Пример #1
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;
}
Пример #2
0
Exec::RetType Exec_DataFilter::Execute(CpptrajState& State, ArgList& argIn) {
  Action_FilterByData filterAction;
  ActionInit state(State.DSL(), State.DFL());
  if (filterAction.Init(argIn, state, State.Debug()) != Action::OK)
    return CpptrajState::ERR;
  size_t nframes = filterAction.DetermineFrames();
  if (nframes < 1) {
    mprinterr("Error: No data to filter. All sets must contain some data.\n");
    return CpptrajState::ERR;
  }
  ProgressBar progress( nframes );
  ActionFrame frm;
  for (size_t frame = 0; frame != nframes; frame++) {
    progress.Update( frame );
    filterAction.DoAction(frame, frm); // Filter does not need frame.
  }
  // Trigger master datafile write just in case
  State.MasterDataFileWrite();
  return CpptrajState::OK;
}
Пример #3
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;
}