Esempio n. 1
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/** For each point p, calculate function Kdist(p) which is the distance of
  * the Kth nearest point to p.
  */
void Cluster_DBSCAN::ComputeKdist( int Kval, std::vector<int> const& FramesToCluster ) const {
  std::vector<double> dists;
  std::vector<double> Kdist;
  dists.reserve( FramesToCluster.size() ); 
  Kdist.reserve( FramesToCluster.size() );
  std::string outfilename = k_prefix_ + "Kdist." + integerToString(Kval) + ".dat";
  mprintf("\tDBSCAN: Calculating Kdist(%i), output to %s\n", Kval, outfilename.c_str());
  for (std::vector<int>::const_iterator point = FramesToCluster.begin();
                                        point != FramesToCluster.end();
                                        ++point)
  {
    // Store distances from this point
    dists.clear();
    for (std::vector<int>::const_iterator otherpoint = FramesToCluster.begin();
                                          otherpoint != FramesToCluster.end();
                                          ++otherpoint)
      dists.push_back( FrameDistances_.GetFdist(*point, *otherpoint) );
    // Sort distances - first dist should always be 0
    std::sort(dists.begin(), dists.end());
    Kdist.push_back( dists[Kval] );
  }
  std::sort( Kdist.begin(), Kdist.end() );
  CpptrajFile Outfile;
  Outfile.OpenWrite(outfilename);
  Outfile.Printf("%-8s %1i%-11s\n", "#Point", Kval,"-dist");
  // Write out largest to smallest
  unsigned int ik = 0;
  for (std::vector<double>::reverse_iterator k = Kdist.rbegin(); 
                                             k != Kdist.rend(); ++k, ++ik)
    Outfile.Printf("%8u %12.4f\n", ik, *k);
  Outfile.CloseFile();
}
Esempio n. 2
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int DataIO_OpenDx::WriteGrid(DataSet const& setIn, CpptrajFile& outfile) const {
  DataSet_3D const& set = static_cast<DataSet_3D const&>( setIn );
  Vec3 oxyz = set.Bin().GridOrigin();
  if (gridWriteMode_ == BIN_CENTER)
    // Origin needs to be shifted to center of bin located at 0,0,0
    oxyz = set.Bin().Center(0,0,0);
  // Print the OpenDX header
  WriteDxHeader(outfile, set.NX(), set.NY(), set.NZ(), set.NX(), set.NY(), set.NZ(),
                set.Bin().Ucell(), oxyz);
  // Now print out the data.
  size_t gridsize = set.Size();
  if (gridsize == 1)
    outfile.Printf("%g\n", set[0]);
  else if (gridsize == 2)
    outfile.Printf("%g %g\n", set[0], set[1]);
  else if (gridsize > 2) {
    // Data is already in row-major form (z-axis changes
    // fastest), so no need to do any kind of data adjustment
    for (size_t i = 0UL; i < gridsize - 2UL; i += 3UL)
      outfile.Printf("%g %g %g\n", set[i], set[i+1], set[i+2]);
    // Print out any points we may have missed
    switch (gridsize % 3) {
      case 2: outfile.Printf("%g %g\n", set[gridsize-2], set[gridsize-1]); break;
      case 1: outfile.Printf("%g\n", set[gridsize-1]); break;
    }
  }
  return 0;
}
Esempio n. 3
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void DataSet_GridDbl::WriteBuffer(CpptrajFile& outfile, SizeArray const& pIn) const {
  size_t x = pIn[0];
  size_t y = pIn[1];
  size_t z = pIn[2];
  if ( x >= grid_.NX() || y >= grid_.NY() || z >= grid_.NZ() )
    outfile.Printf(format_.fmt(), 0.0);
  else
    outfile.Printf(format_.fmt(), grid_.element(x,y,z));
}
Esempio n. 4
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// DataSet_Vector::WriteBuffer()
void DataSet_Vector::WriteBuffer(CpptrajFile &cbuffer, SizeArray const& pIn) const {
  if (pIn[0] >= vectors_.size()) {
    cbuffer.Printf(format_.fmt(), 0.0, 0.0, 0.0, 0.0, 0.0, 0.0); // VXYZ OXYZ
  } else {
    Vec3 const& Vxyz = vectors_[pIn[0]];
    Vec3 const& Oxyz = OXYZ(pIn[0]);
    cbuffer.Printf(format_.fmt(), Vxyz[0], Vxyz[1], Vxyz[2],
                                  Oxyz[0], Oxyz[1], Oxyz[2]);
  }
}
Esempio n. 5
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void TriangleMatrix::Write2D( CpptrajFile& outfile, int xIn, int yIn ) {
  size_t x = (size_t)xIn;
  size_t y = (size_t)yIn;
  if ( xIn==yIn || xIn < 0 || yIn < 0 || x >= nrows_ || y >= nrows_ ) 
    outfile.Printf(data_format_, 0.0);
  else {
    size_t index = calcIndex(x, y);
    outfile.Printf(data_format_, elements_[index]);
  }
}
Esempio n. 6
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void Cluster_DPeaks::ClusterResults(CpptrajFile& outfile) const {
   outfile.Printf("#Algorithm: DPeaks epsilon %g\n", epsilon_);
   if (calc_noise_) {
     outfile.Printf("#NOISE_FRAMES:");
     std::vector<int> noiseFrames;
     for (Carray::const_iterator point = Points_.begin();
                                 point != Points_.end(); ++point)
       if (point->Cnum() == -1) noiseFrames.push_back( point->Fnum()+1 );
    std::sort( noiseFrames.begin(), noiseFrames.end() );
    for (std::vector<int>::const_iterator f = noiseFrames.begin(); f != noiseFrames.end(); ++f)
      outfile.Printf(" %i", *f); 
    outfile.Printf("\n");
    outfile.Printf("#Number_of_noise_frames: %zu\n", noiseFrames.size());
  }
}
Esempio n. 7
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// WriteNameToBuffer()
void DataIO_Std::WriteNameToBuffer(CpptrajFile& fileIn, std::string const& label,
                                   int width,  bool isLeftCol)
{
  std::string temp_name = label;
  // If left aligning, add '#' to name; 
  if (isLeftCol) {
    if (temp_name[0]!='#') {
      temp_name.insert(0,"#");
      // Ensure that name will not be larger than column width.
      if ((int)temp_name.size() > width)
        temp_name.resize( width );
    }
  }
  // Replace any spaces with underscores
  for (std::string::iterator tc = temp_name.begin(); tc != temp_name.end(); ++tc)
    if ( *tc == ' ' )
      *tc = '_';
  if (width >= (int)CpptrajFile::BUF_SIZE)
    // Protect against CpptrajFile buffer overflow
    fileIn.Write(temp_name.c_str(), temp_name.size());
  else {
    // Set up header format string
    TextFormat::AlignType align;
    if (isLeftCol)
      align = TextFormat::LEFT;
    else
      align = TextFormat::RIGHT;
    TextFormat header_format(TextFormat::STRING, width, align);
    fileIn.Printf(header_format.fmt(), temp_name.c_str()); 
  }
}
Esempio n. 8
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// DataIO_Std::WriteByGroup()
int DataIO_Std::WriteByGroup(CpptrajFile& file, DataSetList const& SetList, GroupType gtype)
{
  int err = 0;
  bool firstWrite = true;
  DataSetList tmpdsl;
  std::vector<bool> setIsWritten(SetList.size(), false);
  unsigned int startIdx = 0;
  unsigned int nWritten = 0;
  while (nWritten < SetList.size()) {
    std::string currentName;
    Dimension currentDim;
    int currentNum = -1;
    switch (gtype) {
      case BY_NAME   : currentName = SetList[startIdx]->Meta().Name(); break;
      case BY_ASPECT : currentName = SetList[startIdx]->Meta().Aspect(); break;
      case BY_IDX    : currentNum  = SetList[startIdx]->Meta().Idx(); break;
      case BY_ENS    : currentNum  = SetList[startIdx]->Meta().EnsembleNum(); break;
      case BY_DIM    : currentDim  = SetList[startIdx]->Dim(0); break;
      case NO_TYPE   : return 1;
    }
    int firstNonMatch = -1;
    for (unsigned int idx = startIdx; idx != SetList.size(); idx++)
    {
      if (!setIsWritten[idx])
      {
        bool match = false;
        switch (gtype) {
          case BY_NAME   : match = (currentName == SetList[idx]->Meta().Name()); break;
          case BY_ASPECT : match = (currentName == SetList[idx]->Meta().Aspect()); break;
          case BY_IDX    : match = (currentNum  == SetList[idx]->Meta().Idx()); break;
          case BY_ENS    : match = (currentNum  == SetList[idx]->Meta().EnsembleNum()); break;
          case BY_DIM    : match = (currentDim  == SetList[idx]->Dim(0)); break;
          case NO_TYPE   : return 1;
        }
        if (match)
        {
          tmpdsl.AddCopyOfSet( SetList[idx] );
          setIsWritten[idx] = true;
          nWritten++;
        } else if (firstNonMatch == -1)
          firstNonMatch = (int)idx;
      }
    }
    if (firstNonMatch > -1)
      startIdx = (unsigned int)firstNonMatch;
    if (!firstWrite)
      file.Printf("\n");
    else
      firstWrite = false;
    if (isInverted_)
      err += WriteDataInverted(file, tmpdsl);
    else
      err += WriteDataNormal(file, tmpdsl);
    tmpdsl.ClearAll();
  }
  return err;
}
Esempio n. 9
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// Cluster_DBSCAN::ClusterResults()
void Cluster_DBSCAN::ClusterResults(CpptrajFile& outfile) const {
  outfile.Printf("#Algorithm: DBSCAN minpoints %i epsilon %g sieveToCentroid %i\n",
                 minPoints_, epsilon_, (int)sieveToCentroid_);
  // List the number of noise points.
  outfile.Printf("#NOISE_FRAMES:");
  unsigned int frame = 1;
  unsigned int numNoise = 0;
  for (std::vector<char>::const_iterator stat = Status_.begin();
                                         stat != Status_.end(); 
                                       ++stat, ++frame)
  {
    if ( *stat == NOISE ) {
      outfile.Printf(" %i", frame);
      ++numNoise;
    }
  }
  outfile.Printf("\n");
  outfile.Printf("#Number_of_noise_frames: %u\n", numNoise); 
}
Esempio n. 10
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// DataIO_Std::WriteData3D()
int DataIO_Std::WriteData3D( CpptrajFile& file, DataSetList const& setList) 
{
  int err = 0;
  for (DataSetList::const_iterator set = setList.begin(); set != setList.end(); ++set)
  {
    if (set != setList.begin()) file.Printf("\n");
    err += WriteSet3D( *(*set), file );
  }
  return err;
}
Esempio n. 11
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int DataIO_OpenDx::WriteGridWrap(DataSet const& setIn, CpptrajFile& outfile) const {
  DataSet_3D const& set = static_cast<DataSet_3D const&>( setIn );
  // Need to construct a grid mesh around bins, with points centered on the bins.
  int mesh_x = set.NX();
  int mesh_y = set.NY();
  int mesh_z = set.NZ();
  // Origin needs to be shifted half grid spacing, i.e. it is the center of the
  // bin located at -1, -1, -1.
  Vec3 oxyz = set.Bin().Center(-1, -1, -1);
  // Print the OpenDX header
  WriteDxHeader(outfile, mesh_x+2, mesh_y+2, mesh_z+2, mesh_x, mesh_y, mesh_z,
                set.Bin().Ucell(), oxyz);
  // Print out the data. Start at bin -1, end on bin N.
  int nvals = 0; // Keep track of how many values printed on current line.
  if (gridWriteMode_ == WRAP) {
    int bi, bj, bk;
    for (int ii = -1; ii <= mesh_x; ++ii) {
      if      (ii < 0      ) bi = mesh_x - 1;
      else if (ii == mesh_x) bi = 0;
      else                   bi = ii;
      for (int ij = -1; ij <= mesh_y; ++ij) {
        if      (ij < 0      ) bj = mesh_y - 1;
        else if (ij == mesh_y) bj = 0;
        else                   bj = ij;
        for (int ik = -1; ik <= mesh_z; ++ik) {
          if      (ik < 0      ) bk = mesh_z - 1;
          else if (ik == mesh_z) bk = 0;
          else                   bk = ik;
          outfile.Printf(" %g", set.GetElement(bi, bj, bk));
          ++nvals;
          if (nvals == 5) {
            outfile.Printf("\n");
            nvals = 0;
          }
        }
      }
    }
  } else { // EXTENDED
    for (int ii = -1; ii <= mesh_x; ++ii) {
      bool zero_x = (ii < 0 || ii == mesh_x);
      for (int ij = -1; ij <= mesh_y; ++ij) {
        bool zero_y = (ij < 0 || ij == mesh_y);
        for (int ik = -1; ik <= mesh_z; ++ik) {
          if (zero_x || zero_y || ik < 0 || ik == mesh_z)
            outfile.Printf(" 0");
          else
            outfile.Printf(" %g", set.GetElement(ii, ij, ik));
          ++nvals;
          if (nvals == 5) {
            outfile.Printf("\n");
            nvals = 0;
          }
        }
      }
    }
  }
  if (nvals > 0) outfile.Printf("\n");
  return 0;
}
Esempio n. 12
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void Action_Pairwise::Print() {
  if (nframes_ < 1) return;
  // Divide matrices by # of frames
  double norm = 1.0 / (double)nframes_;
  for (unsigned int i = 0; i != vdwMat_->Size(); i++)
  {
    (*vdwMat_)[i] *= norm;
    (*eleMat_)[i] *= norm;
  }
  // Write out final results
  CpptrajFile AvgOut;
  if (AvgOut.OpenWrite( avgout_ )) return;
  if (nb_calcType_ == NORMAL)
    mprintf("  PAIRWISE: Writing all pairs with |<evdw>| > %.4f, |<eelec>| > %.4f\n",
            cut_evdw_, cut_eelec_);
  else if (nb_calcType_ == COMPARE_REF)
    mprintf("  PAIRWISE: Writing all pairs with |<dEvdw>| > %.4f, |<dEelec>| > %.4f\n",
            cut_evdw_, cut_eelec_);
  AvgOut.Printf("%-16s %5s -- %16s %5s : ENE\n","#Name1", "At1", "Name2", "At2");
  for (AtomMask::const_iterator m1 = Mask0_.begin(); m1 != Mask0_.end(); ++m1) {
    for (AtomMask::const_iterator m2 = m1 + 1; m2 != Mask0_.end(); ++m2)
    {
      double EV = vdwMat_->GetElement(*m1, *m2);
      double EE = eleMat_->GetElement(*m1, *m2);
      bool outputv = ( fabs(EV) > cut_evdw_ );
      bool outpute = ( fabs(EE) > cut_eelec_ );
      if (outputv || outpute) {
        AvgOut.Printf("%16s %5i -- %16s %5i :",
                CurrentParm_->TruncResAtomName(*m1).c_str(), *m1 + 1,
                CurrentParm_->TruncResAtomName(*m2).c_str(), *m2 + 1);
        if (outputv) AvgOut.Printf("  EVDW= %12.5e", EV);
        if (outpute) AvgOut.Printf(" EELEC= %12.5e", EE);
        AvgOut.Printf("\n");
      }
    }
  }
}
Esempio n. 13
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void DataIO_OpenDx::WriteDxHeader(CpptrajFile& outfile,
                                  size_t NX, size_t NY, size_t NZ,
                                  double LX, double LY, double LZ,
                                  Matrix_3x3 const& ucell, Vec3 const& oxyz) const
{
  outfile.Printf("object 1 class gridpositions counts %zu %zu %zu\n"
                 "origin %g %g %g\ndelta %g %g %g\ndelta %g %g %g\ndelta %g %g %g\n"
                 "object 2 class gridconnections counts %zu %zu %zu\n"
                 "object 3 class array type double rank 0 items %zu data follows\n",
                 NX, NY, NZ, oxyz[0], oxyz[1], oxyz[2],
                 ucell[0]/LX, ucell[1]/LX, ucell[2]/LX,
                 ucell[3]/LY, ucell[4]/LY, ucell[5]/LY,
                 ucell[6]/LZ, ucell[7]/LZ, ucell[8]/LZ,
                 NX, NY, NZ, NX*NY*NZ);
}
Esempio n. 14
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// DataIO_Std::WriteCmatrix()
int DataIO_Std::WriteCmatrix(CpptrajFile& file, DataSetList const& Sets) {
  for (DataSetList::const_iterator ds = Sets.begin(); ds != Sets.end(); ++ds)
  {
    if ( (*ds)->Group() != DataSet::CLUSTERMATRIX) {
      mprinterr("Error: Write of cluster matrix and other sets to same file not supported.\n"
                "Error: Skipping '%s'\n", (*ds)->legend());
      continue;
    }
    DataSet_Cmatrix const& cm = static_cast<DataSet_Cmatrix const&>( *(*ds) );
    int nrows = cm.OriginalNframes();
    int col_width = std::max(3, DigitWidth( nrows ) + 1);
    int dat_width = std::max(cm.Format().Width(), (int)cm.Meta().Legend().size()) + 1;
    WriteNameToBuffer(file, "F1",               col_width, true);
    WriteNameToBuffer(file, "F2",               col_width, false);
    WriteNameToBuffer(file, cm.Meta().Legend(), dat_width, false);
    if (cm.SieveType() != ClusterSieve::NONE)
      file.Printf(" nframes %i", cm.OriginalNframes());
    file.Printf("\n");
    TextFormat col_fmt(TextFormat::INTEGER, col_width);
    TextFormat dat_fmt = cm.Format();
    dat_fmt.SetFormatAlign(TextFormat::RIGHT);
    dat_fmt.SetFormatWidth( dat_width );
    std::string total_fmt = col_fmt.Fmt() + col_fmt.Fmt() + dat_fmt.Fmt() + "\n";
    //mprintf("DEBUG: format '%s'\n", total_fmt.c_str());
    ClusterSieve::SievedFrames const& frames = cm.FramesToCluster();
    int ntotal = (int)frames.size();
    for (int idx1 = 0; idx1 != ntotal; idx1++) {
      int row = frames[idx1];
      for (int idx2 = idx1 + 1; idx2 != ntotal; idx2++) {
        int col = frames[idx2];
        file.Printf(total_fmt.c_str(), row+1, col+1, cm.GetFdist(col, row)); 
      }
    }
  }
  return 0;
}
Esempio n. 15
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// DataIO_OpenDx::WriteSet3D()
int DataIO_OpenDx::WriteSet3D(DataSet const& setIn, CpptrajFile& outfile) const {
  if (setIn.Ndim() != 3) {
    mprinterr("Internal Error: DataSet %s in DataFile %s has %zu dimensions, expected 3.\n",
              setIn.legend(), outfile.Filename().full(), setIn.Ndim());
    return 1;
  }
  int err = 0;
  switch ( gridWriteMode_ ) {
    case BIN_CORNER:
    case BIN_CENTER: err = WriteGrid( setIn, outfile ); break;
    case WRAP:
    case EXTENDED  : err = WriteGridWrap( setIn, outfile ); break;
  }
  // Print tail
  if (err == 0) {
    // TODO: Make this an option
    //if (mode_ == CENTER)
    //  outfile.Printf("\nobject \"density (%s) [A^-3]\" class field\n",
    //                 centerMask_.MaskString());
    //else
      outfile.Printf("\nobject \"density [A^-3]\" class field\n");
  }
  return err;
}
Esempio n. 16
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// DataIO_Std::WriteDataInverted()
int DataIO_Std::WriteDataInverted(CpptrajFile& file, DataSetList const& Sets)
{
  if (Sets.empty() || CheckAllDims(Sets, 1)) return 1;
  // Determine size of largest DataSet.
  size_t maxFrames = DetermineMax( Sets );
  // Write each set to a line.
  DataSet::SizeArray positions(1);
  // Set up x column format
  DataSetList::const_iterator set = Sets.begin();
  TextFormat x_col_format;
  if (hasXcolumn_)
    x_col_format = XcolFmt();
  else
    x_col_format = (*set)->Format();
  for (; set != Sets.end(); ++set) {
    // Write dataset name as first column.
    WriteNameToBuffer( file, (*set)->Meta().Legend(), x_col_format.ColumnWidth(), false); 
    // Write each frame to subsequent columns
    for (positions[0] = 0; positions[0] < maxFrames; positions[0]++) 
      (*set)->WriteBuffer(file, positions);
    file.Printf("\n");
  }
  return 0;
}
Esempio n. 17
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// Analysis_Wavelet::Analyze()
Analysis::RetType Analysis_Wavelet::Analyze() {
    // Step 1 - Create a matrix that is #atoms rows by #frames - 1 cols,
    //          where matrix(frame, atom) is the distance that atom has
    //          travelled from the previous frame.
    // TODO: Implement this in Action_Matrix()?
    mprintf("    WAVELET:\n");
    // First set up atom mask.
    if (coords_->Top().SetupIntegerMask( mask_ )) return Analysis::ERR;
    mask_.MaskInfo();
    int natoms = mask_.Nselected();
    int nframes = (int)coords_->Size();
    if (natoms < 1 || nframes < 2) {
        mprinterr("Error: Not enough frames (%i) or atoms (%i) in '%s'\n",
                  nframes, natoms, coords_->legend());
        return Analysis::ERR;
    }
    Matrix<double> d_matrix;
    mprintf("\t%i frames, %i atoms, distance matrix will require %.2f MB\n",
            (double)d_matrix.sizeInBytes(nframes, natoms) / (1024.0*1024.0));
    d_matrix.resize(nframes, natoms);
    // Get initial frame.
    Frame currentFrame, lastFrame;
    currentFrame.SetupFrameFromMask( mask_, coords_->Top().Atoms() );
    lastFrame = currentFrame;
    coords_->GetFrame( 0, lastFrame, mask_ );
    // Iterate over frames
    for (int frm = 1; frm != nframes; frm++) {
        coords_->GetFrame( frm, currentFrame, mask_ );
        int idx = frm; // Position in distance matrix; start at column 'frame'
        for (int at = 0; at != natoms; at++, idx += nframes)
            // Distance of atom in currentFrame from its position in lastFrame.
            d_matrix[idx] = sqrt(DIST2_NoImage( currentFrame.XYZ(at), lastFrame.XYZ(at) ));
        //lastFrame = currentFrame; // TODO: Re-enable?
    }
# ifdef DEBUG_WAVELET
    // DEBUG: Write matrix to file.
    CpptrajFile dmatrixOut; // DEBUG
    dmatrixOut.OpenWrite("dmatrix.dat");
    Matrix<double>::iterator mval = d_matrix.begin();
    for (int row = 0; row != natoms; row++) {
        for (int col = 0; col != nframes; col++)
            dmatrixOut.Printf("%g ", *(mval++));
        dmatrixOut.Printf("\n");
    }
    dmatrixOut.CloseFile();
# endif

    // Precompute some factors for calculating scaled wavelets.
    const double one_over_sqrt_N = 1.0 / sqrt(static_cast<double>( nframes ));
    std::vector<int> arrayK( nframes );
    arrayK[0] = -1 * (nframes/2);
    for (int i = 1; i != nframes; i++)
        arrayK[i] = arrayK[i-1] + 1;
# ifdef DEBUG_WAVELET
    mprintf("DEBUG: K:");
    for (std::vector<int>::const_iterator kval = arrayK.begin(); kval != arrayK.end(); ++kval)
        mprintf(" %i", *kval);
    mprintf("\n");
# endif

    // Step 2 - Get FFT of wavelet for each scale.
    PubFFT pubfft;
    pubfft.SetupFFTforN( nframes );
    mprintf("\tMemory required for scaled wavelet array: %.2f MB\n",
            (double)(2 * nframes * nb_ * sizeof(double)) / (1024 * 1024));
    typedef std::vector<ComplexArray> WaveletArray;
    WaveletArray FFT_of_Scaled_Wavelets;
    FFT_of_Scaled_Wavelets.reserve( nb_ );
    typedef std::vector<double> Darray;
    Darray scaleVector;
    scaleVector.reserve( nb_ );
    Darray MIN( nb_ * 2 );
    for (int iscale = 0; iscale != nb_; iscale++)
    {
        // Calculate and store scale factor.
        scaleVector.push_back( S0_ * pow(2.0, iscale * ds_) );
        // Populate MIN array
        MIN[iscale    ] = (0.00647*pow((correction_*scaleVector.back()),1.41344)+19.7527)*chival_;
        MIN[iscale+nb_] = correction_*scaleVector.back();
        // Calculate scalved wavelet
        ComplexArray scaledWavelet;
        switch (wavelet_type_) {
        case W_MORLET:
            scaledWavelet = F_Morlet(arrayK, scaleVector.back());
            break;
        case W_PAUL  :
            scaledWavelet = F_Paul(arrayK, scaleVector.back());
            break;
        case W_NONE  :
            return Analysis::ERR; // Sanity check
        }
#   ifdef DEBUG_WAVELET
        PrintComplex("wavelet_before_fft", scaledWavelet);
#   endif
        // Perform FFT
        pubfft.Forward( scaledWavelet );
        // Normalize
        scaledWavelet.Normalize( one_over_sqrt_N );
#   ifdef DEBUG_WAVELET
        PrintComplex("wavelet_after_fft", scaledWavelet);
#   endif
        FFT_of_Scaled_Wavelets.push_back( scaledWavelet );
    }
# ifdef DEBUG_WAVELET
    mprintf("DEBUG: Scaling factors:");
    for (Darray::const_iterator sval = scaleVector.begin(); sval != scaleVector.end(); ++sval)
        mprintf(" %g", *sval);
    mprintf("\n");
    mprintf("DEBUG: MIN:");
    for (int i = 0; i != nb_; i++)
        mprintf(" %g", MIN[i]);
    mprintf("\n");
# endif

    // Step 3 - For each atom, calculate the convolution of scaled wavelets
    //          with rows (atom distance vs frame) via dot product of the
    //          frequency domains, i.e. Fourier-transformed, followed by an
    //          inverse FT.
    DataSet_MatrixFlt& OUT = static_cast<DataSet_MatrixFlt&>( *output_ );
    mprintf("\tMemory required for output matrix: %.2f MB\n",
            (double)Matrix<float>::sizeInBytes(nframes, natoms)/(1024.0*1024.0));
    OUT.Allocate2D( nframes, natoms ); // Should initialize to zero
    Matrix<double> MAX;
    mprintf("\tMemory required for Max array: %.2f MB\n",
            (double)MAX.sizeInBytes(nframes, natoms)/(1024.0*1024.0));
    MAX.resize( nframes, natoms );
    Darray magnitude( nframes ); // Scratch space for calculating magnitude across rows
    for (int at = 0; at != natoms; at++) {
        ComplexArray AtomSignal( nframes ); // Initializes to zero
        // Calculate the distance variance for this atom and populate the array.
        int midx = at * nframes; // Index into d_matrix
        int cidx = 0;            // Index into AtomSignal
        double d_avg = 0.0;
        double d_var = 0.0;
        for (int frm = 0; frm != nframes; frm++, cidx += 2, midx++) {
            d_avg += d_matrix[midx];
            d_var += (d_matrix[midx] * d_matrix[midx]);
            AtomSignal[cidx] = d_matrix[midx];
        }
        d_var = (d_var - ((d_avg * d_avg) / (double)nframes)) / ((double)(nframes - 1));
#   ifdef DEBUG_WAVELET
        mprintf("VARIANCE: %g\n", d_var);
#   endif
        double var_norm = 1.0 / d_var;
        // Calculate FT of atom signal
        pubfft.Forward( AtomSignal );
#   ifdef DEBUG_WAVELET
        PrintComplex("AtomSignal", AtomSignal);
#   endif
        // Normalize
        AtomSignal.Normalize( one_over_sqrt_N );
        // Calculate dot product of atom signal with each scaled FT wavelet
        for (int iscale = 0; iscale != nb_; iscale++) {
            ComplexArray dot = AtomSignal.TimesComplexConj( FFT_of_Scaled_Wavelets[iscale] );
            // Inverse FT of dot product
            pubfft.Back( dot );
#     ifdef DEBUG_WAVELET
            PrintComplex("InverseFT_Dot", dot);
#     endif
            // Chi-squared testing
            midx = at * nframes;
            cidx = 0;
            for (int frm = 0; frm != nframes; frm++, cidx += 2, midx++) {
                magnitude[frm] = (dot[cidx]*dot[cidx] + dot[cidx+1]*dot[cidx+1]) * var_norm;
                if (magnitude[frm] < MIN[iscale])
                    magnitude[frm] = 0.0;
                if (magnitude[frm] > MAX[midx]) {
                    MAX[midx] = magnitude[frm];
                    //Indices[midx] = iscale
                    OUT[midx] = (float)(correction_ * scaleVector[iscale]);
                }
            }
#     ifdef DEBUG_WAVELET
            mprintf("DEBUG: AbsoluteValue:");
            for (Darray::const_iterator dval = magnitude.begin(); dval != magnitude.end(); ++dval)
                mprintf(" %g", *dval);
            mprintf("\n");
#     endif
        } // END loop over scales
    } // END loop over atoms
# ifdef DEBUG_WAVELET
    // DEBUG: Print MAX
    CpptrajFile maxmatrixOut; // DEBUG
    maxmatrixOut.OpenWrite("maxmatrix.dat");
    for (int col = 0; col != nframes; col++) {
        for (int row = 0; row != natoms; row++)
            maxmatrixOut.Printf("%g ", MAX.element(col, row));
        maxmatrixOut.Printf("\n");
    }
    maxmatrixOut.CloseFile();
# endif

    return Analysis::OK;
}
Esempio n. 18
0
int Cluster_DPeaks::ChoosePointsAutomatically() {
  // Right now all density values are discrete. Try to choose outliers at each
  // value for which there is density.;
/*
  // For each point, calculate average distance (X,Y) to points in next and
  // previous density values.
  const double dens_cut = 3.0 * 3.0;
  const double dist_cut = 1.32 * 1.32;
  for (Carray::const_iterator point0 = Points_.begin(); point0 != Points_.end(); ++point0)
  {
    int Npts = 0;
    for (Carray::const_iterator point1 = Points_.begin(); point1 != Points_.end(); ++point1)
    {
      if (point0 != point1) {
        // Only do this for close densities
        double dX = (double)(point0->PointsWithinEps() - point1->PointsWithinEps());
        double dX2 = dX * dX;
        double dY = (point0->Dist() - point1->Dist());
        double dY2 = dY * dY;
        if (dX2 < dens_cut && dY2 < dist_cut) {
          Npts++;
        }
      }
    }
    mprintf("%i %i %i\n", point0->PointsWithinEps(), point0->Fnum()+1, Npts);
  }
*/

/*
  CpptrajFile tempOut;
  tempOut.OpenWrite("temp.dat");
  int currentDensity = -1;
  double distAv = 0.0;
  double distSD = 0.0;
  double sumWts = 0.0;
  int nValues = 0;
  Carray::const_iterator lastPoint = Points_.end() + 1;
  for (Carray::const_iterator point = Points_.begin(); point != lastPoint; ++point)
  {
    if (point == Points_.end() || point->PointsWithinEps() != currentDensity) {
      if (nValues > 0) {
        distAv = distAv / sumWts; //(double)nValues;
        distSD = (distSD / sumWts) - (distAv * distAv);
        if (distSD > 0.0)
          distSD = sqrt(distSD);
        else
          distSD = 0.0;
        //mprintf("Density %i: %i values  Avg= %g  SD= %g  SumWts= %g\n", currentDensity,
        //        nValues, distAv, distSD, sumWts);
        tempOut.Printf("%i %g\n", currentDensity, distAv);
      }
      if (point == Points_.end()) break;
      currentDensity = point->PointsWithinEps();
      distAv = 0.0;
      distSD = 0.0;
      sumWts = 0.0;
      nValues = 0;
    }
    double wt = exp(point->Dist());
    double dval = point->Dist() * wt;
    sumWts += wt;
    distAv += dval;
    distSD += (dval * dval);
    nValues++;
  }
  tempOut.CloseFile(); 
*/

  // BEGIN CALCULATING WEIGHTED DISTANCE AVERAGE
  CpptrajFile tempOut;
  tempOut.OpenWrite("temp.dat");
  DataSet_Mesh weightedAverage;
  Carray::const_iterator cp = Points_.begin();
  // Skip local density of 0.
  //while (cp->PointsWithinEps() == 0 && cp != Points_.end()) ++cp;
  while (cp != Points_.end())
  {
    int densityVal = cp->PointsWithinEps();
    Carray densityArray;
    // Add all points of current density.
    while (cp->PointsWithinEps() == densityVal && cp != Points_.end())
      densityArray.push_back( *(cp++) );
    mprintf("Density value %i has %zu points.\n", densityVal, densityArray.size());
    // Sort array by distance
    std::sort(densityArray.begin(), densityArray.end(), Cpoint::dist_sort());
    // Take the average of the points weighted by their position. 
    double wtDistAv = 0.0;
    double sumWts = 0.0;
    //std::vector<double> weights;
    //weights.reserve( densityArray.size() );
    int maxPt = (int)densityArray.size() - 1;
    for (int ip = 0; ip != (int)densityArray.size(); ++ip) 
    {
      double wt = exp( (double)(ip - maxPt) );
      //mprintf("\t%10i %10u %10u %10g\n", densityVal, ip, maxPt, wt);
      wtDistAv += (densityArray[ip].Dist() * wt);
      sumWts += wt;
      //weights.push_back( wt );
    }
    wtDistAv /= sumWts;
    // Calculate the weighted sample variance
    //double distSD = 0.0;
    //for (unsigned int ip = 0; ip != densityArray.size(); ++ip) {
    //  double diff = densityArray[ip].Dist() - wtDistAv;
    //  distSD += weights[ip] * (diff * diff);
    //}
    //distSD /= sumWts;
    weightedAverage.AddXY(densityVal, wtDistAv); 
    //tempOut.Printf("%i %g %g %g\n", densityVal, wtDistAv, sqrt(distSD), sumWts);
    tempOut.Printf("%i %g %g\n", densityVal, wtDistAv, sumWts);
/*
    // Find the median.
    double median, Q1, Q3;
    if (densityArray.size() == 1) {
      median = densityArray[0].Dist();
      Q1 = median;
      Q3 = median;
    } else {
      unsigned int q3_beg;
      unsigned int med_idx = densityArray.size() / 2; // Always 0 <= Q1 < med_idx
      if ((densityArray.size() % 2) == 0) {
        median = (densityArray[med_idx].Dist() + densityArray[med_idx-1].Dist()) / 2.0;
        q3_beg = med_idx;
      } else {
        median = densityArray[med_idx].Dist();
        q3_beg = med_idx + 1;
      }
      if (densityArray.size() == 2) {
        Q1 = densityArray[0].Dist();
        Q3 = densityArray[1].Dist();
      } else {
        // Find lower quartile
        unsigned int q1_idx = med_idx / 2;
        if ((med_idx % 2) == 0)
          Q1 = (densityArray[q1_idx].Dist() + densityArray[q1_idx-1].Dist()) / 2.0;
        else
          Q1 = densityArray[q1_idx].Dist();
        // Find upper quartile
        unsigned int q3_size = densityArray.size() - q3_beg;
        unsigned int q3_idx = (q3_size / 2) + q3_beg;
        if ((q3_size %2) == 0)
          Q3 = (densityArray[q3_idx].Dist() + densityArray[q3_idx-1].Dist()) / 2.0;
        else
          Q3 = densityArray[q3_idx].Dist();
      }
    }
    mprintf("\tMedian dist value is %g. Q1= %g   Q3= %g\n", median, Q1, Q3);
*/
  }
  tempOut.CloseFile();
  // END CALCULATING WEIGHTED DISTANCE AVERAGE

/*
  // TEST
  tempOut.OpenWrite("temp2.dat");
  std::vector<double> Hist( Points_.back().PointsWithinEps()+1, 0.0 );
  int gWidth = 3;
  double cval = 3.0;
  double two_c_squared = 2.0 * cval * cval;
  mprintf("DBG: cval= %g, Gaussian denominator is %g\n", cval, two_c_squared);
  for (int wtIdx = 0; wtIdx != (int)weightedAverage.Size(); wtIdx++)
  {
    int bval = weightedAverage.X(wtIdx);
    for (int xval = std::max(bval - gWidth, 0);
             xval != std::min(bval + gWidth + 1, (int)Hist.size()); xval++)
    {
      // a: height (weighted average)
      // b: center (density value)
      // c: width
      // x: density value in histogram 
      //int xval = weightedAverage.X(idx);
      //double bval = weightedAverage.X(wtIdx);
      //double bval = (double)wtIdx;
      double diff = (double)(xval - bval);
      //Hist[xval] += (weightedAverage.Y(wtIdx) * exp( -( (diff * diff) / two_c_squared ) ));
      Hist[xval] = std::max(Hist[xval],
                            weightedAverage.Y(wtIdx) * exp( -( (diff * diff) / two_c_squared ) ));
    }
  }
  for (unsigned int idx = 0; idx != Hist.size(); idx++)
    tempOut.Printf("%u %g\n", idx, Hist[idx]);
  tempOut.CloseFile();
  // END TEST
*/
/*
  // TEST
  // Construct best-fit line segments
  tempOut.OpenWrite("temp2.dat");
  double slope, intercept, correl;
  int segment_length = 3;
  DataSet_Mesh Segment;
  Segment.Allocate1D( segment_length );
  for (int wtIdx = 0; wtIdx != (int)weightedAverage.Size(); wtIdx++)
  {
    Segment.Clear();
    for (int idx = std::max(wtIdx - 1, 0); // TODO: use segment_length
             idx != std::min(wtIdx + 2, (int)weightedAverage.Size()); idx++)
        Segment.AddXY(weightedAverage.X(idx), weightedAverage.Y(idx));
    Segment.LinearRegression(slope, intercept, correl, true);
    for (int idx = std::max(wtIdx - 1, 0); // TODO: use segment_length
             idx != std::min(wtIdx + 2, (int)weightedAverage.Size()); idx++)
    {
      double x = weightedAverage.X(idx);
      double y = slope * x + intercept;
      tempOut.Printf("%g %g %i\n", x, y, weightedAverage.X(wtIdx));
    }
  }
  tempOut.CloseFile(); 
  // END TEST
*/

  // BEGIN WEIGHTED RUNNING AVG/SD OF DISTANCES
  // For each point, determine if it is greater than the average of the
  // weighted average distances of the previous, current, and next densities.
  int width = 2;
  int currentDensity = 0;
  int wtIdx = 0;
  double currentAvg = 0.0;
  double deltaSD = 0.0;
  double deltaAv = 0.0;
  int    Ndelta = 0;
  CpptrajFile raOut;
  if (!rafile_.empty()) raOut.OpenWrite(rafile_);
  CpptrajFile raDelta;
  if (!radelta_.empty()) raDelta.OpenWrite(radelta_);
  std::vector<unsigned int> candidateIdxs;
  std::vector<double> candidateDeltas;
  cp = Points_.begin();
  // Skip over points with zero density
  while (cp != Points_.end() && cp->PointsWithinEps() == 0) ++cp;
  while (weightedAverage.X(wtIdx) != cp->PointsWithinEps() && wtIdx < (int)Points_.size())
    ++wtIdx;
  for (Carray::const_iterator point = cp; point != Points_.end(); ++point)
  {
    if (point->PointsWithinEps() != currentDensity) {
      //currentAvg = weightedAverage.Y(wtIdx);
      // New density value. Determine average.
      currentAvg = 0.0;
     // unsigned int Npt = 0; 
      double currentWt = 0.0;
      for (int idx = std::max(wtIdx - width, 0);
               idx != std::min(wtIdx + width + 1, (int)weightedAverage.Size()); idx++)
      {
        //currentAvg += weightedAverage.Y(idx);
        //Npt++;
        double wt = weightedAverage.Y(idx);
        currentAvg += (weightedAverage.Y(idx) * wt);
        currentWt += wt;
      }
      //currentAvg /= (double)Npt;
      currentAvg /= currentWt;
      //smoothAv += currentAvg;
      //smoothSD += (currentAvg * currentAvg);
      //Nsmooth++;
      currentDensity = point->PointsWithinEps();
      if (raOut.IsOpen())
        raOut.Printf("%i %g %g\n", currentDensity, currentAvg, weightedAverage.Y(wtIdx));
      wtIdx++;
    }
    double delta = (point->Dist() - currentAvg);
    if (delta > 0.0) {
      //delta *= log((double)currentDensity);
      if (raDelta.IsOpen())
        raDelta.Printf("%8i %8.3f %8i %8.3f %8.3f\n",
                       currentDensity, delta, point->Fnum()+1, point->Dist(), currentAvg);
      candidateIdxs.push_back( point - Points_.begin() );
      candidateDeltas.push_back( delta );
      deltaAv += delta;
      deltaSD += (delta * delta);
      Ndelta++;
    }
  }
  raOut.CloseFile();
  deltaAv /= (double)Ndelta;
  deltaSD = (deltaSD / (double)Ndelta) - (deltaAv * deltaAv);
  if (deltaSD > 0.0)
    deltaSD = sqrt(deltaSD);
  else
    deltaSD = 0.0;
  if (raDelta.IsOpen())
    raDelta.Printf("#DeltaAvg= %g  DeltaSD= %g\n", deltaAv, deltaSD);
  raDelta.CloseFile();
  int cnum = 0;
  for (unsigned int i = 0; i != candidateIdxs.size(); i++) {
    if (candidateDeltas[i] > (deltaSD)) {
      Points_[candidateIdxs[i]].SetCluster( cnum++ );
      mprintf("\tPoint %u (frame %i, density %i) selected as candidate for cluster %i\n",
              candidateIdxs[i], Points_[candidateIdxs[i]].Fnum()+1,
              Points_[candidateIdxs[i]].PointsWithinEps(), cnum-1);
    }
  }
  // END WEIGHTED AVG/SD OF DISTANCES

/* 
  // Currently doing this by calculating the running average of density vs 
  // distance, then choosing points with distance > twice the SD of the 
  // running average.
  // NOTE: Store in a mesh data set for now in case we want to spline etc later.
  if (avg_factor_ < 1) avg_factor_ = 10; 
  unsigned int window_size = Points_.size() / (unsigned int)avg_factor_;
  mprintf("\tRunning avg window size is %u\n", window_size);
  // FIXME: Handle case where window_size < frames
  DataSet_Mesh runavg;
  unsigned int ra_size = Points_.size() - window_size + 1;
  runavg.Allocate1D( ra_size );
  double dwindow = (double)window_size;
  double sumx = 0.0;
  double sumy = 0.0;
  for (unsigned int i = 0; i < window_size; i++) {
    sumx += (double)Points_[i].PointsWithinEps();
    sumy += Points_[i].Dist();
  }
  runavg.AddXY( sumx / dwindow, sumy / dwindow );
  for (unsigned int i = 1; i < ra_size; i++) {
    unsigned int nextwin = i + window_size - 1;
    unsigned int prevwin = i - 1;
    sumx = (double)Points_[nextwin].PointsWithinEps() -
           (double)Points_[prevwin].PointsWithinEps() + sumx;
    sumy =         Points_[nextwin].Dist()    -
                   Points_[prevwin].Dist()    + sumy;
    runavg.AddXY( sumx / dwindow, sumy / dwindow );
  }
  // Write running average
  if (!rafile_.empty()) {
    CpptrajFile raOut;
    if (raOut.OpenWrite(rafile_))
      mprinterr("Error: Could not open running avg file '%s' for write.\n", rafile_.c_str());
    else {
      for (unsigned int i = 0; i != runavg.Size(); i++)
        raOut.Printf("%g %g\n", runavg.X(i), runavg.Y(i));
      raOut.CloseFile();
    }
  }
  double ra_sd;
  double ra_avg = runavg.Avg( ra_sd );
  // Double stdev to use as cutoff for findning anomalously high peaks.
  ra_sd *= 2.0;
  mprintf("\tAvg of running avg set is %g, SD*2.0 (delta cutoff) is %g\n", ra_avg, ra_sd);
  // For each point in density vs distance plot, determine which running
  // average point is closest. If the difference between the point and the
  // running average point is > 2.0 the SD of the running average data,
  // consider it a 'peak'. 
  CpptrajFile raDelta;
  if (!radelta_.empty())
    raDelta.OpenWrite("radelta.dat");
  if (raDelta.IsOpen())
    raDelta.Printf("%-10s %10s %10s\n", "#Frame", "RnAvgPos", "Delta");
  unsigned int ra_position = 0; // Position in the runavg DataSet
  unsigned int ra_end = runavg.Size() - 1;
  int cnum = 0;
  for (Carray::iterator point = Points_.begin();
                        point != Points_.end(); ++point)
  {
    if (ra_position != ra_end) {
      // Is the next running avgd point closer to this point?
      while (ra_position != ra_end) {
        double dens  = (double)point->PointsWithinEps();
        double diff0 = fabs( dens - runavg.X(ra_position  ) );
        double diff1 = fabs( dens - runavg.X(ra_position+1) );
        if (diff1 < diff0)
          ++ra_position; // Next running avg position is closer for this point.
        else
          break; // This position is closer.
      }
    }
    double delta = point->Dist() - runavg.Y(ra_position);
    if (raDelta.IsOpen())
      raDelta.Printf("%-10i %10u %10g", point->Fnum()+1, ra_position, delta);
    if (delta > ra_sd) {
      if (raDelta.IsOpen())
        raDelta.Printf(" POTENTIAL CLUSTER %i", cnum);
      point->SetCluster(cnum++);
    }
    if (raDelta.IsOpen()) raDelta.Printf("\n");
  }
  raDelta.CloseFile();
*/
  return cnum;
}
Esempio n. 19
0
// -----------------------------------------------------------------------------
int Cluster_DPeaks::Cluster_DiscreteDensity() {
  mprintf("\tStarting DPeaks clustering, discrete density calculation.\n");
  Points_.clear();
  // First determine which frames are being clustered.
  for (int frame = 0; frame < (int)FrameDistances_.Nframes(); ++frame)
    if (!FrameDistances_.IgnoringRow( frame ))
      Points_.push_back( Cpoint(frame) );
  // Sanity check.
  if (Points_.size() < 2) {
    mprinterr("Error: Only 1 frame in initial clustering.\n");
    return 1;
  }
  // For each point, determine how many others are within epsilon. Also
  // determine maximum distance between any two points.
  mprintf("\tDetermining local density of each point.\n");
  ProgressBar cluster_progress( Points_.size() );
  double maxDist = -1.0;
  for (Carray::iterator point0 = Points_.begin();
                        point0 != Points_.end(); ++point0)
  {
    cluster_progress.Update(point0 - Points_.begin());
    int density = 0;
    for (Carray::const_iterator point1 = Points_.begin();
                                point1 != Points_.end(); ++point1)
    {
      if (point0 != point1) {
        double dist = FrameDistances_.GetFdist(point0->Fnum(), point1->Fnum());
        maxDist = std::max(maxDist, dist);
        if ( dist < epsilon_ )
          density++;
      }
    }
    point0->SetPointsWithinEps( density );
  }
  mprintf("DBG: Max dist= %g\n", maxDist);
  // DEBUG: Frame/Density
  CpptrajFile fdout;
  fdout.OpenWrite("fd.dat");
  for (Carray::const_iterator point = Points_.begin(); point != Points_.end(); ++point)
    fdout.Printf("%i %i\n", point->Fnum()+1, point->PointsWithinEps());
  fdout.CloseFile();
  // Sort by density here. Otherwise array indices will be invalid later.
  std::sort( Points_.begin(), Points_.end(), Cpoint::pointsWithinEps_sort() );
  // For each point, find the closest point that has higher density. Since 
  // array is now sorted by density the last point has the highest density.
  Points_.back().SetDist( maxDist );
  mprintf("\tFinding closest neighbor point with higher density for each point.\n");
  unsigned int lastidx = Points_.size() - 1;
  cluster_progress.SetupProgress( lastidx );
  for (unsigned int idx0 = 0; idx0 != lastidx; idx0++)
  {
    cluster_progress.Update( idx0 );
    double min_dist = maxDist;
    int nearestIdx = -1; // Index of nearest neighbor with higher density
    Cpoint& point0 = Points_[idx0];
    //mprintf("\nDBG:\tSearching for nearest neighbor to idx %u with higher density than %i.\n",
    //        idx0, point0.PointsWithinEps());
    // Since array is sorted by density we can start at the next point.
    for (unsigned int idx1 = idx0+1; idx1 != Points_.size(); idx1++)
    {
      Cpoint const& point1 = Points_[idx1];
      double dist1_2 = FrameDistances_.GetFdist(point0.Fnum(), point1.Fnum());
      if (point1.PointsWithinEps() > point0.PointsWithinEps())
      {
        if (dist1_2 < min_dist) {
          min_dist = dist1_2;
          nearestIdx = (int)idx1;
          //mprintf("DBG:\t\tNeighbor idx %i is closer (density %i, distance %g)\n",
          //        nearestIdx, point1.PointsWithinEps(), min_dist);
        }
      }
    }
    point0.SetDist( min_dist );
    //mprintf("DBG:\tClosest point to %u with higher density is %i (distance %g)\n",
    //        idx0, nearestIdx, min_dist);
    point0.SetNearestIdx( nearestIdx );
  }
  // Plot density vs distance for each point.
  if (!dvdfile_.empty()) {
    CpptrajFile output;
    if (output.OpenWrite(dvdfile_))
      mprinterr("Error: Could not open density vs distance plot '%s' for write.\n",
                dvdfile_.c_str()); // TODO: Make fatal?
    else {
      output.Printf("%-10s %10s %s %10s %10s\n", "#Density", "Distance",
                    "Frame", "Idx", "Neighbor");
      for (Carray::const_iterator point = Points_.begin();
                                  point != Points_.end(); ++point)
        output.Printf("%-10i %10g \"%i\" %10u %10i\n", point->PointsWithinEps(), point->Dist(),
                      point->Fnum()+1, point-Points_.begin(), point->NearestIdx());
      output.CloseFile();
    }
  }

  return 0;
}
Esempio n. 20
0
// -----------------------------------------------------------------------------
int Cluster_DPeaks::Cluster_GaussianKernel() {
  mprintf("\tStarting DPeaks clustering. Using Gaussian kernel to calculate density.\n");
  // First determine which frames are being clustered.
  Points_.clear();
  int oidx = 0;
  for (int frame = 0; frame < (int)FrameDistances_.Nframes(); ++frame)
    if (!FrameDistances_.IgnoringRow( frame ))
      Points_.push_back( Cpoint(frame, oidx++) );
  // Sanity check.
  if (Points_.size() < 2) {
    mprinterr("Error: Only 1 frame in initial clustering.\n");
    return 1;
  }

  // Sort distances
  std::vector<float> Distances;
  for (ClusterMatrix::const_iterator mat = FrameDistances_.begin();
                                     mat != FrameDistances_.end(); ++mat)
    Distances.push_back( *mat );
  std::sort( Distances.begin(), Distances.end() );
  unsigned int idx = (unsigned int)((double)Distances.size() * 0.02);
  double bandwidth = (double)Distances[idx];
  mprintf("idx= %u, bandwidth= %g\n", idx, bandwidth);

  // Density via Gaussian kernel
  double maxDist = -1.0;
  for (unsigned int i = 0; i != Points_.size(); i++) {
    for (unsigned int j = i+1; j != Points_.size(); j++) {
      double dist = FrameDistances_.GetFdist(Points_[i].Fnum(), Points_[j].Fnum());
      maxDist = std::max( maxDist, dist );
      dist /= bandwidth;
      double gk = exp(-(dist *dist));
      Points_[i].AddDensity( gk );
      Points_[j].AddDensity( gk );
    }
  }
  mprintf("Max dist= %g\n", maxDist);
  CpptrajFile rhoOut;
  rhoOut.OpenWrite("rho.dat");
  for (unsigned int i = 0; i != Points_.size(); i++)
    rhoOut.Printf("%u %g\n", i+1, Points_[i].Density());
  rhoOut.CloseFile();
  
  // Sort by density, descending
  std::stable_sort( Points_.begin(), Points_.end(), Cpoint::density_sort_descend() );
  CpptrajFile ordrhoOut;
  ordrhoOut.OpenWrite("ordrho.dat");
  for (unsigned int i = 0; i != Points_.size(); i++)
    ordrhoOut.Printf("%u %g %i %i\n", i+1, Points_[i].Density(), Points_[i].Fnum()+1,
                     Points_[i].Oidx()+1);
  ordrhoOut.CloseFile();

  // Determine minimum distances
  int first_idx = Points_[0].Oidx();
  Points_[first_idx].SetDist( -1.0 );
  Points_[first_idx].SetNearestIdx(-1);
  for (unsigned int ii = 1; ii != Points_.size(); ii++) {
    int ord_i = Points_[ii].Oidx();
    Points_[ord_i].SetDist( maxDist );
    for (unsigned int jj = 0; jj != ii; jj++) {
      int ord_j = Points_[jj].Oidx();
      double dist = FrameDistances_.GetFdist(Points_[ord_i].Fnum(), Points_[ord_j].Fnum());
      if (dist < Points_[ord_i].Dist()) {
        Points_[ord_i].SetDist( dist );
        Points_[ord_j].SetNearestIdx( ord_j );
      }
    }
  }
  if (!dvdfile_.empty()) {
    CpptrajFile output;
    if (output.OpenWrite(dvdfile_)) return 1;
    for (Carray::const_iterator point = Points_.begin(); point != Points_.end(); ++point)
      output.Printf("%g %g %i\n", point->Density(), point->Dist(), point->NearestIdx()+1);
    output.CloseFile();
  }
      
  return 0;
}
Esempio n. 21
0
/** Given the structure of a molecule and its normal mode vibrational
  * frequencies this routine uses standard statistical mechanical
  * formulas for an ideal gas (in the canonical ensemble, see,
  * for example, d. a. mcquarrie, "statistical thermodynamics",
  * harper & row, new york, 1973, chapters 5, 6, and 8) to compute
  * the entropy, heat capacity, and internal energy.

  * The si system of units is used internally. Conversion to units
  * more familiar to most chemists is made for output.
  *
  * \param outfile output file, should already be open.
  * \param natoms  Number of atoms
  * \param nvecs   Number of eigenvectors (already converted to frequencies)
  * \param crd     coordinates in Angstroms
  * \param amass   atomic weights, in amu.
  * \param freq    vibrational frequencies, in cm**-1 and in ascending order
  * \param temp    temperature
  * \param patm    pressure, in atmospheres
*/
void thermo( CpptrajFile& outfile, int natoms, int nvecs, int ilevel, 
             const double* crd, const double* amass, const double* freq, 
             double temp, double patm)
{
  // pmom    principal moments of inertia, in amu-bohr**2 and in ascending order.
  double pmom[3], rtemp, rtemp1, rtemp2, rtemp3;

  // ----- Constants -------------------
  const double thresh = 900.0;        // vibrational frequency threshold
  const double tokg   = 1.660531e-27; // kilograms per amu.
  const double boltz  = 1.380622e-23; // boltzman constant, in joules per kelvin.
  const double planck = 6.626196e-34; // planck constant, in joule-seconds.
  const double avog   = 6.022169e+23; // avogadro constant, in mol**(-1).
  const double jpcal  = 4.18674e+00;  // joules per calorie.
  const double tomet  = 1.0e-10;      // metres per Angstrom.
  const double hartre = 4.35981e-18;  // joules per hartree.
  const double pstd   = 1.01325e+05;  // Standard pressure in pascals
  // -----------------------------------

  //     compute the gas constant, pi, pi**2, and e.
  //     compute the conversion factors cal per joule and kcal per joule.
  const double gas  = avog * boltz;
  // pi   = four * datan(one)
  const double pipi = PI * PI;
  const double e    = exp(1.0);
  const double tocal  = 1.0 / jpcal;
  const double tokcal = tocal / 1000.0;

  if (!outfile.IsOpen()) {
    mprinterr("Internal Error: thermo: output file is not open.\n");
    return;
  }

  //     print the temperature and pressure.
  outfile.Printf("\n                    *******************\n");
  outfile.Printf(  "                    - Thermochemistry -\n");
  outfile.Printf(  "                    *******************\n\n");
  outfile.Printf("\n temperature %9.3f kelvin\n pressure    %9.5f atm\n",temp,patm);
  double pressure = pstd * patm;
  double rt = gas * temp;

  //     compute and print the molecular mass in amu, then convert to
  //     kilograms.
  double weight = 0.0;
  for (int iat = 0; iat < natoms; ++iat)
    weight += amass[iat];
  outfile.Printf(" molecular mass (principal isotopes) %11.5f amu\n", weight);
  weight *= tokg;

  //trap non-unit multiplicities.
  //if (multip != 1) {
  //  outfile.Printf("\n Warning-- assumptions made about the electronic partition function\n");
  //  outfile.Printf(  "           are not valid for multiplets!\n\n");
  //}
  //     compute contributions due to translation:
  //        etran-- internal energy
  //        ctran-- constant v heat capacity
  //        stran-- entropy
  double dum1 = boltz * temp;
  double dum2 = pow(TWOPI, 1.5);
  double arg = pow(dum1, 1.5) / planck;
  arg = (arg / pressure) * (dum1 / planck);
  arg = arg * dum2 * (weight / planck);
  arg = arg * sqrt(weight) * exp(2.5);
  double stran = gas * log(arg);
  double etran = 1.5 * rt;
  double ctran = 1.5 * gas;

  //     Compute contributions due to electronic motion:
  //        It is assumed that the first electronic excitation energy
  //        is much greater than kt and that the ground state has a
  //        degeneracy of one.  Under these conditions the electronic
  //        partition function can be considered to be unity.  The
  //        ground electronic state is taken to be the zero of
  //        electronic energy.

  //     for monatomics print and return.
  if (natoms <= 1){ 
    outfile.Printf("\n internal energy:   %10.3f joule/mol         %10.3f kcal/mol\n",
           etran, etran * tokcal);
    outfile.Printf(  " entropy:           %10.3f joule/k-mol       %10.3f cal/k-mol\n",
           stran, stran * tocal);
    outfile.Printf(  " heat capacity cv:  %10.3f joule/k-mol       %10.3f  cal/k-mol\n",
           ctran, ctran * tocal);
    return;
  }

  // Allocate workspace memory
  // vtemp   vibrational temperatures, in kelvin.
  // evibn   contribution to e from the vibration n.
  // cvibn   contribution to cv from the vibration n.
  // svibn   contribution to s from the vibration n.
  double* WorkSpace = new double[ 4 * nvecs ];
  double* vtemp = WorkSpace;
  double* evibn = WorkSpace + nvecs;
  double* cvibn = WorkSpace + nvecs*2;
  double* svibn = WorkSpace + nvecs*3;

  //     compute contributions due to rotation.

  //     Compute the principal moments of inertia, get the rotational
  //     symmetry number, see if the molecule is linear, and compute
  //     the rotational temperatures.  Note the imbedded conversion
  //     of the moments to SI units.
  MomentOfInertia( natoms, crd, amass, pmom );
  outfile.Printf("\n principal moments of inertia (nuclei only) in amu-A**2:\n");
  outfile.Printf(  "      %12.2f%12.2f%12.2f\n", pmom[0], pmom[1], pmom[2]);
  
  bool linear = false;
  // Symmetry number: only for linear molecules. for others symmetry number is unity
  double sn = 1.0;
  if (natoms <= 2) {
    linear = true;
    if (amass[0] == amass[1]) sn = 2.0;
  }
  outfile.Printf("\n rotational symmetry number %3.0f\n", sn);

  double con = planck / (boltz*8.0*pipi);
  con = (con / tokg)  *  (planck / (tomet*tomet));
  if (linear) {
    rtemp = con / pmom[2];
    if (rtemp < 0.2) {
      outfile.Printf("\n Warning-- assumption of classical behavior for rotation\n");
      outfile.Printf(  "           may cause significant error\n");
    }
    outfile.Printf("\n rotational temperature (kelvin) %12.5f\n", rtemp);                 
  } else {
    rtemp1 = con / pmom[0];
    rtemp2 = con / pmom[1];
    rtemp3 = con / pmom[2];
    if (rtemp1 < 0.2) {
      outfile.Printf("\n Warning-- assumption of classical behavior for rotation\n");
      outfile.Printf(  "           may cause significant error\n");
    }
    outfile.Printf("\n rotational temperatures (kelvin) %12.5f%12.5f%12.5f\n", 
           rtemp1, rtemp2, rtemp3);
  }

  //         erot-- rotational contribution to internal energy.
  //         crot-- rotational contribution to cv.
  //         srot-- rotational contribution to entropy.
  double erot, crot, srot;

  if (linear) { 
     erot = rt;
     crot = gas;
     arg  = (temp/rtemp) * (e/sn);
     srot = gas * log(arg);
  } else {
     erot = 1.5 * rt;
     crot = 1.5 * gas;
     arg  = sqrt(PI*e*e*e) / sn;
     double dum  = (temp/rtemp1) * (temp/rtemp2) * (temp/rtemp3);
     arg  = arg * sqrt(dum);
     srot = gas * log(arg);
  }

  //     compute contributions due to vibration.

  //     compute vibrational temperatures and zero point vibrational
  //     energy.  only real frequencies are included in the analysis.

  //     ndof = 3*natoms - 6 - nimag
  //     if (nimag .ne. 0) write(iout,1210) nimag
  //     if (linear) ndof = ndof + 1
  int ndof = nvecs;

  //       (---iff is the first frequency to include in thermo:)
  int iff;
  if (ilevel != 0)
     iff = 0;
  else if (linear)
     iff = 5;
  else
     iff = 6;
  con = planck / boltz;
  double ezpe = 0.0;
  for (int i = 0; i < ndof; ++i) {
     vtemp[i] = freq[i+iff] * con * 3.0e10;
     ezpe    += freq[i+iff] * 3.0e10;
  }
  ezpe = 0.5 * planck * ezpe;
  outfile.Printf("\n zero point vibrational energy %12.1f (joules/mol) \n",ezpe * avog);
  outfile.Printf(  "                               %12.5f (kcal/mol)\n",ezpe * tokcal * avog);
  outfile.Printf(  "                               %12.7f (hartree/particle)\n", ezpe / hartre); 
  //     compute the number of vibrations for which more than 5% of an
  //     assembly of molecules would exist in vibrational excited states.
  //     special printing for these modes is done to allow the user to
  //     easily take internal rotations into account.  the criterion
  //     corresponds roughly to a low frequency of 1.9(10**13) hz, or
  //     625 cm**(-1), or a vibrational temperature of 900 k.

  int lofreq = 0;
  for (int i = 0; i < ndof; ++i)
    if (vtemp[i] < thresh)
      ++lofreq;
  if (lofreq != 0) {
    outfile.Printf("\n Warning-- %3i vibrations have low frequencies and may represent hindered \n",
           lofreq);
    outfile.Printf(  "         internal rotations.  The contributions printed below assume that these \n");
    outfile.Printf(  "         really are vibrations.\n");
  }

  //     compute:
  //        evib-- the vibrational component of the internal energy.
  //        cvib-- the vibrational component of the heat capacity.
  //        svib-- the vibrational component of the entropy.
  double evib = 0.0;
  double cvib = 0.0;
  double svib = 0.0;
  double scont;
  for (int i = 0; i < ndof; ++i) {
     //       compute some common factors.

     double tovt  = vtemp[i] / temp;
     double etovt = exp(tovt);
     double em1   = etovt - 1.0;

     //       compute contributions due to the i'th vibration.

     double econt = tovt  *  (0.5 + 1.0/em1);
     double ccont = etovt *  pow(tovt/em1,2.0);
     double argd = 1.0 - 1.0/etovt;
     if (argd > 1.0e-7) 
        scont = tovt/em1 - log(argd);
     else {
        scont = 0.0;
        outfile.Printf(" warning: setting vibrational entropy to zero for mode %i with vtemp = %f\n",
               i+1, vtemp[i]);
     }
     //       if (lofreq .ge. i) then
     evibn[i] = econt * rt;
     cvibn[i] = ccont * gas;
     svibn[i] = scont * gas;
     //       end if
     evib += econt;
     cvib += ccont;
     svib += scont;
  } 
  evib *= rt;
  cvib *= gas;
  svib *= gas;

  //     the units are now:
  //         e-- joules/mol
  //         c-- joules/mol-kelvin
  //         s-- joules/mol-kelvin

  double etot = etran + erot + evib;
  double ctot = ctran + crot + cvib;
  double stot = stran + srot + svib;

  //     print the sum of the hartree-fock energy and the thermal energy.

  //     call tread(501,gen,47,1,47,1,0)
  //     esum = gen(32) + etot/avog/hartre
  //     write(iout,1230) esum

  //     convert to the following and print
  //         e-- kcal/mol
  //         c-- cal/mol-kelvin
  //         s-- cal/mol-kelvin
  etran = etran * tokcal;
  ctran = ctran * tocal;
  stran = stran * tocal;
  erot   = erot * tokcal;
  crot   = crot * tocal;
  srot   = srot * tocal;
  evib   = evib * tokcal;
  cvib   = cvib * tocal;
  svib   = svib * tocal;
  etot   = etran + erot + evib;
  ctot   = ctran + crot + cvib;
  stot   = stran + srot + svib;
  for (int i = 0; i < ndof; ++i) {
     evibn[i] *= tokcal;
     cvibn[i] *= tocal;
     svibn[i] *= tocal;
  }

  outfile.Printf("\n\n           freq.         E                  Cv                 S\n");
  outfile.Printf(    "          cm**-1      kcal/mol        cal/mol-kelvin    cal/mol-kelvin\n");
  outfile.Printf(    "--------------------------------------------------------------------------------\n");
  outfile.Printf(    " Total              %11.3f        %11.3f        %11.3f\n",etot,ctot,stot);
  outfile.Printf(    " translational      %11.3f        %11.3f        %11.3f\n",etran,ctran,stran);
  outfile.Printf(    " rotational         %11.3f        %11.3f        %11.3f\n",erot,crot,srot);
  outfile.Printf(    " vibrational        %11.3f        %11.3f        %11.3f\n",evib,cvib,svib);

  for (int i = 0; i < iff; ++i) 
    outfile.Printf(" %5i%10.3f\n", i+1, freq[i]);

  for (int i = 0; i < ndof; ++i) {
    outfile.Printf(" %5i%10.3f    %11.3f        %11.3f        %11.3f\n",i+iff+1,
           freq[i+iff], evibn[i], cvibn[i], svibn[i]);
  }
  delete[] WorkSpace;
}
Esempio n. 22
0
// Action_AtomMap::Init()
Action::RetType Action_AtomMap::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
    DataFile* rmsout = 0;
    int refatom,targetatom;
    debug_ = debugIn;
    RefMap_.SetDebug(debug_);
    TgtMap_.SetDebug(debug_);

    // Get Args
    CpptrajFile* outputfile = init.DFL().AddCpptrajFile(actionArgs.GetStringKey("mapout"), "Atom Map");
    maponly_ = actionArgs.hasKey("maponly");
    rmsfit_ = actionArgs.hasKey("rmsfit");
    if (rmsfit_)
        rmsout = init.DFL().AddDataFile( actionArgs.GetStringKey("rmsout"), actionArgs );
    std::string targetName = actionArgs.GetStringNext();
    std::string refName = actionArgs.GetStringNext();
    if (targetName.empty()) {
        mprinterr("Error: No target specified.\n");
        return Action::ERR;
    }
    if (refName.empty()) {
        mprinterr("Error: No reference specified.\n");
        return Action::ERR;
    }
    // Get Reference
    RefFrame_ = (DataSet_Coords_REF*)init.DSL().FindSetOfType( refName, DataSet::REF_FRAME );
    if (RefFrame_ == 0) {
        mprinterr("Error: Could not get reference frame %s\n",refName.c_str());
        return Action::ERR;
    }
    // Get Target
    TgtFrame_ = (DataSet_Coords_REF*)init.DSL().FindSetOfType( targetName, DataSet::REF_FRAME );
    if (TgtFrame_ == 0) {
        mprinterr("Error: Could not get target frame %s\n",targetName.c_str());
        return Action::ERR;
    }

    mprintf("    ATOMMAP: Atoms in trajectories associated with parm %s will be\n",
            TgtFrame_->Top().c_str());
    mprintf("             mapped according to parm %s.\n",RefFrame_->Top().c_str());
    if (outputfile != 0)
        mprintf("             Map will be written to %s\n",outputfile->Filename().full());
    if (maponly_)
        mprintf("             maponly: Map will only be written, not used in trajectory read.\n");
    if (!maponly_ && rmsfit_) {
        mprintf("             rmsfit: Will rms fit mapped atoms in tgt to reference.\n");
        if (rmsout != 0) {
            rmsdata_ = init.DSL().AddSet(DataSet::DOUBLE, actionArgs.GetStringNext(), "RMSD");
            if (rmsdata_==0) return Action::ERR;
            rmsout->AddDataSet(rmsdata_);
        }
    }

    // For each map, set up (get element for each atom, initialize map mem),
    // determine what atoms are bonded to each other via simple distance
    // cutoffs, the give each atom an ID based on what atoms are bonded to
    // it, noting which IDs are unique for that map.

    if (RefMap_.Setup(RefFrame_->Top())!=0) return Action::ERR;
    //RefMap_.WriteMol2((char*)"RefMap.mol2\0"); // DEBUG
    RefMap_.DetermineAtomIDs();

    if (TgtMap_.Setup(TgtFrame_->Top())!=0) return Action::ERR;
    //TgtMap_.WriteMol2((char*)"TgtMap.mol2\0"); // DEBUG
    TgtMap_.DetermineAtomIDs();

    // Check if number of atoms in each map is equal
    if (RefMap_.Natom() != TgtMap_.Natom()) {
        mprintf("Warning: # atoms in reference (%i) not equal\n",
                RefMap_.Natom());
        mprintf("Warning:\tto # atoms in target (%i).\n",TgtMap_.Natom());
    }

    // Set up RMS frames to be able to hold max # of possible atoms
    rmsRefFrame_.SetupFrame(RefMap_.Natom());
    rmsTgtFrame_.SetupFrame(RefMap_.Natom());

    // Allocate memory for atom map
    //   AMap_[reference]=target
    AMap_.resize( RefMap_.Natom(), -1);
    // Map unique atoms
    int numMappedAtoms = MapUniqueAtoms(RefMap_, TgtMap_);
    if (debug_>0)
        mprintf("*         MapUniqueAtoms: %i atoms mapped.\n",numMappedAtoms);
    // If no unique atoms mapped system is highly symmetric and needs to be
    // iteratively mapped. Otherwise just map remaining atoms.
    if (numMappedAtoms==0) {
        if (MapWithNoUniqueAtoms(RefMap_,TgtMap_)) return Action::ERR;
    } else {
        if (MapAtoms(RefMap_,TgtMap_)) return Action::ERR;
    }

    // Print atom map and count # mapped atoms
    numMappedAtoms = 0;
    outputfile->Printf("%-6s %4s %6s %4s\n","#TgtAt","Tgt","RefAt","Ref");
    for (refatom=0; refatom < RefMap_.Natom(); refatom++) {
        targetatom = AMap_[refatom];
        if (targetatom < 0)
            outputfile->Printf("%6s %4s %6i %4s\n","---","---",refatom+1,RefMap_[refatom].c_str());
        else
            outputfile->Printf("%6i %4s %6i %4s\n",targetatom+1,TgtMap_[targetatom].c_str(),
                               refatom+1, RefMap_[refatom].c_str());
        if (targetatom>=0) {
            //mprintf("* TargetAtom %6i(%4s) maps to RefAtom %6i(%4s)\n",
            //                targetatom,TgtMap_.P->names[targetatom],
            //                refatom,RefMap_.P->names[refatom]);
            ++numMappedAtoms;
        } //else {
        //  mprintf("* Could not map any TargetAtom to RefAtom %6i(%4s)\n",
        //                  refatom,RefMap_.P->names[refatom]);
        //}
    }
    mprintf("      %i total atoms were mapped.\n",numMappedAtoms);
    if (maponly_) return Action::OK;

    // If rmsfit is specified, an rms fit of target to reference will be
    // performed using all atoms that were successfully mapped from
    // target to reference.
    if (rmsfit_) {
        // Set up a reference frame containing only mapped reference atoms
        rmsRefFrame_.StripUnmappedAtoms(RefFrame_->RefFrame(), AMap_);
        mprintf("      rmsfit: Will rms fit %i atoms from target to reference.\n",numMappedAtoms);
        return Action::OK;
    }

    // Check if not all atoms could be mapped
    if (numMappedAtoms != RefMap_.Natom()) {
        // If the number of mapped atoms is less than the number of reference
        // atoms but equal to the number of target atoms, can modify the reference
        // frame to only include mapped atoms
        if (numMappedAtoms<RefMap_.Natom() && numMappedAtoms==TgtMap_.Natom()) {
            // Create mask that includes only reference atoms that could be mapped
            AtomMask M1;
            for (refatom = 0; refatom < RefMap_.Natom(); refatom++) {
                if (AMap_[refatom] != -1) M1.AddAtom(refatom);
            }
            // Strip reference parm
            mprintf("    Modifying reference '%s' topology and frame to match mapped atoms.\n",
                    RefFrame_->legend());
            if (RefFrame_->StripRef( M1 )) return Action::ERR;
            // Since AMap[ ref ] = tgt but ref is now missing any stripped atoms,
            // the indices of AMap must be shifted to match
            int refIndex = 0; // The new index
            for (refatom = 0; refatom < RefMap_.Natom(); refatom++) {
                targetatom = AMap_[refatom];
                if (targetatom<0)
                    continue;
                else
                    AMap_[refIndex++]=targetatom;
            }
        } else {
            mprintf("Warning: AtomMap: Not all atoms were mapped. Frames will not be modified.\n");
            maponly_=true;
        }
    }

    if (!maponly_) {
        // Set up new Frame
        newFrame_ = new Frame();
        newFrame_->SetupFrameM( TgtFrame_->Top().Atoms() );

        // Set up new Parm
        newParm_ = TgtFrame_->Top().ModifyByMap(AMap_);
    }

    return Action::OK;
}
Esempio n. 23
0
int Parm_CharmmPsf::WriteParm(FileName const& fname, Topology const& parm) {
  // TODO: CMAP etc info
  CpptrajFile outfile;
  if (outfile.OpenWrite(fname)) return 1;
  // Write PSF
  outfile.Printf("PSF\n\n");
  // Write title
  std::string titleOut = parm.ParmName();
  titleOut.resize(78);
  outfile.Printf("%8i !NTITLE\n* %-78s\n\n", 1, titleOut.c_str());
  // Write NATOM section
  outfile.Printf("%8i !NATOM\n", parm.Natom());
  unsigned int idx = 1;
  // Make fake segment ids for now.
  char segid[2];
  segid[0] = 'A';
  segid[1] = '\0';
  mprintf("Warning: Assigning single letter segment IDs.\n");
  int currentMol = 0;
  bool inSolvent = false;
  for (Topology::atom_iterator atom = parm.begin(); atom != parm.end(); ++atom, ++idx) {
    int resnum = atom->ResNum();
    if (atom->MolNum() != currentMol) {
      if (!inSolvent) {
        inSolvent = parm.Mol(atom->MolNum()).IsSolvent();
        currentMol = atom->MolNum();
        segid[0]++;
      } else
        inSolvent = parm.Mol(atom->MolNum()).IsSolvent();
    }
    // TODO: Print type name for xplor-like PSF
    int typeindex = atom->TypeIndex() + 1;
    // If type begins with digit, assume charmm numbers were read as
    // type. Currently Amber types all begin with letters.
    if (isdigit(atom->Type()[0]))
      typeindex = convertToInteger( *(atom->Type()) );
    // ATOM# SEGID RES# RES ATNAME ATTYPE CHRG MASS (REST OF COLUMNS ARE LIKELY FOR CMAP AND CHEQ)
    outfile.Printf("%8i %-4s %-4i %-4s %-4s %4i %14.6G %9g  %10i\n", idx, segid,
                   parm.Res(resnum).OriginalResNum(), parm.Res(resnum).c_str(),
                   atom->c_str(), typeindex, atom->Charge(),
                   atom->Mass(), 0);
  }
  outfile.Printf("\n");
  // Write NBOND section
  outfile.Printf("%8u !NBOND: bonds\n", parm.Bonds().size() + parm.BondsH().size());
  idx = 1;
  for (BondArray::const_iterator bond = parm.BondsH().begin();
                                 bond != parm.BondsH().end(); ++bond, ++idx)
  {
    outfile.Printf("%8i%8i", bond->A1()+1, bond->A2()+1);
    if ((idx % 4)==0) outfile.Printf("\n"); 
  }
  for (BondArray::const_iterator bond = parm.Bonds().begin();
                                 bond != parm.Bonds().end(); ++bond, ++idx)
  {
    outfile.Printf("%8i%8i", bond->A1()+1, bond->A2()+1);
    if ((idx % 4)==0) outfile.Printf("\n"); 
  }
  if ((idx % 4)!=0) outfile.Printf("\n");
  outfile.Printf("\n");
  // Write NTHETA section
  outfile.Printf("%8u !NTHETA: angles\n", parm.Angles().size() + parm.AnglesH().size());
  idx = 1;
  for (AngleArray::const_iterator ang = parm.AnglesH().begin();
                                  ang != parm.AnglesH().end(); ++ang, ++idx)
  {
    outfile.Printf("%8i%8i%8i", ang->A1()+1, ang->A2()+1, ang->A3()+1);
    if ((idx % 3)==0) outfile.Printf("\n");
  }
  for (AngleArray::const_iterator ang = parm.Angles().begin();
                                  ang != parm.Angles().end(); ++ang, ++idx)
  {
    outfile.Printf("%8i%8i%8i", ang->A1()+1, ang->A2()+1, ang->A3()+1);
    if ((idx % 3)==0) outfile.Printf("\n");
  }
  if ((idx % 3)==0) outfile.Printf("\n");
  outfile.Printf("\n");
  // Write out NPHI section
  outfile.Printf("%8u !NPHI: dihedrals\n", parm.Dihedrals().size() + parm.DihedralsH().size());
  idx = 1;
  for (DihedralArray::const_iterator dih = parm.DihedralsH().begin();
                                     dih != parm.DihedralsH().end(); ++dih, ++idx)
  {
    outfile.Printf("%8i%8i%8i%8i", dih->A1()+1, dih->A2()+1, dih->A3()+1, dih->A4()+1);
    if ((idx % 2)==0) outfile.Printf("\n");
  }
  for (DihedralArray::const_iterator dih = parm.Dihedrals().begin();
                                     dih != parm.Dihedrals().end(); ++dih, ++idx)
  {
    outfile.Printf("%8i%8i%8i%8i", dih->A1()+1, dih->A2()+1, dih->A3()+1, dih->A4()+1);
    if ((idx % 2)==0) outfile.Printf("\n");
  }
  if ((idx % 2)==0) outfile.Printf("\n");
  outfile.Printf("\n");

  outfile.CloseFile();
  return 0;
}
Esempio n. 24
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// DataIO_Std::WriteDataNormal()
int DataIO_Std::WriteDataNormal(CpptrajFile& file, DataSetList const& Sets) {
  // Assume all 1D data sets.
  if (Sets.empty() || CheckAllDims(Sets, 1)) return 1;
  // For this output to work the X-dimension of all sets needs to match.
  // The most important things for output are min and step so just check that.
  // Use X dimension of set 0 for all set dimensions.
  CheckXDimension( Sets );
  // TODO: Check for empty dim.
  DataSet* Xdata = Sets[0];
  Dimension const& Xdim = static_cast<Dimension const&>( Xdata->Dim(0) );
  int xcol_width = Xdim.Label().size() + 1; // Only used if hasXcolumn_
  if (xcol_width < 8) xcol_width = 8;
  int xcol_precision = 3;

  // Determine size of largest DataSet.
  size_t maxFrames = DetermineMax( Sets );

  // Set up X column.
  TextFormat x_col_format(XcolFmt());
  if (hasXcolumn_) {
    if (XcolPrecSet()) {
      xcol_width = XcolWidth();
      x_col_format = TextFormat(XcolFmt(), XcolWidth(), XcolPrec());
    } else {
      // Create format string for X column based on dimension in first data set.
      // Adjust X col precision as follows: if the step is set and has a 
      // fractional component set the X col width/precision to either the data
      // width/precision or the current width/precision, whichever is larger. If
      // the set is XYMESH but step has not been set (so we do not know spacing 
      // between X values) use default precision. Otherwise the step has no
      // fractional component so make the precision zero.
      double step_i;
      double step_f = modf( Xdim.Step(), &step_i );
      double min_f  = modf( Xdim.Min(),  &step_i );
      if (Xdim.Step() > 0.0 && (step_f > 0.0 || min_f > 0.0)) {
        xcol_precision = std::max(xcol_precision, Xdata->Format().Precision());
        xcol_width = std::max(xcol_width, Xdata->Format().Width());
      } else if (Xdata->Type() != DataSet::XYMESH)
        xcol_precision = 0;
      x_col_format.SetCoordFormat( maxFrames, Xdim.Min(), Xdim.Step(), xcol_width, xcol_precision );
    }
  } else {
    // If not writing an X-column, no leading space for the first dataset.
    Xdata->SetupFormat().SetFormatAlign( TextFormat::RIGHT );
  }

  // Write header to buffer
  std::vector<int> Original_Column_Widths;
  if (writeHeader_) {
    // If x-column present, write x-label
    if (hasXcolumn_)
      WriteNameToBuffer( file, Xdim.Label(), xcol_width, true );
    // To prevent truncation of DataSet legends, adjust the width of each
    // DataSet if necessary.
    for (DataSetList::const_iterator ds = Sets.begin(); ds != Sets.end(); ++ds) {
      // Record original column widths in case they are changed.
      Original_Column_Widths.push_back( (*ds)->Format().Width() );
      int colLabelSize;
      if (ds == Sets.begin() && !hasXcolumn_)
        colLabelSize = (int)(*ds)->Meta().Legend().size() + 1;
      else
        colLabelSize = (int)(*ds)->Meta().Legend().size();
      //mprintf("DEBUG: Set '%s', fmt width= %i, colWidth= %i, colLabelSize= %i\n",
      //        (*ds)->legend(), (*ds)->Format().Width(), (*ds)->Format().ColumnWidth(),
      //        colLabelSize);
      if (colLabelSize >= (*ds)->Format().ColumnWidth())
        (*ds)->SetupFormat().SetFormatWidth( colLabelSize );
    }
    // Write dataset names to header, left-aligning first set if no X-column
    DataSetList::const_iterator set = Sets.begin();
    if (!hasXcolumn_)
      WriteNameToBuffer( file, (*set)->Meta().Legend(), (*set)->Format().ColumnWidth(), true  );
    else
      WriteNameToBuffer( file, (*set)->Meta().Legend(), (*set)->Format().ColumnWidth(), false );
    ++set;
    for (; set != Sets.end(); ++set) 
      WriteNameToBuffer( file, (*set)->Meta().Legend(), (*set)->Format().ColumnWidth(), false );
    file.Printf("\n"); 
  }

  // Write Data
  DataSet::SizeArray positions(1);
  for (positions[0] = 0; positions[0] < maxFrames; positions[0]++) {
    // Output Frame for each set
    if (hasXcolumn_)
      file.Printf( x_col_format.fmt(), Xdata->Coord(0, positions[0]) );
    for (DataSetList::const_iterator set = Sets.begin(); set != Sets.end(); ++set) 
      (*set)->WriteBuffer(file, positions);
    file.Printf("\n"); 
  }
  // Restore original column widths if necessary
  if (!Original_Column_Widths.empty())
    for (unsigned int i = 0; i != Original_Column_Widths.size(); i++)
      Sets[i]->SetupFormat().SetFormatWidth( Original_Column_Widths[i] );
  return 0;
}
Esempio n. 25
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void Cluster_ReadInfo::ClusterResults(CpptrajFile& outfile) const {
  outfile.Printf("#Algorithm: Read from file '%s'\n", filename_.c_str());
  if (!algorithm_.empty())
    outfile.Printf("#Original algorithm: %s", algorithm_.c_str());
}
Esempio n. 26
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// 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();
}
Esempio n. 27
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// DataIO_Std::WriteSet3D()
int DataIO_Std::WriteSet3D( DataSet const& setIn, CpptrajFile& file ) {
  if (setIn.Ndim() != 3) {
    mprinterr("Internal Error: DataSet %s in DataFile %s has %zu dimensions, expected 3.\n",
              setIn.legend(), file.Filename().full(), setIn.Ndim());
    return 1;
  }
  DataSet_3D const& set = static_cast<DataSet_3D const&>( setIn );
  Dimension const& Xdim = static_cast<Dimension const&>(set.Dim(0));
  Dimension const& Ydim = static_cast<Dimension const&>(set.Dim(1));
  Dimension const& Zdim = static_cast<Dimension const&>(set.Dim(2));
  //if (Xdim.Step() == 1.0) xcol_precision = 0;
  if (sparse_)
    mprintf("\tOnly writing voxels with value > %g\n", cut_);
  // Print X Y Z Values
  // x y z val(x,y,z)
  DataSet::SizeArray pos(3);
  if (writeHeader_) {
    file.Printf("#counts %zu %zu %zu\n", set.NX(), set.NY(), set.NZ());
    file.Printf("#origin %12.7f %12.7f %12.7f\n",
                set.Bin().GridOrigin()[0],
                set.Bin().GridOrigin()[1],
                set.Bin().GridOrigin()[2]);
    if (set.Bin().IsOrthoGrid()) {
      GridBin_Ortho const& b = static_cast<GridBin_Ortho const&>( set.Bin() );
      file.Printf("#delta %12.7f %12.7f %12.7f\n", b.DX(), b.DY(), b.DZ());
    } else {
      GridBin_Nonortho const& b = static_cast<GridBin_Nonortho const&>( set.Bin() );
      file.Printf("#delta %12.7f %12.7f %12.7f %12.7f %12.7f %12.7f %12.7f %12.7f %12.7f\n",
                  b.Ucell()[0]/set.NX(),
                  b.Ucell()[1]/set.NX(),
                  b.Ucell()[2]/set.NX(),
                  b.Ucell()[3]/set.NY(),
                  b.Ucell()[4]/set.NY(),
                  b.Ucell()[5]/set.NY(),
                  b.Ucell()[6]/set.NZ(),
                  b.Ucell()[7]/set.NZ(),
                  b.Ucell()[8]/set.NZ());
    }
    file.Printf("#%s %s %s %s\n", Xdim.Label().c_str(), 
                Ydim.Label().c_str(), Zdim.Label().c_str(), set.legend());
  }
  std::string xyz_fmt;
  if (XcolPrecSet()) {
    TextFormat nfmt( XcolFmt(), XcolWidth(), XcolPrec() );
    xyz_fmt = nfmt.Fmt() + " " + nfmt.Fmt() + " " + nfmt.Fmt() + " ";
  } else {
    TextFormat xfmt( XcolFmt(), set.NX(), Xdim.Min(), Xdim.Step(), 8, 3 );
    TextFormat yfmt( XcolFmt(), set.NY(), Ydim.Min(), Ydim.Step(), 8, 3 );
    TextFormat zfmt( XcolFmt(), set.NZ(), Zdim.Min(), Zdim.Step(), 8, 3 );
    xyz_fmt = xfmt.Fmt() + " " + yfmt.Fmt() + " " + zfmt.Fmt() + " ";
  }
  if (sparse_) {
    for (pos[2] = 0; pos[2] < set.NZ(); ++pos[2]) {
      for (pos[1] = 0; pos[1] < set.NY(); ++pos[1]) {
        for (pos[0] = 0; pos[0] < set.NX(); ++pos[0]) {
          double val = set.GetElement(pos[0], pos[1], pos[2]);
          if (val > cut_) {
            Vec3 xyz = set.Bin().Corner(pos[0], pos[1], pos[2]);
            file.Printf( xyz_fmt.c_str(), xyz[0], xyz[1], xyz[2] );
            set.WriteBuffer( file, pos );
            file.Printf("\n");
          }
        }
      }
    }
  } else {
    for (pos[2] = 0; pos[2] < set.NZ(); ++pos[2]) {
      for (pos[1] = 0; pos[1] < set.NY(); ++pos[1]) {
        for (pos[0] = 0; pos[0] < set.NX(); ++pos[0]) {
          Vec3 xyz = set.Bin().Corner(pos[0], pos[1], pos[2]);
          file.Printf( xyz_fmt.c_str(), xyz[0], xyz[1], xyz[2] );
          set.WriteBuffer( file, pos );
          file.Printf("\n");
        }
      }
    }
  }
  return 0;
}
Esempio n. 28
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// DataIO_Std::WriteSet2D()
int DataIO_Std::WriteSet2D( DataSet const& setIn, CpptrajFile& file ) {
  if (setIn.Ndim() != 2) {
    mprinterr("Internal Error: DataSet %s in DataFile %s has %zu dimensions, expected 2.\n",
              setIn.legend(), file.Filename().full(), setIn.Ndim());
    return 1;
  }
  DataSet_2D const& set = static_cast<DataSet_2D const&>( setIn );
  int xcol_width = 8;
  int xcol_precision = 3;
  Dimension const& Xdim = static_cast<Dimension const&>(set.Dim(0));
  Dimension const& Ydim = static_cast<Dimension const&>(set.Dim(1));
  if (Xdim.Step() == 1.0) xcol_precision = 0;
  
  DataSet::SizeArray positions(2);
  TextFormat ycoord_fmt(XcolFmt()), xcoord_fmt(XcolFmt());
  if (square2d_) {
    // Print XY values in a grid:
    // x0y0 x1y0 x2y0
    // x0y1 x1y1 x2y1
    // x0y2 x1y2 x2y2
    // If file has header, top-left value will be '#<Xlabel>-<Ylabel>',
    // followed by X coordinate values.
    if (writeHeader_) {
      ycoord_fmt.SetCoordFormat( set.Nrows(), Ydim.Min(), Ydim.Step(), xcol_width, xcol_precision );
      std::string header;
      if (Xdim.Label().empty() && Ydim.Label().empty())
        header = "#Frame";
      else
        header = "#" + Xdim.Label() + "-" + Ydim.Label();
      WriteNameToBuffer( file, header, xcol_width, true );
      xcoord_fmt.SetCoordFormat( set.Ncols(), Xdim.Min(), Xdim.Step(),
                                 set.Format().ColumnWidth(), xcol_precision );
      for (size_t ix = 0; ix < set.Ncols(); ix++)
        file.Printf( xcoord_fmt.fmt(), set.Coord(0, ix) );
      file.Printf("\n");
    }
    for (positions[1] = 0; positions[1] < set.Nrows(); positions[1]++) {
      if (writeHeader_)
        file.Printf( ycoord_fmt.fmt(), set.Coord(1, positions[1]) );
      for (positions[0] = 0; positions[0] < set.Ncols(); positions[0]++)
        set.WriteBuffer( file, positions );
      file.Printf("\n");
    }
  } else {
    // Print X Y Values
    // x y val(x,y)
    if (writeHeader_)
      file.Printf("#%s %s %s\n", Xdim.Label().c_str(), 
                  Ydim.Label().c_str(), set.legend());
    if (XcolPrecSet()) {
      xcoord_fmt = TextFormat(XcolFmt(), XcolWidth(), XcolPrec());
      ycoord_fmt = xcoord_fmt;
    } else {
      xcoord_fmt.SetCoordFormat( set.Ncols(), Xdim.Min(), Xdim.Step(), 8, 3 );
      ycoord_fmt.SetCoordFormat( set.Nrows(), Ydim.Min(), Ydim.Step(), 8, 3 );
    }
    std::string xy_fmt = xcoord_fmt.Fmt() + " " + ycoord_fmt.Fmt() + " ";
    for (positions[1] = 0; positions[1] < set.Nrows(); ++positions[1]) {
      for (positions[0] = 0; positions[0] < set.Ncols(); ++positions[0]) {
        file.Printf( xy_fmt.c_str(), set.Coord(0, positions[0]), set.Coord(1, positions[1]) );
        set.WriteBuffer( file, positions );
        file.Printf("\n");
      }
    }
  }
  return 0;
}
Esempio n. 29
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// Cluster_Kmeans::ClusterResults()
void Cluster_Kmeans::ClusterResults(CpptrajFile& outfile) const {
  outfile.Printf("#Algorithm: Kmeans nclusters %i maxit %i\n", nclusters_, maxIt_);
}
Esempio n. 30
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/** Write data at frame to CharBuffer. If no data for frame write 0.0.
  */
void DataSet_double::WriteBuffer(CpptrajFile &cbuffer, SizeArray const& frame) const {
  if (frame[0] >= Data_.size())
    cbuffer.Printf(format_.fmt(), 0.0);
  else
    cbuffer.Printf(format_.fmt(), Data_[frame[0]]);
}