Exemplo n.º 1
0
void Action_Dihedral::Print() {
  if (range360_) {
    DataSet_double* ds = (DataSet_double*)dih_;
    for (int i = 0; i < ds->Size(); i++) {
      if ( (*ds)[i] < 0.0 )
        (*ds)[i] += 360.0;
    }
  }
}
Exemplo n.º 2
0
int KDE::CalcKDE(DataSet_double& Out, DataSet_1D const& Pdata,
                 std::vector<double> const& Increments,
                 HistBin const& Xdim, double bandwidth) const
{
  int inSize = (int)Pdata.Size();
  // Allocate output set, set all to zero.
  Out.Zero( Xdim.Bins() );
  Out.SetDim( Dimension::X, Xdim );
  int outSize = (int)Out.Size();

  int frame, bin;
  double increment, val;
  double total = 0.0;
# ifdef _OPENMP
  int original_num_threads;
# pragma omp parallel
  {
#   pragma omp master
    {
      original_num_threads = omp_get_num_threads();
    }
  }
  // Ensure we only execute with the desired number of threads
  if (numthreads_ < original_num_threads)
    omp_set_num_threads( numthreads_ );
# endif
  // Calculate KDE, loop over input data
# ifdef _OPENMP
  int mythread;
  double **P_thread;
# pragma omp parallel private(frame, bin, val, increment, mythread) reduction(+:total)
  {
    mythread = omp_get_thread_num();
    // Prevent race conditions by giving each thread its own histogram
#   pragma omp master
    {
      P_thread = new double*[ numthreads_ ];
      for (int nt = 0; nt < numthreads_; nt++) {
        P_thread[nt] = new double[ outSize ];
        std::fill(P_thread[nt], P_thread[nt] + outSize, 0.0);
      }
    }
#   pragma omp barrier
#   pragma omp for
# endif
    for (frame = 0; frame < inSize; frame++) {
      val = Pdata.Dval(frame);
      increment = Increments[frame];
      total += increment;
      // Apply kernel across histogram
      for (bin = 0; bin < outSize; bin++)
#       ifdef _OPENMP
        P_thread[mythread][bin] +=
#       else
        Out[bin] +=
#       endif
          (increment * (this->*Kernel_)( (Xdim.Coord(bin) - val) / bandwidth ));
    }
# ifdef _OPENMP
  } // END parallel block
  // Combine results from each thread histogram into Out
  for (int i = 0; i < numthreads_; i++) {
    for (int j = 0; j < outSize; j++)
      Out[j] += P_thread[i][j];
    delete[] P_thread[i];
  }
  delete[] P_thread;
  // Restore original number of threads
  if (original_num_threads != numthreads_)
    omp_set_num_threads( original_num_threads );
# endif
  // Normalize
  for (unsigned int j = 0; j < Out.Size(); j++)
    Out[j] /= (total * bandwidth);
  return 0;
}