applications/nanoparticleBuilder/nanoparticleBuilderCmd.c

/*
  File autogenerated by gengetopt version 2.13
  generated with the following command:
  gengetopt -u -F nanoparticleBuilderCmd 

  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 "nanoparticleBuilderCmd.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 ShellRadius_list
{
  double ShellRadius_arg;
  struct ShellRadius_list * next;
};

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

struct vacancyRadius_list
{
  double vacancyRadius_arg;
  struct vacancyRadius_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->latticeCnst_given = 0 ;
  args_info->radius_given = 0 ;
  args_info->ShellRadius_given = 0 ;
  args_info->molFraction_given = 0 ;
  args_info->vacancyPCT_given = 0 ;
  args_info->vacancyRadius_given = 0 ;
}

static
void clear_args (struct gengetopt_args_info *args_info)
{
  args_info->output_arg = NULL;
  args_info->latticetype_arg = gengetopt_strdup ("fcc");
  args_info->ShellRadius_arg = NULL;
  args_info->molFraction_arg = NULL;
  args_info->vacancyRadius_arg = 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("\n%s\n", "Builds spherical random or core-shell nanoparticles and outputs a xyz input \nfile");
  printf("\nUsage: nanoparticleBuilder [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                                 (default=`fcc')");
  printf("%s\n","      --latticeCnst=DOUBLE    Lattice spacing in Angstroms for cubic lattice.");
  printf("%s\n","      --radius=DOUBLE         Nanoparticle radius in Angstroms");
  printf("%s\n","      --ShellRadius=DOUBLE    Radius from the center of the particle to start a \n                                new shell in multi-component core-shell \n                                particle. Specified for each component > 1 in \n                                md file.");
  printf("%s\n","      --molFraction=DOUBLE    (Default) Builds a multi-component random mixed \n                                nanoparticle. Mole Fraction must be specified \n                                for each componet > 1 in MD file.");
  printf("%s\n","      --vacancyPCT=DOUBLE     Percentage of vacancies to build");
  printf("%s\n","      --vacancyRadius=DOUBLE  Radius arround core-shell where vacancies should \n                                be located.");
  
}

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;
}

void
cmdline_parser_free (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->latticetype_arg)
    {
      free (args_info->latticetype_arg); /* free previous argument */
      args_info->latticetype_arg = 0;
    }
  if (args_info->ShellRadius_arg)
    {
      free (args_info->ShellRadius_arg); /* free previous argument */
      args_info->ShellRadius_arg = 0;
    }
  if (args_info->molFraction_arg)
    {
      free (args_info->molFraction_arg); /* free previous argument */
      args_info->molFraction_arg = 0;
    }
  if (args_info->vacancyRadius_arg)
    {
      free (args_info->vacancyRadius_arg); /* free previous argument */
      args_info->vacancyRadius_arg = 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);
}

/* 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->latticeCnst_given)
    {
      fprintf (stderr, "%s: '--latticeCnst' option required%s\n", prog_name, (additional_error ? additional_error : ""));
      error = 1;
    }
  if (! args_info->radius_given)
    {
      fprintf (stderr, "%s: '--radius' 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 ShellRadius_list * ShellRadius_list = NULL,* ShellRadius_new = NULL;
  struct molFraction_list * molFraction_list = NULL,* molFraction_new = NULL;
  struct vacancyRadius_list * vacancyRadius_list = NULL,* vacancyRadius_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 },
        { "latticeCnst",        1, NULL, 0 },
        { "radius",     1, NULL, 0 },
        { "ShellRadius",        1, NULL, 0 },
        { "molFraction",        1, NULL, 0 },
        { "vacancyPCT", 1, NULL, 0 },
        { "vacancyRadius",      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 ();
          exit (EXIT_SUCCESS);

        case 'V':       /* Print version and exit.  */
          cmdline_parser_print_version ();
          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);
          break;


        case 0: /* Long option with no short option */
          /* Lattice type string. Valid types are fcc,hcp,bcc..  */
          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);
          }
          /* Lattice spacing in Angstroms for cubic lattice..  */
          else if (strcmp (long_options[option_index].name, "latticeCnst") == 0)
          {
            if (local_args_info.latticeCnst_given)
              {
                fprintf (stderr, "%s: `--latticeCnst' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
                goto failure;
              }
            if (args_info->latticeCnst_given && ! override)
              continue;
            local_args_info.latticeCnst_given = 1;
            args_info->latticeCnst_given = 1;
            args_info->latticeCnst_arg = strtod (optarg, NULL);
          }
          /* Nanoparticle radius in Angstroms.  */
          else if (strcmp (long_options[option_index].name, "radius") == 0)
          {
            if (local_args_info.radius_given)
              {
                fprintf (stderr, "%s: `--radius' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
                goto failure;
              }
            if (args_info->radius_given && ! override)
              continue;
            local_args_info.radius_given = 1;
            args_info->radius_given = 1;
            args_info->radius_arg = strtod (optarg, NULL);
          }
          /* Radius from the center of the particle to start a new shell in multi-component core-shell particle. Specified for each component > 1 in md file..  */
          else if (strcmp (long_options[option_index].name, "ShellRadius") == 0)
          {
            local_args_info.ShellRadius_given++;
          
            multi_token = get_multiple_arg_token(optarg);
            multi_next = get_multiple_arg_token_next (optarg);
          
            while (1)
              {
                ShellRadius_new = (struct ShellRadius_list *) malloc (sizeof (struct ShellRadius_list));
                ShellRadius_new->next = ShellRadius_list;
                ShellRadius_list = ShellRadius_new;
                ShellRadius_new->ShellRadius_arg = strtod (multi_token, NULL);
                free (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.ShellRadius_given++;
                  }
                else
                  break;
              }
            break;
          }
          /* (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, NULL);
                free (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;
          }
          /* Percentage of vacancies to build.  */
          else if (strcmp (long_options[option_index].name, "vacancyPCT") == 0)
          {
            if (local_args_info.vacancyPCT_given)
              {
                fprintf (stderr, "%s: `--vacancyPCT' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
                goto failure;
              }
            if (args_info->vacancyPCT_given && ! override)
              continue;
            local_args_info.vacancyPCT_given = 1;
            args_info->vacancyPCT_given = 1;
            args_info->vacancyPCT_arg = strtod (optarg, NULL);
          }
          /* Radius arround core-shell where vacancies should be located..  */
          else if (strcmp (long_options[option_index].name, "vacancyRadius") == 0)
          {
            local_args_info.vacancyRadius_given++;
          
            multi_token = get_multiple_arg_token(optarg);
            multi_next = get_multiple_arg_token_next (optarg);
          
            while (1)
              {
                vacancyRadius_new = (struct vacancyRadius_list *) malloc (sizeof (struct vacancyRadius_list));
                vacancyRadius_new->next = vacancyRadius_list;
                vacancyRadius_list = vacancyRadius_new;
                vacancyRadius_new->vacancyRadius_arg = strtod (multi_token, NULL);
                free (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.vacancyRadius_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.ShellRadius_given && ShellRadius_list)
    {
      struct ShellRadius_list *tmp;
      args_info->ShellRadius_arg = (double *) realloc (args_info->ShellRadius_arg, (args_info->ShellRadius_given + local_args_info.ShellRadius_given) * sizeof (double));
      for (i = (local_args_info.ShellRadius_given - 1); i >= 0; --i)
        {
          tmp = ShellRadius_list;
          args_info->ShellRadius_arg [i + args_info->ShellRadius_given] = ShellRadius_list->ShellRadius_arg;
          ShellRadius_list = ShellRadius_list->next;
          free (tmp);
        }
    }
  
  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));
      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;
          molFraction_list = molFraction_list->next;
          free (tmp);
        }
    }
  
  if (local_args_info.vacancyRadius_given && vacancyRadius_list)
    {
      struct vacancyRadius_list *tmp;
      args_info->vacancyRadius_arg = (double *) realloc (args_info->vacancyRadius_arg, (args_info->vacancyRadius_given + local_args_info.vacancyRadius_given) * sizeof (double));
      for (i = (local_args_info.vacancyRadius_given - 1); i >= 0; --i)
        {
          tmp = vacancyRadius_list;
          args_info->vacancyRadius_arg [i + args_info->vacancyRadius_given] = vacancyRadius_list->vacancyRadius_arg;
          vacancyRadius_list = vacancyRadius_list->next;
          free (tmp);
        }
    }
  

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

  cmdline_parser_free (&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 (ShellRadius_list)
    {
      struct ShellRadius_list *tmp;
      while (ShellRadius_list)
        {
          tmp = ShellRadius_list;
          ShellRadius_list = ShellRadius_list->next;
          free (tmp);
        }
    }
  if (molFraction_list)
    {
      struct molFraction_list *tmp;
      while (molFraction_list)
        {
          tmp = molFraction_list;
          molFraction_list = molFraction_list->next;
          free (tmp);
        }
    }
  if (vacancyRadius_list)
    {
      struct vacancyRadius_list *tmp;
      while (vacancyRadius_list)
        {
          tmp = vacancyRadius_list;
          vacancyRadius_list = vacancyRadius_list->next;
          free (tmp);
        }
    }
  
  cmdline_parser_free (&local_args_info);
  return (EXIT_FAILURE);
}
Revision:	2352
Committed:	Tue Oct 11 21:57:22 2005 UTC (18 years, 8 months ago) by chuckv
Content type:	text/plain
File size:	19606 byte(s)
Log Message:	Added code for nanoparticle builder to cvs.
#	Content
1	/*
2	File autogenerated by gengetopt version 2.13
3	generated with the following command:
4	gengetopt -u -F nanoparticleBuilderCmd
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 "nanoparticleBuilderCmd.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 ShellRadius_list
36	{
37	double ShellRadius_arg;
38	struct ShellRadius_list * next;
39	};
40
41	struct molFraction_list
42	{
43	double molFraction_arg;
44	struct molFraction_list * next;
45	};
46
47	struct vacancyRadius_list
48	{
49	double vacancyRadius_arg;
50	struct vacancyRadius_list * next;
51	};
52
53	static char *
54	gengetopt_strdup (const char *s);
55
56	static
57	void clear_given (struct gengetopt_args_info *args_info)
58	{
59	args_info->help_given = 0 ;
60	args_info->version_given = 0 ;
61	args_info->output_given = 0 ;
62	args_info->latticetype_given = 0 ;
63	args_info->latticeCnst_given = 0 ;
64	args_info->radius_given = 0 ;
65	args_info->ShellRadius_given = 0 ;
66	args_info->molFraction_given = 0 ;
67	args_info->vacancyPCT_given = 0 ;
68	args_info->vacancyRadius_given = 0 ;
69	}
70
71	static
72	void clear_args (struct gengetopt_args_info *args_info)
73	{
74	args_info->output_arg = NULL;
75	args_info->latticetype_arg = gengetopt_strdup ("fcc");
76	args_info->ShellRadius_arg = NULL;
77	args_info->molFraction_arg = NULL;
78	args_info->vacancyRadius_arg = NULL;
79	}
80
81	void
82	cmdline_parser_print_version (void)
83	{
84	printf ("%s %s\n", CMDLINE_PARSER_PACKAGE, CMDLINE_PARSER_VERSION);
85	}
86
87	void
88	cmdline_parser_print_help (void)
89	{
90	cmdline_parser_print_version ();
91	printf("\n%s\n", "Builds spherical random or core-shell nanoparticles and outputs a xyz input \nfile");
92	printf("\nUsage: nanoparticleBuilder [OPTIONS]... [FILES]...\n\n");
93	printf("%s\n"," -h, --help Print help and exit");
94	printf("%s\n"," -V, --version Print version and exit");
95	printf("%s\n"," -o, --output=STRING Output file name");
96	printf("%s\n"," --latticetype=STRING Lattice type string. Valid types are fcc,hcp,bcc. \n (default=`fcc')");
97	printf("%s\n"," --latticeCnst=DOUBLE Lattice spacing in Angstroms for cubic lattice.");
98	printf("%s\n"," --radius=DOUBLE Nanoparticle radius in Angstroms");
99	printf("%s\n"," --ShellRadius=DOUBLE Radius from the center of the particle to start a \n new shell in multi-component core-shell \n particle. Specified for each component > 1 in \n md file.");
100	printf("%s\n"," --molFraction=DOUBLE (Default) Builds a multi-component random mixed \n nanoparticle. Mole Fraction must be specified \n for each componet > 1 in MD file.");
101	printf("%s\n"," --vacancyPCT=DOUBLE Percentage of vacancies to build");
102	printf("%s\n"," --vacancyRadius=DOUBLE Radius arround core-shell where vacancies should \n be located.");
103
104	}
105
106	void
107	cmdline_parser_init (struct gengetopt_args_info *args_info)
108	{
109	clear_given (args_info);
110	clear_args (args_info);
111
112	args_info->inputs = NULL;
113	args_info->inputs_num = 0;
114	}
115
116	void
117	cmdline_parser_free (struct gengetopt_args_info *args_info)
118	{
119
120	unsigned int i;
121	if (args_info->output_arg)
122	{
123	free (args_info->output_arg); /* free previous argument */
124	args_info->output_arg = 0;
125	}
126	if (args_info->latticetype_arg)
127	{
128	free (args_info->latticetype_arg); /* free previous argument */
129	args_info->latticetype_arg = 0;
130	}
131	if (args_info->ShellRadius_arg)
132	{
133	free (args_info->ShellRadius_arg); /* free previous argument */
134	args_info->ShellRadius_arg = 0;
135	}
136	if (args_info->molFraction_arg)
137	{
138	free (args_info->molFraction_arg); /* free previous argument */
139	args_info->molFraction_arg = 0;
140	}
141	if (args_info->vacancyRadius_arg)
142	{
143	free (args_info->vacancyRadius_arg); /* free previous argument */
144	args_info->vacancyRadius_arg = 0;
145	}
146
147	for (i = 0; i < args_info->inputs_num; ++i)
148	free (args_info->inputs [i]);
149
150	if (args_info->inputs_num)
151	free (args_info->inputs);
152
153	clear_given (args_info);
154	}
155
156	/* gengetopt_strdup() */
157	/* strdup.c replacement of strdup, which is not standard */
158	char *
159	gengetopt_strdup (const char *s)
160	{
161	char *result = NULL;
162	if (!s)
163	return result;
164
165	result = (char*)malloc(strlen(s) + 1);
166	if (result == (char*)0)
167	return (char*)0;
168	strcpy(result, s);
169	return result;
170	}
171
172	static char *
173	get_multiple_arg_token(const char *arg)
174	{
175	char tok, ret;
176	size_t len;
177
178	if (!arg)
179	return NULL;
180
181	tok = strchr (arg, ',');
182
183	if (tok)
184	len = (size_t)(tok - arg + 1);
185	else
186	len = strlen (arg) + 1;
187
188	ret = (char *) malloc (len);
189	strncpy (ret, arg, len-1);
190	ret[len-1] = '\0';
191
192	return ret;
193	}
194
195	static char *
196	get_multiple_arg_token_next(const char *arg)
197	{
198	char *tok;
199
200	if (!arg)
201	return NULL;
202
203	tok = strchr (arg, ',');
204
205	if (! tok \|\| strlen(tok) == 1)
206	return 0;
207
208	return tok+1;
209	}
210
211	int
212	cmdline_parser (int argc, char * const argv, struct gengetopt_args_info args_info)
213	{
214	return cmdline_parser2 (argc, argv, args_info, 0, 1, 1);
215	}
216
217	int
218	cmdline_parser2 (int argc, char * const argv, struct gengetopt_args_info args_info, int override, int initialize, int check_required)
219	{
220	int result;
221
222	result = cmdline_parser_internal (argc, argv, args_info, override, initialize, check_required, NULL);
223
224	if (result == EXIT_FAILURE)
225	{
226	cmdline_parser_free (args_info);
227	exit (EXIT_FAILURE);
228	}
229
230	return result;
231	}
232
233	int
234	cmdline_parser_required (struct gengetopt_args_info args_info, const char prog_name)
235	{
236	int result = EXIT_SUCCESS;
237
238	if (cmdline_parser_required2(args_info, prog_name, NULL) > 0)
239	result = EXIT_FAILURE;
240
241	if (result == EXIT_FAILURE)
242	{
243	cmdline_parser_free (args_info);
244	exit (EXIT_FAILURE);
245	}
246
247	return result;
248	}
249
250	int
251	cmdline_parser_required2 (struct gengetopt_args_info args_info, const char prog_name, const char *additional_error)
252	{
253	int error = 0;
254
255	if (! args_info->latticeCnst_given)
256	{
257	fprintf (stderr, "%s: '--latticeCnst' option required%s\n", prog_name, (additional_error ? additional_error : ""));
258	error = 1;
259	}
260	if (! args_info->radius_given)
261	{
262	fprintf (stderr, "%s: '--radius' option required%s\n", prog_name, (additional_error ? additional_error : ""));
263	error = 1;
264	}
265
266	return error;
267	}
268
269	int
270	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)
271	{
272	int c; /* Character of the parsed option. */
273	char multi_token, multi_next; /* for multiple options */
274
275	int i; /* Counter */
276
277	struct ShellRadius_list * ShellRadius_list = NULL,* ShellRadius_new = NULL;
278	struct molFraction_list * molFraction_list = NULL,* molFraction_new = NULL;
279	struct vacancyRadius_list * vacancyRadius_list = NULL,* vacancyRadius_new = NULL;
280	int error = 0;
281	struct gengetopt_args_info local_args_info;
282
283	if (initialize)
284	cmdline_parser_init (args_info);
285
286	cmdline_parser_init (&local_args_info);
287
288	optarg = 0;
289	optind = 1;
290	opterr = 1;
291	optopt = '?';
292
293	while (1)
294	{
295	int option_index = 0;
296	char *stop_char;
297
298	static struct option long_options[] = {
299	{ "help", 0, NULL, 'h' },
300	{ "version", 0, NULL, 'V' },
301	{ "output", 1, NULL, 'o' },
302	{ "latticetype", 1, NULL, 0 },
303	{ "latticeCnst", 1, NULL, 0 },
304	{ "radius", 1, NULL, 0 },
305	{ "ShellRadius", 1, NULL, 0 },
306	{ "molFraction", 1, NULL, 0 },
307	{ "vacancyPCT", 1, NULL, 0 },
308	{ "vacancyRadius", 1, NULL, 0 },
309	{ NULL, 0, NULL, 0 }
310	};
311
312	stop_char = 0;
313	c = getopt_long (argc, argv, "hVo:", long_options, &option_index);
314
315	if (c == -1) break; /* Exit from `while (1)' loop. */
316
317	switch (c)
318	{
319	case 'h': /* Print help and exit. */
320	cmdline_parser_print_help ();
321	exit (EXIT_SUCCESS);
322
323	case 'V': /* Print version and exit. */
324	cmdline_parser_print_version ();
325	exit (EXIT_SUCCESS);
326
327	case 'o': /* Output file name. */
328	if (local_args_info.output_given)
329	{
330	fprintf (stderr, "%s: `--output' (`-o') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
331	goto failure;
332	}
333	if (args_info->output_given && ! override)
334	continue;
335	local_args_info.output_given = 1;
336	args_info->output_given = 1;
337	if (args_info->output_arg)
338	free (args_info->output_arg); /* free previous string */
339	args_info->output_arg = gengetopt_strdup (optarg);
340	break;
341
342
343	case 0: /* Long option with no short option */
344	/* Lattice type string. Valid types are fcc,hcp,bcc.. */
345	if (strcmp (long_options[option_index].name, "latticetype") == 0)
346	{
347	if (local_args_info.latticetype_given)
348	{
349	fprintf (stderr, "%s: `--latticetype' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
350	goto failure;
351	}
352	if (args_info->latticetype_given && ! override)
353	continue;
354	local_args_info.latticetype_given = 1;
355	args_info->latticetype_given = 1;
356	if (args_info->latticetype_arg)
357	free (args_info->latticetype_arg); /* free previous string */
358	args_info->latticetype_arg = gengetopt_strdup (optarg);
359	}
360	/* Lattice spacing in Angstroms for cubic lattice.. */
361	else if (strcmp (long_options[option_index].name, "latticeCnst") == 0)
362	{
363	if (local_args_info.latticeCnst_given)
364	{
365	fprintf (stderr, "%s: `--latticeCnst' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
366	goto failure;
367	}
368	if (args_info->latticeCnst_given && ! override)
369	continue;
370	local_args_info.latticeCnst_given = 1;
371	args_info->latticeCnst_given = 1;
372	args_info->latticeCnst_arg = strtod (optarg, NULL);
373	}
374	/* Nanoparticle radius in Angstroms. */
375	else if (strcmp (long_options[option_index].name, "radius") == 0)
376	{
377	if (local_args_info.radius_given)
378	{
379	fprintf (stderr, "%s: `--radius' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
380	goto failure;
381	}
382	if (args_info->radius_given && ! override)
383	continue;
384	local_args_info.radius_given = 1;
385	args_info->radius_given = 1;
386	args_info->radius_arg = strtod (optarg, NULL);
387	}
388	/* Radius from the center of the particle to start a new shell in multi-component core-shell particle. Specified for each component > 1 in md file.. */
389	else if (strcmp (long_options[option_index].name, "ShellRadius") == 0)
390	{
391	local_args_info.ShellRadius_given++;
392
393	multi_token = get_multiple_arg_token(optarg);
394	multi_next = get_multiple_arg_token_next (optarg);
395
396	while (1)
397	{
398	ShellRadius_new = (struct ShellRadius_list *) malloc (sizeof (struct ShellRadius_list));
399	ShellRadius_new->next = ShellRadius_list;
400	ShellRadius_list = ShellRadius_new;
401	ShellRadius_new->ShellRadius_arg = strtod (multi_token, NULL);
402	free (multi_token);
403
404	if (multi_next)
405	{
406	multi_token = get_multiple_arg_token(multi_next);
407	multi_next = get_multiple_arg_token_next (multi_next);
408	local_args_info.ShellRadius_given++;
409	}
410	else
411	break;
412	}
413	break;
414	}
415	/* (Default) Builds a multi-component random mixed nanoparticle. Mole Fraction must be specified for each componet > 1 in MD file.. */
416	else if (strcmp (long_options[option_index].name, "molFraction") == 0)
417	{
418	local_args_info.molFraction_given++;
419
420	multi_token = get_multiple_arg_token(optarg);
421	multi_next = get_multiple_arg_token_next (optarg);
422
423	while (1)
424	{
425	molFraction_new = (struct molFraction_list *) malloc (sizeof (struct molFraction_list));
426	molFraction_new->next = molFraction_list;
427	molFraction_list = molFraction_new;
428	molFraction_new->molFraction_arg = strtod (multi_token, NULL);
429	free (multi_token);
430
431	if (multi_next)
432	{
433	multi_token = get_multiple_arg_token(multi_next);
434	multi_next = get_multiple_arg_token_next (multi_next);
435	local_args_info.molFraction_given++;
436	}
437	else
438	break;
439	}
440	break;
441	}
442	/* Percentage of vacancies to build. */
443	else if (strcmp (long_options[option_index].name, "vacancyPCT") == 0)
444	{
445	if (local_args_info.vacancyPCT_given)
446	{
447	fprintf (stderr, "%s: `--vacancyPCT' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
448	goto failure;
449	}
450	if (args_info->vacancyPCT_given && ! override)
451	continue;
452	local_args_info.vacancyPCT_given = 1;
453	args_info->vacancyPCT_given = 1;
454	args_info->vacancyPCT_arg = strtod (optarg, NULL);
455	}
456	/* Radius arround core-shell where vacancies should be located.. */
457	else if (strcmp (long_options[option_index].name, "vacancyRadius") == 0)
458	{
459	local_args_info.vacancyRadius_given++;
460
461	multi_token = get_multiple_arg_token(optarg);
462	multi_next = get_multiple_arg_token_next (optarg);
463
464	while (1)
465	{
466	vacancyRadius_new = (struct vacancyRadius_list *) malloc (sizeof (struct vacancyRadius_list));
467	vacancyRadius_new->next = vacancyRadius_list;
468	vacancyRadius_list = vacancyRadius_new;
469	vacancyRadius_new->vacancyRadius_arg = strtod (multi_token, NULL);
470	free (multi_token);
471
472	if (multi_next)
473	{
474	multi_token = get_multiple_arg_token(multi_next);
475	multi_next = get_multiple_arg_token_next (multi_next);
476	local_args_info.vacancyRadius_given++;
477	}
478	else
479	break;
480	}
481	break;
482	}
483
484	break;
485	case '?': /* Invalid option. */
486	/* `getopt_long' already printed an error message. */
487	goto failure;
488
489	default: /* bug: option not considered. */
490	fprintf (stderr, "%s: option unknown: %c%s\n", CMDLINE_PARSER_PACKAGE, c, (additional_error ? additional_error : ""));
491	abort ();
492	} /* switch */
493	} /* while */
494
495
496	if (local_args_info.ShellRadius_given && ShellRadius_list)
497	{
498	struct ShellRadius_list *tmp;
499	args_info->ShellRadius_arg = (double ) realloc (args_info->ShellRadius_arg, (args_info->ShellRadius_given + local_args_info.ShellRadius_given) sizeof (double));
500	for (i = (local_args_info.ShellRadius_given - 1); i >= 0; --i)
501	{
502	tmp = ShellRadius_list;
503	args_info->ShellRadius_arg [i + args_info->ShellRadius_given] = ShellRadius_list->ShellRadius_arg;
504	ShellRadius_list = ShellRadius_list->next;
505	free (tmp);
506	}
507	}
508
509	if (local_args_info.molFraction_given && molFraction_list)
510	{
511	struct molFraction_list *tmp;
512	args_info->molFraction_arg = (double ) realloc (args_info->molFraction_arg, (args_info->molFraction_given + local_args_info.molFraction_given) sizeof (double));
513	for (i = (local_args_info.molFraction_given - 1); i >= 0; --i)
514	{
515	tmp = molFraction_list;
516	args_info->molFraction_arg [i + args_info->molFraction_given] = molFraction_list->molFraction_arg;
517	molFraction_list = molFraction_list->next;
518	free (tmp);
519	}
520	}
521
522	if (local_args_info.vacancyRadius_given && vacancyRadius_list)
523	{
524	struct vacancyRadius_list *tmp;
525	args_info->vacancyRadius_arg = (double ) realloc (args_info->vacancyRadius_arg, (args_info->vacancyRadius_given + local_args_info.vacancyRadius_given) sizeof (double));
526	for (i = (local_args_info.vacancyRadius_given - 1); i >= 0; --i)
527	{
528	tmp = vacancyRadius_list;
529	args_info->vacancyRadius_arg [i + args_info->vacancyRadius_given] = vacancyRadius_list->vacancyRadius_arg;
530	vacancyRadius_list = vacancyRadius_list->next;
531	free (tmp);
532	}
533	}
534
535
536	args_info->ShellRadius_given += local_args_info.ShellRadius_given;
537	local_args_info.ShellRadius_given = 0;
538	args_info->molFraction_given += local_args_info.molFraction_given;
539	local_args_info.molFraction_given = 0;
540	args_info->vacancyRadius_given += local_args_info.vacancyRadius_given;
541	local_args_info.vacancyRadius_given = 0;
542
543	if (check_required)
544	{
545	error += cmdline_parser_required2 (args_info, argv[0], additional_error);
546	}
547
548	cmdline_parser_free (&local_args_info);
549
550	if ( error )
551	return (EXIT_FAILURE);
552
553	if (optind < argc)
554	{
555	int i = 0 ;
556
557	args_info->inputs_num = argc - optind ;
558	args_info->inputs =
559	(char *)(malloc ((args_info->inputs_num)sizeof(char *))) ;
560	while (optind < argc)
561	args_info->inputs[ i++ ] = gengetopt_strdup (argv[optind++]) ;
562	}
563
564	return 0;
565
566	failure:
567	if (ShellRadius_list)
568	{
569	struct ShellRadius_list *tmp;
570	while (ShellRadius_list)
571	{
572	tmp = ShellRadius_list;
573	ShellRadius_list = ShellRadius_list->next;
574	free (tmp);
575	}
576	}
577	if (molFraction_list)
578	{
579	struct molFraction_list *tmp;
580	while (molFraction_list)
581	{
582	tmp = molFraction_list;
583	molFraction_list = molFraction_list->next;
584	free (tmp);
585	}
586	}
587	if (vacancyRadius_list)
588	{
589	struct vacancyRadius_list *tmp;
590	while (vacancyRadius_list)
591	{
592	tmp = vacancyRadius_list;
593	vacancyRadius_list = vacancyRadius_list->next;
594	free (tmp);
595	}
596	}
597
598	cmdline_parser_free (&local_args_info);
599	return (EXIT_FAILURE);
600	}