示例#1
0
/** Allocate a character buffer based on number of coords and whether 
  * velocities/box info is present.
  */
int Traj_AmberRestart::setupTrajout(FileName const& fname, Topology* trajParm,
                                    CoordinateInfo const& cInfoIn, 
                                    int NframesToWrite, bool append)
{
  if (append) {
    mprinterr("Error: Append not supported for Amber Restart.\n");
    return 1;
  }
  CoordinateInfo cInfo = cInfoIn;
  if (!cInfo.HasTemp() && outputTemp_) cInfo.SetTemperature(true);
  // If temperature requested write time as well or format will break.
  if (cInfo.HasTemp()) {
    outputTime_ = true;
    if (!cInfo.HasTime() && time0_ < 0.0) time0_ = 1.0;
  }
  if (cInfo.HasVel() && !outputVel_) cInfo.SetVelocity(false);
  if (outputTime_) {
    if (!cInfo.HasTime() && time0_ >= 0) cInfo.SetTime(true);
  } else
    cInfo.SetTime(false);
  SetCoordInfo( cInfo );
  if (file_.SetupWrite( fname, debug_ )) return 1;
  readAccess_ = false;
  // Set trajectory info
  natom3_ = trajParm->Natom() * 3;
  // Calculate the length of coordinate frame in bytes
  file_.SetupFrameBuffer( natom3_, 12, 6 ); 
  // Dont know ahead of time if velocities will be used, allocate space
  // just in case. Velocity will not be written if V input is null.
  file_.ResizeBuffer( natom3_ );
  // If box coords are present, allocate extra space for them
  if (CoordInfo().HasBox()) {
    numBoxCoords_ = 6;
    file_.ResizeBuffer( numBoxCoords_ );
  }
  // If number of frames to write == 1 set singleWrite so we dont append
  // frame # to filename.
  if (NframesToWrite==1) singleWrite_ = true;
  // Set up title
  std::string outTitle = Title();
  if (outTitle.empty()) {
    outTitle.assign("Cpptraj Generated Restart");
    outTitle.resize(80, ' ');
  } else {
    if ( outTitle.size() > 80) {
      mprintf("Warning: Amber restart title for %s too long: truncating.\n[%s]\n",
              file_.Filename().base(), outTitle.c_str());
      outTitle.resize(80);
    }
  }
  SetTitle( outTitle );

  return 0;
}
示例#2
0
/** Create Netcdf file specified by filename and set up dimension and
  * variable IDs. 
  */
int Traj_AmberNetcdf::setupTrajout(FileName const& fname, Topology* trajParm,
                                   CoordinateInfo const& cInfoIn, 
                                   int NframesToWrite, bool append)
{
  readAccess_ = false;
  if (!append) {
    CoordinateInfo cInfo = cInfoIn;
    // Deal with output options
    // For backwards compatibility always write temperature if remdtraj is true.
    if (outputTemp_ && !cInfo.HasTemp()) cInfo.SetTemperature(true);
    // Explicitly write velocity - initial frames may not have velocity info.
    if (outputVel_ && !cInfo.HasVel()) cInfo.SetVelocity(true);
    if (outputFrc_ && !cInfo.HasForce()) cInfo.SetForce(true);
    SetCoordInfo( cInfo );
    filename_ = fname;
    // Set up title
    if (Title().empty())
      SetTitle("Cpptraj Generated trajectory");
    // Create NetCDF file.
    if (NC_create( filename_.Full(), NC_AMBERTRAJ, trajParm->Natom(), CoordInfo(), Title() ))
      return 1;
    if (debug_>1) NetcdfDebug();
    // Close Netcdf file. It will be reopened write.
    NC_close();
    // Allocate memory
    if (Coord_!=0) delete[] Coord_;
    Coord_ = new float[ Ncatom3() ];
  } else { // NOTE: File existence is checked for in Trajout
    // Call setupTrajin to set input parameters. This will also allocate
    // memory for coords.
    if (setupTrajin(fname, trajParm) == TRAJIN_ERR) return 1;
    // Check output options.
    if (outputTemp_ && !CoordInfo().HasTemp())
      mprintf("Warning: Cannot append temperature data to NetCDF file '%s'; no temperature dimension.\n",
              filename_.base());
    if (outputVel_ && !CoordInfo().HasVel())
      mprintf("Warning: Cannot append velocity data to NetCDF file '%s'; no velocity dimension.\n",
              filename_.base());
    if (outputFrc_ && !CoordInfo().HasForce())
      mprintf("Warning: Cannot append force data to NetCDF file '%s'; no force dimension.\n",
              filename_.base());
    if (debug_ > 0)
      mprintf("\tNetCDF: Appending %s starting at frame %i\n", filename_.base(), Ncframe()); 
  }
  // Open file
  if ( NC_openWrite( filename_.Full() ) != 0 ) {
    mprinterr("Error: Opening Netcdf file %s for Write.\n", filename_.base());
    return 1;
  }
  return 0;
}
示例#3
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;
}