void ActionWithVessel::readVesselKeywords(){
// Set maxderivatives if it is too big
if( maxderivatives>getNumberOfDerivatives() ) maxderivatives=getNumberOfDerivatives();
// Loop over all keywords find the vessels and create appropriate functions
for(unsigned i=0;i<keywords.size();++i){
std::string thiskey,input; thiskey=keywords.getKeyword(i);
// Check if this is a key for a vessel
if( vesselRegister().check(thiskey) ){
plumed_assert( keywords.style(thiskey,"vessel") );
bool dothis=false; parseFlag(thiskey,dothis);
if(dothis) addVessel( thiskey, input );
parse(thiskey,input);
if(input.size()!=0){
addVessel( thiskey, input );
} else {
for(unsigned i=1;;++i){
if( !parseNumbered(thiskey,i,input) ) break;
std::string ss; Tools::convert(i,ss);
addVessel( thiskey, input, i );
input.clear();
}
}
}
}
// Make sure all vessels have had been resized at start
if( functions.size()>0 ) resizeFunctions();
}
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;
}
BridgeVessel* ActionWithVessel::addBridgingVessel( ActionWithVessel* tome ){
VesselOptions da("","",0,"",this);
BridgeVessel* bv=new BridgeVessel(da);
bv->setOutputAction( tome );
functions.push_back( dynamic_cast<Vessel*>(bv) );
resizeFunctions();
return bv;
}
void ActionWithVessel::unlockContributors(){
if( contributorsAreUnlocked ) return;
nactive_tasks = fullTaskList.size();
for(unsigned i=0;i<fullTaskList.size();++i){
partialTaskList[i] = fullTaskList[i]; taskFlags[i]=0;
indexOfTaskInFullList[i]=i;
}
finishTaskListUpdate();
contributorsAreUnlocked=true;
resizeFunctions();
}
void ActionWithVessel::needsDerivatives(){
// Turn on the derivatives and resize
noderiv=false; resizeFunctions();
// Setting contributors unlocked here ensures that link cells are ignored
contributorsAreUnlocked=true; finishTaskListUpdate(); contributorsAreUnlocked=false;
// And turn on the derivatives in all actions on which we are dependent
for(unsigned i=0;i<getDependencies().size();++i){
ActionWithVessel* vv=dynamic_cast<ActionWithVessel*>( getDependencies()[i] );
if(vv) vv->needsDerivatives();
}
}
StoreDataVessel* ActionWithVessel::buildDataStashes( const bool& allow_wcutoff, const double& wtol ){
if(mydata) return mydata;
VesselOptions da("","",0,"",this);
StoreDataVessel* mm=new StoreDataVessel(da);
if( allow_wcutoff ) mm->setHardCutoffOnWeight( wtol );
addVessel(mm);
// Make sure resizing of vessels is done
resizeFunctions();
return mydata;
}
void ActionWithVessel::lockContributors(){
nactive_tasks = 0;
for(unsigned i=0;i<fullTaskList.size();++i){
// Deactivate sets inactive tasks to number not equal to zero
if( taskFlags[i]==0 ){
partialTaskList[nactive_tasks] = fullTaskList[i];
indexOfTaskInFullList[nactive_tasks]=i;
nactive_tasks++;
}
}
contributorsAreUnlocked=false;
finishTaskListUpdate();
resizeFunctions();
}
void ActionWithAveraging::setAveragingAction( AveragingVessel* av_vessel, const bool& usetasks ) {
myaverage=av_vessel; addVessel( myaverage );
useRunAllTasks=usetasks; resizeFunctions();
}