ClusteringBase::ClusteringBase(const ActionOptions&ao):
Action(ao),
ActionWithInputMatrix(ao),
number_of_cluster(-1)
{
if( getAdjacencyVessel() ) {
cluster_sizes.resize(getNumberOfNodes()); which_cluster.resize(getNumberOfNodes());
if( getNumberOfNodeTypes()!=1 ) error("should only be running clustering with one base multicolvar in function");
if( !getAdjacencyVessel()->undirectedGraph() ) error("input contact matrix is incompatible with clustering");
}
if( keywords.exists("MATRIX") ) {
std::vector<AtomNumber> fake_atoms; setupMultiColvarBase( fake_atoms );
}
}
void ClusteringBase::turnOnDerivatives() {
// Check base multicolvar isn't density probably other things shouldn't be allowed here as well
if( (getAdjacencyVessel()->getMatrixAction())->getNumberOfBaseMultiColvars()>0 ) {
if( getBaseMultiColvar(0)->isDensity() ) error("DFS clustering cannot be differentiated if base multicolvar is DENSITY");
}
// Ensure that derivatives are turned on in base classes
ActionWithInputMatrix::turnOnDerivatives();
}
Vector ActionWithInputMatrix::getPositionOfAtomForLinkCells( const unsigned& iatom ) const {
return (getAdjacencyVessel()->function)->getPositionOfAtomForLinkCells( iatom );
}
double ClusteringBase::getCutoffForConnection() const {
return getAdjacencyVessel()->getCutoffForConnection();
}
bool ClusteringBase::areConnected( const unsigned& iatom, const unsigned& jatom ) const {
return getAdjacencyVessel()->nodesAreConnected( iatom, jatom );
}
