Ejemplo n.º 1
0
/** Like the strip action, closest will modify the current parm keeping info
  * for atoms in mask plus the closestWaters solvent molecules. Set up the
  * vector of MolDist objects, one for every solvent molecule in the original
  * parm file. Atom masks for each solvent molecule will be set up.
  */
Action_Closest::RetType Action_Closest::Setup(Topology const& topIn, CoordinateInfo const& cInfoIn)
{
  // If there are no solvent molecules this action is not valid.
  if (topIn.Nsolvent()==0) {
    mprintf("Warning: Parm %s does not contain solvent.\n",topIn.c_str());
    return Action_Closest::SKIP;
  }
  // If # solvent to keep >= solvent in this parm the action is not valid.
  if (closestWaters_ >= topIn.Nsolvent()) {
    mprintf("Warning: # solvent to keep (%i) >= # solvent molecules in '%s' (%i)\n",
            closestWaters_, topIn.c_str(), topIn.Nsolvent());
    return Action_Closest::SKIP;
  }
  image_.SetupImaging( cInfoIn.TrajBox().Type() );
  if (image_.ImagingEnabled())
    mprintf("\tDistances will be imaged.\n");
  else
    mprintf("\tImaging off.\n"); 
  // LOOP OVER MOLECULES
  // 1: Check that all solvent molecules contain same # atoms. Solvent 
  //    molecules must be identical for the command to work properly; 
  //    the prmtop strip occurs only once so the solvent params become fixed.
  // 2: Set up a mask for all solvent molecules.
  SolventMols_.clear();
  // NOTE: May not be necessary to init 'solvent'
  MolDist solvent;
  solvent.D = 0.0;
  solvent.mol = 0;
  SolventMols_.resize(topIn.Nsolvent(), solvent);
  std::vector<MolDist>::iterator mdist = SolventMols_.begin();
  // 3: Set up the soluteMask for all non-solvent molecules.
  int molnum = 1;
  int nclosest = 0;
  int NsolventAtoms = -1;
  for (Topology::mol_iterator Mol = topIn.MolStart();
                              Mol != topIn.MolEnd(); ++Mol)
  {
    if ( Mol->IsSolvent() ) {
      // Solvent, check for same # of atoms.
      if (NsolventAtoms == -1)
        NsolventAtoms = Mol->NumAtoms();
      else if ( NsolventAtoms != Mol->NumAtoms() ) {
        mprinterr("Error: Solvent molecules in '%s' are not of uniform size.\n"
                  "Error:   First solvent mol = %i atoms, solvent mol %i = %i atoms.\n",
                  topIn.c_str(), NsolventAtoms, molnum, (*Mol).NumAtoms());
        return Action_Closest::ERR;
      }
      // mol here is the output molecule number which is why it starts from 1.
      mdist->mol = molnum;
      // Solvent molecule mask
      mdist->mask.AddAtomRange( Mol->BeginAtom(), Mol->EndAtom() );
      // Atoms in the solvent molecule to actually calculate distances to.
      if (firstAtom_) {
        mdist->solventAtoms.assign(1, Mol->BeginAtom() );
      } else {
        mdist->solventAtoms.clear();
        mdist->solventAtoms.reserve( Mol->NumAtoms() );
        for (int svatom = Mol->BeginAtom(); svatom < Mol->EndAtom(); svatom++)
          mdist->solventAtoms.push_back( svatom );
      }
      if (debug_ > 0) {
        mprintf("DEBUG:\tSet up mol %i:", mdist->mol); // DEBUG
        mdist->mask.PrintMaskAtoms("solvent"); // DEBUG
        mprintf("\n"); // DEBUG
      }
      ++mdist;
    }
    ++molnum;
  }

  // Setup distance atom mask
  // NOTE: Should ensure that no solvent atoms are selected!
  if ( topIn.SetupIntegerMask(distanceMask_) ) return Action_Closest::ERR;
  if (distanceMask_.None()) {
    mprintf("Warning: Distance mask '%s' contains no atoms.\n",
            distanceMask_.MaskString());
    return Action_Closest::SKIP;
  }
  distanceMask_.MaskInfo();

  // Check the total number of solvent atoms to be kept.
  NsolventAtoms *= closestWaters_;
  mprintf("\tKeeping %i solvent atoms.\n",NsolventAtoms);
  if (NsolventAtoms < 1) {
    mprintf("Warning: # of solvent atoms to be kept is < 1.\n");
    return Action_Closest::SKIP;
  }
  NsolventMolecules_ = (int)SolventMols_.size();

  return Action_Closest::OK;
}
Ejemplo n.º 2
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;
}