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();
}
void ActionWithVessel::addVessel( const std::string& name, const std::string& input, const int numlab ){
VesselOptions da(name,"",numlab,input,this);
Vessel* vv=vesselRegister().create(name,da);
FunctionVessel* fv=dynamic_cast<FunctionVessel*>(vv);
if( fv ){
std::string mylabel=Vessel::transformName( name );
plumed_massert( keywords.outputComponentExists(mylabel,false), "a description of the value calculated by vessel " + name + " has not been added to the manual");
}
addVessel(vv);
}
void ActionWithVessel::registerKeywords(Keywords& keys){
keys.add("optional","TOL","this keyword can be used to speed up your calculation. When accumulating sums in which the individual "
"terms are numbers inbetween zero and one it is assumed that terms less than a certain tolerance "
"make only a small contribution to the sum. They can thus be safely ignored as can the the derivatives "
"wrt these small quantities.");
keys.reserve("hidden","NL_TOL","this keyword can be used to speed up your calculation. It must be used in conjuction with the TOL "
"keyword and the value for NL_TOL must be set less than the value for TOL. This keyword ensures that "
"quantities, which are much less than TOL and which will thus not added to the sums being accumulated "
"are not calculated at every step. They are only calculated when the neighbor list is updated.");
keys.add("hidden","MAXDERIVATIVES","The maximum number of derivatives that can be used when storing data. This controls when "
"we have to start using lowmem");
keys.addFlag("SERIAL",false,"do the calculation in serial. Do not parallelize");
keys.addFlag("LOWMEM",false,"lower the memory requirements");
keys.add( vesselRegister().getKeywords() );
}
void ActionWithVessel::addVessel( const std::string& name, const std::string& input, const int numlab, const std::string thislab ){
VesselOptions da(name,thislab,numlab,input,this);
Vessel* vv=vesselRegister().create(name,da); vv->checkRead();
addVessel(vv);
}
