void ClusterDiameter::calculate(){
// Retrieve the atoms in the largest cluster
std::vector<unsigned> myatoms; retrieveAtomsInCluster( clustr, myatoms );
// Activate the relevant tasks
deactivateAllTasks();
for(unsigned i=1;i<myatoms.size();++i){
for(unsigned j=0;j<i;++j) taskFlags[ myatoms[i]*getNumberOfNodes() + myatoms[j] ] = 1;
}
lockContributors();
// Now do the calculation
runAllTasks();
}
void Histogram::prepareForAveraging() {
if( myvessels.size()>0 ) {
deactivateAllTasks(); double norm=0;
for(unsigned i=0; i<stashes[0]->getNumberOfStoredValues(); ++i) {
std::vector<double> cvals( myvessels[0]->getNumberOfQuantities() );
stashes[0]->retrieveSequentialValue( i, false, cvals );
unsigned itask=myvessels[0]->getActiveTask(i); double tnorm = cvals[0];
for(unsigned j=1; j<myvessels.size(); ++j) {
if( myvessels[j]->getActiveTask(i)!=itask ) error("mismatched task identities in histogram suggests histogram is meaningless");
if( cvals.size()!=myvessels[j]->getNumberOfQuantities() ) cvals.resize( myvessels[j]->getNumberOfQuantities() );
stashes[j]->retrieveSequentialValue( i, false, cvals ); tnorm *= cvals[0];
}
norm += tnorm; taskFlags[i]=1;
}
lockContributors();
// Sort out normalization of histogram
if( !noNormalization() ) ww = cweight / norm;
else ww = cweight;
} else {
// Now fetch the kernel and the active points
std::vector<double> point( getNumberOfArguments() );
for(unsigned i=0; i<point.size(); ++i) point[i]=getArgument(i);
unsigned num_neigh; std::vector<unsigned> neighbors(1);
kernel = myhist->getKernelAndNeighbors( point, num_neigh, neighbors );
if( num_neigh>1 ) {
// Activate relevant tasks
deactivateAllTasks();
for(unsigned i=0; i<num_neigh; ++i) taskFlags[neighbors[i]]=1;
lockContributors();
} else {
// This is used when we are not doing kernel density evaluation
mygrid->addToGridElement( neighbors[0], 0, cweight );
}
}
}
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];
}
}
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 ) {
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.emplace_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() );
// And prepare the task list
deactivateAllTasks();
for(unsigned i=0; i<getFullNumberOfTasks(); ++i) taskFlags[i]=1;
lockContributors();
}
void SecondaryStructureRMSD::prepare(){
if( contributorsAreUnlocked ) lockContributors();
if( updateFreq>0 ){
if( firsttime || getStep()%updateFreq==0 ){ firsttime=false; unlockContributors(); }
}
}