/* * 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();
}
/** Prepare trajectory for reading. Determine number of frames. */
int Traj_GmxTrX::setupTrajin(FileName const& fname, Topology* trajParm)
{
int nframes = 0;
if (file_.SetupRead( fname, debug_ )) return TRAJIN_ERR;
// Open and read in header
if ( file_.OpenFile() ) return TRAJIN_ERR;
ReadTrxHeader();
if (debug_ > 0) GmxInfo(); // DEBUG
// Warn if # atoms in parm does not match
if (trajParm->Natom() != natoms_) {
mprinterr("Error: # atoms in TRX file (%i) does not match # atoms in parm %s (%i)\n",
natoms_, trajParm->c_str(), trajParm->Natom());
return TRAJIN_ERR;
}
// If float precision, create temp array. Temp array not needed for double reads.
if (precision_ == sizeof(float)) {
if (farray_ != 0) delete[] farray_;
farray_ = new float[ natom3_ ];
}
// Attempt to determine # of frames in traj
headerBytes_ = (size_t)file_.Tell();
frameSize_ = headerBytes_ + (size_t)box_size_ + (size_t)vir_size_ + (size_t)pres_size_ +
(size_t)x_size_ + (size_t)v_size_ + (size_t)f_size_;
//(size_t)ir_size_ + (size_t)e_size_ + (size_t)top_size_ +
//(size_t)sym_size_;
size_t file_size = (size_t)file_.UncompressedSize();
if (file_size > 0) {
nframes = (int)(file_size / frameSize_);
if ( (file_size % frameSize_) != 0 ) {
mprintf("Warning: %s: Number of frames in TRX file could not be accurately determined.\n"
"Warning: Will attempt to read %i frames.\n", file_.Filename().base(), nframes);
}
} else {
mprintf("Warning: Uncompressed size could not be determined. This is normal for\n");
mprintf("Warning: bzip2 files. Cannot check # of frames. Frames will be read until EOF.\n");
nframes = TRAJIN_UNK;
}
// Load box info so that it can be checked.
double box[6];
box[0]=0.0;
box[1]=0.0;
box[2]=0.0;
box[3]=0.0;
box[4]=0.0;
box[5]=0.0;
if ( box_size_ > 0 ) {
if ( ReadBox( box ) ) return TRAJIN_ERR;
}
// Set traj info - No time or temperature
SetCoordInfo( CoordinateInfo(Box(box), (v_size_ > 0), false, false) );
closeTraj();
return nframes;
}
/** 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;
}
void Traj_GmxTrX::parallelCloseTraj() {
closeTraj();
}
// 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;
}
void Traj_AmberCoord::parallelCloseTraj() { closeTraj(); }
