/** 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;
}
// Traj_NcEnsemble::closeTraj()
void Traj_NcEnsemble::closeTraj() {
# ifdef HAS_PNETCDF
if (ncid_ == -1) return;
//ncmpi_end_indep_data( ncid_ ); // Disable independent data mode.
ncmpi_close( ncid_ );
ncid_ = -1;
# else
NC_close();
# endif
}
/** 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;
}
// 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;
}
/** First master performs all necessary setup, then sends info to all children.
*/
int Traj_AmberNetcdf::parallelSetupTrajout(FileName const& fname, Topology* trajParm,
CoordinateInfo const& cInfoIn,
int NframesToWrite, bool append,
Parallel::Comm const& commIn)
{
int err = 0;
if (commIn.Master()) {
err = setupTrajout(fname, trajParm, cInfoIn, NframesToWrite, append);
// NOTE: setupTrajout leaves file open. Should this change?
NC_close();
}
commIn.MasterBcast(&err, 1, MPI_INT);
if (err != 0) return 1;
// Synchronize netcdf info on non-master threads.
Sync(commIn);
if (!commIn.Master()) {
// Non masters need filename and allocate Coord
filename_ = fname;
if (Coord_ != 0) delete[] Coord_;
Coord_ = new float[ Ncatom3() ];
}
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;
}
/** Close netcdf file. Set ncid to -1 since it can change between open
* and close calls.
*/
void Traj_AmberNetcdf::closeTraj() {
NC_close();
}
// 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();
}
// Traj_AmberRestartNC::closeTraj()
void Traj_AmberRestartNC::closeTraj() {
NC_close();
}