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