applications/randomBuilder/randomBuilderCmd.c

/*
  File autogenerated by gengetopt version 2.16
  generated with the following command:
  gengetopt -F randomBuilderCmd --unamed-opts 

  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>

#include "getopt.h"

#include "randomBuilderCmd.h"

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 * const *argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required, const char *additional_error);

static int
cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error);

struct molFraction_list
{
  double molFraction_arg;
  char *molFraction_orig;
  struct molFraction_list * next;
};

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->latticetype_given = 0 ;
  args_info->density_given = 0 ;
  args_info->nx_given = 0 ;
  args_info->ny_given = 0 ;
  args_info->nz_given = 0 ;
  args_info->molFraction_given = 0 ;
}

static
void clear_args (struct gengetopt_args_info *args_info)
{
  args_info->output_arg = NULL;
  args_info->output_orig = NULL;
  args_info->latticetype_arg = gengetopt_strdup ("fcc");
  args_info->latticetype_orig = NULL;
  args_info->density_orig = NULL;
  args_info->nx_orig = NULL;
  args_info->ny_orig = NULL;
  args_info->nz_orig = NULL;
  args_info->molFraction_arg = NULL;
  args_info->molFraction_orig = NULL;
  
}

void
cmdline_parser_print_version (void)
{
  printf ("%s %s\n", CMDLINE_PARSER_PACKAGE, CMDLINE_PARSER_VERSION);
}

void
cmdline_parser_print_help (void)
{
  cmdline_parser_print_version ();
  printf("\nUsage: randomBuilder [OPTIONS]... [FILES]...\n\n");
  printf("%s\n","  -h, --help                Print help and exit");
  printf("%s\n","  -V, --version             Print version and exit");
  printf("%s\n","  -o, --output=STRING       Output file name");
  printf("%s\n","      --latticetype=STRING  Lattice type string. Valid types are fcc,hcp,bcc \n                              and hcp-water.  (default=`fcc')");
  printf("%s\n","      --density=DOUBLE      density (g/cm^3)");
  printf("%s\n","      --nx=INT              number of unit cells in x");
  printf("%s\n","      --ny=INT              number of unit cells in y");
  printf("%s\n","      --nz=INT              number of unit cells in z");
  printf("%s\n","      --molFraction=DOUBLE  (Default) Builds a multi-component random mixed \n                              nanoparticle. Mole Fraction must be specified for \n                              each componet > 1 in MD file.");
  
}

void
cmdline_parser_init (struct gengetopt_args_info *args_info)
{
  clear_given (args_info);
  clear_args (args_info);

  args_info->inputs = NULL;
  args_info->inputs_num = 0;
}

static void
cmdline_parser_release (struct gengetopt_args_info *args_info)
{
  
  unsigned int i;
  if (args_info->output_arg)
    {
      free (args_info->output_arg); /* free previous argument */
      args_info->output_arg = 0;
    }
  if (args_info->output_orig)
    {
      free (args_info->output_orig); /* free previous argument */
      args_info->output_orig = 0;
    }
  if (args_info->latticetype_arg)
    {
      free (args_info->latticetype_arg); /* free previous argument */
      args_info->latticetype_arg = 0;
    }
  if (args_info->latticetype_orig)
    {
      free (args_info->latticetype_orig); /* free previous argument */
      args_info->latticetype_orig = 0;
    }
  if (args_info->density_orig)
    {
      free (args_info->density_orig); /* free previous argument */
      args_info->density_orig = 0;
    }
  if (args_info->nx_orig)
    {
      free (args_info->nx_orig); /* free previous argument */
      args_info->nx_orig = 0;
    }
  if (args_info->ny_orig)
    {
      free (args_info->ny_orig); /* free previous argument */
      args_info->ny_orig = 0;
    }
  if (args_info->nz_orig)
    {
      free (args_info->nz_orig); /* free previous argument */
      args_info->nz_orig = 0;
    }
  if (args_info->molFraction_arg)
    {
      for (i = 0; i < args_info->molFraction_given; ++i)
        {
          if (args_info->molFraction_orig [i])
            {
              free (args_info->molFraction_orig [i]); /* free previous argument */
              args_info->molFraction_orig [i] = 0;
            }
        }
      free (args_info->molFraction_arg); /* free previous argument */
      args_info->molFraction_arg = 0;
      free (args_info->molFraction_orig); /* free previous argument */
      args_info->molFraction_orig = 0;
    }
  
  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);
}

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;
    }

  if (args_info->help_given) {
    fprintf(outfile, "%s\n", "help");
  }
  if (args_info->version_given) {
    fprintf(outfile, "%s\n", "version");
  }
  if (args_info->output_given) {
    if (args_info->output_orig) {
      fprintf(outfile, "%s=\"%s\"\n", "output", args_info->output_orig);
    } else {
      fprintf(outfile, "%s\n", "output");
    }
  }
  if (args_info->latticetype_given) {
    if (args_info->latticetype_orig) {
      fprintf(outfile, "%s=\"%s\"\n", "latticetype", args_info->latticetype_orig);
    } else {
      fprintf(outfile, "%s\n", "latticetype");
    }
  }
  if (args_info->density_given) {
    if (args_info->density_orig) {
      fprintf(outfile, "%s=\"%s\"\n", "density", args_info->density_orig);
    } else {
      fprintf(outfile, "%s\n", "density");
    }
  }
  if (args_info->nx_given) {
    if (args_info->nx_orig) {
      fprintf(outfile, "%s=\"%s\"\n", "nx", args_info->nx_orig);
    } else {
      fprintf(outfile, "%s\n", "nx");
    }
  }
  if (args_info->ny_given) {
    if (args_info->ny_orig) {
      fprintf(outfile, "%s=\"%s\"\n", "ny", args_info->ny_orig);
    } else {
      fprintf(outfile, "%s\n", "ny");
    }
  }
  if (args_info->nz_given) {
    if (args_info->nz_orig) {
      fprintf(outfile, "%s=\"%s\"\n", "nz", args_info->nz_orig);
    } else {
      fprintf(outfile, "%s\n", "nz");
    }
  }
  if (args_info->molFraction_orig)
    {
      for (i = 0; i < args_info->molFraction_given; ++i)
        {
          if (args_info->molFraction_orig [i])
            {
              fprintf(outfile, "%s=\"%s\"\n", "molFraction", args_info->molFraction_orig [i]);
            }
        }
    }
  
  fclose (outfile);

  i = EXIT_SUCCESS;
  return i;
}

void
cmdline_parser_free (struct gengetopt_args_info *args_info)
{
  cmdline_parser_release (args_info);
}


/* gengetopt_strdup() */
/* strdup.c replacement of strdup, which is not standard */
char *
gengetopt_strdup (const char *s)
{
  char *result = NULL;
  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)
{
  char *tok, *ret;
  size_t len;

  if (!arg)
    return NULL;

  tok = strchr (arg, ',');

  if (tok)
    len = (size_t)(tok - arg + 1);
  else
    len = strlen (arg) + 1;

  ret = (char *) malloc (len);
  strncpy (ret, arg, len-1);
  ret[len-1] = '\0';

  return ret;
}

static char *
get_multiple_arg_token_next(const char *arg)
{
  char *tok;

  if (!arg)
    return NULL;

  tok = strchr (arg, ',');

  if (! tok || strlen(tok) == 1)
    return 0;

  return tok+1;
}

int
cmdline_parser (int argc, char * const *argv, struct gengetopt_args_info *args_info)
{
  return cmdline_parser2 (argc, argv, args_info, 0, 1, 1);
}

int
cmdline_parser2 (int argc, char * const *argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required)
{
  int result;

  result = cmdline_parser_internal (argc, argv, args_info, override, initialize, check_required, NULL);

  if (result == EXIT_FAILURE)
    {
      cmdline_parser_free (args_info);
      exit (EXIT_FAILURE);
    }
  
  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, NULL) > 0)
    result = EXIT_FAILURE;

  if (result == EXIT_FAILURE)
    {
      cmdline_parser_free (args_info);
      exit (EXIT_FAILURE);
    }
  
  return result;
}

int
cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error)
{
  int error = 0;

  if (! args_info->output_given)
    {
      fprintf (stderr, "%s: '--output' ('-o') option required%s\n", prog_name, (additional_error ? additional_error : ""));
      error = 1;
    }
  if (! args_info->density_given)
    {
      fprintf (stderr, "%s: '--density' option required%s\n", prog_name, (additional_error ? additional_error : ""));
      error = 1;
    }
  if (! args_info->nx_given)
    {
      fprintf (stderr, "%s: '--nx' option required%s\n", prog_name, (additional_error ? additional_error : ""));
      error = 1;
    }
  if (! args_info->ny_given)
    {
      fprintf (stderr, "%s: '--ny' option required%s\n", prog_name, (additional_error ? additional_error : ""));
      error = 1;
    }
  if (! args_info->nz_given)
    {
      fprintf (stderr, "%s: '--nz' option required%s\n", prog_name, (additional_error ? additional_error : ""));
      error = 1;
    }

  return error;
}

int
cmdline_parser_internal (int argc, char * const *argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required, const char *additional_error)
{
  int c;        /* Character of the parsed option.  */
  char *multi_token, *multi_next; /* for multiple options */

  int i;        /* Counter */

  struct molFraction_list * molFraction_list = NULL,* molFraction_new = NULL;
  int error = 0;
  struct gengetopt_args_info local_args_info;

  if (initialize)
    cmdline_parser_init (args_info);

  cmdline_parser_init (&local_args_info);

  optarg = 0;
  optind = 0;
  opterr = 1;
  optopt = '?';

  while (1)
    {
      int option_index = 0;
      char *stop_char;

      static struct option long_options[] = {
        { "help",       0, NULL, 'h' },
        { "version",    0, NULL, 'V' },
        { "output",     1, NULL, 'o' },
        { "latticetype",        1, NULL, 0 },
        { "density",    1, NULL, 0 },
        { "nx", 1, NULL, 0 },
        { "ny", 1, NULL, 0 },
        { "nz", 1, NULL, 0 },
        { "molFraction",        1, NULL, 0 },
        { NULL, 0, NULL, 0 }
      };

      stop_char = 0;
      c = getopt_long (argc, argv, "hVo:", long_options, &option_index);

      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 (local_args_info.output_given)
            {
              fprintf (stderr, "%s: `--output' (`-o') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
              goto failure;
            }
          if (args_info->output_given && ! override)
            continue;
          local_args_info.output_given = 1;
          args_info->output_given = 1;
          if (args_info->output_arg)
            free (args_info->output_arg); /* free previous string */
          args_info->output_arg = gengetopt_strdup (optarg);
          if (args_info->output_orig)
            free (args_info->output_orig); /* free previous string */
          args_info->output_orig = gengetopt_strdup (optarg);
          break;


        case 0: /* Long option with no short option */
          /* Lattice type string. Valid types are fcc,hcp,bcc and hcp-water..  */
          if (strcmp (long_options[option_index].name, "latticetype") == 0)
          {
            if (local_args_info.latticetype_given)
              {
                fprintf (stderr, "%s: `--latticetype' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
                goto failure;
              }
            if (args_info->latticetype_given && ! override)
              continue;
            local_args_info.latticetype_given = 1;
            args_info->latticetype_given = 1;
            if (args_info->latticetype_arg)
              free (args_info->latticetype_arg); /* free previous string */
            args_info->latticetype_arg = gengetopt_strdup (optarg);
            if (args_info->latticetype_orig)
              free (args_info->latticetype_orig); /* free previous string */
            args_info->latticetype_orig = gengetopt_strdup (optarg);
          }
          /* density (g/cm^3).  */
          else if (strcmp (long_options[option_index].name, "density") == 0)
          {
            if (local_args_info.density_given)
              {
                fprintf (stderr, "%s: `--density' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
                goto failure;
              }
            if (args_info->density_given && ! override)
              continue;
            local_args_info.density_given = 1;
            args_info->density_given = 1;
            args_info->density_arg = strtod (optarg, &stop_char);
            if (!(stop_char && *stop_char == '\0')) {
              fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
              goto failure;
            }
            if (args_info->density_orig)
              free (args_info->density_orig); /* free previous string */
            args_info->density_orig = gengetopt_strdup (optarg);
          }
          /* number of unit cells in x.  */
          else if (strcmp (long_options[option_index].name, "nx") == 0)
          {
            if (local_args_info.nx_given)
              {
                fprintf (stderr, "%s: `--nx' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
                goto failure;
              }
            if (args_info->nx_given && ! override)
              continue;
            local_args_info.nx_given = 1;
            args_info->nx_given = 1;
            args_info->nx_arg = strtol (optarg, &stop_char, 0);
            if (!(stop_char && *stop_char == '\0')) {
              fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
              goto failure;
            }
            if (args_info->nx_orig)
              free (args_info->nx_orig); /* free previous string */
            args_info->nx_orig = gengetopt_strdup (optarg);
          }
          /* number of unit cells in y.  */
          else if (strcmp (long_options[option_index].name, "ny") == 0)
          {
            if (local_args_info.ny_given)
              {
                fprintf (stderr, "%s: `--ny' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
                goto failure;
              }
            if (args_info->ny_given && ! override)
              continue;
            local_args_info.ny_given = 1;
            args_info->ny_given = 1;
            args_info->ny_arg = strtol (optarg, &stop_char, 0);
            if (!(stop_char && *stop_char == '\0')) {
              fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
              goto failure;
            }
            if (args_info->ny_orig)
              free (args_info->ny_orig); /* free previous string */
            args_info->ny_orig = gengetopt_strdup (optarg);
          }
          /* number of unit cells in z.  */
          else if (strcmp (long_options[option_index].name, "nz") == 0)
          {
            if (local_args_info.nz_given)
              {
                fprintf (stderr, "%s: `--nz' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
                goto failure;
              }
            if (args_info->nz_given && ! override)
              continue;
            local_args_info.nz_given = 1;
            args_info->nz_given = 1;
            args_info->nz_arg = strtol (optarg, &stop_char, 0);
            if (!(stop_char && *stop_char == '\0')) {
              fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
              goto failure;
            }
            if (args_info->nz_orig)
              free (args_info->nz_orig); /* free previous string */
            args_info->nz_orig = gengetopt_strdup (optarg);
          }
          /* (Default) Builds a multi-component random mixed nanoparticle. Mole Fraction must be specified for each componet > 1 in MD file..  */
          else if (strcmp (long_options[option_index].name, "molFraction") == 0)
          {
            local_args_info.molFraction_given++;
          
            multi_token = get_multiple_arg_token(optarg);
            multi_next = get_multiple_arg_token_next (optarg);
          
            while (1)
              {
                molFraction_new = (struct molFraction_list *) malloc (sizeof (struct molFraction_list));
                molFraction_new->next = molFraction_list;
                molFraction_list = molFraction_new;
                molFraction_new->molFraction_arg = strtod (multi_token, &stop_char);
                if (!(stop_char && *stop_char == '\0')) {
                  fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], multi_token);
                  goto failure;
                }
                molFraction_new->molFraction_orig = multi_token;
          
                if (multi_next)
                  {
                    multi_token = get_multiple_arg_token(multi_next);
                    multi_next = get_multiple_arg_token_next (multi_next);
                    local_args_info.molFraction_given++;
                  }
                else
                  break;
              }
            break;
          }
          
          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 */


  if (local_args_info.molFraction_given && molFraction_list)
    {
      struct molFraction_list *tmp;
      args_info->molFraction_arg = (double *) realloc (args_info->molFraction_arg, (args_info->molFraction_given + local_args_info.molFraction_given) * sizeof (double));
      args_info->molFraction_orig = (char **) realloc (args_info->molFraction_orig, (args_info->molFraction_given + local_args_info.molFraction_given) * sizeof (char *));
      for (i = (local_args_info.molFraction_given - 1); i >= 0; --i)
        {
          tmp = molFraction_list;
          args_info->molFraction_arg [i + args_info->molFraction_given] = molFraction_list->molFraction_arg;
          args_info->molFraction_orig [i + args_info->molFraction_given] = molFraction_list->molFraction_orig;
          molFraction_list = molFraction_list->next;
          free (tmp);
        }
    }
  

  args_info->molFraction_given += local_args_info.molFraction_given;
  local_args_info.molFraction_given = 0;
  
  if (check_required)
    {
      error += cmdline_parser_required2 (args_info, argv[0], additional_error);
    }

  cmdline_parser_release (&local_args_info);

  if ( error )
    return (EXIT_FAILURE);

  if (optind < argc)
    {
      int i = 0 ;

      args_info->inputs_num = argc - optind ;
      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:
  if (molFraction_list)
    {
      struct molFraction_list *tmp;
      while (molFraction_list)
        {
          tmp = molFraction_list;
          free (molFraction_list->molFraction_orig);
          molFraction_list = molFraction_list->next;
          free (tmp);
        }
    }
  
  cmdline_parser_release (&local_args_info);
  return (EXIT_FAILURE);
}
Revision:	3036
Committed:	Tue Oct 10 02:44:13 2006 UTC (17 years, 8 months ago) by gezelter
Content type:	text/plain
File size:	21005 byte(s)
Log Message:	fixing bugs in randomBuilder
#	Content
1	/*
2	File autogenerated by gengetopt version 2.16
3	generated with the following command:
4	gengetopt -F randomBuilderCmd --unamed-opts
5
6	The developers of gengetopt consider the fixed text that goes in all
7	gengetopt output files to be in the public domain:
8	we make no copyright claims on it.
9	*/
10
11	/* If we use autoconf. */
12	#ifdef HAVE_CONFIG_H
13	#include "config.h"
14	#endif
15
16	#include <stdio.h>
17	#include <stdlib.h>
18	#include <string.h>
19
20	#include "getopt.h"
21
22	#include "randomBuilderCmd.h"
23
24	static
25	void clear_given (struct gengetopt_args_info *args_info);
26	static
27	void clear_args (struct gengetopt_args_info *args_info);
28
29	static int
30	cmdline_parser_internal (int argc, char * const argv, struct gengetopt_args_info args_info, int override, int initialize, int check_required, const char *additional_error);
31
32	static int
33	cmdline_parser_required2 (struct gengetopt_args_info args_info, const char prog_name, const char *additional_error);
34
35	struct molFraction_list
36	{
37	double molFraction_arg;
38	char *molFraction_orig;
39	struct molFraction_list * next;
40	};
41
42	static char *
43	gengetopt_strdup (const char *s);
44
45	static
46	void clear_given (struct gengetopt_args_info *args_info)
47	{
48	args_info->help_given = 0 ;
49	args_info->version_given = 0 ;
50	args_info->output_given = 0 ;
51	args_info->latticetype_given = 0 ;
52	args_info->density_given = 0 ;
53	args_info->nx_given = 0 ;
54	args_info->ny_given = 0 ;
55	args_info->nz_given = 0 ;
56	args_info->molFraction_given = 0 ;
57	}
58
59	static
60	void clear_args (struct gengetopt_args_info *args_info)
61	{
62	args_info->output_arg = NULL;
63	args_info->output_orig = NULL;
64	args_info->latticetype_arg = gengetopt_strdup ("fcc");
65	args_info->latticetype_orig = NULL;
66	args_info->density_orig = NULL;
67	args_info->nx_orig = NULL;
68	args_info->ny_orig = NULL;
69	args_info->nz_orig = NULL;
70	args_info->molFraction_arg = NULL;
71	args_info->molFraction_orig = NULL;
72
73	}
74
75	void
76	cmdline_parser_print_version (void)
77	{
78	printf ("%s %s\n", CMDLINE_PARSER_PACKAGE, CMDLINE_PARSER_VERSION);
79	}
80
81	void
82	cmdline_parser_print_help (void)
83	{
84	cmdline_parser_print_version ();
85	printf("\nUsage: randomBuilder [OPTIONS]... [FILES]...\n\n");
86	printf("%s\n"," -h, --help Print help and exit");
87	printf("%s\n"," -V, --version Print version and exit");
88	printf("%s\n"," -o, --output=STRING Output file name");
89	printf("%s\n"," --latticetype=STRING Lattice type string. Valid types are fcc,hcp,bcc \n and hcp-water. (default=`fcc')");
90	printf("%s\n"," --density=DOUBLE density (g/cm^3)");
91	printf("%s\n"," --nx=INT number of unit cells in x");
92	printf("%s\n"," --ny=INT number of unit cells in y");
93	printf("%s\n"," --nz=INT number of unit cells in z");
94	printf("%s\n"," --molFraction=DOUBLE (Default) Builds a multi-component random mixed \n nanoparticle. Mole Fraction must be specified for \n each componet > 1 in MD file.");
95
96	}
97
98	void
99	cmdline_parser_init (struct gengetopt_args_info *args_info)
100	{
101	clear_given (args_info);
102	clear_args (args_info);
103
104	args_info->inputs = NULL;
105	args_info->inputs_num = 0;
106	}
107
108	static void
109	cmdline_parser_release (struct gengetopt_args_info *args_info)
110	{
111
112	unsigned int i;
113	if (args_info->output_arg)
114	{
115	free (args_info->output_arg); /* free previous argument */
116	args_info->output_arg = 0;
117	}
118	if (args_info->output_orig)
119	{
120	free (args_info->output_orig); /* free previous argument */
121	args_info->output_orig = 0;
122	}
123	if (args_info->latticetype_arg)
124	{
125	free (args_info->latticetype_arg); /* free previous argument */
126	args_info->latticetype_arg = 0;
127	}
128	if (args_info->latticetype_orig)
129	{
130	free (args_info->latticetype_orig); /* free previous argument */
131	args_info->latticetype_orig = 0;
132	}
133	if (args_info->density_orig)
134	{
135	free (args_info->density_orig); /* free previous argument */
136	args_info->density_orig = 0;
137	}
138	if (args_info->nx_orig)
139	{
140	free (args_info->nx_orig); /* free previous argument */
141	args_info->nx_orig = 0;
142	}
143	if (args_info->ny_orig)
144	{
145	free (args_info->ny_orig); /* free previous argument */
146	args_info->ny_orig = 0;
147	}
148	if (args_info->nz_orig)
149	{
150	free (args_info->nz_orig); /* free previous argument */
151	args_info->nz_orig = 0;
152	}
153	if (args_info->molFraction_arg)
154	{
155	for (i = 0; i < args_info->molFraction_given; ++i)
156	{
157	if (args_info->molFraction_orig [i])
158	{
159	free (args_info->molFraction_orig [i]); /* free previous argument */
160	args_info->molFraction_orig [i] = 0;
161	}
162	}
163	free (args_info->molFraction_arg); /* free previous argument */
164	args_info->molFraction_arg = 0;
165	free (args_info->molFraction_orig); /* free previous argument */
166	args_info->molFraction_orig = 0;
167	}
168
169	for (i = 0; i < args_info->inputs_num; ++i)
170	free (args_info->inputs [i]);
171
172	if (args_info->inputs_num)
173	free (args_info->inputs);
174
175	clear_given (args_info);
176	}
177
178	int
179	cmdline_parser_file_save(const char filename, struct gengetopt_args_info args_info)
180	{
181	FILE *outfile;
182	int i = 0;
183
184	outfile = fopen(filename, "w");
185
186	if (!outfile)
187	{
188	fprintf (stderr, "%s: cannot open file for writing: %s\n", CMDLINE_PARSER_PACKAGE, filename);
189	return EXIT_FAILURE;
190	}
191
192	if (args_info->help_given) {
193	fprintf(outfile, "%s\n", "help");
194	}
195	if (args_info->version_given) {
196	fprintf(outfile, "%s\n", "version");
197	}
198	if (args_info->output_given) {
199	if (args_info->output_orig) {
200	fprintf(outfile, "%s=\"%s\"\n", "output", args_info->output_orig);
201	} else {
202	fprintf(outfile, "%s\n", "output");
203	}
204	}
205	if (args_info->latticetype_given) {
206	if (args_info->latticetype_orig) {
207	fprintf(outfile, "%s=\"%s\"\n", "latticetype", args_info->latticetype_orig);
208	} else {
209	fprintf(outfile, "%s\n", "latticetype");
210	}
211	}
212	if (args_info->density_given) {
213	if (args_info->density_orig) {
214	fprintf(outfile, "%s=\"%s\"\n", "density", args_info->density_orig);
215	} else {
216	fprintf(outfile, "%s\n", "density");
217	}
218	}
219	if (args_info->nx_given) {
220	if (args_info->nx_orig) {
221	fprintf(outfile, "%s=\"%s\"\n", "nx", args_info->nx_orig);
222	} else {
223	fprintf(outfile, "%s\n", "nx");
224	}
225	}
226	if (args_info->ny_given) {
227	if (args_info->ny_orig) {
228	fprintf(outfile, "%s=\"%s\"\n", "ny", args_info->ny_orig);
229	} else {
230	fprintf(outfile, "%s\n", "ny");
231	}
232	}
233	if (args_info->nz_given) {
234	if (args_info->nz_orig) {
235	fprintf(outfile, "%s=\"%s\"\n", "nz", args_info->nz_orig);
236	} else {
237	fprintf(outfile, "%s\n", "nz");
238	}
239	}
240	if (args_info->molFraction_orig)
241	{
242	for (i = 0; i < args_info->molFraction_given; ++i)
243	{
244	if (args_info->molFraction_orig [i])
245	{
246	fprintf(outfile, "%s=\"%s\"\n", "molFraction", args_info->molFraction_orig [i]);
247	}
248	}
249	}
250
251	fclose (outfile);
252
253	i = EXIT_SUCCESS;
254	return i;
255	}
256
257	void
258	cmdline_parser_free (struct gengetopt_args_info *args_info)
259	{
260	cmdline_parser_release (args_info);
261	}
262
263
264	/* gengetopt_strdup() */
265	/* strdup.c replacement of strdup, which is not standard */
266	char *
267	gengetopt_strdup (const char *s)
268	{
269	char *result = NULL;
270	if (!s)
271	return result;
272
273	result = (char*)malloc(strlen(s) + 1);
274	if (result == (char*)0)
275	return (char*)0;
276	strcpy(result, s);
277	return result;
278	}
279
280	static char *
281	get_multiple_arg_token(const char *arg)
282	{
283	char tok, ret;
284	size_t len;
285
286	if (!arg)
287	return NULL;
288
289	tok = strchr (arg, ',');
290
291	if (tok)
292	len = (size_t)(tok - arg + 1);
293	else
294	len = strlen (arg) + 1;
295
296	ret = (char *) malloc (len);
297	strncpy (ret, arg, len-1);
298	ret[len-1] = '\0';
299
300	return ret;
301	}
302
303	static char *
304	get_multiple_arg_token_next(const char *arg)
305	{
306	char *tok;
307
308	if (!arg)
309	return NULL;
310
311	tok = strchr (arg, ',');
312
313	if (! tok \|\| strlen(tok) == 1)
314	return 0;
315
316	return tok+1;
317	}
318
319	int
320	cmdline_parser (int argc, char * const argv, struct gengetopt_args_info args_info)
321	{
322	return cmdline_parser2 (argc, argv, args_info, 0, 1, 1);
323	}
324
325	int
326	cmdline_parser2 (int argc, char * const argv, struct gengetopt_args_info args_info, int override, int initialize, int check_required)
327	{
328	int result;
329
330	result = cmdline_parser_internal (argc, argv, args_info, override, initialize, check_required, NULL);
331
332	if (result == EXIT_FAILURE)
333	{
334	cmdline_parser_free (args_info);
335	exit (EXIT_FAILURE);
336	}
337
338	return result;
339	}
340
341	int
342	cmdline_parser_required (struct gengetopt_args_info args_info, const char prog_name)
343	{
344	int result = EXIT_SUCCESS;
345
346	if (cmdline_parser_required2(args_info, prog_name, NULL) > 0)
347	result = EXIT_FAILURE;
348
349	if (result == EXIT_FAILURE)
350	{
351	cmdline_parser_free (args_info);
352	exit (EXIT_FAILURE);
353	}
354
355	return result;
356	}
357
358	int
359	cmdline_parser_required2 (struct gengetopt_args_info args_info, const char prog_name, const char *additional_error)
360	{
361	int error = 0;
362
363	if (! args_info->output_given)
364	{
365	fprintf (stderr, "%s: '--output' ('-o') option required%s\n", prog_name, (additional_error ? additional_error : ""));
366	error = 1;
367	}
368	if (! args_info->density_given)
369	{
370	fprintf (stderr, "%s: '--density' option required%s\n", prog_name, (additional_error ? additional_error : ""));
371	error = 1;
372	}
373	if (! args_info->nx_given)
374	{
375	fprintf (stderr, "%s: '--nx' option required%s\n", prog_name, (additional_error ? additional_error : ""));
376	error = 1;
377	}
378	if (! args_info->ny_given)
379	{
380	fprintf (stderr, "%s: '--ny' option required%s\n", prog_name, (additional_error ? additional_error : ""));
381	error = 1;
382	}
383	if (! args_info->nz_given)
384	{
385	fprintf (stderr, "%s: '--nz' option required%s\n", prog_name, (additional_error ? additional_error : ""));
386	error = 1;
387	}
388
389	return error;
390	}
391
392	int
393	cmdline_parser_internal (int argc, char * const argv, struct gengetopt_args_info args_info, int override, int initialize, int check_required, const char *additional_error)
394	{
395	int c; /* Character of the parsed option. */
396	char multi_token, multi_next; /* for multiple options */
397
398	int i; /* Counter */
399
400	struct molFraction_list * molFraction_list = NULL,* molFraction_new = NULL;
401	int error = 0;
402	struct gengetopt_args_info local_args_info;
403
404	if (initialize)
405	cmdline_parser_init (args_info);
406
407	cmdline_parser_init (&local_args_info);
408
409	optarg = 0;
410	optind = 0;
411	opterr = 1;
412	optopt = '?';
413
414	while (1)
415	{
416	int option_index = 0;
417	char *stop_char;
418
419	static struct option long_options[] = {
420	{ "help", 0, NULL, 'h' },
421	{ "version", 0, NULL, 'V' },
422	{ "output", 1, NULL, 'o' },
423	{ "latticetype", 1, NULL, 0 },
424	{ "density", 1, NULL, 0 },
425	{ "nx", 1, NULL, 0 },
426	{ "ny", 1, NULL, 0 },
427	{ "nz", 1, NULL, 0 },
428	{ "molFraction", 1, NULL, 0 },
429	{ NULL, 0, NULL, 0 }
430	};
431
432	stop_char = 0;
433	c = getopt_long (argc, argv, "hVo:", long_options, &option_index);
434
435	if (c == -1) break; /* Exit from `while (1)' loop. */
436
437	switch (c)
438	{
439	case 'h': /* Print help and exit. */
440	cmdline_parser_print_help ();
441	cmdline_parser_free (&local_args_info);
442	exit (EXIT_SUCCESS);
443
444	case 'V': /* Print version and exit. */
445	cmdline_parser_print_version ();
446	cmdline_parser_free (&local_args_info);
447	exit (EXIT_SUCCESS);
448
449	case 'o': /* Output file name. */
450	if (local_args_info.output_given)
451	{
452	fprintf (stderr, "%s: `--output' (`-o') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
453	goto failure;
454	}
455	if (args_info->output_given && ! override)
456	continue;
457	local_args_info.output_given = 1;
458	args_info->output_given = 1;
459	if (args_info->output_arg)
460	free (args_info->output_arg); /* free previous string */
461	args_info->output_arg = gengetopt_strdup (optarg);
462	if (args_info->output_orig)
463	free (args_info->output_orig); /* free previous string */
464	args_info->output_orig = gengetopt_strdup (optarg);
465	break;
466
467
468	case 0: /* Long option with no short option */
469	/* Lattice type string. Valid types are fcc,hcp,bcc and hcp-water.. */
470	if (strcmp (long_options[option_index].name, "latticetype") == 0)
471	{
472	if (local_args_info.latticetype_given)
473	{
474	fprintf (stderr, "%s: `--latticetype' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
475	goto failure;
476	}
477	if (args_info->latticetype_given && ! override)
478	continue;
479	local_args_info.latticetype_given = 1;
480	args_info->latticetype_given = 1;
481	if (args_info->latticetype_arg)
482	free (args_info->latticetype_arg); /* free previous string */
483	args_info->latticetype_arg = gengetopt_strdup (optarg);
484	if (args_info->latticetype_orig)
485	free (args_info->latticetype_orig); /* free previous string */
486	args_info->latticetype_orig = gengetopt_strdup (optarg);
487	}
488	/* density (g/cm^3). */
489	else if (strcmp (long_options[option_index].name, "density") == 0)
490	{
491	if (local_args_info.density_given)
492	{
493	fprintf (stderr, "%s: `--density' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
494	goto failure;
495	}
496	if (args_info->density_given && ! override)
497	continue;
498	local_args_info.density_given = 1;
499	args_info->density_given = 1;
500	args_info->density_arg = strtod (optarg, &stop_char);
501	if (!(stop_char && *stop_char == '\0')) {
502	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
503	goto failure;
504	}
505	if (args_info->density_orig)
506	free (args_info->density_orig); /* free previous string */
507	args_info->density_orig = gengetopt_strdup (optarg);
508	}
509	/* number of unit cells in x. */
510	else if (strcmp (long_options[option_index].name, "nx") == 0)
511	{
512	if (local_args_info.nx_given)
513	{
514	fprintf (stderr, "%s: `--nx' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
515	goto failure;
516	}
517	if (args_info->nx_given && ! override)
518	continue;
519	local_args_info.nx_given = 1;
520	args_info->nx_given = 1;
521	args_info->nx_arg = strtol (optarg, &stop_char, 0);
522	if (!(stop_char && *stop_char == '\0')) {
523	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
524	goto failure;
525	}
526	if (args_info->nx_orig)
527	free (args_info->nx_orig); /* free previous string */
528	args_info->nx_orig = gengetopt_strdup (optarg);
529	}
530	/* number of unit cells in y. */
531	else if (strcmp (long_options[option_index].name, "ny") == 0)
532	{
533	if (local_args_info.ny_given)
534	{
535	fprintf (stderr, "%s: `--ny' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
536	goto failure;
537	}
538	if (args_info->ny_given && ! override)
539	continue;
540	local_args_info.ny_given = 1;
541	args_info->ny_given = 1;
542	args_info->ny_arg = strtol (optarg, &stop_char, 0);
543	if (!(stop_char && *stop_char == '\0')) {
544	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
545	goto failure;
546	}
547	if (args_info->ny_orig)
548	free (args_info->ny_orig); /* free previous string */
549	args_info->ny_orig = gengetopt_strdup (optarg);
550	}
551	/* number of unit cells in z. */
552	else if (strcmp (long_options[option_index].name, "nz") == 0)
553	{
554	if (local_args_info.nz_given)
555	{
556	fprintf (stderr, "%s: `--nz' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
557	goto failure;
558	}
559	if (args_info->nz_given && ! override)
560	continue;
561	local_args_info.nz_given = 1;
562	args_info->nz_given = 1;
563	args_info->nz_arg = strtol (optarg, &stop_char, 0);
564	if (!(stop_char && *stop_char == '\0')) {
565	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
566	goto failure;
567	}
568	if (args_info->nz_orig)
569	free (args_info->nz_orig); /* free previous string */
570	args_info->nz_orig = gengetopt_strdup (optarg);
571	}
572	/* (Default) Builds a multi-component random mixed nanoparticle. Mole Fraction must be specified for each componet > 1 in MD file.. */
573	else if (strcmp (long_options[option_index].name, "molFraction") == 0)
574	{
575	local_args_info.molFraction_given++;
576
577	multi_token = get_multiple_arg_token(optarg);
578	multi_next = get_multiple_arg_token_next (optarg);
579
580	while (1)
581	{
582	molFraction_new = (struct molFraction_list *) malloc (sizeof (struct molFraction_list));
583	molFraction_new->next = molFraction_list;
584	molFraction_list = molFraction_new;
585	molFraction_new->molFraction_arg = strtod (multi_token, &stop_char);
586	if (!(stop_char && *stop_char == '\0')) {
587	fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], multi_token);
588	goto failure;
589	}
590	molFraction_new->molFraction_orig = multi_token;
591
592	if (multi_next)
593	{
594	multi_token = get_multiple_arg_token(multi_next);
595	multi_next = get_multiple_arg_token_next (multi_next);
596	local_args_info.molFraction_given++;
597	}
598	else
599	break;
600	}
601	break;
602	}
603
604	break;
605	case '?': /* Invalid option. */
606	/* `getopt_long' already printed an error message. */
607	goto failure;
608
609	default: /* bug: option not considered. */
610	fprintf (stderr, "%s: option unknown: %c%s\n", CMDLINE_PARSER_PACKAGE, c, (additional_error ? additional_error : ""));
611	abort ();
612	} /* switch */
613	} /* while */
614
615
616	if (local_args_info.molFraction_given && molFraction_list)
617	{
618	struct molFraction_list *tmp;
619	args_info->molFraction_arg = (double ) realloc (args_info->molFraction_arg, (args_info->molFraction_given + local_args_info.molFraction_given) sizeof (double));
620	args_info->molFraction_orig = (char *) realloc (args_info->molFraction_orig, (args_info->molFraction_given + local_args_info.molFraction_given) sizeof (char *));
621	for (i = (local_args_info.molFraction_given - 1); i >= 0; --i)
622	{
623	tmp = molFraction_list;
624	args_info->molFraction_arg [i + args_info->molFraction_given] = molFraction_list->molFraction_arg;
625	args_info->molFraction_orig [i + args_info->molFraction_given] = molFraction_list->molFraction_orig;
626	molFraction_list = molFraction_list->next;
627	free (tmp);
628	}
629	}
630
631
632	args_info->molFraction_given += local_args_info.molFraction_given;
633	local_args_info.molFraction_given = 0;
634
635	if (check_required)
636	{
637	error += cmdline_parser_required2 (args_info, argv[0], additional_error);
638	}
639
640	cmdline_parser_release (&local_args_info);
641
642	if ( error )
643	return (EXIT_FAILURE);
644
645	if (optind < argc)
646	{
647	int i = 0 ;
648
649	args_info->inputs_num = argc - optind ;
650	args_info->inputs =
651	(char *)(malloc ((args_info->inputs_num)sizeof(char *))) ;
652	while (optind < argc)
653	args_info->inputs[ i++ ] = gengetopt_strdup (argv[optind++]) ;
654	}
655
656	return 0;
657
658	failure:
659	if (molFraction_list)
660	{
661	struct molFraction_list *tmp;
662	while (molFraction_list)
663	{
664	tmp = molFraction_list;
665	free (molFraction_list->molFraction_orig);
666	molFraction_list = molFraction_list->next;
667	free (tmp);
668	}
669	}
670
671	cmdline_parser_release (&local_args_info);
672	return (EXIT_FAILURE);
673	}