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->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->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","      --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->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->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' },
        { "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 */
          /* density (g/cm^3).  */
          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:	3041
Committed:	Tue Oct 10 18:34:12 2006 UTC (17 years, 9 months ago) by gezelter
Content type:	text/plain
File size:	19130 byte(s)
Log Message:	fixing missing lattice arguments, adding a builder sample
#	User	Rev	Content
1	chuckv	2738	/*
2	gezelter	3036	File autogenerated by gengetopt version 2.16
3	chuckv	2738	generated with the following command:
4	gezelter	3036	gengetopt -F randomBuilderCmd --unamed-opts
5	chuckv	2738
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->density_given = 0 ;
52			args_info->nx_given = 0 ;
53			args_info->ny_given = 0 ;
54			args_info->nz_given = 0 ;
55			args_info->molFraction_given = 0 ;
56			}
57
58			static
59			void clear_args (struct gengetopt_args_info *args_info)
60			{
61			args_info->output_arg = NULL;
62			args_info->output_orig = NULL;
63			args_info->density_orig = NULL;
64			args_info->nx_orig = NULL;
65			args_info->ny_orig = NULL;
66			args_info->nz_orig = NULL;
67			args_info->molFraction_arg = NULL;
68			args_info->molFraction_orig = NULL;
69
70			}
71
72			void
73			cmdline_parser_print_version (void)
74			{
75			printf ("%s %s\n", CMDLINE_PARSER_PACKAGE, CMDLINE_PARSER_VERSION);
76			}
77
78			void
79			cmdline_parser_print_help (void)
80			{
81			cmdline_parser_print_version ();
82	gezelter	3036	printf("\nUsage: randomBuilder [OPTIONS]... [FILES]...\n\n");
83	chuckv	2738	printf("%s\n"," -h, --help Print help and exit");
84			printf("%s\n"," -V, --version Print version and exit");
85			printf("%s\n"," -o, --output=STRING Output file name");
86			printf("%s\n"," --density=DOUBLE density (g/cm^3)");
87			printf("%s\n"," --nx=INT number of unit cells in x");
88			printf("%s\n"," --ny=INT number of unit cells in y");
89			printf("%s\n"," --nz=INT number of unit cells in z");
90			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.");
91
92			}
93
94			void
95			cmdline_parser_init (struct gengetopt_args_info *args_info)
96			{
97			clear_given (args_info);
98			clear_args (args_info);
99
100			args_info->inputs = NULL;
101			args_info->inputs_num = 0;
102			}
103
104			static void
105			cmdline_parser_release (struct gengetopt_args_info *args_info)
106			{
107
108			unsigned int i;
109			if (args_info->output_arg)
110			{
111			free (args_info->output_arg); /* free previous argument */
112			args_info->output_arg = 0;
113			}
114			if (args_info->output_orig)
115			{
116			free (args_info->output_orig); /* free previous argument */
117			args_info->output_orig = 0;
118			}
119			if (args_info->density_orig)
120			{
121			free (args_info->density_orig); /* free previous argument */
122			args_info->density_orig = 0;
123			}
124			if (args_info->nx_orig)
125			{
126			free (args_info->nx_orig); /* free previous argument */
127			args_info->nx_orig = 0;
128			}
129			if (args_info->ny_orig)
130			{
131			free (args_info->ny_orig); /* free previous argument */
132			args_info->ny_orig = 0;
133			}
134			if (args_info->nz_orig)
135			{
136			free (args_info->nz_orig); /* free previous argument */
137			args_info->nz_orig = 0;
138			}
139			if (args_info->molFraction_arg)
140			{
141			for (i = 0; i < args_info->molFraction_given; ++i)
142			{
143			if (args_info->molFraction_orig [i])
144			{
145			free (args_info->molFraction_orig [i]); /* free previous argument */
146			args_info->molFraction_orig [i] = 0;
147			}
148			}
149			free (args_info->molFraction_arg); /* free previous argument */
150			args_info->molFraction_arg = 0;
151			free (args_info->molFraction_orig); /* free previous argument */
152			args_info->molFraction_orig = 0;
153			}
154
155			for (i = 0; i < args_info->inputs_num; ++i)
156			free (args_info->inputs [i]);
157
158			if (args_info->inputs_num)
159			free (args_info->inputs);
160
161			clear_given (args_info);
162			}
163
164			int
165			cmdline_parser_file_save(const char filename, struct gengetopt_args_info args_info)
166			{
167			FILE *outfile;
168			int i = 0;
169
170			outfile = fopen(filename, "w");
171
172			if (!outfile)
173			{
174			fprintf (stderr, "%s: cannot open file for writing: %s\n", CMDLINE_PARSER_PACKAGE, filename);
175			return EXIT_FAILURE;
176			}
177
178			if (args_info->help_given) {
179			fprintf(outfile, "%s\n", "help");
180			}
181			if (args_info->version_given) {
182			fprintf(outfile, "%s\n", "version");
183			}
184			if (args_info->output_given) {
185			if (args_info->output_orig) {
186			fprintf(outfile, "%s=\"%s\"\n", "output", args_info->output_orig);
187			} else {
188			fprintf(outfile, "%s\n", "output");
189			}
190			}
191			if (args_info->density_given) {
192			if (args_info->density_orig) {
193			fprintf(outfile, "%s=\"%s\"\n", "density", args_info->density_orig);
194			} else {
195			fprintf(outfile, "%s\n", "density");
196			}
197			}
198			if (args_info->nx_given) {
199			if (args_info->nx_orig) {
200			fprintf(outfile, "%s=\"%s\"\n", "nx", args_info->nx_orig);
201			} else {
202			fprintf(outfile, "%s\n", "nx");
203			}
204			}
205			if (args_info->ny_given) {
206			if (args_info->ny_orig) {
207			fprintf(outfile, "%s=\"%s\"\n", "ny", args_info->ny_orig);
208			} else {
209			fprintf(outfile, "%s\n", "ny");
210			}
211			}
212			if (args_info->nz_given) {
213			if (args_info->nz_orig) {
214			fprintf(outfile, "%s=\"%s\"\n", "nz", args_info->nz_orig);
215			} else {
216			fprintf(outfile, "%s\n", "nz");
217			}
218			}
219			if (args_info->molFraction_orig)
220			{
221			for (i = 0; i < args_info->molFraction_given; ++i)
222			{
223			if (args_info->molFraction_orig [i])
224			{
225			fprintf(outfile, "%s=\"%s\"\n", "molFraction", args_info->molFraction_orig [i]);
226			}
227			}
228			}
229
230			fclose (outfile);
231
232			i = EXIT_SUCCESS;
233			return i;
234			}
235
236			void
237			cmdline_parser_free (struct gengetopt_args_info *args_info)
238			{
239			cmdline_parser_release (args_info);
240			}
241
242
243			/* gengetopt_strdup() */
244			/* strdup.c replacement of strdup, which is not standard */
245			char *
246			gengetopt_strdup (const char *s)
247			{
248			char *result = NULL;
249			if (!s)
250			return result;
251
252			result = (char*)malloc(strlen(s) + 1);
253			if (result == (char*)0)
254			return (char*)0;
255			strcpy(result, s);
256			return result;
257			}
258
259			static char *
260			get_multiple_arg_token(const char *arg)
261			{
262			char tok, ret;
263			size_t len;
264
265			if (!arg)
266			return NULL;
267
268			tok = strchr (arg, ',');
269
270			if (tok)
271			len = (size_t)(tok - arg + 1);
272			else
273			len = strlen (arg) + 1;
274
275			ret = (char *) malloc (len);
276			strncpy (ret, arg, len-1);
277			ret[len-1] = '\0';
278
279			return ret;
280			}
281
282			static char *
283			get_multiple_arg_token_next(const char *arg)
284			{
285			char *tok;
286
287			if (!arg)
288			return NULL;
289
290			tok = strchr (arg, ',');
291
292			if (! tok \|\| strlen(tok) == 1)
293			return 0;
294
295			return tok+1;
296			}
297
298			int
299			cmdline_parser (int argc, char * const argv, struct gengetopt_args_info args_info)
300			{
301			return cmdline_parser2 (argc, argv, args_info, 0, 1, 1);
302			}
303
304			int
305			cmdline_parser2 (int argc, char * const argv, struct gengetopt_args_info args_info, int override, int initialize, int check_required)
306			{
307			int result;
308
309			result = cmdline_parser_internal (argc, argv, args_info, override, initialize, check_required, NULL);
310
311			if (result == EXIT_FAILURE)
312			{
313			cmdline_parser_free (args_info);
314			exit (EXIT_FAILURE);
315			}
316
317			return result;
318			}
319
320			int
321			cmdline_parser_required (struct gengetopt_args_info args_info, const char prog_name)
322			{
323			int result = EXIT_SUCCESS;
324
325			if (cmdline_parser_required2(args_info, prog_name, NULL) > 0)
326			result = EXIT_FAILURE;
327
328			if (result == EXIT_FAILURE)
329			{
330			cmdline_parser_free (args_info);
331			exit (EXIT_FAILURE);
332			}
333
334			return result;
335			}
336
337			int
338			cmdline_parser_required2 (struct gengetopt_args_info args_info, const char prog_name, const char *additional_error)
339			{
340			int error = 0;
341
342	gezelter	3036	if (! args_info->output_given)
343			{
344			fprintf (stderr, "%s: '--output' ('-o') option required%s\n", prog_name, (additional_error ? additional_error : ""));
345			error = 1;
346			}
347	chuckv	2738	if (! args_info->density_given)
348			{
349			fprintf (stderr, "%s: '--density' option required%s\n", prog_name, (additional_error ? additional_error : ""));
350			error = 1;
351			}
352			if (! args_info->nx_given)
353			{
354			fprintf (stderr, "%s: '--nx' option required%s\n", prog_name, (additional_error ? additional_error : ""));
355			error = 1;
356			}
357			if (! args_info->ny_given)
358			{
359			fprintf (stderr, "%s: '--ny' option required%s\n", prog_name, (additional_error ? additional_error : ""));
360			error = 1;
361			}
362			if (! args_info->nz_given)
363			{
364			fprintf (stderr, "%s: '--nz' option required%s\n", prog_name, (additional_error ? additional_error : ""));
365			error = 1;
366			}
367
368			return error;
369			}
370
371			int
372			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)
373			{
374			int c; /* Character of the parsed option. */
375			char multi_token, multi_next; /* for multiple options */
376
377			int i; /* Counter */
378
379			struct molFraction_list * molFraction_list = NULL,* molFraction_new = NULL;
380			int error = 0;
381			struct gengetopt_args_info local_args_info;
382
383			if (initialize)
384			cmdline_parser_init (args_info);
385
386			cmdline_parser_init (&local_args_info);
387
388			optarg = 0;
389	gezelter	3036	optind = 0;
390	chuckv	2738	opterr = 1;
391			optopt = '?';
392
393			while (1)
394			{
395			int option_index = 0;
396			char *stop_char;
397
398			static struct option long_options[] = {
399			{ "help", 0, NULL, 'h' },
400			{ "version", 0, NULL, 'V' },
401			{ "output", 1, NULL, 'o' },
402			{ "density", 1, NULL, 0 },
403			{ "nx", 1, NULL, 0 },
404			{ "ny", 1, NULL, 0 },
405			{ "nz", 1, NULL, 0 },
406			{ "molFraction", 1, NULL, 0 },
407			{ NULL, 0, NULL, 0 }
408			};
409
410			stop_char = 0;
411			c = getopt_long (argc, argv, "hVo:", long_options, &option_index);
412
413			if (c == -1) break; /* Exit from `while (1)' loop. */
414
415			switch (c)
416			{
417			case 'h': /* Print help and exit. */
418			cmdline_parser_print_help ();
419			cmdline_parser_free (&local_args_info);
420			exit (EXIT_SUCCESS);
421
422			case 'V': /* Print version and exit. */
423			cmdline_parser_print_version ();
424			cmdline_parser_free (&local_args_info);
425			exit (EXIT_SUCCESS);
426
427			case 'o': /* Output file name. */
428			if (local_args_info.output_given)
429			{
430			fprintf (stderr, "%s: `--output' (`-o') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
431			goto failure;
432			}
433			if (args_info->output_given && ! override)
434			continue;
435			local_args_info.output_given = 1;
436			args_info->output_given = 1;
437			if (args_info->output_arg)
438			free (args_info->output_arg); /* free previous string */
439			args_info->output_arg = gengetopt_strdup (optarg);
440			if (args_info->output_orig)
441			free (args_info->output_orig); /* free previous string */
442			args_info->output_orig = gengetopt_strdup (optarg);
443			break;
444
445
446			case 0: /* Long option with no short option */
447			/* density (g/cm^3). */
448	gezelter	3041	if (strcmp (long_options[option_index].name, "density") == 0)
449	chuckv	2738	{
450			if (local_args_info.density_given)
451			{
452			fprintf (stderr, "%s: `--density' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
453			goto failure;
454			}
455			if (args_info->density_given && ! override)
456			continue;
457			local_args_info.density_given = 1;
458			args_info->density_given = 1;
459			args_info->density_arg = strtod (optarg, &stop_char);
460			if (!(stop_char && *stop_char == '\0')) {
461			fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
462			goto failure;
463			}
464			if (args_info->density_orig)
465			free (args_info->density_orig); /* free previous string */
466			args_info->density_orig = gengetopt_strdup (optarg);
467			}
468			/* number of unit cells in x. */
469			else if (strcmp (long_options[option_index].name, "nx") == 0)
470			{
471			if (local_args_info.nx_given)
472			{
473			fprintf (stderr, "%s: `--nx' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
474			goto failure;
475			}
476			if (args_info->nx_given && ! override)
477			continue;
478			local_args_info.nx_given = 1;
479			args_info->nx_given = 1;
480			args_info->nx_arg = strtol (optarg, &stop_char, 0);
481			if (!(stop_char && *stop_char == '\0')) {
482			fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
483			goto failure;
484			}
485			if (args_info->nx_orig)
486			free (args_info->nx_orig); /* free previous string */
487			args_info->nx_orig = gengetopt_strdup (optarg);
488			}
489			/* number of unit cells in y. */
490			else if (strcmp (long_options[option_index].name, "ny") == 0)
491			{
492			if (local_args_info.ny_given)
493			{
494			fprintf (stderr, "%s: `--ny' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
495			goto failure;
496			}
497			if (args_info->ny_given && ! override)
498			continue;
499			local_args_info.ny_given = 1;
500			args_info->ny_given = 1;
501			args_info->ny_arg = strtol (optarg, &stop_char, 0);
502			if (!(stop_char && *stop_char == '\0')) {
503			fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
504			goto failure;
505			}
506			if (args_info->ny_orig)
507			free (args_info->ny_orig); /* free previous string */
508			args_info->ny_orig = gengetopt_strdup (optarg);
509			}
510			/* number of unit cells in z. */
511			else if (strcmp (long_options[option_index].name, "nz") == 0)
512			{
513			if (local_args_info.nz_given)
514			{
515			fprintf (stderr, "%s: `--nz' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
516			goto failure;
517			}
518			if (args_info->nz_given && ! override)
519			continue;
520			local_args_info.nz_given = 1;
521			args_info->nz_given = 1;
522			args_info->nz_arg = strtol (optarg, &stop_char, 0);
523			if (!(stop_char && *stop_char == '\0')) {
524			fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
525			goto failure;
526			}
527			if (args_info->nz_orig)
528			free (args_info->nz_orig); /* free previous string */
529			args_info->nz_orig = gengetopt_strdup (optarg);
530			}
531			/* (Default) Builds a multi-component random mixed nanoparticle. Mole Fraction must be specified for each componet > 1 in MD file.. */
532			else if (strcmp (long_options[option_index].name, "molFraction") == 0)
533			{
534			local_args_info.molFraction_given++;
535
536			multi_token = get_multiple_arg_token(optarg);
537			multi_next = get_multiple_arg_token_next (optarg);
538
539			while (1)
540			{
541			molFraction_new = (struct molFraction_list *) malloc (sizeof (struct molFraction_list));
542			molFraction_new->next = molFraction_list;
543			molFraction_list = molFraction_new;
544			molFraction_new->molFraction_arg = strtod (multi_token, &stop_char);
545			if (!(stop_char && *stop_char == '\0')) {
546			fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], multi_token);
547			goto failure;
548			}
549			molFraction_new->molFraction_orig = multi_token;
550
551			if (multi_next)
552			{
553			multi_token = get_multiple_arg_token(multi_next);
554			multi_next = get_multiple_arg_token_next (multi_next);
555			local_args_info.molFraction_given++;
556			}
557			else
558			break;
559			}
560			break;
561			}
562
563			break;
564			case '?': /* Invalid option. */
565			/* `getopt_long' already printed an error message. */
566			goto failure;
567
568			default: /* bug: option not considered. */
569			fprintf (stderr, "%s: option unknown: %c%s\n", CMDLINE_PARSER_PACKAGE, c, (additional_error ? additional_error : ""));
570			abort ();
571			} /* switch */
572			} /* while */
573
574
575			if (local_args_info.molFraction_given && molFraction_list)
576			{
577			struct molFraction_list *tmp;
578			args_info->molFraction_arg = (double ) realloc (args_info->molFraction_arg, (args_info->molFraction_given + local_args_info.molFraction_given) sizeof (double));
579			args_info->molFraction_orig = (char *) realloc (args_info->molFraction_orig, (args_info->molFraction_given + local_args_info.molFraction_given) sizeof (char *));
580			for (i = (local_args_info.molFraction_given - 1); i >= 0; --i)
581			{
582			tmp = molFraction_list;
583			args_info->molFraction_arg [i + args_info->molFraction_given] = molFraction_list->molFraction_arg;
584			args_info->molFraction_orig [i + args_info->molFraction_given] = molFraction_list->molFraction_orig;
585			molFraction_list = molFraction_list->next;
586			free (tmp);
587			}
588			}
589
590
591			args_info->molFraction_given += local_args_info.molFraction_given;
592			local_args_info.molFraction_given = 0;
593
594			if (check_required)
595			{
596			error += cmdline_parser_required2 (args_info, argv[0], additional_error);
597			}
598
599			cmdline_parser_release (&local_args_info);
600
601			if ( error )
602			return (EXIT_FAILURE);
603
604			if (optind < argc)
605			{
606			int i = 0 ;
607
608			args_info->inputs_num = argc - optind ;
609			args_info->inputs =
610			(char *)(malloc ((args_info->inputs_num)sizeof(char *))) ;
611			while (optind < argc)
612			args_info->inputs[ i++ ] = gengetopt_strdup (argv[optind++]) ;
613			}
614
615			return 0;
616
617			failure:
618			if (molFraction_list)
619			{
620			struct molFraction_list *tmp;
621			while (molFraction_list)
622			{
623			tmp = molFraction_list;
624			free (molFraction_list->molFraction_orig);
625			molFraction_list = molFraction_list->next;
626			free (tmp);
627			}
628			}
629
630			cmdline_parser_release (&local_args_info);
631			return (EXIT_FAILURE);
632			}