// 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;
}
// 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;
}