nanorodBuilderCmd.cpp

/*
  File autogenerated by gengetopt version 2.22.6
  generated with the following command:
  /opt/local/bin/gengetopt -C --input=nanorodBuilder.ggo --no-handle-error --include-getopt --show-required --unamed-opts --file-name=nanorodBuilderCmd --c-extension=cpp --header-extension=hpp
 
  The developers of gengetopt consider the fixed text that goes in all
  gengetopt output files to be in the public domain:
  we make no copyright claims on it.
*/
 
/* If we use autoconf.  */
#ifdef HAVE_CONFIG_H
#include "config.h"
#endif
 
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
 
#ifndef FIX_UNUSED
#define FIX_UNUSED(X) (void) (X) /* avoid warnings for unused params */
#endif
 
 
#include "nanorodBuilderCmd.hpp"
 
const char *gengetopt_args_info_purpose = "Builds pill-shaped, ellipsoidal, or pentagonal nanoparticles and outputs an\nOpenMD startup file";
 
const char *gengetopt_args_info_usage = "Usage: nanorodBuilder [OPTIONS]... [FILES]...";
 
const char *gengetopt_args_info_versiontext = "";
 
const char *gengetopt_args_info_description = "";
 
const char *gengetopt_args_info_help[] = {
  "  -h, --help                    Print help and exit",
  "  -V, --version                 Print version and exit",
  "  -o, --output=STRING           Output file name (mandatory)",
  "      --latticeConstant=DOUBLE  Lattice spacing in Angstroms for cubic lattice.\n                                  (mandatory)",
  "      --radius=DOUBLE           Nanorod radius in Angstroms (mandatory)",
  "      --length=DOUBLE           Nanorod length in Angstroms (mandatory)",
  "  -e, --ellipsoid               Build an Ellipsoid instead of a rod.\n                                  (default=off)",
  "      --shellRadius=DOUBLE      Radius containing within it only molecules of a\n                                  specific component. Specified for each\n                                  component > 1 in the template file.",
  "      --molFraction=DOUBLE      Builds a multi-component random alloy\n                                  nanoparticle. A mole Fraction must be\n                                  specified for each component > 1 in the\n                                  template file.",
  "      --vacancyPercent=DOUBLE   Percentage of atoms to remove from within\n                                  vacancy range",
  "      --vacancyInnerRadius=DOUBLE\n                                Radius arround core-shell where vacancies\n                                  should be located.",
  "      --vacancyOuterRadius=DOUBLE\n                                Radius arround core-shell where vacancies\n                                  should be located.",
    0
};
 
typedef enum {ARG_NO
  , ARG_FLAG
  , ARG_STRING
  , ARG_DOUBLE
} cmdline_parser_arg_type;
 
static
void clear_given (struct gengetopt_args_info *args_info);
static
void clear_args (struct gengetopt_args_info *args_info);
 
static int
cmdline_parser_internal (int argc, char **argv, struct gengetopt_args_info *args_info,
                        struct cmdline_parser_params *params, const char *additional_error);
 
static int
cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error);
struct line_list
{
  char * string_arg;
  struct line_list * next;
};
 
static struct line_list *cmd_line_list = 0;
static struct line_list *cmd_line_list_tmp = 0;
 
static void
free_cmd_list(void)
{
  /* free the list of a previous call */
  if (cmd_line_list)
    {
      while (cmd_line_list) {
        cmd_line_list_tmp = cmd_line_list;
        cmd_line_list = cmd_line_list->next;
        free (cmd_line_list_tmp->string_arg);
        free (cmd_line_list_tmp);
      }
    }
}
 
 
static char *
gengetopt_strdup (const char *s);
 
static
void clear_given (struct gengetopt_args_info *args_info)
{
  args_info->help_given = 0 ;
  args_info->version_given = 0 ;
  args_info->output_given = 0 ;
  args_info->latticeConstant_given = 0 ;
  args_info->radius_given = 0 ;
  args_info->length_given = 0 ;
  args_info->ellipsoid_given = 0 ;
  args_info->shellRadius_given = 0 ;
  args_info->molFraction_given = 0 ;
  args_info->vacancyPercent_given = 0 ;
  args_info->vacancyInnerRadius_given = 0 ;
  args_info->vacancyOuterRadius_given = 0 ;
}
 
static
void clear_args (struct gengetopt_args_info *args_info)
{
  FIX_UNUSED (args_info);
  args_info->output_arg = NULL;
  args_info->output_orig = NULL;
  args_info->latticeConstant_orig = NULL;
  args_info->radius_orig = NULL;
  args_info->length_orig = NULL;
  args_info->ellipsoid_flag = 0;
  args_info->shellRadius_arg = NULL;
  args_info->shellRadius_orig = NULL;
  args_info->molFraction_arg = NULL;
  args_info->molFraction_orig = NULL;
  args_info->vacancyPercent_orig = NULL;
  args_info->vacancyInnerRadius_orig = NULL;
  args_info->vacancyOuterRadius_orig = NULL;
  
}
 
static
void init_args_info(struct gengetopt_args_info *args_info)
{
 
 
  args_info->help_help = gengetopt_args_info_help[0] ;
  args_info->version_help = gengetopt_args_info_help[1] ;
  args_info->output_help = gengetopt_args_info_help[2] ;
  args_info->latticeConstant_help = gengetopt_args_info_help[3] ;
  args_info->radius_help = gengetopt_args_info_help[4] ;
  args_info->length_help = gengetopt_args_info_help[5] ;
  args_info->ellipsoid_help = gengetopt_args_info_help[6] ;
  args_info->shellRadius_help = gengetopt_args_info_help[7] ;
  args_info->shellRadius_min = 0;
  args_info->shellRadius_max = 0;
  args_info->molFraction_help = gengetopt_args_info_help[8] ;
  args_info->molFraction_min = 0;
  args_info->molFraction_max = 0;
  args_info->vacancyPercent_help = gengetopt_args_info_help[9] ;
  args_info->vacancyInnerRadius_help = gengetopt_args_info_help[10] ;
  args_info->vacancyOuterRadius_help = gengetopt_args_info_help[11] ;
  
}
 
void
cmdline_parser_print_version (void)
{
  printf ("%s %s\n",
     (strlen(CMDLINE_PARSER_PACKAGE_NAME) ? CMDLINE_PARSER_PACKAGE_NAME : CMDLINE_PARSER_PACKAGE),
     CMDLINE_PARSER_VERSION);
 
  if (strlen(gengetopt_args_info_versiontext) > 0)
    printf("\n%s\n", gengetopt_args_info_versiontext);
}
 
static void print_help_common(void) {
  cmdline_parser_print_version ();
 
  if (strlen(gengetopt_args_info_purpose) > 0)
    printf("\n%s\n", gengetopt_args_info_purpose);
 
  if (strlen(gengetopt_args_info_usage) > 0)
    printf("\n%s\n", gengetopt_args_info_usage);
 
  printf("\n");
 
  if (strlen(gengetopt_args_info_description) > 0)
    printf("%s\n\n", gengetopt_args_info_description);
}
 
void
cmdline_parser_print_help (void)
{
  int i = 0;
  print_help_common();
  while (gengetopt_args_info_help[i])
    printf("%s\n", gengetopt_args_info_help[i++]);
}
 
void
cmdline_parser_init (struct gengetopt_args_info *args_info)
{
  clear_given (args_info);
  clear_args (args_info);
  init_args_info (args_info);
 
  args_info->inputs = 0;
  args_info->inputs_num = 0;
}
 
void
cmdline_parser_params_init(struct cmdline_parser_params *params)
{
  if (params)
    { 
      params->override = 0;
      params->initialize = 1;
      params->check_required = 1;
      params->check_ambiguity = 0;
      params->print_errors = 1;
    }
}
 
struct cmdline_parser_params *
cmdline_parser_params_create(void)
{
  struct cmdline_parser_params *params = 
    (struct cmdline_parser_params *)malloc(sizeof(struct cmdline_parser_params));
  cmdline_parser_params_init(params);  
  return params;
}
 
static void
free_string_field (char **s)
{
  if (*s)
    {
      free (*s);
      *s = 0;
    }
}
 
/** @brief generic value variable */
union generic_value {
    double double_arg;
    char *string_arg;
    const char *default_string_arg;
};
 
/** @brief holds temporary values for multiple options */
struct generic_list
{
  union generic_value arg;
  char *orig;
  struct generic_list *next;
};
 
/**
 * @brief add a node at the head of the list 
 */
static void add_node(struct generic_list **list) {
  struct generic_list *new_node = (struct generic_list *) malloc (sizeof (struct generic_list));
  new_node->next = *list;
  *list = new_node;
  new_node->arg.string_arg = 0;
  new_node->orig = 0;
}
 
/**
 * The passed arg parameter is NOT set to 0 from this function
 */
static void
free_multiple_field(unsigned int len, void *arg, char ***orig)
{
  unsigned int i;
  if (arg) {
    for (i = 0; i < len; ++i)
      {
        free_string_field(&((*orig)[i]));
      }
 
    free (arg);
    free (*orig);
    *orig = 0;
  }
}
 
 
static void
cmdline_parser_release (struct gengetopt_args_info *args_info)
{
  unsigned int i;
  free_string_field (&(args_info->output_arg));
  free_string_field (&(args_info->output_orig));
  free_string_field (&(args_info->latticeConstant_orig));
  free_string_field (&(args_info->radius_orig));
  free_string_field (&(args_info->length_orig));
  free_multiple_field (args_info->shellRadius_given, (void *)(args_info->shellRadius_arg), &(args_info->shellRadius_orig));
  args_info->shellRadius_arg = 0;
  free_multiple_field (args_info->molFraction_given, (void *)(args_info->molFraction_arg), &(args_info->molFraction_orig));
  args_info->molFraction_arg = 0;
  free_string_field (&(args_info->vacancyPercent_orig));
  free_string_field (&(args_info->vacancyInnerRadius_orig));
  free_string_field (&(args_info->vacancyOuterRadius_orig));
  
  
  for (i = 0; i < args_info->inputs_num; ++i)
    free (args_info->inputs [i]);
 
  if (args_info->inputs_num)
    free (args_info->inputs);
 
  clear_given (args_info);
}
 
 
static void
write_into_file(FILE *outfile, const char *opt, const char *arg, const char *values[])
{
  FIX_UNUSED (values);
  if (arg) {
    fprintf(outfile, "%s=\"%s\"\n", opt, arg);
  } else {
    fprintf(outfile, "%s\n", opt);
  }
}
 
static void
write_multiple_into_file(FILE *outfile, int len, const char *opt, char **arg, const char *values[])
{
  int i;
  
  for (i = 0; i < len; ++i)
    write_into_file(outfile, opt, (arg ? arg[i] : 0), values);
}
 
int
cmdline_parser_dump(FILE *outfile, struct gengetopt_args_info *args_info)
{
  int i = 0;
 
  if (!outfile)
    {
      fprintf (stderr, "%s: cannot dump options to stream\n", CMDLINE_PARSER_PACKAGE);
      return EXIT_FAILURE;
    }
 
  if (args_info->help_given)
    write_into_file(outfile, "help", 0, 0 );
  if (args_info->version_given)
    write_into_file(outfile, "version", 0, 0 );
  if (args_info->output_given)
    write_into_file(outfile, "output", args_info->output_orig, 0);
  if (args_info->latticeConstant_given)
    write_into_file(outfile, "latticeConstant", args_info->latticeConstant_orig, 0);
  if (args_info->radius_given)
    write_into_file(outfile, "radius", args_info->radius_orig, 0);
  if (args_info->length_given)
    write_into_file(outfile, "length", args_info->length_orig, 0);
  if (args_info->ellipsoid_given)
    write_into_file(outfile, "ellipsoid", 0, 0 );
  write_multiple_into_file(outfile, args_info->shellRadius_given, "shellRadius", args_info->shellRadius_orig, 0);
  write_multiple_into_file(outfile, args_info->molFraction_given, "molFraction", args_info->molFraction_orig, 0);
  if (args_info->vacancyPercent_given)
    write_into_file(outfile, "vacancyPercent", args_info->vacancyPercent_orig, 0);
  if (args_info->vacancyInnerRadius_given)
    write_into_file(outfile, "vacancyInnerRadius", args_info->vacancyInnerRadius_orig, 0);
  if (args_info->vacancyOuterRadius_given)
    write_into_file(outfile, "vacancyOuterRadius", args_info->vacancyOuterRadius_orig, 0);
  
 
  i = EXIT_SUCCESS;
  return i;
}
 
int
cmdline_parser_file_save(const char *filename, struct gengetopt_args_info *args_info)
{
  FILE *outfile;
  int i = 0;
 
  outfile = fopen(filename, "w");
 
  if (!outfile)
    {
      fprintf (stderr, "%s: cannot open file for writing: %s\n", CMDLINE_PARSER_PACKAGE, filename);
      return EXIT_FAILURE;
    }
 
  i = cmdline_parser_dump(outfile, args_info);
  fclose (outfile);
 
  return i;
}
 
void
cmdline_parser_free (struct gengetopt_args_info *args_info)
{
  cmdline_parser_release (args_info);
}
 
/** @brief replacement of strdup, which is not standard */
char *
gengetopt_strdup (const char *s)
{
  char *result = 0;
  if (!s)
    return result;
 
  result = (char*)malloc(strlen(s) + 1);
  if (result == (char*)0)
    return (char*)0;
  strcpy(result, s);
  return result;
}
 
static char *
get_multiple_arg_token(const char *arg)
{
  const char *tok;
  char *ret;
  size_t len, num_of_escape, i, j;
 
  if (!arg)
    return 0;
 
  tok = strchr (arg, ',');
  num_of_escape = 0;
 
  /* make sure it is not escaped */
  while (tok)
    {
      if (*(tok-1) == '\\')
        {
          /* find the next one */
          tok = strchr (tok+1, ',');
          ++num_of_escape;
        }
      else
        break;
    }
 
  if (tok)
    len = (size_t)(tok - arg + 1);
  else
    len = strlen (arg) + 1;
 
  len -= num_of_escape;
 
  ret = (char *) malloc (len);
 
  i = 0;
  j = 0;
  while (arg[i] && (j < len-1))
    {
      if (arg[i] == '\\' && 
          arg[ i + 1 ] && 
          arg[ i + 1 ] == ',')
        ++i;
 
      ret[j++] = arg[i++];
    }
 
  ret[len-1] = '\0';
 
  return ret;
}
 
static const char *
get_multiple_arg_token_next(const char *arg)
{
  const char *tok;
 
  if (!arg)
    return 0;
 
  tok = strchr (arg, ',');
 
  /* make sure it is not escaped */
  while (tok)
    {
      if (*(tok-1) == '\\')
        {
          /* find the next one */
          tok = strchr (tok+1, ',');
        }
      else
        break;
    }
 
  if (! tok || strlen(tok) == 1)
    return 0;
 
  return tok+1;
}
 
static int
check_multiple_option_occurrences(const char *prog_name, unsigned int option_given, unsigned int min, unsigned int max, const char *option_desc);
 
int
check_multiple_option_occurrences(const char *prog_name, unsigned int option_given, unsigned int min, unsigned int max, const char *option_desc)
{
  int error_occurred = 0;
 
  if (option_given && (min > 0 || max > 0))
    {
      if (min > 0 && max > 0)
        {
          if (min == max)
            {
              /* specific occurrences */
              if (option_given != (unsigned int) min)
                {
                  fprintf (stderr, "%s: %s option occurrences must be %d\n",
                    prog_name, option_desc, min);
                  error_occurred = 1;
                }
            }
          else if (option_given < (unsigned int) min
                || option_given > (unsigned int) max)
            {
              /* range occurrences */
              fprintf (stderr, "%s: %s option occurrences must be between %d and %d\n",
                prog_name, option_desc, min, max);
              error_occurred = 1;
            }
        }
      else if (min > 0)
        {
          /* at least check */
          if (option_given < min)
            {
              fprintf (stderr, "%s: %s option occurrences must be at least %d\n",
                prog_name, option_desc, min);
              error_occurred = 1;
            }
        }
      else if (max > 0)
        {
          /* at most check */
          if (option_given > max)
            {
              fprintf (stderr, "%s: %s option occurrences must be at most %d\n",
                prog_name, option_desc, max);
              error_occurred = 1;
            }
        }
    }
    
  return error_occurred;
}
int
cmdline_parser (int argc, char **argv, struct gengetopt_args_info *args_info)
{
  return cmdline_parser2 (argc, argv, args_info, 0, 1, 1);
}
 
int
cmdline_parser_ext (int argc, char **argv, struct gengetopt_args_info *args_info,
                   struct cmdline_parser_params *params)
{
  int result;
  result = cmdline_parser_internal (argc, argv, args_info, params, 0);
 
  return result;
}
 
int
cmdline_parser2 (int argc, char **argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required)
{
  int result;
  struct cmdline_parser_params params;
  
  params.override = override;
  params.initialize = initialize;
  params.check_required = check_required;
  params.check_ambiguity = 0;
  params.print_errors = 1;
 
  result = cmdline_parser_internal (argc, argv, args_info, &params, 0);
 
  return result;
}
 
int
cmdline_parser_required (struct gengetopt_args_info *args_info, const char *prog_name)
{
  int result = EXIT_SUCCESS;
 
  if (cmdline_parser_required2(args_info, prog_name, 0) > 0)
    result = EXIT_FAILURE;
 
  return result;
}
 
int
cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error)
{
  int error_occurred = 0;
  FIX_UNUSED (additional_error);
 
  /* checks for required options */
  if (! args_info->output_given)
    {
      fprintf (stderr, "%s: '--output' ('-o') option required%s\n", prog_name, (additional_error ? additional_error : ""));
      error_occurred = 1;
    }
  
  if (! args_info->latticeConstant_given)
    {
      fprintf (stderr, "%s: '--latticeConstant' option required%s\n", prog_name, (additional_error ? additional_error : ""));
      error_occurred = 1;
    }
  
  if (! args_info->radius_given)
    {
      fprintf (stderr, "%s: '--radius' option required%s\n", prog_name, (additional_error ? additional_error : ""));
      error_occurred = 1;
    }
  
  if (! args_info->length_given)
    {
      fprintf (stderr, "%s: '--length' option required%s\n", prog_name, (additional_error ? additional_error : ""));
      error_occurred = 1;
    }
  
  if (check_multiple_option_occurrences(prog_name, args_info->shellRadius_given, args_info->shellRadius_min, args_info->shellRadius_max, "'--shellRadius'"))
     error_occurred = 1;
  
  if (check_multiple_option_occurrences(prog_name, args_info->molFraction_given, args_info->molFraction_min, args_info->molFraction_max, "'--molFraction'"))
     error_occurred = 1;
  
  
  /* checks for dependences among options */
 
  return error_occurred;
}
 
/*
 * Extracted from the glibc source tree, version 2.3.6
 *
 * Licensed under the GPL as per the whole glibc source tree.
 *
 * This file was modified so that getopt_long can be called
 * many times without risking previous memory to be spoiled.
 *
 * Modified by Andre Noll and Lorenzo Bettini for use in
 * GNU gengetopt generated files.
 *
 */
 
/* 
 * we must include anything we need since this file is not thought to be
 * inserted in a file already using getopt.h
 *
 * Lorenzo
 */
 
struct option
{
  const char *name;
  /* has_arg can't be an enum because some compilers complain about
     type mismatches in all the code that assumes it is an int.  */
  int has_arg;
  int *flag;
  int val;
};
 
/* This version of `getopt' appears to the caller like standard Unix `getopt'
   but it behaves differently for the user, since it allows the user
   to intersperse the options with the other arguments.
 
   As `getopt' works, it permutes the elements of ARGV so that,
   when it is done, all the options precede everything else.  Thus
   all application programs are extended to handle flexible argument order.
*/
/*
   If the field `flag' is not NULL, it points to a variable that is set
   to the value given in the field `val' when the option is found, but
   left unchanged if the option is not found.
 
   To have a long-named option do something other than set an `int' to
   a compiled-in constant, such as set a value from `custom_optarg', set the
   option's `flag' field to zero and its `val' field to a nonzero
   value (the equivalent single-letter option character, if there is
   one).  For long options that have a zero `flag' field, `getopt'
   returns the contents of the `val' field.  */
 
/* Names for the values of the `has_arg' field of `struct option'.  */
#ifndef no_argument
#define no_argument             0
#endif
 
#ifndef required_argument
#define required_argument       1
#endif
 
#ifndef optional_argument
#define optional_argument       2
#endif
 
struct custom_getopt_data {
        /*
         * These have exactly the same meaning as the corresponding global variables,
         * except that they are used for the reentrant versions of getopt.
         */
        int custom_optind;
        int custom_opterr;
        int custom_optopt;
        char *custom_optarg;
 
        /* True if the internal members have been initialized.  */
        int initialized;
 
        /*
         * The next char to be scanned in the option-element in which the last option
         * character we returned was found.  This allows us to pick up the scan where
         * we left off.  If this is zero, or a null string, it means resume the scan by
         * advancing to the next ARGV-element.
         */
        char *nextchar;
 
        /*
         * Describe the part of ARGV that contains non-options that have been skipped.
         * `first_nonopt' is the index in ARGV of the first of them; `last_nonopt' is
         * the index after the last of them.
         */
        int first_nonopt;
        int last_nonopt;
};
 
/*
 * the variables optarg, optind, opterr and optopt are renamed with
 * the custom_ prefix so that they don't interfere with getopt ones.
 *
 * Moreover they're static so they are visible only from within the
 * file where this very file will be included.
 */
 
/*
 * For communication from `custom_getopt' to the caller.  When `custom_getopt' finds an
 * option that takes an argument, the argument value is returned here.
 */
static char *custom_optarg;
 
/*
 * Index in ARGV of the next element to be scanned.  This is used for
 * communication to and from the caller and for communication between
 * successive calls to `custom_getopt'.
 *
 * On entry to `custom_getopt', 1 means this is the first call; initialize.
 *
 * When `custom_getopt' returns -1, this is the index of the first of the non-option
 * elements that the caller should itself scan.
 *
 * Otherwise, `custom_optind' communicates from one call to the next how much of ARGV
 * has been scanned so far.
 *
 * 1003.2 says this must be 1 before any call.
 */
static int custom_optind = 1;
 
/*
 * Callers store zero here to inhibit the error message for unrecognized
 * options.
 */
static int custom_opterr = 1;
 
/*
 * Set to an option character which was unrecognized.  This must be initialized
 * on some systems to avoid linking in the system's own getopt implementation.
 */
static int custom_optopt = '?';
 
/*
 * Exchange two adjacent subsequences of ARGV.  One subsequence is elements
 * [first_nonopt,last_nonopt) which contains all the non-options that have been
 * skipped so far.  The other is elements [last_nonopt,custom_optind), which contains
 * all the options processed since those non-options were skipped.
 * `first_nonopt' and `last_nonopt' are relocated so that they describe the new
 * indices of the non-options in ARGV after they are moved.
 */
static void exchange(char **argv, struct custom_getopt_data *d)
{
        int bottom = d->first_nonopt;
        int middle = d->last_nonopt;
        int top = d->custom_optind;
        char *tem;
 
        /*
         * Exchange the shorter segment with the far end of the longer segment.
         * That puts the shorter segment into the right place.  It leaves the
         * longer segment in the right place overall, but it consists of two
         * parts that need to be swapped next.
         */
        while (top > middle && middle > bottom) {
                if (top - middle > middle - bottom) {
                        /* Bottom segment is the short one.  */
                        int len = middle - bottom;
                        int i;
 
                        /* Swap it with the top part of the top segment.  */
                        for (i = 0; i < len; i++) {
                                tem = argv[bottom + i];
                                argv[bottom + i] =
                                        argv[top - (middle - bottom) + i];
                                argv[top - (middle - bottom) + i] = tem;
                        }
                        /* Exclude the moved bottom segment from further swapping.  */
                        top -= len;
                } else {
                        /* Top segment is the short one.  */
                        int len = top - middle;
                        int i;
 
                        /* Swap it with the bottom part of the bottom segment.  */
                        for (i = 0; i < len; i++) {
                                tem = argv[bottom + i];
                                argv[bottom + i] = argv[middle + i];
                                argv[middle + i] = tem;
                        }
                        /* Exclude the moved top segment from further swapping.  */
                        bottom += len;
                }
        }
        /* Update records for the slots the non-options now occupy.  */
        d->first_nonopt += (d->custom_optind - d->last_nonopt);
        d->last_nonopt = d->custom_optind;
}
 
/* Initialize the internal data when the first call is made.  */
static void custom_getopt_initialize(struct custom_getopt_data *d)
{
        /*
         * Start processing options with ARGV-element 1 (since ARGV-element 0
         * is the program name); the sequence of previously skipped non-option
         * ARGV-elements is empty.
         */
        d->first_nonopt = d->last_nonopt = d->custom_optind;
        d->nextchar = NULL;
        d->initialized = 1;
}
 
#define NONOPTION_P (argv[d->custom_optind][0] != '-' || argv[d->custom_optind][1] == '\0')
 
/* return: zero: continue, nonzero: return given value to user */
static int shuffle_argv(int argc, char *const *argv,const struct option *longopts,
        struct custom_getopt_data *d)
{
        /*
         * Give FIRST_NONOPT & LAST_NONOPT rational values if CUSTOM_OPTIND has been
         * moved back by the user (who may also have changed the arguments).
         */
        if (d->last_nonopt > d->custom_optind)
                d->last_nonopt = d->custom_optind;
        if (d->first_nonopt > d->custom_optind)
                d->first_nonopt = d->custom_optind;
        /*
         * If we have just processed some options following some
         * non-options, exchange them so that the options come first.
         */
        if (d->first_nonopt != d->last_nonopt &&
                        d->last_nonopt != d->custom_optind)
                exchange((char **) argv, d);
        else if (d->last_nonopt != d->custom_optind)
                d->first_nonopt = d->custom_optind;
        /*
         * Skip any additional non-options and extend the range of
         * non-options previously skipped.
         */
        while (d->custom_optind < argc && NONOPTION_P)
                d->custom_optind++;
        d->last_nonopt = d->custom_optind;
        /*
         * The special ARGV-element `--' means premature end of options.  Skip
         * it like a null option, then exchange with previous non-options as if
         * it were an option, then skip everything else like a non-option.
         */
        if (d->custom_optind != argc && !strcmp(argv[d->custom_optind], "--")) {
                d->custom_optind++;
                if (d->first_nonopt != d->last_nonopt
                                && d->last_nonopt != d->custom_optind)
                        exchange((char **) argv, d);
                else if (d->first_nonopt == d->last_nonopt)
                        d->first_nonopt = d->custom_optind;
                d->last_nonopt = argc;
                d->custom_optind = argc;
        }
        /*
         * If we have done all the ARGV-elements, stop the scan and back over
         * any non-options that we skipped and permuted.
         */
        if (d->custom_optind == argc) {
                /*
                 * Set the next-arg-index to point at the non-options that we
                 * previously skipped, so the caller will digest them.
                 */
                if (d->first_nonopt != d->last_nonopt)
                        d->custom_optind = d->first_nonopt;
                return -1;
        }
        /*
         * If we have come to a non-option and did not permute it, either stop
         * the scan or describe it to the caller and pass it by.
         */
        if (NONOPTION_P) {
                d->custom_optarg = argv[d->custom_optind++];
                return 1;
        }
        /*
         * We have found another option-ARGV-element. Skip the initial
         * punctuation.
         */
        d->nextchar = (argv[d->custom_optind] + 1 + (longopts != NULL && argv[d->custom_optind][1] == '-'));
        return 0;
}
 
/*
 * Check whether the ARGV-element is a long option.
 *
 * If there's a long option "fubar" and the ARGV-element is "-fu", consider
 * that an abbreviation of the long option, just like "--fu", and not "-f" with
 * arg "u".
 *
 * This distinction seems to be the most useful approach.
 *
 */
static int check_long_opt(int argc, char *const *argv, const char *optstring,
                const struct option *longopts, int *longind,
                int print_errors, struct custom_getopt_data *d)
{
        char *nameend;
        const struct option *p;
        const struct option *pfound = NULL;
        int exact = 0;
        int ambig = 0;
        int indfound = -1;
        int option_index;
 
        for (nameend = d->nextchar; *nameend && *nameend != '='; nameend++)
                /* Do nothing.  */ ;
 
        /* Test all long options for either exact match or abbreviated matches */
        for (p = longopts, option_index = 0; p->name; p++, option_index++)
                if (!strncmp(p->name, d->nextchar, nameend - d->nextchar)) {
                        if ((unsigned int) (nameend - d->nextchar)
                                        == (unsigned int) strlen(p->name)) {
                                /* Exact match found.  */
                                pfound = p;
                                indfound = option_index;
                                exact = 1;
                                break;
                        } else if (pfound == NULL) {
                                /* First nonexact match found.  */
                                pfound = p;
                                indfound = option_index;
                        } else if (pfound->has_arg != p->has_arg
                                        || pfound->flag != p->flag
                                        || pfound->val != p->val)
                                /* Second or later nonexact match found.  */
                                ambig = 1;
                }
        if (ambig && !exact) {
                if (print_errors) {
                        fprintf(stderr,
                                "%s: option `%s' is ambiguous\n",
                                argv[0], argv[d->custom_optind]);
                }
                d->nextchar += strlen(d->nextchar);
                d->custom_optind++;
                d->custom_optopt = 0;
                return '?';
        }
        if (pfound) {
                option_index = indfound;
                d->custom_optind++;
                if (*nameend) {
                        if (pfound->has_arg != no_argument)
                                d->custom_optarg = nameend + 1;
                        else {
                                if (print_errors) {
                                        if (argv[d->custom_optind - 1][1] == '-') {
                                                /* --option */
                                                fprintf(stderr, "%s: option `--%s' doesn't allow an argument\n",
                                                        argv[0], pfound->name);
                                        } else {
                                                /* +option or -option */
                                                fprintf(stderr, "%s: option `%c%s' doesn't allow an argument\n",
                                                        argv[0], argv[d->custom_optind - 1][0], pfound->name);
                                        }
 
                                }
                                d->nextchar += strlen(d->nextchar);
                                d->custom_optopt = pfound->val;
                                return '?';
                        }
                } else if (pfound->has_arg == required_argument) {
                        if (d->custom_optind < argc)
                                d->custom_optarg = argv[d->custom_optind++];
                        else {
                                if (print_errors) {
                                        fprintf(stderr,
                                                "%s: option `%s' requires an argument\n",
                                                argv[0],
                                                argv[d->custom_optind - 1]);
                                }
                                d->nextchar += strlen(d->nextchar);
                                d->custom_optopt = pfound->val;
                                return optstring[0] == ':' ? ':' : '?';
                        }
                }
                d->nextchar += strlen(d->nextchar);
                if (longind != NULL)
                        *longind = option_index;
                if (pfound->flag) {
                        *(pfound->flag) = pfound->val;
                        return 0;
                }
                return pfound->val;
        }
        /*
         * Can't find it as a long option.  If this is not getopt_long_only, or
         * the option starts with '--' or is not a valid short option, then
         * it's an error.  Otherwise interpret it as a short option.
         */
        if (print_errors) {
                if (argv[d->custom_optind][1] == '-') {
                        /* --option */
                        fprintf(stderr,
                                "%s: unrecognized option `--%s'\n",
                                argv[0], d->nextchar);
                } else {
                        /* +option or -option */
                        fprintf(stderr,
                                "%s: unrecognized option `%c%s'\n",
                                argv[0], argv[d->custom_optind][0],
                                d->nextchar);
                }
        }
        d->nextchar = (char *) "";
        d->custom_optind++;
        d->custom_optopt = 0;
        return '?';
}
 
static int check_short_opt(int argc, char *const *argv, const char *optstring,
                int print_errors, struct custom_getopt_data *d)
{
        char c = *d->nextchar++;
        const char *temp = strchr(optstring, c);
 
        /* Increment `custom_optind' when we start to process its last character.  */
        if (*d->nextchar == '\0')
                ++d->custom_optind;
        if (!temp || c == ':') {
                if (print_errors)
                        fprintf(stderr, "%s: invalid option -- %c\n", argv[0], c);
 
                d->custom_optopt = c;
                return '?';
        }
        if (temp[1] == ':') {
                if (temp[2] == ':') {
                        /* This is an option that accepts an argument optionally.  */
                        if (*d->nextchar != '\0') {
                                d->custom_optarg = d->nextchar;
                                d->custom_optind++;
                        } else
                                d->custom_optarg = NULL;
                        d->nextchar = NULL;
                } else {
                        /* This is an option that requires an argument.  */
                        if (*d->nextchar != '\0') {
                                d->custom_optarg = d->nextchar;
                                /*
                                 * If we end this ARGV-element by taking the
                                 * rest as an arg, we must advance to the next
                                 * element now.
                                 */
                                d->custom_optind++;
                        } else if (d->custom_optind == argc) {
                                if (print_errors) {
                                        fprintf(stderr,
                                                "%s: option requires an argument -- %c\n",
                                                argv[0], c);
                                }
                                d->custom_optopt = c;
                                if (optstring[0] == ':')
                                        c = ':';
                                else
                                        c = '?';
                        } else
                                /*
                                 * We already incremented `custom_optind' once;
                                 * increment it again when taking next ARGV-elt
                                 * as argument.
                                 */
                                d->custom_optarg = argv[d->custom_optind++];
                        d->nextchar = NULL;
                }
        }
        return c;
}
 
/*
 * Scan elements of ARGV for option characters given in OPTSTRING.
 *
 * If an element of ARGV starts with '-', and is not exactly "-" or "--",
 * then it is an option element.  The characters of this element
 * (aside from the initial '-') are option characters.  If `getopt'
 * is called repeatedly, it returns successively each of the option characters
 * from each of the option elements.
 *
 * If `getopt' finds another option character, it returns that character,
 * updating `custom_optind' and `nextchar' so that the next call to `getopt' can
 * resume the scan with the following option character or ARGV-element.
 *
 * If there are no more option characters, `getopt' returns -1.
 * Then `custom_optind' is the index in ARGV of the first ARGV-element
 * that is not an option.  (The ARGV-elements have been permuted
 * so that those that are not options now come last.)
 *
 * OPTSTRING is a string containing the legitimate option characters.
 * If an option character is seen that is not listed in OPTSTRING,
 * return '?' after printing an error message.  If you set `custom_opterr' to
 * zero, the error message is suppressed but we still return '?'.
 *
 * If a char in OPTSTRING is followed by a colon, that means it wants an arg,
 * so the following text in the same ARGV-element, or the text of the following
 * ARGV-element, is returned in `custom_optarg'.  Two colons mean an option that
 * wants an optional arg; if there is text in the current ARGV-element,
 * it is returned in `custom_optarg', otherwise `custom_optarg' is set to zero.
 *
 * If OPTSTRING starts with `-' or `+', it requests different methods of
 * handling the non-option ARGV-elements.
 * See the comments about RETURN_IN_ORDER and REQUIRE_ORDER, above.
 *
 * Long-named options begin with `--' instead of `-'.
 * Their names may be abbreviated as long as the abbreviation is unique
 * or is an exact match for some defined option.  If they have an
 * argument, it follows the option name in the same ARGV-element, separated
 * from the option name by a `=', or else the in next ARGV-element.
 * When `getopt' finds a long-named option, it returns 0 if that option's
 * `flag' field is nonzero, the value of the option's `val' field
 * if the `flag' field is zero.
 *
 * The elements of ARGV aren't really const, because we permute them.
 * But we pretend they're const in the prototype to be compatible
 * with other systems.
 *
 * LONGOPTS is a vector of `struct option' terminated by an
 * element containing a name which is zero.
 *
 * LONGIND returns the index in LONGOPT of the long-named option found.
 * It is only valid when a long-named option has been found by the most
 * recent call.
 *
 * Return the option character from OPTS just read.  Return -1 when there are
 * no more options.  For unrecognized options, or options missing arguments,
 * `custom_optopt' is set to the option letter, and '?' is returned.
 *
 * The OPTS string is a list of characters which are recognized option letters,
 * optionally followed by colons, specifying that that letter takes an
 * argument, to be placed in `custom_optarg'.
 *
 * If a letter in OPTS is followed by two colons, its argument is optional.
 * This behavior is specific to the GNU `getopt'.
 *
 * The argument `--' causes premature termination of argument scanning,
 * explicitly telling `getopt' that there are no more options.  If OPTS begins
 * with `--', then non-option arguments are treated as arguments to the option
 * '\0'.  This behavior is specific to the GNU `getopt'.
 */
 
static int getopt_internal_r(int argc, char *const *argv, const char *optstring,
                const struct option *longopts, int *longind,
                struct custom_getopt_data *d)
{
        int ret, print_errors = d->custom_opterr;
 
        if (optstring[0] == ':')
                print_errors = 0;
        if (argc < 1)
                return -1;
        d->custom_optarg = NULL;
 
        /* 
         * This is a big difference with GNU getopt, since optind == 0
         * means initialization while here 1 means first call.
         */
        if (d->custom_optind == 0 || !d->initialized) {
                if (d->custom_optind == 0)
                        d->custom_optind = 1;   /* Don't scan ARGV[0], the program name.  */
                custom_getopt_initialize(d);
        }
        if (d->nextchar == NULL || *d->nextchar == '\0') {
                ret = shuffle_argv(argc, argv, longopts, d);
                if (ret)
                        return ret;
        }
        if (longopts && (argv[d->custom_optind][1] == '-' ))
                return check_long_opt(argc, argv, optstring, longopts,
                        longind, print_errors, d);
        return check_short_opt(argc, argv, optstring, print_errors, d);
}
 
static int custom_getopt_internal(int argc, char *const *argv, const char *optstring,
        const struct option *longopts, int *longind)
{
        int result;
        /* Keep a global copy of all internal members of d */
        static struct custom_getopt_data d;
 
        d.custom_optind = custom_optind;
        d.custom_opterr = custom_opterr;
        result = getopt_internal_r(argc, argv, optstring, longopts,
                longind, &d);
        custom_optind = d.custom_optind;
        custom_optarg = d.custom_optarg;
        custom_optopt = d.custom_optopt;
        return result;
}
 
static int custom_getopt_long (int argc, char *const *argv, const char *options,
        const struct option *long_options, int *opt_index)
{
        return custom_getopt_internal(argc, argv, options, long_options,
                opt_index);
}
 
 
static char *package_name = 0;
 
/**
 * @brief updates an option
 * @param field the generic pointer to the field to update
 * @param orig_field the pointer to the orig field
 * @param field_given the pointer to the number of occurrence of this option
 * @param prev_given the pointer to the number of occurrence already seen
 * @param value the argument for this option (if null no arg was specified)
 * @param possible_values the possible values for this option (if specified)
 * @param default_value the default value (in case the option only accepts fixed values)
 * @param arg_type the type of this option
 * @param check_ambiguity @see cmdline_parser_params.check_ambiguity
 * @param override @see cmdline_parser_params.override
 * @param no_free whether to free a possible previous value
 * @param multiple_option whether this is a multiple option
 * @param long_opt the corresponding long option
 * @param short_opt the corresponding short option (or '-' if none)
 * @param additional_error possible further error specification
 */
static
int update_arg(void *field, char **orig_field,
               unsigned int *field_given, unsigned int *prev_given, 
               char *value, const char *possible_values[],
               const char *default_value,
               cmdline_parser_arg_type arg_type,
               int check_ambiguity, int override,
               int no_free, int multiple_option,
               const char *long_opt, char short_opt,
               const char *additional_error)
{
  char *stop_char = 0;
  const char *val = value;
  int found;
  char **string_field;
  FIX_UNUSED (field);
 
  stop_char = 0;
  found = 0;
 
  if (!multiple_option && prev_given && (*prev_given || (check_ambiguity && *field_given)))
    {
      if (short_opt != '-')
        fprintf (stderr, "%s: `--%s' (`-%c') option given more than once%s\n", 
               package_name, long_opt, short_opt,
               (additional_error ? additional_error : ""));
      else
        fprintf (stderr, "%s: `--%s' option given more than once%s\n", 
               package_name, long_opt,
               (additional_error ? additional_error : ""));
      return 1; /* failure */
    }
 
  FIX_UNUSED (default_value);
    
  if (field_given && *field_given && ! override)
    return 0;
  if (prev_given)
    (*prev_given)++;
  if (field_given)
    (*field_given)++;
  if (possible_values)
    val = possible_values[found];
 
  switch(arg_type) {
  case ARG_FLAG:
    *((int *)field) = !*((int *)field);
    break;
  case ARG_DOUBLE:
    if (val) *((double *)field) = strtod (val, &stop_char);
    break;
  case ARG_STRING:
    if (val) {
      string_field = (char **)field;
      if (!no_free && *string_field)
        free (*string_field); /* free previous string */
      *string_field = gengetopt_strdup (val);
    }
    break;
  default:
    break;
  };
 
  /* check numeric conversion */
  switch(arg_type) {
  case ARG_DOUBLE:
    if (val && !(stop_char && *stop_char == '\0')) {
      fprintf(stderr, "%s: invalid numeric value: %s\n", package_name, val);
      return 1; /* failure */
    }
    break;
  default:
    ;
  };
 
  /* store the original value */
  switch(arg_type) {
  case ARG_NO:
  case ARG_FLAG:
    break;
  default:
    if (value && orig_field) {
      if (no_free) {
        *orig_field = value;
      } else {
        if (*orig_field)
          free (*orig_field); /* free previous string */
        *orig_field = gengetopt_strdup (value);
      }
    }
  };
 
  return 0; /* OK */
}
 
/**
 * @brief store information about a multiple option in a temporary list
 * @param list where to (temporarily) store multiple options
 */
static
int update_multiple_arg_temp(struct generic_list **list,
               unsigned int *prev_given, const char *val,
               const char *possible_values[], const char *default_value,
               cmdline_parser_arg_type arg_type,
               const char *long_opt, char short_opt,
               const char *additional_error)
{
  /* store single arguments */
  char *multi_token;
  const char *multi_next;
 
  if (arg_type == ARG_NO) {
    (*prev_given)++;
    return 0; /* OK */
  }
 
  multi_token = get_multiple_arg_token(val);
  multi_next = get_multiple_arg_token_next (val);
 
  while (1)
    {
      add_node (list);
      if (update_arg((void *)&((*list)->arg), &((*list)->orig), 0,
          prev_given, multi_token, possible_values, default_value, 
          arg_type, 0, 1, 1, 1, long_opt, short_opt, additional_error)) {
        if (multi_token) free(multi_token);
        return 1; /* failure */
      }
 
      if (multi_next)
        {
          multi_token = get_multiple_arg_token(multi_next);
          multi_next = get_multiple_arg_token_next (multi_next);
        }
      else
        break;
    }
 
  return 0; /* OK */
}
 
/**
 * @brief free the passed list (including possible string argument)
 */
static
void free_list(struct generic_list *list, short string_arg)
{
  if (list) {
    struct generic_list *tmp;
    while (list)
      {
        tmp = list;
        if (string_arg && list->arg.string_arg)
          free (list->arg.string_arg);
        if (list->orig)
          free (list->orig);
        list = list->next;
        free (tmp);
      }
  }
}
 
/**
 * @brief updates a multiple option starting from the passed list
 */
static
void update_multiple_arg(void *field, char ***orig_field,
               unsigned int field_given, unsigned int prev_given, union generic_value *default_value,
               cmdline_parser_arg_type arg_type,
               struct generic_list *list)
{
  int i;
  struct generic_list *tmp;
 
  if (prev_given && list) {
    *orig_field = (char **) realloc (*orig_field, (field_given + prev_given) * sizeof (char *));
 
    switch(arg_type) {
    case ARG_DOUBLE:
      *((double **)field) = (double *)realloc (*((double **)field), (field_given + prev_given) * sizeof (double)); break;
    case ARG_STRING:
      *((char ***)field) = (char **)realloc (*((char ***)field), (field_given + prev_given) * sizeof (char *)); break;
    default:
      break;
    };
    
    for (i = (prev_given - 1); i >= 0; --i)
      {
        tmp = list;
        
        switch(arg_type) {
        case ARG_DOUBLE:
          (*((double **)field))[i + field_given] = tmp->arg.double_arg; break;
        case ARG_STRING:
          (*((char ***)field))[i + field_given] = tmp->arg.string_arg; break;
        default:
          break;
        }        
        (*orig_field) [i + field_given] = list->orig;
        list = list->next;
        free (tmp);
      }
  } else { /* set the default value */
    if (default_value && ! field_given) {
      switch(arg_type) {
      case ARG_DOUBLE:
        if (! *((double **)field)) {
          *((double **)field) = (double *)malloc (sizeof (double));
          (*((double **)field))[0] = default_value->double_arg;
        }
        break;
      case ARG_STRING:
        if (! *((char ***)field)) {
          *((char ***)field) = (char **)malloc (sizeof (char *));
          (*((char ***)field))[0] = gengetopt_strdup(default_value->string_arg);
        }
        break;
      default: break;
      }
      if (!(*orig_field)) {
        *orig_field = (char **) malloc (sizeof (char *));
        (*orig_field)[0] = 0;
      }
    }
  }
}
 
int
cmdline_parser_internal (
  int argc, char **argv, struct gengetopt_args_info *args_info,
                        struct cmdline_parser_params *params, const char *additional_error)
{
  int c;        /* Character of the parsed option.  */
 
  struct generic_list * shellRadius_list = NULL;
  struct generic_list * molFraction_list = NULL;
  int error_occurred = 0;
  struct gengetopt_args_info local_args_info;
  
  int override;
  int initialize;
  int check_required;
  int check_ambiguity;
 
  char *optarg;
  int optind;
  int opterr;
  int optopt;
  
  package_name = argv[0];
  
  override = params->override;
  initialize = params->initialize;
  check_required = params->check_required;
  check_ambiguity = params->check_ambiguity;
 
  if (initialize)
    cmdline_parser_init (args_info);
 
  cmdline_parser_init (&local_args_info);
 
  optarg = 0;
  optind = 0;
  opterr = params->print_errors;
  optopt = '?';
 
  while (1)
    {
      int option_index = 0;
 
      static struct option long_options[] = {
        { "help",       0, NULL, 'h' },
        { "version",    0, NULL, 'V' },
        { "output",     1, NULL, 'o' },
        { "latticeConstant",    1, NULL, 0 },
        { "radius",     1, NULL, 0 },
        { "length",     1, NULL, 0 },
        { "ellipsoid",  0, NULL, 'e' },
        { "shellRadius",        1, NULL, 0 },
        { "molFraction",        1, NULL, 0 },
        { "vacancyPercent",     1, NULL, 0 },
        { "vacancyInnerRadius", 1, NULL, 0 },
        { "vacancyOuterRadius", 1, NULL, 0 },
        { 0,  0, 0, 0 }
      };
 
      custom_optarg = optarg;
      custom_optind = optind;
      custom_opterr = opterr;
      custom_optopt = optopt;
 
      c = custom_getopt_long (argc, argv, "hVo:e", long_options, &option_index);
 
      optarg = custom_optarg;
      optind = custom_optind;
      opterr = custom_opterr;
      optopt = custom_optopt;
 
      if (c == -1) break;       /* Exit from `while (1)' loop.  */
 
      switch (c)
        {
        case 'h':       /* Print help and exit.  */
          cmdline_parser_print_help ();
          cmdline_parser_free (&local_args_info);
          exit (EXIT_SUCCESS);
 
        case 'V':       /* Print version and exit.  */
          cmdline_parser_print_version ();
          cmdline_parser_free (&local_args_info);
          exit (EXIT_SUCCESS);
 
        case 'o':       /* Output file name.  */
        
        
          if (update_arg( (void *)&(args_info->output_arg), 
               &(args_info->output_orig), &(args_info->output_given),
              &(local_args_info.output_given), optarg, 0, 0, ARG_STRING,
              check_ambiguity, override, 0, 0,
              "output", 'o',
              additional_error))
            goto failure;
        
          break;
        case 'e':       /* Build an Ellipsoid instead of a rod..  */
        
        
          if (update_arg((void *)&(args_info->ellipsoid_flag), 0, &(args_info->ellipsoid_given),
              &(local_args_info.ellipsoid_given), optarg, 0, 0, ARG_FLAG,
              check_ambiguity, override, 1, 0, "ellipsoid", 'e',
              additional_error))
            goto failure;
        
          break;
 
        case 0: /* Long option with no short option */
          /* Lattice spacing in Angstroms for cubic lattice..  */
          if (strcmp (long_options[option_index].name, "latticeConstant") == 0)
          {
          
          
            if (update_arg( (void *)&(args_info->latticeConstant_arg), 
                 &(args_info->latticeConstant_orig), &(args_info->latticeConstant_given),
                &(local_args_info.latticeConstant_given), optarg, 0, 0, ARG_DOUBLE,
                check_ambiguity, override, 0, 0,
                "latticeConstant", '-',
                additional_error))
              goto failure;
          
          }
          /* Nanorod radius in Angstroms.  */
          else if (strcmp (long_options[option_index].name, "radius") == 0)
          {
          
          
            if (update_arg( (void *)&(args_info->radius_arg), 
                 &(args_info->radius_orig), &(args_info->radius_given),
                &(local_args_info.radius_given), optarg, 0, 0, ARG_DOUBLE,
                check_ambiguity, override, 0, 0,
                "radius", '-',
                additional_error))
              goto failure;
          
          }
          /* Nanorod length in Angstroms.  */
          else if (strcmp (long_options[option_index].name, "length") == 0)
          {
          
          
            if (update_arg( (void *)&(args_info->length_arg), 
                 &(args_info->length_orig), &(args_info->length_given),
                &(local_args_info.length_given), optarg, 0, 0, ARG_DOUBLE,
                check_ambiguity, override, 0, 0,
                "length", '-',
                additional_error))
              goto failure;
          
          }
          /* Radius containing within it only molecules of a specific component. Specified for each component > 1 in the template file..  */
          else if (strcmp (long_options[option_index].name, "shellRadius") == 0)
          {
          
            if (update_multiple_arg_temp(&shellRadius_list, 
                &(local_args_info.shellRadius_given), optarg, 0, 0, ARG_DOUBLE,
                "shellRadius", '-',
                additional_error))
              goto failure;
          
          }
          /* Builds a multi-component random alloy nanoparticle. A mole Fraction must be specified for each component > 1 in the template file..  */
          else if (strcmp (long_options[option_index].name, "molFraction") == 0)
          {
          
            if (update_multiple_arg_temp(&molFraction_list, 
                &(local_args_info.molFraction_given), optarg, 0, 0, ARG_DOUBLE,
                "molFraction", '-',
                additional_error))
              goto failure;
          
          }
          /* Percentage of atoms to remove from within vacancy range.  */
          else if (strcmp (long_options[option_index].name, "vacancyPercent") == 0)
          {
          
          
            if (update_arg( (void *)&(args_info->vacancyPercent_arg), 
                 &(args_info->vacancyPercent_orig), &(args_info->vacancyPercent_given),
                &(local_args_info.vacancyPercent_given), optarg, 0, 0, ARG_DOUBLE,
                check_ambiguity, override, 0, 0,
                "vacancyPercent", '-',
                additional_error))
              goto failure;
          
          }
          /* Radius arround core-shell where vacancies should be located..  */
          else if (strcmp (long_options[option_index].name, "vacancyInnerRadius") == 0)
          {
          
          
            if (update_arg( (void *)&(args_info->vacancyInnerRadius_arg), 
                 &(args_info->vacancyInnerRadius_orig), &(args_info->vacancyInnerRadius_given),
                &(local_args_info.vacancyInnerRadius_given), optarg, 0, 0, ARG_DOUBLE,
                check_ambiguity, override, 0, 0,
                "vacancyInnerRadius", '-',
                additional_error))
              goto failure;
          
          }
          /* Radius arround core-shell where vacancies should be located..  */
          else if (strcmp (long_options[option_index].name, "vacancyOuterRadius") == 0)
          {
          
          
            if (update_arg( (void *)&(args_info->vacancyOuterRadius_arg), 
                 &(args_info->vacancyOuterRadius_orig), &(args_info->vacancyOuterRadius_given),
                &(local_args_info.vacancyOuterRadius_given), optarg, 0, 0, ARG_DOUBLE,
                check_ambiguity, override, 0, 0,
                "vacancyOuterRadius", '-',
                additional_error))
              goto failure;
          
          }
          
          break;
        case '?':       /* Invalid option.  */
          /* `getopt_long' already printed an error message.  */
          goto failure;
 
        default:        /* bug: option not considered.  */
          fprintf (stderr, "%s: option unknown: %c%s\n", CMDLINE_PARSER_PACKAGE, c, (additional_error ? additional_error : ""));
          abort ();
        } /* switch */
    } /* while */
 
 
  update_multiple_arg((void *)&(args_info->shellRadius_arg),
    &(args_info->shellRadius_orig), args_info->shellRadius_given,
    local_args_info.shellRadius_given, 0,
    ARG_DOUBLE, shellRadius_list);
  update_multiple_arg((void *)&(args_info->molFraction_arg),
    &(args_info->molFraction_orig), args_info->molFraction_given,
    local_args_info.molFraction_given, 0,
    ARG_DOUBLE, molFraction_list);
 
  args_info->shellRadius_given += local_args_info.shellRadius_given;
  local_args_info.shellRadius_given = 0;
  args_info->molFraction_given += local_args_info.molFraction_given;
  local_args_info.molFraction_given = 0;
  
  if (check_required)
    {
      error_occurred += cmdline_parser_required2 (args_info, argv[0], additional_error);
    }
 
  cmdline_parser_release (&local_args_info);
 
  if ( error_occurred )
    return (EXIT_FAILURE);
 
  if (optind < argc)
    {
      int i = 0 ;
      int found_prog_name = 0;
      /* whether program name, i.e., argv[0], is in the remaining args
         (this may happen with some implementations of getopt,
          but surely not with the one included by gengetopt) */
 
 
      args_info->inputs_num = argc - optind - found_prog_name;
      args_info->inputs =
        (char **)(malloc ((args_info->inputs_num)*sizeof(char *))) ;
      while (optind < argc)
        args_info->inputs[ i++ ] = gengetopt_strdup (argv[optind++]) ;
    }
 
  return 0;
 
failure:
  free_list (shellRadius_list, 0 );
  free_list (molFraction_list, 0 );
  
  cmdline_parser_release (&local_args_info);
  return (EXIT_FAILURE);
}
 
#ifndef CONFIG_FILE_LINE_SIZE
#define CONFIG_FILE_LINE_SIZE 2048
#endif
#define ADDITIONAL_ERROR " in configuration file "
 
#define CONFIG_FILE_LINE_BUFFER_SIZE (CONFIG_FILE_LINE_SIZE+3)
/* 3 is for "--" and "=" */
 
static int
_cmdline_parser_configfile (const char *filename, int *my_argc)
{
  FILE* file;
  char my_argv[CONFIG_FILE_LINE_BUFFER_SIZE+1];
  char linebuf[CONFIG_FILE_LINE_SIZE];
  int line_num = 0;
  int result = 0, equal;
  char *fopt, *farg;
  char *str_index;
  size_t len, next_token;
  char delimiter;
 
  if ((file = fopen(filename, "r")) == 0)
    {
      fprintf (stderr, "%s: Error opening configuration file '%s'\n",
               CMDLINE_PARSER_PACKAGE, filename);
      return EXIT_FAILURE;
    }
 
  while ((fgets(linebuf, CONFIG_FILE_LINE_SIZE, file)) != 0)
    {
      ++line_num;
      my_argv[0] = '\0';
      len = strlen(linebuf);
      if (len > (CONFIG_FILE_LINE_BUFFER_SIZE-1))
        {
          fprintf (stderr, "%s:%s:%d: Line too long in configuration file\n",
                   CMDLINE_PARSER_PACKAGE, filename, line_num);
          result = EXIT_FAILURE;
          break;
        }
 
      /* find first non-whitespace character in the line */
      next_token = strspn (linebuf, " \t\r\n");
      str_index  = linebuf + next_token;
 
      if ( str_index[0] == '\0' || str_index[0] == '#')
        continue; /* empty line or comment line is skipped */
 
      fopt = str_index;
 
      /* truncate fopt at the end of the first non-valid character */
      next_token = strcspn (fopt, " \t\r\n=");
 
      if (fopt[next_token] == '\0') /* the line is over */
        {
          farg  = 0;
          equal = 0;
          goto noarg;
        }
 
      /* remember if equal sign is present */
      equal = (fopt[next_token] == '=');
      fopt[next_token++] = '\0';
 
      /* advance pointers to the next token after the end of fopt */
      next_token += strspn (fopt + next_token, " \t\r\n");
 
      /* check for the presence of equal sign, and if so, skip it */
      if ( !equal )
        if ((equal = (fopt[next_token] == '=')))
          {
            next_token++;
            next_token += strspn (fopt + next_token, " \t\r\n");
          }
      str_index  += next_token;
 
      /* find argument */
      farg = str_index;
      if ( farg[0] == '\"' || farg[0] == '\'' )
        { /* quoted argument */
          str_index = strchr (++farg, str_index[0] ); /* skip opening quote */
          if (! str_index)
            {
              fprintf
                (stderr,
                 "%s:%s:%d: unterminated string in configuration file\n",
                 CMDLINE_PARSER_PACKAGE, filename, line_num);
              result = EXIT_FAILURE;
              break;
            }
        }
      else
        { /* read up the remaining part up to a delimiter */
          next_token = strcspn (farg, " \t\r\n#\'\"");
          str_index += next_token;
        }
 
      /* truncate farg at the delimiter and store it for further check */
      delimiter = *str_index, *str_index++ = '\0';
 
      /* everything but comment is illegal at the end of line */
      if (delimiter != '\0' && delimiter != '#')
        {
          str_index += strspn(str_index, " \t\r\n");
          if (*str_index != '\0' && *str_index != '#')
            {
              fprintf
                (stderr,
                 "%s:%s:%d: malformed string in configuration file\n",
                 CMDLINE_PARSER_PACKAGE, filename, line_num);
              result = EXIT_FAILURE;
              break;
            }
        }
 
    noarg:
      if (!strcmp(fopt,"include")) {
        if (farg && *farg) {
          result = _cmdline_parser_configfile(farg, my_argc);
        } else {
          fprintf(stderr, "%s:%s:%d: include requires a filename argument.\n",
                  CMDLINE_PARSER_PACKAGE, filename, line_num);
        }
        continue;
      }
      len = strlen(fopt);
      strcat (my_argv, len > 1 ? "--" : "-");
      strcat (my_argv, fopt);
      if (len > 1 && ((farg && *farg) || equal))
        strcat (my_argv, "=");
      if (farg && *farg)
        strcat (my_argv, farg);
      ++(*my_argc);
 
      cmd_line_list_tmp = (struct line_list *) malloc (sizeof (struct line_list));
      cmd_line_list_tmp->next = cmd_line_list;
      cmd_line_list = cmd_line_list_tmp;
      cmd_line_list->string_arg = gengetopt_strdup(my_argv);
    } /* while */
 
  if (file)
    fclose(file);
  return result;
}
 
int
cmdline_parser_configfile (
  const char *filename,
                           struct gengetopt_args_info *args_info,
                           int override, int initialize, int check_required)
{
  struct cmdline_parser_params params;
 
  params.override = override;
  params.initialize = initialize;
  params.check_required = check_required;
  params.check_ambiguity = 0;
  params.print_errors = 1;
  
  return cmdline_parser_config_file (filename, args_info, &params);
}
 
int
cmdline_parser_config_file (const char *filename,
                           struct gengetopt_args_info *args_info,
                           struct cmdline_parser_params *params)
{
  int i, result;
  int my_argc = 1;
  char **my_argv_arg;
  char *additional_error;
 
  /* store the program name */
  cmd_line_list_tmp = (struct line_list *) malloc (sizeof (struct line_list));
  cmd_line_list_tmp->next = cmd_line_list;
  cmd_line_list = cmd_line_list_tmp;
  cmd_line_list->string_arg = gengetopt_strdup (CMDLINE_PARSER_PACKAGE);
 
  result = _cmdline_parser_configfile(filename, &my_argc);
 
  if (result != EXIT_FAILURE) {
    my_argv_arg = (char **) malloc((my_argc+1) * sizeof(char *));
    cmd_line_list_tmp = cmd_line_list;
 
    for (i = my_argc - 1; i >= 0; --i) {
      my_argv_arg[i] = cmd_line_list_tmp->string_arg;
      cmd_line_list_tmp = cmd_line_list_tmp->next;
    }
 
    my_argv_arg[my_argc] = 0;
 
    additional_error = (char *)malloc(strlen(filename) + strlen(ADDITIONAL_ERROR) + 1);
    strcpy (additional_error, ADDITIONAL_ERROR);
    strcat (additional_error, filename);
    result =
      cmdline_parser_internal (my_argc, my_argv_arg, args_info,
                              params,
                              additional_error);
 
    free (additional_error);
    free (my_argv_arg);
  }
 
  free_cmd_list();
  return result;
}