C++ DataFile::AddDataSet方法代码示例

// Action_Angle::init()
Action::RetType Action_Angle::Init(ArgList& actionArgs, TopologyList* PFL, DataSetList* DSL, DataFileList* DFL, int debugIn)
{
  // Get keywords
  DataFile* outfile = DFL->AddDataFile( actionArgs.GetStringKey("out"), actionArgs );
  useMass_ = actionArgs.hasKey("mass");

  // Get Masks
  std::string mask1 = actionArgs.GetMaskNext();
  std::string mask2 = actionArgs.GetMaskNext();
  std::string mask3 = actionArgs.GetMaskNext();
  if (mask1.empty() || mask2.empty() || mask3.empty()) {
    mprinterr("Error: angle: Requires 3 masks\n");
    return Action::ERR;
  }
  Mask1_.SetMaskString(mask1);
  Mask2_.SetMaskString(mask2);
  Mask3_.SetMaskString(mask3);

  // Dataset to store angles
  ang_ = DSL->AddSet(DataSet::DOUBLE, MetaData(actionArgs.GetStringNext(),MetaData::M_ANGLE),"Ang");
  if (ang_==0) return Action::ERR;
  // Add dataset to data file list
  if (outfile != 0) outfile->AddDataSet( ang_ );

  mprintf("    ANGLE: [%s]-[%s]-[%s]\n",Mask1_.MaskString(), Mask2_.MaskString(), 
          Mask3_.MaskString());
  if (useMass_)
    mprintf("\tUsing center of mass of atoms in masks.\n");

  return Action::OK;
}

/** Called once before traj processing. Set up reference info. */
Action::RetType Action_DistRmsd::Init(ArgList& actionArgs, TopologyList* PFL, DataSetList* DSL, DataFileList* DFL, int debugIn)
{
  // Check for keywords
  DataFile* outfile = DFL->AddDataFile( actionArgs.GetStringKey("out"), actionArgs );
  // Reference keywords
  // TODO: Can these just be put in the InitRef call?
  bool first = actionArgs.hasKey("first");
  ReferenceFrame REF = DSL->GetReferenceFrame( actionArgs );
  std::string reftrajname = actionArgs.GetStringKey("reftraj");
  Topology* RefParm = PFL->GetParm( actionArgs );
  // Get the RMS mask string for target 
  std::string mask0 = actionArgs.GetMaskNext();
  TgtMask_.SetMaskString(mask0);
  // Get the RMS mask string for reference
  std::string mask1 = actionArgs.GetMaskNext();
  if (mask1.empty())
    mask1 = mask0;

  // Initialize reference
  if (refHolder_.InitRef(false, first, false, false, reftrajname, REF, RefParm,
                         mask1, actionArgs, "distrmsd"))
    return Action::ERR;
 
  // Set up the RMSD data set
  drmsd_ = DSL->AddSet(DataSet::DOUBLE, actionArgs.GetStringNext(),"DRMSD");
  if (drmsd_==0) return Action::ERR;
  // Add dataset to data file list
  if (outfile != 0) outfile->AddDataSet( drmsd_ );

  mprintf("    DISTRMSD: (%s), reference is %s\n",TgtMask_.MaskString(),
          refHolder_.RefModeString());

  return Action::OK;
}

Action::RetType Action_Channel::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
  // Keywords.
  DataFile* outfile = init.DFL().AddDataFile( actionArgs.GetStringKey("out"), actionArgs );
  dxyz_[0] = actionArgs.getKeyDouble("dx", 0.35);
  dxyz_[1] = actionArgs.getKeyDouble("dy", dxyz_[0]);
  dxyz_[2] = actionArgs.getKeyDouble("dz", dxyz_[1]);
  // solute mask
  std::string sMask = actionArgs.GetMaskNext();
  if (sMask.empty()) {
    mprinterr("Error: No solute mask specified.\n");
    return Action::ERR;
  }
  soluteMask_.SetMaskString( sMask );
  // solvent mask
  sMask = actionArgs.GetMaskNext();
  if (sMask.empty())
    sMask.assign(":[email protected]");
  solventMask_.SetMaskString( sMask );

  // Grid Data Set
  grid_ = init.DSL().AddSet(DataSet::GRID_FLT, actionArgs.GetStringNext(), "Channel");
  if (grid_ == 0) return Action::ERR;
  if (outfile != 0) outfile->AddDataSet( grid_ );

  mprintf("Warning: *** THIS ACTION IS EXPERIMENTAL AND NOT FULLY IMPLEMENTED. ***\n");
  mprintf("    CHANNEL: Solute mask [%s], solvent mask [%s]\n",
          soluteMask_.MaskString(), solventMask_.MaskString());
  mprintf("\tSpacing: XYZ={ %g %g %g }\n", dxyz_[0], dxyz_[1], dxyz_[2]);
  return Action::OK;
}

// Action_AreaPerMol::Init()
Action::RetType Action_AreaPerMol::Init(ArgList& actionArgs, TopologyList* PFL, DataSetList* DSL, DataFileList* DFL, int debugIn)
{
  // Get keywords
  DataFile* outfile = DFL->AddDataFile( actionArgs.GetStringKey("out"), actionArgs );
  if (actionArgs.hasKey("xy")) areaType_ = XY;
  else if (actionArgs.hasKey("xz")) areaType_ = XZ;
  else if (actionArgs.hasKey("yz")) areaType_ = YZ;
  else areaType_ = XY;

  Nmols_ = (double)actionArgs.getKeyInt("nmols", -1);

  // Get Masks
  if (Nmols_ < 0.0) {
    Nlayers_ = (double)actionArgs.getKeyInt("nlayers", 1);
    if (Nlayers_ < 1.0) {
      mprinterr("Error: Number of layers must be > 0\n");
      return Action::ERR;
    }
    Mask1_.SetMaskString( actionArgs.GetMaskNext() );
  }

  // DataSet
  area_per_mol_ = DSL->AddSet(DataSet::DOUBLE, actionArgs.GetStringNext(),"APM");
  if (area_per_mol_==0) return Action::ERR;
  // Add DataSet to DataFileList
  if (outfile != 0) outfile->AddDataSet( area_per_mol_ );

  mprintf("    AREAPERMOL: Calculating %s area per molecule", APMSTRING[areaType_]);
  if (Mask1_.MaskStringSet())
    mprintf(" using mask '%s', %.0f layers.\n", Mask1_.MaskString(), Nlayers_);
  else
    mprintf(" for %.0f mols\n", Nmols_);

  return Action::OK;
}

// Action_Grid::Init()
Action::RetType Action_Grid::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
  debug_ = debugIn;
  nframes_ = 0;
  // Get output filename
  std::string filename = actionArgs.GetStringKey("out");
  // Get grid options
  grid_ = GridInit( "GRID", actionArgs, init.DSL() );
  if (grid_ == 0) return Action::ERR;
# ifdef MPI
  if (ParallelGridInit(init.TrajComm(), grid_)) return Action::ERR;
# endif
  // Get extra options
  max_ = actionArgs.getKeyDouble("max", 0.80);
  madura_ = actionArgs.getKeyDouble("madura", 0);
  smooth_ = actionArgs.getKeyDouble("smoothdensity", 0);
  invert_ = actionArgs.hasKey("invert");
  pdbfile_ = init.DFL().AddCpptrajFile(actionArgs.GetStringKey("pdb"),"Grid PDB",DataFileList::PDB,true);
  density_ = actionArgs.getKeyDouble("density",0.033456);
  if (actionArgs.hasKey("normframe")) normalize_ = TO_FRAME;
  else if (actionArgs.hasKey("normdensity")) normalize_ = TO_DENSITY;
  else normalize_ = NONE;
  if (normalize_ != NONE && (smooth_ > 0.0 || madura_ > 0.0)) {
    mprinterr("Error: Normalize options are not compatible with smoothdensity/madura options.\n");
    init.DSL().RemoveSet( grid_ );
    return Action::ERR;
  }
  // Get mask
  std::string maskexpr = actionArgs.GetMaskNext();
  if (maskexpr.empty()) {
    mprinterr("Error: GRID: No mask specified.\n");
    init.DSL().RemoveSet( grid_ );
    return Action::ERR;
  }
  mask_.SetMaskString(maskexpr);

  // Setup output file
  // For backwards compat., if no 'out' assume next string is filename
  if (filename.empty() && actionArgs.Nargs() > 1 && !actionArgs.Marked(1))
    filename = actionArgs.GetStringNext();
  DataFile* outfile = init.DFL().AddDataFile(filename, actionArgs);
  if (outfile != 0) outfile->AddDataSet((DataSet*)grid_);

  // Info
  mprintf("    GRID:\n");
  GridInfo( *grid_ );
  if (outfile != 0) mprintf("\tGrid will be printed to file %s\n", outfile->DataFilename().full());
  mprintf("\tGrid data set: '%s'\n", grid_->legend());
  mprintf("\tMask expression: [%s]\n",mask_.MaskString());
  if (pdbfile_ != 0)
      mprintf("\tPseudo-PDB will be printed to %s\n", pdbfile_->Filename().full());
  if (normalize_ == TO_FRAME)
    mprintf("\tGrid will be normalized by number of frames.\n");
  else if (normalize_ == TO_DENSITY)
    mprintf("\tGrid will be normalized to a density of %g molecules/Ang^3.\n", density_);
  // TODO: print extra options

  return Action::OK;
}

// Action_FilterByData::Init()
Action::RetType Action_FilterByData::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
  maxmin_ = init.DSL().AddSet( DataSet::INTEGER, actionArgs.GetStringKey("name"), "Filter" );
  if (maxmin_ == 0) return Action::ERR;
  DataFile* maxminfile = init.DFL().AddDataFile( actionArgs.GetStringKey("out"), actionArgs );
  if (maxminfile != 0)
    maxminfile->AddDataSet( maxmin_ );
  // Get min and max args.
  while (actionArgs.Contains("min"))
    Min_.push_back( actionArgs.getKeyDouble("min", 0.0) );
  while (actionArgs.Contains("max"))
    Max_.push_back( actionArgs.getKeyDouble("max", 0.0) );
  if (Min_.empty()) {
    mprinterr("Error: At least one 'min' arg must be specified.\n");
    return Action::ERR;
  }
  if (Max_.empty()) {
    mprinterr("Error: At least one 'max' arg must be specified.\n");
    return Action::ERR;
  }
  if (Min_.size() != Max_.size()) {
    mprinterr("Error: # of 'min' args (%zu) != # of 'max' args (%zu)\n",
              Min_.size(), Max_.size());
    return Action::ERR;
  }
  // Get DataSets from remaining arguments
  Dsets_.AddSetsFromArgs( actionArgs.RemainingArgs(), init.DSL() );

  if (Dsets_.empty()) {
    mprinterr("Error: No data sets specified.\n");
    return Action::ERR;
  }

  if ( Dsets_.size() < Min_.size() ) {
    mprinterr("Error: More 'min'/'max' args (%zu) than data sets (%zu).\n",
              Min_.size(), Dsets_.size());
    return Action::ERR;
  }
  if ( Dsets_.size() > Min_.size() ) {
    unsigned int Nremaining = Dsets_.size() - Min_.size();
    double useMin = Min_.back();
    double useMax = Max_.back();
    mprintf("Warning: More data sets than 'min'/'max' args.\n"
            "Warning:  Using min=%f and max=%f for last %zu data sets.\n",
            useMin, useMax, Nremaining);
    for (unsigned int ds = 0; ds < Nremaining; ++ds) {
      Min_.push_back( useMin );
      Max_.push_back( useMax );
    }
  }

  mprintf("    FILTER: Filtering out frames using %zu data sets.\n", Dsets_.size());
  for (unsigned int ds = 0; ds < Dsets_.size(); ds++)
    mprintf("\t%.4f < '%s' < %.4f\n", Min_[ds], Dsets_[ds]->legend(), Max_[ds]);
  if (maxminfile != 0)
    mprintf("\tFilter frame info will be written to %s\n", maxminfile->DataFilename().full());

  return Action::OK;
}

// Action_VelocityAutoCorr::Init()
Action::RetType Action_VelocityAutoCorr::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
  if (actionArgs.hasKey("usevelocity")) {
    mprinterr("Error: The 'usevelocity' keyword is deprecated. Velocity information\n"
              "Error:   is now used by default if present. To force cpptraj to use\n"
              "Error:   coordinates to estimate velocities (not recommended) use the\n"
              "Error:   'usecoords' keyword.\n");
    return Action::ERR;
  }
  useVelInfo_ = !actionArgs.hasKey("usecoords");
  if (mask_.SetMaskString( actionArgs.GetMaskNext() )) return Action::ERR;
  DataFile* outfile =  init.DFL().AddDataFile( actionArgs.GetStringKey("out"), actionArgs );
  diffout_ = init.DFL().AddCpptrajFile( actionArgs.GetStringKey("diffout"),
                                        "VAC diffusion constants", DataFileList::TEXT, true );
  maxLag_ = actionArgs.getKeyInt("maxlag", -1);
  tstep_ = actionArgs.getKeyDouble("tstep", 1.0);
  useFFT_ = !actionArgs.hasKey("direct");
  normalize_ = actionArgs.hasKey("norm");
  // Set up output data set
  VAC_ = init.DSL().AddSet(DataSet::DOUBLE, actionArgs.GetStringNext(), "VAC");
  if (VAC_ == 0) return Action::ERR;
  // TODO: This should just be a scalar
  diffConst_ = init.DSL().AddSet(DataSet::DOUBLE,
                                 MetaData(VAC_->Meta().Name(), "D", MetaData::NOT_TS));
  if (diffConst_ == 0) return Action::ERR;
  if (outfile != 0) outfile->AddDataSet( VAC_ );
# ifdef MPI
  trajComm_ = init.TrajComm(); 
  if (trajComm_.Size() > 1 && !useVelInfo_)
    mprintf("\nWarning: When calculating velocities between consecutive frames,\n"
            "\nWarning:   'velocityautocorr' in parallel will not work correctly if\n"
            "\nWarning:   coordinates have been modified by previous actions (e.g. 'rms').\n\n");
  diffConst_->SetNeedsSync( false );
# endif
  mprintf("    VELOCITYAUTOCORR:\n"
          "\tCalculate velocity auto-correlation function for atoms in mask '%s'\n",
          mask_.MaskString());
  if (useVelInfo_)
    mprintf("\tUsing velocity information present in frames.\n");
  else
    mprintf("\tCalculating velocities between consecutive frames from coordinates.\n");
  if (outfile != 0)
    mprintf("\tOutput velocity autocorrelation function '%s' to '%s'\n", VAC_->legend(), 
            outfile->DataFilename().full());
  mprintf("\tWriting diffusion constants to '%s'\n", diffout_->Filename().full());
  if (maxLag_ < 1)
    mprintf("\tMaximum lag will be half total # of frames");
  else
    mprintf("\tMaximum lag is %i frames", maxLag_);
  mprintf(", time step between frames is %f ps\n", tstep_);
  if (useFFT_)
    mprintf("\tUsing FFT to calculate autocorrelation function.\n");
  else
    mprintf("\tUsing direct method to calculate autocorrelation function.\n");
  if (normalize_)
    mprintf("\tNormalizing autocorrelation function to 1.0\n");
  return Action::OK;
}

// Analysis_Wavelet::Setup
Analysis::RetType Analysis_Wavelet::Setup(ArgList& analyzeArgs, DataSetList* datasetlist,
        TopologyList* PFLin, DataFileList* DFLin, int debugIn)
{
    // Attempt to get COORDS DataSet from DataSetList. If none specified the
    // default COORDS set will be used.
    std::string setname = analyzeArgs.GetStringKey("crdset");
    coords_ = (DataSet_Coords*)datasetlist->FindCoordsSet( setname );
    if (coords_ == 0) {
        mprinterr("Error: Could not locate COORDS set corresponding to %s\n", setname.c_str());
        return Analysis::ERR;
    }
    // Get keywords
    DataFile* outfile = DFLin->AddDataFile( analyzeArgs.GetStringKey("out"), analyzeArgs );
    setname = analyzeArgs.GetStringKey("name");
    // TODO: Check defaults
    nb_ = analyzeArgs.getKeyInt("nb", 0); // FIXME: Should be more descriptive? nscale?
    if (nb_ < 1) {
        mprinterr("Error: Scaling number must be > 0\n");
        return Analysis::ERR;
    }
    S0_ = analyzeArgs.getKeyDouble("s0", 0.2);
    ds_ = analyzeArgs.getKeyDouble("ds", 1.0/3.0);
    correction_ = analyzeArgs.getKeyDouble("correction", 1.01);
    chival_ = analyzeArgs.getKeyDouble("chival", 0.2231);
    // Wavelet type: default to Morlet
    std::string wavelet_name = analyzeArgs.GetStringKey("type");
    if (wavelet_name.empty())
        wavelet_type_ = W_MORLET;
    else {
        wavelet_type_ = W_NONE;
        for (int itoken = 0; itoken != (int)W_NONE; itoken++)
            if (wavelet_name.compare(Tokens_[itoken].key_) == 0) {
                wavelet_type_ = (WaveletType)itoken;
                break;
            }
        if (wavelet_type_ == W_NONE) {
            mprinterr("Error: Unrecognized wavelet type: %s\n", wavelet_name.c_str());
            return Analysis::ERR;
        }
    }
    // Atom mask
    mask_.SetMaskString( analyzeArgs.GetMaskNext() );
    // Set up output data set
    output_ = datasetlist->AddSet( DataSet::MATRIX_FLT, setname, "WAVELET" );
    if (output_ == 0) return Analysis::ERR;
    if (outfile != 0) outfile->AddDataSet( output_ );

    mprintf("    WAVELET: Using COORDS set '%s', wavelet type %s\n",
            coords_->legend(), Tokens_[wavelet_type_].description_);
    mprintf("\tCalculating for atoms in mask '%s'\n", mask_.MaskString());
    mprintf("\tScaling wavelet %i times starting from %g with delta of %g\n",
            nb_, S0_, ds_);
    mprintf("\tCorrection: %g\n", correction_);
    mprintf("\tChiVal:     %g\n", chival_);
    if (outfile != 0) mprintf("\tOutput to '%s'\n", outfile->DataFilename().full());

    return Analysis::OK;
}

// Action_AtomicFluct::Init()
Action::RetType Action_AtomicFluct::Init(ArgList& actionArgs, TopologyList* PFL, DataSetList* DSL, DataFileList* DFL, int debugIn)
{
    // Get frame # keywords
    if (InitFrameCounter(actionArgs)) return Action::ERR;
    // Get other keywords
    bfactor_ = actionArgs.hasKey("bfactor");
    calc_adp_ = actionArgs.hasKey("calcadp");
    adpoutfile_ = DFL->AddCpptrajFile(actionArgs.GetStringKey("adpout"), "PDB w/ADP",
                                      DataFileList::PDB);;
    if (adpoutfile_!=0) calc_adp_ = true; // adpout implies calcadp
    if (calc_adp_ && !bfactor_) bfactor_ = true;
    DataFile* outfile = DFL->AddDataFile( actionArgs.GetStringKey("out"), actionArgs );
    if (actionArgs.hasKey("byres"))
        outtype_ = BYRES;
    else if (actionArgs.hasKey("bymask"))
        outtype_ = BYMASK;
    else if (actionArgs.hasKey("byatom") || actionArgs.hasKey("byatm"))
        outtype_ = BYATOM;
    // Get Mask
    Mask_.SetMaskString( actionArgs.GetMaskNext()  );
    // Get DataSet name
    std::string setname = actionArgs.GetStringNext();
    // Add output dataset
    MetaData md( setname );
    md.SetTimeSeries( MetaData::NOT_TS );
    if (bfactor_)
        md.SetLegend("B-factors");
    else
        md.SetLegend("AtomicFlx");
    dataout_ = DSL->AddSet( DataSet::XYMESH, md, "Fluct" );
    if (dataout_ == 0) {
        mprinterr("Error: AtomicFluct: Could not allocate dataset for output.\n");
        return Action::ERR;
    }
    if (outfile != 0)
        outfile->AddDataSet( dataout_ );

    mprintf("    ATOMICFLUCT: calculating");
    if (bfactor_)
        mprintf(" B factors");
    else
        mprintf(" atomic positional fluctuations");
    if (outfile != 0)
        mprintf(", output to file %s", outfile->DataFilename().full());
    mprintf("\n                 Atom mask: [%s]\n",Mask_.MaskString());
    FrameCounterInfo();
    if (calc_adp_) {
        mprintf("\tCalculating anisotropic displacement parameters.\n");
        if (adpoutfile_!=0) mprintf("\tWriting PDB with ADP to '%s'\n", adpoutfile_->Filename().full());
    }
    if (!setname.empty())
        mprintf("\tData will be saved to set named %s\n", setname.c_str());

    return Action::OK;
}

Analysis::RetType Analysis_AutoCorr::Setup(ArgList& analyzeArgs, DataSetList* datasetlist,
                            TopologyList* PFLin, DataFileList* DFLin, int debugIn)
{
  const char* calctype;

  std::string setname = analyzeArgs.GetStringKey("name");
  DataFile* outfile = DFLin->AddDataFile( analyzeArgs.GetStringKey("out"), analyzeArgs );
  lagmax_ = analyzeArgs.getKeyInt("lagmax",-1);
  calc_covar_ = !analyzeArgs.hasKey("nocovar");
  usefft_ = !analyzeArgs.hasKey("direct");
  // Select datasets from remaining args
  ArgList dsetArgs = analyzeArgs.RemainingArgs();
  for (ArgList::const_iterator dsa = dsetArgs.begin(); dsa != dsetArgs.end(); ++dsa)
    dsets_ += datasetlist->GetMultipleSets( *dsa );
  if (dsets_.empty()) {
    mprinterr("Error: autocorr: No data sets selected.\n");
    return Analysis::ERR;
  }
  // If setname is empty generate a default name
  if (setname.empty())
    setname = datasetlist->GenerateDefaultName( "autocorr" );
  // Setup output datasets
  int idx = 0;
  MetaData md( setname );
  for (DataSetList::const_iterator DS = dsets_.begin(); DS != dsets_.end(); ++DS) {
    md.SetIdx( idx++ );
    DataSet* dsout = datasetlist->AddSet( DataSet::DOUBLE, md );
    if (dsout==0) return Analysis::ERR;
    dsout->SetLegend( (*DS)->Meta().Legend() );
    outputData_.push_back( dsout );
    // Add set to output file
    if (outfile != 0) outfile->AddDataSet( outputData_.back() );
  }
 
  if (calc_covar_)
    calctype = "covariance";
  else
    calctype = "correlation";
 
  mprintf("    AUTOCORR: Calculating auto-%s for %i data sets:\n", calctype, dsets_.size());
  dsets_.List();
  if (lagmax_!=-1)
    mprintf("\tLag max= %i\n", lagmax_);
  if ( !setname.empty() )
    mprintf("\tSet name: %s\n", setname.c_str() );
  if ( outfile != 0 )
    mprintf("\tOutfile name: %s\n", outfile->DataFilename().base());
  if (usefft_)
    mprintf("\tUsing FFT to calculate %s.\n", calctype);
  else
    mprintf("\tUsing direct method to calculate %s.\n", calctype);

  return Analysis::OK;
}

// Action_SymmetricRmsd::Init()
Action::RetType Action_SymmetricRmsd::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
  // Check for keywords
  bool fit = !actionArgs.hasKey("nofit");
  bool useMass = actionArgs.hasKey("mass");
  DataFile* outfile = init.DFL().AddDataFile(actionArgs.GetStringKey("out"), actionArgs);
  remap_ = actionArgs.hasKey("remap");
  // Reference keywords
  bool previous = actionArgs.hasKey("previous");
  bool first = actionArgs.hasKey("first");
  ReferenceFrame REF = init.DSL().GetReferenceFrame( actionArgs );
  std::string reftrajname = actionArgs.GetStringKey("reftraj");
  Topology* RefParm = init.DSL().GetTopology( actionArgs );
  // Get the RMS mask string for target
  std::string tMaskExpr = actionArgs.GetMaskNext();
  if (tgtMask_.SetMaskString( tMaskExpr )) return Action::ERR;
  // Initialize Symmetric RMSD calc.
  if (SRMSD_.InitSymmRMSD( fit, useMass, debugIn )) return Action::ERR;
  // Initialize reference
  std::string rMaskExpr = actionArgs.GetMaskNext();
  if (rMaskExpr.empty())
    rMaskExpr = tMaskExpr;
  if (REF_.InitRef(previous, first, useMass, fit, reftrajname, REF, RefParm,
                   rMaskExpr, actionArgs, "symmrmsd"))
    return Action::ERR;
  // Set up the RMSD data set.
  MetaData md(actionArgs.GetStringNext(), MetaData::M_RMS); 
  rmsd_ = init.DSL().AddSet(DataSet::DOUBLE, md, "RMSD");
  if (rmsd_==0) return Action::ERR;
  // Add dataset to data file list
  if (outfile != 0) outfile->AddDataSet( rmsd_ );
  if (remap_ || SRMSD_.Fit())
    action_return_ = Action::MODIFY_COORDS;
  else
    action_return_ = Action::OK;
  
  mprintf("    SYMMRMSD: (%s), reference is %s", tgtMask_.MaskString(),
          REF_.RefModeString());
  if (!SRMSD_.Fit())
    mprintf(", no fitting");
  else
    mprintf(", with fitting");
  if (SRMSD_.UseMass())
    mprintf(", mass-weighted");
  mprintf(".\n");
  if (remap_) mprintf("\tAtoms will be re-mapped for symmetry.\n");
  return Action::OK;
}

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();
  }
}

// Action_Distance::Init()
Action::RetType Action_Distance::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
  AssociatedData_NOE noe;
  // Get Keywords
  image_.InitImaging( !(actionArgs.hasKey("noimage")) );
  useMass_ = !(actionArgs.hasKey("geom"));
  DataFile* outfile = init.DFL().AddDataFile( actionArgs.GetStringKey("out"), actionArgs );
  MetaData::scalarType stype = MetaData::UNDEFINED;
  std::string stypename = actionArgs.GetStringKey("type");
  if ( stypename == "noe" ) {
    stype = MetaData::NOE;
    if (noe.NOE_Args( actionArgs )) return Action::ERR;
  }
  // Get Masks
  std::string mask1 = actionArgs.GetMaskNext();
  std::string mask2 = actionArgs.GetMaskNext();
  if (mask1.empty() || mask2.empty()) {
    mprinterr("Error: distance requires 2 masks\n");
    return Action::ERR;
  }
  Mask1_.SetMaskString(mask1);
  Mask2_.SetMaskString(mask2);

  // Dataset to store distances TODO store masks in data set?
  dist_ = init.DSL().AddSet(DataSet::DOUBLE, MetaData(actionArgs.GetStringNext(),
                                                MetaData::M_DISTANCE, stype), "Dis");
  if (dist_==0) return Action::ERR;
  if ( stype == MetaData::NOE ) {
    dist_->AssociateData( &noe );
    dist_->SetLegend(Mask1_.MaskExpression() + " and " + Mask2_.MaskExpression());
  }
  // Add dataset to data file
  if (outfile != 0) outfile->AddDataSet( dist_ );

  mprintf("    DISTANCE: %s to %s",Mask1_.MaskString(), Mask2_.MaskString());
  if (!image_.UseImage()) 
    mprintf(", non-imaged");
  if (useMass_) 
    mprintf(", center of mass");
  else
    mprintf(", geometric center");
  mprintf(".\n");

  return Action::OK;
}

// Analysis_VectorMath::Setup()
Analysis::RetType Analysis_VectorMath::Setup(ArgList& analyzeArgs, DataSetList* DSLin, DataFileList* DFLin, int debugIn)
{
  // Get Vectors
  vinfo1_ = (DataSet_Vector*)DSLin->FindSetOfType( analyzeArgs.GetStringKey("vec1"),
                                                   DataSet::VECTOR );
  vinfo2_ = (DataSet_Vector*)DSLin->FindSetOfType( analyzeArgs.GetStringKey("vec2"),
                                                   DataSet::VECTOR );
  if (vinfo1_ == 0 ) {
    mprinterr("Error: 'vec1' not found.\n");
    return Analysis::ERR;
  }
  if (vinfo2_ == 0) {
    mprinterr("Error: 'vec2' not found.\n");
    return Analysis::ERR;
  }
  std::string setname = analyzeArgs.GetStringKey("name");
  norm_ = analyzeArgs.hasKey("norm");
  // Check for dotproduct/crossproduct keywords
  DataOut_ = 0;
  if (analyzeArgs.hasKey("dotproduct")) {
    mode_ = DOTPRODUCT;
    if ((DataOut_ = DSLin->AddSet(DataSet::DOUBLE, setname, "Dot")) == 0) return Analysis::ERR;
  } else if (analyzeArgs.hasKey("dotangle")) {
    mode_ = DOTANGLE;
    norm_ = true; // Vecs must be normalized for angle calc to work
    if ((DataOut_ = DSLin->AddSet(DataSet::DOUBLE, setname, "Angle")) == 0) return Analysis::ERR;
  } else if (analyzeArgs.hasKey("crossproduct")) {
    mode_ = CROSSPRODUCT;
    if ((DataOut_ = DSLin->AddSet(DataSet::VECTOR, setname, "Cross")) == 0) return Analysis::ERR;
  } else
    mode_ = DOTPRODUCT;
  // Set up output file in DataFileList if necessary
  DataFile* outfile = DFLin->AddDataFile( analyzeArgs.GetStringKey("out"), analyzeArgs );
  if (outfile != 0) outfile->AddDataSet( DataOut_ );

  // Print Status
  mprintf("    VECTORMATH: Calculating %s of vectors %s and %s\n", 
            ModeString[mode_], vinfo1_->legend(), vinfo2_->legend());
  if (norm_) mprintf("\tVectors will be normalized.\n");
  if (outfile != 0)
    mprintf("\tResults are written to %s\n", outfile->DataFilename().full());

  return Analysis::OK;
}

// Action_VelocityAutoCorr::Init()
Action::RetType Action_VelocityAutoCorr::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
  useVelInfo_ = actionArgs.hasKey("usevelocity");
  mask_.SetMaskString( actionArgs.GetMaskNext() );
  DataFile* outfile =  init.DFL().AddDataFile( actionArgs.GetStringKey("out"), actionArgs );
  maxLag_ = actionArgs.getKeyInt("maxlag", -1);
  tstep_ = actionArgs.getKeyDouble("tstep", 1.0);
  useFFT_ = !actionArgs.hasKey("direct");
  normalize_ = actionArgs.hasKey("norm");
  // Set up output data set
  VAC_ = init.DSL().AddSet(DataSet::DOUBLE, actionArgs.GetStringNext(), "VAC");
  if (VAC_ == 0) return Action::ERR;
  if (outfile != 0) outfile->AddDataSet( VAC_ );
# ifdef MPI
  trajComm_ = init.TrajComm(); 
  if (trajComm_.Size() > 1 && !useVelInfo_)
    mprintf("\nWarning: When calculating velocities between consecutive frames,\n"
            "\nWarning:   'velocityautocorr' in parallel will not work correctly if\n"
            "\nWarning:   coordinates have been modified by previous actions (e.g. 'rms').\n\n");
# endif
  mprintf("    VELOCITYAUTOCORR:\n"
          "\tCalculate velocity auto-correlation function for atoms in mask '%s'\n",
          mask_.MaskString());
  if (useVelInfo_)
    mprintf("\tUsing velocity information present in frames.\n");
  else
    mprintf("\tCalculating velocities between consecutive frames.\n");
  if (outfile != 0)
    mprintf("\tOutput data set '%s' to '%s'\n", VAC_->legend(), 
            outfile->DataFilename().full());
  if (maxLag_ < 1)
    mprintf("\tMaximum lag will be half total # of frames");
  else
    mprintf("\tMaximum lag is %i frames", maxLag_);
  mprintf(", time step is %f ps\n", tstep_);
  if (useFFT_)
    mprintf("\tUsing FFT to calculate autocorrelation function.\n");
  else
    mprintf("\tUsing direct method to calculate autocorrelation function.\n");
  if (normalize_)
    mprintf("\tNormalizing autocorrelation function to 1.0\n");
  return Action::OK;
}