PathBase::PathBase(const ActionOptions& ao):
Action(ao),
Mapping(ao)
{
bool noz; parseFlag("NOZPATH",noz);
parse("LAMBDA",lambda);
// Create the list of tasks
for(unsigned i=0;i<getNumberOfReferencePoints();++i) addTaskToList( i );
std::string empty="LABEL=zpath";
if(!noz) addVessel("ZPATH",empty,0);
}
ActionWithIntegral::ActionWithIntegral(const ActionOptions&ao):
Action(ao),
ActionWithInputGrid(ao)
{
plumed_assert( ingrid->getNumberOfComponents()==1 );
// Retrieve the volume of the grid (for integration)
volume = ingrid->getCellVolume();
// Create something that is going to calculate the sum of all the values
// at the various grid points - this is going to be the integral
std::string fake_input; addVessel( "SUM", fake_input, -1 ); readVesselKeywords();
// Now create task list - number of tasks is equal to the number of grid points
// as we have to evaluate the function at each grid points
for(unsigned i=0;i<ingrid->getNumberOfPoints();++i) addTaskToList(i);
// And activate all tasks
deactivateAllTasks();
for(unsigned i=0;i<ingrid->getNumberOfPoints();++i) taskFlags[i]=1;
lockContributors();
}
void FindContourSurface::prepareForAveraging() {
// Create a task list if first time
if( firsttime ) {
std::vector<unsigned> find( ingrid->getDimension() );
std::vector<unsigned> ind( mygrid->getDimension() );
for(unsigned i=0; i<mygrid->getNumberOfPoints(); ++i) {
find.assign( find.size(), 0 ); mygrid->getIndices( i, ind );
for(unsigned j=0; j<gdirs.size(); ++j) find[gdirs[j]]=ind[j];
// Current will be set equal to the start point for this grid index
addTaskToList( ingrid->getIndex(find) );
}
// And prepare the task list
deactivateAllTasks();
for(unsigned i=0; i<getFullNumberOfTasks(); ++i) taskFlags[i]=1;
lockContributors();
// Set the direction in which to look for the contour
direction.resize( ingrid->getDimension(), 0 );
direction[dir_n] = 0.999999999*ingrid->getGridSpacing()[dir_n];
}
}
BridgedMultiColvarFunction::BridgedMultiColvarFunction(const ActionOptions&ao):
Action(ao),
MultiColvarBase(ao)
{
std::string mlab; parse("DATA",mlab);
mycolv = plumed.getActionSet().selectWithLabel<MultiColvarBase*>(mlab);
if(!mycolv) error("action labeled " + mlab + " does not exist or is not a multicolvar");
BridgedMultiColvarFunction* check = dynamic_cast<BridgedMultiColvarFunction*>( mycolv );
if(check) error("cannot create a bridge of a bridge");
// When using numerical derivatives here we must use numerical derivatives
// in base multicolvar
if( checkNumericalDerivatives() ) mycolv->useNumericalDerivatives();
myBridgeVessel = mycolv->addBridgingVessel( this ); addDependency(mycolv);
weightHasDerivatives=true;
// Number of tasks is the same as the number in the underlying MultiColvar
for(unsigned i=0;i<mycolv->getFullNumberOfTasks();++i) addTaskToList( mycolv->getTaskCode(i) );
// Do all setup stuff in MultiColvarBase
resizeLocalArrays();
}
