Esempio n. 1
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;
}
Esempio n. 2
0
/** Get the specified frame from amber netcdf file
  * Coords are a 1 dimensional array of format X1,Y1,Z1,X2,Y2,Z2,...
  */
int Traj_AmberNetcdf::readFrame(int set,double *X, double *V,double *box, double *T) {
  // Get temperature
  if (TempVID_!=-1) {
    start_[0] = set;
    count_[0] = 1;
    if ( checkNCerr(nc_get_vara_double(ncid_, TempVID_, start_, count_, T)) ) {
      mprinterr("Error: Getting replica temperature.\n"); 
      return 1;
    }
    //fprintf(stderr,"DEBUG: Replica Temperature %lf\n",F->T);
  }

  // Read Coords 
  start_[0] = set;
  start_[1] = 0;
  start_[2] = 0;
  count_[0] = 1;
  count_[1] = Ncatom();
  count_[2] = 3;
  if ( checkNCerr(nc_get_vara_float(ncid_, coordVID_, start_, count_, Coord_)) ) {
    mprinterr("Error: Getting frame %i\n", set);
    return 1;
  }
  FloatToDouble(X, Coord_);

  // Read Velocities
  if (velocityVID_ != -1) {
    if ( checkNCerr(nc_get_vara_float(ncid_, velocityVID_, start_, count_, Veloc_)) ) {
      mprinterr("Error: Getting velocities for frame %i\n", set);
      return 1;
    }
    FloatToDouble(V, Veloc_);
  }

  // Read box info 
  if (cellLengthVID_ != -1) {
    count_[1] = 3;
    count_[2] = 0;
    if ( checkNCerr(nc_get_vara_double(ncid_, cellLengthVID_, start_, count_, box)) ) {
      mprinterr("Getting cell lengths.\n");
      return 1;
    }
    if ( checkNCerr(nc_get_vara_double(ncid_, cellAngleVID_, start_, count_, box+3)) ) {
      mprinterr("Getting cell angles.\n");
      return 1;
    }
  }


  return 0;
}
Esempio n. 3
0
  JNIEXPORT jint JNICALL Java_edu_berkeley_bid_CUMATD_FloatToDouble 
  (JNIEnv *env, jobject obj, jobject jA, jobject jB, jint N)
  {
    float *A = (float*)getPointer(env, jA);
    double *B = (double*)getPointer(env, jB);

    return FloatToDouble(A, B, N);
  }
Esempio n. 4
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// As DeSerialize, but reads an old (float) format WeightMatrix for
// backward compatibility.
bool WeightMatrix::DeSerializeOld(bool training, bool swap, TFile* fp) {
  GENERIC_2D_ARRAY<float> float_array;
  if (int_mode_) {
    if (!wi_.DeSerialize(swap, fp)) return false;
    GenericVector<float> old_scales;
    if (!old_scales.DeSerialize(swap, fp)) return false;
    scales_.init_to_size(old_scales.size(), 0.0);
    for (int i = 0; i < old_scales.size(); ++i) scales_[i] = old_scales[i];
  } else {
    if (!float_array.DeSerialize(swap, fp)) return false;
    FloatToDouble(float_array, &wf_);
  }
  if (training) {
    InitBackward(use_ada_grad_);
    if (!float_array.DeSerialize(swap, fp)) return false;
    FloatToDouble(float_array, &updates_);
    // Errs was only used in int training, which is now dead.
    if (!float_array.DeSerialize(swap, fp)) return false;
  }
  return true;
}
Esempio n. 5
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// Traj_AmberNetcdf::readVelocity()
int Traj_AmberNetcdf::readVelocity(int set, Frame& frameIn) {
  start_[0] = set;
  start_[1] = 0;
  start_[2] = 0;
  count_[0] = 1;
  count_[1] = Ncatom();
  count_[2] = 3;
  // Read Velocities
  if (velocityVID_ != -1) {
    if ( checkNCerr(nc_get_vara_float(ncid_, velocityVID_, start_, count_, Coord_)) ) {
      mprinterr("Error: Getting velocities for frame %i\n", set+1);
      return 1;
    }
    FloatToDouble(frameIn.vAddress(), Coord_);
  }
  return 0;
}
Esempio n. 6
0
// Traj_AmberNetcdf::readForce()
int Traj_AmberNetcdf::readForce(int set, Frame& frameIn) {
  start_[0] = set;
  start_[1] = 0;
  start_[2] = 0;
  count_[0] = 1;
  count_[1] = Ncatom();
  count_[2] = 3;
  // Read forces
  if (frcVID_ != -1) {
    if ( NC::CheckErr(nc_get_vara_float(ncid_, frcVID_, start_, count_, Coord_)) ) {
      mprinterr("Error: Getting forces for frame %i\n", set+1);
      return 1;
    }
    FloatToDouble(frameIn.fAddress(), Coord_);
  }
  return 0;
}
Esempio n. 7
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TEST(DSP, FloatDoubleConversion)
{
    float in[10] = {1.0, -1.0, 1.0, -1.0, 1.0, -1.0, 1.0, -1.0, 1.0, -1.0};
    double out[10];
    float fout[10];
    
    FloatToDouble(out, in, 10);
    for (unsigned i = 0; i < 10; ++i)
    {
        ASSERT_DOUBLE_EQ((double)in[i], out[i]);
    }
    
    DoubleToFloat(fout, out, 10);
    for (unsigned i = 0; i < 10; ++i)
    {
        ASSERT_FLOAT_EQ(in[i], fout[i]);
    }
}
Esempio n. 8
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;
}
Esempio n. 9
0
/** Get the specified frame from amber netcdf file
  * Coords are a 1 dimensional array of format X1,Y1,Z1,X2,Y2,Z2,...
  */
int Traj_AmberNetcdf::readFrame(int set, Frame& frameIn) {
  start_[0] = set;
  start_[1] = 0;
  start_[2] = 0;
  count_[0] = 1;
  count_[1] = Ncatom();
  count_[2] = 3;

  // Get temperature
  if (TempVID_!=-1) {
    if ( checkNCerr(nc_get_vara_double(ncid_, TempVID_, start_, count_, frameIn.tAddress())) ) {
      mprinterr("Error: Getting replica temperature for frame %i.\n", set+1); 
      return 1;
    }
    //fprintf(stderr,"DEBUG: Replica Temperature %lf\n",F->T);
  }

  // Get time
  if (timeVID_!=-1) {
    float time;
    if (checkNCerr(nc_get_vara_float(ncid_, timeVID_, start_, count_, &time))) {
      mprinterr("Error: Getting time for frame %i.\n", set + 1);
      return 1;
    }
    frameIn.SetTime( (double)time );
  }

  // Read Coords 
  if ( checkNCerr(nc_get_vara_float(ncid_, coordVID_, start_, count_, Coord_)) ) {
    mprinterr("Error: Getting coordinates for frame %i\n", set+1);
    return 1;
  }
  FloatToDouble(frameIn.xAddress(), Coord_);

  // Read Velocities
  if (velocityVID_ != -1) {
    if ( checkNCerr(nc_get_vara_float(ncid_, velocityVID_, start_, count_, Coord_)) ) {
      mprinterr("Error: Getting velocities for frame %i\n", set+1);
      return 1;
    }
    FloatToDouble(frameIn.vAddress(), Coord_);
  }

  // Read indices. Input array must be allocated to be size remd_dimension.
  if (indicesVID_!=-1) {
    count_[1] = remd_dimension_;
    if ( checkNCerr(nc_get_vara_int(ncid_, indicesVID_, start_, count_, frameIn.iAddress())) ) {
      mprinterr("Error: Getting replica indices for frame %i.\n", set+1);
      return 1;
    }
    //mprintf("DEBUG:\tReplica indices:");
    //for (int dim=0; dim < remd_dimension_; dim++) mprintf(" %i",remd_indices[dim]);
    //mprintf("\n");
  }

  // Read box info 
  if (cellLengthVID_ != -1) {
    count_[1] = 3;
    count_[2] = 0;
    if (checkNCerr(nc_get_vara_double(ncid_, cellLengthVID_, start_, count_, frameIn.bAddress())))
    {
      mprinterr("Error: Getting cell lengths for frame %i.\n", set+1);
      return 1;
    }
    if (checkNCerr(nc_get_vara_double(ncid_, cellAngleVID_, start_, count_, frameIn.bAddress()+3)))
    {
      mprinterr("Error: Getting cell angles for frame %i.\n", set+1);
      return 1;
    }
  }

  return 0;
}