applications/randomBuilder/randomBuilderCmd.cpp

/*
  File autogenerated by gengetopt version 2.15
  generated with the following command:
  gengetopt --file-name=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: simpleBuilder [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->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 = 1;
  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:	950
Committed:	Tue Apr 25 22:59:27 2006 UTC (19 years ago) by chuckv
Content type:	text/plain
Original Path:	*trunk/src/applications/randomBuilder/randomBuilderCmd.c*
File size:	20828 byte(s)
Log Message:	Added random builder to cvs.
#	User	Rev	Content
1	chuckv	950	/*
2			File autogenerated by gengetopt version 2.15
3			generated with the following command:
4			gengetopt --file-name=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: simpleBuilder [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->density_given)
364			{
365			fprintf (stderr, "%s: '--density' option required%s\n", prog_name, (additional_error ? additional_error : ""));
366			error = 1;
367			}
368			if (! args_info->nx_given)
369			{
370			fprintf (stderr, "%s: '--nx' option required%s\n", prog_name, (additional_error ? additional_error : ""));
371			error = 1;
372			}
373			if (! args_info->ny_given)
374			{
375			fprintf (stderr, "%s: '--ny' option required%s\n", prog_name, (additional_error ? additional_error : ""));
376			error = 1;
377			}
378			if (! args_info->nz_given)
379			{
380			fprintf (stderr, "%s: '--nz' option required%s\n", prog_name, (additional_error ? additional_error : ""));
381			error = 1;
382			}
383
384			return error;
385			}
386
387			int
388			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)
389			{
390			int c; /* Character of the parsed option. */
391			char multi_token, multi_next; /* for multiple options */
392
393			int i; /* Counter */
394
395			struct molFraction_list * molFraction_list = NULL,* molFraction_new = NULL;
396			int error = 0;
397			struct gengetopt_args_info local_args_info;
398
399			if (initialize)
400			cmdline_parser_init (args_info);
401
402			cmdline_parser_init (&local_args_info);
403
404			optarg = 0;
405			optind = 1;
406			opterr = 1;
407			optopt = '?';
408
409			while (1)
410			{
411			int option_index = 0;
412			char *stop_char;
413
414			static struct option long_options[] = {
415			{ "help", 0, NULL, 'h' },
416			{ "version", 0, NULL, 'V' },
417			{ "output", 1, NULL, 'o' },
418			{ "latticetype", 1, NULL, 0 },
419			{ "density", 1, NULL, 0 },
420			{ "nx", 1, NULL, 0 },
421			{ "ny", 1, NULL, 0 },
422			{ "nz", 1, NULL, 0 },
423			{ "molFraction", 1, NULL, 0 },
424			{ NULL, 0, NULL, 0 }
425			};
426
427			stop_char = 0;
428			c = getopt_long (argc, argv, "hVo:", long_options, &option_index);
429
430			if (c == -1) break; /* Exit from `while (1)' loop. */
431
432			switch (c)
433			{
434			case 'h': /* Print help and exit. */
435			cmdline_parser_print_help ();
436			cmdline_parser_free (&local_args_info);
437			exit (EXIT_SUCCESS);
438
439			case 'V': /* Print version and exit. */
440			cmdline_parser_print_version ();
441			cmdline_parser_free (&local_args_info);
442			exit (EXIT_SUCCESS);
443
444			case 'o': /* Output file name. */
445			if (local_args_info.output_given)
446			{
447			fprintf (stderr, "%s: `--output' (`-o') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
448			goto failure;
449			}
450			if (args_info->output_given && ! override)
451			continue;
452			local_args_info.output_given = 1;
453			args_info->output_given = 1;
454			if (args_info->output_arg)
455			free (args_info->output_arg); /* free previous string */
456			args_info->output_arg = gengetopt_strdup (optarg);
457			if (args_info->output_orig)
458			free (args_info->output_orig); /* free previous string */
459			args_info->output_orig = gengetopt_strdup (optarg);
460			break;
461
462
463			case 0: /* Long option with no short option */
464			/* Lattice type string. Valid types are fcc,hcp,bcc and hcp-water.. */
465			if (strcmp (long_options[option_index].name, "latticetype") == 0)
466			{
467			if (local_args_info.latticetype_given)
468			{
469			fprintf (stderr, "%s: `--latticetype' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
470			goto failure;
471			}
472			if (args_info->latticetype_given && ! override)
473			continue;
474			local_args_info.latticetype_given = 1;
475			args_info->latticetype_given = 1;
476			if (args_info->latticetype_arg)
477			free (args_info->latticetype_arg); /* free previous string */
478			args_info->latticetype_arg = gengetopt_strdup (optarg);
479			if (args_info->latticetype_orig)
480			free (args_info->latticetype_orig); /* free previous string */
481			args_info->latticetype_orig = gengetopt_strdup (optarg);
482			}
483			/* density (g/cm^3). */
484			else if (strcmp (long_options[option_index].name, "density") == 0)
485			{
486			if (local_args_info.density_given)
487			{
488			fprintf (stderr, "%s: `--density' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
489			goto failure;
490			}
491			if (args_info->density_given && ! override)
492			continue;
493			local_args_info.density_given = 1;
494			args_info->density_given = 1;
495			args_info->density_arg = strtod (optarg, &stop_char);
496			if (!(stop_char && *stop_char == '\0')) {
497			fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
498			goto failure;
499			}
500			if (args_info->density_orig)
501			free (args_info->density_orig); /* free previous string */
502			args_info->density_orig = gengetopt_strdup (optarg);
503			}
504			/* number of unit cells in x. */
505			else if (strcmp (long_options[option_index].name, "nx") == 0)
506			{
507			if (local_args_info.nx_given)
508			{
509			fprintf (stderr, "%s: `--nx' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
510			goto failure;
511			}
512			if (args_info->nx_given && ! override)
513			continue;
514			local_args_info.nx_given = 1;
515			args_info->nx_given = 1;
516			args_info->nx_arg = strtol (optarg, &stop_char, 0);
517			if (!(stop_char && *stop_char == '\0')) {
518			fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
519			goto failure;
520			}
521			if (args_info->nx_orig)
522			free (args_info->nx_orig); /* free previous string */
523			args_info->nx_orig = gengetopt_strdup (optarg);
524			}
525			/* number of unit cells in y. */
526			else if (strcmp (long_options[option_index].name, "ny") == 0)
527			{
528			if (local_args_info.ny_given)
529			{
530			fprintf (stderr, "%s: `--ny' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
531			goto failure;
532			}
533			if (args_info->ny_given && ! override)
534			continue;
535			local_args_info.ny_given = 1;
536			args_info->ny_given = 1;
537			args_info->ny_arg = strtol (optarg, &stop_char, 0);
538			if (!(stop_char && *stop_char == '\0')) {
539			fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
540			goto failure;
541			}
542			if (args_info->ny_orig)
543			free (args_info->ny_orig); /* free previous string */
544			args_info->ny_orig = gengetopt_strdup (optarg);
545			}
546			/* number of unit cells in z. */
547			else if (strcmp (long_options[option_index].name, "nz") == 0)
548			{
549			if (local_args_info.nz_given)
550			{
551			fprintf (stderr, "%s: `--nz' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
552			goto failure;
553			}
554			if (args_info->nz_given && ! override)
555			continue;
556			local_args_info.nz_given = 1;
557			args_info->nz_given = 1;
558			args_info->nz_arg = strtol (optarg, &stop_char, 0);
559			if (!(stop_char && *stop_char == '\0')) {
560			fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
561			goto failure;
562			}
563			if (args_info->nz_orig)
564			free (args_info->nz_orig); /* free previous string */
565			args_info->nz_orig = gengetopt_strdup (optarg);
566			}
567			/* (Default) Builds a multi-component random mixed nanoparticle. Mole Fraction must be specified for each componet > 1 in MD file.. */
568			else if (strcmp (long_options[option_index].name, "molFraction") == 0)
569			{
570			local_args_info.molFraction_given++;
571
572			multi_token = get_multiple_arg_token(optarg);
573			multi_next = get_multiple_arg_token_next (optarg);
574
575			while (1)
576			{
577			molFraction_new = (struct molFraction_list *) malloc (sizeof (struct molFraction_list));
578			molFraction_new->next = molFraction_list;
579			molFraction_list = molFraction_new;
580			molFraction_new->molFraction_arg = strtod (multi_token, &stop_char);
581			if (!(stop_char && *stop_char == '\0')) {
582			fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], multi_token);
583			goto failure;
584			}
585			molFraction_new->molFraction_orig = multi_token;
586
587			if (multi_next)
588			{
589			multi_token = get_multiple_arg_token(multi_next);
590			multi_next = get_multiple_arg_token_next (multi_next);
591			local_args_info.molFraction_given++;
592			}
593			else
594			break;
595			}
596			break;
597			}
598
599			break;
600			case '?': /* Invalid option. */
601			/* `getopt_long' already printed an error message. */
602			goto failure;
603
604			default: /* bug: option not considered. */
605			fprintf (stderr, "%s: option unknown: %c%s\n", CMDLINE_PARSER_PACKAGE, c, (additional_error ? additional_error : ""));
606			abort ();
607			} /* switch */
608			} /* while */
609
610
611			if (local_args_info.molFraction_given && molFraction_list)
612			{
613			struct molFraction_list *tmp;
614			args_info->molFraction_arg = (double ) realloc (args_info->molFraction_arg, (args_info->molFraction_given + local_args_info.molFraction_given) sizeof (double));
615			args_info->molFraction_orig = (char *) realloc (args_info->molFraction_orig, (args_info->molFraction_given + local_args_info.molFraction_given) sizeof (char *));
616			for (i = (local_args_info.molFraction_given - 1); i >= 0; --i)
617			{
618			tmp = molFraction_list;
619			args_info->molFraction_arg [i + args_info->molFraction_given] = molFraction_list->molFraction_arg;
620			args_info->molFraction_orig [i + args_info->molFraction_given] = molFraction_list->molFraction_orig;
621			molFraction_list = molFraction_list->next;
622			free (tmp);
623			}
624			}
625
626
627			args_info->molFraction_given += local_args_info.molFraction_given;
628			local_args_info.molFraction_given = 0;
629
630			if (check_required)
631			{
632			error += cmdline_parser_required2 (args_info, argv[0], additional_error);
633			}
634
635			cmdline_parser_release (&local_args_info);
636
637			if ( error )
638			return (EXIT_FAILURE);
639
640			if (optind < argc)
641			{
642			int i = 0 ;
643
644			args_info->inputs_num = argc - optind ;
645			args_info->inputs =
646			(char *)(malloc ((args_info->inputs_num)sizeof(char *))) ;
647			while (optind < argc)
648			args_info->inputs[ i++ ] = gengetopt_strdup (argv[optind++]) ;
649			}
650
651			return 0;
652
653			failure:
654			if (molFraction_list)
655			{
656			struct molFraction_list *tmp;
657			while (molFraction_list)
658			{
659			tmp = molFraction_list;
660			free (molFraction_list->molFraction_orig);
661			molFraction_list = molFraction_list->next;
662			free (tmp);
663			}
664			}
665
666			cmdline_parser_release (&local_args_info);
667			return (EXIT_FAILURE);
668			}