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;
}
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;
}
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;
}
// 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;
}