Example #1
0
// Traj_NcEnsemble::setupTrajin()
int Traj_NcEnsemble::setupTrajin(FileName const& fname, Topology* trajParm)
{
# ifdef MPI
  if (NoPnetcdf()) return TRAJIN_ERR;
# endif
  readAccess_ = true;
  filename_ = fname;
  // NOTE: Setup opens and closes single thread for now
  // Setup for Amber NetCDF ensemble
  if ( NC_setupRead(filename_.Full(), NC_AMBERENSEMBLE, trajParm->Natom(),
                    useVelAsCoords_, useFrcAsCoords_, debug_) )
    return TRAJIN_ERR;
  // Get title
  SetTitle( GetNcTitle() );
  // Set coordinate info 
  SetCoordInfo( NC_coordInfo() ); 
  // Set up local ensemble parameters
# ifdef MPI
  ensembleStart_ = Parallel::World().Rank();
  ensembleEnd_ = Parallel::World().Rank() + 1;
# else
  ensembleStart_ = 0;
  ensembleEnd_ = ensembleSize_;
# endif
  // DEBUG: Print info for all ranks
  DebugVIDs();
  // Allocate float array
  if (Coord_ != 0) delete[] Coord_;
  Coord_ = new float[ Ncatom3() ];
  return Ncframe();
}
Example #2
0
/* * Open the netcdf file, read all dimension and variable IDs, close.
  * Return the number of frames in the file. 
  */
int Traj_AmberNetcdf::setupTrajin(FileName const& fname, Topology* trajParm)
{
  filename_ = fname;
  if (openTrajin()) return TRAJIN_ERR;
  readAccess_ = true;
  // Sanity check - Make sure this is a Netcdf trajectory
  if ( GetNetcdfConventions() != NC_AMBERTRAJ ) {
    mprinterr("Error: Netcdf file %s conventions do not include \"AMBER\"\n",filename_.base());
    return TRAJIN_ERR;
  }
  // This will warn if conventions are not 1.0 
  CheckConventionsVersion();
  // Get title
  SetTitle( GetNcTitle() );
  // Get Frame info
  if ( SetupFrameDim()!=0 ) return TRAJIN_ERR;
  if ( Ncframe() < 1 ) {
    mprinterr("Error: Netcdf file is empty.\n");
    return TRAJIN_ERR;
  }
  // Setup Coordinates/Velocities
  if ( SetupCoordsVelo( useVelAsCoords_, useFrcAsCoords_ )!=0 ) return TRAJIN_ERR;
  // Check that specified number of atoms matches expected number.
  if (Ncatom() != trajParm->Natom()) {
    mprinterr("Error: Number of atoms in NetCDF file %s (%i) does not\n"
              "Error:   match number in associated parmtop (%i)!\n", 
              filename_.base(), Ncatom(), trajParm->Natom());
    return TRAJIN_ERR;
  }
  // Setup Time - FIXME: Allowed to fail silently
  SetupTime();
  // Box info
  Box nc_box;
  if (SetupBox(nc_box, NC_AMBERTRAJ) == 1) // 1 indicates an error
    return TRAJIN_ERR;
  // Replica Temperatures - FIXME: Allowed to fail silently
  SetupTemperature();
  // Replica Dimensions
  ReplicaDimArray remdDim;
  if ( SetupMultiD(remdDim) == -1 ) return TRAJIN_ERR;
  SetCoordInfo( CoordinateInfo(remdDim, nc_box, HasVelocities(),
                               HasTemperatures(), HasTimes(), HasForces()) ); 
  // NOTE: TO BE ADDED
  // labelDID;
  //int cell_spatialDID, cell_angularDID;
  //int spatialVID, cell_spatialVID, cell_angularVID;
  // Amber Netcdf coords are float. Allocate a float array for converting
  // float to/from double.
  if (Coord_ != 0) delete[] Coord_;
  Coord_ = new float[ Ncatom3() ];
  if (debug_>1) NetcdfDebug();
  closeTraj();
  return Ncframe();
}
Example #3
0
// Traj_NcEnsemble::setupTrajin()
int Traj_NcEnsemble::setupTrajin(FileName const& fname, Topology* trajParm)
{
# ifdef MPI
  if (NoPnetcdf()) return TRAJIN_ERR;
# endif
  readAccess_ = true;
  filename_ = fname;
  //if (openTrajin()) return TRAJIN_ERR;
  // Open single thread for now
  if (NC_openRead( filename_.Full() )) return TRAJIN_ERR;
  // Sanity check - Make sure this is a Netcdf ensemble trajectory
  if ( GetNetcdfConventions() != NC_AMBERENSEMBLE ) {
    mprinterr("Error: Netcdf file %s conventions do not include \"AMBERENSEMBLE\"\n",
              filename_.base());
    return TRAJIN_ERR;
  }
  // This will warn if conventions are not 1.0 
  CheckConventionsVersion();
  // Get title
  SetTitle( GetNcTitle() );
  // Get Frame info
  if ( SetupFrameDim()!=0 ) return TRAJIN_ERR;
  if ( Ncframe() < 1 ) {
    mprinterr("Error: Netcdf file is empty.\n");
    return TRAJIN_ERR;
  }
  // Get ensemble info
  int ensembleSize = SetupEnsembleDim();
  if (ensembleSize < 1) {
    mprinterr("Error: Could not get ensemble dimension info.\n");
    return TRAJIN_ERR;
  }
  // Setup Coordinates/Velocities
  if ( SetupCoordsVelo( useVelAsCoords_, useFrcAsCoords_ )!=0 ) return TRAJIN_ERR;
  // Check that specified number of atoms matches expected number.
  if (Ncatom() != trajParm->Natom()) {
    mprinterr("Error: Number of atoms in NetCDF file %s (%i) does not\n"
              "Error:   match number in associated parmtop (%i)!\n",
              filename_.base(), Ncatom(), trajParm->Natom());
    return TRAJIN_ERR;
  }
  // Setup Time - FIXME: Allowed to fail silently
  SetupTime();
  // Box info
  Box nc_box; 
  if (SetupBox(nc_box, NC_AMBERENSEMBLE) == 1) // 1 indicates an error
    return TRAJIN_ERR;
  // Replica Temperatures - FIXME: Allowed to fail silently
  SetupTemperature();
  // Replica Dimensions
  ReplicaDimArray remdDim;
  if ( SetupMultiD(remdDim) == -1 ) return TRAJIN_ERR;
  // Set traj info: FIXME - no forces yet
  SetCoordInfo( CoordinateInfo(ensembleSize, remdDim, nc_box, HasVelocities(),
                               HasTemperatures(), HasTimes(), false) ); 
  if (debug_>1) NetcdfDebug();
  //closeTraj();
  // Close single thread for now
  NC_close();
  // Set up local ensemble parameters
# ifdef MPI
  ensembleStart_ = Parallel::World().Rank();
  ensembleEnd_ = Parallel::World().Rank() + 1;
# else
  ensembleStart_ = 0;
  ensembleEnd_ = ensembleSize;
# endif
  // DEBUG: Print info for all ranks
  WriteVIDs();
  // Allocate float array
  if (Coord_ != 0) delete[] Coord_;
  Coord_ = new float[ Ncatom3() ];
  return Ncframe();
}