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
#	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->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	gezelter	3036	printf("\nUsage: randomBuilder [OPTIONS]... [FILES]...\n\n");
86	chuckv	2738	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	gezelter	3036	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	chuckv	2738	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	gezelter	3036	optind = 0;
411	chuckv	2738	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			}