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;
}
// Action_CreateReservoir::Setup()
Action::RetType Action_CreateReservoir::Setup(ActionSetup& setup) {
  // Check that input parm matches current parm
  if (original_trajparm_->Pindex() != setup.Top().Pindex()) {
    mprintf("Info: createreservoir was set up for topology %s\n", original_trajparm_->c_str());
    mprintf("Info: skipping topology %s\n", setup.Top().c_str());
    return Action::SKIP;
  }
  if (!trajIsOpen_) {
    mprintf("\tCreating reservoir file %s\n", filename_.full());
    CoordinateInfo cinfo = setup.CoordInfo();
    if (!useVelocity_) cinfo.SetVelocity(false);
    if (!useForce_)    cinfo.SetForce(false);
    if (reservoir_.InitReservoir(filename_, title_, cinfo, setup.Top().Natom(),
                                 (bin_ != 0), reservoirT_, iseed_))
    {
      mprinterr("Error: Could not set up NetCDF reservoir.\n");
      return Action::ERR;
    }
    trajIsOpen_ = true;
    nframes_ = 0;
  }
  return Action::OK;
}