/*
 * Copyright (c) 2005-2017 National Technology & Engineering Solutions
 * of Sandia, LLC (NTESS).  Under the terms of Contract DE-NA0003525 with
 * NTESS, the U.S. Government retains certain rights in this software.
 *
 * Redistribution and use in source and binary forms, with or without
 * modification, are permitted provided that the following conditions are
 * met:
 *
 *     * Redistributions of source code must retain the above copyright
 *       notice, this list of conditions and the following disclaimer.
 *
 *     * Redistributions in binary form must reproduce the above
 *       copyright notice, this list of conditions and the following
 *       disclaimer in the documentation and/or other materials provided
 *       with the distribution.
 *
 *     * Neither the name of NTESS nor the names of its
 *       contributors may be used to endorse or promote products derived
 *       from this software without specific prior written permission.
 *
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
 * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
 * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
 * A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
 * OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
 * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
 * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
 * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
 * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
 * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
 * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 *
 */

#include "exodusII.h"     // for EX_FATAL, exerrval, ex_err, etc
#include "exodusII_int.h" // for ex_get_counter_list, etc
#include "vtk_netcdf.h"       // for NC_NOERR, nc_inq_varid, etc
#include <assert.h>       // for assert
#include <stddef.h>       // for size_t
#include <stdint.h>       // for int64_t
#include <stdio.h>        // for fprintf, stderr, snprintf
#include <stdlib.h>       // for free, calloc, malloc
#include <string.h>       // for strcmp, strncmp, NULL

#define STRINGIFY(x) #x
#define TOSTRING(x) STRINGIFY(x)

#define EXCHECK(funcall)                                                                           \
  if ((funcall) != NC_NOERR) {                                                                     \
    fprintf(stderr, "Error calling %s\n", TOSTRING(funcall));                                      \
    EX_FUNC_LEAVE(EX_FATAL);                                                                       \
  }

#define EXCHECKI(funcall)                                                                          \
  if ((funcall) != NC_NOERR) {                                                                     \
    fprintf(stderr, "Error calling %s\n", TOSTRING(funcall));                                      \
    return (EX_FATAL);                                                                             \
  }

#define EXCHECKF(funcall)                                                                          \
  if ((funcall) != NC_NOERR) {                                                                     \
    fprintf(stderr, "Error calling %s\n", TOSTRING(funcall));                                      \
    goto err_ret;                                                                                  \
  }

/*! \cond INTERNAL */
struct ncdim
{ /* dimension */
  char   name[MAX_VAR_NAME_LENGTH];
  size_t size;
};

struct ncvar
{ /* variable */
  char    name[MAX_VAR_NAME_LENGTH];
  nc_type type;
  int     ndims;
  int     dims[NC_MAX_VAR_DIMS];
  int     natts;
};

struct ncatt
{ /* attribute */
  int     var;
  char    name[MAX_VAR_NAME_LENGTH];
  nc_type type;
  size_t  len;
  void *  val;
};

static size_t type_size(nc_type type);
static int    cpy_variable_data(int in_exoid, int out_exoid, int in_large, int mesh_only);
static int    cpy_variables(int in_exoid, int out_exoid, int in_large, int mesh_only);
static int    cpy_dimension(int in_exoid, int out_exoid, int mesh_only);
static int    cpy_global_att(int in_exoid, int out_exoid);
static int    cpy_att(int in_id, int out_id, int var_in_id, int var_out_id);
static int    cpy_var_def(int in_id, int out_id, int rec_dim_id, char *var_nm);
static int    cpy_var_val(int in_id, int out_id, char *var_nm);
static int    cpy_coord_def(int in_id, int out_id, int rec_dim_id, char *var_nm, int in_large);
static int    cpy_coord_val(int in_id, int out_id, char *var_nm, int in_large);
static void   update_structs(int out_exoid);
static void update_internal_structs(int out_exoid, ex_inquiry inqcode, struct list_item **ctr_list);

static int is_truth_table_variable(const char *var_name)
{
  /* If copying just the "mesh" or "non-transient" portion of the
   * input DB, these are the variables that won't be copied:
   */
  return (strcmp(var_name, VAR_EBLK_TAB) == 0) || (strcmp(var_name, VAR_FBLK_TAB) == 0) ||
         (strcmp(var_name, VAR_ELEM_TAB) == 0) || (strcmp(var_name, VAR_ELSET_TAB) == 0) ||
         (strcmp(var_name, VAR_SSET_TAB) == 0) || (strcmp(var_name, VAR_FSET_TAB) == 0) ||
         (strcmp(var_name, VAR_ESET_TAB) == 0) || (strcmp(var_name, VAR_NSET_TAB) == 0);
}

static int is_non_mesh_variable(const char *var_name)
{
  /* If copying just the "mesh" or "non-transient" portion of the
   * input DB, these are the variables that won't be copied:
   */
  return (strcmp(var_name, VAR_NAME_GLO_VAR) == 0) || (strcmp(var_name, VAR_GLO_VAR) == 0) ||
         (strcmp(var_name, VAR_NAME_NOD_VAR) == 0) || (strcmp(var_name, VAR_NOD_VAR) == 0) ||
         (strcmp(var_name, VAR_NAME_EDG_VAR) == 0) || (strcmp(var_name, VAR_NAME_FAC_VAR) == 0) ||
         (strcmp(var_name, VAR_NAME_ELE_VAR) == 0) || (strcmp(var_name, VAR_NAME_NSET_VAR) == 0) ||
         (strcmp(var_name, VAR_NAME_ESET_VAR) == 0) || (strcmp(var_name, VAR_NAME_FSET_VAR) == 0) ||
         (strcmp(var_name, VAR_NAME_SSET_VAR) == 0) ||
         (strcmp(var_name, VAR_NAME_ELSET_VAR) == 0) ||
         (strncmp(var_name, "vals_elset_var", 14) == 0) ||
         (strncmp(var_name, "vals_sset_var", 13) == 0) ||
         (strncmp(var_name, "vals_fset_var", 13) == 0) ||
         (strncmp(var_name, "vals_eset_var", 13) == 0) ||
         (strncmp(var_name, "vals_nset_var", 13) == 0) ||
         (strncmp(var_name, "vals_nod_var", 12) == 0) ||
         (strncmp(var_name, "vals_edge_var", 13) == 0) ||
         (strncmp(var_name, "vals_face_var", 13) == 0) ||
         (strncmp(var_name, "vals_elem_var", 13) == 0);
}
/*! \endcond */

/*!
  \undoc

 *  efficiently copies all non-transient information (attributes,
 * dimensions, and variables from an opened EXODUS file to another
 * opened EXODUS file.  Will not overwrite a dimension or variable
 * already defined in the new file.
 * \param      in_exoid     exodus file id for input file
 * \param      out_exoid    exodus file id for output file
 */

int ex_copy(int in_exoid, int out_exoid)
{
  int  mesh_only = 1;
  int  status;
  int  in_large;
  char errmsg[MAX_ERR_LENGTH];

  EX_FUNC_ENTER();
  ex_check_valid_file_id(in_exoid, __func__);
  ex_check_valid_file_id(out_exoid, __func__);

  /*
   * Get exodus_large_model setting on both input and output
   * databases so know how to handle coordinates.
   */
  in_large = ex_large_model(in_exoid);

  /*
   * Get integer sizes for both input and output databases.
   * Currently they should both match or there will be an error.
   */
  if (ex_int64_status(in_exoid) != ex_int64_status(out_exoid)) {
    snprintf(errmsg, MAX_ERR_LENGTH,
             "ERROR: integer sizes do not match for input and output databases.");
    ex_err(__func__, errmsg, EX_WRONGFILETYPE);
    EX_FUNC_LEAVE(EX_FATAL);
  }

  /* put output file into define mode */
  EXCHECK(nc_redef(out_exoid));

  /* copy global attributes */
  EXCHECK(cpy_global_att(in_exoid, out_exoid));

  /* copy dimensions */
  EXCHECK(cpy_dimension(in_exoid, out_exoid, mesh_only));

  /* copy variable definitions and variable attributes */
  EXCHECK(cpy_variables(in_exoid, out_exoid, in_large, mesh_only));

  /* take the output file out of define mode */
  if ((status = nc_enddef(out_exoid)) != NC_NOERR) {
    snprintf(errmsg, MAX_ERR_LENGTH, "ERROR: failed to complete definition in file id %d",
             out_exoid);
    ex_err(__func__, errmsg, status);
    EX_FUNC_LEAVE(EX_FATAL);
  }

  /* output variable data */
  EXCHECK(cpy_variable_data(in_exoid, out_exoid, in_large, mesh_only));

  /* ensure internal data structures are updated */
  update_structs(out_exoid);

  ex_update(out_exoid);

  EX_FUNC_LEAVE(EX_NOERR);
}

int ex_copy_transient(int in_exoid, int out_exoid)
{
  int  mesh_only = 0;
  int  status;
  int  in_large;
  char errmsg[MAX_ERR_LENGTH];

  EX_FUNC_ENTER();
  ex_check_valid_file_id(in_exoid, __func__);
  ex_check_valid_file_id(out_exoid, __func__);

  /*
   * Get exodus_large_model setting on both input and output
   * databases so know how to handle coordinates.
   */
  in_large = ex_large_model(in_exoid);

  /*
   * Get integer sizes for both input and output databases.
   * Currently they should both match or there will be an error.
   */
  if (ex_int64_status(in_exoid) != ex_int64_status(out_exoid)) {
    snprintf(errmsg, MAX_ERR_LENGTH,
             "ERROR: integer sizes do not match for input and output databases.");
    ex_err(__func__, errmsg, EX_WRONGFILETYPE);
    EX_FUNC_LEAVE(EX_FATAL);
  }

  /* put output file into define mode */
  EXCHECK(nc_redef(out_exoid));

  /* copy global attributes */
  EXCHECK(cpy_global_att(in_exoid, out_exoid));

  /* copy dimensions */
  EXCHECK(cpy_dimension(in_exoid, out_exoid, mesh_only));

  /* copy variable definitions and variable attributes */
  EXCHECK(cpy_variables(in_exoid, out_exoid, in_large, mesh_only));

  /* take the output file out of define mode */
  if ((status = nc_enddef(out_exoid)) != NC_NOERR) {
    snprintf(errmsg, MAX_ERR_LENGTH, "ERROR: failed to complete definition in file id %d",
             out_exoid);
    ex_err(__func__, errmsg, status);
    EX_FUNC_LEAVE(EX_FATAL);
  }

  /* output variable data */
  EXCHECK(cpy_variable_data(in_exoid, out_exoid, in_large, mesh_only));

  /* ensure internal data structures are updated */
  update_structs(out_exoid);

  ex_update(out_exoid);

  EX_FUNC_LEAVE(EX_NOERR);
}

/*! \cond INTERNAL */
int cpy_variable_data(int in_exoid, int out_exoid, int in_large, int mesh_only)
{
  int          nvars; /* number of variables */
  int          varid; /* variable id */
  int          is_filtered = 0;
  struct ncvar var; /* variable */

  EXCHECKI(nc_inq(in_exoid, NULL, &nvars, NULL, NULL));
  for (varid = 0; varid < nvars; varid++) {
    EXCHECKI(nc_inq_var(in_exoid, varid, var.name, &var.type, &var.ndims, var.dims, &var.natts));
    if ((strcmp(var.name, VAR_QA_TITLE) == 0) || (strcmp(var.name, VAR_INFO) == 0)) {
      is_filtered = 1;
    }
    else if (is_truth_table_variable(var.name)) {
      is_filtered = 1;
    }
    else if (mesh_only == 1 &&
             (is_non_mesh_variable(var.name) || (strcmp(var.name, VAR_WHOLE_TIME) == 0))) {
      is_filtered = 1;
    }
    else if (mesh_only == 0 &&
             (!is_non_mesh_variable(var.name) && strcmp(var.name, VAR_WHOLE_TIME) != 0)) {
      is_filtered = 1;
    }
    else {
      is_filtered = 0;
    }

    if (!is_filtered) {
      if (strncmp(var.name, VAR_COORD, 5) == 0) {
        cpy_coord_val(in_exoid, out_exoid, var.name, in_large);
      }
      else {
        cpy_var_val(in_exoid, out_exoid, var.name);
      }
    }
  }
  return EX_NOERR;
}

/*! \cond INTERNAL */
int cpy_variables(int in_exoid, int out_exoid, int in_large, int mesh_only)
{
  int          nvars;      /* number of variables */
  int          recdimid;   /* id of unlimited dimension */
  int          varid;      /* variable id */
  int          var_out_id; /* variable id */
  int          is_filtered = 0;
  struct ncvar var; /* variable */

  EXCHECKI(nc_inq(in_exoid, NULL, &nvars, NULL, &recdimid));
  for (varid = 0; varid < nvars; varid++) {

    EXCHECKI(nc_inq_var(in_exoid, varid, var.name, &var.type, &var.ndims, var.dims, &var.natts));

    if ((strcmp(var.name, VAR_QA_TITLE) == 0) || (strcmp(var.name, VAR_INFO) == 0)) {
      is_filtered = 1;
    }
    else if (is_truth_table_variable(var.name)) {
      is_filtered = 1;
    }
    else if (mesh_only == 1 && is_non_mesh_variable(var.name)) {
      is_filtered = 1;
    }
    else {
      is_filtered = 0;
    }

    if (!is_filtered) {
      if (strncmp(var.name, VAR_COORD, 5) == 0) {
        var_out_id = cpy_coord_def(in_exoid, out_exoid, recdimid, var.name, in_large);
      }
      else {
        var_out_id = cpy_var_def(in_exoid, out_exoid, recdimid, var.name);
      }

      /* copy the variable's attributes */
      cpy_att(in_exoid, out_exoid, varid, var_out_id);
    }
  }
  return EX_NOERR;
}

/*! \cond INTERNAL */
int cpy_dimension(int in_exoid, int out_exoid, int mesh_only)
{
  int    status;
  int    ndims;      /* number of dimensions */
  int    recdimid;   /* id of unlimited dimension */
  int    dimid;      /* dimension id */
  int    dim_out_id; /* dimension id */
  int    is_filtered = 0;
  char   dim_nm[NC_MAX_NAME];
  size_t dim_sz;
  char   errmsg[MAX_ERR_LENGTH];

  EXCHECKI(nc_inq(in_exoid, &ndims, NULL, NULL, &recdimid));
  for (dimid = 0; dimid < ndims; dimid++) {

    EXCHECK(nc_inq_dim(in_exoid, dimid, dim_nm, &dim_sz));

    /* If the dimension isn't one we specifically don't want
     * to copy (ie, number of QA or INFO records) and it
     * hasn't been defined, copy it */
    if (strcmp(dim_nm, DIM_NUM_QA) == 0 || strcmp(dim_nm, DIM_NUM_INFO) == 0 ||
        strcmp(dim_nm, DIM_N4) == 0 || strcmp(dim_nm, DIM_STR) == 0 ||
        strcmp(dim_nm, DIM_LIN) == 0) {
      is_filtered = 1;
    }
    else if (mesh_only == 1 &&
             ((strcmp(dim_nm, DIM_NUM_NOD_VAR) == 0) || (strcmp(dim_nm, DIM_NUM_EDG_VAR) == 0) ||
              (strcmp(dim_nm, DIM_NUM_FAC_VAR) == 0) || (strcmp(dim_nm, DIM_NUM_ELE_VAR) == 0) ||
              (strcmp(dim_nm, DIM_NUM_NSET_VAR) == 0) || (strcmp(dim_nm, DIM_NUM_ESET_VAR) == 0) ||
              (strcmp(dim_nm, DIM_NUM_FSET_VAR) == 0) || (strcmp(dim_nm, DIM_NUM_SSET_VAR) == 0) ||
              (strcmp(dim_nm, DIM_NUM_ELSET_VAR) == 0) || (strcmp(dim_nm, DIM_NUM_GLO_VAR) == 0))) {
      is_filtered = 1;
    }
    else {
      is_filtered = 0;
    }

    if (!is_filtered) {
      /* See if the dimension has already been defined */
      status = nc_inq_dimid(out_exoid, dim_nm, &dim_out_id);

      if (status != NC_NOERR) {
        if (dimid != recdimid) {
          status = nc_def_dim(out_exoid, dim_nm, dim_sz, &dim_out_id);
        }
        else {
          status = nc_def_dim(out_exoid, dim_nm, NC_UNLIMITED, &dim_out_id);
        }
        if (status != NC_NOERR) {
          snprintf(errmsg, MAX_ERR_LENGTH, "ERROR: failed to define %s dimension in file id %d",
                   dim_nm, out_exoid);
          ex_err(__func__, errmsg, status);
          EX_FUNC_LEAVE(EX_FATAL);
        }
      }
    }
  }

  /* DIM_STR_NAME is a newly added dimension required by current API.
   * If it doesn't exist on the source database, we need to add it to
   * the target...
   */
  status = nc_inq_dimid(in_exoid, DIM_STR_NAME, &dim_out_id);
  if (status != NC_NOERR) {
    /*
     * See if it already exists in the output file
     * (ex_put_init_ext may have been called on the
     * output file prior to calling ex_copy)
     */
    status = nc_inq_dimid(out_exoid, DIM_STR_NAME, &dim_out_id);
    if (status != NC_NOERR) {
      /* Not found; set to default value of 32+1. */

      if ((status = nc_def_dim(out_exoid, DIM_STR_NAME, 33, &dim_out_id)) != NC_NOERR) {
        snprintf(errmsg, MAX_ERR_LENGTH,
                 "ERROR: failed to define string name dimension in file id %d", out_exoid);
        ex_err(__func__, errmsg, status);
        EX_FUNC_LEAVE(EX_FATAL);
      }
    }
  }
  return EX_NOERR;
}

/*! \cond INTERNAL */
int cpy_global_att(int in_exoid, int out_exoid)
{
  int          status;
  int          ngatts;
  size_t       i;
  struct ncatt att; /* attribute */

  EXCHECKI(nc_inq(in_exoid, NULL, NULL, &ngatts, NULL));

  /* copy global attributes */
  for (i = 0; i < (size_t)ngatts; i++) {

    EXCHECKI(nc_inq_attname(in_exoid, NC_GLOBAL, i, att.name));

    /* if attribute exists in output file, don't overwrite it; compute
     * word size, I/O word size etc. are global attributes stored when
     * file is created with ex_create;  we don't want to overwrite those
     */
    if ((status = nc_inq_att(out_exoid, NC_GLOBAL, att.name, &att.type, &att.len)) != NC_NOERR) {

      /* The "last_written_time" attribute is a special attribute used
         by the IOSS library to determine whether a timestep has been
         fully written to the database in order to try to detect a
         database crash that happens in the middle of a database
         output step. Don't want to copy that attribute.
      */
      if (strcmp(att.name, "last_written_time") != 0) {
        /* attribute doesn't exist in new file so OK to create it */
        EXCHECKI(nc_copy_att(in_exoid, NC_GLOBAL, att.name, out_exoid, NC_GLOBAL));
      }
    }
  }

  /* If the `ATT_MAX_NAME_LENGTH` attribute exists on input database,
   * add its value to the output database.  Won't be set above since
   * it is added during ex_create(), so it already exists in the
   * output database, but with potentially wrong value.
   */
  {
    nc_type att_type = NC_NAT;
    size_t  att_len  = 0;
    status           = nc_inq_att(in_exoid, NC_GLOBAL, ATT_MAX_NAME_LENGTH, &att_type, &att_len);
    if (status == NC_NOERR) {
      EXCHECKI(nc_copy_att(in_exoid, NC_GLOBAL, ATT_MAX_NAME_LENGTH, out_exoid, NC_GLOBAL));
    }
  }

  return EX_NOERR;
}

/*! \cond INTERNAL */
int cpy_att(int in_id, int out_id, int var_in_id, int var_out_id)
{
  /* Routine to copy all the attributes from the input netCDF
     file to the output netCDF file. If var_in_id == NC_GLOBAL,
     then the global attributes are copied. Otherwise the variable's
     attributes are copied. */

  int idx;
  int nbr_att;

  if (var_in_id == NC_GLOBAL) {
    EXCHECKI(nc_inq_natts(in_id, &nbr_att));
  }
  else {
    EXCHECKI(nc_inq_varnatts(in_id, var_in_id, &nbr_att));
  }

  /* Get the attributes names, types, lengths, and values */
  for (idx = 0; idx < nbr_att; idx++) {
    char att_nm[MAX_VAR_NAME_LENGTH];

    EXCHECKI(nc_inq_attname(in_id, var_in_id, idx, att_nm));
    nc_copy_att(in_id, var_in_id, att_nm, out_id, var_out_id);
  }

  return (EX_NOERR);
}

/*! \internal */
int cpy_coord_def(int in_id, int out_id, int rec_dim_id, char *var_nm, int in_large)
{
  const char *routine = NULL;
  size_t      spatial_dim;
  int         nbr_dim;
  int         temp;

  int dim_out_id[2];
  int var_out_id = -1;

  /* Handle easiest situation first: in_large matches out_large (1) */
  if (in_large == 1) {
    return cpy_var_def(in_id, out_id, rec_dim_id, var_nm); /* OK */
  }

  /* At this point, know that in_large != out_large, so only supported
     option is that in_large == 0 and out_large == 1.  Also will need
     the spatial dimension, so get that now.
   */
  ex_get_dimension(in_id, DIM_NUM_DIM, "dimension", &spatial_dim, &temp, routine);

  /* output file will have coordx, coordy, coordz (if 3d).  See if
     they are already defined in output file. Assume either all or
     none are defined. */

  {
    int var_out_idx, var_out_idy, var_out_idz;
    int status1 = nc_inq_varid(out_id, VAR_COORD_X, &var_out_idx);
    int status2 = nc_inq_varid(out_id, VAR_COORD_Y, &var_out_idy);
    int status3 = nc_inq_varid(out_id, VAR_COORD_Y, &var_out_idz);

    if (status1 == NC_NOERR && status2 == NC_NOERR && (spatial_dim == 2 || status3 == NC_NOERR)) {
      return NC_NOERR; /* already defined in output file */ /* OK */
    }
  }

  /* Get dimid of the num_nodes dimension in output file... */
  EXCHECKI(nc_inq_dimid(out_id, DIM_NUM_NODES, &dim_out_id[0]));

  /* Define the variables in the output file */

  /* Define according to the EXODUS file's IO_word_size */
  nbr_dim = 1;
  EXCHECKI(nc_def_var(out_id, VAR_COORD_X, nc_flt_code(out_id), nbr_dim, dim_out_id, &var_out_id));
  ex_compress_variable(out_id, var_out_id, 2);
  if (spatial_dim > 1) {
    EXCHECKI(
        nc_def_var(out_id, VAR_COORD_Y, nc_flt_code(out_id), nbr_dim, dim_out_id, &var_out_id));
    ex_compress_variable(out_id, var_out_id, 2);
  }
  if (spatial_dim > 2) {
    EXCHECKI(
        nc_def_var(out_id, VAR_COORD_Z, nc_flt_code(out_id), nbr_dim, dim_out_id, &var_out_id));
    ex_compress_variable(out_id, var_out_id, 2);
  }

  return var_out_id; /* OK */
}

/*! \internal */
int cpy_var_def(int in_id, int out_id, int rec_dim_id, char *var_nm)
{
  /* Routine to copy the variable metadata from an input netCDF file
   * to an output netCDF file.
   */

  int status;
  int dim_in_id[NC_MAX_VAR_DIMS];
  int dim_out_id[NC_MAX_VAR_DIMS];
  int idx;
  int nbr_dim;
  int var_in_id;
  int var_out_id;

  nc_type var_type;

  /* See if the requested variable is already in the output file. */
  status = nc_inq_varid(out_id, var_nm, &var_out_id);
  if (status == NC_NOERR) {
    return var_out_id; /* OK */
  }

  /* See if the requested variable is in the input file. */
  EXCHECKI(nc_inq_varid(in_id, var_nm, &var_in_id));

  /* Get the type of the variable and the number of dimensions. */
  EXCHECKI(nc_inq_vartype(in_id, var_in_id, &var_type));
  EXCHECKI(nc_inq_varndims(in_id, var_in_id, &nbr_dim));

  /* Recall:
     1. The dimensions must be defined before the variable.
     2. The variable must be defined before the attributes. */

  /* Get the dimension IDs */
  EXCHECKI(nc_inq_vardimid(in_id, var_in_id, dim_in_id));

  /* Get the dimension sizes and names */
  for (idx = 0; idx < nbr_dim; idx++) {
    char   dim_nm[NC_MAX_NAME];
    size_t dim_sz;

    EXCHECKI(nc_inq_dim(in_id, dim_in_id[idx], dim_nm, &dim_sz));

    /* See if the dimension has already been defined */
    status = nc_inq_dimid(out_id, dim_nm, &dim_out_id[idx]);

    /* If the dimension hasn't been defined, copy it */
    if (status != NC_NOERR) {
      if (dim_in_id[idx] != rec_dim_id) {
        EXCHECKI(nc_def_dim(out_id, dim_nm, dim_sz, &dim_out_id[idx]));
      }
      else {
        EXCHECKI(nc_def_dim(out_id, dim_nm, NC_UNLIMITED, &dim_out_id[idx]));
      }
    }
  }

  /* Define the variable in the output file */

  /* If variable is float or double, define it according to the EXODUS
     file's IO_word_size */

  if ((var_type == NC_FLOAT) || (var_type == NC_DOUBLE)) {
    EXCHECKI(nc_def_var(out_id, var_nm, nc_flt_code(out_id), nbr_dim, dim_out_id, &var_out_id));
    ex_compress_variable(out_id, var_out_id, 2);
  }
  else {
    EXCHECKI(nc_def_var(out_id, var_nm, var_type, nbr_dim, dim_out_id, &var_out_id));
    ex_compress_variable(out_id, var_out_id, 1);
  }
  return var_out_id; /* OK */

} /* end cpy_var_def() */

/*! \internal */
int cpy_var_val(int in_id, int out_id, char *var_nm)
{
  /* Routine to copy the variable data from an input netCDF file
   * to an output netCDF file.
   */

  int     dim_id_in[NC_MAX_VAR_DIMS];
  int     dim_id_out[NC_MAX_VAR_DIMS];
  int     idx;
  int     nbr_dim;
  int     var_in_id;
  int     var_out_id;
  size_t  dim_str[NC_MAX_VAR_DIMS];
  size_t  dim_cnt[NC_MAX_VAR_DIMS];
  size_t  var_sz = 1L;
  nc_type var_type_in, var_type_out;

  void *void_ptr = NULL;

  /* Get the var_id for the requested variable from both files. */
  EXCHECKI(nc_inq_varid(in_id, var_nm, &var_in_id));
  EXCHECKI(nc_inq_varid(out_id, var_nm, &var_out_id));

  /* Get the number of dimensions for the variable. */
  EXCHECKI(nc_inq_vartype(out_id, var_out_id, &var_type_out));

  EXCHECKI(nc_inq_vartype(in_id, var_in_id, &var_type_in));
  EXCHECKI(nc_inq_varndims(in_id, var_in_id, &nbr_dim));

  /* Get the dimension IDs from the input file */
  EXCHECKF(nc_inq_vardimid(in_id, var_in_id, dim_id_in));
  EXCHECKF(nc_inq_vardimid(out_id, var_out_id, dim_id_out));

  /* Get the dimension sizes and names from the input file */
  for (idx = 0; idx < nbr_dim; idx++) {
    /* NB: For the unlimited dimension, ncdiminq() returns the maximum
       value used so far in writing data for that dimension.
       Thus if you read the dimension sizes from the output file, then
       the ncdiminq() returns dim_sz=0 for the unlimited dimension
       until a variable has been written with that dimension. This is
       the reason for always reading the input file for the dimension
       sizes. */
    size_t dim_in  = 0;
    size_t dim_out = 0;

    /* If client is increasing any sizes, then need to make sure
       the void_ptr is large enough to hold new dimension */
    EXCHECKF(nc_inq_dimlen(in_id, dim_id_in[idx], &dim_in));
    EXCHECKF(nc_inq_dimlen(out_id, dim_id_out[idx], &dim_out));
    dim_cnt[idx] = dim_in > dim_out ? dim_in : dim_out;
    dim_str[idx] = 0;

    /* Initialize the indicial offset and stride arrays */
    var_sz *= dim_cnt[idx];
  } /* end loop over dim */

  /* Allocate enough space to hold the variable */
  if (var_sz > 0) {
    void_ptr = calloc(var_sz, type_size(var_type_in));
  }

  /* Get the variable */

  /* if variable is float or double, convert if necessary */

  if (nbr_dim == 0) { /* variable is a scalar */

    if (var_type_in == NC_INT && var_type_out == NC_INT) {
      EXCHECKF(nc_get_var1_int(in_id, var_in_id, 0L, void_ptr));
      EXCHECKF(nc_put_var1_int(out_id, var_out_id, 0L, void_ptr));
    }

    else if (var_type_in == NC_INT64 && var_type_out == NC_INT64) {
      EXCHECKF(nc_get_var1_longlong(in_id, var_in_id, 0L, void_ptr));
      EXCHECKF(nc_put_var1_longlong(out_id, var_out_id, 0L, void_ptr));
    }

    else if (var_type_in == NC_FLOAT) {
      EXCHECKF(nc_get_var1_float(in_id, var_in_id, 0L, void_ptr));
      EXCHECKF(nc_put_var1_float(out_id, var_out_id, 0L, void_ptr));
    }

    else if (var_type_in == NC_DOUBLE) {
      EXCHECKF(nc_get_var1_double(in_id, var_in_id, 0L, void_ptr));
      EXCHECKF(nc_put_var1_double(out_id, var_out_id, 0L, void_ptr));
    }

    else if (var_type_in == NC_CHAR) {
      EXCHECKF(nc_get_var1_text(in_id, var_in_id, 0L, void_ptr));
      EXCHECKF(nc_put_var1_text(out_id, var_out_id, 0L, void_ptr));
    }

    else {
      assert(1 == 0);
    }
  }
  else { /* variable is a vector */

    if (var_type_in == NC_INT && var_type_out == NC_INT) {
      EXCHECKF(nc_get_var_int(in_id, var_in_id, void_ptr));
      EXCHECKF(nc_put_vara_int(out_id, var_out_id, dim_str, dim_cnt, void_ptr));
    }

    else if (var_type_in == NC_INT64 && var_type_out == NC_INT64) {
      EXCHECKF(nc_get_var_longlong(in_id, var_in_id, void_ptr));
      EXCHECKF(nc_put_vara_longlong(out_id, var_out_id, dim_str, dim_cnt, void_ptr));
    }

    else if (var_type_in == NC_FLOAT) {
      EXCHECKF(nc_get_var_float(in_id, var_in_id, void_ptr));
      EXCHECKF(nc_put_vara_float(out_id, var_out_id, dim_str, dim_cnt, void_ptr));
    }

    else if (var_type_in == NC_DOUBLE) {
      EXCHECKF(nc_get_var_double(in_id, var_in_id, void_ptr));
      EXCHECKF(nc_put_vara_double(out_id, var_out_id, dim_str, dim_cnt, void_ptr));
    }

    else if (var_type_in == NC_CHAR) {
      EXCHECKF(nc_get_var_text(in_id, var_in_id, void_ptr));
      EXCHECKF(nc_put_vara_text(out_id, var_out_id, dim_str, dim_cnt, void_ptr));
    }

    else {
      assert(1 == 0);
    }
  } /* end if variable is an array */

  /* Free the space that held the variable */
  free(void_ptr);

  return (EX_NOERR);

err_ret:
  free(void_ptr);
  return (EX_FATAL);

} /* end cpy_var_val() */

/*! \internal */
int cpy_coord_val(int in_id, int out_id, char *var_nm, int in_large)
{
  /* Routine to copy the coordinate data from an input netCDF file
   * to an output netCDF file.
   */

  const char *routine = NULL;
  int         temp;
  size_t      i;
  size_t      spatial_dim, num_nodes;
  size_t      start[2], count[2];
  nc_type     var_type_in, var_type_out;

  void *void_ptr = NULL;

  /* Handle easiest situation first: in_large matches out_large (1) */
  if (in_large == 1) {
    return cpy_var_val(in_id, out_id, var_nm); /* OK */
  }

  /* At this point, know that in_large == 0, so will need to
     copy a vector to multiple scalars.  Also
     will need a couple dimensions, so get them now.*/
  ex_get_dimension(in_id, DIM_NUM_DIM, "dimension", &spatial_dim, &temp, routine);
  ex_get_dimension(in_id, DIM_NUM_NODES, "nodes", &num_nodes, &temp, routine);

  /* output file will have coordx, coordy, coordz (if 3d). */
  /* Get the var_id for the requested variable from both files. */
  int var_in_id, var_out_id[3];
  EXCHECKI(nc_inq_varid(in_id, VAR_COORD, &var_in_id));

  EXCHECKI(nc_inq_varid(out_id, VAR_COORD_X, &var_out_id[0]));
  if (spatial_dim > 1)
    EXCHECKI(nc_inq_varid(out_id, VAR_COORD_Y, &var_out_id[1]));
  if (spatial_dim > 2)
    EXCHECKI(nc_inq_varid(out_id, VAR_COORD_Z, &var_out_id[2]));

  EXCHECKI(nc_inq_vartype(in_id, var_in_id, &var_type_in));
  EXCHECKI(nc_inq_vartype(out_id, var_out_id[0], &var_type_out));

  if (num_nodes > 0) {
    void_ptr = malloc(num_nodes * type_size(var_type_in));
  }

  /* Copy each component of the variable... */
  for (i = 0; i < spatial_dim; i++) {
    start[0] = i;
    start[1] = 0;
    count[0] = 1;
    count[1] = num_nodes;
    if (var_type_in == NC_FLOAT) {
      EXCHECKI(nc_get_vara_float(in_id, var_in_id, start, count, void_ptr));
      EXCHECKI(nc_put_var_float(out_id, var_out_id[i], void_ptr));
    }
    else {
      assert(var_type_in == NC_DOUBLE);
      EXCHECKI(nc_get_vara_double(in_id, var_in_id, start, count, void_ptr));
      EXCHECKI(nc_put_var_double(out_id, var_out_id[i], void_ptr));
    }
  }

  /* Free the space that held the variable */
  free(void_ptr);
  return (EX_NOERR);

} /* end cpy_coord_val() */

/*! \internal */
void update_structs(int out_exoid)
{
  update_internal_structs(out_exoid, EX_INQ_EDGE_BLK, ex_get_counter_list(EX_EDGE_BLOCK));
  update_internal_structs(out_exoid, EX_INQ_FACE_BLK, ex_get_counter_list(EX_FACE_BLOCK));
  update_internal_structs(out_exoid, EX_INQ_ELEM_BLK, ex_get_counter_list(EX_ELEM_BLOCK));

  update_internal_structs(out_exoid, EX_INQ_NODE_SETS, ex_get_counter_list(EX_NODE_SET));
  update_internal_structs(out_exoid, EX_INQ_EDGE_SETS, ex_get_counter_list(EX_EDGE_SET));
  update_internal_structs(out_exoid, EX_INQ_FACE_SETS, ex_get_counter_list(EX_FACE_SET));
  update_internal_structs(out_exoid, EX_INQ_SIDE_SETS, ex_get_counter_list(EX_SIDE_SET));
  update_internal_structs(out_exoid, EX_INQ_ELEM_SETS, ex_get_counter_list(EX_ELEM_SET));

  update_internal_structs(out_exoid, EX_INQ_NODE_MAP, ex_get_counter_list(EX_NODE_MAP));
  update_internal_structs(out_exoid, EX_INQ_EDGE_MAP, ex_get_counter_list(EX_EDGE_MAP));
  update_internal_structs(out_exoid, EX_INQ_FACE_MAP, ex_get_counter_list(EX_FACE_MAP));
  update_internal_structs(out_exoid, EX_INQ_ELEM_MAP, ex_get_counter_list(EX_ELEM_MAP));
}

/*! \internal */
void update_internal_structs(int out_exoid, ex_inquiry inqcode, struct list_item **ctr_list)
{
  int i;
  int number = ex_inquire_int(out_exoid, inqcode);

  if (number > 0) {
    for (i = 0; i < number; i++) {
      ex_inc_file_item(out_exoid, ctr_list);
    }
  }
}

size_t type_size(nc_type type)
{
  if (type == NC_CHAR) {
    return sizeof(char); /* OK */
  }
  if (type == NC_INT) {
    return sizeof(int); /* OK */
  }
  if (type == NC_INT64) {
    return sizeof(int64_t); /* OK */
  }
  if (type == NC_FLOAT) {
    return sizeof(float); /* OK */
  }
  else if (type == NC_DOUBLE) {
    return sizeof(double); /* OK */
  }
  else {
    return 0; /* OK */
  }
}

/* \endcond */
