// EnsembleOut_Single::PrintInfo()
void EnsembleOut_Single::PrintInfo(int expectedNframes) const {
mprintf(" '%s' (Single Ensemble, %i members",Traj().Filename().base(), ensembleSize_);
if (expectedNframes > 0) mprintf(", %i frames", expectedNframes);
mprintf(") ");
eio_->Info();
Traj().CommonInfo();
}
void EnsembleIn_Single::EnsembleInfo(int showExtended) const {
mprintf("'%s' (REMD ensemble size %i) ",Traj().Filename().base(), ensembleSize_);
eio_->Info();
mprintf(", Parm %s",Traj().Parm()->c_str());
if (cInfo_.HasBox()) mprintf(" (%s box)", cInfo_.TrajBox().TypeName());
if (showExtended==1) Traj().Counter().PrintFrameInfo();
if (debug_>0)
mprintf(", %i atoms, Box %i",Traj().Parm()->Natom(),(int)cInfo_.HasBox());
}
// Trajin_Multi::PrintInfo()
void Trajin_Multi::PrintInfo(int showExtended) const {
mprintf("REMD trajectories (%u total), lowest replica '%s'", REMDtraj_.size(),
Traj().Filename().base());
if (showExtended == 1) Traj().Counter().PrintFrameInfo();
mprintf("\n");
if (debug_ > 0) REMDtraj_.PrintIOinfo();
if (remdtrajidx_.empty())
mprintf("\tLooking for frames at %.2lf K\n",remdtrajtemp_);
else {
mprintf("\tLooking for indices [");
for (RemdIdxType::const_iterator idx = remdtrajidx_.begin(); idx != remdtrajidx_.end(); ++idx)
mprintf(" %i", *idx);
mprintf(" ]\n");
}
}
// EnsembleOut_Single::InitEnsembleWrite()
int EnsembleOut_Single::InitEnsembleWrite(std::string const& tnameIn,
ArgList const& argIn, int ensembleSizeIn,
TrajectoryFile::TrajFormatType writeFormatIn)
{
// Require a base filename
if (tnameIn.empty()) {
mprinterr("Internal Error: InitTrajWrite: No filename given.\n");
return 1;
}
// Require that ensemble size is set.
ensembleSize_ = ensembleSizeIn;
if (ensembleSize_ < 1) {
mprinterr("Internal Error: Ensemble size has not been set.\n");
return 1;
}
ArgList trajout_args = argIn;
// Get onlymembers range
Range members_to_write = MembersToWrite(trajout_args.GetStringKey("onlymembers"), ensembleSize_);
if (members_to_write.Empty()) return 1;
// Process common args
if (SetTraj().CommonTrajoutSetup(tnameIn, trajout_args, writeFormatIn))
return 1;
if (eio_ != 0) delete eio_;
// If appending, file must exist and must match the current format.
// TODO Do not pass in writeformat directly to be changed.
if (Traj().Append()) {
if (Traj().CheckAppendFormat( Traj().Filename(), SetTraj().WriteFormat() ))
SetTraj().SetAppend( false );
}
// Set up for the specified format.
eio_ = TrajectoryFile::AllocTrajIO( Traj().WriteFormat() );
if (eio_ == 0) return 1;
// Check that the TrajectoryIO object can read/write single ensemble
if (!eio_->CanProcessEnsemble()) {
mprinterr("Error: Format '%s' cannot be used for ensemble single file output.\n",
TrajectoryFile::FormatString(Traj().WriteFormat()));
return 1;
}
mprintf("\tWriting '%s' as %s\n", Traj().Filename().full(),
TrajectoryFile::FormatString(Traj().WriteFormat()));
eio_->SetDebug( debug_ );
// Set specified title - will not set if empty
eio_->SetTitle( Traj().Title() );
// Process any write arguments specific to certain formats not related
// to parm file. Options related to parm file are handled in SetupTrajWrite
if (eio_->processWriteArgs(trajout_args)) {
mprinterr("Error: trajout %s: Could not process arguments.\n",Traj().Filename().full());
return 1;
}
return 0;
}
int EnsembleIn_Single::BeginEnsemble() {
// Open the trajectory
if (eio_->openTrajin()) {
mprinterr("Error: Could not open %s\n",Traj().Filename().base());
return 1;
}
// Initialize counter.
SetTraj().Counter().Begin();
return 0;
}
/** Expect lowest replica file name to be passed in. 'remdtraj' should have
* already been parsed out of input arguments.
*/
int Trajin_Multi::SetupTrajRead(FileName const& tnameIn, ArgList& argIn, Topology *tparmIn)
{
// Set file name and topology pointer.
if (SetTraj().SetNameAndParm(tnameIn, tparmIn)) return 1;
REMDtraj_.ClearIOarray();
// Check for deprecated args
if (argIn.hasKey("remdout")) {
mprinterr("%s", TrajIOarray::DEPRECATED_remdout);
return 1;
}
// Process REMD-specific arguments
if (argIn.Contains("remdtrajidx")) {
// Looking for specific indices
ArgList indicesArg(argIn.GetStringKey("remdtrajidx"), ",");
if (indicesArg.empty()) {
mprinterr("Error: remdtrajidx expects comma-separated list of target indices in each\n"
"Error: dimension, '<dim1 idx>,<dim2 idx>,...,<dimN idx>'. Indices start\n"
"Error: from 1.\n");
return 1;
}
for (ArgList::const_iterator arg = indicesArg.begin(); // TODO: validInteger?
arg != indicesArg.end(); ++arg)
remdtrajidx_.push_back( convertToInteger( *arg ) );
targetType_ = ReplicaInfo::INDICES;
} else if (argIn.Contains("remdtrajtemp")) {
// Looking for target temperature
remdtrajtemp_ = argIn.getKeyDouble("remdtrajtemp",0.0);
targetType_ = ReplicaInfo::TEMP;
}
// Set up replica file names.
if (REMDtraj_.SetupReplicaFilenames( tnameIn, argIn )) return 1;
// Set up TrajectoryIO classes for all file names.
if (REMDtraj_.SetupIOarray(argIn, SetTraj().Counter(), cInfo_, Traj().Parm())) return 1;
// Check that replica dimension valid for desired indices.
if (targetType_ == ReplicaInfo::INDICES &&
cInfo_.ReplicaDimensions().Ndims() != (int)remdtrajidx_.size())
{
mprinterr("Error: Replica # of dim (%i) not equal to target # dim (%zu)\n",
cInfo_.ReplicaDimensions().Ndims(), remdtrajidx_.size());
return 1;
}
// If target type is temperature make sure there is temperature info.
if (targetType_ == ReplicaInfo::TEMP && !cInfo_.HasTemp()) {
mprinterr("Error: Some or all replicas are missing temperature info.\n");
return 1;
}
return 0;
}
// EnsembleOut_Single::SetupEnsembleWrite()
int EnsembleOut_Single::SetupEnsembleWrite(Topology* tparmIn, CoordinateInfo const& cInfoIn, int nFrames) {
// Set up topology and coordinate info.
if (SetTraj().SetupCoordInfo(tparmIn, nFrames, cInfoIn))
return 1;
if (debug_ > 0)
rprintf("\tSetting up single ensemble %s for WRITE, topology '%s' (%i atoms).\n",
Traj().Filename().base(), tparmIn->c_str(), tparmIn->Natom());
// Set up TrajectoryIO
if (eio_->setupTrajout(Traj().Filename(), Traj().Parm(), Traj().CoordInfo(),
Traj().NframesToWrite(), Traj().Append()))
return 1;
if (debug_ > 0)
Frame::PrintCoordInfo(Traj().Filename().base(), Traj().Parm()->c_str(), eio_->CoordInfo());
// First frame setup
//if (!TrajIsOpen()) { //}
return 0;
}
// EnsembleIn_Single::SetupEnsembleRead()
int EnsembleIn_Single::SetupEnsembleRead(FileName const& tnameIn, ArgList& argIn,
Topology *tparmIn)
{
if (eio_ != 0) delete eio_;
// Set file name and topology pointer.
if (SetTraj().SetNameAndParm(tnameIn, tparmIn)) return 1;
// Detect file format
TrajectoryFile::TrajFormatType tformat;
if ( (eio_ = TrajectoryFile::DetectFormat( Traj().Filename(), tformat )) == 0 ) {
mprinterr("Error: Could not determine trajectory %s format.\n", Traj().Filename().full());
return 1;
}
eio_->SetDebug( debug_ );
mprintf("\tReading '%s' as %s\n", Traj().Filename().full(), TrajectoryFile::FormatString(tformat));
// Process ensemble args // TODO: Should be common to Ensemble?
bool nosort = argIn.hasKey("nosort");
// Process format-specific read args
if (eio_->processReadArgs( argIn )) return 1;
// Set up the format for reading and get the number of frames.
int nframes = eio_->setupTrajin(Traj().Filename(), Traj().Parm());
if (nframes == TrajectoryIO::TRAJIN_ERR) {
mprinterr("Error: Could not set up %s for reading.\n", Traj().Filename().full());
return 1;
}
if (debug_ > 0) {
if (nframes != TrajectoryIO::TRAJIN_UNK)
mprintf("\t'%s' contains %i frames.\n", Traj().Filename().base(), nframes);
else
mprintf("\t'%s' contains an unknown number of frames.\n",Traj().Filename().base());
}
// Set the start, stop, and offset args based on user input. Do some bounds
// checking.
if (SetTraj().Counter().CheckFrameArgs( nframes, argIn )) return 1;
// Set trajectory coordinate info.
cInfo_ = eio_->CoordInfo();
// NOTE: ensembleSize_ is saved here as a shortcut. Should always equal whats in cInfo_
// Determine if this trajectory actually contains an ensemble.
// FIXME: Should check for < 2?
ensembleSize_ = cInfo_.EnsembleSize();
if (ensembleSize_ < 1) {
mprinterr("Error: Cannot process single file ensemble with '%s'\n",
TrajectoryFile::FormatString(tformat));
return 1;
}
# ifdef MPI
// Set up communicators
if (Parallel::SetupComms( ensembleSize_ )) return 1;
// Set ensemble member number.
SetEnsembleMemberNum( EnsembleComm().Rank() );
# endif
// If dimensions are present, assume search by indices, otherwise by temp.
targetType_ = ReplicaInfo::NONE;
if (cInfo_.ReplicaDimensions().Ndims() > 0)
targetType_ = ReplicaInfo::INDICES;
else if (cInfo_.HasTemp())
targetType_ = ReplicaInfo::TEMP;
else if (!nosort) {
mprinterr("Error: Ensemble trajectory does not have indices or temperature.\n");
return 1;
}
if (debug_ > 0)
cInfo_.PrintCoordInfo( Traj().Filename().base(), Traj().Parm()->c_str() );
# ifdef MPI
// This array will let each thread know who has what frame.
frameidx_.resize( ensembleSize_ ); // TODO: Get rid of, should do all in TrajIO class.
# endif
// Get a list of all temperatures/indices.
TemperatureMap_.ClearMap();
IndicesMap_.ClearMap();
if (targetType_ == ReplicaInfo::TEMP || targetType_ == ReplicaInfo::INDICES )
{
# ifdef MPI
FrameArray f_ensemble(1);
# else
FrameArray f_ensemble( ensembleSize_ );
# endif
f_ensemble.SetupFrames( Traj().Parm()->Atoms(), cInfo_ );
if ( eio_->openTrajin() ) return 1;
if ( eio_->readArray( Traj().Counter().Start(), f_ensemble ) ) return 1;
eio_->closeTraj();
if (targetType_ == ReplicaInfo::TEMP) {
std::vector<double> allTemps( ensembleSize_, -1.0 );
# ifdef MPI
// Consolidate temperatures
if (GatherTemperatures(f_ensemble[0].tAddress(), allTemps, EnsembleComm())) return 1;
# else
for (int en = 0; en != ensembleSize_; ++en)
allTemps[en] = f_ensemble[en].Temperature();
# endif
if (SetTemperatureMap( allTemps )) return 1;
} else if (targetType_ == ReplicaInfo::INDICES) {
std::vector<RemdIdxType> allIndices( ensembleSize_ );
# ifdef MPI
// Consolidate replica indices
if (GatherIndices(f_ensemble[0].iAddress(), allIndices, cInfo_.ReplicaDimensions().Ndims(),
EnsembleComm()))
return 1;
# else
for (int en = 0; en != ensembleSize_; ++en)
allIndices[en] = f_ensemble[en].RemdIndices();
# endif
if (SetIndicesMap( allIndices)) return 1;
}
}
return 0;
}