// Exec_DataSetCmd::ChangeOutputFormat() Exec::RetType Exec_DataSetCmd::ChangeOutputFormat(CpptrajState const& State, ArgList& argIn) { TextFormat::FmtType fmt; if (argIn.hasKey("double")) fmt = TextFormat::DOUBLE; else if (argIn.hasKey("scientific")) fmt = TextFormat::SCIENTIFIC; else if (argIn.hasKey("general")) fmt = TextFormat::GDOUBLE; else { mprinterr("Error: Expected either 'double', 'scientific', or 'general'\n"); return CpptrajState::ERR; } // Loop over all DataSet arguments std::string ds_arg = argIn.GetStringNext(); while (!ds_arg.empty()) { DataSetList dsl = State.DSL().GetMultipleSets( ds_arg ); for (DataSetList::const_iterator ds = dsl.begin(); ds != dsl.end(); ++ds) if ((*ds)->SetupFormat().SetFormatType(fmt)) mprintf("\tSet '%s' output format changed to '%s'\n", (*ds)->legend(), TextFormat::typeDescription(fmt)); ds_arg = argIn.GetStringNext(); } return CpptrajState::OK; }
/// \return 1 if problem with or not a Tinker Atom/Title line. static inline int SetNatomAndTitle(ArgList& lineIn, int& natom, std::string& title) { if (lineIn.Nargs() < 1) return 1; natom = lineIn.getNextInteger( -1 ); if (natom < 1) return 1; std::string nextWord = lineIn.GetStringNext(); //if (nextWord.empty()) return 1; while (!nextWord.empty()) { if (!title.empty()) title += ' '; title.append( nextWord ); nextWord = lineIn.GetStringNext(); } return 0; }
// Exec_DataSetCmd::MakeXY() Exec::RetType Exec_DataSetCmd::MakeXY(CpptrajState& State, ArgList& argIn) { std::string name = argIn.GetStringKey("name"); DataSet* ds1 = State.DSL().GetDataSet( argIn.GetStringNext() ); DataSet* ds2 = State.DSL().GetDataSet( argIn.GetStringNext() ); if (ds1 == 0 || ds2 == 0) return CpptrajState::ERR; if (ds1->Ndim() != 1 || ds2->Ndim() != 1) { mprinterr("Error: makexy only works for 1D data sets.\n"); return CpptrajState::ERR; } DataSet* ds3 = State.DSL().AddSet( DataSet::XYMESH, name, "XY" ); if (ds3 == 0) return CpptrajState::ERR; mprintf("\tUsing values from '%s' as X, values from '%s' as Y, output set '%s'\n", ds1->legend(), ds2->legend(), ds3->legend()); DataSet_1D const& ds_x = static_cast<DataSet_1D const&>( *ds1 ); DataSet_1D const& ds_y = static_cast<DataSet_1D const&>( *ds2 ); DataSet_1D& out = static_cast<DataSet_1D&>( *ds3 ); size_t nframes = std::min( ds_x.Size(), ds_y.Size() ); if (ds_x.Size() != ds_y.Size()) mprintf("Warning: Data sets do not have equal sizes, only using %zu frames.\n", nframes); double XY[2]; for (size_t i = 0; i != nframes; i++) { XY[0] = ds_x.Dval(i); XY[1] = ds_y.Dval(i); out.Add( i, XY ); } return CpptrajState::OK; }
Exec::RetType Exec_Precision::Execute(CpptrajState& State, ArgList& argIn) { // Next string is DataSet(s)/DataFile that command pertains to. std::string name1 = argIn.GetStringNext(); if (name1.empty()) { mprinterr("Error: No filename/setname given.\n"); return CpptrajState::ERR; } // This will break if dataset name starts with a digit... int width = argIn.getNextInteger(12); if (width < 1) { mprintf("Error: Cannot set width < 1 (%i).\n", width); return CpptrajState::ERR; } int precision = argIn.getNextInteger(4); if (precision < 0) precision = 0; DataFile* df = State.DFL().GetDataFile(name1); if (df != 0) { mprintf("\tSetting precision for all sets in %s to %i.%i\n", df->DataFilename().base(), width, precision); df->SetDataFilePrecision(width, precision); } else { State.DSL().SetPrecisionOfDataSets( name1, width, precision ); } return CpptrajState::OK; }
// Exec_DataSetCmd::Make2D() Exec::RetType Exec_DataSetCmd::Make2D(CpptrajState& State, ArgList& argIn) { std::string name = argIn.GetStringKey("name"); int ncols = argIn.getKeyInt("ncols", 0); int nrows = argIn.getKeyInt("nrows", 0); if (ncols <= 0 || nrows <= 0) { mprinterr("Error: Must specify both ncols and nrows\n"); return CpptrajState::ERR; } DataSet* ds1 = State.DSL().GetDataSet( argIn.GetStringNext() ); if (ds1 == 0) return CpptrajState::ERR; if (ds1->Ndim() != 1) { mprinterr("Error: make2d only works for 1D data sets.\n"); return CpptrajState::ERR; } if (nrows * ncols != (int)ds1->Size()) { mprinterr("Error: Size of '%s' (%zu) != nrows X ncols.\n", ds1->legend(), ds1->Size()); return CpptrajState::ERR; } if (name.empty()) name = State.DSL().GenerateDefaultName("make2d"); MetaData md(name, MetaData::M_MATRIX); DataSet* ds3 = State.DSL().AddSet( DataSet::MATRIX_DBL, md ); if (ds3 == 0) return CpptrajState::ERR; mprintf("\tConverting values from 1D set '%s' to 2D matrix '%s' with %i cols, %i rows.\n", ds1->legend(), ds3->legend(), ncols, nrows); DataSet_1D const& data = static_cast<DataSet_1D const&>( *ds1 ); DataSet_MatrixDbl& matrix = static_cast<DataSet_MatrixDbl&>( *ds3 ); if (matrix.Allocate2D( ncols, nrows )) return CpptrajState::ERR; for (unsigned int idx = 0; idx != data.Size(); idx++) matrix.AddElement( data.Dval(idx) ); return CpptrajState::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::RetType Action_CreateCrd::Init(ArgList& actionArgs, ActionInit& init, int debugIn) { // Keywords Topology* parm = init.DSL().GetTopology( actionArgs ); if (parm == 0) { mprinterr("Error: createcrd: No parm files loaded.\n"); return Action::ERR; } pindex_ = parm->Pindex(); check_ = !actionArgs.hasKey("nocheck"); // DataSet std::string setname = actionArgs.GetStringNext(); if (setname == "_DEFAULTCRD_") { // Special case: Creation of COORDS DataSet has been requested by an // analysis and should already be present. coords_ = (DataSet_Coords_CRD*)init.DSL().FindSetOfType(setname, DataSet::COORDS); } else coords_ = (DataSet_Coords_CRD*)init.DSL().AddSet(DataSet::COORDS, setname, "CRD"); if (coords_ == 0) return Action::ERR; // Do not set topology here since it may be modified later. mprintf(" CREATECRD: Saving coordinates from Top %s to \"%s\"\n", parm->c_str(), coords_->legend()); if (!check_) mprintf("\tNot strictly enforcing that all frames have same # atoms.\n"); # ifdef MPI if (init.TrajComm().Size() > 1) mprintf("Warning: Synchronization of COORDS data sets over multiple threads is\n" "Warning: experimental and may be slower than reading in via a single\n" "Warning: thread. Users are encouraged to run benchmarks before\n" "Warning: extensive usage.\n"); # endif 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; }
// Exec_CrdAction::ProcessArgs() Exec::RetType Exec_CrdAction::ProcessArgs(CpptrajState& State, ArgList& argIn) { std::string setname = argIn.GetStringNext(); if (setname.empty()) { mprinterr("Error: %s: Specify COORDS dataset name.\n", argIn.Command()); return CpptrajState::ERR; } DataSet_Coords* CRD = (DataSet_Coords*)State.DSL().FindCoordsSet( setname ); if (CRD == 0) { mprinterr("Error: %s: No COORDS set with name %s found.\n", argIn.Command(), setname.c_str()); return CpptrajState::ERR; } mprintf("\tUsing set '%s'\n", CRD->legend()); // Start, stop, offset TrajFrameCounter frameCount; ArgList crdarg( argIn.GetStringKey("crdframes"), "," ); if (frameCount.CheckFrameArgs( CRD->Size(), crdarg )) return CpptrajState::ERR; frameCount.PrintInfoLine(CRD->legend()); ArgList actionargs = argIn.RemainingArgs(); actionargs.MarkArg(0); Cmd const& cmd = Command::SearchTokenType( DispatchObject::ACTION, actionargs.Command() ); if ( cmd.Empty() ) return CpptrajState::ERR; Action* act = (Action*)cmd.Alloc(); if (act == 0) return CpptrajState::ERR; CpptrajState::RetType err = DoCrdAction(State, actionargs, CRD, act, frameCount); delete act; return err; }
// 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; }
Action::RetType Action_MultiVector::Init(ArgList& actionArgs, TopologyList* PFL, DataSetList* DSL, DataFileList* DFL, int debugIn) { debug_ = debugIn; // Get keywords outfile_ = 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()); DSL->SetDataSetsPending(true); masterDSL_ = DSL; return Action::OK; }
// Action_Average::init() Action::RetType Action_Average::Init(ArgList& actionArgs, TopologyList* PFL, FrameList* FL, DataSetList* DSL, DataFileList* DFL, int debugIn) { debug_ = debugIn; // Get Keywords avgfilename_ = actionArgs.GetStringNext(); if (avgfilename_.empty()) { mprinterr("Error: average: No filename given.\n"); return Action::ERR; } // Get start/stop/offset args if (InitFrameCounter(actionArgs)) return Action::ERR; // Get Masks Mask1_.SetMaskString( actionArgs.GetMaskNext() ); // Save all remaining arguments for setting up the trajectory at the end. trajArgs_ = actionArgs.RemainingArgs(); mprintf(" AVERAGE: Averaging over coordinates in mask [%s]\n",Mask1_.MaskString()); FrameCounterInfo(); mprintf("\tWriting averaged coords to [%s]\n",avgfilename_.c_str()); Nframes_ = 0; 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(":WAT@O"); 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_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_Outtraj::Init() Action::RetType Action_Outtraj::Init(ArgList& actionArgs, ActionInit& init, int debugIn) { // Set up output traj outtraj_.SetDebug(debugIn); std::string trajfilename = actionArgs.GetStringNext(); if (trajfilename.empty()) { mprinterr("Error: No filename given.\nError: Usage: "); Help(); return Action::ERR; } associatedParm_ = init.DSL().GetTopology(actionArgs); if (associatedParm_ == 0) { mprinterr("Error: Could not get associated topology for %s\n",trajfilename.c_str()); return Action::ERR; } // If maxmin, get the name of the dataset as well as the max and min values. double lastmin = 0.0; double lastmax = 0.0; while ( actionArgs.Contains("maxmin") ) { std::string datasetName = actionArgs.GetStringKey("maxmin"); if (!datasetName.empty()) { DataSet* dset = init.DSL().GetDataSet(datasetName); if (dset==0) { mprintf("Error: maxmin: Could not get dataset %s\n",datasetName.c_str()); return Action::ERR; } else { // Currently only allow int, float, or double datasets if (dset->Type() != DataSet::INTEGER && dset->Type() != DataSet::FLOAT && dset->Type() != DataSet::DOUBLE) { mprinterr("Error: maxmin: Only int, float, or double dataset (%s) supported.\n", datasetName.c_str()); return Action::ERR; } Dsets_.push_back( (DataSet_1D*)dset ); Max_.push_back( actionArgs.getKeyDouble("max",lastmax) ); Min_.push_back( actionArgs.getKeyDouble("min",lastmin) ); lastmax = Max_.back(); lastmin = Min_.back(); } } else { mprinterr("Error: maxmin Usage: maxmin <setname> max <max> min <min>\n"); return Action::ERR; } } // Initialize output trajectory with remaining arguments if ( outtraj_.InitEnsembleTrajWrite(trajfilename, actionArgs.RemainingArgs(), TrajectoryFile::UNKNOWN_TRAJ, init.DSL().EnsembleNum()) ) return Action::ERR; isSetup_ = false; mprintf(" OUTTRAJ: Writing frames associated with topology '%s'\n", associatedParm_->c_str()); for (unsigned int ds = 0; ds < Dsets_.size(); ++ds) mprintf("\tmaxmin: Printing trajectory frames based on %g <= %s <= %g\n", Min_[ds], Dsets_[ds]->legend(), Max_[ds]); 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; }
// Exec_SortEnsembleData::Execute() Exec::RetType Exec_SortEnsembleData::Execute(CpptrajState& State, ArgList& argIn) { debug_ = State.Debug(); DataSetList setsToSort; std::string dsarg = argIn.GetStringNext(); while (!dsarg.empty()) { setsToSort += State.DSL().GetMultipleSets( dsarg ); dsarg = argIn.GetStringNext(); } int err = 0; # ifdef MPI // For now, require ensemble mode in parallel. if (!Parallel::EnsembleIsSetup()) { rprinterr("Error: Data set ensemble sort requires ensemble mode in parallel.\n"); return CpptrajState::ERR; } // Only TrajComm masters have complete data. if (Parallel::TrajComm().Master()) { comm_ = Parallel::MasterComm(); # endif DataSetList OutputSets; err = SortData( setsToSort, OutputSets ); if (err == 0) { // Remove unsorted sets. for (DataSetList::const_iterator ds = setsToSort.begin(); ds != setsToSort.end(); ++ds) State.DSL().RemoveSet( *ds ); // Add sorted sets. for (DataSetList::const_iterator ds = OutputSets.begin(); ds != OutputSets.end(); ++ds) State.DSL().AddSet( *ds ); // Since sorted sets have been transferred to master DSL, OutputSets now // just has copies. OutputSets.SetHasCopies( true ); mprintf("\tSorted sets:\n"); OutputSets.List(); } # ifdef MPI } if (Parallel::World().CheckError( err )) # else if (err != 0) # endif return CpptrajState::ERR; return CpptrajState::OK; }
int DataSetList::SetActiveReference(ArgList &argIn) { int err = 0; DataSet* ds = GetReferenceSet( argIn, err ); if (ds == 0) { // For backwards compat, see if there is a single integer arg. ArgList refArg( "refindex " + argIn.GetStringNext() ); ds = GetReferenceSet( refArg, err ); } return SetActiveReference( ds ); }
// 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_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; }
// Action_Dihedral::init() Action::RetType Action_Dihedral::Init(ArgList& actionArgs, TopologyList* PFL, FrameList* FL, DataSetList* DSL, DataFileList* DFL, int debugIn) { // Get keywords DataFile* outfile = DFL->AddDataFile( actionArgs.GetStringKey("out"), actionArgs ); useMass_ = actionArgs.hasKey("mass"); DataSet::scalarType stype = DataSet::UNDEFINED; range360_ = actionArgs.hasKey("range360"); std::string stypename = actionArgs.GetStringKey("type"); if ( stypename == "alpha" ) stype = DataSet::ALPHA; else if ( stypename == "beta" ) stype = DataSet::BETA; else if ( stypename == "gamma" ) stype = DataSet::GAMMA; else if ( stypename == "delta" ) stype = DataSet::DELTA; else if ( stypename == "epsilon" ) stype = DataSet::EPSILON; else if ( stypename == "zeta" ) stype = DataSet::ZETA; else if ( stypename == "chi" ) stype = DataSet::CHI; else if ( stypename == "c2p" ) stype = DataSet::C2P; else if ( stypename == "h1p" ) stype = DataSet::H1P; else if ( stypename == "phi" ) stype = DataSet::PHI; else if ( stypename == "psi" ) stype = DataSet::PSI; else if ( stypename == "pchi" ) stype = DataSet::PCHI; // Get Masks std::string mask1 = actionArgs.GetMaskNext(); std::string mask2 = actionArgs.GetMaskNext(); std::string mask3 = actionArgs.GetMaskNext(); std::string mask4 = actionArgs.GetMaskNext(); if (mask1.empty() || mask2.empty() || mask3.empty() || mask4.empty()) { mprinterr("Error: dihedral: Requires 4 masks\n"); return Action::ERR; } M1_.SetMaskString(mask1); M2_.SetMaskString(mask2); M3_.SetMaskString(mask3); M4_.SetMaskString(mask4); // Setup dataset dih_ = DSL->AddSet(DataSet::DOUBLE, actionArgs.GetStringNext(),"Dih"); if (dih_==0) return Action::ERR; dih_->SetScalar( DataSet::M_TORSION, stype ); // Add dataset to datafile list if (outfile != 0) outfile->AddSet( dih_ ); mprintf(" DIHEDRAL: [%s]-[%s]-[%s]-[%s]\n", M1_.MaskString(), M2_.MaskString(), M3_.MaskString(), M4_.MaskString()); if (useMass_) mprintf(" Using center of mass of atoms in masks.\n"); if (range360_) mprintf(" Output range is 0 to 360 degrees.\n"); else mprintf(" Output range is -180 to 180 degrees.\n"); return Action::OK; }
Analysis::RetType Analysis_CurveFit::Setup(ArgList& analyzeArgs, DataSetList* datasetlist, TopologyList* PFLin, DataFileList* DFLin, int debugIn) { // First argument should be DataSet to fit to. std::string dsinName = analyzeArgs.GetStringNext(); dset_ = datasetlist->GetDataSet( dsinName ); if (dset_ == 0) { mprinterr("Error: Data set '%s' not found.\n", dsinName.c_str()); return Analysis::ERR; } return Internal_setup( "", analyzeArgs, datasetlist, DFLin, debugIn ); }
// Exec_DataSetCmd::Concatenate() Exec::RetType Exec_DataSetCmd::Concatenate(CpptrajState& State, ArgList& argIn) { std::string name = argIn.GetStringKey("name"); bool use_offset = !argIn.hasKey("nooffset"); DataSet* ds3 = State.DSL().AddSet( DataSet::XYMESH, name, "CAT" ); if (ds3 == 0) return CpptrajState::ERR; DataSet_1D& out = static_cast<DataSet_1D&>( *ds3 ); mprintf("\tConcatenating sets into '%s'\n", out.legend()); if (use_offset) mprintf("\tX values will be offset.\n"); else mprintf("\tX values will not be offset.\n"); std::string dsarg = argIn.GetStringNext(); double offset = 0.0; while (!dsarg.empty()) { DataSetList dsl = State.DSL().GetMultipleSets( dsarg ); double XY[2]; for (DataSetList::const_iterator ds = dsl.begin(); ds != dsl.end(); ++ds) { if ( (*ds)->Group() != DataSet::SCALAR_1D ) { mprintf("Warning: '%s': Concatenation only supported for 1D scalar data sets.\n", (*ds)->legend()); } else { DataSet_1D const& set = static_cast<DataSet_1D const&>( *(*ds) ); mprintf("\t\t'%s'\n", set.legend()); for (size_t i = 0; i != set.Size(); i++) { XY[0] = set.Xcrd( i ) + offset; XY[1] = set.Dval( i ); out.Add( i, XY ); // NOTE: value of i does not matter for mesh } if (use_offset) offset = XY[0]; } } dsarg = argIn.GetStringNext(); } return CpptrajState::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; }
// Exec_DataSetCmd::Execute() Exec::RetType Exec_DataSetCmd::Execute(CpptrajState& State, ArgList& argIn) { RetType err = CpptrajState::OK; if (argIn.Contains("legend")) { // Set legend for one data set std::string legend = argIn.GetStringKey("legend"); DataSet* ds = State.DSL().GetDataSet( argIn.GetStringNext() ); if (ds == 0) return CpptrajState::ERR; mprintf("\tChanging legend '%s' to '%s'\n", ds->legend(), legend.c_str()); ds->SetLegend( legend ); // --------------------------------------------- } else if (argIn.hasKey("outformat")) { // Change double precision set output format err = ChangeOutputFormat(State, argIn); // --------------------------------------------- } else if (argIn.hasKey("remove")) { // Remove data sets by various criteria err = Remove(State, argIn); // --------------------------------------------- } else if (argIn.hasKey("makexy")) { // Combine values from two sets into 1 err = MakeXY(State, argIn); // --------------------------------------------- } else if (argIn.hasKey("make2d")) { // Create 2D matrix from 1D set err = Make2D(State, argIn); // --------------------------------------------- } else if (argIn.hasKey("vectorcoord")) { // Extract vector X/Y/Z coord as new set err = VectorCoord(State, argIn); // --------------------------------------------- } else if (argIn.hasKey("filter")) { // Filter points in data set to make new data set err = Filter(State, argIn); // --------------------------------------------- } else if (argIn.hasKey("cat")) { // Concatenate two or more data sets err = Concatenate(State, argIn); // --------------------------------------------- } else if (argIn.hasKey("droppoints")) { // Drop points from set err = ModifyPoints(State, argIn, true); // --------------------------------------------- } else if (argIn.hasKey("keeppoints")) { // Keep points in set err = ModifyPoints(State, argIn, false); // --------------------------------------------- } else if (argIn.hasKey("dim")) { // Modify dimension of set(s) err = ChangeDim(State, argIn); // --------------------------------------------- } else if (argIn.hasKey("invert")) { // Invert set(s) X/Y, create new sets err = InvertSets(State, argIn); // --------------------------------------------- } else { // Default: change mode/type for one or more sets. err = ChangeModeType(State, argIn); } return err; }
Action::RetType Action_MultiDihedral::Init(ArgList& actionArgs, TopologyList* PFL, FrameList* FL, DataSetList* DSL, DataFileList* DFL, int debugIn) { debug_ = debugIn; // Get keywords outfile_ = DFL->AddDataFile( actionArgs.GetStringKey("out"), actionArgs); range360_ = actionArgs.hasKey("range360"); std::string resrange_arg = actionArgs.GetStringKey("resrange"); if (!resrange_arg.empty()) if (resRange_.SetRange( resrange_arg )) return Action::ERR; // Search for known dihedral keywords dihSearch_.SearchForArgs(actionArgs); // Get custom dihedral arguments: dihtype <name>:<a0>:<a1>:<a2>:<a3>[:<offset>] std::string dihtype_arg = actionArgs.GetStringKey("dihtype"); while (!dihtype_arg.empty()) { ArgList dihtype(dihtype_arg, ":"); if (dihtype.Nargs() < 5) { mprinterr("Error: Malformed dihtype arg.\n"); return Action::ERR; } int offset = 0; if (dihtype.Nargs() == 6) offset = convertToInteger(dihtype[5]); dihSearch_.SearchForNewType(offset,dihtype[1],dihtype[2],dihtype[3],dihtype[4], dihtype[0]); dihtype_arg = actionArgs.GetStringKey("dihtype"); } // If no dihedral types yet selected, this will select all. dihSearch_.SearchForAll(); // Setup DataSet(s) name dsetname_ = actionArgs.GetStringNext(); mprintf(" MULTIDIHEDRAL: Calculating"); dihSearch_.PrintTypes(); if (!resRange_.Empty()) mprintf(" dihedrals for residues in range %s\n", resRange_.RangeArg()); else mprintf(" dihedrals for all residues.\n"); if (!dsetname_.empty()) mprintf("\tDataSet name: %s\n", dsetname_.c_str()); if (outfile_ != 0) mprintf("\tOutput to %s\n", outfile_->DataFilename().base()); if (range360_) mprintf("\tRange 0-360 deg.\n"); else mprintf("\tRange -180-180 deg.\n"); masterDSL_ = DSL; 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_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_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; }