/** Loop over all filenames in replica_filenames, set up TrajectoryIO. */
int TrajIOarray::SetupIOarray(ArgList& argIn, TrajFrameCounter& counter,
CoordinateInfo& cInfo, Topology* trajParm)
{
// Sanity check
if (!IOarray_.empty()) {
mprinterr("Internal Error: SetupIOarray() has been called twice.\n");
return 1;
}
// Save arguments that have not been processed so they can be passed
// to each replica in turn. Only the lowest replica will use argIn.
ArgList argCopy( argIn );
bool lowestRep = true;
int rep0Frames = TrajectoryIO::TRAJIN_UNK; // Total frames in replica 0
int totalFrames = TrajectoryIO::TRAJIN_UNK; // Total # frames to be read from ensemble
TrajectoryFile::TrajFormatType lastRepFmt = TrajectoryFile::UNKNOWN_TRAJ;
// Right now enforce that all replicas have the same metadata as lowest
// replica, e.g. if replica 0 has temperature, replica 1 does too etc.
for (File::NameArray::const_iterator repfile = replica_filenames_.begin();
repfile != replica_filenames_.end(); ++repfile)
{
// Detect format
TrajectoryFile::TrajFormatType repformat = TrajectoryFile::UNKNOWN_TRAJ;
TrajectoryIO* replica0 = TrajectoryFile::DetectFormat( *repfile, repformat );
if ( replica0 == 0 ) {
mprinterr("Error: Could not set up replica file %s\n", repfile->full());
return 1;
}
if (repformat != lastRepFmt)
mprintf("\tReading '%s' as %s\n", repfile->full(), TrajectoryFile::FormatString(repformat));
lastRepFmt = repformat;
replica0->SetDebug( debug_ );
// Pushing replica0 here allows the destructor to handle it on errors
IOarray_.push_back( replica0 );
// Process format-specific read args. Do not exit on error in case
// replicas have different formats supporting different args.
if (lowestRep) {
replica0->processReadArgs( argIn );
} else {
ArgList argtmp( argCopy );
replica0->processReadArgs( argtmp );
}
// Set up replica for reading and get the number of frames.
int nframes = replica0->setupTrajin( *repfile, trajParm );
if (nframes == TrajectoryIO::TRAJIN_ERR) {
mprinterr("Error: Could not set up %s for reading.\n", repfile->full());
return 1;
}
// TODO: Do not allow unknown number of frames?
if (lowestRep) {
cInfo = replica0->CoordInfo();
rep0Frames = nframes;
totalFrames = nframes;
if (cInfo.ReplicaDimensions().Ndims() > 0) {
mprintf("\tReplica dimensions:\n");
for (int rd = 0; rd < cInfo.ReplicaDimensions().Ndims(); rd++)
mprintf("\t\t%i: %s\n", rd+1, cInfo.ReplicaDimensions().Description(rd));
}
} else {
// Check total frames in this replica against lowest rep.
if (nframes != rep0Frames)
mprintf("Warning: Replica %s frames (%i) does not match # frames in first replica (%i).\n",
repfile->base(), nframes, rep0Frames);
//if (repframes < 0) {
// mprinterr("Error: RemdTraj: Unknown # of frames in replica.\n");
// return 1;
//}
if (nframes < totalFrames) {
totalFrames = nframes;
mprintf("Warning: Setting total # of frames to read from replica ensemble to %i\n",
totalFrames);
}
// Check box info against lowest rep.
if ( replica0->CoordInfo().HasBox() != cInfo.HasBox() ) {
mprinterr("Error: Replica %s box info does not match first replica.\n",
repfile->full());
return 1;
}
// TODO: Check specific box type
// Check velocity info against lowest rep.
if ( replica0->CoordInfo().HasVel() != cInfo.HasVel() ) {
mprinterr("Error: Replica %s velocity info does not match first replica.\n",
repfile->full());
return 1;
}
// Check # dimensions and types against lowest rep
if ( replica0->CoordInfo().ReplicaDimensions() != cInfo.ReplicaDimensions() ) {
mprinterr("Error: Replica %s dimension info does not match first replica.\n",
repfile->full());
ReplicaDimArray const& thisRepDims = replica0->CoordInfo().ReplicaDimensions();
for (int rd = 0; rd < thisRepDims.Ndims(); rd++)
mprinterr("\t\t%i: %s\n", rd+1, thisRepDims.Description(rd));
return 1;
}
// If temperature/time info does not match set to false.
if (cInfo.HasTemp() != replica0->CoordInfo().HasTemp())
cInfo.SetTemperature( false );
if (cInfo.HasTime() != replica0->CoordInfo().HasTime())
cInfo.SetTime( false );
}
lowestRep = false;
}
// Check how many frames will actually be read
if (counter.CheckFrameArgs( totalFrames, argIn )) return 1;
// Check for errors.
if (IOarray_.empty()) {
mprinterr("Error: No replica trajectories set up.\n");
return 1;
}
if (IOarray_.size() != replica_filenames_.size()) { // SANITY CHECK
mprinterr("Error: Not all replica files were set up.\n");
return 1;
}
// Update ensemble size
cInfo.SetEnsembleSize( (int)IOarray_.size() );
if (debug_ > 0)
cInfo.PrintCoordInfo( replica_filenames_[0].full(), trajParm->c_str() );
return 0;
}
Analysis::RetType Analysis_State::Setup(ArgList& analyzeArgs, DataSetList* datasetlist, DataFileList* DFLin, int debugIn)
{
debug_ = debugIn;
masterDSL_ = datasetlist;
DataFile* outfile = DFLin->AddDataFile( analyzeArgs.GetStringKey("out"), analyzeArgs );
curveOut_ = DFLin->AddDataFile( analyzeArgs.GetStringKey("curveout"), analyzeArgs );
stateOut_ = DFLin->AddCpptrajFile( analyzeArgs.GetStringKey("stateout"), "State Output",
DataFileList::TEXT, true);
transOut_ = DFLin->AddCpptrajFile( analyzeArgs.GetStringKey("transout"), "Transitions Output",
DataFileList::TEXT, true);
normalize_ = analyzeArgs.hasKey("norm");
// Get definitions of states if present.
// Define states as 'state <#>,<dataset>,<min>,<max>'
std::string state_arg = analyzeArgs.GetStringKey("state");
if (!state_arg.empty()) {
while (!state_arg.empty()) {
// Expect form <#>,<dataset>
ArgList argtmp(state_arg, ",");
if (argtmp.Nargs() != 4) {
mprinterr("Error: Malformed state argument '%s': expect <ID>,<dataset>,<min>,<max>\n",
state_arg.c_str());
return Analysis::ERR;
}
std::string state_id = argtmp.GetStringNext();
// TODO: Check duplicate names
if (state_id.empty()) {
mprinterr("Error: In state argument, could not get ID.\n");
return Analysis::ERR;
}
DataSet* ds = datasetlist->GetDataSet( argtmp.GetStringNext() );
if (ds == 0) return Analysis::ERR;
if (ds->Ndim() != 1) {
mprinterr("Error: Only 1D data sets allowed.\n");
return Analysis::ERR;
}
double min = argtmp.getNextDouble(0.0);
double max = argtmp.getNextDouble(0.0);
if (max < min) {
mprinterr("Error: max value cannot be less than min.\n");
return Analysis::ERR;
}
States_.push_back( StateType(state_id, (DataSet_1D*)ds, min, max) );
state_arg = analyzeArgs.GetStringKey("state");
}
}
if (States_.empty()) {
mprinterr("Error: No states defined.\n");
return Analysis::ERR;
}
state_data_ = datasetlist->AddSet(DataSet::INTEGER, analyzeArgs.GetStringKey("name"), "State");
if (state_data_ == 0) return Analysis::ERR;
if (outfile != 0) outfile->AddDataSet( state_data_ );
mprintf(" STATE: The following states have been set up:\n");
for (StateArray::const_iterator state = States_.begin(); state != States_.end(); ++state)
mprintf("\t%u: %20s %12.4f <= %-20s < %12.4f\n", state - States_.begin(), state->DS().legend(),
state->Min(), state->id(), state->Max());
mprintf("\tState data set: %s\n", state_data_->legend());
if (outfile != 0)
mprintf("\tStates vs time output to file '%s'\n", outfile->DataFilename().full());
if (curveOut_ != 0)
mprintf("\tCurves output to file '%s'\n", curveOut_->DataFilename().full());
mprintf("\tState output to file '%s'\n", stateOut_->Filename().full());
mprintf("\tTransitions output to file '%s'\n", transOut_->Filename().full());
if (normalize_)
mprintf("\tCurves will be normalized to 1.0\n");
return Analysis::OK;
}
