/* ----------------------------------------------------------------------
   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
   http://lammps.sandia.gov, Sandia National Laboratories
   Steve Plimpton, sjplimp@sandia.gov

   Copyright (2003) Sandia Corporation.  Under the terms of Contract
   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
   certain rights in this software.  This software is distributed under
   the GNU General Public License.

   See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */

/* ----------------------------------------------------------------------
   Contributing author: Lars Pastewka (University of Freiburg)
------------------------------------------------------------------------- */

#if defined(LMP_HAS_NETCDF)

#include <unistd.h>
#include <stdlib.h>
#include <string.h>
#include <netcdf.h>
#include "dump_netcdf.h"
#include "atom.h"
#include "comm.h"
#include "compute.h"
#include "domain.h"
#include "error.h"
#include "fix.h"
#include "group.h"
#include "input.h"
#include "math_const.h"
#include "memory.h"
#include "modify.h"
#include "update.h"
#include "universe.h"
#include "variable.h"
#include "force.h"
#include "output.h"
#include "thermo.h"

using namespace LAMMPS_NS;
using namespace MathConst;

enum{INT,FLOAT,BIGINT}; // same as in thermo.cpp

const char NC_FRAME_STR[]         = "frame";
const char NC_SPATIAL_STR[]       = "spatial";
const char NC_VOIGT_STR[]         = "Voigt";
const char NC_ATOM_STR[]          = "atom";
const char NC_CELL_SPATIAL_STR[]  = "cell_spatial";
const char NC_CELL_ANGULAR_STR[]  = "cell_angular";
const char NC_LABEL_STR[]         = "label";

const char NC_TIME_STR[]          = "time";
const char NC_CELL_ORIGIN_STR[]   = "cell_origin";
const char NC_CELL_LENGTHS_STR[]  = "cell_lengths";
const char NC_CELL_ANGLES_STR[]   = "cell_angles";

const char NC_UNITS_STR[]         = "units";
const char NC_SCALE_FACTOR_STR[]  = "scale_factor";

const int THIS_IS_A_FIX      = -1;
const int THIS_IS_A_COMPUTE  = -2;
const int THIS_IS_A_VARIABLE = -3;
const int THIS_IS_A_BIGINT   = -4;

/* ---------------------------------------------------------------------- */

#define NCERR(x) ncerr(x, NULL, __LINE__)
#define NCERRX(x, descr) ncerr(x, descr, __LINE__)
#if !defined(NC_64BIT_DATA)
#define NC_64BIT_DATA NC_64BIT_OFFSET
#endif

/* ---------------------------------------------------------------------- */

DumpNetCDF::DumpNetCDF(LAMMPS *lmp, int narg, char **arg) :
  DumpCustom(lmp, narg, arg)
{
  // arrays for data rearrangement

  sort_flag = 1;
  sortcol = 0;
  binary = 1;
  flush_flag = 0;

  if (multiproc)
    error->all(FLERR,"Multi-processor writes are not supported.");
  if (multifile)
    error->all(FLERR,"Multiple files are not supported.");

  perat = new nc_perat_t[nfield];

  for (int i = 0; i < nfield; i++) {
    perat[i].dims = 0;
  }

  n_perat = 0;
  for (int iarg = 5; iarg < narg; iarg++) {
    int i = iarg-5;
    int idim = 0;
    int ndims = 1;
    char mangled[1024];
    bool constant = false;

    strcpy(mangled, arg[iarg]);

    // name mangling
    // in the AMBER specification
    if (!strcmp(mangled, "x") || !strcmp(mangled, "y") ||
        !strcmp(mangled, "z")) {
      idim = mangled[0] - 'x';
      ndims = 3;
      strcpy(mangled, "coordinates");
    }
    else if (!strcmp(mangled, "vx") || !strcmp(mangled, "vy") ||
             !strcmp(mangled, "vz")) {
      idim = mangled[1] - 'x';
      ndims = 3;
      strcpy(mangled, "velocities");
    }
    // extensions to the AMBER specification
    else if (!strcmp(mangled, "type")) {
      strcpy(mangled, "atom_types");
    }
    else if (!strcmp(mangled, "xs") || !strcmp(mangled, "ys") ||
             !strcmp(mangled, "zs")) {
      idim = mangled[0] - 'x';
      ndims = 3;
      strcpy(mangled, "scaled_coordinates");
    }
    else if (!strcmp(mangled, "xu") || !strcmp(mangled, "yu") ||
             !strcmp(mangled, "zu")) {
      idim = mangled[0] - 'x';
      ndims = 3;
      strcpy(mangled, "unwrapped_coordinates");
    }
    else if (!strcmp(mangled, "fx") || !strcmp(mangled, "fy") ||
             !strcmp(mangled, "fz")) {
      idim = mangled[1] - 'x';
      ndims = 3;
      strcpy(mangled, "forces");
    }
    else if (!strcmp(mangled, "mux") || !strcmp(mangled, "muy") ||
             !strcmp(mangled, "muz")) {
      idim = mangled[2] - 'x';
      ndims = 3;
      strcpy(mangled, "mu");
    }
    else if (!strncmp(mangled, "c_", 2)) {
      char *ptr = strchr(mangled, '[');
      if (ptr) {
        if (mangled[strlen(mangled)-1] != ']')
          error->all(FLERR,"Missing ']' in dump command");
        *ptr = '\0';
        idim = ptr[1] - '1';
        ndims = THIS_IS_A_COMPUTE;
      }
    }
    else if (!strncmp(mangled, "f_", 2)) {
      char *ptr = strchr(mangled, '[');
      if (ptr) {
        if (mangled[strlen(mangled)-1] != ']')
          error->all(FLERR,"Missing ']' in dump command");
        *ptr = '\0';
        idim = ptr[1] - '1';
        ndims = THIS_IS_A_FIX;
      }
    }

    // find mangled name
    int inc = -1;
    for (int j = 0; j < n_perat && inc < 0; j++) {
      if (!strcmp(perat[j].name, mangled)) {
        inc = j;
      }
    }

    if (inc < 0) {
      // this has not yet been defined
      inc = n_perat;
      perat[inc].dims = ndims;
      if (ndims < 0) ndims = DUMP_NC_MAX_DIMS;
      for (int j = 0; j < DUMP_NC_MAX_DIMS; j++) {
        perat[inc].field[j] = -1;
      }
      strcpy(perat[inc].name, mangled);
      n_perat++;
    }

    perat[inc].constant = constant;
    perat[inc].ndumped = 0;
    perat[inc].field[idim] = i;
  }

  n_buffer = 0;
  int_buffer = NULL;
  double_buffer = NULL;

  double_precision = false;

  thermo = false;
  thermovar = NULL;

  framei = 0;
}

/* ---------------------------------------------------------------------- */

DumpNetCDF::~DumpNetCDF()
{
  closefile();

  delete [] perat;
  if (thermovar)  delete [] thermovar;

  if (int_buffer) memory->sfree(int_buffer);
  if (double_buffer) memory->sfree(double_buffer);
}

/* ---------------------------------------------------------------------- */

void DumpNetCDF::openfile()
{
  if (thermo && !singlefile_opened) {
    if (thermovar)  delete [] thermovar;
    thermovar = new int[output->thermo->nfield];
  }

  // now the computes and fixes have been initialized, so we can query
  // for the size of vector quantities
  for (int i = 0; i < n_perat; i++) {
    if (perat[i].dims == THIS_IS_A_COMPUTE) {
      int j = -1;
      for (int k = 0; k < DUMP_NC_MAX_DIMS; k++) {
        if (perat[i].field[k] >= 0) {
          j = field2index[perat[i].field[0]];
        }
      }
      if (j < 0)
        error->all(FLERR,"Internal error.");
      if (!compute[j]->peratom_flag)
        error->all(FLERR,"compute does not provide per atom data");
      perat[i].dims = compute[j]->size_peratom_cols;
      if (perat[i].dims > DUMP_NC_MAX_DIMS)
        error->all(FLERR,"perat[i].dims > DUMP_NC_MAX_DIMS");
    }
    else if (perat[i].dims == THIS_IS_A_FIX) {
      int j = -1;
      for (int k = 0; k < DUMP_NC_MAX_DIMS; k++) {
        if (perat[i].field[k] >= 0) {
          j = field2index[perat[i].field[0]];
        }
      }
      if (j < 0)
        error->all(FLERR,"Internal error.");
      if (!fix[j]->peratom_flag)
        error->all(FLERR,"fix does not provide per atom data");
      perat[i].dims = fix[j]->size_peratom_cols;
      if (perat[i].dims > DUMP_NC_MAX_DIMS)
        error->all(FLERR,"perat[i].dims > DUMP_NC_MAX_DIMS");
    }
  }

  // get total number of atoms
  ntotalgr = group->count(igroup);

  if (filewriter) {
    if (append_flag && access(filename, F_OK) != -1) {
      // Fixme! Perform checks if dimensions and variables conform with
      // data structure standard.

      if (singlefile_opened) return;
      singlefile_opened = 1;

      NCERRX( nc_open(filename, NC_WRITE, &ncid), filename );

      // dimensions
      NCERRX( nc_inq_dimid(ncid, NC_FRAME_STR, &frame_dim), NC_FRAME_STR );
      NCERRX( nc_inq_dimid(ncid, NC_SPATIAL_STR, &spatial_dim),
          NC_SPATIAL_STR );
      NCERRX( nc_inq_dimid(ncid, NC_VOIGT_STR, &Voigt_dim), NC_VOIGT_STR );
      NCERRX( nc_inq_dimid(ncid, NC_ATOM_STR, &atom_dim), NC_ATOM_STR );
      NCERRX( nc_inq_dimid(ncid, NC_CELL_SPATIAL_STR, &cell_spatial_dim),
          NC_CELL_SPATIAL_STR );
      NCERRX( nc_inq_dimid(ncid, NC_CELL_ANGULAR_STR, &cell_angular_dim),
          NC_CELL_ANGULAR_STR );
      NCERRX( nc_inq_dimid(ncid, NC_LABEL_STR, &label_dim), NC_LABEL_STR );

      // default variables
      NCERRX( nc_inq_varid(ncid, NC_SPATIAL_STR, &spatial_var),
          NC_SPATIAL_STR );
      NCERRX( nc_inq_varid(ncid, NC_CELL_SPATIAL_STR, &cell_spatial_var),
          NC_CELL_SPATIAL_STR);
      NCERRX( nc_inq_varid(ncid, NC_CELL_ANGULAR_STR, &cell_angular_var),
          NC_CELL_ANGULAR_STR);

      NCERRX( nc_inq_varid(ncid, NC_TIME_STR, &time_var), NC_TIME_STR );
      NCERRX( nc_inq_varid(ncid, NC_CELL_ORIGIN_STR, &cell_origin_var),
          NC_CELL_ORIGIN_STR );
      NCERRX( nc_inq_varid(ncid, NC_CELL_LENGTHS_STR, &cell_lengths_var),
          NC_CELL_LENGTHS_STR);
      NCERRX( nc_inq_varid(ncid, NC_CELL_ANGLES_STR, &cell_angles_var),
          NC_CELL_ANGLES_STR);

      // variables specified in the input file
      for (int i = 0; i < n_perat; i++) {
        nc_type xtype;

        // Type mangling
        if (vtype[perat[i].field[0]] == INT) {
          xtype = NC_INT;
        }
        else {
          if (double_precision)
            xtype = NC_DOUBLE;
          else
            xtype = NC_FLOAT;
        }

        NCERRX( nc_inq_varid(ncid, perat[i].name, &perat[i].var),
                perat[i].name );
      }

      // perframe variables
      if (thermo) {
        Thermo *th = output->thermo;
        for (int i = 0; i < th->nfield; i++) {
          NCERRX( nc_inq_varid(ncid, th->keyword[i], &thermovar[i]),
                  th->keyword[i] );
        }
      }

      size_t nframes;
      NCERR( nc_inq_dimlen(ncid, frame_dim, &nframes) );
      // framei == -1 means append to file, == -2 means override last frame
      // Note that in the input file this translates to 'yes', '-1', etc.
      if (framei < 0 || (append_flag && framei == 0))  framei = nframes+framei+1;
      if (framei < 1)  framei = 1;
    }
    else {
      int dims[NC_MAX_VAR_DIMS];
      size_t index[NC_MAX_VAR_DIMS], count[NC_MAX_VAR_DIMS];
      double d[1];

      if (singlefile_opened) return;
      singlefile_opened = 1;

      NCERRX( nc_create(filename, NC_64BIT_DATA, &ncid),
          filename );

      // dimensions
      NCERRX( nc_def_dim(ncid, NC_FRAME_STR, NC_UNLIMITED, &frame_dim),
          NC_FRAME_STR );
      NCERRX( nc_def_dim(ncid, NC_SPATIAL_STR, 3, &spatial_dim),
          NC_SPATIAL_STR );
      NCERRX( nc_def_dim(ncid, NC_VOIGT_STR, 6, &Voigt_dim),
          NC_VOIGT_STR );
      NCERRX( nc_def_dim(ncid, NC_ATOM_STR, ntotalgr, &atom_dim),
          NC_ATOM_STR );
      NCERRX( nc_def_dim(ncid, NC_CELL_SPATIAL_STR, 3, &cell_spatial_dim),
          NC_CELL_SPATIAL_STR );
      NCERRX( nc_def_dim(ncid, NC_CELL_ANGULAR_STR, 3, &cell_angular_dim),
          NC_CELL_ANGULAR_STR );
      NCERRX( nc_def_dim(ncid, NC_LABEL_STR, 10, &label_dim),
          NC_LABEL_STR );

      // default variables
      dims[0] = spatial_dim;
      NCERRX( nc_def_var(ncid, NC_SPATIAL_STR, NC_CHAR, 1, dims, &spatial_var),
          NC_SPATIAL_STR );
      NCERRX( nc_def_var(ncid, NC_CELL_SPATIAL_STR, NC_CHAR, 1, dims,
             &cell_spatial_var), NC_CELL_SPATIAL_STR );
      dims[0] = spatial_dim;
      dims[1] = label_dim;
      NCERRX( nc_def_var(ncid, NC_CELL_ANGULAR_STR, NC_CHAR, 2, dims,
             &cell_angular_var), NC_CELL_ANGULAR_STR );

      dims[0] = frame_dim;
      NCERRX( nc_def_var(ncid, NC_TIME_STR, NC_DOUBLE, 1, dims, &time_var),
          NC_TIME_STR);
      dims[0] = frame_dim;
      dims[1] = cell_spatial_dim;
      NCERRX( nc_def_var(ncid, NC_CELL_ORIGIN_STR, NC_DOUBLE, 2, dims,
             &cell_origin_var), NC_CELL_ORIGIN_STR );
      NCERRX( nc_def_var(ncid, NC_CELL_LENGTHS_STR, NC_DOUBLE, 2, dims,
             &cell_lengths_var), NC_CELL_LENGTHS_STR );
      dims[0] = frame_dim;
      dims[1] = cell_angular_dim;
      NCERRX( nc_def_var(ncid, NC_CELL_ANGLES_STR, NC_DOUBLE, 2, dims,
             &cell_angles_var), NC_CELL_ANGLES_STR );

      // variables specified in the input file
      dims[0] = frame_dim;
      dims[1] = atom_dim;
      dims[2] = spatial_dim;

      for (int i = 0; i < n_perat; i++) {
        nc_type xtype;

        // Type mangling
        if (vtype[perat[i].field[0]] == INT) {
          xtype = NC_INT;
        }
        else {
          if (double_precision)
            xtype = NC_DOUBLE;
          else
            xtype = NC_FLOAT;
        }

        if (perat[i].constant) {
          // this quantity will only be written once
          if (perat[i].dims == 6) {
            // this is a tensor in Voigt notation
            dims[2] = Voigt_dim;
            NCERRX( nc_def_var(ncid, perat[i].name, xtype, 2, dims+1,
                   &perat[i].var), perat[i].name );
          }
          else if (perat[i].dims == 3) {
            // this is a vector, we need to store x-, y- and z-coordinates
            dims[2] = spatial_dim;
            NCERRX( nc_def_var(ncid, perat[i].name, xtype, 2, dims+1,
                   &perat[i].var), perat[i].name );
          }
          else if (perat[i].dims == 1) {
            NCERRX( nc_def_var(ncid, perat[i].name, xtype, 1, dims+1,
                   &perat[i].var), perat[i].name );
          }
          else {
            char errstr[1024];
            sprintf(errstr, "%i dimensions for '%s'. Not sure how to write "
                    "this to the NetCDF trajectory file.", perat[i].dims,
                    perat[i].name);
            error->all(FLERR,errstr);
          }
        }
        else {
          if (perat[i].dims == 6) {
            // this is a tensor in Voigt notation
            dims[2] = Voigt_dim;
            NCERRX( nc_def_var(ncid, perat[i].name, xtype, 3, dims,
                   &perat[i].var), perat[i].name );
          }
          else if (perat[i].dims == 3) {
            // this is a vector, we need to store x-, y- and z-coordinates
            dims[2] = spatial_dim;
            NCERRX( nc_def_var(ncid, perat[i].name, xtype, 3, dims,
                   &perat[i].var), perat[i].name );
          }
          else if (perat[i].dims == 1) {
            NCERRX( nc_def_var(ncid, perat[i].name, xtype, 2, dims,
                   &perat[i].var), perat[i].name );
          }
          else {
            char errstr[1024];
            sprintf(errstr, "%i dimensions for '%s'. Not sure how to write "
                    "this to the NetCDF trajectory file.", perat[i].dims,
                    perat[i].name);
            error->all(FLERR,errstr);
          }
        }
      }

      // perframe variables
      if (thermo) {
        Thermo *th = output->thermo;
        for (int i = 0; i < th->nfield; i++) {
          if (th->vtype[i] == FLOAT) {
            NCERRX( nc_def_var(ncid, th->keyword[i], NC_DOUBLE, 1, dims,
                               &thermovar[i]), th->keyword[i] );
          }
          else if (th->vtype[i] == INT) {
            NCERRX( nc_def_var(ncid, th->keyword[i], NC_INT, 1, dims,
                               &thermovar[i]), th->keyword[i] );
          }
          else if (th->vtype[i] == BIGINT) {
            NCERRX( nc_def_var(ncid, th->keyword[i], NC_LONG, 1, dims,
                               &thermovar[i]), th->keyword[i] );
          }
        }
      }

      // attributes
      NCERR( nc_put_att_text(ncid, NC_GLOBAL, "Conventions",
                 5, "AMBER") );
      NCERR( nc_put_att_text(ncid, NC_GLOBAL, "ConventionVersion",
                 3, "1.0") );

      NCERR( nc_put_att_text(ncid, NC_GLOBAL, "program",
                 6, "LAMMPS") );
      NCERR( nc_put_att_text(ncid, NC_GLOBAL, "programVersion",
                 strlen(universe->version), universe->version) );

      // units
      if (!strcmp(update->unit_style, "lj")) {
        NCERR( nc_put_att_text(ncid, time_var, NC_UNITS_STR,
                               2, "lj") );
        NCERR( nc_put_att_text(ncid, cell_origin_var, NC_UNITS_STR,
                               2, "lj") );
        NCERR( nc_put_att_text(ncid, cell_lengths_var, NC_UNITS_STR,
                               2, "lj") );
      }
      else if (!strcmp(update->unit_style, "real")) {
        NCERR( nc_put_att_text(ncid, time_var, NC_UNITS_STR,
                               11, "femtosecond") );
        NCERR( nc_put_att_text(ncid, cell_origin_var, NC_UNITS_STR,
                               8, "Angstrom") );
        NCERR( nc_put_att_text(ncid, cell_lengths_var, NC_UNITS_STR,
                               8, "Angstrom") );
      }
      else if (!strcmp(update->unit_style, "metal")) {
        NCERR( nc_put_att_text(ncid, time_var, NC_UNITS_STR,
                               10, "picosecond") );
        NCERR( nc_put_att_text(ncid, cell_origin_var, NC_UNITS_STR,
                               8, "Angstrom") );
        NCERR( nc_put_att_text(ncid, cell_lengths_var, NC_UNITS_STR,
                               8, "Angstrom") );
      }
      else if (!strcmp(update->unit_style, "si")) {
        NCERR( nc_put_att_text(ncid, time_var, NC_UNITS_STR,
                               6, "second") );
        NCERR( nc_put_att_text(ncid, cell_origin_var, NC_UNITS_STR,
                               5, "meter") );
        NCERR( nc_put_att_text(ncid, cell_lengths_var, NC_UNITS_STR,
                               5, "meter") );
      }
      else if (!strcmp(update->unit_style, "cgs")) {
        NCERR( nc_put_att_text(ncid, time_var, NC_UNITS_STR,
                               6, "second") );
        NCERR( nc_put_att_text(ncid, cell_origin_var, NC_UNITS_STR,
                               10, "centimeter") );
        NCERR( nc_put_att_text(ncid, cell_lengths_var, NC_UNITS_STR,
                               10, "centimeter") );
      }
      else if (!strcmp(update->unit_style, "electron")) {
        NCERR( nc_put_att_text(ncid, time_var, NC_UNITS_STR,
                               11, "femtosecond") );
        NCERR( nc_put_att_text(ncid, cell_origin_var, NC_UNITS_STR,
                               4, "Bohr") );
        NCERR( nc_put_att_text(ncid, cell_lengths_var, NC_UNITS_STR,
                               4, "Bohr") );
      }
      else {
        char errstr[1024];
        sprintf(errstr, "Unsupported unit style '%s'", update->unit_style);
        error->all(FLERR,errstr);
      }

      NCERR( nc_put_att_text(ncid, cell_angles_var, NC_UNITS_STR,
                             6, "degree") );

      d[0] = update->dt;
      NCERR( nc_put_att_double(ncid, time_var, NC_SCALE_FACTOR_STR,
                               NC_DOUBLE, 1, d) );
      d[0] = 1.0;
      NCERR( nc_put_att_double(ncid, cell_origin_var, NC_SCALE_FACTOR_STR,
                               NC_DOUBLE, 1, d) );
      d[0] = 1.0;
      NCERR( nc_put_att_double(ncid, cell_lengths_var, NC_SCALE_FACTOR_STR,
                               NC_DOUBLE, 1, d) );

      /*
       * Finished with definition
       */

      NCERR( nc_enddef(ncid) );

      /*
       * Write label variables
       */

      NCERR( nc_put_var_text(ncid, spatial_var, "xyz") );
      NCERR( nc_put_var_text(ncid, cell_spatial_var, "abc") );
      index[0] = 0;
      index[1] = 0;
      count[0] = 1;
      count[1] = 5;
      NCERR( nc_put_vara_text(ncid, cell_angular_var, index, count, "alpha") );
      index[0] = 1;
      count[1] = 4;
      NCERR( nc_put_vara_text(ncid, cell_angular_var, index, count, "beta") );
      index[0] = 2;
      count[1] = 5;
      NCERR( nc_put_vara_text(ncid, cell_angular_var, index, count, "gamma") );

      framei = 1;
    }
  }
}

/* ---------------------------------------------------------------------- */

void DumpNetCDF::closefile()
{
  if (filewriter && singlefile_opened) {
    NCERR( nc_close(ncid) );
    singlefile_opened = 0;
    // append next time DumpNetCDF::openfile is called
    append_flag = 1;
    // write to next frame upon next open
    framei++;
  }
}

/* ---------------------------------------------------------------------- */

void DumpNetCDF::write()
{
  // open file

  openfile();

  // need to write per-frame (global) properties here since they may come
  // from computes. write_header below is only called from the writing
  // processes, but modify->compute[j]->compute_* must be called from all
  // processes.

  size_t start[2];

  start[0] = framei-1;
  start[1] = 0;

  if (thermo) {
    Thermo *th = output->thermo;
    for (int i = 0; i < th->nfield; i++) {
      th->call_vfunc(i);
      if (filewriter) {
        if (th->vtype[i] == FLOAT) {
          NCERRX( nc_put_var1_double(ncid, thermovar[i], start,
                                     &th->dvalue),
                  th->keyword[i] );
        }
        else if (th->vtype[i] == INT) {
          NCERRX( nc_put_var1_int(ncid, thermovar[i], start, &th->ivalue),
                  th->keyword[i] );
        }
        else if (th->vtype[i] == BIGINT) {
#if defined(LAMMPS_SMALLBIG) || defined(LAMMPS_BIGBIG)
          NCERRX( nc_put_var1_long(ncid, thermovar[i], start, &th->bivalue),
                  th->keyword[i] );
#else
          NCERRX( nc_put_var1_int(ncid, thermovar[i], start, &th->bivalue),
                  th->keyword[i] );
#endif
        }
      }
    }
  }

  // call write of superclass

  Dump::write();

  // close file. this ensures data is flushed and mimized data corruption

  closefile();
}

/* ---------------------------------------------------------------------- */

void DumpNetCDF::write_header(bigint n)
{
  size_t start[2];

  start[0] = framei-1;
  start[1] = 0;

  if (filewriter) {
    size_t count[2];
    double time, cell_origin[3], cell_lengths[3], cell_angles[3];

    time = update->ntimestep;
    if (domain->triclinic == 0) {
      cell_origin[0] = domain->boxlo[0];
      cell_origin[1] = domain->boxlo[1];
      cell_origin[2] = domain->boxlo[2];

      cell_lengths[0] = domain->xprd;
      cell_lengths[1] = domain->yprd;
      cell_lengths[2] = domain->zprd;

      cell_angles[0] = 90;
      cell_angles[1] = 90;
      cell_angles[2] = 90;
    }
    else {
      double cosalpha, cosbeta, cosgamma;
      double *h = domain->h;

      cell_origin[0] = domain->boxlo[0];
      cell_origin[1] = domain->boxlo[1];
      cell_origin[2] = domain->boxlo[2];

      cell_lengths[0] = domain->xprd;
      cell_lengths[1] = sqrt(h[1]*h[1]+h[5]*h[5]);
      cell_lengths[2] = sqrt(h[2]*h[2]+h[3]*h[3]+h[4]*h[4]);

      cosalpha = (h[5]*h[4]+h[1]*h[3])/
          sqrt((h[1]*h[1]+h[5]*h[5])*(h[2]*h[2]+h[3]*h[3]+h[4]*h[4]));
      cosbeta = h[4]/sqrt(h[2]*h[2]+h[3]*h[3]+h[4]*h[4]);
      cosgamma = h[5]/sqrt(h[1]*h[1]+h[5]*h[5]);

      cell_angles[0] = acos(cosalpha)*180.0/MY_PI;
      cell_angles[1] = acos(cosbeta)*180.0/MY_PI;
      cell_angles[2] = acos(cosgamma)*180.0/MY_PI;
    }

    // Recent AMBER conventions say that nonperiodic boundaries should have
    // 'cell_lengths' set to zero.
    for (int dim = 0; dim < 3; dim++) {
        if (!domain->periodicity[dim])
            cell_lengths[dim] = 0.0;
    }

    count[0] = 1;
    count[1] = 3;
    NCERR( nc_put_var1_double(ncid, time_var, start, &time) );
    NCERR( nc_put_vara_double(ncid, cell_origin_var, start, count,
                              cell_origin) );
    NCERR( nc_put_vara_double(ncid, cell_lengths_var, start, count,
                              cell_lengths) );
    NCERR( nc_put_vara_double(ncid, cell_angles_var, start, count,
                              cell_angles) );
  }

  ndata = n;
  blocki = 0;
}


/* ----------------------------------------------------------------------
   write data lines to file in a block-by-block style
   write head of block (mass & element name) only if has atoms of the type
------------------------------------------------------------------------- */

void DumpNetCDF::write_data(int n, double *mybuf)
{
  size_t start[NC_MAX_VAR_DIMS], count[NC_MAX_VAR_DIMS];
  ptrdiff_t stride[NC_MAX_VAR_DIMS];

  if (!int_buffer) {
    n_buffer = n;
    int_buffer = (int *)
      memory->smalloc(n*sizeof(int),"dump::int_buffer");
    double_buffer = (double *)
      memory->smalloc(n*sizeof(double),"dump::double_buffer");
  }

  if (n > n_buffer) {
    n_buffer = n;
    int_buffer = (int *)
      memory->srealloc(int_buffer, n*sizeof(int),"dump::int_buffer");
    double_buffer = (double *)
      memory->srealloc(double_buffer, n*sizeof(double),"dump::double_buffer");
  }

  start[0] = framei-1;
  start[1] = blocki;
  start[2] = 0;

  count[0] = 1;
  count[1] = n;
  count[2] = 1;

  stride[0] = 1;
  stride[1] = 1;
  stride[2] = 3;

  for (int i = 0; i < n_perat; i++) {
    int iaux = perat[i].field[0];

    if (vtype[iaux] == INT) {
      // integers
      if (perat[i].dims > 1) {

        for (int idim = 0; idim < perat[i].dims; idim++) {
          iaux = perat[i].field[idim];

          if (iaux >= 0) {
            for (int j = 0; j < n; j++, iaux+=size_one) {
              int_buffer[j] = mybuf[iaux];
            }

            start[2] = idim;

            if (perat[i].constant) {
              if (perat[i].ndumped < ntotalgr) {
                NCERR( nc_put_vars_int(ncid, perat[i].var,
                                       start+1, count+1, stride+1,
                                       int_buffer) );
                perat[i].ndumped += n;
              }
            }
            else
              NCERR( nc_put_vars_int(ncid, perat[i].var, start, count, stride,
                                     int_buffer) );
          }
        }
      }
      else {
        for (int j = 0; j < n; j++, iaux+=size_one) {
            int_buffer[j] = mybuf[iaux];
        }

        if (perat[i].constant) {
          if (perat[i].ndumped < ntotalgr) {
            NCERR( nc_put_vara_int(ncid, perat[i].var, start+1, count+1,
                                   int_buffer) );
            perat[i].ndumped += n;
          }
        }
        else
          NCERR( nc_put_vara_int(ncid, perat[i].var, start, count,
                                 int_buffer) );
      }
    }
    else {
      // doubles
      if (perat[i].dims > 1) {

        for (int idim = 0; idim < perat[i].dims; idim++) {
          iaux = perat[i].field[idim];

          if (iaux >= 0) {
            for (int j = 0; j < n; j++, iaux+=size_one) {
                double_buffer[j] = mybuf[iaux];
            }

            start[2] = idim;

            if (perat[i].constant) {
              if (perat[i].ndumped < ntotalgr) {
                  NCERR( nc_put_vars_double(ncid, perat[i].var,
                                            start+1, count+1, stride+1,
                                            double_buffer) );
                  perat[i].ndumped += n;
              }
            }
            else
              NCERR( nc_put_vars_double(ncid, perat[i].var, start, count,
                                        stride, double_buffer) );
          }
        }
      }
      else {
        for (int j = 0; j < n; j++, iaux+=size_one) {
            double_buffer[j] = mybuf[iaux];
        }

        if (perat[i].constant) {
          if (perat[i].ndumped < ntotalgr) {
            NCERR( nc_put_vara_double(ncid, perat[i].var, start+1, count+1,
                                      double_buffer) );
            perat[i].ndumped += n;
          }
        }
        else
          NCERR( nc_put_vara_double(ncid, perat[i].var, start, count,
                                    double_buffer) );
      }
    }
  }

  blocki += n;
}

/* ---------------------------------------------------------------------- */

int DumpNetCDF::modify_param(int narg, char **arg)
{
  int iarg = 0;
  if (strcmp(arg[iarg],"double") == 0) {
    iarg++;
    if (iarg >= narg)
      error->all(FLERR,"expected 'yes' or 'no' after 'double' keyword.");
    if (strcmp(arg[iarg],"yes") == 0) {
      double_precision = true;
    }
    else if (strcmp(arg[iarg],"no") == 0) {
      double_precision = false;
    }
    else error->all(FLERR,"expected 'yes' or 'no' after 'double' keyword.");
    iarg++;
    return 2;
  }
  else if (strcmp(arg[iarg],"at") == 0) {
    iarg++;
    framei = force->inumeric(FLERR,arg[iarg]);
    if (framei < 0)  framei--;
    iarg++;
    return 2;
  }
  else if (strcmp(arg[iarg],"thermo") == 0) {
    iarg++;
    if (iarg >= narg)
      error->all(FLERR,"expected 'yes' or 'no' after 'thermo' keyword.");
    if (strcmp(arg[iarg],"yes") == 0) {
      thermo = true;
    }
    else if (strcmp(arg[iarg],"no") == 0) {
      thermo = false;
    }
    else error->all(FLERR,"expected 'yes' or 'no' after 'thermo' keyword.");
    iarg++;
    return 2;
  } else return 0;
}

/* ---------------------------------------------------------------------- */

void DumpNetCDF::write_prmtop()
{
  char fn[1024];
  char tmp[81];
  FILE *f;

  strcpy(fn, filename);
  strcat(fn, ".prmtop");

  f = fopen(fn, "w");
  fprintf(f, "%%VERSION  LAMMPS\n");
  fprintf(f, "%%FLAG TITLE\n");
  fprintf(f, "%%FORMAT(20a4)\n");
  memset(tmp, ' ', 76);
  tmp[76] = '\0';
  fprintf(f, "NASN%s\n", tmp);

  fprintf(f, "%%FLAG POINTERS\n");
  fprintf(f, "%%FORMAT(10I8)\n");
#if defined(LAMMPS_SMALLBIG) || defined(LAMMPS_BIGBIG)
  fprintf(f, "%8li", ntotalgr);
#else
  fprintf(f, "%8i", ntotalgr);
#endif
  for (int i = 0; i < 11; i++)
    fprintf(f, "%8i", 0);
  fprintf(f, "\n");
  for (int i = 0; i < 12; i++)
    fprintf(f, "%8i", 0);
  fprintf(f, "\n");
  for (int i = 0; i < 6; i++)
    fprintf(f, "%8i", 0);
  fprintf(f, "\n");

  fprintf(f, "%%FLAG ATOM_NAME\n");
  fprintf(f, "%%FORMAT(20a4)\n");
  for (int i = 0; i < ntotalgr; i++) {
    fprintf(f, "%4s", "He");
    if ((i+1) % 20 == 0)
      fprintf(f, "\n");
  }

  fprintf(f, "%%FLAG CHARGE\n");
  fprintf(f, "%%FORMAT(5E16.5)\n");
  for (int i = 0; i < ntotalgr; i++) {
    fprintf(f, "%16.5e", 0.0);
    if ((i+1) % 5 == 0)
      fprintf(f, "\n");
  }

  fprintf(f, "%%FLAG MASS\n");
  fprintf(f, "%%FORMAT(5E16.5)\n");
  for (int i = 0; i < ntotalgr; i++) {
    fprintf(f, "%16.5e", 1.0);
    if ((i+1) % 5 == 0)
        fprintf(f, "\n");
  }
  fclose(f);
}

/* ---------------------------------------------------------------------- */

void DumpNetCDF::ncerr(int err, const char *descr, int line)
{
  if (err != NC_NOERR) {
    char errstr[1024];
    if (descr) {
      sprintf(errstr, "NetCDF failed with error '%s' (while accessing '%s') "
          " in line %i of %s.", nc_strerror(err), descr, line, __FILE__);
    }
    else {
      sprintf(errstr, "NetCDF failed with error '%s' in line %i of %s.",
          nc_strerror(err), line, __FILE__);
    }
    error->one(FLERR,errstr);
  }
}

#endif /* defined(LMP_HAS_NETCDF) */
