// Traj_NcEnsemble::setupTrajin()
int Traj_NcEnsemble::setupTrajin(FileName const& fname, Topology* trajParm)
{
# ifdef MPI
if (NoPnetcdf()) return TRAJIN_ERR;
# endif
readAccess_ = true;
filename_ = fname;
// NOTE: Setup opens and closes single thread for now
// Setup for Amber NetCDF ensemble
if ( NC_setupRead(filename_.Full(), NC_AMBERENSEMBLE, trajParm->Natom(),
useVelAsCoords_, useFrcAsCoords_, debug_) )
return TRAJIN_ERR;
// Get title
SetTitle( GetNcTitle() );
// Set coordinate info
SetCoordInfo( NC_coordInfo() );
// 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
DebugVIDs();
// Allocate float array
if (Coord_ != 0) delete[] Coord_;
Coord_ = new float[ Ncatom3() ];
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 trajectory for write. Calculate the length of each cooordinate
* frame. Set the title and titleSize. Calculate the full output file
* size, necessary only for seeking when MPI writing. Allocate memory for
* the frame buffer.
*/
int Traj_AmberCoord::setupTrajout(FileName const& fname, Topology* trajParm,
CoordinateInfo const& cInfoIn,
int NframesToWrite, bool append)
{
// Set Temperature Write
// FIXME: Check for temperatures in input frames and when appending.
SetCoordInfo( cInfoIn );
if (outputTemp_) {
headerSize_ = REMD_HEADER_SIZE;
if (!CoordInfo().HasTemp())
mprintf("Warning: No temperature information in input frames.\n");
}
if (!append) {
// Write the title if not appending
if (file_.SetupWrite( fname, debug_ )) return 1;
std::string title = Title();
if (title.empty()) {
// Set up default title
title.assign("Cpptraj Generated trajectory");
title.resize(80,' ');
SetTitle( title );
} else {
// Check title length
if (title.size() > 80) {
mprintf("Warning: Amber traj title for %s too long: truncating.\n[%s]\n",
file_.Filename().base(), title.c_str());
title.resize(80);
}
}
if (file_.OpenFile()) return 1;
file_.Printf("%-s\n", title.c_str());
} else {
// Just set up for append
if (file_.SetupAppend( fname, debug_ )) return 1;
if (file_.OpenFile()) return 1;
}
// Allocate buffer. Will not buffer REMD header or need to seek.
// NOTE: This is done here since SetupFrameBuffer allocates based
// on write mode, which is not known until now.
natom3_ = trajParm->Natom() * 3;
file_.SetupFrameBuffer( natom3_, 8, 10 );
// If box coords are present, allocate extra space for them
switch (CoordInfo().TrajBox().Type()) {
case Box::NOBOX : numBoxCoords_ = 0; break;
case Box::ORTHO :
case Box::TRUNCOCT: numBoxCoords_ = 3; break;
default : numBoxCoords_ = 6;
}
file_.ResizeBuffer( numBoxCoords_ );
if (debug_>0)
rprintf("(%s): Each frame has %lu bytes.\n", file_.Filename().base(), file_.FrameSize());
return 0;
}
int Traj_GmxTrX::setupTrajout(FileName const& fname, Topology* trajParm,
CoordinateInfo const& cInfoIn,
int NframesToWrite, bool append)
{
if (!append) {
SetCoordInfo( cInfoIn );
natoms_ = trajParm->Natom();
natom3_ = natoms_ * 3;
// Default to little endian, precision 4, TRR
format_ = TRR;
isBigEndian_ = false;
precision_ = 4;
// Set up title
if (Title().empty())
SetTitle("Cpptraj generated TRR file.");
// Set size defaults, box, velocity etc
ir_size_ = 0;
e_size_ = 0;
if (CoordInfo().HasBox())
box_size_ = precision_ * 9;
else
box_size_ = 0;
vir_size_ = 0;
pres_size_ = 0;
top_size_ = 0;
sym_size_ = 0;
x_size_ = natom3_ * precision_;
if (CoordInfo().HasVel())
v_size_ = natom3_ * precision_;
else
v_size_ = 0;
f_size_ = 0;
step_ = 0;
nre_ = 0;
dt_ = 0.0;
lambda_ = 0.0;
// Allocate temp space for coords/velo
AllocateCoords();
if (file_.SetupWrite( fname, debug_)) return 1;
if (file_.OpenFile()) return 1;
} else {
int nframes = setupTrajin( fname, trajParm );
if ( format_ == TRJ ) {
mprinterr("Error: Only writes to TRR files supported.\n");
return 1;
}
if ( nframes == TRAJIN_ERR ) return 1;
mprintf("\tAppending to TRR file starting at frame %i\n", nframes);
// Re-open for appending
if (file_.SetupAppend( fname, debug_ )) return 1;
if (file_.OpenFile()) return 1;
}
return 0;
}
/** Allocate a character buffer based on number of coords and whether
* velocities/box info is present.
*/
int Traj_AmberRestart::setupTrajout(FileName const& fname, Topology* trajParm,
CoordinateInfo const& cInfoIn,
int NframesToWrite, bool append)
{
if (append) {
mprinterr("Error: Append not supported for Amber Restart.\n");
return 1;
}
CoordinateInfo cInfo = cInfoIn;
if (!cInfo.HasTemp() && outputTemp_) cInfo.SetTemperature(true);
// If temperature requested write time as well or format will break.
if (cInfo.HasTemp()) {
outputTime_ = true;
if (!cInfo.HasTime() && time0_ < 0.0) time0_ = 1.0;
}
if (cInfo.HasVel() && !outputVel_) cInfo.SetVelocity(false);
if (outputTime_) {
if (!cInfo.HasTime() && time0_ >= 0) cInfo.SetTime(true);
} else
cInfo.SetTime(false);
SetCoordInfo( cInfo );
if (file_.SetupWrite( fname, debug_ )) return 1;
readAccess_ = false;
// Set trajectory info
natom3_ = trajParm->Natom() * 3;
// Calculate the length of coordinate frame in bytes
file_.SetupFrameBuffer( natom3_, 12, 6 );
// Dont know ahead of time if velocities will be used, allocate space
// just in case. Velocity will not be written if V input is null.
file_.ResizeBuffer( natom3_ );
// If box coords are present, allocate extra space for them
if (CoordInfo().HasBox()) {
numBoxCoords_ = 6;
file_.ResizeBuffer( numBoxCoords_ );
}
// If number of frames to write == 1 set singleWrite so we dont append
// frame # to filename.
if (NframesToWrite==1) singleWrite_ = true;
// Set up title
std::string outTitle = Title();
if (outTitle.empty()) {
outTitle.assign("Cpptraj Generated Restart");
outTitle.resize(80, ' ');
} else {
if ( outTitle.size() > 80) {
mprintf("Warning: Amber restart title for %s too long: truncating.\n[%s]\n",
file_.Filename().base(), outTitle.c_str());
outTitle.resize(80);
}
}
SetTitle( outTitle );
return 0;
}
/** 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;
}
/** 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;
}
// Traj_SQM::setupTrajout()
int Traj_SQM::setupTrajout(FileName const& fname, Topology* trajParm,
CoordinateInfo const& cInfoIn,
int NframesToWrite, bool append)
{
if (trajParm==0) return 1;
if (append) {
mprinterr("Error: Append not supported for SQM.\n");
return 1;
}
SetCoordInfo( cInfoIn );
if (outfile_.SetupWrite( fname, debug_ )) return 1;
sqmParm_ = trajParm;
if (NframesToWrite==1) singleWrite_ = true;
// Set up title
std::string outTitle = Title();
if (outTitle.empty()) {
outTitle.assign("Cpptraj generated SQM input");
} else {
if ( outTitle.size() > 80) {
mprintf("Warning: Amber SQM title for '%s' too long: truncating.\n[%s]\n",
outfile_.Filename().base(), outTitle.c_str());
outTitle.resize(80);
}
}
SetTitle( outTitle );
// If charge not set, try to determine charge.
// TODO: Warn if not integer charge
if (!chargeIsSet_) {
mprintf("Warning: No charge specified; attempting to calculate charge.\n");
double qtotal = 0.0;
for (int i = 0; i < sqmParm_->Natom(); i++)
qtotal += (*sqmParm_)[i].Charge();
charge_ = (int)qtotal;
}
// Set up header
header_.assign(" &qmmm\n"
" qm_theory='AM1', qmcharge = "+integerToString(charge_)+", maxcyc = 0,\n"
" tight_p_conv = 1, scfconv = 1.0e-10, pseudo_diag = 0, errconv = 1.0e-10\n"
" /\n");
return 0;
}
// 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;
}
/** Set up and read Amber restart file. Coordinate/velocities will be saved
* here to avoid having to open the file again. Check that number of atoms
* matches number of atoms in associated parmtop. Check for box/velocity info.
*/
int Traj_AmberRestart::setupTrajin(FileName const& fname, Topology* trajParm)
{
BufferedFrame infile;
if (infile.SetupRead( fname, debug_ )) return TRAJIN_ERR;
if (infile.OpenFile()) return TRAJIN_ERR;
readAccess_ = true;
// Read in title
std::string title = infile.GetLine();
SetTitle( NoTrailingWhitespace(title) );
// Read in natoms, time, and Replica Temp if present
std::string nextLine = infile.GetLine();
if (nextLine.empty()) {
mprinterr("Error: Could not read restart atoms/time.\n");
return TRAJIN_ERR;
}
int restartAtoms = 0;
bool hasTemp = false;
bool hasTime = false;
int nread = sscanf(nextLine.c_str(),"%i %lE %lE",&restartAtoms,&restartTime_,&restartTemp_);
if (nread < 1) {
mprinterr("Error: Unable to read restart atoms/time.\n");
return TRAJIN_ERR;
} else if (nread == 1) { // # atoms only
restartTime_ = 0.0;
restartTemp_ = -1.0;
} else if (nread == 2) { // # atoms and time
hasTime = true;
restartTemp_ = -1.0;
} else { // # atoms, time, and temperature
hasTime = true;
hasTemp = true;
}
if (debug_ > 0)
mprintf("\tAmber restart: Atoms=%i Time=%lf Temp=%lf\n",restartAtoms,
restartTime_, restartTemp_);
// Check that natoms matches parm natoms
if (restartAtoms != trajParm->Natom()) {
mprinterr("Error: Number of atoms in Amber Restart %s (%i) does not\n",
infile.Filename().base(), restartAtoms);
mprinterr(" match number in associated parmtop (%i)\n",trajParm->Natom());
return TRAJIN_ERR;
}
natom3_ = restartAtoms * 3;
// Calculate the length of coordinate frame in bytes
infile.SetupFrameBuffer( natom3_, 12, 6 );
// Read past restart coords
if ( infile.ReadFrame() ) {
mprinterr("Error: AmberRestart::setupTrajin(): Error reading coordinates.\n");
return TRAJIN_ERR;
}
// Save coordinates
CRD_.resize( natom3_ );
infile.BufferBegin();
infile.BufferToDouble(&CRD_[0], natom3_);
// Attempt a second read to get velocities or box coords
bool hasVel = false;
boxInfo_.SetNoBox();
nread = infile.AttemptReadFrame();
if ( nread < 0 ) {
mprinterr("Error: Error attempting to read box line of Amber restart file.\n");
return TRAJIN_ERR;
}
size_t readSize = (size_t)nread;
//mprintf("DEBUG: Restart readSize on second read = %i\n",readSize);
// If 0 no box or velo
if (readSize > 0) {
if (readSize == infile.FrameSize()) {
// If filled framebuffer again, has velocity info.
hasVel = true;
VEL_.resize( natom3_ );
infile.BufferBegin();
infile.BufferToDouble(&VEL_[0], natom3_);
// If we can read 1 more line after velocity, should be box info.
nextLine = infile.GetLine();
if (!nextLine.empty()) {
if (getBoxAngles(nextLine, boxInfo_)) return TRAJIN_ERR;
}
} else if (readSize<82) {
// If we read something but didnt fill framebuffer, should have box coords.
nextLine.assign(infile.Buffer(), readSize);
if (getBoxAngles(nextLine, boxInfo_)) return TRAJIN_ERR;
} else {
// Otherwise, who knows what was read?
mprinterr("Error: AmberRestart::setupTrajin(): When attempting to read in\n"
"Error: box coords/velocity info got %lu chars, expected 0, 37,\n"
"Error: 73, or %lu.\n", readSize, infile.FrameSize());
mprinterr("Error: This usually indicates a malformed or corrupted restart file.\n");
return TRAJIN_ERR;
}
}
if (useVelAsCoords_ && !hasVel) {
mprinterr("Error: 'usevelascoords' specified but no velocities in this restart.\n");
return TRAJIN_ERR;
}
infile.CloseFile();
// Set coordinate info
SetCoordInfo( CoordinateInfo(boxInfo_, hasVel, hasTemp, hasTime) );
// Only 1 frame in restart by definition
return 1;
}
// 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();
}
int Traj_Gro::setupTrajin(FileName const& fnameIn, Topology* trajParm)
{
float fXYZ[9];
fname_ = fnameIn; // TODO SetupRead for BufferedLine
// Open file for reading
if (file_.OpenFileRead( fname_ )) return TRAJIN_ERR;
// Read the title. May contain time value, 't= <time>'
const char* ptr = file_.Line();
if (ptr == 0) {
mprinterr("Error: Reading title.\n");
return TRAJIN_ERR;
}
std::string title( ptr );
RemoveTrailingWhitespace(title);
mprintf("DBG: Title: %s\n", title.c_str());
bool hasTime = true;
// TODO Is it OK to assume there will never be a negative time value?
double timeVal = GetTimeValue( ptr );
if (timeVal < 0.0) hasTime = false;
mprintf("DBG: Timeval= %g HasTime= %i\n", timeVal, (int)hasTime);
// Read number of atoms
ptr = file_.Line();
if (ptr == 0) return TRAJIN_ERR;
natom_ = atoi(ptr);
if (natom_ < 1) {
mprinterr("Error: Reading number of atoms.\n");
return TRAJIN_ERR;
}
if (natom_ != trajParm->Natom()) {
mprinterr("Error: Number of atoms %i does not match associated parm %s (%i)\n",
natom_, trajParm->c_str(), trajParm->Natom());
return TRAJIN_ERR;
}
// Read first atom to see if there are velocities
ptr = file_.Line();
int nread = sscanf(ptr, "%*5c%*5c%*5c%*5c%f %f %f %f %f %f",
fXYZ, fXYZ+1, fXYZ+2, fXYZ+3, fXYZ+4, fXYZ+5);
bool hasV = false;
if (nread == 6)
hasV = true;
else if (nread != 3) {
mprinterr("Error: Reading first atom, expected 3 or 6 coordinates, got %i\n", nread);
return TRAJIN_ERR;
}
// Read past the rest of the atoms
for (int i = 1; i != natom_; i++)
if (file_.Line() == 0) {
mprinterr("Error: Reading atom %i of first frame.\n", i+1);
return TRAJIN_ERR;
}
// Attempt to read box line
// v1(x) v2(y) v3(z) [v1(y) v1(z) v2(x) v2(z) v3(x) v3(y)]
ptr = file_.Line();
Box groBox;
if (ptr != 0)
groBox = GetBox( ptr );
// Set trajectory information. No temperature info.
SetCoordInfo( CoordinateInfo(groBox, hasV, false, hasTime) );
SetTitle( title );
// Check for multiple frames. If nothing was read above, 1 frame, no box. If
// box info was read but nothing more can be read, 1 frame. Otherwise there
// are more frames.
bool hasMultipleFrames = false;
if (ptr != 0) {
if (groBox.Type() == Box::NOBOX) // Assume another title read.
hasMultipleFrames = true;
else {
ptr = file_.Line(); // Read line after box info
if (ptr != 0)
hasMultipleFrames = true;
}
}
// Set up some info for performing blank reads.
linesToRead_ = natom_;
if (groBox.Type() != Box::NOBOX)
linesToRead_ += 1;
int nframes = 1;
if (hasMultipleFrames) {
// Since there is no guarantee that each frame is the same size we cannot
// just seek. Blank reads for as many times as possible. Should currently
// be positioned at the title line of the next frame.
while (ptr != 0 ) {
ptr = file_.Line(); // Natoms
int Nat = atoi(ptr);
if (Nat != natom_) {
mprinterr("Error: Frame %i # atoms (%i) does not match first frame (%i).\n"
"Error: Only reading %i frames.\n", nframes+1, Nat, natom_, nframes);
break;
}
for (int i = 0; i != linesToRead_; i++)
ptr = file_.Line();
if (ptr == 0) break;
nframes++;
ptr = file_.Line(); // Next title or EOF
}
}
file_.CloseFile();
return nframes;
}
// Traj_AmberCoord::setupTrajin()
int Traj_AmberCoord::setupTrajin(FileName const& fname, Topology* trajParm)
{
// Set up file for reading
if (file_.SetupRead( fname, debug_ )) return TRAJIN_ERR;
// Attempt to open the file. Read and set the title and titleSize
if ( file_.OpenFile() ) return TRAJIN_ERR;
std::string title = file_.GetLine();
// Allocate mem to read in frame (plus REMD header if present). REMD
// header is checked for when file is IDd. Title size is used in seeking.
natom3_ = trajParm->Natom() * 3;
file_.SetupFrameBuffer( natom3_, 8, 10, headerSize_, title.size() );
if (debug_ > 0) {
mprintf("Each frame is %zu bytes", file_.FrameSize());
if (headerSize_ != 0) mprintf(" (including REMD header)");
mprintf(".\n");
}
// Read the first frame of coordinates
if ( file_.ReadFrame() ) {
mprinterr("Error: in read of Coords frame 1 of trajectory %s.\n", file_.Filename().base());
return TRAJIN_ERR;
}
// Check for box coordinates. If present, update the frame size and
// reallocate the frame buffer. If less than 3 atoms there is no way
// to tell if a line is a box line or coordinates, so skip.
Box boxInfo;
if ( trajParm->Natom() < 3 ) {
mprintf("Warning: Less than 3 atoms, skipping box check.\n");
numBoxCoords_ = 0;
} else {
std::string nextLine = file_.GetLine();
if ( !nextLine.empty() ) {
if (debug_>0) rprintf("DEBUG: Line after first frame: (%s)\n", nextLine.c_str());
if ( IsRemdHeader(nextLine.c_str()) || IsRxsgldHeader(nextLine.c_str()) ) {
// REMD header - no box coords
numBoxCoords_ = 0;
} else {
double box[8];
numBoxCoords_ = sscanf(nextLine.c_str(), "%8lf%8lf%8lf%8lf%8lf%8lf%8lf%8lf",
box, box+1, box+2, box+3, box+4, box+5, box+6, box+7);
if (numBoxCoords_ == -1) {
mprinterr("Error: Could not read Box coord line of trajectory %s.\n",
file_.Filename().base());
return TRAJIN_ERR;
} else if (numBoxCoords_ == 8) {
// Full line of coords was read, no box coords.
numBoxCoords_ = 0;
} else if (numBoxCoords_ == 3) {
// Box lengths only, ortho. or truncated oct. Use default parm angles.
if (trajParm->ParmBox().Type() == Box::NOBOX)
mprintf("Warning: Trajectory only contains box lengths and topology has no box info.\n"
"Warning: To set box angles for topology use the 'parmbox' command.\n");
box[3] = boxAngle_[0] = trajParm->ParmBox().Alpha();
box[4] = boxAngle_[1] = trajParm->ParmBox().Beta();
box[5] = boxAngle_[2] = trajParm->ParmBox().Gamma();
boxInfo.SetBox( box );
} else if (numBoxCoords_ == 6) {
// General triclinic. Set lengths and angles.
boxInfo.SetBox( box );
} else {
mprinterr("Error: In %s, expect only 3 or 6 box coords, got %i\n"
"Error: Box line=[%s]\n",
file_.Filename().base(), numBoxCoords_, nextLine.c_str());
return TRAJIN_ERR;
}
}
}
// Reallocate frame buffer accordingly
file_.ResizeBuffer( numBoxCoords_ );
}
// Calculate Frames and determine seekable. If not possible and this is not a
// compressed file the trajectory is probably corrupted. Frames will
// be read until EOF.
int Frames = 0;
if (debug_>0)
rprintf("Title offset=%lu FrameSize=%lu UncompressedFileSize=%lu\n",
title.size(), file_.FrameSize(), file_.UncompressedSize());
off_t title_size = (off_t) title.size();
off_t frame_size = (off_t) file_.FrameSize();
off_t uncompressed_size = file_.UncompressedSize();
off_t file_size = uncompressed_size - title_size;
bool seekable = false;
if (file_.Compression() != CpptrajFile::NO_COMPRESSION) {
// -----==== AMBER TRAJ COMPRESSED ====------
// If the uncompressed size of compressed file is reported as <= 0,
// uncompressed size cannot be determined. Read coordinates until
// EOF.
if (uncompressed_size <= 0) {
mprintf("Warning: %s: Uncompressed size of trajectory could not be determined.\n",
file_.Filename().base());
if (file_.Compression() == CpptrajFile::BZIP2)
mprintf(" (This is normal for bzipped files)\n");
mprintf(" Number of frames could not be calculated.\n");
mprintf(" Frames will be read until EOF.\n");
Frames = TRAJIN_UNK;
seekable = false;
} else {
// Frame calculation for large gzip files
if (file_.Compression() == CpptrajFile::GZIP) {
// Since this is gzip compressed, if the file_size % frame size != 0,
// it could be that the uncompressed filesize > 4GB. Since
// ISIZE = uncompressed % 2^32,
// try ((file_size + (2^32 * i)) % frame_size) and see if any are 0.
if ( (file_size % frame_size) != 0) {
// Determine the maximum number of iterations to try based on the
// fact that Amber trajectories typically compress about 3x with
// gzip.
off_t tmpfsize = ((file_.FileSize() * 4) - uncompressed_size) / 4294967296LL;
int maxi = (int) tmpfsize;
++maxi;
if (debug_>1)
mprintf("\tLooking for uncompressed gzip size > 4GB, %i iterations.\n",maxi);
tmpfsize = 0;
bool sizeFound = false;
for (int i = 0; i < maxi; i++ ) {
tmpfsize = (4294967296LL * i) + file_size;
if ( (tmpfsize % frame_size) == 0) {sizeFound=true; break;}
}
if (sizeFound) file_size = tmpfsize;
}
}
if ((file_size % frame_size) == 0) {
Frames = (int) (file_size / frame_size);
seekable = true;
} else {
mprintf("Warning: %s: Number of frames in compressed traj could not be determined.\n"
"Warning: Frames will be read until EOF.\n", file_.Filename().base());
Frames = TRAJIN_UNK;
seekable = false;
}
}
} else {
// ----==== AMBER TRAJ NOT COMPRESSED ====----
Frames = (int) (file_size / frame_size);
if ( (file_size % frame_size) == 0 ) {
seekable = true;
} else {
mprintf("Warning: %s: Could not accurately predict # frames. This usually\n"
"Warning: indicates a corrupted trajectory or trajectory/topology\n"
"Warning: mismatch. Will attempt to read %i frames.\n",
file_.Filename().base(), Frames);
seekable = false;
}
}
if (debug_>0)
rprintf("Atoms: %i FrameSize: %lu TitleSize: %lu NumBox: %i Seekable: %i Frames: %i\n\n",
trajParm->Natom(), frame_size, title_size, numBoxCoords_, (int)seekable, Frames);
// Close the file
file_.CloseFile();
// Set trajectory info: no velocity, no time.
SetCoordInfo( CoordinateInfo(boxInfo, false, (headerSize_ != 0), false) );
SetTitle( title );
return Frames;
}
