return ;
unsigned iblock;
if( usespecies ){
iblock=0;
} else if( ablocks.size()<4 ){
iblock=1;
} else {
plumed_error();
}
// Count number of currently active atoms
unsigned nactive_atoms=0;
for(unsigned i=0;i<ablocks[iblock].size();++i){
if( isCurrentlyActive( iblock, ablocks[iblock][i] ) ) nactive_atoms++;
}
std::vector<Vector> ltmp_pos( nactive_atoms );
std::vector<unsigned> ltmp_ind( nactive_atoms );
nactive_atoms=0;
if( usespecies ){
for(unsigned i=0;i<ablocks[0].size();++i){
if( !isCurrentlyActive( 0, ablocks[0][i] ) ) continue;
ltmp_ind[nactive_atoms]=ablocks[0][i];
ltmp_pos[nactive_atoms]=getPositionOfAtomForLinkCells( ltmp_ind[nactive_atoms] );
nactive_atoms++;
}
} else {
for(unsigned i=0;i<ablocks[1].size();++i){
if( !isCurrentlyActive( 1, ablocks[1][i] ) ) continue;
ltmp_ind[nactive_atoms]=i;
ltmp_pos[nactive_atoms]=getPositionOfAtomForLinkCells( ablocks[1][i] );
nactive_atoms++;
}
}
// Build the lists for the link cells
linkcells.buildCellLists( ltmp_pos, ltmp_ind, getPbc() );
if( !usespecies ){
// Get some parallel info
unsigned stride=comm.Get_size();
unsigned rank=comm.Get_rank();
if( serialCalculation() ){ stride=1; rank=0; }
// Ensure we only do tasks where atoms are in appropriate link cells
std::vector<unsigned> linked_atoms( 1+ablocks[1].size() );
std::vector<unsigned> active_tasks( getFullNumberOfTasks(), 0 );
for(unsigned i=rank;i<ablocks[0].size();i+=stride){
if( !isCurrentlyActive( 0, ablocks[0][i] ) ) continue;
unsigned natomsper=1; linked_atoms[0]=ltmp_ind[0]; // Note we always check atom 0 because it is simpler than changing LinkCells.cpp
linkcells.retrieveNeighboringAtoms( getPositionOfAtomForLinkCells( ablocks[0][i] ), natomsper, linked_atoms );
for(unsigned j=0;j<natomsper;++j){
for(unsigned k=bookeeping(i,linked_atoms[j]).first;k<bookeeping(i,linked_atoms[j]).second;++k) active_tasks[k]=1;
}
}
if( !serialCalculation() ) comm.Sum( active_tasks );
deactivateAllTasks();
activateTheseTasks( active_tasks );
contributorsAreUnlocked=false;
} else {
// Now check for calculating volumes (currently this is only done for usespecies style commands
// as it is difficult to do with things like DISTANCES or ANGLES and I think pointless
bool justVolumes=true;
for(unsigned i=0;i<getNumberOfVessels();++i){
vesselbase::BridgeVessel* myb=dynamic_cast<vesselbase::BridgeVessel*>( getPntrToVessel(i) );
if( !myb ){ justVolumes=false; break; }
ActionVolume* myv=dynamic_cast<ActionVolume*>( myb->getOutputAction() );
if( !myv ){ justVolumes=false; break; }
}
// Now ensure that we only do calculations for those atoms in the relevant volume
if( justVolumes ){
bool justVolumes=true;
// Setup the regions in the action volume objects
for(unsigned i=0;i<getNumberOfVessels();++i){
vesselbase::BridgeVessel* myb=dynamic_cast<vesselbase::BridgeVessel*>( getPntrToVessel(i) );
ActionVolume* myv=dynamic_cast<ActionVolume*>( myb->getOutputAction() );
myv->retrieveAtoms(); myv->setupRegions();
}
unsigned stride=comm.Get_size();
unsigned rank=comm.Get_rank();
if( serialCalculation() ){ stride=1; rank=0; }
unsigned nactive=0;
std::vector<unsigned> active_tasks( getFullNumberOfTasks(), 0 );
for(unsigned i=rank;i<getFullNumberOfTasks();i+=stride){
bool invol=false;
for(unsigned j=0;j<getNumberOfVessels();++j){
vesselbase::BridgeVessel* myb=dynamic_cast<vesselbase::BridgeVessel*>( getPntrToVessel(j) );
ActionVolume* myv=dynamic_cast<ActionVolume*>( myb->getOutputAction() );
if( myv->inVolumeOfInterest(i) ){ invol=true; }
}
if( invol ){ nactive++; active_tasks[i]=1; }
}
if( !serialCalculation() ) comm.Sum( active_tasks );
deactivateAllTasks();
activateTheseTasks( active_tasks );
contributorsAreUnlocked=false;
}
}
}