/* * 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();
}
// 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();
}