/** Determine if Netcdf file contains time; set up timeVID and check units. */ int NetcdfFile::SetupTime() { if ( nc_inq_varid(ncid_, NCTIME, &timeVID_) == NC_NOERR ) { std::string attrText = GetAttrText(timeVID_, "units"); if (attrText!="picosecond") mprintf("Warning: NetCDF file has time units of %s - expected picosecond.\n", attrText.c_str()); // Check for time values which have NOT been filled, which was possible // with netcdf trajectories created by older versions of ptraj/cpptraj. if (ncframe_ > 0 && GetNetcdfConventions() == NC_AMBERTRAJ) { float time; start_[0] = 0; count_[0] = 1; if (checkNCerr(nc_get_vara_float(ncid_, timeVID_, start_, count_, &time))) { mprinterr("Error: Getting time value for NetCDF file.\n"); return -1; } if (time == NC_FILL_FLOAT) { mprintf("Warning: NetCDF file time variable defined but empty. Disabling.\n"); timeVID_ = -1; } } return 0; } timeVID_=-1; return 1; }
/* * Open the netcdf file, read all dimension and variable IDs, close. * Return the number of frames in the file. */ int Traj_AmberNetcdf::setupTrajin(std::string const& fname, Topology* trajParm) { filename_.SetFileNameWithExpansion( fname ); if (openTrajin()) return TRAJIN_ERR; // 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; } // Get global attributes std::string attrText = GetAttrText("ConventionVersion"); if ( attrText != "1.0") mprintf("Warning: Netcdf file %s has ConventionVersion that is not 1.0 (%s)\n", filename_.base(), attrText.c_str()); // Get title SetTitle( GetAttrText("title") ); // Get Frame info if ( SetupFrame()!=0 ) return TRAJIN_ERR; // Setup Coordinates/Velocities if ( SetupCoordsVelo()!=0 ) return TRAJIN_ERR; SetVelocity( HasVelocities() ); // 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", filename_.base(),Ncatom()); mprinterr(" match number in associated parmtop (%i)!\n",trajParm->Natom()); return TRAJIN_ERR; } // Setup Time if ( SetupTime()!=0 ) return TRAJIN_ERR; // Box info double boxcrd[6]; if (SetupBox(boxcrd, NC_AMBERTRAJ) == 1) // 1 indicates an error return TRAJIN_ERR; SetBox( boxcrd ); // Replica Temperatures - Allowed to fail silently if (SetupTemperature() == 0) SetTemperature( true ); // Replica Dimensions if ( SetupMultiD() == -1 ) return TRAJIN_ERR; // 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 (Veloc_ != 0) delete[] Veloc_; if (velocityVID_ != -1) Veloc_ = new float[ Ncatom3() ]; else Veloc_ = 0; if (debug_>1) NetcdfDebug(); closeTraj(); // NetCDF files are always seekable SetSeekable( true ); return Ncframe(); }
/* * 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; } // Get global attributes std::string attrText = GetAttrText("ConventionVersion"); if ( attrText != "1.0") mprintf("Warning: Netcdf file %s has ConventionVersion that is not 1.0 (%s)\n", filename_.base(), attrText.c_str()); // Get title SetTitle( GetAttrText("title") ); // 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_ )!=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 double boxcrd[6]; if (SetupBox(boxcrd, 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; // Set traj info: FIXME - no forces yet SetCoordInfo( CoordinateInfo(remdDim, Box(boxcrd), HasVelocities(), HasTemperatures(), HasTimes(), false) ); // 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(); }
// NetcdfFile::GetNetcdfConventions() NetcdfFile::NCTYPE NetcdfFile::GetNetcdfConventions(const char* fname) { NCTYPE nctype = NC_UNKNOWN; #ifdef BINTRAJ // NOTE: Do not use checkNCerr so this fails silently. Allows routine to // be used in file autodetection. if ( nc_open( fname, NC_NOWRITE, &ncid_ ) != NC_NOERR ) return NC_UNKNOWN; nctype = GetNetcdfConventions(); NC_close(); #else mprintf("Error: Compiled without NETCDF support. Recompile with -DBINTRAJ\n"); #endif return nctype; }
/** Set up netcdf restart file for reading, get all variable and dimension IDs. * Also check number of atoms against associated parmtop. */ int Traj_AmberRestartNC::setupTrajin(std::string const& fname, Topology* trajParm) { filename_.SetFileNameWithExpansion( fname ); if (openTrajin()) return TRAJIN_ERR; // Sanity check - Make sure this is a Netcdf restart if ( GetNetcdfConventions() != NC_AMBERRESTART ) { mprinterr("Error: Netcdf restart file %s conventions do not include \"AMBERRESTART\"\n", filename_.base()); return TRAJIN_ERR; } // Get global attributes std::string attrText = GetAttrText("ConventionVersion"); if (attrText!="1.0") mprintf("Warning: Netcdf restart file %s has ConventionVersion that is not 1.0 (%s)\n", filename_.base(), attrText.c_str()); // Get title SetTitle( GetAttrText("title") ); // Setup Coordinates/Velocities if ( SetupCoordsVelo()!=0 ) return TRAJIN_ERR; SetVelocity( HasVelocities() ); // Check that specified number of atoms matches expected number. if (Ncatom() != trajParm->Natom()) { mprinterr("Error: Number of atoms in NetCDF restart file %s (%i) does not\n", filename_.base(), Ncatom()); mprinterr(" match number in associated parmtop (%i)!\n",trajParm->Natom()); return TRAJIN_ERR; } // Setup Time if ( SetupTime()!=0 ) return TRAJIN_ERR; // Box info double boxcrd[6]; if (SetupBox(boxcrd, NC_AMBERRESTART) == 1) // 1 indicates an error return TRAJIN_ERR; SetBox( boxcrd ); // Replica Temperatures - allowed to fail silently if (SetupTemperature() == 0) SetTemperature( true ); if ( SetupMultiD() == -1 ) return TRAJIN_ERR; // NOTE: TO BE ADDED // labelDID; //int cell_spatialDID, cell_angularDID; //int spatialVID, cell_spatialVID, cell_angularVID; closeTraj(); // Only 1 frame for NC restarts return 1; }
// Traj_NcEnsemble::ID_TrajFormat() bool Traj_NcEnsemble::ID_TrajFormat(CpptrajFile& fileIn) { return ( GetNetcdfConventions( fileIn.Filename().full() ) == NC_AMBERENSEMBLE ); }
bool Traj_AmberNetcdf::ID_TrajFormat(CpptrajFile& fileIn) { if ( GetNetcdfConventions( fileIn.Filename().full() ) == NC_AMBERTRAJ ) return true; return false; }
// 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(); }
bool Traj_AmberRestartNC::ID_TrajFormat(CpptrajFile& fileIn) { if ( GetNetcdfConventions( fileIn.Filename().full() ) == NC_AMBERRESTART ) return true; return false; }