/** Create Netcdf file specified by filename and set up dimension and * variable IDs. */ int Traj_AmberNetcdf::setupTrajout(std::string const& fname, Topology* trajParm, int NframesToWrite, bool append) { if (!append) { filename_.SetFileName( fname ); // Set up title if (Title().empty()) SetTitle("Cpptraj Generated trajectory"); // Create NetCDF file. if ( NC_create( filename_.Full(), NC_AMBERTRAJ, trajParm->Natom(), HasV(), HasBox(), HasT(), true, 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; 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; }
int Traj_GmxTrX::setupTrajout(FileName const& fname, Topology* trajParm, CoordinateInfo const& cInfoIn, int NframesToWrite, bool append) { if (!append) { SetCoordInfo( cInfoIn ); natoms_ = trajParm->Natom(); natom3_ = natoms_ * 3; // Default to little endian, precision 4, TRR format_ = TRR; isBigEndian_ = false; precision_ = 4; // Set up title if (Title().empty()) SetTitle("Cpptraj generated TRR file."); // Set size defaults, box, velocity etc ir_size_ = 0; e_size_ = 0; if (CoordInfo().HasBox()) box_size_ = precision_ * 9; else box_size_ = 0; vir_size_ = 0; pres_size_ = 0; top_size_ = 0; sym_size_ = 0; x_size_ = natom3_ * precision_; if (CoordInfo().HasVel()) v_size_ = natom3_ * precision_; else v_size_ = 0; f_size_ = 0; step_ = 0; nre_ = 0; dt_ = 0.0; lambda_ = 0.0; // Allocate temp space for coords/velo AllocateCoords(); if (file_.SetupWrite( fname, debug_)) return 1; if (file_.OpenFile()) return 1; } else { int nframes = setupTrajin( fname, trajParm ); if ( format_ == TRJ ) { mprinterr("Error: Only writes to TRR files supported.\n"); return 1; } if ( nframes == TRAJIN_ERR ) return 1; mprintf("\tAppending to TRR file starting at frame %i\n", nframes); // Re-open for appending if (file_.SetupAppend( fname, debug_ )) return 1; if (file_.OpenFile()) return 1; } return 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; }
// Traj_NcEnsemble::setupTrajout() int Traj_NcEnsemble::setupTrajout(FileName const& fname, Topology* trajParm, CoordinateInfo const& cInfoIn, int NframesToWrite, bool append) { int err = 0; # ifdef MPI if (NoPnetcdf()) return 1; # endif readAccess_ = false; if (!append) { CoordinateInfo cInfo = cInfoIn; // TODO: File output modifications SetCoordInfo( cInfo ); # ifdef MPI ensembleStart_ = Parallel::World().Rank(); ensembleEnd_ = Parallel::World().Rank() + 1; # else ensembleStart_ = 0; ensembleEnd_ = cInfo.EnsembleSize();; # endif filename_ = fname; // Set up title if (Title().empty()) SetTitle("Cpptraj Generated trajectory"); # ifdef MPI if (Parallel::World().Master()) { // Only master creates file. # endif // Create NetCDF file. err = NC_create(filename_.Full(), NC_AMBERENSEMBLE, trajParm->Natom(), CoordInfo(), Title(), debug_); // Close Netcdf file. It will be reopened write. FIXME should NC_create leave it closed? NC_close(); # ifdef MPI } Parallel::World().MasterBcast(&err, 1, MPI_INT); # endif if (err != 0) return 1; # ifdef MPI // Synchronize netcdf info on non-master threads Sync(Parallel::World()); // DEBUG: Print info for all ranks DebugVIDs(); # endif // 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; if (debug_ > 0) mprintf("\tNetCDF: Appending %s starting at frame %i\n", filename_.base(), Ncframe()); } // Open file # ifdef HAS_PNETCDF err = ncmpi_open(MPI_COMM_WORLD, filename_.full(), NC_WRITE, MPI_INFO_NULL, &ncid_); // TODO: Graceful error handling # else err = NC_openWrite( filename_.Full() ); # endif if ( err != 0 ) { mprinterr("Error: Opening Netcdf file %s for Write.\n", filename_.base()); return 1; } return 0; }