void Action_Spam::Print() {
// Print the spam info file if we didn't do pure water
if (!purewater_) {
// Warn about any overflows
if (overflow_)
mprinterr("Warning: SPAM: Some frames had a box too small for the cutoff.\n");
// Print information about each missing peak
infofile_->Printf("# There are %d density peaks and %d frames\n\n",
(int)peaks_.size(), Nframes_);
// Loop over every Data set
for (unsigned int i = 0; i < peakFrameData_.size(); i++) {
// Skip peaks with 0 unoccupied sites
if (peakFrameData_[i].size() == 0) continue;
// Find out how many double-occupied frames there are
int ndouble = 0;
for (unsigned int j = 0; j < peakFrameData_[i].size(); j++)
if (peakFrameData_[i][j] < 0) ndouble++;
infofile_->Printf("# Peak %u has %d omitted frames (%d double-occupied)\n",
i, peakFrameData_[i].size(), ndouble);
for (unsigned int j = 0; j < peakFrameData_[i].size(); j++) {
if (j > 0 && j % 10 == 0) infofile_->Printf("\n");
infofile_->Printf("%7d ", peakFrameData_[i][j]);
}
infofile_->Printf("\n\n");
}
}
// Print the summary file with the calculated SPAM energies
if (!summaryfile_.empty()) {
// Not enabled yet -- just print out the data files.
mprinterr("Warning: SPAM: SPAM calculation not yet enabled.\n");
if (datafile_.empty()) datafile_ = summaryfile_;
}
// Now print the energy data
if (!datafile_.empty()) {
// Now write the data file with all of the SPAM energies
DataFile dfl;
ArgList dummy;
dfl.SetupDatafile(datafile_, dummy, 0);
for (int i = 0; i < (int)myDSL_.size(); i++) {
dfl.AddDataSet(myDSL_[i]);
}
dfl.WriteDataOut();
}
}
// Cluster_DBSCAN::ComputeKdistMap()
void Cluster_DBSCAN::ComputeKdistMap( Range const& Kvals,
std::vector<int> const& FramesToCluster ) const
{
int pt1_idx, pt2_idx, d_idx, point;
mprintf("\tCalculating Kdist map for %s\n", Kvals.RangeArg());
double* kdist_array; // Store distance of pt1 to every other point.
int nframes = (int)FramesToCluster.size();
// Ensure all Kdist points are within proper range
Range::const_iterator kval;
for (kval = Kvals.begin(); kval != Kvals.end(); ++kval)
if (*kval < 1 || *kval >= nframes) {
mprinterr("Error: Kdist value %i is out of range (1 <= Kdist < %i)\n",
*kval, nframes);
return;
}
int nvals = (int)Kvals.Size();
double** KMAP; // KMAP[i] has the ith nearest point for each point.
KMAP = new double*[ nvals ];
for (int i = 0; i != nvals; i++)
KMAP[i] = new double[ nframes ];
ParallelProgress progress( nframes );
# ifdef _OPENMP
# pragma omp parallel private(pt1_idx, pt2_idx, d_idx, kval, point, kdist_array) firstprivate(progress)
{
progress.SetThread( omp_get_thread_num() );
#endif
kdist_array = new double[ nframes ];
# ifdef _OPENMP
# pragma omp for
# endif
for (pt1_idx = 0; pt1_idx < nframes; pt1_idx++) // X
{
progress.Update( pt1_idx );
point = FramesToCluster[pt1_idx];
d_idx = 0;
// Store distances from pt1 to pt2
for (pt2_idx = 0; pt2_idx != nframes; pt2_idx++)
kdist_array[d_idx++] = FrameDistances_.GetFdist(point, FramesToCluster[pt2_idx]);
// Sort distances; will be smallest to largest
std::sort( kdist_array, kdist_array + nframes );
// Save the distance of specified nearest neighbors to this point.
d_idx = 0;
for (kval = Kvals.begin(); kval != Kvals.end(); ++kval) // Y
KMAP[d_idx++][pt1_idx] = kdist_array[ *kval ];
}
delete[] kdist_array;
# ifdef _OPENMP
} // END omp parallel
# endif
progress.Finish();
// Sort all of the individual kdist plots, smallest to largest.
for (int i = 0; i != nvals; i++)
std::sort(KMAP[i], KMAP[i] + nframes);
// Save in matrix, largest to smallest.
DataSet_MatrixDbl kmatrix;
kmatrix.Allocate2D( FramesToCluster.size(), Kvals.Size() );
for (int y = 0; y != nvals; y++) {
for (int x = nframes - 1; x != -1; x--)
kmatrix.AddElement( KMAP[y][x] );
delete[] KMAP[y];
}
delete[] KMAP;
// Write matrix to file
DataFile outfile;
ArgList outargs("usemap");
outfile.SetupDatafile(k_prefix_ + "Kmatrix.gnu", outargs, debug_);
outfile.AddDataSet( (DataSet*)&kmatrix );
outfile.WriteDataOut();
// Write out the largest and smallest values for each K.
// This means for each value of K the point with the furthest Kth-nearest
// neighbor etc.
CpptrajFile maxfile;
if (maxfile.OpenWrite(k_prefix_ + "Kmatrix.max.dat")) return;
maxfile.Printf("%-12s %12s %12s\n", "#Kval", "MaxD", "MinD");
d_idx = 0;
for (kval = Kvals.begin(); kval != Kvals.end(); ++kval, d_idx++)
maxfile.Printf("%12i %12g %12g\n", *kval, kmatrix.GetElement(0, d_idx),
kmatrix.GetElement(nframes-1, d_idx));
maxfile.CloseFile();
}
