read_mosaic.c

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/***********************************************************************
 *                   GNU Lesser General Public License
 *
 * This file is part of the GFDL Flexible Modeling System (FMS).
 *
 * FMS is free software: you can redistribute it and/or modify it under
 * the terms of the GNU Lesser General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or (at
 * your option) any later version.
 *
 * FMS is distributed in the hope that it will be useful, but WITHOUT
 * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
 * FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
 * for more details.
 *
 * You should have received a copy of the GNU Lesser General Public
 * License along with FMS.  If not, see <http://www.gnu.org/licenses/>.
 **********************************************************************/
#include <stdlib.h>
#include <stdio.h>
#include <math.h>
#include <string.h>
#include "read_mosaic.h"
#include "constant.h"
#include "mosaic_util.h"
#include <netcdf.h>
 
/** \file
 *  \ingroup mosaic
 *  \brief Support for reading mosaic netcdf grid files.
 */
 
/*********************************************************************
    void netcdf_error( int status )
    status is the returning value of netcdf call. this routine will
    handle the error when status is not NC_NOERR.
********************************************************************/
void handle_netcdf_error(const char *msg, int status )
{
  char errmsg[512];
 
  sprintf( errmsg, "%s: %s", msg, (char *)nc_strerror(status) );
  error_handler(errmsg);
 
} /* handle_netcdf_error */
 
/***************************************************************************
  void get_file_dir(const char *file, char *dir)
  get the directory where file is located. The dir will be the complate path
  before the last "/". If no "/" exist in file, the path will be current ".".
***************************************************************************/
void get_file_dir(const char *file, char *dir)
{
  int len;
  const char *strptr = NULL;
 
  /* get the diretory */
 
  strptr = strrchr(file, '/');
  if(strptr) {
    len = strptr - file;
    strncpy(dir, file, len);
  }
  else {
    len = 1;
    strcpy(dir, ".");
  }
  dir[len] = 0;
 
} /* get_file_dir */
 
 
int field_exist(const char* file, const char *name)
{
  int ncid, varid, status;
  char msg[512];
  int existed=0;
 
#ifdef use_netCDF
 
  status = nc_open(file, NC_NOWRITE, &ncid);
  if(status != NC_NOERR) {
    sprintf(msg, "field_exist: in opening file %s", file);
    handle_netcdf_error(msg, status);
  }
 
  status = nc_inq_varid(ncid, name, &varid);
  if(status == NC_NOERR){
    existed = 1;
  }
 
  status = nc_close(ncid);
  if(status != NC_NOERR) {
    sprintf(msg, "field_exist: in closing file %s.", file);
    handle_netcdf_error(msg, status);
  }
 
#else  /* ndef use_netCDF */
  error_handler("read_mosaic: Add flag -Duse_netCDF when compiling");
#endif  /* use_netcdf */
 
  return existed;
 
} /* field_exist */
 
int get_dimlen(const char* file, const char *name)
{
  int ncid, dimid, status, len;
  size_t size;
  char msg[512];
 
  len = 0;
#ifdef use_netCDF
  status = nc_open(file, NC_NOWRITE, &ncid);
  if(status != NC_NOERR) {
    sprintf(msg, "in opening file %s", file);
    handle_netcdf_error(msg, status);
  }
 
  status = nc_inq_dimid(ncid, name, &dimid);
  if(status != NC_NOERR) {
    sprintf(msg, "in getting dimid of %s from file %s.", name, file);
    handle_netcdf_error(msg, status);
  }
 
  status = nc_inq_dimlen(ncid, dimid, &size);
  if(status != NC_NOERR) {
    sprintf(msg, "in getting dimension size of %s from file %s.", name, file);
    handle_netcdf_error(msg, status);
  }
  status = nc_close(ncid);
  if(status != NC_NOERR) {
    sprintf(msg, "in closing file %s.", file);
    handle_netcdf_error(msg, status);
  }
 
  len = size;
  if(status != NC_NOERR) {
    sprintf(msg, "in closing file %s", file);
    handle_netcdf_error(msg, status);
  }
#else
  error_handler("read_mosaic: Add flag -Duse_netCDF when compiling");
#endif
 
  return len;
 
} /* get_dimlen */
 
/*******************************************************************************
   void get_string_data(const char *file, const char *name, char *data)
   get string data of field with "name" from "file".
******************************************************************************/
void get_string_data(const char *file, const char *name, char *data)
{
  int ncid, varid, status;
  char msg[512];
 
#ifdef use_netCDF
  status = nc_open(file, NC_NOWRITE, &ncid);
  if(status != NC_NOERR) {
    sprintf(msg, "in opening file %s", file);
    handle_netcdf_error(msg, status);
  }
  status = nc_inq_varid(ncid, name, &varid);
  if(status != NC_NOERR) {
    sprintf(msg, "in getting varid of %s from file %s.", name, file);
    handle_netcdf_error(msg, status);
  }
  status = nc_get_var_text(ncid, varid, data);
  if(status != NC_NOERR) {
    sprintf(msg, "in getting data of %s from file %s.", name, file);
    handle_netcdf_error(msg, status);
  }
  status = nc_close(ncid);
  if(status != NC_NOERR) {
    sprintf(msg, "in closing file %s.", file);
    handle_netcdf_error(msg, status);
  }
#else
  error_handler("read_mosaic: Add flag -Duse_netCDF when compiling");
#endif
 
} /* get_string_data */
 
/*******************************************************************************
   void get_string_data_level(const char *file, const char *name, const size_t *start, const size_t *nread, char *data)
   get string data of field with "name" from "file".
******************************************************************************/
void get_string_data_level(const char *file, const char *name, char *data, const unsigned int *level)
{
  int ncid, varid, status, i;
  size_t start[4], nread[4];
  char msg[512];
 
#ifdef use_netCDF
  status = nc_open(file, NC_NOWRITE, &ncid);
  if(status != NC_NOERR) {
    sprintf(msg, "in opening file %s", file);
    handle_netcdf_error(msg, status);
  }
  status = nc_inq_varid(ncid, name, &varid);
  if(status != NC_NOERR) {
    sprintf(msg, "in getting varid of %s from file %s.", name, file);
    handle_netcdf_error(msg, status);
  }
  for(i=0; i<4; i++) {
    start[i] = 0; nread[i] = 1;
  }
  start[0] = *level; nread[1] = STRING;
  status = nc_get_vara_text(ncid, varid, start, nread, data);
  if(status != NC_NOERR) {
    sprintf(msg, "in getting data of %s from file %s.", name, file);
    handle_netcdf_error(msg, status);
  }
  status = nc_close(ncid);
  if(status != NC_NOERR) {
    sprintf(msg, "in closing file %s.", file);
    handle_netcdf_error(msg, status);
  }
#else
  error_handler("read_mosaic: Add flag -Duse_netCDF when compiling");
#endif
 
} /* get_string_data_level */
 
 
/*******************************************************************************
   void get_var_data(const char *file, const char *name, double *data)
   get var data of field with "name" from "file".
******************************************************************************/
void get_var_data(const char *file, const char *name, void *data)
{
 
  int ncid, varid, status;
  nc_type vartype;
  char msg[512];
 
#ifdef use_netCDF
  status = nc_open(file, NC_NOWRITE, &ncid);
  if(status != NC_NOERR) {
    sprintf(msg, "in opening file %s", file);
    handle_netcdf_error(msg, status);
  }
  status = nc_inq_varid(ncid, name, &varid);
  if(status != NC_NOERR) {
    sprintf(msg, "in getting varid of %s from file %s.", name, file);
    handle_netcdf_error(msg, status);
  }
 
  status = nc_inq_vartype(ncid, varid, &vartype);
  if(status != NC_NOERR) {
    sprintf(msg, "get_var_data: in getting vartype of of %s in file %s ", name, file);
    handle_netcdf_error(msg, status);
  }
 
  switch (vartype) {
    case NC_DOUBLE:case NC_FLOAT:
      status = nc_get_var_double(ncid, varid, (double *)data);
      break;
    case NC_INT:
      status = nc_get_var_int(ncid, varid, (int *)data);
      break;
    default:
      sprintf(msg, "get_var_data: field %s in file %s has an invalid type, "
              "the type should be NC_DOUBLE, NC_FLOAT or NC_INT", name, file);
      error_handler(msg);
  }
  if(status != NC_NOERR) {
    sprintf(msg, "in getting data of %s from file %s.", name, file);
    handle_netcdf_error(msg, status);
  }
  status = nc_close(ncid);
  if(status != NC_NOERR) {
    sprintf(msg, "in closing file %s.", file);
    handle_netcdf_error(msg, status);
  }
#else
  error_handler("read_mosaic: Add flag -Duse_netCDF when compiling");
#endif
 
} /* get_var_data */
 
/*******************************************************************************
   void get_var_data(const char *file, const char *name, double *data)
   get var data of field with "name" from "file".
******************************************************************************/
void get_var_data_region(const char *file, const char *name, const size_t *start, const size_t *nread, void *data)
{
 
  int ncid, varid, status;
  nc_type vartype;
  char msg[512];
 
#ifdef use_netCDF
  status = nc_open(file, NC_NOWRITE, &ncid);
  if(status != NC_NOERR) {
    sprintf(msg, "get_var_data_region: in opening file %s", file);
    handle_netcdf_error(msg, status);
  }
  status = nc_inq_varid(ncid, name, &varid);
  if(status != NC_NOERR) {
    sprintf(msg, "in getting varid of %s from file %s.", name, file);
    handle_netcdf_error(msg, status);
  }
 
  status = nc_inq_vartype(ncid, varid, &vartype);
  if(status != NC_NOERR) {
    sprintf(msg, "get_var_data_region: in getting vartype of of %s in file %s ", name, file);
    handle_netcdf_error(msg, status);
  }
 
  switch (vartype) {
    case NC_DOUBLE:case NC_FLOAT:
      status = nc_get_vara_double(ncid, varid, start, nread, (double *)data);
      break;
    case NC_INT:
      status = nc_get_vara_int(ncid, varid, start, nread, (int *)data);
      break;
    default:
      sprintf(msg, "get_var_data_region: field %s in file %s has an invalid type, "
              "the type should be NC_DOUBLE, NC_FLOAT or NC_INT", name, file);
      error_handler(msg);
  }
 
  if(status != NC_NOERR) {
    sprintf(msg, "get_var_data_region: in getting data of %s from file %s.", name, file);
    handle_netcdf_error(msg, status);
  }
  status = nc_close(ncid);
  if(status != NC_NOERR) {
    sprintf(msg, "get_var_data_region: in closing file %s.", file);
    handle_netcdf_error(msg, status);
  }
#else
  error_handler("read_mosaic: Add flag -Duse_netCDF when compiling");
#endif
 
} /* get_var_data_region */
 
/******************************************************************************
   void get_var_text_att(const char *file, const char *name, const char *attname, char *att)
   get text attribute of field 'name' from 'file
******************************************************************************/
void get_var_text_att(const char *file, const char *name, const char *attname, char *att)
{
  int ncid, varid, status;
  char msg[512];
 
#ifdef use_netCDF
  status = nc_open(file, NC_NOWRITE, &ncid);
  if(status != NC_NOERR) {
    sprintf(msg, "in opening file %s", file);
    handle_netcdf_error(msg, status);
  }
  status = nc_inq_varid(ncid, name, &varid);
  if(status != NC_NOERR) {
    sprintf(msg, "in getting varid of %s from file %s.", name, file);
    handle_netcdf_error(msg, status);
  }
  status = nc_get_att_text(ncid, varid, attname, att);
  if(status != NC_NOERR) {
    sprintf(msg, "in getting attribute %s of %s from file %s.", attname, name, file);
    handle_netcdf_error(msg, status);
  }
  status = nc_close(ncid);
  if(status != NC_NOERR) {
    sprintf(msg, "in closing file %s.", file);
    handle_netcdf_error(msg, status);
  }
#else
  error_handler("read_mosaic: Add flag -Duse_netCDF when compiling");
#endif
 
} /* get_var_text_att */
 
/***********************************************************************
  return number of overlapping cells.
***********************************************************************/
int read_mosaic_xgrid_size_( const char *xgrid_file )
{
  return read_mosaic_xgrid_size(xgrid_file);
}
 
int read_mosaic_xgrid_size( const char *xgrid_file )
{
  int ncells;
 
  ncells = get_dimlen(xgrid_file, "ncells");
  return ncells;
}
 
  double get_global_area(void)
  {
    double garea;
    garea = 4*M_PI*RADIUS*RADIUS;
 
    return garea;
  }
 
  double get_global_area_(void)
  {
    double garea;
    garea = 4*M_PI*RADIUS*RADIUS;
 
    return garea;
  }
 
 
    /****************************************************************************/
  void read_mosaic_xgrid_order1_(const char *xgrid_file, int *i1, int *j1, int *i2, int *j2, double *area )
    {
      read_mosaic_xgrid_order1(xgrid_file, i1, j1, i2, j2, area);
 
    }
 
  void read_mosaic_xgrid_order1(const char *xgrid_file, int *i1, int *j1, int *i2, int *j2, double *area )
    {
      int    ncells, n;
      int    *tile1_cell, *tile2_cell;
      double garea;
 
      ncells = get_dimlen(xgrid_file, "ncells");
 
      tile1_cell       = (int *)malloc(ncells*2*sizeof(int));
      tile2_cell       = (int *)malloc(ncells*2*sizeof(int));
      get_var_data(xgrid_file, "tile1_cell", tile1_cell);
      get_var_data(xgrid_file, "tile2_cell", tile2_cell);
 
      get_var_data(xgrid_file, "xgrid_area", area);
 
      garea = 4*M_PI*RADIUS*RADIUS;
 
      for(n=0; n<ncells; n++) {
        i1[n] = tile1_cell[n*2] - 1;
        j1[n] = tile1_cell[n*2+1] - 1;
        i2[n] = tile2_cell[n*2] - 1;
        j2[n] = tile2_cell[n*2+1] - 1;
        area[n] /= garea; /* rescale the exchange grid area to unit earth area */
      }
 
      free(tile1_cell);
      free(tile2_cell);
 
    } /* read_mosaic_xgrid_order1 */
 
 
  void read_mosaic_xgrid_order1_region_(const char *xgrid_file, int *i1, int *j1, int *i2, int *j2, double *area, int *isc, int *iec )
    {
      read_mosaic_xgrid_order1_region(xgrid_file, i1, j1, i2, j2, area, isc, iec);
 
    }
 
  void read_mosaic_xgrid_order1_region(const char *xgrid_file, int *i1, int *j1, int *i2, int *j2, double *area, int *isc, int *iec )
    {
      int    ncells, n, i;
      int    *tile1_cell, *tile2_cell;
      size_t start[4], nread[4];
      double garea;
 
      ncells = *iec-*isc+1;
 
      tile1_cell       = (int *)malloc(ncells*2*sizeof(int));
      tile2_cell       = (int *)malloc(ncells*2*sizeof(int));
      for(i=0; i<4; i++) {
        start[i] = 0; nread[i] = 1;
      }
 
      start[0] = *isc;
      nread[0] = ncells;
      nread[1] = 2;
 
      get_var_data_region(xgrid_file, "tile1_cell", start, nread, tile1_cell);
      get_var_data_region(xgrid_file, "tile2_cell", start, nread, tile2_cell);
 
      nread[1] = 1;
 
      get_var_data_region(xgrid_file, "xgrid_area", start, nread, area);
 
      garea = 4*M_PI*RADIUS*RADIUS;
 
      for(n=0; n<ncells; n++) {
        i1[n] = tile1_cell[n*2] - 1;
        j1[n] = tile1_cell[n*2+1] - 1;
        i2[n] = tile2_cell[n*2] - 1;
        j2[n] = tile2_cell[n*2+1] - 1;
        area[n] /= garea; /* rescale the exchange grid area to unit earth area */
      }
 
      free(tile1_cell);
      free(tile2_cell);
 
    } /* read_mosaic_xgrid_order1 */
 
    /* NOTE: di, dj is for tile1, */
    /****************************************************************************/
  void read_mosaic_xgrid_order2_(const char *xgrid_file, int *i1, int *j1, int *i2, int *j2, double *area, double *di, double *dj )
  {
      read_mosaic_xgrid_order2(xgrid_file, i1, j1, i2, j2, area, di, dj);
 
    }
  void read_mosaic_xgrid_order2(const char *xgrid_file, int *i1, int *j1, int *i2, int *j2, double *area, double *di, double *dj )
    {
      int    ncells, n;
      int    *tile1_cell, *tile2_cell;
      double *tile1_distance;
      double garea;
      ncells = get_dimlen(xgrid_file, "ncells");
 
      tile1_cell       = (int    *)malloc(ncells*2*sizeof(int   ));
      tile2_cell       = (int    *)malloc(ncells*2*sizeof(int   ));
      tile1_distance   = (double *)malloc(ncells*2*sizeof(double));
      get_var_data(xgrid_file, "tile1_cell", tile1_cell);
      get_var_data(xgrid_file, "tile2_cell", tile2_cell);
      get_var_data(xgrid_file, "xgrid_area", area);
      get_var_data(xgrid_file, "tile1_distance", tile1_distance);
 
      garea = 4*M_PI*RADIUS*RADIUS;
 
      for(n=0; n<ncells; n++) {
        i1[n] = tile1_cell[n*2] - 1;
        j1[n] = tile1_cell[n*2+1] - 1;
        i2[n] = tile2_cell[n*2] - 1;
        j2[n] = tile2_cell[n*2+1] - 1;
        di[n] = tile1_distance[n*2];
        dj[n] = tile1_distance[n*2+1];
        area[n] /= garea; /* rescale the exchange grid area to unit earth area */
      }
 
      free(tile1_cell);
      free(tile2_cell);
      free(tile1_distance);
 
    } /* read_mosaic_xgrid_order2 */
 
    /******************************************************************************
  int read_mosaic_ntiles(const char *mosaic_file)
  return number tiles in mosaic_file
    ******************************************************************************/
    int read_mosaic_ntiles_(const char *mosaic_file)
    {
      return read_mosaic_ntiles(mosaic_file);
    }
    int read_mosaic_ntiles(const char *mosaic_file)
    {
 
      int ntiles;
 
      ntiles = get_dimlen(mosaic_file, "ntiles");
 
      return ntiles;
 
    } /* read_mosaic_ntiles */
 
    /******************************************************************************
  int read_mosaic_ncontacts(const char *mosaic_file)
  return number of contacts in mosaic_file
    ******************************************************************************/
    int read_mosaic_ncontacts_(const char *mosaic_file)
    {
      return read_mosaic_ncontacts(mosaic_file);
    }
    int read_mosaic_ncontacts(const char *mosaic_file)
    {
 
      int ncontacts;
 
      if(field_exist(mosaic_file, "contacts") )
        ncontacts = get_dimlen(mosaic_file, "ncontact");
      else
        ncontacts = 0;
 
      return ncontacts;
 
    } /* read_mosaic_ncontacts */
 
 
    /*****************************************************************************
  void read_mosaic_grid_sizes(const char *mosaic_file, int *nx, int *ny)
  read mosaic grid size of each tile, currently we are assuming the refinement is 2.
  We assume the grid files are located at the same directory as mosaic_file.
    *****************************************************************************/
    void read_mosaic_grid_sizes_(const char *mosaic_file, int *nx, int *ny)
    {
      read_mosaic_grid_sizes(mosaic_file, nx, ny);
    }
    void read_mosaic_grid_sizes(const char *mosaic_file, int *nx, int *ny)
    {
      unsigned int ntiles, n;
      char gridfile[STRING], tilefile[2*STRING];
      char dir[STRING];
      const int x_refine = 2, y_refine = 2;
 
      get_file_dir(mosaic_file, dir);
      ntiles = get_dimlen(mosaic_file, "ntiles");
      for(n = 0; n < ntiles; n++) {
        get_string_data_level(mosaic_file, "gridfiles", gridfile, &n);
        sprintf(tilefile, "%s/%s", dir, gridfile);
        nx[n] = get_dimlen(tilefile, "nx");
        ny[n] = get_dimlen(tilefile, "ny");
        if(nx[n]%x_refine != 0) error_handler("Error from read_mosaic_grid_sizes: nx is not divided by x_refine");
        if(ny[n]%y_refine != 0) error_handler("Error from read_mosaic_grid_sizes: ny is not divided by y_refine");
        nx[n] /= x_refine;
        ny[n] /= y_refine;
      }
 
    } /* read_mosaic_grid_sizes */
 
 
    /******************************************************************************
  void read_mosaic_contact(const char *mosaic_file)
  read mosaic contact information
    ******************************************************************************/
    void read_mosaic_contact_(const char *mosaic_file, int *tile1, int *tile2, int *istart1, int *iend1,
                              int *jstart1, int *jend1, int *istart2, int *iend2, int *jstart2, int *jend2)
    {
      read_mosaic_contact(mosaic_file, tile1, tile2, istart1, iend1, jstart1, jend1, istart2, iend2, jstart2, jend2);
    }
 
    /* transfer the index from supergrid to model grid
       return 0 if istart = iend
       otherwise return 1.
    */
 
    int transfer_to_model_index(int istart_in, int iend_in, int *istart_out, int *iend_out, int refine_ratio)
    {
 
      int type;
 
      if( istart_in == iend_in ) {
        type = 0;
        istart_out[0] = (istart_in+1)/refine_ratio-1;
        iend_out[0]  = istart_out[0];
      }
      else {
        type = 1;
        if( iend_in > istart_in ) {
          istart_out[0] = istart_in - 1;
          iend_out[0]   = iend_in - refine_ratio;
        }
        else {
          istart_out[0] = istart_in - refine_ratio;
          iend_out[0]   = iend_in - 1;
        }
 
        if( istart_out[0]%refine_ratio || iend_out[0]%refine_ratio)
          error_handler("Error from read_mosaic: mismatch between refine_ratio and istart_in/iend_in");
        istart_out[0] /= refine_ratio;
        iend_out[0]   /= refine_ratio;
      }
 
      return type;
 
    }
 
 
    void read_mosaic_contact(const char *mosaic_file, int *tile1, int *tile2, int *istart1, int *iend1,
                             int *jstart1, int *jend1, int *istart2, int *iend2, int *jstart2, int *jend2)
    {
      char contacts[STRING];
      char **gridtiles;
#define MAXVAR 40
      char pstring[MAXVAR][STRING];
      unsigned int nstr, ntiles, ncontacts, n, m, l, found;
      const int x_refine = 2, y_refine = 2;
      int i1_type, j1_type, i2_type, j2_type;
 
      ntiles = get_dimlen(mosaic_file, "ntiles");
      gridtiles = (char **)malloc(ntiles*sizeof(char *));
      for(n=0; n<ntiles; n++) {
        gridtiles[n] = (char *)malloc(STRING*sizeof(char));
        get_string_data_level(mosaic_file, "gridtiles", gridtiles[n], &n);
      }
 
      ncontacts = get_dimlen(mosaic_file, "ncontact");
      for(n = 0; n < ncontacts; n++) {
        get_string_data_level(mosaic_file, "contacts", contacts, &n);
        /* parse the string contacts to get tile number */
        tokenize( contacts, ":", STRING, MAXVAR, (char *)pstring, &nstr);
        if(nstr != 4) error_handler("Error from read_mosaic: number of elements "
                                    "in contact seperated by :/:: should be 4");
        found = 0;
        for(m=0; m<ntiles; m++) {
          if(strcmp(gridtiles[m], pstring[1]) == 0) { /*found the tile name */
            found = 1;
            tile1[n] = m+1;
            break;
          }
        }
        if(!found) error_handler("error from read_mosaic: the first tile name specified "
                                 "in contact is not found in tile list");
        found = 0;
        for(m=0; m<ntiles; m++) {
          if(strcmp(gridtiles[m], pstring[3]) == 0) { /*found the tile name */
            found = 1;
            tile2[n] = m+1;
            break;
          }
        }
        if(!found) error_handler("error from read_mosaic: the second tile name specified "
                                 "in contact is not found in tile list");
        get_string_data_level(mosaic_file, "contact_index", contacts, &n);
        /* parse the string to get contact index */
        tokenize( contacts, ":,", STRING, MAXVAR, (char *)pstring, &nstr);
        if(nstr != 8) error_handler("Error from read_mosaic: number of elements "
                                    "in contact_index seperated by :/, should be 8");
        /* make sure the string is only composed of numbers */
        for(m=0; m<nstr; m++){
          for(l=0; l<strlen(pstring[m]); l++){
            if(pstring[m][l] > '9' ||  pstring[m][l] < '0' ) {
              error_handler("Error from read_mosaic: some of the character in "
                            "contact_indices except token is not digit number");
            }
          }
        }
        istart1[n] = atoi(pstring[0]);
        iend1[n]   = atoi(pstring[1]);
        jstart1[n] = atoi(pstring[2]);
        jend1[n]   = atoi(pstring[3]);
        istart2[n] = atoi(pstring[4]);
        iend2[n]   = atoi(pstring[5]);
        jstart2[n] = atoi(pstring[6]);
        jend2[n]   = atoi(pstring[7]);
        i1_type = transfer_to_model_index(istart1[n], iend1[n], istart1+n, iend1+n, x_refine);
        j1_type = transfer_to_model_index(jstart1[n], jend1[n], jstart1+n, jend1+n, y_refine);
        i2_type = transfer_to_model_index(istart2[n], iend2[n], istart2+n, iend2+n, x_refine);
        j2_type = transfer_to_model_index(jstart2[n], jend2[n], jstart2+n, jend2+n, y_refine);
        if( i1_type == 0 && j1_type == 0 )
          error_handler("Error from read_mosaic_contact:istart1==iend1 and jstart1==jend1");
        if( i2_type == 0 && j2_type == 0 )
          error_handler("Error from read_mosaic_contact:istart2==iend2 and jstart2==jend2");
        if( i1_type + j1_type != i2_type + j2_type )
          error_handler("Error from read_mosaic_contact: It is not a line or overlap contact");
 
      }
 
      for(m=0; m<ntiles; m++) {
        free(gridtiles[m]);
      }
 
      free(gridtiles);
 
 
    } /* read_mosaic_contact */
 
 
    /******************************************************************************
  void read_mosaic_grid_data(const char *mosaic_file, const char *name, int nx, int ny,
                             double *data, int level, int ioff, int joff)
  read mosaic grid information onto model grid. We assume the refinement is 2 right now.
  We may remove this restriction in the future. nx and ny are model grid size. level
  is the tile number. ioff and joff to indicate grid location. ioff =0 and joff = 0
  for C-cell. ioff=0 and joff=1 for E-cell, ioff=1 and joff=0 for N-cell,
  ioff=1 and joff=1 for T-cell
    ******************************************************************************/
    void read_mosaic_grid_data(const char *mosaic_file, const char *name, int nx, int ny,
                               double *data, unsigned int level, int ioff, int joff)
    {
      char   tilefile[STRING], gridfile[STRING], dir[STRING];
      double *tmp;
      int    ni, nj, nxp, nyp, i, j;
 
      get_file_dir(mosaic_file, dir);
 
      get_string_data_level(mosaic_file, "gridfiles", gridfile, &level);
      sprintf(tilefile, "%s/%s", dir, gridfile);
 
      ni = get_dimlen(tilefile, "nx");
      nj = get_dimlen(tilefile, "ny");
 
      if( ni != nx*2 || nj != ny*2) error_handler("supergrid size should be double of the model grid size");
      tmp = (double *)malloc((ni+1)*(nj+1)*sizeof(double));
      get_var_data( tilefile, name, tmp);
      nxp = nx + 1 - ioff;
      nyp = ny + 1 - joff;
      for(j=0; j<nyp; j++) for(i=0; i<nxp; i++) data[j*nxp+i] = tmp[(2*j+joff)*(ni+1)+2*i+ioff];
      free(tmp);
 
    } /* read_mosaic_grid_data */