示例#1
0
int TrajinList::AddTrajin(std::string const& fname, Topology* topIn, ArgList const& argIn)
{
  if (topIn == 0) {
    mprinterr("Error: No topology for input trajectory '%s'\n", fname.c_str());
    return 1;
  }
  // CRDIDXARG
  finalCrdIndicesArg_.clear();
  ArgList trajin_args = argIn;
  bool isRemdtraj = trajin_args.hasKey("remdtraj");
  int err = 0;
  File::NameArray fnames = File::ExpandToFilenames( fname );
  if (fnames.empty()) return 1;
  Trajin* traj = 0;
  for (File::NameArray::const_iterator fn = fnames.begin(); fn != fnames.end(); ++fn) {
    ArgList args = trajin_args;
    if (isRemdtraj)
      traj = new Trajin_Multi();
    else
      traj = new Trajin_Single();
    if (traj == 0) {
      mprinterr("Error: Memory allocation for input trajectory failed.\n");
      return 1;
    }
    traj->SetDebug(debug_);
    if ( traj->SetupTrajRead(*fn, args, topIn) ) {
      mprinterr("Error: Could not set up input trajectory '%s'.\n", fn->full());
      delete traj;
      err++;
      continue;
    }
    // Add to trajin list and update # of frames.
    trajin_.push_back( traj );
    UpdateMaxFrames( traj->Traj() );
  }
  if (err > 0) return 1;
  // FIXME: For backwards compat. overwrite Topology box info with traj box info.
  topIn->SetBoxFromTraj( trajin_.back()->TrajCoordInfo().TrajBox() );
  return 0;
}
示例#2
0
Exec::RetType Exec_ReadData::Execute(CpptrajState& State, ArgList& argIn) {
  DataFile dataIn;
  dataIn.SetDebug( State.DFL().Debug() );
  std::string filenameIn = argIn.GetStringNext();
  File::NameArray fnames = File::ExpandToFilenames( filenameIn );
  if (fnames.empty()) {
    mprinterr("Error: '%s' matches no files.\n", filenameIn.c_str());
    return CpptrajState::ERR;
  }
  int err = 0;
  int idx = -1;
  bool useIndex = argIn.hasKey("separate");
  for (File::NameArray::const_iterator fn = fnames.begin(); fn != fnames.end(); ++fn) {
    if (useIndex) idx++;
    if (dataIn.ReadDataIn( *fn, argIn, State.DSL(), idx, fnames.size() )!=0) {
      mprinterr("Error: Could not read data file '%s'.\n", fn->full());
      err++;
    }
  }
  if (err > 0) return CpptrajState::ERR;
  return CpptrajState::OK;
}
示例#3
0
// TrajinList::AddEnsembleIn()
int TrajinList::AddEnsembleIn(std::string const& fname, Topology* topIn, ArgList const& argIn)
{
  if (topIn == 0) {
    mprinterr("Error: No topology for input ensemble '%s'\n", fname.c_str());
    return 1;
  }
  int err = 0;
  File::NameArray fnames = File::ExpandToFilenames( fname );
  if (fnames.empty()) return 1;
  TrajectoryFile::TrajFormatType trajinFmt;
  TrajectoryIO* tio = 0;
  for (File::NameArray::const_iterator fn = fnames.begin(); fn != fnames.end(); ++fn) {
    ArgList args = argIn;
    // Determine whether this file is multiple file or single file ensemble.
    tio = TrajectoryFile::DetectFormat( *fn, trajinFmt );
    if (tio == 0) {
      mprinterr("Error: Could not determine trajectory %s format\n", fn->full());
      err++;
      continue;
    }
    EnsembleIn* ensemble = 0;
#   ifdef ENABLE_SINGLE_ENSEMBLE
    if (tio->CanProcessEnsemble())
      ensemble = new EnsembleIn_Single();
    else
#   endif
      ensemble = new EnsembleIn_Multi();
    if (ensemble == 0) {
      mprinterr("Error: Memory allocation for input ensemble failed.\n");
      delete tio;
      return 1;
    }
    ensemble->SetDebug( debug_ );
    // CRDIDXARG: Append coordinate indices arg if there is one
    args.AddArg( finalCrdIndicesArg_ );
    if ( ensemble->SetupEnsembleRead(*fn, args, topIn) ) {
      mprinterr("Error: Could not set up input ensemble '%s'.\n", fname.c_str());
      delete ensemble;
      delete tio;
      err++;
      continue;
    }
    // Currently all input ensembles must be same size.
    if (ensembleSize_ == -1)
      ensembleSize_ = ensemble->EnsembleCoordInfo().EnsembleSize();
    else if (ensembleSize_ != ensemble->EnsembleCoordInfo().EnsembleSize()) {
      mprinterr("Error: Ensemble size (%i) does not match first ensemble size (%i).\n",
                ensemble->EnsembleCoordInfo().EnsembleSize(), ensembleSize_);
      return 1;
    }
    // CRDIDXARG: If trajectory is REMD ensemble and sorting by CRDIDX, need to
    //            save final CRDIDX for next ensemble command.
    // TODO: This is very clunky - remlog dataset should contain all exchanges
    //       so trajin doesnt have to worry about it.
#   ifdef ENABLE_SINGLE_ENSEMBLE
    if ( !tio->CanProcessEnsemble() ) {
#   endif
      EnsembleIn_Multi const& mTraj = static_cast<EnsembleIn_Multi const&>( *ensemble );
      if ( mTraj.TargetMode() == ReplicaInfo::CRDIDX ) {
        finalCrdIndicesArg_ = mTraj.FinalCrdIndices();
        if (finalCrdIndicesArg_.empty()) {
          mprinterr("Error: Could not obtain final remlog indices.\n");
          delete ensemble;
          delete tio;
          err++;
          continue;
        }
        //mprintf("DEBUG: Final crd indices arg: %s\n", finalCrdIndicesArg_.c_str());
      }
#   ifdef ENABLE_SINGLE_ENSEMBLE
    } else
      mprintf("Warning: Single ensemble cannot process crdidx.\n");
#   endif
    // Add to ensemble list and update # of frames.
    ensemble_.push_back( ensemble );
    UpdateMaxFrames( ensemble->Traj() );
    delete tio;
  }
  if (err > 0) return 1;
  // FIXME: For backwards compat. overwrite Topology box info with traj box info.
  topIn->SetBoxFromTraj( ensemble_.back()->EnsembleCoordInfo().TrajBox() );
  return 0;
}
示例#4
0
/** Loop over all filenames in replica_filenames, set up TrajectoryIO. */
int TrajIOarray::SetupIOarray(ArgList& argIn, TrajFrameCounter& counter,
                              CoordinateInfo& cInfo, Topology* trajParm)
{
  // Sanity check
  if (!IOarray_.empty()) {
    mprinterr("Internal Error: SetupIOarray() has been called twice.\n");
    return 1;
  }
  // Save arguments that have not been processed so they can be passed
  // to each replica in turn. Only the lowest replica will use argIn.
  ArgList argCopy( argIn );
  bool lowestRep = true;
  int rep0Frames = TrajectoryIO::TRAJIN_UNK;  // Total frames in replica 0
  int totalFrames = TrajectoryIO::TRAJIN_UNK; // Total # frames to be read from ensemble
  TrajectoryFile::TrajFormatType lastRepFmt = TrajectoryFile::UNKNOWN_TRAJ;
  // Right now enforce that all replicas have the same metadata as lowest
  // replica, e.g. if replica 0 has temperature, replica 1 does too etc.
  for (File::NameArray::const_iterator repfile = replica_filenames_.begin();
                                       repfile != replica_filenames_.end(); ++repfile)
  {
    // Detect format
    TrajectoryFile::TrajFormatType repformat = TrajectoryFile::UNKNOWN_TRAJ;
    TrajectoryIO* replica0 = TrajectoryFile::DetectFormat( *repfile, repformat );
    if ( replica0 == 0 ) {
      mprinterr("Error: Could not set up replica file %s\n", repfile->full());
      return 1;
    }
    if (repformat != lastRepFmt)
      mprintf("\tReading '%s' as %s\n", repfile->full(), TrajectoryFile::FormatString(repformat));
    lastRepFmt = repformat;
    replica0->SetDebug( debug_ );
    // Pushing replica0 here allows the destructor to handle it on errors
    IOarray_.push_back( replica0 );
    // Process format-specific read args. Do not exit on error in case
    // replicas have different formats supporting different args.
    if (lowestRep) {
      replica0->processReadArgs( argIn );
    } else {
      ArgList argtmp( argCopy );
      replica0->processReadArgs( argtmp );
    }
    // Set up replica for reading and get the number of frames.
    int nframes = replica0->setupTrajin( *repfile, trajParm );
    if (nframes == TrajectoryIO::TRAJIN_ERR) {
      mprinterr("Error: Could not set up %s for reading.\n", repfile->full());
      return 1;
    }
    // TODO: Do not allow unknown number of frames?
    if (lowestRep) {
      cInfo = replica0->CoordInfo();
      rep0Frames = nframes;
      totalFrames = nframes;
      if (cInfo.ReplicaDimensions().Ndims() > 0) {
        mprintf("\tReplica dimensions:\n");
        for (int rd = 0; rd < cInfo.ReplicaDimensions().Ndims(); rd++)
          mprintf("\t\t%i: %s\n", rd+1, cInfo.ReplicaDimensions().Description(rd));
      }
    } else {
      // Check total frames in this replica against lowest rep.
      if (nframes != rep0Frames)
        mprintf("Warning: Replica %s frames (%i) does not match # frames in first replica (%i).\n",
                repfile->base(), nframes, rep0Frames);
      //if (repframes < 0) {
      //  mprinterr("Error: RemdTraj: Unknown # of frames in replica.\n");
      //  return 1;
      //}
      if (nframes < totalFrames) {
        totalFrames = nframes; 
        mprintf("Warning: Setting total # of frames to read from replica ensemble to %i\n",
                totalFrames);
      }
      // Check box info against lowest rep.
      if ( replica0->CoordInfo().HasBox() != cInfo.HasBox() ) {
        mprinterr("Error: Replica %s box info does not match first replica.\n",
                  repfile->full());
        return 1;
      }
      // TODO: Check specific box type
      // Check velocity info against lowest rep.
      if ( replica0->CoordInfo().HasVel() != cInfo.HasVel() ) {
        mprinterr("Error: Replica %s velocity info does not match first replica.\n",
                  repfile->full());
        return 1;
      }
      // Check # dimensions and types against lowest rep
      if ( replica0->CoordInfo().ReplicaDimensions() != cInfo.ReplicaDimensions() ) {
        mprinterr("Error: Replica %s dimension info does not match first replica.\n",
                  repfile->full());
        ReplicaDimArray const& thisRepDims = replica0->CoordInfo().ReplicaDimensions();
        for (int rd = 0; rd < thisRepDims.Ndims(); rd++)
          mprinterr("\t\t%i: %s\n", rd+1, thisRepDims.Description(rd)); 
        return 1;
      }
      // If temperature/time info does not match set to false.
      if (cInfo.HasTemp() != replica0->CoordInfo().HasTemp())
        cInfo.SetTemperature( false );
      if (cInfo.HasTime() != replica0->CoordInfo().HasTime())
        cInfo.SetTime( false );
    }
    lowestRep = false;
  }
  // Check how many frames will actually be read
  if (counter.CheckFrameArgs( totalFrames, argIn )) return 1;
  // Check for errors.
  if (IOarray_.empty()) {
    mprinterr("Error: No replica trajectories set up.\n");
    return 1;
  }
  if (IOarray_.size() != replica_filenames_.size()) { // SANITY CHECK
    mprinterr("Error: Not all replica files were set up.\n");
    return 1;
  }
  // Update ensemble size
  cInfo.SetEnsembleSize( (int)IOarray_.size() );
  if (debug_ > 0)
    cInfo.PrintCoordInfo( replica_filenames_[0].full(), trajParm->c_str() );

  return 0;
}
示例#5
0
/** Set up each mask/integer loop. */
int ControlBlock_For::SetupBlock(CpptrajState& State, ArgList& argIn) {
  mprintf("    Setting up 'for' loop.\n");
  Vars_.clear();
  Topology* currentTop = 0;
  static const char* TypeStr[] = { "ATOMS ", "RESIDUES ", "MOLECULES ",
                                   "MOL_FIRST_RES ", "MOL_LAST_RES " };
  static const char* OpStr[] = {"+=", "-=", "<", ">"};
  description_.assign("for (");
  int MaxIterations = -1;
  int iarg = 0;
  while (iarg < argIn.Nargs())
  {
    // Advance to next unmarked argument.
    while (iarg < argIn.Nargs() && argIn.Marked(iarg)) iarg++;
    if (iarg == argIn.Nargs()) break;
    // Determine 'for' type
    ForType ftype = UNKNOWN;
    bool isMaskFor = true;
    int argToMark = iarg;
    if      ( argIn[iarg] == "atoms"       ) ftype = ATOMS;
    else if ( argIn[iarg] == "residues"    ) ftype = RESIDUES;
    else if ( argIn[iarg] == "molecules"   ) ftype = MOLECULES;
    else if ( argIn[iarg] == "molfirstres" ) ftype = MOLFIRSTRES;
    else if ( argIn[iarg] == "mollastres"  ) ftype = MOLLASTRES;
    else if ( argIn[iarg].find(";") != std::string::npos ) {
      isMaskFor = false;
      ftype = INTEGER;
    }
    // If type is still unknown, check for list.
    if (ftype == UNKNOWN) {
      if (iarg+1 < argIn.Nargs() && argIn[iarg+1] == "in") {
        ftype = LIST;
        isMaskFor = false;
        argToMark = iarg+1;
      }
    }
    // Exit if type could not be determined.
    if (ftype == UNKNOWN) {
      mprinterr("Error: for loop type not specfied.\n");
      return 1;
    }
    argIn.MarkArg(argToMark);
    Vars_.push_back( LoopVar() );
    LoopVar& MH = Vars_.back();
    int Niterations = -1;
    // Set up for specific type
    if (description_ != "for (") description_.append(", ");
    // -------------------------------------------
    if (isMaskFor)
    {
      // {atoms|residues|molecules} <var> inmask <mask> [TOP KEYWORDS]
      if (argIn[iarg+2] != "inmask") {
        mprinterr("Error: Expected 'inmask', got %s\n", argIn[iarg+2].c_str());
        return 1;
      }
      AtomMask currentMask;
      if (currentMask.SetMaskString( argIn.GetStringKey("inmask") )) return 1;
      MH.varType_ = ftype;
      Topology* top = State.DSL().GetTopByIndex( argIn );
      if (top != 0) currentTop = top;
      if (currentTop == 0) return 1;
      MH.varname_ = argIn.GetStringNext();
      if (MH.varname_.empty()) {
        mprinterr("Error: 'for inmask': missing variable name.\n");
        return 1;
      }
      MH.varname_ = "$" + MH.varname_;
      // Set up mask
      if (currentTop->SetupIntegerMask( currentMask )) return 1;
      currentMask.MaskInfo();
      if (currentMask.None()) return 1;
      // Set up indices
      if (MH.varType_ == ATOMS)
        MH.Idxs_ = currentMask.Selected();
      else if (MH.varType_ == RESIDUES) {
        int curRes = -1;
        for (AtomMask::const_iterator at = currentMask.begin(); at != currentMask.end(); ++at) {
          int res = (*currentTop)[*at].ResNum();
          if (res != curRes) {
            MH.Idxs_.push_back( res );
            curRes = res;
          }
        }
      } else if (MH.varType_ == MOLECULES ||
                 MH.varType_ == MOLFIRSTRES ||
                 MH.varType_ == MOLLASTRES)
      {
        int curMol = -1;
        for (AtomMask::const_iterator at = currentMask.begin(); at != currentMask.end(); ++at) {
          int mol = (*currentTop)[*at].MolNum();
          if (mol != curMol) {
            if (MH.varType_ == MOLECULES)
              MH.Idxs_.push_back( mol );
            else {
              int res;
              if (MH.varType_ == MOLFIRSTRES)
                res = (*currentTop)[ currentTop->Mol( mol ).BeginAtom() ].ResNum();
              else // MOLLASTRES
                res = (*currentTop)[ currentTop->Mol( mol ).EndAtom()-1 ].ResNum();
              MH.Idxs_.push_back( res );
            }
            curMol = mol;
          }
        }
      }
      Niterations = (int)MH.Idxs_.size();
      description_.append(std::string(TypeStr[MH.varType_]) +
                        MH.varname_ + " inmask " + currentMask.MaskExpression());
    // -------------------------------------------
    } else if (ftype == INTEGER) {
      // [<var>=<start>;[<var><OP><end>;]<var><OP>[<value>]]
      MH.varType_ = ftype;
      ArgList varArg( argIn[iarg], ";" );
      if (varArg.Nargs() < 2 || varArg.Nargs() > 3) {
        mprinterr("Error: Malformed 'for' loop variable.\n"
                  "Error: Expected '[<var>=<start>;[<var><OP><end>;]<var><OP>[<value>]]'\n"
                  "Error: Got '%s'\n", argIn[iarg].c_str());
        return 1;
      }
      // First argument: <var>=<start>
      ArgList startArg( varArg[0], "=" );
      if (startArg.Nargs() != 2) {
        mprinterr("Error: Malformed 'start' argument.\n"
                  "Error: Expected <var>=<start>, got '%s'\n", varArg[0].c_str());
        return 1;
      }
      MH.varname_ = startArg[0];
      if (!validInteger(startArg[1])) {
        // TODO allow variables
        mprinterr("Error: Start argument must be an integer.\n");
        return 1;
      } else
        MH.start_ = convertToInteger(startArg[1]);
      // Second argument: <var><OP><end>
      size_t pos0 = MH.varname_.size();
      size_t pos1 = pos0 + 1;
      MH.endOp_ = NO_OP;
      int iargIdx = 1;
      if (varArg.Nargs() == 3) {
        iargIdx = 2;
        if ( varArg[1][pos0] == '<' )
          MH.endOp_ = LESS_THAN;
        else if (varArg[1][pos0] == '>')
          MH.endOp_ = GREATER_THAN;
        if (MH.endOp_ == NO_OP) {
          mprinterr("Error: Unrecognized end op: '%s'\n",
                    varArg[1].substr(pos0, pos1-pos0).c_str());
          return 1;
        }
        std::string endStr = varArg[1].substr(pos1);
        if (!validInteger(endStr)) {
          // TODO allow variables
          mprinterr("Error: End argument must be an integer.\n");
          return 1;
        } else
          MH.end_ = convertToInteger(endStr);
      }
      // Third argument: <var><OP>[<value>]
      pos1 = pos0 + 2;
      MH.incOp_ = NO_OP;
      bool needValue = false;
      if ( varArg[iargIdx][pos0] == '+' ) {
        if (varArg[iargIdx][pos0+1] == '+') {
          MH.incOp_ = INCREMENT;
          MH.inc_ = 1;
        } else if (varArg[iargIdx][pos0+1] == '=') {
          MH.incOp_ = INCREMENT;
          needValue = true;
        }
      } else if ( varArg[iargIdx][pos0] == '-' ) {
        if (varArg[iargIdx][pos0+1] == '-' ) {
          MH.incOp_ = DECREMENT;
          MH.inc_ = 1;
        } else if (varArg[iargIdx][pos0+1] == '=') {
          MH.incOp_ = DECREMENT;
          needValue = true;
        }
      }
      if (MH.incOp_ == NO_OP) {
        mprinterr("Error: Unrecognized increment op: '%s'\n",
                  varArg[iargIdx].substr(pos0, pos1-pos0).c_str());
        return 1;
      }
      if (needValue) {
        std::string incStr = varArg[iargIdx].substr(pos1);
        if (!validInteger(incStr)) {
          mprinterr("Error: increment value is not a valid integer.\n");
          return 1;
        }
        MH.inc_ = convertToInteger(incStr);
        if (MH.inc_ < 1) {
          mprinterr("Error: Extra '-' detected in increment.\n");
          return 1;
        }
      }
      // Description
      MH.varname_ = "$" + MH.varname_;
      std::string sval = integerToString(MH.start_);
      description_.append("(" + MH.varname_ + "=" + sval + "; ");
      std::string eval;
      if (iargIdx == 2) {
        // End argument present
        eval = integerToString(MH.end_);
        description_.append(MH.varname_ + std::string(OpStr[MH.endOp_]) + eval + "; ");
        // Check end > start for increment, start > end for decrement
        int maxval, minval;
        if (MH.incOp_ == INCREMENT) {
          if (MH.start_ >= MH.end_) {
            mprinterr("Error: start must be less than end for increment.\n");
            return 1;
          }
          minval = MH.start_;
          maxval = MH.end_;
        } else {
          if (MH.end_ >= MH.start_) {
            mprinterr("Error: end must be less than start for decrement.\n");
            return 1;
          }
          minval = MH.end_;
          maxval = MH.start_;
        }
        // Figure out number of iterations
        Niterations = (maxval - minval) / MH.inc_;
        if (((maxval-minval) % MH.inc_) > 0) Niterations++;
      }
      description_.append( MH.varname_ + std::string(OpStr[MH.incOp_]) +
                           integerToString(MH.inc_) + ")" );
      // If decrementing just negate value
      if (MH.incOp_ == DECREMENT)
        MH.inc_ = -MH.inc_;
      // DEBUG
      //mprintf("DEBUG: start=%i endOp=%i end=%i incOp=%i val=%i startArg=%s endArg=%s\n",
      //        MH.start_, (int)MH.endOp_, MH.end_, (int)MH.incOp_, MH.inc_,
      //        MH.startArg_.c_str(), MH.endArg_.c_str());
    // -------------------------------------------
    } else if (ftype == LIST) {
      // <var> in <string0>[,<string1>...]
      MH.varType_ = ftype;
      // Variable name
      MH.varname_ = argIn.GetStringNext();
      if (MH.varname_.empty()) {
        mprinterr("Error: 'for in': missing variable name.\n");
        return 1;
      }
      MH.varname_ = "$" + MH.varname_;
      // Comma-separated list of strings
      std::string listArg = argIn.GetStringNext();
      if (listArg.empty()) {
        mprinterr("Error: 'for in': missing comma-separated list of strings.\n");
        return 1;
      }
      ArgList list(listArg, ",");
      if (list.Nargs() < 1) {
        mprinterr("Error: Could not parse '%s' for 'for in'\n", listArg.c_str());
        return 1;
      }
      for (int il = 0; il != list.Nargs(); il++) {
        // Check if file name expansion should occur
        if (list[il].find_first_of("*?") != std::string::npos) {
          File::NameArray files = File::ExpandToFilenames( list[il] );
          for (File::NameArray::const_iterator fn = files.begin(); fn != files.end(); ++fn)
            MH.List_.push_back( fn->Full() );
        } else
          MH.List_.push_back( list[il] );
      }
      Niterations = (int)MH.List_.size();
      // Description
      description_.append( MH.varname_ + " in " + listArg );

    }
    // Check number of values
    if (MaxIterations == -1)
      MaxIterations = Niterations;
    else if (Niterations != -1 && Niterations != MaxIterations) {
      mprintf("Warning: # iterations %i != previous # iterations %i\n",
              Niterations, MaxIterations);
      MaxIterations = std::min(Niterations, MaxIterations);
    }
  }
  mprintf("\tLoop will execute for %i iterations.\n", MaxIterations);
  if (MaxIterations < 1) {
    mprinterr("Error: Loop has less than 1 iteration.\n");
    return 1; 
  }
  description_.append(") do");

  return 0;
}