void ActionWithAveraging::update() {
if( (clearstride!=1 && getStep()==0) || !onStep() ) return;
// Clear if it is time to reset
if( myaverage ) {
if( myaverage->wasreset() ) clearAverage();
}
// Calculate the weight for all reweighting
if ( weights.size()>0 ) {
double sum=0; for(unsigned i=0; i<weights.size(); ++i) sum+=weights[i]->get();
lweight=sum; cweight = exp( sum );
} else {
lweight=0; cweight=1.0;
}
// Prepare to do the averaging
prepareForAveraging();
// Run all the tasks (if required
if( useRunAllTasks ) runAllTasks();
// This the averaging if it is not done using task list
else performOperations( true );
// Update the norm
if( myaverage ) myaverage->setNorm( cweight + myaverage->getNorm() );
// Finish the averaging
finishAveraging();
// By resetting here we are ensuring that the grid will be cleared at the start of the next step
if( myaverage ) {
if( getStride()==0 || (clearstride>0 && getStep()%clearstride==0) ) myaverage->reset();
}
}
void Histogram::apply() {
if( !myhist->wasForced() ) return ;
in_apply=true;
// Run the loop to calculate the forces
runAllTasks(); finishAveraging();
// We now need to retrieve the buffer and set the forces on the atoms
myhist->applyForce( forcesToApply );
// Now make the forces make sense for the virial
unsigned fbase=0, tbase=0, vbase = getNumberOfDerivatives() - myvessels.size()*9;
for(unsigned i=vbase; i<vbase+9; ++i) finalForces[i]=0.0;
for(unsigned i=0; i<myvessels.size(); ++i) {
for(unsigned j=0; j<myvessels[i]->getNumberOfDerivatives()-9; ++j) {
finalForces[fbase + j] = forcesToApply[tbase + j];
}
unsigned k=0;
for(unsigned j=myvessels[i]->getNumberOfDerivatives()-9; j<myvessels[i]->getNumberOfDerivatives(); ++j) {
finalForces[vbase + k] += forcesToApply[tbase + j]; k++;
}
fbase += myvessels[i]->getNumberOfDerivatives() - 9;
tbase += myvessels[i]->getNumberOfDerivatives();
}
// And set the final forces on the atoms
setForcesOnAtoms( finalForces );
// Reset everything for next regular loop
in_apply=false;
}
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 DFSClusterDiameter::calculate(){
// Do the clustring
performClustering();
// Retrieve the atoms in the largest cluster
std::vector<unsigned> myatoms; retrieveAtomsInCluster( clustr, myatoms );
// Activate the relevant tasks
deactivateAllTasks(); std::vector<unsigned> active_tasks( getFullNumberOfTasks(), 0 );
for(unsigned i=1;i<myatoms.size();++i){
for(unsigned j=0;j<i;++j) active_tasks[ myatoms[i]*getNumberOfNodes() + myatoms[j] ] = 1;
}
activateTheseTasks( active_tasks );
// Now do the calculation
runAllTasks();
}
void ActionWithGrid::calculate(){
// Do nothing if derivatives are not required
if( doNotCalculateDerivatives() ) return;
// Clear on every step
if( mygrid ) clearAverage();
// Should not be any reweighting so just set these accordingly
lweight=0; cweight=1.0;
// Prepare to do the averaging
prepareForAveraging();
// Run all the tasks (if required
if( useRunAllTasks ) runAllTasks();
// This the averaging if it is not done using task list
else performOperations( true );
// Update the norm
if( mygrid ) mygrid->setNorm( cweight );
// Finish the averaging
finishAveraging();
// And reset for next step
if( mygrid ) mygrid->reset();
}
void SecondaryStructureRMSD::calculate(){
runAllTasks();
}
void PathBase::calculate(){
// Loop over all frames is now performed by ActionWithVessel
runAllTasks();
}
