int TrajinList::AddTrajin(std::string const& fname, Topology* topIn, ArgList const& argIn)
{
if (topIn == 0) {
mprinterr("Error: No topology for input trajectory '%s'\n", fname.c_str());
return 1;
}
// CRDIDXARG
finalCrdIndicesArg_.clear();
ArgList trajin_args = argIn;
bool isRemdtraj = trajin_args.hasKey("remdtraj");
int err = 0;
File::NameArray fnames = File::ExpandToFilenames( fname );
if (fnames.empty()) return 1;
Trajin* traj = 0;
for (File::NameArray::const_iterator fn = fnames.begin(); fn != fnames.end(); ++fn) {
ArgList args = trajin_args;
if (isRemdtraj)
traj = new Trajin_Multi();
else
traj = new Trajin_Single();
if (traj == 0) {
mprinterr("Error: Memory allocation for input trajectory failed.\n");
return 1;
}
traj->SetDebug(debug_);
if ( traj->SetupTrajRead(*fn, args, topIn) ) {
mprinterr("Error: Could not set up input trajectory '%s'.\n", fn->full());
delete traj;
err++;
continue;
}
// Add to trajin list and update # of frames.
trajin_.push_back( traj );
UpdateMaxFrames( traj->Traj() );
}
if (err > 0) return 1;
// FIXME: For backwards compat. overwrite Topology box info with traj box info.
topIn->SetBoxFromTraj( trajin_.back()->TrajCoordInfo().TrajBox() );
return 0;
}
Exec::RetType Exec_ReadData::Execute(CpptrajState& State, ArgList& argIn) {
DataFile dataIn;
dataIn.SetDebug( State.DFL().Debug() );
std::string filenameIn = argIn.GetStringNext();
File::NameArray fnames = File::ExpandToFilenames( filenameIn );
if (fnames.empty()) {
mprinterr("Error: '%s' matches no files.\n", filenameIn.c_str());
return CpptrajState::ERR;
}
int err = 0;
int idx = -1;
bool useIndex = argIn.hasKey("separate");
for (File::NameArray::const_iterator fn = fnames.begin(); fn != fnames.end(); ++fn) {
if (useIndex) idx++;
if (dataIn.ReadDataIn( *fn, argIn, State.DSL(), idx, fnames.size() )!=0) {
mprinterr("Error: Could not read data file '%s'.\n", fn->full());
err++;
}
}
if (err > 0) return CpptrajState::ERR;
return CpptrajState::OK;
}
// TrajinList::AddEnsembleIn()
int TrajinList::AddEnsembleIn(std::string const& fname, Topology* topIn, ArgList const& argIn)
{
if (topIn == 0) {
mprinterr("Error: No topology for input ensemble '%s'\n", fname.c_str());
return 1;
}
int err = 0;
File::NameArray fnames = File::ExpandToFilenames( fname );
if (fnames.empty()) return 1;
TrajectoryFile::TrajFormatType trajinFmt;
TrajectoryIO* tio = 0;
for (File::NameArray::const_iterator fn = fnames.begin(); fn != fnames.end(); ++fn) {
ArgList args = argIn;
// Determine whether this file is multiple file or single file ensemble.
tio = TrajectoryFile::DetectFormat( *fn, trajinFmt );
if (tio == 0) {
mprinterr("Error: Could not determine trajectory %s format\n", fn->full());
err++;
continue;
}
EnsembleIn* ensemble = 0;
# ifdef ENABLE_SINGLE_ENSEMBLE
if (tio->CanProcessEnsemble())
ensemble = new EnsembleIn_Single();
else
# endif
ensemble = new EnsembleIn_Multi();
if (ensemble == 0) {
mprinterr("Error: Memory allocation for input ensemble failed.\n");
delete tio;
return 1;
}
ensemble->SetDebug( debug_ );
// CRDIDXARG: Append coordinate indices arg if there is one
args.AddArg( finalCrdIndicesArg_ );
if ( ensemble->SetupEnsembleRead(*fn, args, topIn) ) {
mprinterr("Error: Could not set up input ensemble '%s'.\n", fname.c_str());
delete ensemble;
delete tio;
err++;
continue;
}
// Currently all input ensembles must be same size.
if (ensembleSize_ == -1)
ensembleSize_ = ensemble->EnsembleCoordInfo().EnsembleSize();
else if (ensembleSize_ != ensemble->EnsembleCoordInfo().EnsembleSize()) {
mprinterr("Error: Ensemble size (%i) does not match first ensemble size (%i).\n",
ensemble->EnsembleCoordInfo().EnsembleSize(), ensembleSize_);
return 1;
}
// CRDIDXARG: If trajectory is REMD ensemble and sorting by CRDIDX, need to
// save final CRDIDX for next ensemble command.
// TODO: This is very clunky - remlog dataset should contain all exchanges
// so trajin doesnt have to worry about it.
# ifdef ENABLE_SINGLE_ENSEMBLE
if ( !tio->CanProcessEnsemble() ) {
# endif
EnsembleIn_Multi const& mTraj = static_cast<EnsembleIn_Multi const&>( *ensemble );
if ( mTraj.TargetMode() == ReplicaInfo::CRDIDX ) {
finalCrdIndicesArg_ = mTraj.FinalCrdIndices();
if (finalCrdIndicesArg_.empty()) {
mprinterr("Error: Could not obtain final remlog indices.\n");
delete ensemble;
delete tio;
err++;
continue;
}
//mprintf("DEBUG: Final crd indices arg: %s\n", finalCrdIndicesArg_.c_str());
}
# ifdef ENABLE_SINGLE_ENSEMBLE
} else
mprintf("Warning: Single ensemble cannot process crdidx.\n");
# endif
// Add to ensemble list and update # of frames.
ensemble_.push_back( ensemble );
UpdateMaxFrames( ensemble->Traj() );
delete tio;
}
if (err > 0) return 1;
// FIXME: For backwards compat. overwrite Topology box info with traj box info.
topIn->SetBoxFromTraj( ensemble_.back()->EnsembleCoordInfo().TrajBox() );
return 0;
}
