void SecondaryStructureRMSD::setSecondaryStructure( std::vector<Vector>& structure, double bondlength, double units ){
// If we are in natural units get conversion factor from nm into natural length units
if( plumed.getAtoms().usingNaturalUnits() ){
error("cannot use this collective variable when using natural units");
}
plumed_massert( !(align_strands && align_atom_1==0 && align_atom_2==0), "you must use setAtomsFromStrands with strands cutoff");
// Convert into correct units
for(unsigned i=0;i<structure.size();++i){
structure[i][0]*=units; structure[i][1]*=units; structure[i][2]*=units;
}
if( references.size()==0 ){
finishTaskListUpdate();
readVesselKeywords();
if( getNumberOfVessels()==0 ){
double r0; parse("R_0",r0); double d0; parse("D_0",d0);
int nn; parse("NN",nn); int mm; parse("MM",mm);
std::ostringstream ostr;
ostr<<"RATIONAL R_0="<<r0<<" D_0="<<d0<<" NN="<<nn<<" MM="<<mm;
std::string input=ostr.str(); addVessel( "LESS_THAN", input, -1 ); // -1 here means that this value will be named getLabel()
readVesselKeywords(); // This makes sure resizing is done
}
}
// Set the reference structure
references.push_back( metricRegister().create<SingleDomainRMSD>( alignType ) );
unsigned nn=references.size()-1;
std::vector<double> align( structure.size(), 1.0 ), displace( structure.size(), 1.0 );
references[nn]->setBoundsOnDistances( true , bondlength ); // We always use pbc
references[nn]->setReferenceAtoms( structure, align, displace );
// references[nn]->setNumberOfAtoms( structure.size() );
}
vesselbase::StoreDataVessel* MultiColvarBase::buildDataStashes( const bool& allow_wcutoff, const double& wtol ){
// Check if vessels have already been setup
for(unsigned i=0;i<getNumberOfVessels();++i){
StoreColvarVessel* ssc=dynamic_cast<StoreColvarVessel*>( getPntrToVessel(i) );
if(ssc){
if( allow_wcutoff && !ssc->weightCutoffIsOn() ) error("Cannot have more than one data stash with different properties");
if( !allow_wcutoff && ssc->weightCutoffIsOn() ) error("Cannot have more than one data stash with different properties");
return ssc;
}
}
// Setup central atoms
vesselbase::VesselOptions da("","",0,"",this);
mycatoms=new StoreCentralAtomsVessel(da);
if( allow_wcutoff ) mycatoms->setHardCutoffOnWeight( wtol );
addVessel(mycatoms);
// Setup store values vessel
vesselbase::VesselOptions ta("","",0,"",this);
myvalues=new StoreColvarVessel(ta);
if( allow_wcutoff ) myvalues->setHardCutoffOnWeight( wtol );
addVessel(myvalues);
// Make sure resizing of vessels is done
resizeFunctions();
return myvalues;
}
void ClusterAnalysisBase::turnOnDerivatives(){
// Check for dubious vessels
for(unsigned i=0;i<getNumberOfVessels();++i){
if( getPntrToVessel(i)->getName()=="MEAN" ) error("MEAN of cluster is not differentiable");
if( getPntrToVessel(i)->getName()=="VMEAN" ) error("VMEAN of cluster is not differentiable");
}
MultiColvarBase::turnOnDerivatives();
}
bool ActionWithVessel::getForcesFromVessels( std::vector<double>& forcesToApply ){
plumed_dbg_assert( forcesToApply.size()==getNumberOfDerivatives() );
forcesToApply.assign( forcesToApply.size(),0.0 );
bool wasforced=false;
for(unsigned i=0;i<getNumberOfVessels();++i){
if( (functions[i]->applyForce( tmpforces )) ){
wasforced=true;
for(unsigned j=0;j<forcesToApply.size();++j) forcesToApply[j]+=tmpforces[j];
}
}
return wasforced;
}
void MultiColvarBase::addTaskToList( const unsigned& taskCode ){
plumed_assert( getNumberOfVessels()==0 );
ActionWithVessel::addTaskToList( taskCode );
}
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;
}
}
}
