/* * 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();
}
/** 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;
}
/** 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;
}
// NetcdfFile::GetNetcdfConventions()
NetcdfFile::NCTYPE NetcdfFile::GetNetcdfConventions() {
NCTYPE nctype = NC_UNKNOWN;
std::string attrText = GetAttrText(NC_GLOBAL, "Conventions");
if (attrText == "AMBERENSEMBLE")
nctype = NC_AMBERENSEMBLE;
else if (attrText == "AMBER")
nctype = NC_AMBERTRAJ;
else if (attrText == "AMBERRESTART")
nctype = NC_AMBERRESTART;
else if (attrText.empty())
mprinterr("Error: Could not get conventions from Netcdf file.\n");
else {
mprinterr("Error: Netcdf file: Unrecognized conventions \"%s\".\n",
attrText.c_str());
mprinterr("Error: Expected \"AMBER\", \"AMBERRESTART\", or \"AMBERENSEMBLE\".\n");
}
return nctype;
}
/** Setup ncatom, ncatom3, atomDID, coordVID, spatialDID, spatialVID,
* velocityVID, frcVID. Check units and spatial dimensions.
*/
int NetcdfFile::SetupCoordsVelo(bool useVelAsCoords) {
int spatial;
atomDID_ = GetDimInfo(NCATOM, &ncatom_);
if (atomDID_==-1) return 1;
ncatom3_ = ncatom_ * 3;
// Get coord info
coordVID_ = -1;
if ( nc_inq_varid(ncid_, NCCOORDS, &coordVID_) == NC_NOERR ) {
if (ncdebug_ > 0) mprintf("\tNetcdf file has coordinates.\n");
std::string attrText = GetAttrText(coordVID_, "units");
if (attrText!="angstrom")
mprintf("Warning: Netcdf file has length units of %s - expected angstrom.\n",
attrText.c_str());
}
// Get spatial info
spatialDID_ = GetDimInfo(NCSPATIAL, &spatial);
if (spatialDID_==-1) return 1;
if (spatial!=3) {
mprinterr("Error: Expected 3 spatial dimensions, got %i\n",spatial);
return 1;
}
if ( checkNCerr(nc_inq_varid(ncid_, NCSPATIAL, &spatialVID_)) ) {
mprintf("Warning: Could not get spatial VID. File may not be Amber NetCDF compliant.\n");
mprintf("Warning: Assuming spatial variables are 'x', 'y', 'z'\n");
} else {
start_[0] = 0;
count_[0] = 3;
char xyz[3];
if (checkNCerr(nc_get_vara_text(ncid_, spatialVID_, start_, count_, xyz))) {
mprinterr("Error: Getting spatial variables.\n");
return 1;
}
if (xyz[0] != 'x' || xyz[1] != 'y' || xyz[2] != 'z') {
mprinterr("Error: NetCDF spatial variables are '%c', '%c', '%c', not 'x', 'y', 'z'\n",
xyz[0], xyz[1], xyz[2]);
return 1;
}
}
// Get velocity info
velocityVID_ = -1;
if ( nc_inq_varid(ncid_, NCVELO, &velocityVID_) == NC_NOERR ) {
if (ncdebug_>0) mprintf("\tNetcdf file has velocities.\n");
}
// Return a error if no coords and no velocity
if ( coordVID_ == -1 && velocityVID_ == -1 ) {
mprinterr("Error: NetCDF file has no coords and no velocities.\n");
return 1;
}
// If using velocities as coordinates, swap them now.
if (useVelAsCoords) {
if (velocityVID_ == -1) {
mprinterr("Error: Cannot use velocities as coordinates; no velocities present.\n");
return 1;
}
mprintf("\tUsing velocities as coordinates.\n");
coordVID_ = velocityVID_;
velocityVID_ = -1;
}
// Get force info
frcVID_ = -1;
if ( nc_inq_varid(ncid_, NCFRC, &frcVID_) == NC_NOERR ) {
if (ncdebug_>0) mprintf("\tNetcdf file has forces.\n");
}
// Get overall replica and coordinate indices
crdidxVID_ = -1;
if ( nc_inq_varid(ncid_, NCREMD_REPIDX, &repidxVID_) == NC_NOERR ) {
//if (ncdebug_ > 0)
mprintf(" Netcdf file has overall replica indices.\n");
if ( checkNCerr(nc_inq_varid(ncid_, NCREMD_CRDIDX, &crdidxVID_)) ) {
mprinterr("Error: Getting overall coordinate index variable ID.\n");
return 1;
}
} else
repidxVID_ = -1;
return 0;
}
/** Get information about a netcdf global attribute. */
std::string NetcdfFile::GetAttrText(const char *attribute) {
return GetAttrText(NC_GLOBAL, attribute);
}
// 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;
}
// 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;
}
// 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_ )!=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_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, Box(boxcrd), 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();
}
