C++ ActionSetup::CoordInfo方法代码示例

// Action_Unwrap::Setup()
Action::RetType Action_Unwrap::Setup(ActionSetup& setup) {
  // Ensure same number of atoms in current parm and ref parm
  if ( RefParm_!=0 ) {
    if ( setup.Top().Natom() != RefParm_->Natom() ) {
      mprinterr("Error: unwrap: # atoms in reference parm %s is not\n", RefParm_->c_str());
      mprinterr("Error:         equal to # atoms in parm %s\n", setup.Top().c_str());
      return Action::ERR;
    }
  }
  // Check box type
  if (setup.CoordInfo().TrajBox().Type()==Box::NOBOX) {
    mprintf("Error: unwrap: Parm %s does not contain box information.\n",
            setup.Top().c_str());
    return Action::ERR;
  }
  orthogonal_ = false;
  if (setup.CoordInfo().TrajBox().Type()==Box::ORTHO)
    orthogonal_ = true;

  // Setup atom pairs to be unwrapped.
  imageList_ = Image::CreatePairList(setup.Top(), imageMode_, maskExpression_);
  if (imageList_.empty()) {
    mprintf("Warning: Mask selects no atoms for topology '%s'.\n", setup.Top().c_str());
    return Action::SKIP;
  }
  mprintf("\tNumber of %ss to be unwrapped is %zu\n",
          Image::ModeString(imageMode_), imageList_.size()/2);

  // Use current parm as reference if not already set
  if (RefParm_ == 0)
    RefParm_ = setup.TopAddress();
  return Action::OK;
}

/** Set angle up for this parmtop. Get masks etc.
  */
Action::RetType Action_Esander::Setup(ActionSetup& setup) {
  if (currentParm_ != 0 && currentParm_->Pindex() != setup.Top().Pindex())
  {
    mprintf("Warning: Current topology is %i:%s but reference is %i:%s. Skipping.\n",
            setup.Top().Pindex(), setup.Top().c_str(),
            currentParm_->Pindex(), currentParm_->c_str());
    return Action::SKIP;
  }
  // Check for LJ terms
  if (!setup.Top().Nonbond().HasNonbond())
  {
    mprinterr("Error: Topology '%s' does not have non-bonded parameters.\n", setup.Top().c_str());
    return Action::ERR;
  }
  // If reference specified, init now. Otherwise using first frame.
  if (currentParm_ != 0 ) {
    if ( InitForRef() ) return Action::ERR;
  } else
    currentParm_ = setup.TopAddress();
  // If saving of forces is requested, make sure CoordinateInfo has force.
  if (save_forces_) {
    cInfo_ = setup.CoordInfo();
    cInfo_.SetForce( true );
    newFrame_.SetupFrameV( setup.Top().Atoms(), cInfo_ );
    setup.SetCoordInfo( &cInfo_ );
    ret_ = Action::MODIFY_COORDS;
    return Action::MODIFY_TOPOLOGY;
  }
  ret_ = Action::OK;
  return Action::OK;
}

Action::RetType Action_DNAionTracker::Setup(ActionSetup& setup) {
  // Setup masks
  if (setup.Top().SetupIntegerMask( p1_ )) return Action::ERR; 
  if ( p1_.None() ) {
    mprinterr("Error: dnaiontracker: No atoms in mask1\n");
    return Action::ERR;
  }
  if (setup.Top().SetupIntegerMask( p2_ )) return Action::ERR;  
  if ( p2_.None() ) {
    mprinterr("Error: dnaiontracker: No atoms in mask2\n");
    return Action::ERR;
  }
  if (setup.Top().SetupIntegerMask( base_ )) return Action::ERR;  
  if ( base_.None() ) {
    mprinterr("Error: dnaiontracker: No atoms in mask3\n");
    return Action::ERR;
  }
  if (setup.Top().SetupIntegerMask( ions_ )) return Action::ERR;  
  if ( ions_.None() ) {
    mprinterr("Error: dnaiontracker: No atoms in mask4\n");
    return Action::ERR;
  }
  SetupImaging( setup.CoordInfo().TrajBox().Type() );
  mprintf("\tPhosphate1 Mask [%s] %i atoms.\n", p1_.MaskString(), p1_.Nselected());
  mprintf("\tPhosphate2 Mask [%s] %i atoms.\n", p2_.MaskString(), p2_.Nselected());
  mprintf("\t      Base Mask [%s] %i atoms.\n", base_.MaskString(), base_.Nselected());
  mprintf("\t      Ions Mask [%s] %i atoms.\n", ions_.MaskString(), ions_.Nselected());

  return Action::OK;
}

/** For this to be valid the same # of atoms should be selected each time. */
Action::RetType Action_VelocityAutoCorr::Setup(ActionSetup& setup) {
  if (setup.Top().SetupIntegerMask( mask_ )) return Action::ERR;
  mask_.MaskInfo();
  if (mask_.None()) {
    mprintf("Warning: No atoms selected by mask.\n");
    return Action::SKIP;
  }
  // If using velocity info, check that it is present.
  if (useVelInfo_ && !setup.CoordInfo().HasVel()) {
    mprinterr("Error: 'usevelocity' specified but no velocity info assocated with %s\n",
              setup.Top().c_str());
    return Action::ERR;
  }
  // If we have already started recording velocities, check that the current 
  // number of selected atoms has remained the same.
  if (!Vel_.empty()) {
    if ((int)Vel_.size() != mask_.Nselected()) {
      mprinterr("Error: # of selected atoms %i has changed (previously %zu)\n",
                mask_.Nselected(), Vel_.size());
      return Action::ERR;
    }
  } else
    Vel_.resize( mask_.Nselected() );
  return Action::OK;
}

/** Determine what atoms each mask pertains to for the current parm file.
  */
Action::RetType Action_LIE::Setup(ActionSetup& setup) {
  if (setup.Top().SetupIntegerMask( Mask1_ )) return Action::ERR;
  if (setup.Top().SetupIntegerMask( Mask2_ )) return Action::ERR;

  mprintf("\tLIE: %i Ligand Atoms, %i Surrounding Atoms\n",
          Mask1_.Nselected(), Mask2_.Nselected());

  if (setup.CoordInfo().TrajBox().Type() == Box::NOBOX) {
    mprinterr("Error: LIE: Must have explicit solvent system with box info\n");
    return Action::ERR;
  }

  if (Mask1_.None() || Mask2_.None()) {
    mprintf("Warning: LIE: One or both masks have no atoms.\n");
    return Action::SKIP;
  }

  if (SetupParms(setup.Top()))
    return Action::ERR;

  // Back up the parm
  CurrentParm_ = setup.TopAddress();

  return Action::OK;
}

// Action_Outtraj::Setup()
Action::RetType Action_Outtraj::Setup(ActionSetup& setup) {
  if (associatedParm_->Pindex() != setup.Top().Pindex())
    return Action::SKIP;
  if (!isSetup_) { // TODO: Trajout IsOpen?
    if (outtraj_.SetupTrajWrite(setup.TopAddress(), setup.CoordInfo(), setup.Nframes()))
      return Action::ERR;
    outtraj_.PrintInfo(0);
    isSetup_ = true;
  }
  return Action::OK;
}

/** Set up solute and solvent masks. If no solvent mask was specified use 
  * solvent information in the current topology.
  */
Action::RetType Action_Watershell::Setup(ActionSetup& setup) {
  // Set up solute mask
  if (setup.Top().SetupIntegerMask( soluteMask_ )) return Action::ERR;
  if ( soluteMask_.None() ) {
    mprintf("Warning: No atoms in solute mask [%s].\n",soluteMask_.MaskString());
    return Action::SKIP;
  }
  // Set up solvent mask
  if (!solventmaskexpr_.empty()) {
    if (setup.Top().SetupIntegerMask( solventMask_ )) return Action::ERR;
  } else {
    solventMask_.ResetMask();
    for (Topology::mol_iterator mol = setup.Top().MolStart();
                                mol != setup.Top().MolEnd(); ++mol)
    {
      if ( mol->IsSolvent() )
        solventMask_.AddAtomRange( mol->BeginAtom(), mol->EndAtom() );
    }
  }
  if ( solventMask_.None() ) {
    if (!solventmaskexpr_.empty())
      mprintf("Warning: No solvent atoms selected by mask [%s]\n",
                solventmaskexpr_.c_str());
    else
      mprintf("Warning: No solvent atoms in topology %s\n",setup.Top().c_str());
    return Action::SKIP;
  }
  SetupImaging( setup.CoordInfo().TrajBox().Type() );
  // Create space for residues
# ifdef _OPENMP
  // Only re-allocate for larger # of residues
  if ( setup.Top().Nres() > NactiveResidues_ ) {
    if (activeResidues_thread_ != 0) {
      // Deallocate each thread
      for (int i = 0; i < NactiveResidues_; ++i)
        delete[] activeResidues_thread_[i];
    } else {
      // Initial thread allocation needed
      activeResidues_thread_ = new int*[ numthreads_ ];
    }
    // Allocate each thread
    for (int i = 0; i < numthreads_; ++i) {
      activeResidues_thread_[i] = new int[ setup.Top().Nres() ];
      std::fill( activeResidues_thread_[i], activeResidues_thread_[i] + setup.Top().Nres(), 0 );
    }
  }
  NactiveResidues_ = setup.Top().Nres();
# else
  activeResidues_.resize( setup.Top().Nres(), 0 );
# endif
  // Store current Parm
  CurrentParm_ = setup.TopAddress();
  return Action::OK;    
}

/** Determine what atoms each mask pertains to for the current parm file.
  */
Action::RetType Action_ReplicateCell::Setup(ActionSetup& setup) {
  if (setup.Top().SetupIntegerMask( Mask1_ )) return Action::ERR;
  mprintf("\t%s (%i atoms)\n",Mask1_.MaskString(), Mask1_.Nselected());
  if (Mask1_.None()) {
    mprintf("Warning: One or both masks have no atoms.\n");
    return Action::SKIP;
  }
  // Set up imaging info for this parm
  image_.SetupImaging( setup.CoordInfo().TrajBox().Type() );
  if (!image_.ImagingEnabled()) {
    mprintf("Warning: Imaging cannot be performed for topology %s\n", setup.Top().c_str());
    return Action::SKIP;
  }
  // Create combined topology.
  if (combinedTop_.Natom() > 0) {
    // Topology already set up. Check that # atoms matches.
    if (Mask1_.Nselected() * ncopies_ != combinedTop_.Natom()) {
      mprintf("Warning: Unit cell can currently only be replicated for"
              " topologies with same # atoms.\n");
      return Action::SKIP;
    }
    // Otherwise assume top does not change.
  } else {
    // Set up topology and frame.
    Topology* stripParm = setup.Top().modifyStateByMask( Mask1_ );
    if (stripParm == 0) return Action::ERR;
    for (int cell = 0; cell != ncopies_; cell++)
      combinedTop_.AppendTop( *stripParm );
    combinedTop_.Brief("Combined parm:");
    delete stripParm;
    if (!parmfilename_.empty()) {
      ParmFile pfile;
      if (pfile.WriteTopology(combinedTop_, parmfilename_, ParmFile::UNKNOWN_PARM, 0)) {
        mprinterr("Error: Topology file %s not written.\n", parmfilename_.c_str());
        return Action::ERR;
      }
    }
    // Only coordinates for now. FIXME
    combinedFrame_.SetupFrameM(combinedTop_.Atoms());
    // Set up COORDS / output traj if necessary.
    if (coords_ != 0)
      coords_->CoordsSetup( combinedTop_, CoordinateInfo() );
    if (!trajfilename_.empty()) {
      if ( outtraj_.PrepareEnsembleTrajWrite(trajfilename_, trajArgs_,
                                             &combinedTop_, CoordinateInfo(),
                                             setup.Nframes(), TrajectoryFile::UNKNOWN_TRAJ,
                                             ensembleNum_) )
        return Action::ERR;
    }
  }

  return Action::OK;
}

// Action_CheckStructure::Setup()
Action::RetType Action_CheckStructure::Setup(ActionSetup& setup) {
  CurrentParm_ = setup.TopAddress();
  if (SeparateSetup( setup.Top(), setup.CoordInfo().TrajBox().Type(),bondcheck_ ))
    return Action::ERR;
  // Print imaging info for this parm
  if (bondcheck_)
    mprintf("\tChecking %u bonds.\n", bondList_.size());
  if (image_.ImagingEnabled())
    mprintf("\tImaging on.\n");
  else
    mprintf("\timaging off.\n");
  return Action::OK;
}

// Action_Outtraj::Setup()
Action::RetType Action_Outtraj::Setup(ActionSetup& setup) {
  if (!isActive_ || associatedParm_->Pindex() != setup.Top().Pindex()) {
    mprintf("\tOutput trajectory not active for topology '%s'\n", setup.Top().c_str());
    return Action::SKIP;
  }
  if (!isSetup_) { // TODO: Trajout IsOpen?
    if (outtraj_.SetupTrajWrite(setup.TopAddress(), setup.CoordInfo(), setup.Nframes()))
      return Action::ERR;
    mprintf("      "); //TODO this is a kludge; PrintInfo should be a string.
    outtraj_.PrintInfo(0);
    mprintf("\tHas %s\n", outtraj_.Traj().CoordInfo().InfoString().c_str());
    isSetup_ = true;
  }
  return Action::OK;
}

// Action_GridFreeEnergy::setup()
Action::RetType Action_GridFreeEnergy::Setup(ActionSetup& setup) {
  // Setup grid, checks box info.
  if (GridSetup( setup.Top(), setup.CoordInfo() )) return Action::ERR;

  // Setup mask
  if (setup.Top().SetupIntegerMask( mask_ ))
    return Action::ERR;
  mask_.MaskInfo();
  if (mask_.None()) {
    mprinterr("Warning: No atoms selected for parm %s\n", setup.Top().c_str());
    return Action::SKIP;
  }

  return Action::OK;
}

// Action_Center::Setup()
Action::RetType Action_Center::Setup(ActionSetup& setup) {

  if ( setup.Top().SetupIntegerMask(Mask_) ) return Action::ERR;
  Mask_.MaskInfo();
  if (Mask_.None()) {
    mprintf("Warning: Mask contains 0 atoms.\n");
    return Action::SKIP;
  }

  if (centerMode_ == BOXCTR && setup.CoordInfo().TrajBox().Type()==Box::NOBOX) {
    mprintf("Warning: Box center specified but no box information.\n");
    return Action::SKIP;
  }

  return Action::OK;  
}

// Action_Density::DensitySetup()
Action::RetType Action_Density::DensitySetup(ActionSetup& setup) {
  // Total system density setup
  image_.SetupImaging( setup.CoordInfo().TrajBox().Type() );
  if (!image_.ImagingEnabled()) {
    mprintf("Warning: No unit cell information, total density cannot be calculated for '%s'\n",
            setup.Top().c_str());
    return Action::SKIP;
  }
  // delta_ will hold sum of masses
  delta_ = 0.0;
  for (int idx = 0; idx != setup.Top().Natom(); idx++)
    delta_ += setup.Top()[idx].Mass();
  mprintf("\tSum of masses is %g amu\n", delta_);

  return Action::OK;
}

// Action_NativeContacts::Setup()
Action::RetType Action_NativeContacts::Setup(ActionSetup& setup) {
  // Setup potential contact lists for this topology
  if (SetupContactLists( setup.Top(), Frame()))
    return Action::SKIP;
  mprintf("\t%zu potential contact sites for '%s'\n", Mask1_.Nselected(), Mask1_.MaskString());
  if (Mask2_.MaskStringSet())
    mprintf("\t%zu potential contact sites for '%s'\n", Mask2_.Nselected(), Mask2_.MaskString());
  // Set up imaging info for this parm
  image_.SetupImaging( setup.CoordInfo().TrajBox().Type() );
  if (image_.ImagingEnabled())
    mprintf("\tImaging enabled.\n");
  else
    mprintf("\tImaging disabled.\n");
  CurrentParm_ = setup.TopAddress();
  return Action::OK;
}

/** Determine what atoms each mask pertains to for the current parm file.
  * Imaging is checked for in Action::Setup. 
  */
Action::RetType Action_Distance::Setup(ActionSetup& setup) {
  if (setup.Top().SetupIntegerMask( Mask1_ )) return Action::ERR;
  if (setup.Top().SetupIntegerMask( Mask2_ )) return Action::ERR;
  mprintf("\t%s (%i atoms) to %s (%i atoms)",Mask1_.MaskString(), Mask1_.Nselected(),
          Mask2_.MaskString(),Mask2_.Nselected());
  if (Mask1_.None() || Mask2_.None()) {
    mprintf("\nWarning: One or both masks have no atoms.\n");
    return Action::SKIP;
  }
  // Set up imaging info for this parm
  image_.SetupImaging( setup.CoordInfo().TrajBox().Type() );
  if (image_.ImagingEnabled())
    mprintf(", imaged");
  else
    mprintf(", imaging off");
  mprintf(".\n");

  return Action::OK;  
}