/** 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;
}
/** 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;
}
/* This function creates a file for use with parallel I/O. */
int
nc_create_par(const char *path, int cmode, MPI_Comm comm,
MPI_Info info, int *ncidp)
{
#ifndef USE_PARALLEL
return NC_ENOPAR;
#else
NC_MPI_INFO data;
/* One of these two parallel IO modes must be chosen by the user,
* or else pnetcdf must be in use. */
if (!(cmode & NC_MPIIO || cmode & NC_MPIPOSIX) &&
!(cmode & NC_PNETCDF))
return NC_EINVAL;
data.comm = comm;
data.info = info;
return NC_create(path, cmode, 0, 0, NULL, 1, &data, ncidp);
#endif /* USE_PARALLEL */
}
// 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;
}
// Traj_AmberRestartNC::writeFrame()
int Traj_AmberRestartNC::writeFrame(int set, double *X, double *V,double *box, double T) {
// Set up file for this set
bool V_present = (HasV() && V != 0);
std::string fname;
// Create filename for this set
// If just writing 1 frame dont modify output filename
if (singleWrite_)
fname = filename_.Full();
else
fname = NumberFilename(filename_.Full(), set+1);
if ( NC_create( fname.c_str(), NC_AMBERRESTART, Ncatom(), V_present,
HasBox(), HasT(), (time0_ >= 0), Title() ) )
return 1;
// write coords
start_[0] = 0;
start_[1] = 0;
count_[0] = Ncatom();
count_[1] = 3;
if (checkNCerr(nc_put_vara_double(ncid_,coordVID_,start_,count_,X)) ) {
mprinterr("Error: Netcdf restart Writing coordinates %i\n",set);
return 1;
}
// write velocity
if (V_present) {
mprintf("DEBUG: Writing V, VID=%i\n",velocityVID_);
if (checkNCerr(nc_put_vara_double(ncid_,velocityVID_,start_,count_,V)) ) {
mprinterr("Error: Netcdf restart writing velocity %i\n",set);
return 1;
}
}
// write box
if (cellLengthVID_ != -1) {
count_[0] = 3;
count_[1] = 0;
if (checkNCerr(nc_put_vara_double(ncid_,cellLengthVID_,start_,count_,box)) ) {
mprinterr("Error: Writing cell lengths.\n");
return 1;
}
if (checkNCerr(nc_put_vara_double(ncid_,cellAngleVID_,start_,count_, box+3)) ) {
mprinterr("Error: Writing cell angles.\n");
return 1;
}
}
// write time
if (timeVID_ != -1) {
restartTime_ = (time0_ + (double)set) * dt_;
if (checkNCerr(nc_put_var_double(ncid_,timeVID_,&restartTime_)) ) {
mprinterr("Error: Writing restart time.\n");
return 1;
}
}
// write temperature
if (TempVID_ != -1) {
if (checkNCerr(nc_put_var_double(ncid_,TempVID_,&T)) ) {
mprinterr("Error: Writing restart temperature.\n");
return 1;
}
}
//nc_sync(ncid_); // Necessary? File about to close anyway...
// Close file for this set
closeTraj();
return 0;
}
