// Exec_CrdAction::ProcessArgs()
Exec::RetType Exec_CrdAction::ProcessArgs(CpptrajState& State, ArgList& argIn) {
std::string setname = argIn.GetStringNext();
if (setname.empty()) {
mprinterr("Error: %s: Specify COORDS dataset name.\n", argIn.Command());
return CpptrajState::ERR;
}
DataSet_Coords* CRD = (DataSet_Coords*)State.DSL().FindCoordsSet( setname );
if (CRD == 0) {
mprinterr("Error: %s: No COORDS set with name %s found.\n", argIn.Command(), setname.c_str());
return CpptrajState::ERR;
}
mprintf("\tUsing set '%s'\n", CRD->legend());
// Start, stop, offset
TrajFrameCounter frameCount;
ArgList crdarg( argIn.GetStringKey("crdframes"), "," );
if (frameCount.CheckFrameArgs( CRD->Size(), crdarg )) return CpptrajState::ERR;
frameCount.PrintInfoLine(CRD->legend());
ArgList actionargs = argIn.RemainingArgs();
actionargs.MarkArg(0);
Cmd const& cmd = Command::SearchTokenType( DispatchObject::ACTION, actionargs.Command() );
if ( cmd.Empty() ) return CpptrajState::ERR;
Action* act = (Action*)cmd.Alloc();
if (act == 0) return CpptrajState::ERR;
CpptrajState::RetType err = DoCrdAction(State, actionargs, CRD, act, frameCount);
delete act;
return err;
}
// DataSet_Coords_TRJ::UpdateTrjFrames()
int DataSet_Coords_TRJ::UpdateTrjFrames(TrajFrameCounter const& count) {
if (count.TotalReadFrames() > 0)
IDX_.AddTraj( count.TotalReadFrames(), count.Start(), count.Offset() );
else {
mprinterr("Error: Cannot use trajectories with unknown # of frames as data set.\n");
return 1;
}
return 0;
}
Exec::RetType Exec_CrdAction::DoCrdAction(CpptrajState& State, ArgList& actionargs,
DataSet_Coords* CRD, Action* act,
TrajFrameCounter const& frameCount) const
{
Timer total_time;
total_time.Start();
# ifdef MPI
ActionInit state(State.DSL(), State.DFL(), trajComm_);
# else
ActionInit state(State.DSL(), State.DFL());
# endif
if ( act->Init( actionargs, state, State.Debug() ) != Action::OK )
return CpptrajState::ERR;
actionargs.CheckForMoreArgs();
// Set up frame and parm for COORDS.
ActionSetup originalSetup( CRD->TopPtr(), CRD->CoordsInfo(), CRD->Size() );
Frame originalFrame = CRD->AllocateFrame();
ActionFrame frm( &originalFrame, 0 );
// Set up for this topology
Action::RetType setup_ret = act->Setup( originalSetup );
if ( setup_ret == Action::ERR || setup_ret == Action::SKIP )
return CpptrajState::ERR;
// Loop over all frames in COORDS.
ProgressBar progress( frameCount.TotalReadFrames() );
int set = 0;
for (int frame = frameCount.Start(); frame < frameCount.Stop();
frame += frameCount.Offset(), ++set)
{
progress.Update( set );
CRD->GetFrame( frame, originalFrame );
frm.SetTrajoutNum( set );
Action::RetType ret = act->DoAction( set, frm );
if (ret == Action::ERR) {
mprinterr("Error: crdaction: Frame %i, set %i\n", frame + 1, set + 1);
break;
}
// Check if frame was modified. If so, update COORDS.
if ( ret == Action::MODIFY_COORDS )
CRD->SetCRD( frame, frm.Frm() );
}
# ifdef MPI
act->SyncAction();
# endif
// Check if parm was modified. If so, update COORDS.
if ( setup_ret == Action::MODIFY_TOPOLOGY ) {
mprintf("Info: crdaction: Parm for %s was modified by action %s\n",
CRD->legend(), actionargs.Command());
CRD->CoordsSetup( originalSetup.Top(), originalSetup.CoordInfo() );
}
act->Print();
State.MasterDataFileWrite();
total_time.Stop();
mprintf("TIME: Total action execution time: %.4f seconds.\n", total_time.Total());
return CpptrajState::OK;
}
/** 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;
}
/** Each rank only sets up file that it will process. */
int TrajIOarray::SetupIOarray(ArgList& argIn, TrajFrameCounter& counter,
CoordinateInfo& cInfo, Topology* trajParm,
Parallel::Comm const& ensComm, Parallel::Comm const& trajComm)
{
// Sanity check
if (!IOarray_.empty()) {
mprinterr("Internal Error: SetupIOarray() has been called twice.\n");
return 1;
}
// Detect format
FileName const& repFname = replica_filenames_[ensComm.Rank()];
TrajectoryFile::TrajFormatType repformat = TrajectoryFile::UNKNOWN_TRAJ;
TrajectoryIO* replica0 = TrajectoryFile::DetectFormat( repFname, repformat );
if ( replica0 == 0 ) {
mprinterr("Error: Could not set up replica file %s\n", repFname.full());
return 1;
}
mprintf("\tReading '%s' as %s\n", repFname.full(), TrajectoryFile::FormatString(repformat));
replica0->SetDebug( debug_ );
// Construct the IOarray_ with blanks for all except this rank.
for (int member = 0; member != ensComm.Size(); member++)
if (member == ensComm.Rank())
IOarray_.push_back( replica0 );
else
IOarray_.push_back( 0 );
// Process format-specific read args.
replica0->processReadArgs( argIn );
// Set up replica for reading and get # frames
int nframes = replica0->setupTrajin( repFname, trajParm );
if (nframes == TrajectoryIO::TRAJIN_ERR) {
mprinterr("Error: Could not set up %s for reading.\n", repFname.full());
return 1;
}
// Set coordinate info
cInfo = replica0->CoordInfo();
int totalFrames = nframes;
if (cInfo.ReplicaDimensions().Ndims() > 0) { // TODO put in common routine
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));
}
// Check # frames in all files, use lowest.
Parallel::World().AllReduce( &totalFrames, &nframes, 1, MPI_INT, MPI_MIN );
if (totalFrames != nframes) {
rprintf("Warning: Replica '%s' frames (%i) is > # frames in shortest replica.\n",
repFname.full(), nframes);
mprintf("Warning: Setting total # of frames to read from replica ensemble to %i\n",
totalFrames);
}
if (trajComm.Master()) {
static const int iSize = 6;
static const char* iTitle[iSize] = {"box", "velocity", "temperature", "time", "force",
"replica dimensions"};
// Check coordinate info of all files 0 1 2 3 4 5
std::vector<int> Info( iSize * ensComm.Size() ); // box, vel, temp, time, force, nRepDims
int rank_info[iSize];
rank_info[0] = (int)cInfo.TrajBox().Type();
rank_info[1] = (int)cInfo.HasVel();
rank_info[2] = (int)cInfo.HasTemp();
rank_info[3] = (int)cInfo.HasTime();
rank_info[4] = (int)cInfo.HasForce();
rank_info[5] = cInfo.ReplicaDimensions().Ndims();
ensComm.AllGather( rank_info, iSize, MPI_INT, &Info[0] );
// TODO Should mismatches be errors instead?
for (int midx = 0; midx != iSize; midx++) {
for (int ridx = midx + iSize; ridx < (int)Info.size(); ridx += iSize) {
if (Info[midx] != Info[ridx]) {
rprintf("Warning: Replica %i %s info does not match first replica.\n",
ridx/iSize, iTitle[midx]);
}
}
}
}
// TODO: Put code below into a common routine with serial version
// Check how many frames will actually be read
if (counter.CheckFrameArgs( totalFrames, argIn )) return 1;
// SANITY CHECK
if (IOarray_.size() != replica_filenames_.size()) {
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( repFname.full(), trajParm->c_str() );
return 0;
}
Exec::RetType Exec_CrdAction::DoCrdAction(CpptrajState& State, ArgList& actionargs,
DataSet_Coords* CRD, Action* act,
TrajFrameCounter const& frameCount) const
{
Timer total_time;
total_time.Start();
# ifdef MPI
ActionInit state(State.DSL(), State.DFL(), trajComm_);
# else
ActionInit state(State.DSL(), State.DFL());
# endif
if ( act->Init( actionargs, state, State.Debug() ) != Action::OK )
return CpptrajState::ERR;
actionargs.CheckForMoreArgs();
// Set up frame and parm for COORDS.
ActionSetup originalSetup( CRD->TopPtr(), CRD->CoordsInfo(), CRD->Size() );
Frame originalFrame = CRD->AllocateFrame();
// Set up for this topology
Action::RetType setup_ret = act->Setup( originalSetup );
if ( setup_ret == Action::ERR || setup_ret == Action::SKIP )
return CpptrajState::ERR;
// If the topology was modified, we will need a new COORDS set.
DataSet_Coords* crdOut = 0;
if ( setup_ret == Action::MODIFY_TOPOLOGY ) {
// This will not work for a TRJ set.
switch ( CRD->Type() ) {
case DataSet::TRAJ : mprinterr("Error: Cannot modify TRAJ data sets.\n"); break;
case DataSet::COORDS : crdOut = (DataSet_Coords*)new DataSet_Coords_CRD(); break;
case DataSet::REF_FRAME : crdOut = (DataSet_Coords*)new DataSet_Coords_REF(); break;
default: crdOut = 0; // SANITY
}
if (crdOut == 0) return CpptrajState::ERR;
mprintf("Info: crdaction: COORDS set '%s' will be modified by action '%s'\n",
CRD->legend(), actionargs.Command());
if (frameCount.TotalReadFrames() != (int)CRD->Size())
mprintf("Info: crdaction: Previous size= %zu, new size is %i\n",
CRD->Size(), frameCount.TotalReadFrames());
// Set up set, copy original metadata
crdOut->SetMeta( CRD->Meta() );
if (crdOut->CoordsSetup( originalSetup.Top(), originalSetup.CoordInfo() ))
return CpptrajState::ERR;
DataSet::SizeArray mfArray(1, frameCount.TotalReadFrames());
if (crdOut->Allocate( mfArray )) return CpptrajState::ERR;
}
// Loop over all frames in COORDS.
ProgressBar* progress = 0;
if (State.ShowProgress())
progress = new ProgressBar( frameCount.TotalReadFrames() );
int set = 0;
for (int frame = frameCount.Start(); frame < frameCount.Stop();
frame += frameCount.Offset(), ++set)
{
// Since Frame can be modified by actions, save original and use currentFrame
ActionFrame frm( &originalFrame, set );
if (progress != 0) progress->Update( set );
CRD->GetFrame( frame, originalFrame );
Action::RetType ret = act->DoAction( set, frm );
if (ret == Action::ERR) {
mprinterr("Error: crdaction: Frame %i, set %i\n", frame + 1, set + 1);
break;
}
// Check if frame was modified. If so, update COORDS.
if ( ret == Action::MODIFY_COORDS ) {
if (crdOut != 0)
crdOut->AddFrame( frm.Frm() );
else
CRD->SetCRD( frame, frm.Frm() );
}
}
if (progress != 0) delete progress;
# ifdef MPI
act->SyncAction();
# endif
// If topology was modified, replace old set with new.
if ( setup_ret == Action::MODIFY_TOPOLOGY ) {
mprintf("Info: crdaction: Topology for '%s' was modified by action '%s'\n",
CRD->legend(), actionargs.Command());
State.DSL().RemoveSet( CRD );
State.DSL().AddSet( crdOut );
}
act->Print();
State.MasterDataFileWrite();
total_time.Stop();
mprintf("TIME: Total action execution time: %.4f seconds.\n", total_time.Total());
return CpptrajState::OK;
}
