applications/nanoparticleBuilder/nanoparticleBuilderCmd.c

/*
  File autogenerated by gengetopt version 2.13.1
  generated with the following command:
  gengetopt -F nanoparticleBuilderCmd --unamed-opts --no-handle-error 

  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;
};

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->latticeConstant_given = 0 ;
  args_info->radius_given = 0 ;
  args_info->shellRadius_given = 0 ;
  args_info->molFraction_given = 0 ;
  args_info->vacancyPercent_given = 0 ;
  args_info->vacancyInnerRadius_given = 0 ;
  args_info->vacancyOuterRadius_given = 0 ;
}

static
void clear_args (struct gengetopt_args_info *args_info)
{
  args_info->output_arg = NULL;
  args_info->shellRadius_arg = NULL;
  args_info->molFraction_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 an OOPSE \nstartup file");
  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","      --latticeConstant=DOUBLE  Lattice spacing in Angstroms for cubic lattice.");
  printf("%s\n","      --radius=DOUBLE           Nanoparticle radius in Angstroms");
  printf("%s\n","      --shellRadius=DOUBLE      Radius containing within it only molecules of a \n                                  specific component. Specified for each \n                                  component > 1 in the template file.");
  printf("%s\n","      --molFraction=DOUBLE      Builds a multi-component random alloy \n                                  nanoparticle. A mole Fraction must be \n                                  specified for each component > 1 in the \n                                  template file.");
  printf("%s\n","      --vacancyPercent=DOUBLE   Percentage of atoms to remove from within \n                                  vacancy range");
  printf("%s\n","      --vacancyInnerRadius=DOUBLE\n                                Radius arround core-shell where vacancies \n                                  should be located.");
  printf("%s\n","      --vacancyOuterRadius=DOUBLE\n                                Radius arround core-shell where vacancies \n                                  should 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->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;
    }
  
  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);

  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;

  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->latticeConstant_given)
    {
      fprintf (stderr, "%s: '--latticeConstant' 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;
  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' },
        { "latticeConstant",    1, NULL, 0 },
        { "radius",     1, NULL, 0 },
        { "shellRadius",        1, NULL, 0 },
        { "molFraction",        1, NULL, 0 },
        { "vacancyPercent",     1, NULL, 0 },
        { "vacancyInnerRadius", 1, NULL, 0 },
        { "vacancyOuterRadius", 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);
          break;


        case 0: /* Long option with no short option */
          /* Lattice spacing in Angstroms for cubic lattice..  */
          if (strcmp (long_options[option_index].name, "latticeConstant") == 0)
          {
            if (local_args_info.latticeConstant_given)
              {
                fprintf (stderr, "%s: `--latticeConstant' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
                goto failure;
              }
            if (args_info->latticeConstant_given && ! override)
              continue;
            local_args_info.latticeConstant_given = 1;
            args_info->latticeConstant_given = 1;
            args_info->latticeConstant_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 containing within it only molecules of a specific component. Specified for each component > 1 in the template 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;
          }
          /* Builds a multi-component random alloy nanoparticle. A mole Fraction must be specified for each component > 1 in the template 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 atoms to remove from within vacancy range.  */
          else if (strcmp (long_options[option_index].name, "vacancyPercent") == 0)
          {
            if (local_args_info.vacancyPercent_given)
              {
                fprintf (stderr, "%s: `--vacancyPercent' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
                goto failure;
              }
            if (args_info->vacancyPercent_given && ! override)
              continue;
            local_args_info.vacancyPercent_given = 1;
            args_info->vacancyPercent_given = 1;
            args_info->vacancyPercent_arg = strtod (optarg, NULL);
          }
          /* Radius arround core-shell where vacancies should be located..  */
          else if (strcmp (long_options[option_index].name, "vacancyInnerRadius") == 0)
          {
            if (local_args_info.vacancyInnerRadius_given)
              {
                fprintf (stderr, "%s: `--vacancyInnerRadius' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
                goto failure;
              }
            if (args_info->vacancyInnerRadius_given && ! override)
              continue;
            local_args_info.vacancyInnerRadius_given = 1;
            args_info->vacancyInnerRadius_given = 1;
            args_info->vacancyInnerRadius_arg = strtod (optarg, NULL);
          }
          /* Radius arround core-shell where vacancies should be located..  */
          else if (strcmp (long_options[option_index].name, "vacancyOuterRadius") == 0)
          {
            if (local_args_info.vacancyOuterRadius_given)
              {
                fprintf (stderr, "%s: `--vacancyOuterRadius' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
                goto failure;
              }
            if (args_info->vacancyOuterRadius_given && ! override)
              continue;
            local_args_info.vacancyOuterRadius_given = 1;
            args_info->vacancyOuterRadius_given = 1;
            args_info->vacancyOuterRadius_arg = strtod (optarg, NULL);
          }
          
          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);
        }
    }
  

  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;
  
  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);
        }
    }
  
  cmdline_parser_free (&local_args_info);
  return (EXIT_FAILURE);
}
Revision:	3053
Committed:	Wed Oct 18 19:35:07 2006 UTC (18 years, 6 months ago) by gezelter
Content type:	text/plain
File size:	17918 byte(s)
Log Message:	bug fixes for vacancies
#	Content
1	/*
2	File autogenerated by gengetopt version 2.13.1
3	generated with the following command:
4	gengetopt -F nanoparticleBuilderCmd --unamed-opts --no-handle-error
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	static char *
48	gengetopt_strdup (const char *s);
49
50	static
51	void clear_given (struct gengetopt_args_info *args_info)
52	{
53	args_info->help_given = 0 ;
54	args_info->version_given = 0 ;
55	args_info->output_given = 0 ;
56	args_info->latticeConstant_given = 0 ;
57	args_info->radius_given = 0 ;
58	args_info->shellRadius_given = 0 ;
59	args_info->molFraction_given = 0 ;
60	args_info->vacancyPercent_given = 0 ;
61	args_info->vacancyInnerRadius_given = 0 ;
62	args_info->vacancyOuterRadius_given = 0 ;
63	}
64
65	static
66	void clear_args (struct gengetopt_args_info *args_info)
67	{
68	args_info->output_arg = NULL;
69	args_info->shellRadius_arg = NULL;
70	args_info->molFraction_arg = NULL;
71	}
72
73	void
74	cmdline_parser_print_version (void)
75	{
76	printf ("%s %s\n", CMDLINE_PARSER_PACKAGE, CMDLINE_PARSER_VERSION);
77	}
78
79	void
80	cmdline_parser_print_help (void)
81	{
82	cmdline_parser_print_version ();
83	printf("\n%s\n", "Builds spherical random or core-shell nanoparticles and outputs an OOPSE \nstartup file");
84	printf("\nUsage: nanoparticleBuilder [OPTIONS]... [FILES]...\n\n");
85	printf("%s\n"," -h, --help Print help and exit");
86	printf("%s\n"," -V, --version Print version and exit");
87	printf("%s\n"," -o, --output=STRING Output file name");
88	printf("%s\n"," --latticeConstant=DOUBLE Lattice spacing in Angstroms for cubic lattice.");
89	printf("%s\n"," --radius=DOUBLE Nanoparticle radius in Angstroms");
90	printf("%s\n"," --shellRadius=DOUBLE Radius containing within it only molecules of a \n specific component. Specified for each \n component > 1 in the template file.");
91	printf("%s\n"," --molFraction=DOUBLE Builds a multi-component random alloy \n nanoparticle. A mole Fraction must be \n specified for each component > 1 in the \n template file.");
92	printf("%s\n"," --vacancyPercent=DOUBLE Percentage of atoms to remove from within \n vacancy range");
93	printf("%s\n"," --vacancyInnerRadius=DOUBLE\n Radius arround core-shell where vacancies \n should be located.");
94	printf("%s\n"," --vacancyOuterRadius=DOUBLE\n Radius arround core-shell where vacancies \n should be located.");
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	void
109	cmdline_parser_free (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->shellRadius_arg)
119	{
120	free (args_info->shellRadius_arg); /* free previous argument */
121	args_info->shellRadius_arg = 0;
122	}
123	if (args_info->molFraction_arg)
124	{
125	free (args_info->molFraction_arg); /* free previous argument */
126	args_info->molFraction_arg = 0;
127	}
128
129	for (i = 0; i < args_info->inputs_num; ++i)
130	free (args_info->inputs [i]);
131
132	if (args_info->inputs_num)
133	free (args_info->inputs);
134
135	clear_given (args_info);
136	}
137
138	/* gengetopt_strdup() */
139	/* strdup.c replacement of strdup, which is not standard */
140	char *
141	gengetopt_strdup (const char *s)
142	{
143	char *result = NULL;
144	if (!s)
145	return result;
146
147	result = (char*)malloc(strlen(s) + 1);
148	if (result == (char*)0)
149	return (char*)0;
150	strcpy(result, s);
151	return result;
152	}
153
154	static char *
155	get_multiple_arg_token(const char *arg)
156	{
157	char tok, ret;
158	size_t len;
159
160	if (!arg)
161	return NULL;
162
163	tok = strchr (arg, ',');
164
165	if (tok)
166	len = (size_t)(tok - arg + 1);
167	else
168	len = strlen (arg) + 1;
169
170	ret = (char *) malloc (len);
171	strncpy (ret, arg, len-1);
172	ret[len-1] = '\0';
173
174	return ret;
175	}
176
177	static char *
178	get_multiple_arg_token_next(const char *arg)
179	{
180	char *tok;
181
182	if (!arg)
183	return NULL;
184
185	tok = strchr (arg, ',');
186
187	if (! tok \|\| strlen(tok) == 1)
188	return 0;
189
190	return tok+1;
191	}
192
193	int
194	cmdline_parser (int argc, char * const argv, struct gengetopt_args_info args_info)
195	{
196	return cmdline_parser2 (argc, argv, args_info, 0, 1, 1);
197	}
198
199	int
200	cmdline_parser2 (int argc, char * const argv, struct gengetopt_args_info args_info, int override, int initialize, int check_required)
201	{
202	int result;
203
204	result = cmdline_parser_internal (argc, argv, args_info, override, initialize, check_required, NULL);
205
206	return result;
207	}
208
209	int
210	cmdline_parser_required (struct gengetopt_args_info args_info, const char prog_name)
211	{
212	int result = EXIT_SUCCESS;
213
214	if (cmdline_parser_required2(args_info, prog_name, NULL) > 0)
215	result = EXIT_FAILURE;
216
217	return result;
218	}
219
220	int
221	cmdline_parser_required2 (struct gengetopt_args_info args_info, const char prog_name, const char *additional_error)
222	{
223	int error = 0;
224
225	if (! args_info->output_given)
226	{
227	fprintf (stderr, "%s: '--output' ('-o') option required%s\n", prog_name, (additional_error ? additional_error : ""));
228	error = 1;
229	}
230	if (! args_info->latticeConstant_given)
231	{
232	fprintf (stderr, "%s: '--latticeConstant' option required%s\n", prog_name, (additional_error ? additional_error : ""));
233	error = 1;
234	}
235	if (! args_info->radius_given)
236	{
237	fprintf (stderr, "%s: '--radius' option required%s\n", prog_name, (additional_error ? additional_error : ""));
238	error = 1;
239	}
240
241	return error;
242	}
243
244	int
245	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)
246	{
247	int c; /* Character of the parsed option. */
248	char multi_token, multi_next; /* for multiple options */
249
250	int i; /* Counter */
251
252	struct shellRadius_list * shellRadius_list = NULL,* shellRadius_new = NULL;
253	struct molFraction_list * molFraction_list = NULL,* molFraction_new = NULL;
254	int error = 0;
255	struct gengetopt_args_info local_args_info;
256
257	if (initialize)
258	cmdline_parser_init (args_info);
259
260	cmdline_parser_init (&local_args_info);
261
262	optarg = 0;
263	optind = 1;
264	opterr = 1;
265	optopt = '?';
266
267	while (1)
268	{
269	int option_index = 0;
270	char *stop_char;
271
272	static struct option long_options[] = {
273	{ "help", 0, NULL, 'h' },
274	{ "version", 0, NULL, 'V' },
275	{ "output", 1, NULL, 'o' },
276	{ "latticeConstant", 1, NULL, 0 },
277	{ "radius", 1, NULL, 0 },
278	{ "shellRadius", 1, NULL, 0 },
279	{ "molFraction", 1, NULL, 0 },
280	{ "vacancyPercent", 1, NULL, 0 },
281	{ "vacancyInnerRadius", 1, NULL, 0 },
282	{ "vacancyOuterRadius", 1, NULL, 0 },
283	{ NULL, 0, NULL, 0 }
284	};
285
286	stop_char = 0;
287	c = getopt_long (argc, argv, "hVo:", long_options, &option_index);
288
289	if (c == -1) break; /* Exit from `while (1)' loop. */
290
291	switch (c)
292	{
293	case 'h': /* Print help and exit. */
294	cmdline_parser_print_help ();
295	cmdline_parser_free (&local_args_info);
296	exit (EXIT_SUCCESS);
297
298	case 'V': /* Print version and exit. */
299	cmdline_parser_print_version ();
300	cmdline_parser_free (&local_args_info);
301	exit (EXIT_SUCCESS);
302
303	case 'o': /* Output file name. */
304	if (local_args_info.output_given)
305	{
306	fprintf (stderr, "%s: `--output' (`-o') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
307	goto failure;
308	}
309	if (args_info->output_given && ! override)
310	continue;
311	local_args_info.output_given = 1;
312	args_info->output_given = 1;
313	if (args_info->output_arg)
314	free (args_info->output_arg); /* free previous string */
315	args_info->output_arg = gengetopt_strdup (optarg);
316	break;
317
318
319	case 0: /* Long option with no short option */
320	/* Lattice spacing in Angstroms for cubic lattice.. */
321	if (strcmp (long_options[option_index].name, "latticeConstant") == 0)
322	{
323	if (local_args_info.latticeConstant_given)
324	{
325	fprintf (stderr, "%s: `--latticeConstant' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
326	goto failure;
327	}
328	if (args_info->latticeConstant_given && ! override)
329	continue;
330	local_args_info.latticeConstant_given = 1;
331	args_info->latticeConstant_given = 1;
332	args_info->latticeConstant_arg = strtod (optarg, NULL);
333	}
334	/* Nanoparticle radius in Angstroms. */
335	else if (strcmp (long_options[option_index].name, "radius") == 0)
336	{
337	if (local_args_info.radius_given)
338	{
339	fprintf (stderr, "%s: `--radius' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
340	goto failure;
341	}
342	if (args_info->radius_given && ! override)
343	continue;
344	local_args_info.radius_given = 1;
345	args_info->radius_given = 1;
346	args_info->radius_arg = strtod (optarg, NULL);
347	}
348	/* Radius containing within it only molecules of a specific component. Specified for each component > 1 in the template file.. */
349	else if (strcmp (long_options[option_index].name, "shellRadius") == 0)
350	{
351	local_args_info.shellRadius_given++;
352
353	multi_token = get_multiple_arg_token(optarg);
354	multi_next = get_multiple_arg_token_next (optarg);
355
356	while (1)
357	{
358	shellRadius_new = (struct shellRadius_list *) malloc (sizeof (struct shellRadius_list));
359	shellRadius_new->next = shellRadius_list;
360	shellRadius_list = shellRadius_new;
361	shellRadius_new->shellRadius_arg = strtod (multi_token, NULL);
362	free (multi_token);
363
364	if (multi_next)
365	{
366	multi_token = get_multiple_arg_token(multi_next);
367	multi_next = get_multiple_arg_token_next (multi_next);
368	local_args_info.shellRadius_given++;
369	}
370	else
371	break;
372	}
373	break;
374	}
375	/* Builds a multi-component random alloy nanoparticle. A mole Fraction must be specified for each component > 1 in the template file.. */
376	else if (strcmp (long_options[option_index].name, "molFraction") == 0)
377	{
378	local_args_info.molFraction_given++;
379
380	multi_token = get_multiple_arg_token(optarg);
381	multi_next = get_multiple_arg_token_next (optarg);
382
383	while (1)
384	{
385	molFraction_new = (struct molFraction_list *) malloc (sizeof (struct molFraction_list));
386	molFraction_new->next = molFraction_list;
387	molFraction_list = molFraction_new;
388	molFraction_new->molFraction_arg = strtod (multi_token, NULL);
389	free (multi_token);
390
391	if (multi_next)
392	{
393	multi_token = get_multiple_arg_token(multi_next);
394	multi_next = get_multiple_arg_token_next (multi_next);
395	local_args_info.molFraction_given++;
396	}
397	else
398	break;
399	}
400	break;
401	}
402	/* Percentage of atoms to remove from within vacancy range. */
403	else if (strcmp (long_options[option_index].name, "vacancyPercent") == 0)
404	{
405	if (local_args_info.vacancyPercent_given)
406	{
407	fprintf (stderr, "%s: `--vacancyPercent' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
408	goto failure;
409	}
410	if (args_info->vacancyPercent_given && ! override)
411	continue;
412	local_args_info.vacancyPercent_given = 1;
413	args_info->vacancyPercent_given = 1;
414	args_info->vacancyPercent_arg = strtod (optarg, NULL);
415	}
416	/* Radius arround core-shell where vacancies should be located.. */
417	else if (strcmp (long_options[option_index].name, "vacancyInnerRadius") == 0)
418	{
419	if (local_args_info.vacancyInnerRadius_given)
420	{
421	fprintf (stderr, "%s: `--vacancyInnerRadius' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
422	goto failure;
423	}
424	if (args_info->vacancyInnerRadius_given && ! override)
425	continue;
426	local_args_info.vacancyInnerRadius_given = 1;
427	args_info->vacancyInnerRadius_given = 1;
428	args_info->vacancyInnerRadius_arg = strtod (optarg, NULL);
429	}
430	/* Radius arround core-shell where vacancies should be located.. */
431	else if (strcmp (long_options[option_index].name, "vacancyOuterRadius") == 0)
432	{
433	if (local_args_info.vacancyOuterRadius_given)
434	{
435	fprintf (stderr, "%s: `--vacancyOuterRadius' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
436	goto failure;
437	}
438	if (args_info->vacancyOuterRadius_given && ! override)
439	continue;
440	local_args_info.vacancyOuterRadius_given = 1;
441	args_info->vacancyOuterRadius_given = 1;
442	args_info->vacancyOuterRadius_arg = strtod (optarg, NULL);
443	}
444
445	break;
446	case '?': /* Invalid option. */
447	/* `getopt_long' already printed an error message. */
448	goto failure;
449
450	default: /* bug: option not considered. */
451	fprintf (stderr, "%s: option unknown: %c%s\n", CMDLINE_PARSER_PACKAGE, c, (additional_error ? additional_error : ""));
452	abort ();
453	} /* switch */
454	} /* while */
455
456
457	if (local_args_info.shellRadius_given && shellRadius_list)
458	{
459	struct shellRadius_list *tmp;
460	args_info->shellRadius_arg = (double ) realloc (args_info->shellRadius_arg, (args_info->shellRadius_given + local_args_info.shellRadius_given) sizeof (double));
461	for (i = (local_args_info.shellRadius_given - 1); i >= 0; --i)
462	{
463	tmp = shellRadius_list;
464	args_info->shellRadius_arg [i + args_info->shellRadius_given] = shellRadius_list->shellRadius_arg;
465	shellRadius_list = shellRadius_list->next;
466	free (tmp);
467	}
468	}
469
470	if (local_args_info.molFraction_given && molFraction_list)
471	{
472	struct molFraction_list *tmp;
473	args_info->molFraction_arg = (double ) realloc (args_info->molFraction_arg, (args_info->molFraction_given + local_args_info.molFraction_given) sizeof (double));
474	for (i = (local_args_info.molFraction_given - 1); i >= 0; --i)
475	{
476	tmp = molFraction_list;
477	args_info->molFraction_arg [i + args_info->molFraction_given] = molFraction_list->molFraction_arg;
478	molFraction_list = molFraction_list->next;
479	free (tmp);
480	}
481	}
482
483
484	args_info->shellRadius_given += local_args_info.shellRadius_given;
485	local_args_info.shellRadius_given = 0;
486	args_info->molFraction_given += local_args_info.molFraction_given;
487	local_args_info.molFraction_given = 0;
488
489	if (check_required)
490	{
491	error += cmdline_parser_required2 (args_info, argv[0], additional_error);
492	}
493
494	cmdline_parser_free (&local_args_info);
495
496	if ( error )
497	return (EXIT_FAILURE);
498
499	if (optind < argc)
500	{
501	int i = 0 ;
502
503	args_info->inputs_num = argc - optind ;
504	args_info->inputs =
505	(char *)(malloc ((args_info->inputs_num)sizeof(char *))) ;
506	while (optind < argc)
507	args_info->inputs[ i++ ] = gengetopt_strdup (argv[optind++]) ;
508	}
509
510	return 0;
511
512	failure:
513	if (shellRadius_list)
514	{
515	struct shellRadius_list *tmp;
516	while (shellRadius_list)
517	{
518	tmp = shellRadius_list;
519	shellRadius_list = shellRadius_list->next;
520	free (tmp);
521	}
522	}
523	if (molFraction_list)
524	{
525	struct molFraction_list *tmp;
526	while (molFraction_list)
527	{
528	tmp = molFraction_list;
529	molFraction_list = molFraction_list->next;
530	free (tmp);
531	}
532	}
533
534	cmdline_parser_free (&local_args_info);
535	return (EXIT_FAILURE);
536	}