コード例 #1
0
ファイル: Traj_NcEnsemble.cpp プロジェクト: Amber-MD/cpptraj
// Traj_NcEnsemble::setupTrajout()
int Traj_NcEnsemble::setupTrajout(FileName const& fname, Topology* trajParm,
                                  CoordinateInfo const& cInfoIn,
                                  int NframesToWrite, bool append)
{
  int err = 0;
# ifdef MPI
  if (NoPnetcdf()) return 1;
# endif
  readAccess_ = false;
  if (!append) {
    CoordinateInfo cInfo = cInfoIn;
    // TODO: File output modifications
    SetCoordInfo( cInfo );
#   ifdef MPI
    ensembleStart_ = Parallel::World().Rank();
    ensembleEnd_ = Parallel::World().Rank() + 1;
#   else
    ensembleStart_ = 0;
    ensembleEnd_ = cInfo.EnsembleSize();;
#   endif
    filename_ = fname;
    // Set up title
    if (Title().empty())
      SetTitle("Cpptraj Generated trajectory");
#   ifdef MPI
    if (Parallel::World().Master()) { // Only master creates file.
#   endif
      // Create NetCDF file.
      err = NC_create(filename_.Full(), NC_AMBERENSEMBLE, trajParm->Natom(), CoordInfo(),
                      Title(), debug_);
      // Close Netcdf file. It will be reopened write. FIXME should NC_create leave it closed?
      NC_close();
#   ifdef MPI
    }
    Parallel::World().MasterBcast(&err, 1, MPI_INT);
#   endif
    if (err != 0) return 1;
#   ifdef MPI
    // Synchronize netcdf info on non-master threads
    Sync(Parallel::World());
    // DEBUG: Print info for all ranks
    DebugVIDs();
#   endif
    // Allocate memory
    if (Coord_!=0) delete[] Coord_;
    Coord_ = new float[ Ncatom3() ];
  } else { // NOTE: File existence is checked for in Trajout
    // Call setupTrajin to set input parameters. This will also allocate
    // memory for coords.
    if (setupTrajin(fname, trajParm) == TRAJIN_ERR) return 1;
    if (debug_ > 0)
      mprintf("\tNetCDF: Appending %s starting at frame %i\n", filename_.base(), Ncframe());
  }
  // Open file
# ifdef HAS_PNETCDF
  err = ncmpi_open(MPI_COMM_WORLD, filename_.full(), NC_WRITE, MPI_INFO_NULL, &ncid_);
  // TODO: Graceful error handling
# else
  err = NC_openWrite( filename_.Full() );
# endif  
  if ( err != 0 ) {
    mprinterr("Error: Opening Netcdf file %s for Write.\n", filename_.base());
    return 1;
  }

  return 0;
}
コード例 #2
0
ファイル: NetcdfFile.cpp プロジェクト: rmcgibbo/cpptraj
// NetcdfFile::NC_create()
int NetcdfFile::NC_create(std::string const& Name, NCTYPE type, int natomIn,
                          CoordinateInfo const& coordInfo, std::string const& title)
{
    if (Name.empty()) return 1;
    int dimensionID[NC_MAX_VAR_DIMS];
    int NDIM;
    nc_type dataType;

    if (ncdebug_>1)
        mprintf("DEBUG: NC_create: %s  natom=%i V=%i F=%i box=%i  temp=%i  time=%i\n",
                Name.c_str(),natomIn,(int)coordInfo.HasVel(),
                (int)coordInfo.HasForce(),(int)coordInfo.HasBox(),
                (int)coordInfo.HasTemp(),(int)coordInfo.HasTime());

    if ( checkNCerr( nc_create( Name.c_str(), NC_64BIT_OFFSET, &ncid_) ) )
        return 1;

    ncatom_ = natomIn;
    ncatom3_ = ncatom_ * 3;

    // Set number of dimensions based on file type
    switch (type) {
    case NC_AMBERENSEMBLE:
        NDIM = 4;
        dataType = NC_FLOAT;
        break;
    case NC_AMBERTRAJ:
        NDIM = 3;
        dataType = NC_FLOAT;
        break;
    case NC_AMBERRESTART:
        NDIM = 2;
        dataType = NC_DOUBLE;
        break;
    default:
        mprinterr("Error: NC_create (%s): Unrecognized type (%i)\n",Name.c_str(),(int)type);
        return 1;
    }

    if (type == NC_AMBERENSEMBLE) {
        // Ensemble dimension for ensemble
        if (coordInfo.EnsembleSize() < 1) {
            mprinterr("Internal Error: NetcdfFile: ensembleSize < 1\n");
            return 1;
        }
        if ( checkNCerr(nc_def_dim(ncid_, NCENSEMBLE, coordInfo.EnsembleSize(), &ensembleDID_)) ) {
            mprinterr("Error: Defining ensemble dimension.\n");
            return 1;
        }
        dimensionID[1] = ensembleDID_;
    }
    ncframe_ = 0;
    if (type == NC_AMBERTRAJ || type == NC_AMBERENSEMBLE) {
        // Frame dimension for traj
        if ( checkNCerr( nc_def_dim( ncid_, NCFRAME, NC_UNLIMITED, &frameDID_)) ) {
            mprinterr("Error: Defining frame dimension.\n");
            return 1;
        }
        // Since frame is UNLIMITED, it must be lowest dim.
        dimensionID[0] = frameDID_;
    }
    // Time variable and units
    if (coordInfo.HasTime()) {
        if ( checkNCerr( nc_def_var(ncid_, NCTIME, dataType, NDIM-2, dimensionID, &timeVID_)) ) {
            mprinterr("Error: Defining time variable.\n");
            return 1;
        }
        if ( checkNCerr( nc_put_att_text(ncid_, timeVID_, "units", 10, "picosecond")) ) {
            mprinterr("Error: Writing time VID units.\n");
            return 1;
        }
    }
    // Spatial dimension and variable
    if ( checkNCerr( nc_def_dim( ncid_, NCSPATIAL, 3, &spatialDID_)) ) {
        mprinterr("Error: Defining spatial dimension.\n");
        return 1;
    }
    dimensionID[0] = spatialDID_;
    if ( checkNCerr( nc_def_var( ncid_, NCSPATIAL, NC_CHAR, 1, dimensionID, &spatialVID_)) ) {
        mprinterr("Error: Defining spatial variable.\n");
        return 1;
    }
    // Atom dimension
    if ( checkNCerr( nc_def_dim( ncid_, NCATOM, ncatom_, &atomDID_)) ) {
        mprinterr("Error: Defining atom dimension.\n");
        return 1;
    }
    // Setup dimensions for Coords/Velocity
    // NOTE: THIS MUST BE MODIFIED IF NEW TYPES ADDED
    if (type == NC_AMBERENSEMBLE) {
        dimensionID[0] = frameDID_;
        dimensionID[1] = ensembleDID_;
        dimensionID[2] = atomDID_;
        dimensionID[3] = spatialDID_;
    } else if (type == NC_AMBERTRAJ) {
        dimensionID[0] = frameDID_;
        dimensionID[1] = atomDID_;
        dimensionID[2] = spatialDID_;
    } else {
        dimensionID[0] = atomDID_;
        dimensionID[1] = spatialDID_;
    }
    // Coord variable
    if ( checkNCerr( nc_def_var( ncid_, NCCOORDS, dataType, NDIM, dimensionID, &coordVID_)) ) {
        mprinterr("Error: Defining coordinates variable.\n");
        return 1;
    }
    if ( checkNCerr( nc_put_att_text( ncid_, coordVID_, "units", 8, "angstrom")) ) {
        mprinterr("Error: Writing coordinates variable units.\n");
        return 1;
    }
    // Velocity variable
    if (coordInfo.HasVel()) {
        if ( checkNCerr( nc_def_var( ncid_, NCVELO, dataType, NDIM, dimensionID, &velocityVID_)) ) {
            mprinterr("Error: Defining velocities variable.\n");
            return 1;
        }
        if ( checkNCerr( nc_put_att_text( ncid_, velocityVID_, "units", 19, "angstrom/picosecond")) )
        {
            mprinterr("Error: Writing velocities variable units.\n");
            return 1;
        }
        if ( checkNCerr( nc_put_att_double( ncid_, velocityVID_, "scale_factor", NC_DOUBLE, 1,
                                            &Constants::AMBERTIME_TO_PS)) )
        {
            mprinterr("Error: Writing velocities scale factor.\n");
            return 1;
        }
    }
    // Force variable
    if (coordInfo.HasForce()) {
        if ( checkNCerr( nc_def_var( ncid_, NCFRC, dataType, NDIM, dimensionID, &frcVID_)) ) {
            mprinterr("Error: Defining forces variable\n");
            return 1;
        }
        if ( checkNCerr( nc_put_att_text( ncid_, frcVID_, "units", 25, "kilocalorie/mole/angstrom")) )
        {
            mprinterr("Error: Writing forces variable units.\n");
            return 1;
        }
    }
    // Replica Temperature
    if (coordInfo.HasTemp()) {
        // NOTE: Setting dimensionID should be OK for Restart, will not be used.
        dimensionID[0] = frameDID_;
        if ( NC_defineTemperature( dimensionID, NDIM-2 ) ) return 1;
    }
    // Replica indices
    int remDimTypeVID = -1;
    if (coordInfo.HasReplicaDims()) {
        // Define number of replica dimensions
        remd_dimension_ = coordInfo.ReplicaDimensions().Ndims();
        int remDimDID = -1;
        if ( checkNCerr(nc_def_dim(ncid_, NCREMD_DIMENSION, remd_dimension_, &remDimDID)) ) {
            mprinterr("Error: Defining replica indices dimension.\n");
            return 1;
        }
        dimensionID[0] = remDimDID;
        // For each dimension, store the type
        if ( checkNCerr(nc_def_var(ncid_, NCREMD_DIMTYPE, NC_INT, 1, dimensionID, &remDimTypeVID)) )
        {
            mprinterr("Error: Defining replica dimension type variable.\n");
            return 1;
        }
        // Need to store the indices of replica in each dimension each frame
        // NOTE: THIS MUST BE MODIFIED IF NEW TYPES ADDED
        if (type == NC_AMBERENSEMBLE) {
            dimensionID[0] = frameDID_;
            dimensionID[1] = ensembleDID_;
            dimensionID[2] = remDimDID;
        } else if (type == NC_AMBERTRAJ) {
            dimensionID[0] = frameDID_;
            dimensionID[1] = remDimDID;
        } else {
            dimensionID[0] = remDimDID;
        }
        if (checkNCerr(nc_def_var(ncid_, NCREMD_INDICES, NC_INT, NDIM-1, dimensionID, &indicesVID_)))
        {
            mprinterr("Error: Defining replica indices variable ID.\n");
            return 1;
        }
        // TODO: Determine if groups are really necessary for restarts. If not,
        // remove from AmberNetcdf.F90.
    }
    // Box Info
    if (coordInfo.HasBox()) {
        // Cell Spatial
        if ( checkNCerr( nc_def_dim( ncid_, NCCELL_SPATIAL, 3, &cell_spatialDID_)) ) {
            mprinterr("Error: Defining cell spatial dimension.\n");
            return 1;
        }
        dimensionID[0] = cell_spatialDID_;
        if ( checkNCerr( nc_def_var(ncid_, NCCELL_SPATIAL, NC_CHAR, 1, dimensionID, &cell_spatialVID_)))
        {
            mprinterr("Error: Defining cell spatial variable.\n");
            return 1;
        }
        // Cell angular
        if ( checkNCerr( nc_def_dim( ncid_, NCLABEL, NCLABELLEN, &labelDID_)) ) {
            mprinterr("Error: Defining label dimension.\n");
            return 1;
        }
        if ( checkNCerr( nc_def_dim( ncid_, NCCELL_ANGULAR, 3, &cell_angularDID_)) ) {
            mprinterr("Error: Defining cell angular dimension.\n");
            return 1;
        }
        dimensionID[0] = cell_angularDID_;
        dimensionID[1] = labelDID_;
        if ( checkNCerr( nc_def_var( ncid_, NCCELL_ANGULAR, NC_CHAR, 2, dimensionID,
                                     &cell_angularVID_)) )
        {
            mprinterr("Error: Defining cell angular variable.\n");
            return 1;
        }
        // Setup dimensions for Box
        // NOTE: This must be modified if more types added
        int boxdim;
        if (type == NC_AMBERENSEMBLE) {
            dimensionID[0] = frameDID_;
            dimensionID[1] = ensembleDID_;
            boxdim = 2;
        } else if (type == NC_AMBERTRAJ) {
            dimensionID[0] = frameDID_;
            boxdim = 1;
        } else {
            boxdim = 0;
        }
        dimensionID[boxdim] = cell_spatialDID_;
        if ( checkNCerr( nc_def_var( ncid_, NCCELL_LENGTHS, NC_DOUBLE, NDIM-1, dimensionID,
                                     &cellLengthVID_)) )
        {
            mprinterr("Error: Defining cell length variable.\n");
            return 1;
        }
        if ( checkNCerr( nc_put_att_text( ncid_, cellLengthVID_, "units", 8, "angstrom")) ) {
            mprinterr("Error: Writing cell length variable units.\n");
            return 1;
        }
        dimensionID[boxdim] = cell_angularDID_;
        if ( checkNCerr( nc_def_var( ncid_, NCCELL_ANGLES, NC_DOUBLE, NDIM-1, dimensionID,
                                     &cellAngleVID_)) )
        {
            mprinterr("Error: Defining cell angle variable.\n");
            return 1;
        }
        if ( checkNCerr( nc_put_att_text( ncid_, cellAngleVID_, "units", 6, "degree")) ) {
            mprinterr("Error: Writing cell angle variable units.\n");
            return 1;
        }
    }

    // Attributes
    if (checkNCerr(nc_put_att_text(ncid_,NC_GLOBAL,"title",title.size(),title.c_str())) ) {
        mprinterr("Error: Writing title.\n");
        return 1;
    }
    if (checkNCerr(nc_put_att_text(ncid_,NC_GLOBAL,"application",5,"AMBER")) ) {
        mprinterr("Error: Writing application.\n");
        return 1;
    }
    if (checkNCerr(nc_put_att_text(ncid_,NC_GLOBAL,"program",7,"cpptraj")) ) {
        mprinterr("Error: Writing program.\n");
        return 1;
    }
    if (checkNCerr(nc_put_att_text(ncid_,NC_GLOBAL,"programVersion",
                                   NETCDF_VERSION_STRLEN, NETCDF_VERSION_STRING)) )
    {
        mprinterr("Error: Writing program version.\n");
        return 1;
    }
    // TODO: Make conventions a static string
    bool errOccurred = false;
    if ( type == NC_AMBERENSEMBLE )
        errOccurred = checkNCerr(nc_put_att_text(ncid_,NC_GLOBAL,"Conventions",13,"AMBERENSEMBLE"));
    else if ( type == NC_AMBERTRAJ )
        errOccurred = checkNCerr(nc_put_att_text(ncid_,NC_GLOBAL,"Conventions",5,"AMBER"));
    else
        errOccurred = checkNCerr(nc_put_att_text(ncid_,NC_GLOBAL,"Conventions",12,"AMBERRESTART"));
    if (errOccurred) {
        mprinterr("Error: Writing conventions.\n");
        return 1;
    }
    if (checkNCerr(nc_put_att_text(ncid_,NC_GLOBAL,"ConventionVersion",3,"1.0")) ) {
        mprinterr("Error: Writing conventions version.\n");
        return 1;
    }

    // Set fill mode
    if (checkNCerr(nc_set_fill(ncid_, NC_NOFILL, dimensionID))) {
        mprinterr("Error: NetCDF setting fill value.\n");
        return 1;
    }

    // End netcdf definitions
    if (checkNCerr(nc_enddef(ncid_))) {
        mprinterr("NetCDF error on ending definitions.");
        return 1;
    }

    // Specify spatial dimension labels
    start_[0] = 0;
    count_[0] = 3;
    char xyz[3];
    xyz[0] = 'x';
    xyz[1] = 'y';
    xyz[2] = 'z';
    if (checkNCerr(nc_put_vara_text(ncid_, spatialVID_, start_, count_, xyz))) {
        mprinterr("Error on NetCDF output of spatial VID 'x', 'y' and 'z'");
        return 1;
    }
    if ( coordInfo.HasBox() ) {
        xyz[0] = 'a';
        xyz[1] = 'b';
        xyz[2] = 'c';
        if (checkNCerr(nc_put_vara_text(ncid_, cell_spatialVID_, start_, count_, xyz))) {
            mprinterr("Error on NetCDF output of cell spatial VID 'a', 'b' and 'c'");
            return 1;
        }
        char abc[15] = { 'a', 'l', 'p', 'h', 'a',
                         'b', 'e', 't', 'a', ' ',
                         'g', 'a', 'm', 'm', 'a'
                       };
        start_[0] = 0;
        start_[1] = 0;
        count_[0] = 3;
        count_[1] = NCLABELLEN;
        if (checkNCerr(nc_put_vara_text(ncid_, cell_angularVID_, start_, count_, abc))) {
            mprinterr("Error on NetCDF output of cell angular VID 'alpha', 'beta ' and 'gamma'");
            return 1;
        }
    }

    // Store the type of each replica dimension.
    if (coordInfo.HasReplicaDims()) {
        ReplicaDimArray const& remdDim = coordInfo.ReplicaDimensions();
        start_[0] = 0;
        count_[0] = remd_dimension_;
        int* tempDims = new int[ remd_dimension_ ];
        for (int i = 0; i < remd_dimension_; ++i)
            tempDims[i] = remdDim[i];
        if (checkNCerr(nc_put_vara_int(ncid_, remDimTypeVID, start_, count_, tempDims))) {
            mprinterr("Error: writing replica dimension types.\n");
            delete[] tempDims;
            return 1;
        }
        delete[] tempDims;
    }

    return 0;
}