MultiValue& ActionWithInputMatrix::getInputDerivatives( const unsigned& ind, const bool& normed, const multicolvar::AtomValuePack& myatoms ) const {
if( (mymatrix->function)->mybasemulticolvars.size()==0 ) {
MultiValue& myder=mymatrix->getTemporyMultiValue(0);
if( myder.getNumberOfValues()!=2 || myder.getNumberOfDerivatives()!=(mymatrix->function)->getNumberOfDerivatives() ) {
myder.resize( 2, (mymatrix->function)->getNumberOfDerivatives() );
}
myder.clearAll();
MultiValue myvals( (mymatrix->function)->getNumberOfQuantities(), (mymatrix->function)->getNumberOfDerivatives() );
for(unsigned i=0; i<mymatrix->getNumberOfColumns(); ++i) {
if( mymatrix->undirectedGraph() && ind==i ) continue;
addConnectionDerivatives( ind, i, myvals, myder );
}
myder.updateDynamicList(); return myder;
}
return (mymatrix->function)->getInputDerivatives( ind, normed, myatoms );
}
void ActionWithVessel::runAllTasks(){
if( getExchangeStep() && nactive_tasks!=fullTaskList.size() ) error("contributors must be unlocked during exchange steps");
plumed_massert( functions.size()>0, "you must have a call to readVesselKeywords somewhere" );
unsigned stride=comm.Get_size();
unsigned rank=comm.Get_rank();
if(serial){ stride=1; rank=0; }
// Make sure jobs are done
if(timers) stopwatch.start("1 Prepare Tasks");
doJobsRequiredBeforeTaskList();
if(timers) stopwatch.stop("1 Prepare Tasks");
// Get number of threads for OpenMP
unsigned nt=OpenMP::getNumThreads();
if( nt*stride*10>nactive_tasks) nt=nactive_tasks/stride/10;
if( nt==0 ) nt=1;
// Get size for buffer
unsigned bsize=0, bufsize=getSizeOfBuffer( bsize );
// Clear buffer
buffer.assign( buffer.size(), 0.0 );
// Switch off calculation of derivatives in main loop
if( dertime_can_be_off ) dertime=false;
// std::vector<unsigned> der_list;
// if( mydata ) der_list.resize( mydata->getSizeOfDerivativeList(), 0 );
// Build storage stuff for loop
// std::vector<double> buffer( bufsize, 0.0 );
if(timers) stopwatch.start("2 Loop over tasks");
#pragma omp parallel num_threads(nt)
{
std::vector<double> omp_buffer;
if( nt>1 ) omp_buffer.resize( bufsize, 0.0 );
MultiValue myvals( getNumberOfQuantities(), getNumberOfDerivatives() );
MultiValue bvals( getNumberOfQuantities(), getNumberOfDerivatives() );
myvals.clearAll(); bvals.clearAll();
#pragma omp for nowait
for(unsigned i=rank;i<nactive_tasks;i+=stride){
// Calculate the stuff in the loop for this action
performTask( indexOfTaskInFullList[i], partialTaskList[i], myvals );
// Weight should be between zero and one
plumed_dbg_assert( myvals.get(0)>=0 && myvals.get(0)<=1.0 );
// Check for conditions that allow us to just to skip the calculation
// the condition is that the weight of the contribution is low
// N.B. Here weights are assumed to be between zero and one
if( myvals.get(0)<tolerance ){
// Deactivate task if it is less than the neighbor list tolerance
if( myvals.get(0)<nl_tolerance && contributorsAreUnlocked ) deactivate_task( indexOfTaskInFullList[i] );
// Clear the derivatives
myvals.clearAll();
continue;
}
// Now calculate all the functions
// If the contribution of this quantity is very small at neighbour list time ignore it
// untill next neighbour list time
if( nt>1 ){
if( !calculateAllVessels( indexOfTaskInFullList[i], myvals, bvals, omp_buffer, der_list ) && contributorsAreUnlocked ) deactivate_task( indexOfTaskInFullList[i] );
} else {
if( !calculateAllVessels( indexOfTaskInFullList[i], myvals, bvals, buffer, der_list ) && contributorsAreUnlocked ) deactivate_task( indexOfTaskInFullList[i] );
}
// Clear the value
myvals.clearAll();
}
#pragma omp critical
if(nt>1) for(unsigned i=0;i<bufsize;++i) buffer[i]+=omp_buffer[i];
}
if(timers) stopwatch.stop("2 Loop over tasks");
// Turn back on derivative calculation
dertime=true;
if(timers) stopwatch.start("3 MPI gather");
// MPI Gather everything
if( !serial && buffer.size()>0 ) comm.Sum( buffer );
// MPI Gather index stores
if( mydata && !lowmem && !noderiv ){
comm.Sum( der_list ); mydata->setActiveValsAndDerivatives( der_list );
}
// Update the elements that are makign contributions to the sum here
// this causes problems if we do it in prepare
if( !serial && contributorsAreUnlocked ) comm.Sum( taskFlags );
if(timers) stopwatch.stop("3 MPI gather");
if(timers) stopwatch.start("4 Finishing computations");
finishComputations( buffer );
if(timers) stopwatch.stop("4 Finishing computations");
}