C++ ActionInit::DFL方法代码示例

// 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_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;
}

// -----------------------------------------------------------------------------
// Action_Jcoupling::Init()
Action::RetType Action_Jcoupling::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
  debug_ = debugIn;
  outfile_ = 0;
  // Get Keywords
  outputfile_ = init.DFL().AddCpptrajFile(actionArgs.GetStringKey("outfile"), "J-coupling");
  outfile_ = init.DFL().AddDataFile( actionArgs.GetStringKey("out"), actionArgs );
  std::string karpluspath = actionArgs.GetStringKey("kfile");
  setname_ = actionArgs.GetStringKey("name");
  // Get Masks
  if (Mask1_.SetMaskString( actionArgs.GetMaskNext() )) return Action::ERR;

  // If no Karplus params specified check environment vars. 
  if (karpluspath.empty()) {
    // Check if the KARPLUS env var is set.
    const char* env = getenv("KARPLUS");
    if (env != 0) {
      mprintf("Info: Using parameter file defined by $KARPLUS environment variable.\n");
      karpluspath.assign(env);
    } else {
      // If KARPLUS not set check for $AMBERHOME/dat/Karplus.txt
      env = getenv("AMBERHOME");
      if (env == 0) {
        mprinterr("Error: Either AMBERHOME must be set or KARPLUS must point\n"
                  "Error:   to the file containing Karplus parameters.\n");
        return Action::ERR;
      }
      mprintf("Info: Using parameter file in '$AMBERHOME/dat/'.\n");
      karpluspath.assign(env);
      karpluspath += "/dat/Karplus.txt";
    }
  }
  // Load Karplus parameters
  if (loadKarplus(karpluspath)) 
    return Action::ERR;

  mprintf("    J-COUPLING: Searching for dihedrals in mask [%s].\n"
          "\tUsing Karplus parameters in \"%s\"\n"
          "\t%i parameters found for %zu residues.\n",
          Mask1_.MaskString(), karpluspath.c_str(), Nconstants_, KarplusConstants_.size());
  if (outfile_ != 0)
    mprintf("\tDataSets will be written to %s\n", outfile_->DataFilename().full());
  if (outputfile_ != 0)
    mprintf("\tWriting fixed-format output to %s\n",outputfile_->Filename().full());
  mprintf("# Citations: Chou et al. JACS (2003) 125 p.8959-8966\n"
          "#            Perez et al. JACS (2001) 123 p.7081-7093\n");
  init.DSL().SetDataSetsPending(true);
  masterDSL_ = init.DslPtr();
  return Action::OK;
}

Action::RetType Action_MultiVector::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
  debug_ = debugIn;
  // Get keywords
  outfile_ = init.DFL().AddDataFile( actionArgs.GetStringKey("out"), actionArgs);
  std::string resrange_arg = actionArgs.GetStringKey("resrange");
  if (!resrange_arg.empty())
    if (resRange_.SetRange( resrange_arg )) return Action::ERR;
  ired_ = actionArgs.hasKey("ired");
  // Get atom names
  if (SetName(name1_, actionArgs.GetStringKey("name1"), "name1")) return Action::ERR;
  if (SetName(name2_, actionArgs.GetStringKey("name2"), "name2")) return Action::ERR;
  // Setup DataSet(s) name
  dsetname_ = actionArgs.GetStringNext();

  mprintf("    MULTIVECTOR: Calculating");
  if (ired_) mprintf(" IRED");
  if (!resRange_.Empty())
    mprintf(" vectors for residues in range %s\n", resRange_.RangeArg());
  else
    mprintf(" vectors for all solute residues.\n");
  mprintf("\tName1='%s' (origin)  Name2='%s'\n", *name1_, *name2_);
  if (!dsetname_.empty())
    mprintf("\tDataSet name: %s\n", dsetname_.c_str());
  if (outfile_ != 0) mprintf("\tOutput to %s\n", outfile_->DataFilename().base());
  init.DSL().SetDataSetsPending(true);
  masterDSL_ = init.DslPtr();
  return Action::OK;
}

/** Called once before traj processing. Set up reference info. */
Action::RetType Action_DistRmsd::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
  // Check for keywords
  DataFile* outfile = init.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 = 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 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_ = init.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_Esander::Init()
Action::RetType Action_Esander::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
# ifdef MPI
  trajComm_ = init.TrajComm();
# endif
  SANDER_.SetDebug( debugIn );
  Init_ = init;
  // Get keywords
  outfile_ = init.DFL().AddDataFile( actionArgs.GetStringKey("out"), actionArgs );
  save_forces_ = actionArgs.hasKey("saveforces");
  ReferenceFrame REF = init.DSL().GetReferenceFrame( actionArgs );
  if (REF.error()) return Action::ERR;
  if (!REF.empty()) {
    refFrame_ = REF.Coord();
    currentParm_ = REF.ParmPtr();
  }
  if (SANDER_.SetInput( actionArgs )) return Action::ERR;
  // DataSet name and array
  setname_ = actionArgs.GetStringNext();
  if (setname_.empty())
    setname_ = init.DSL().GenerateDefaultName("ENE");
  Esets_.clear();
  Esets_.resize( (int)Energy_Sander::N_ENERGYTYPES, 0 );

  mprintf("    ESANDER: Calculating energy using Sander.\n");
  mprintf("\tTemporary topology file name is '%s'\n", SANDER_.TopFilename().full());
  if (save_forces_) mprintf("\tSaving force information to frame.\n");
  mprintf("\tReference for initialization");
  if (!REF.empty())
    mprintf(" is '%s'\n", REF.refName());
  else
    mprintf(" will be first frame.\n");
  return Action::OK;
}

// Action_Angle::init()
Action::RetType Action_Angle::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
  // Get keywords
  DataFile* outfile = init.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_ = init.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;
}

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_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_Energy::Init()
Action::RetType Action_Energy::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
  ENE_.SetDebug( debugIn );
  // Get keywords
  DataFile* outfile = init.DFL().AddDataFile( actionArgs.GetStringKey("out"), actionArgs );
  // Which terms will be calculated?
  Ecalcs_.clear();
  if (actionArgs.hasKey("bond"))     Ecalcs_.push_back(BND);
  if (actionArgs.hasKey("angle"))    Ecalcs_.push_back(ANG);
  if (actionArgs.hasKey("dihedral")) Ecalcs_.push_back(DIH);
  if (actionArgs.hasKey("nb14"))     Ecalcs_.push_back(N14);
  if (actionArgs.hasKey("nonbond"))  Ecalcs_.push_back(NBD);
  // If nothing is selected, select all.
  if (Ecalcs_.empty()) {
    for (int c = 0; c <= (int)NBD; c++)
      Ecalcs_.push_back( (CalcType)c );
  }

  // Get Masks
  Mask1_.SetMaskString( actionArgs.GetMaskNext() );

  // DataSet
  std::string setname = actionArgs.GetStringNext();
  if (setname.empty())
    setname = init.DSL().GenerateDefaultName("ENE");
  Energy_.clear();
  Energy_.resize( (int)TOTAL + 1, 0 );
  for (calc_it calc = Ecalcs_.begin(); calc != Ecalcs_.end(); ++calc)
  {
    switch (*calc) {
      case BND: if (AddSet(BOND, init.DSL(), outfile, setname)) return Action::ERR; break;
      case ANG: if (AddSet(ANGLE, init.DSL(), outfile, setname)) return Action::ERR; break;
      case DIH: if (AddSet(DIHEDRAL, init.DSL(), outfile, setname)) return Action::ERR; break;
      case N14:
        if (AddSet(V14, init.DSL(), outfile, setname)) return Action::ERR;
        if (AddSet(Q14, init.DSL(), outfile, setname)) return Action::ERR;
        break;
      case NBD:
        if (AddSet(VDW, init.DSL(), outfile, setname)) return Action::ERR;
        if (AddSet(ELEC, init.DSL(), outfile, setname)) return Action::ERR;
        break;
    }
  }
//  if (Ecalcs_.size() > 1) {
    if (AddSet(TOTAL, init.DSL(), outfile, setname)) return Action::ERR;
//  }
      
  mprintf("    ENERGY: Calculating energy for atoms in mask '%s'\n", Mask1_.MaskString());
  mprintf("\tCalculating terms:");
  for (calc_it calc = Ecalcs_.begin(); calc != Ecalcs_.end(); ++calc)
    mprintf(" %s", Cstring[*calc]);
  mprintf("\n");

  return Action::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;
}

// Action_AtomicCorr::Init()
Action::RetType Action_AtomicCorr::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
  debug_ = debugIn;
  outfile_ = init.DFL().AddDataFile( actionArgs.GetStringKey("out"), actionArgs );
  cut_ = actionArgs.getKeyDouble("cut", 0.0);
  if (cut_ < 0.0 || cut_ > 1.0) {
    mprinterr("Error: cut value must be between 0 and 1.\n");
    return Action::ERR;
  }
  min_ = actionArgs.getKeyInt("min",0);
  if (actionArgs.hasKey("byatom"))
    acorr_mode_ = ATOM;
  else if (actionArgs.hasKey("byres"))
    acorr_mode_ = RES;
  mask_.SetMaskString( actionArgs.GetMaskNext() );
  
  // Set up DataSet
  dset_ = init.DSL().AddSet( DataSet::MATRIX_FLT, actionArgs.GetStringNext(), "ACorr" );
  if (dset_ == 0) {
    mprinterr("Error: Could not allocate output data set.\n");
    return Action::ERR;
  }
  // Add DataSet to output file
  if (outfile_ != 0) outfile_->AddDataSet( dset_ );

  mprintf("    ATOMICCORR: Correlation of %s motions will be calculated for\n",
          ModeString[acorr_mode_]);
  mprintf("\tatoms in mask [%s]", mask_.MaskString());
  if (outfile_ != 0) mprintf(", output to file %s", outfile_->DataFilename().full());
  mprintf("\n\tData saved in set '%s'\n", dset_->legend());
  if (cut_ != 0)
    mprintf("\tOnly correlations greater than %.2f or less than -%.2f will be printed.\n",
            cut_,cut_);
  if (min_!=0)
    mprintf("\tOnly correlations for %ss > %i apart will be calculated.\n",
            ModeString[acorr_mode_],min_);
# ifdef MPI
  trajComm_ = init.TrajComm();
  if (trajComm_.Size() > 1)
    mprintf("\nWarning: 'atomiccorr' in parallel will not work correctly if coordinates have\n"
              "Warning:   been modified by previous actions (e.g. 'rms').\n\n");
  // Since matrix calc only happens in Print(), no sync needed.
  dset_->SetNeedsSync( false );
# endif
  return Action::OK;
}

// Action_CheckStructure::Init()
Action::RetType Action_CheckStructure::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
  // Get Keywords
  std::string around = actionArgs.GetStringKey("around");
  SeparateInit( !(actionArgs.hasKey("noimage")), actionArgs.GetMaskNext(),
                around, actionArgs.GetStringKey("reportfile"),
                actionArgs.getKeyDouble("cut",0.8),
                actionArgs.getKeyDouble("offset",1.15),
                actionArgs.hasKey("silent"), init.DFL() );
  // DoAction-only keywords.
  bondcheck_ = !actionArgs.hasKey("nobondcheck");
  skipBadFrames_ = actionArgs.hasKey("skipbadframes");

  mprintf("    CHECKSTRUCTURE: Checking atoms in mask '%s'",Mask1_.MaskString());
  if (Mask2_.MaskStringSet())
    mprintf(" around mask '%s'", Mask2_.MaskString());
  if (!image_.UseImage())
    mprintf(", imaging off");
  if (outfile_ != 0)
    mprintf(", output to %s", outfile_->Filename().full());
  mprintf(".\n");
  if (!bondcheck_) {
    mprintf("\tChecking inter-atomic distances only.\n");
    mprintf("\tWarnings will be printed for non-bond distances < %.2f Ang.\n", sqrt(nonbondcut2_));
  } else {
    mprintf("\tChecking inter-atomic and bond distances.\n");
    mprintf("\tWarnings will be printed for bond lengths > eq + %.2f Ang\n",
            bondoffset_);
    mprintf("\tand non-bond distances < %.2f Ang.\n", sqrt(nonbondcut2_));
  }
  if (skipBadFrames_)
    mprintf("\tFrames with problems will be skipped.\n");
  if (silent_)
    mprintf("\tWarning messages will be suppressed.\n");
# ifdef _OPENMP
# pragma omp parallel
  {
#   pragma omp master
    {
    mprintf("\tParallelizing calculation with %i threads.\n", omp_get_num_threads());
    }
  }
# endif
  return Action::OK;
}

// 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;
}

// Action_Principal::Init()
Action::RetType Action_Principal::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
  debug_ = debugIn;
  // Keywords
  std::string dsname = actionArgs.GetStringKey("name");
  doRotation_ = actionArgs.hasKey("dorotation");
  // CPPTRAJ always uses mass no matter what this keyword says.
  useMass_ = actionArgs.hasKey("mass");
  std::string filename = actionArgs.GetStringKey("out");
  if (!doRotation_ && filename.empty() && dsname.empty()) {
    mprinterr("Error: At least one of 'dorotation', 'out <filename>', or 'name <dsname>' must be specified.\n");
    return Action::ERR;
  }
  // Masks
  mask_.SetMaskString( actionArgs.GetMaskNext() );
  // Set up data
  if (!dsname.empty()) {
     vecData_ = (DataSet_Mat3x3*)init.DSL().AddSet(DataSet::MAT3X3, MetaData(dsname, "evec"));
     valData_ = (DataSet_Vector*)init.DSL().AddSet(DataSet::VECTOR, MetaData(dsname, "eval"));
     if (vecData_ == 0 || valData_ == 0) return Action::ERR;
  }

  mprintf("    PRINCIPAL:");
  if (!filename.empty()) {
    outfile_ = init.DFL().AddCpptrajFile(filename, "Eigenvectors/Eigenvalues");
    if (outfile_ == 0) return Action::ERR;
    mprintf(" output eigenvectors/eigenvalues to %s,", outfile_->Filename().full());
  }
  if (doRotation_)
    mprintf(" with rotation by");
  else
    mprintf(" without rotation by");
  if (useMass_)
    mprintf(" center of mass");
  else
    mprintf(" center of geometry");
  mprintf(", atoms selected by [%s]\n", mask_.MaskString());
  if (vecData_ != 0)
    mprintf("\tSaving eigenvectors to '%s' (in rows of 3x3 matrices).\n"
            "\tSaving eigenvalues to '%s'\n", vecData_->legend(), valData_->legend());

  return Action::OK;
}