Пример #1
0
int Traj_AmberNetcdf::parallelOpenTrajout(Parallel::Comm const& commIn) {
  if (Ncid() != -1) return 0;
  int err = ncmpi_open(commIn.MPIcomm(), filename_.full(), NC_WRITE, MPI_INFO_NULL, &ncid_);
  if (checkPNCerr(err)) {
    mprinterr("Error: Opening NetCDF file '%s' for writing in parallel.\n", filename_.full());
    return 1;
  }
  err = ncmpi_begin_indep_data( ncid_ ); // Independent data mode
  return 0;
}
Пример #2
0
int Traj_AmberNetcdf::parallelReadFrame(int set, Frame& frameIn) {
  MPI_Offset pstart_[3];
  MPI_Offset pcount_[3];
  pstart_[0] = set;
  pstart_[1] = 0;
  pstart_[2] = 0;
  pcount_[0] = 1;
  pcount_[1] = Ncatom();
  pcount_[2] = 3;

  //int err = ncmpi_get_vara_float_all(ncid_, coordVID_, pstart_, pcount_, Coord_);
  int err = ncmpi_get_vara_float(ncid_, coordVID_, pstart_, pcount_, Coord_);
  if (checkPNCerr(err)) return Parallel::Abort(err);
  FloatToDouble(frameIn.xAddress(), Coord_);
  if (velocityVID_ != -1) {
    //err = ncmpi_get_vara_float_all(ncid_, velocityVID_, pstart_, pcount_, Coord_);
    err = ncmpi_get_vara_float(ncid_, velocityVID_, pstart_, pcount_, Coord_);
    if (checkPNCerr(err)) return Parallel::Abort(err);
    FloatToDouble(frameIn.vAddress(), Coord_);
  }
  if (frcVID_ != -1) {
    err = ncmpi_get_vara_float(ncid_, frcVID_, pstart_, pcount_, Coord_);
    if (checkPNCerr(err)) return Parallel::Abort(err);
    FloatToDouble(frameIn.fAddress(), Coord_);
  } 

  pcount_[2] = 0;
  if (cellLengthVID_ != -1) {
    pcount_[1] = 3;
    //err = ncmpi_get_vara_double_all(ncid_, cellLengthVID_, pstart_, pcount_, frameIn.bAddress());
    err = ncmpi_get_vara_double(ncid_, cellLengthVID_, pstart_, pcount_, frameIn.bAddress());
    if (checkPNCerr(err)) return Parallel::Abort(err);
    //err = ncmpi_get_vara_double_all(ncid_, cellAngleVID_, pstart_, pcount_, frameIn.bAddress()+3);
    err = ncmpi_get_vara_double(ncid_, cellAngleVID_, pstart_, pcount_, frameIn.bAddress()+3);
  }
  if (TempVID_ != -1) {
    //err = ncmpi_get_vara_double_all(ncid_, TempVID_, pstart_, pcount_, frameIn.tAddress());
    err = ncmpi_get_vara_double(ncid_, TempVID_, pstart_, pcount_, frameIn.tAddress());
    if (checkPNCerr(err)) return Parallel::Abort(err);
  }
  if (timeVID_ != -1) {
    float time;
    err = ncmpi_get_vara_float(ncid_, timeVID_, pstart_, pcount_, &time);
    if (checkPNCerr(err)) return Parallel::Abort(err);
    frameIn.SetTime( (double)time );
  }
  if (indicesVID_ != -1) {
    pcount_[1] = remd_dimension_;
    //err = ncmpi_get_vara_int_all(ncid_, indicesVID_, pstart_, pcount_, frameIn.iAddress());
    err = ncmpi_get_vara_int(ncid_, indicesVID_, pstart_, pcount_, frameIn.iAddress());
    if (checkPNCerr(err)) return Parallel::Abort(err);
  }
  return 0;
}
Пример #3
0
int Traj_AmberNetcdf::parallelWriteFrame(int set, Frame const& frameOut) {
  MPI_Offset pstart_[3];
  MPI_Offset pcount_[3];
  pstart_[0] = set;
  pstart_[1] = 0;
  pstart_[2] = 0;
  pcount_[0] = 1;
  pcount_[1] = Ncatom();
  pcount_[2] = 3;
  // TODO check error better
  DoubleToFloat(Coord_, frameOut.xAddress());
  //int err = ncmpi_put_vara_float_all(ncid_, coordVID_, pstart_, pcount_, Coord_);
  int err = ncmpi_put_vara_float(ncid_, coordVID_, pstart_, pcount_, Coord_);
  if (checkPNCerr(err)) return Parallel::Abort(err);
  if (velocityVID_ != -1) {
    DoubleToFloat(Coord_, frameOut.vAddress());
    //err = ncmpi_put_vara_float_all(ncid_, velocityVID_, pstart_, pcount_, Coord_);
    err = ncmpi_put_vara_float(ncid_, velocityVID_, pstart_, pcount_, Coord_);
    if (checkPNCerr(err)) return Parallel::Abort(err);
  }
  if (frcVID_ != -1) {
    DoubleToFloat(Coord_, frameOut.fAddress());
    err = ncmpi_put_vara_float(ncid_, frcVID_, pstart_, pcount_, Coord_);
    if (checkPNCerr(err)) return Parallel::Abort(err);
  }

  pcount_[2] = 0;
  if (cellLengthVID_ != -1) {
    pcount_[1] = 3;
    //err = ncmpi_put_vara_double_all(ncid_, cellLengthVID_, pstart_, pcount_, frameOut.bAddress());
    err = ncmpi_put_vara_double(ncid_, cellLengthVID_, pstart_, pcount_, frameOut.bAddress());
    if (checkPNCerr(err)) return Parallel::Abort(err);
    //err = ncmpi_put_vara_double_all(ncid_, cellAngleVID_, pstart_, pcount_, frameOut.bAddress()+3);
    err = ncmpi_put_vara_double(ncid_, cellAngleVID_, pstart_, pcount_, frameOut.bAddress()+3);
  }
  if (TempVID_ != -1) {
    //err = ncmpi_put_vara_double_all(ncid_, TempVID_, pstart_, pcount_, frameOut.tAddress());
    err = ncmpi_put_vara_double(ncid_, TempVID_, pstart_, pcount_, frameOut.tAddress());
    if (checkPNCerr(err)) return Parallel::Abort(err);
  }
  if (timeVID_ != -1) {
    float tVal = (float)frameOut.Time();
    err = ncmpi_put_vara_float(ncid_, timeVID_, pstart_, pcount_, &tVal);
    if (checkPNCerr(err)) return Parallel::Abort(err);
  }
  if (indicesVID_ != -1) {
    pcount_[1] = remd_dimension_;
    //err = ncmpi_put_vara_int_all(ncid_, indicesVID_, pstart_, pcount_, frameOut.iAddress());
    err = ncmpi_put_vara_int(ncid_, indicesVID_, pstart_, pcount_, frameOut.iAddress());
    if (checkPNCerr(err)) return Parallel::Abort(err);
  }
  return 0;
}
Пример #4
0
// Traj_NcEnsemble::readArray() //TODO RemdValues
int Traj_NcEnsemble::readArray(int set, FrameArray& f_ensemble) {
# ifdef HAS_PNETCDF
  MPI_Offset pstart_[4];
  MPI_Offset pcount_[4];
# define start_ pstart_
# define count_ pcount_
# endif
  start_[0] = set; // Frame
  start_[2] = 0;   // Atoms
  start_[3] = 0;   // XYZ
  count_[0] = 1;        // Frame
  count_[1] = 1;        // Ensemble
  count_[3] = 3;        // XYZ
  //rprintf("DEBUG: Reading frame %i\n", set+1);
  for (int member = ensembleStart_; member != ensembleEnd_; member++) {
#   ifdef MPI
    Frame& frm = f_ensemble[0];
#   else
    Frame& frm = f_ensemble[member];
#   endif
    start_[1] = member;   // Ensemble
    count_[2] = Ncatom(); // Atoms
    // Read Coords
#   ifdef HAS_PNETCDF
    if (checkPNCerr(ncmpi_get_vara_float_all(ncid_, coordVID_, start_, count_, Coord_)))
#   else
    if (NC::CheckErr(nc_get_vara_float(ncid_, coordVID_, start_, count_, Coord_)))
#   endif
    {
      rprinterr("Error: Getting coordinates for frame %i\n", set+1);
      return 1;
    }
    FloatToDouble(frm.xAddress(), Coord_);
    //mprintf("Frm=%8i Rep=%8i ", set+1, member+1); // DEBUG
    //frm.printAtomCoord(0); // DEBUG
    // Read Velocities
    if (velocityVID_ != -1) {
#     ifdef HAS_PNETCDF
      if (checkPNCerr(ncmpi_get_vara_float_all(ncid_, velocityVID_, start_, count_, Coord_)))
#     else
      if (NC::CheckErr(nc_get_vara_float(ncid_, velocityVID_, start_, count_, Coord_)))
#     endif
      {
        rprinterr("Error: Getting velocities for frame %i\n", set+1);
        return 1;
      }
      FloatToDouble(frm.vAddress(), Coord_);
    }
    // Read Box
    if (cellLengthVID_ != -1) {
      count_[2] = 3;
#     ifdef HAS_PNETCDF
      if (checkPNCerr(ncmpi_get_vara_double_all(ncid_, cellLengthVID_, start_, count_, frm.bAddress())))
#     else
      if (NC::CheckErr(nc_get_vara_double(ncid_, cellLengthVID_, start_, count_, frm.bAddress())))
#     endif
      {
        rprinterr("Error: Getting cell lengths for frame %i.\n", set+1);
        return 1;
      }
#     ifdef HAS_PNETCDF
      if (checkPNCerr(ncmpi_get_vara_double_all(ncid_, cellAngleVID_, start_, count_, frm.bAddress()+3)))
#     else
      if (NC::CheckErr(nc_get_vara_double(ncid_, cellAngleVID_, start_, count_, frm.bAddress()+3)))
#     endif
      {
        rprinterr("Error: Getting cell angles for frame %i.\n", set+1);
        return 1;
      }
    }
    // Read Temperature
    if (TempVID_!=-1) {
#     ifdef HAS_PNETCDF
      if (checkPNCerr(ncmpi_get_vara_double_all(ncid_, TempVID_, start_, count_, frm.tAddress())))
#     else
      if (NC::CheckErr(nc_get_vara_double(ncid_, TempVID_, start_, count_, frm.tAddress())))
#     endif
      {
        rprinterr("Error: Getting replica temperature for frame %i.\n", set+1);
        return 1;
      }
      //fprintf(stderr,"DEBUG: Replica Temperature %lf\n",F->T);
    }
    // Read indices
    if (indicesVID_!=-1) {
      count_[2] = remd_dimension_;
#     ifdef HAS_PNETCDF
      if (checkPNCerr(ncmpi_get_vara_int_all(ncid_, indicesVID_, start_, count_, frm.iAddress())))
#     else
      if (NC::CheckErr(nc_get_vara_int(ncid_, indicesVID_, start_, count_, frm.iAddress())))
#     endif
      {
        rprinterr("Error: Getting replica indices for frame %i.\n", set+1);
        return 1;
      }
      // DEBUG
      //char buffer[128];
      //char* ptr = buffer;
      //ptr += sprintf(buffer,"DEBUG:\tReplica indices:");
      //for (int dim=0; dim < remd_dimension_; dim++) ptr += sprintf(ptr, " %i", frm.RemdIndices()[dim]);
      //sprintf(ptr,"\n");
      //rprintf("%s", buffer);
    }
  }
# ifdef HAS_PNETCDF
  // DEBUG
# undef start_
# undef count_
# endif
  return 0;
}