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root/OpenMD/trunk/src/applications/nanoparticleBuilder/nanoparticleBuilderCmd.cpp
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Comparing:
trunk/src/applications/nanoparticleBuilder/nanoparticleBuilderCmd.c (file contents), Revision 653 by chuckv, Tue Oct 11 21:57:22 2005 UTC vs.
trunk/src/applications/nanoparticleBuilder/nanoparticleBuilderCmd.cpp (file contents), Revision 1795 by gezelter, Fri Sep 7 18:13:55 2012 UTC

# Line 1 | Line 1
1   /*
2 <  File autogenerated by gengetopt version 2.13
2 >  File autogenerated by gengetopt version 2.22.4
3    generated with the following command:
4 <  gengetopt -u -F nanoparticleBuilderCmd
4 >  gengetopt -F nanoparticleBuilderCmd -u
5  
6    The developers of gengetopt consider the fixed text that goes in all
7    gengetopt output files to be in the public domain:
# Line 17 | Line 17
17   #include <stdlib.h>
18   #include <string.h>
19  
20 < #include "getopt.h"
20 > #ifndef FIX_UNUSED
21 > #define FIX_UNUSED(X) (void) (X) /* avoid warnings for unused params */
22 > #endif
23  
24 + #ifdef WIN32
25 + #include "utils/wingetopt.h"
26 + #else
27 + #include <getopt.h>
28 + #endif
29 +
30   #include "nanoparticleBuilderCmd.h"
31  
32 + const char *gengetopt_args_info_purpose = "Builds spherical random or core-shell nanoparticles and outputs an OpenMD \nstartup file";
33 +
34 + const char *gengetopt_args_info_usage = "Usage: nanoparticleBuilder [OPTIONS]... [FILES]...";
35 +
36 + const char *gengetopt_args_info_description = "";
37 +
38 + const char *gengetopt_args_info_help[] = {
39 +  "  -h, --help                    Print help and exit",
40 +  "  -V, --version                 Print version and exit",
41 +  "  -o, --output=STRING           Output file name",
42 +  "      --latticeConstant=DOUBLE  Lattice spacing in Angstroms for cubic lattice.",
43 +  "      --radius=DOUBLE           Nanoparticle radius in Angstroms",
44 +  "      --shellRadius=DOUBLE      Radius containing within it only molecules of a \n                                  specific component. Specified for each \n                                  component > 1 in the template file.",
45 +  "      --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.",
46 +  "      --vacancyPercent=DOUBLE   Percentage of atoms to remove from within \n                                  vacancy range",
47 +  "      --vacancyInnerRadius=DOUBLE\n                                Radius arround core-shell where vacancies \n                                  should be located.",
48 +  "      --vacancyOuterRadius=DOUBLE\n                                Radius arround core-shell where vacancies \n                                  should be located.",
49 +    0
50 + };
51 +
52 + typedef enum {ARG_NO
53 +  , ARG_STRING
54 +  , ARG_DOUBLE
55 + } cmdline_parser_arg_type;
56 +
57   static
58   void clear_given (struct gengetopt_args_info *args_info);
59   static
60   void clear_args (struct gengetopt_args_info *args_info);
61  
62   static int
63 < 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);
63 > cmdline_parser_internal (int argc, char **argv, struct gengetopt_args_info *args_info,
64 >                        struct cmdline_parser_params *params, const char *additional_error);
65  
66   static int
67   cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error);
68  
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
69   static char *
70   gengetopt_strdup (const char *s);
71  
# Line 59 | Line 75 | void clear_given (struct gengetopt_args_info *args_inf
75    args_info->help_given = 0 ;
76    args_info->version_given = 0 ;
77    args_info->output_given = 0 ;
78 <  args_info->latticetype_given = 0 ;
63 <  args_info->latticeCnst_given = 0 ;
78 >  args_info->latticeConstant_given = 0 ;
79    args_info->radius_given = 0 ;
80 <  args_info->ShellRadius_given = 0 ;
80 >  args_info->shellRadius_given = 0 ;
81    args_info->molFraction_given = 0 ;
82 <  args_info->vacancyPCT_given = 0 ;
83 <  args_info->vacancyRadius_given = 0 ;
82 >  args_info->vacancyPercent_given = 0 ;
83 >  args_info->vacancyInnerRadius_given = 0 ;
84 >  args_info->vacancyOuterRadius_given = 0 ;
85   }
86  
87   static
88   void clear_args (struct gengetopt_args_info *args_info)
89   {
90 +  FIX_UNUSED (args_info);
91    args_info->output_arg = NULL;
92 <  args_info->latticetype_arg = gengetopt_strdup ("fcc");
93 <  args_info->ShellRadius_arg = NULL;
92 >  args_info->output_orig = NULL;
93 >  args_info->latticeConstant_orig = NULL;
94 >  args_info->radius_orig = NULL;
95 >  args_info->shellRadius_arg = NULL;
96 >  args_info->shellRadius_orig = NULL;
97    args_info->molFraction_arg = NULL;
98 <  args_info->vacancyRadius_arg = NULL;
98 >  args_info->molFraction_orig = NULL;
99 >  args_info->vacancyPercent_orig = NULL;
100 >  args_info->vacancyInnerRadius_orig = NULL;
101 >  args_info->vacancyOuterRadius_orig = NULL;
102 >  
103   }
104  
105 + static
106 + void init_args_info(struct gengetopt_args_info *args_info)
107 + {
108 +
109 +
110 +  args_info->help_help = gengetopt_args_info_help[0] ;
111 +  args_info->version_help = gengetopt_args_info_help[1] ;
112 +  args_info->output_help = gengetopt_args_info_help[2] ;
113 +  args_info->latticeConstant_help = gengetopt_args_info_help[3] ;
114 +  args_info->radius_help = gengetopt_args_info_help[4] ;
115 +  args_info->shellRadius_help = gengetopt_args_info_help[5] ;
116 +  args_info->shellRadius_min = 0;
117 +  args_info->shellRadius_max = 0;
118 +  args_info->molFraction_help = gengetopt_args_info_help[6] ;
119 +  args_info->molFraction_min = 0;
120 +  args_info->molFraction_max = 0;
121 +  args_info->vacancyPercent_help = gengetopt_args_info_help[7] ;
122 +  args_info->vacancyInnerRadius_help = gengetopt_args_info_help[8] ;
123 +  args_info->vacancyOuterRadius_help = gengetopt_args_info_help[9] ;
124 +  
125 + }
126 +
127   void
128   cmdline_parser_print_version (void)
129   {
130 <  printf ("%s %s\n", CMDLINE_PARSER_PACKAGE, CMDLINE_PARSER_VERSION);
130 >  printf ("%s %s\n",
131 >     (strlen(CMDLINE_PARSER_PACKAGE_NAME) ? CMDLINE_PARSER_PACKAGE_NAME : CMDLINE_PARSER_PACKAGE),
132 >     CMDLINE_PARSER_VERSION);
133   }
134  
135 + static void print_help_common(void) {
136 +  cmdline_parser_print_version ();
137 +
138 +  if (strlen(gengetopt_args_info_purpose) > 0)
139 +    printf("\n%s\n", gengetopt_args_info_purpose);
140 +
141 +  if (strlen(gengetopt_args_info_usage) > 0)
142 +    printf("\n%s\n", gengetopt_args_info_usage);
143 +
144 +  printf("\n");
145 +
146 +  if (strlen(gengetopt_args_info_description) > 0)
147 +    printf("%s\n\n", gengetopt_args_info_description);
148 + }
149 +
150   void
151   cmdline_parser_print_help (void)
152   {
153 <  cmdline_parser_print_version ();
154 <  printf("\n%s\n", "Builds spherical random or core-shell nanoparticles and outputs a xyz input \nfile");
155 <  printf("\nUsage: nanoparticleBuilder [OPTIONS]... [FILES]...\n\n");
156 <  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 <  
153 >  int i = 0;
154 >  print_help_common();
155 >  while (gengetopt_args_info_help[i])
156 >    printf("%s\n", gengetopt_args_info_help[i++]);
157   }
158  
159   void
# Line 108 | Line 161 | cmdline_parser_init (struct gengetopt_args_info *args_
161   {
162    clear_given (args_info);
163    clear_args (args_info);
164 +  init_args_info (args_info);
165  
166 <  args_info->inputs = NULL;
166 >  args_info->inputs = 0;
167    args_info->inputs_num = 0;
168   }
169  
170   void
171 < cmdline_parser_free (struct gengetopt_args_info *args_info)
171 > cmdline_parser_params_init(struct cmdline_parser_params *params)
172   {
173 <  
174 <  unsigned int i;
175 <  if (args_info->output_arg)
176 <    {
177 <      free (args_info->output_arg); /* free previous argument */
178 <      args_info->output_arg = 0;
173 >  if (params)
174 >    {
175 >      params->override = 0;
176 >      params->initialize = 1;
177 >      params->check_required = 1;
178 >      params->check_ambiguity = 0;
179 >      params->print_errors = 1;
180      }
181 <  if (args_info->latticetype_arg)
181 > }
182 >
183 > struct cmdline_parser_params *
184 > cmdline_parser_params_create(void)
185 > {
186 >  struct cmdline_parser_params *params =
187 >    (struct cmdline_parser_params *)malloc(sizeof(struct cmdline_parser_params));
188 >  cmdline_parser_params_init(params);  
189 >  return params;
190 > }
191 >
192 > static void
193 > free_string_field (char **s)
194 > {
195 >  if (*s)
196      {
197 <      free (args_info->latticetype_arg); /* free previous argument */
198 <      args_info->latticetype_arg = 0;
197 >      free (*s);
198 >      *s = 0;
199      }
200 <  if (args_info->ShellRadius_arg)
201 <    {
202 <      free (args_info->ShellRadius_arg); /* free previous argument */
203 <      args_info->ShellRadius_arg = 0;
204 <    }
205 <  if (args_info->molFraction_arg)
206 <    {
207 <      free (args_info->molFraction_arg); /* free previous argument */
208 <      args_info->molFraction_arg = 0;
209 <    }
210 <  if (args_info->vacancyRadius_arg)
211 <    {
212 <      free (args_info->vacancyRadius_arg); /* free previous argument */
213 <      args_info->vacancyRadius_arg = 0;
214 <    }
200 > }
201 >
202 > /** @brief generic value variable */
203 > union generic_value {
204 >    double double_arg;
205 >    char *string_arg;
206 >    const char *default_string_arg;
207 > };
208 >
209 > /** @brief holds temporary values for multiple options */
210 > struct generic_list
211 > {
212 >  union generic_value arg;
213 >  char *orig;
214 >  struct generic_list *next;
215 > };
216 >
217 > /**
218 > * @brief add a node at the head of the list
219 > */
220 > static void add_node(struct generic_list **list) {
221 >  struct generic_list *new_node = (struct generic_list *) malloc (sizeof (struct generic_list));
222 >  new_node->next = *list;
223 >  *list = new_node;
224 >  new_node->arg.string_arg = 0;
225 >  new_node->orig = 0;
226 > }
227 >
228 > /**
229 > * The passed arg parameter is NOT set to 0 from this function
230 > */
231 > static void
232 > free_multiple_field(unsigned int len, void *arg, char ***orig)
233 > {
234 >  unsigned int i;
235 >  if (arg) {
236 >    for (i = 0; i < len; ++i)
237 >      {
238 >        free_string_field(&((*orig)[i]));
239 >      }
240 >
241 >    free (arg);
242 >    free (*orig);
243 >    *orig = 0;
244 >  }
245 > }
246 >
247 >
248 > static void
249 > cmdline_parser_release (struct gengetopt_args_info *args_info)
250 > {
251 >  unsigned int i;
252 >  free_string_field (&(args_info->output_arg));
253 >  free_string_field (&(args_info->output_orig));
254 >  free_string_field (&(args_info->latticeConstant_orig));
255 >  free_string_field (&(args_info->radius_orig));
256 >  free_multiple_field (args_info->shellRadius_given, (void *)(args_info->shellRadius_arg), &(args_info->shellRadius_orig));
257 >  args_info->shellRadius_arg = 0;
258 >  free_multiple_field (args_info->molFraction_given, (void *)(args_info->molFraction_arg), &(args_info->molFraction_orig));
259 >  args_info->molFraction_arg = 0;
260 >  free_string_field (&(args_info->vacancyPercent_orig));
261 >  free_string_field (&(args_info->vacancyInnerRadius_orig));
262 >  free_string_field (&(args_info->vacancyOuterRadius_orig));
263    
264 +  
265    for (i = 0; i < args_info->inputs_num; ++i)
266      free (args_info->inputs [i]);
267 <  
267 >
268    if (args_info->inputs_num)
269      free (args_info->inputs);
270 <  
270 >
271    clear_given (args_info);
272   }
273  
274 < /* gengetopt_strdup() */
275 < /* strdup.c replacement of strdup, which is not standard */
274 >
275 > static void
276 > write_into_file(FILE *outfile, const char *opt, const char *arg, const char *values[])
277 > {
278 >  FIX_UNUSED (values);
279 >  if (arg) {
280 >    fprintf(outfile, "%s=\"%s\"\n", opt, arg);
281 >  } else {
282 >    fprintf(outfile, "%s\n", opt);
283 >  }
284 > }
285 >
286 > static void
287 > write_multiple_into_file(FILE *outfile, int len, const char *opt, char **arg, const char *values[])
288 > {
289 >  int i;
290 >  
291 >  for (i = 0; i < len; ++i)
292 >    write_into_file(outfile, opt, (arg ? arg[i] : 0), values);
293 > }
294 >
295 > int
296 > cmdline_parser_dump(FILE *outfile, struct gengetopt_args_info *args_info)
297 > {
298 >  int i = 0;
299 >
300 >  if (!outfile)
301 >    {
302 >      fprintf (stderr, "%s: cannot dump options to stream\n", CMDLINE_PARSER_PACKAGE);
303 >      return EXIT_FAILURE;
304 >    }
305 >
306 >  if (args_info->help_given)
307 >    write_into_file(outfile, "help", 0, 0 );
308 >  if (args_info->version_given)
309 >    write_into_file(outfile, "version", 0, 0 );
310 >  if (args_info->output_given)
311 >    write_into_file(outfile, "output", args_info->output_orig, 0);
312 >  if (args_info->latticeConstant_given)
313 >    write_into_file(outfile, "latticeConstant", args_info->latticeConstant_orig, 0);
314 >  if (args_info->radius_given)
315 >    write_into_file(outfile, "radius", args_info->radius_orig, 0);
316 >  write_multiple_into_file(outfile, args_info->shellRadius_given, "shellRadius", args_info->shellRadius_orig, 0);
317 >  write_multiple_into_file(outfile, args_info->molFraction_given, "molFraction", args_info->molFraction_orig, 0);
318 >  if (args_info->vacancyPercent_given)
319 >    write_into_file(outfile, "vacancyPercent", args_info->vacancyPercent_orig, 0);
320 >  if (args_info->vacancyInnerRadius_given)
321 >    write_into_file(outfile, "vacancyInnerRadius", args_info->vacancyInnerRadius_orig, 0);
322 >  if (args_info->vacancyOuterRadius_given)
323 >    write_into_file(outfile, "vacancyOuterRadius", args_info->vacancyOuterRadius_orig, 0);
324 >  
325 >
326 >  i = EXIT_SUCCESS;
327 >  return i;
328 > }
329 >
330 > int
331 > cmdline_parser_file_save(const char *filename, struct gengetopt_args_info *args_info)
332 > {
333 >  FILE *outfile;
334 >  int i = 0;
335 >
336 >  outfile = fopen(filename, "w");
337 >
338 >  if (!outfile)
339 >    {
340 >      fprintf (stderr, "%s: cannot open file for writing: %s\n", CMDLINE_PARSER_PACKAGE, filename);
341 >      return EXIT_FAILURE;
342 >    }
343 >
344 >  i = cmdline_parser_dump(outfile, args_info);
345 >  fclose (outfile);
346 >
347 >  return i;
348 > }
349 >
350 > void
351 > cmdline_parser_free (struct gengetopt_args_info *args_info)
352 > {
353 >  cmdline_parser_release (args_info);
354 > }
355 >
356 > /** @brief replacement of strdup, which is not standard */
357   char *
358   gengetopt_strdup (const char *s)
359   {
360 <  char *result = NULL;
360 >  char *result = 0;
361    if (!s)
362      return result;
363  
# Line 172 | Line 371 | get_multiple_arg_token(const char *arg)
371   static char *
372   get_multiple_arg_token(const char *arg)
373   {
374 <  char *tok, *ret;
375 <  size_t len;
374 >  const char *tok;
375 >  char *ret;
376 >  size_t len, num_of_escape, i, j;
377  
378    if (!arg)
379 <    return NULL;
379 >    return 0;
380  
381    tok = strchr (arg, ',');
382 +  num_of_escape = 0;
383  
384 +  /* make sure it is not escaped */
385 +  while (tok)
386 +    {
387 +      if (*(tok-1) == '\\')
388 +        {
389 +          /* find the next one */
390 +          tok = strchr (tok+1, ',');
391 +          ++num_of_escape;
392 +        }
393 +      else
394 +        break;
395 +    }
396 +
397    if (tok)
398      len = (size_t)(tok - arg + 1);
399    else
400      len = strlen (arg) + 1;
401  
402 +  len -= num_of_escape;
403 +
404    ret = (char *) malloc (len);
405 <  strncpy (ret, arg, len-1);
405 >
406 >  i = 0;
407 >  j = 0;
408 >  while (arg[i] && (j < len-1))
409 >    {
410 >      if (arg[i] == '\\' &&
411 >          arg[ i + 1 ] &&
412 >          arg[ i + 1 ] == ',')
413 >        ++i;
414 >
415 >      ret[j++] = arg[i++];
416 >    }
417 >
418    ret[len-1] = '\0';
419  
420    return ret;
421   }
422  
423 < static char *
423 > static const char *
424   get_multiple_arg_token_next(const char *arg)
425   {
426 <  char *tok;
426 >  const char *tok;
427  
428    if (!arg)
429 <    return NULL;
429 >    return 0;
430  
431    tok = strchr (arg, ',');
432  
433 +  /* make sure it is not escaped */
434 +  while (tok)
435 +    {
436 +      if (*(tok-1) == '\\')
437 +        {
438 +          /* find the next one */
439 +          tok = strchr (tok+1, ',');
440 +        }
441 +      else
442 +        break;
443 +    }
444 +
445    if (! tok || strlen(tok) == 1)
446      return 0;
447  
448    return tok+1;
449   }
450  
451 + static int
452 + check_multiple_option_occurrences(const char *prog_name, unsigned int option_given, unsigned int min, unsigned int max, const char *option_desc);
453 +
454   int
455 < cmdline_parser (int argc, char * const *argv, struct gengetopt_args_info *args_info)
455 > check_multiple_option_occurrences(const char *prog_name, unsigned int option_given, unsigned int min, unsigned int max, const char *option_desc)
456   {
457 +  int error = 0;
458 +
459 +  if (option_given && (min > 0 || max > 0))
460 +    {
461 +      if (min > 0 && max > 0)
462 +        {
463 +          if (min == max)
464 +            {
465 +              /* specific occurrences */
466 +              if (option_given != (unsigned int) min)
467 +                {
468 +                  fprintf (stderr, "%s: %s option occurrences must be %d\n",
469 +                    prog_name, option_desc, min);
470 +                  error = 1;
471 +                }
472 +            }
473 +          else if (option_given < (unsigned int) min
474 +                || option_given > (unsigned int) max)
475 +            {
476 +              /* range occurrences */
477 +              fprintf (stderr, "%s: %s option occurrences must be between %d and %d\n",
478 +                prog_name, option_desc, min, max);
479 +              error = 1;
480 +            }
481 +        }
482 +      else if (min > 0)
483 +        {
484 +          /* at least check */
485 +          if (option_given < min)
486 +            {
487 +              fprintf (stderr, "%s: %s option occurrences must be at least %d\n",
488 +                prog_name, option_desc, min);
489 +              error = 1;
490 +            }
491 +        }
492 +      else if (max > 0)
493 +        {
494 +          /* at most check */
495 +          if (option_given > max)
496 +            {
497 +              fprintf (stderr, "%s: %s option occurrences must be at most %d\n",
498 +                prog_name, option_desc, max);
499 +              error = 1;
500 +            }
501 +        }
502 +    }
503 +    
504 +  return error;
505 + }
506 + int
507 + cmdline_parser (int argc, char **argv, struct gengetopt_args_info *args_info)
508 + {
509    return cmdline_parser2 (argc, argv, args_info, 0, 1, 1);
510   }
511  
512   int
513 < cmdline_parser2 (int argc, char * const *argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required)
513 > cmdline_parser_ext (int argc, char **argv, struct gengetopt_args_info *args_info,
514 >                   struct cmdline_parser_params *params)
515   {
516    int result;
517 +  result = cmdline_parser_internal (argc, argv, args_info, params, 0);
518  
519 <  result = cmdline_parser_internal (argc, argv, args_info, override, initialize, check_required, NULL);
519 >  if (result == EXIT_FAILURE)
520 >    {
521 >      cmdline_parser_free (args_info);
522 >      exit (EXIT_FAILURE);
523 >    }
524 >  
525 >  return result;
526 > }
527  
528 + int
529 + cmdline_parser2 (int argc, char **argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required)
530 + {
531 +  int result;
532 +  struct cmdline_parser_params params;
533 +  
534 +  params.override = override;
535 +  params.initialize = initialize;
536 +  params.check_required = check_required;
537 +  params.check_ambiguity = 0;
538 +  params.print_errors = 1;
539 +
540 +  result = cmdline_parser_internal (argc, argv, args_info, &params, 0);
541 +
542    if (result == EXIT_FAILURE)
543      {
544        cmdline_parser_free (args_info);
# Line 235 | Line 553 | cmdline_parser_required (struct gengetopt_args_info *a
553   {
554    int result = EXIT_SUCCESS;
555  
556 <  if (cmdline_parser_required2(args_info, prog_name, NULL) > 0)
556 >  if (cmdline_parser_required2(args_info, prog_name, 0) > 0)
557      result = EXIT_FAILURE;
558  
559    if (result == EXIT_FAILURE)
# Line 251 | Line 569 | cmdline_parser_required2 (struct gengetopt_args_info *
569   cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error)
570   {
571    int error = 0;
572 +  FIX_UNUSED (additional_error);
573  
574 <  if (! args_info->latticeCnst_given)
574 >  /* checks for required options */
575 >  if (! args_info->output_given)
576      {
577 <      fprintf (stderr, "%s: '--latticeCnst' option required%s\n", prog_name, (additional_error ? additional_error : ""));
577 >      fprintf (stderr, "%s: '--output' ('-o') option required%s\n", prog_name, (additional_error ? additional_error : ""));
578        error = 1;
579      }
580 +  
581 +  if (! args_info->latticeConstant_given)
582 +    {
583 +      fprintf (stderr, "%s: '--latticeConstant' option required%s\n", prog_name, (additional_error ? additional_error : ""));
584 +      error = 1;
585 +    }
586 +  
587    if (! args_info->radius_given)
588      {
589        fprintf (stderr, "%s: '--radius' option required%s\n", prog_name, (additional_error ? additional_error : ""));
590        error = 1;
591      }
592 +  
593 +  if (check_multiple_option_occurrences(prog_name, args_info->shellRadius_given, args_info->shellRadius_min, args_info->shellRadius_max, "'--shellRadius'"))
594 +     error = 1;
595 +  
596 +  if (check_multiple_option_occurrences(prog_name, args_info->molFraction_given, args_info->molFraction_min, args_info->molFraction_max, "'--molFraction'"))
597 +     error = 1;
598 +  
599 +  
600 +  /* checks for dependences among options */
601  
602    return error;
603   }
604  
605 < int
606 < 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)
605 >
606 > static char *package_name = 0;
607 >
608 > /**
609 > * @brief updates an option
610 > * @param field the generic pointer to the field to update
611 > * @param orig_field the pointer to the orig field
612 > * @param field_given the pointer to the number of occurrence of this option
613 > * @param prev_given the pointer to the number of occurrence already seen
614 > * @param value the argument for this option (if null no arg was specified)
615 > * @param possible_values the possible values for this option (if specified)
616 > * @param default_value the default value (in case the option only accepts fixed values)
617 > * @param arg_type the type of this option
618 > * @param check_ambiguity @see cmdline_parser_params.check_ambiguity
619 > * @param override @see cmdline_parser_params.override
620 > * @param no_free whether to free a possible previous value
621 > * @param multiple_option whether this is a multiple option
622 > * @param long_opt the corresponding long option
623 > * @param short_opt the corresponding short option (or '-' if none)
624 > * @param additional_error possible further error specification
625 > */
626 > static
627 > int update_arg(void *field, char **orig_field,
628 >               unsigned int *field_given, unsigned int *prev_given,
629 >               char *value, const char *possible_values[],
630 >               const char *default_value,
631 >               cmdline_parser_arg_type arg_type,
632 >               int check_ambiguity, int override,
633 >               int no_free, int multiple_option,
634 >               const char *long_opt, char short_opt,
635 >               const char *additional_error)
636   {
637 <  int c;        /* Character of the parsed option.  */
638 <  char *multi_token, *multi_next; /* for multiple options */
637 >  char *stop_char = 0;
638 >  const char *val = value;
639 >  int found;
640 >  char **string_field;
641 >  FIX_UNUSED (field);
642  
643 <  int i;        /* Counter */
643 >  stop_char = 0;
644 >  found = 0;
645  
646 <  struct ShellRadius_list * ShellRadius_list = NULL,* ShellRadius_new = NULL;
647 <  struct molFraction_list * molFraction_list = NULL,* molFraction_new = NULL;
648 <  struct vacancyRadius_list * vacancyRadius_list = NULL,* vacancyRadius_new = NULL;
646 >  if (!multiple_option && prev_given && (*prev_given || (check_ambiguity && *field_given)))
647 >    {
648 >      if (short_opt != '-')
649 >        fprintf (stderr, "%s: `--%s' (`-%c') option given more than once%s\n",
650 >               package_name, long_opt, short_opt,
651 >               (additional_error ? additional_error : ""));
652 >      else
653 >        fprintf (stderr, "%s: `--%s' option given more than once%s\n",
654 >               package_name, long_opt,
655 >               (additional_error ? additional_error : ""));
656 >      return 1; /* failure */
657 >    }
658 >
659 >  FIX_UNUSED (default_value);
660 >    
661 >  if (field_given && *field_given && ! override)
662 >    return 0;
663 >  if (prev_given)
664 >    (*prev_given)++;
665 >  if (field_given)
666 >    (*field_given)++;
667 >  if (possible_values)
668 >    val = possible_values[found];
669 >
670 >  switch(arg_type) {
671 >  case ARG_DOUBLE:
672 >    if (val) *((double *)field) = strtod (val, &stop_char);
673 >    break;
674 >  case ARG_STRING:
675 >    if (val) {
676 >      string_field = (char **)field;
677 >      if (!no_free && *string_field)
678 >        free (*string_field); /* free previous string */
679 >      *string_field = gengetopt_strdup (val);
680 >    }
681 >    break;
682 >  default:
683 >    break;
684 >  };
685 >
686 >  /* check numeric conversion */
687 >  switch(arg_type) {
688 >  case ARG_DOUBLE:
689 >    if (val && !(stop_char && *stop_char == '\0')) {
690 >      fprintf(stderr, "%s: invalid numeric value: %s\n", package_name, val);
691 >      return 1; /* failure */
692 >    }
693 >    break;
694 >  default:
695 >    ;
696 >  };
697 >
698 >  /* store the original value */
699 >  switch(arg_type) {
700 >  case ARG_NO:
701 >    break;
702 >  default:
703 >    if (value && orig_field) {
704 >      if (no_free) {
705 >        *orig_field = value;
706 >      } else {
707 >        if (*orig_field)
708 >          free (*orig_field); /* free previous string */
709 >        *orig_field = gengetopt_strdup (value);
710 >      }
711 >    }
712 >  };
713 >
714 >  return 0; /* OK */
715 > }
716 >
717 > /**
718 > * @brief store information about a multiple option in a temporary list
719 > * @param list where to (temporarily) store multiple options
720 > */
721 > static
722 > int update_multiple_arg_temp(struct generic_list **list,
723 >               unsigned int *prev_given, const char *val,
724 >               const char *possible_values[], const char *default_value,
725 >               cmdline_parser_arg_type arg_type,
726 >               const char *long_opt, char short_opt,
727 >               const char *additional_error)
728 > {
729 >  /* store single arguments */
730 >  char *multi_token;
731 >  const char *multi_next;
732 >
733 >  if (arg_type == ARG_NO) {
734 >    (*prev_given)++;
735 >    return 0; /* OK */
736 >  }
737 >
738 >  multi_token = get_multiple_arg_token(val);
739 >  multi_next = get_multiple_arg_token_next (val);
740 >
741 >  while (1)
742 >    {
743 >      add_node (list);
744 >      if (update_arg((void *)&((*list)->arg), &((*list)->orig), 0,
745 >          prev_given, multi_token, possible_values, default_value,
746 >          arg_type, 0, 1, 1, 1, long_opt, short_opt, additional_error)) {
747 >        if (multi_token) free(multi_token);
748 >        return 1; /* failure */
749 >      }
750 >
751 >      if (multi_next)
752 >        {
753 >          multi_token = get_multiple_arg_token(multi_next);
754 >          multi_next = get_multiple_arg_token_next (multi_next);
755 >        }
756 >      else
757 >        break;
758 >    }
759 >
760 >  return 0; /* OK */
761 > }
762 >
763 > /**
764 > * @brief free the passed list (including possible string argument)
765 > */
766 > static
767 > void free_list(struct generic_list *list, short string_arg)
768 > {
769 >  if (list) {
770 >    struct generic_list *tmp;
771 >    while (list)
772 >      {
773 >        tmp = list;
774 >        if (string_arg && list->arg.string_arg)
775 >          free (list->arg.string_arg);
776 >        if (list->orig)
777 >          free (list->orig);
778 >        list = list->next;
779 >        free (tmp);
780 >      }
781 >  }
782 > }
783 >
784 > /**
785 > * @brief updates a multiple option starting from the passed list
786 > */
787 > static
788 > void update_multiple_arg(void *field, char ***orig_field,
789 >               unsigned int field_given, unsigned int prev_given, union generic_value *default_value,
790 >               cmdline_parser_arg_type arg_type,
791 >               struct generic_list *list)
792 > {
793 >  int i;
794 >  struct generic_list *tmp;
795 >
796 >  if (prev_given && list) {
797 >    *orig_field = (char **) realloc (*orig_field, (field_given + prev_given) * sizeof (char *));
798 >
799 >    switch(arg_type) {
800 >    case ARG_DOUBLE:
801 >      *((double **)field) = (double *)realloc (*((double **)field), (field_given + prev_given) * sizeof (double)); break;
802 >    case ARG_STRING:
803 >      *((char ***)field) = (char **)realloc (*((char ***)field), (field_given + prev_given) * sizeof (char *)); break;
804 >    default:
805 >      break;
806 >    };
807 >    
808 >    for (i = (prev_given - 1); i >= 0; --i)
809 >      {
810 >        tmp = list;
811 >        
812 >        switch(arg_type) {
813 >        case ARG_DOUBLE:
814 >          (*((double **)field))[i + field_given] = tmp->arg.double_arg; break;
815 >        case ARG_STRING:
816 >          (*((char ***)field))[i + field_given] = tmp->arg.string_arg; break;
817 >        default:
818 >          break;
819 >        }        
820 >        (*orig_field) [i + field_given] = list->orig;
821 >        list = list->next;
822 >        free (tmp);
823 >      }
824 >  } else { /* set the default value */
825 >    if (default_value && ! field_given) {
826 >      switch(arg_type) {
827 >      case ARG_DOUBLE:
828 >        if (! *((double **)field)) {
829 >          *((double **)field) = (double *)malloc (sizeof (double));
830 >          (*((double **)field))[0] = default_value->double_arg;
831 >        }
832 >        break;
833 >      case ARG_STRING:
834 >        if (! *((char ***)field)) {
835 >          *((char ***)field) = (char **)malloc (sizeof (char *));
836 >          (*((char ***)field))[0] = gengetopt_strdup(default_value->string_arg);
837 >        }
838 >        break;
839 >      default: break;
840 >      }
841 >      if (!(*orig_field)) {
842 >        *orig_field = (char **) malloc (sizeof (char *));
843 >        (*orig_field)[0] = 0;
844 >      }
845 >    }
846 >  }
847 > }
848 >
849 > int
850 > cmdline_parser_internal (
851 >  int argc, char **argv, struct gengetopt_args_info *args_info,
852 >                        struct cmdline_parser_params *params, const char *additional_error)
853 > {
854 >  int c;        /* Character of the parsed option.  */
855 >
856 >  struct generic_list * shellRadius_list = NULL;
857 >  struct generic_list * molFraction_list = NULL;
858    int error = 0;
859    struct gengetopt_args_info local_args_info;
860 +  
861 +  int override;
862 +  int initialize;
863 +  int check_required;
864 +  int check_ambiguity;
865 +  
866 +  package_name = argv[0];
867 +  
868 +  override = params->override;
869 +  initialize = params->initialize;
870 +  check_required = params->check_required;
871 +  check_ambiguity = params->check_ambiguity;
872  
873    if (initialize)
874      cmdline_parser_init (args_info);
# Line 286 | Line 876 | cmdline_parser_internal (int argc, char * const *argv,
876    cmdline_parser_init (&local_args_info);
877  
878    optarg = 0;
879 <  optind = 1;
880 <  opterr = 1;
879 >  optind = 0;
880 >  opterr = params->print_errors;
881    optopt = '?';
882  
883    while (1)
884      {
885        int option_index = 0;
296      char *stop_char;
886  
887        static struct option long_options[] = {
888          { "help",       0, NULL, 'h' },
889          { "version",    0, NULL, 'V' },
890          { "output",     1, NULL, 'o' },
891 <        { "latticetype",        1, NULL, 0 },
303 <        { "latticeCnst",        1, NULL, 0 },
891 >        { "latticeConstant",    1, NULL, 0 },
892          { "radius",     1, NULL, 0 },
893 <        { "ShellRadius",        1, NULL, 0 },
893 >        { "shellRadius",        1, NULL, 0 },
894          { "molFraction",        1, NULL, 0 },
895 <        { "vacancyPCT", 1, NULL, 0 },
896 <        { "vacancyRadius",      1, NULL, 0 },
897 <        { NULL, 0, NULL, 0 }
895 >        { "vacancyPercent",     1, NULL, 0 },
896 >        { "vacancyInnerRadius", 1, NULL, 0 },
897 >        { "vacancyOuterRadius", 1, NULL, 0 },
898 >        { 0,  0, 0, 0 }
899        };
900  
312      stop_char = 0;
901        c = getopt_long (argc, argv, "hVo:", long_options, &option_index);
902  
903        if (c == -1) break;       /* Exit from `while (1)' loop.  */
# Line 318 | Line 906 | cmdline_parser_internal (int argc, char * const *argv,
906          {
907          case 'h':       /* Print help and exit.  */
908            cmdline_parser_print_help ();
909 +          cmdline_parser_free (&local_args_info);
910            exit (EXIT_SUCCESS);
911  
912          case 'V':       /* Print version and exit.  */
913            cmdline_parser_print_version ();
914 +          cmdline_parser_free (&local_args_info);
915            exit (EXIT_SUCCESS);
916  
917          case 'o':       /* Output file name.  */
918 <          if (local_args_info.output_given)
919 <            {
920 <              fprintf (stderr, "%s: `--output' (`-o') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
921 <              goto failure;
922 <            }
923 <          if (args_info->output_given && ! override)
924 <            continue;
925 <          local_args_info.output_given = 1;
926 <          args_info->output_given = 1;
927 <          if (args_info->output_arg)
338 <            free (args_info->output_arg); /* free previous string */
339 <          args_info->output_arg = gengetopt_strdup (optarg);
918 >        
919 >        
920 >          if (update_arg( (void *)&(args_info->output_arg),
921 >               &(args_info->output_orig), &(args_info->output_given),
922 >              &(local_args_info.output_given), optarg, 0, 0, ARG_STRING,
923 >              check_ambiguity, override, 0, 0,
924 >              "output", 'o',
925 >              additional_error))
926 >            goto failure;
927 >        
928            break;
929  
342
930          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          }
931            /* Lattice spacing in Angstroms for cubic lattice..  */
932 <          else if (strcmp (long_options[option_index].name, "latticeCnst") == 0)
932 >          if (strcmp (long_options[option_index].name, "latticeConstant") == 0)
933            {
934 <            if (local_args_info.latticeCnst_given)
935 <              {
936 <                fprintf (stderr, "%s: `--latticeCnst' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
937 <                goto failure;
938 <              }
939 <            if (args_info->latticeCnst_given && ! override)
940 <              continue;
941 <            local_args_info.latticeCnst_given = 1;
942 <            args_info->latticeCnst_given = 1;
943 <            args_info->latticeCnst_arg = strtod (optarg, NULL);
934 >          
935 >          
936 >            if (update_arg( (void *)&(args_info->latticeConstant_arg),
937 >                 &(args_info->latticeConstant_orig), &(args_info->latticeConstant_given),
938 >                &(local_args_info.latticeConstant_given), optarg, 0, 0, ARG_DOUBLE,
939 >                check_ambiguity, override, 0, 0,
940 >                "latticeConstant", '-',
941 >                additional_error))
942 >              goto failure;
943 >          
944            }
945            /* Nanoparticle radius in Angstroms.  */
946            else if (strcmp (long_options[option_index].name, "radius") == 0)
947            {
948 <            if (local_args_info.radius_given)
949 <              {
950 <                fprintf (stderr, "%s: `--radius' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
951 <                goto failure;
952 <              }
953 <            if (args_info->radius_given && ! override)
954 <              continue;
955 <            local_args_info.radius_given = 1;
956 <            args_info->radius_given = 1;
957 <            args_info->radius_arg = strtod (optarg, NULL);
948 >          
949 >          
950 >            if (update_arg( (void *)&(args_info->radius_arg),
951 >                 &(args_info->radius_orig), &(args_info->radius_given),
952 >                &(local_args_info.radius_given), optarg, 0, 0, ARG_DOUBLE,
953 >                check_ambiguity, override, 0, 0,
954 >                "radius", '-',
955 >                additional_error))
956 >              goto failure;
957 >          
958            }
959 <          /* 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..  */
960 <          else if (strcmp (long_options[option_index].name, "ShellRadius") == 0)
959 >          /* Radius containing within it only molecules of a specific component. Specified for each component > 1 in the template file..  */
960 >          else if (strcmp (long_options[option_index].name, "shellRadius") == 0)
961            {
391            local_args_info.ShellRadius_given++;
962            
963 <            multi_token = get_multiple_arg_token(optarg);
964 <            multi_next = get_multiple_arg_token_next (optarg);
963 >            if (update_multiple_arg_temp(&shellRadius_list,
964 >                &(local_args_info.shellRadius_given), optarg, 0, 0, ARG_DOUBLE,
965 >                "shellRadius", '-',
966 >                additional_error))
967 >              goto failure;
968            
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;
969            }
970 <          /* (Default) Builds a multi-component random mixed nanoparticle. Mole Fraction must be specified for each componet > 1 in MD file..  */
970 >          /* Builds a multi-component random alloy nanoparticle. A mole Fraction must be specified for each component > 1 in the template file..  */
971            else if (strcmp (long_options[option_index].name, "molFraction") == 0)
972            {
418            local_args_info.molFraction_given++;
973            
974 <            multi_token = get_multiple_arg_token(optarg);
975 <            multi_next = get_multiple_arg_token_next (optarg);
974 >            if (update_multiple_arg_temp(&molFraction_list,
975 >                &(local_args_info.molFraction_given), optarg, 0, 0, ARG_DOUBLE,
976 >                "molFraction", '-',
977 >                additional_error))
978 >              goto failure;
979            
980 <            while (1)
981 <              {
982 <                molFraction_new = (struct molFraction_list *) malloc (sizeof (struct molFraction_list));
983 <                molFraction_new->next = molFraction_list;
427 <                molFraction_list = molFraction_new;
428 <                molFraction_new->molFraction_arg = strtod (multi_token, NULL);
429 <                free (multi_token);
980 >          }
981 >          /* Percentage of atoms to remove from within vacancy range.  */
982 >          else if (strcmp (long_options[option_index].name, "vacancyPercent") == 0)
983 >          {
984            
985 <                if (multi_next)
986 <                  {
987 <                    multi_token = get_multiple_arg_token(multi_next);
988 <                    multi_next = get_multiple_arg_token_next (multi_next);
989 <                    local_args_info.molFraction_given++;
990 <                  }
991 <                else
992 <                  break;
993 <              }
440 <            break;
985 >          
986 >            if (update_arg( (void *)&(args_info->vacancyPercent_arg),
987 >                 &(args_info->vacancyPercent_orig), &(args_info->vacancyPercent_given),
988 >                &(local_args_info.vacancyPercent_given), optarg, 0, 0, ARG_DOUBLE,
989 >                check_ambiguity, override, 0, 0,
990 >                "vacancyPercent", '-',
991 >                additional_error))
992 >              goto failure;
993 >          
994            }
995 <          /* Percentage of vacancies to build.  */
996 <          else if (strcmp (long_options[option_index].name, "vacancyPCT") == 0)
995 >          /* Radius arround core-shell where vacancies should be located..  */
996 >          else if (strcmp (long_options[option_index].name, "vacancyInnerRadius") == 0)
997            {
998 <            if (local_args_info.vacancyPCT_given)
999 <              {
1000 <                fprintf (stderr, "%s: `--vacancyPCT' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1001 <                goto failure;
1002 <              }
1003 <            if (args_info->vacancyPCT_given && ! override)
1004 <              continue;
1005 <            local_args_info.vacancyPCT_given = 1;
1006 <            args_info->vacancyPCT_given = 1;
1007 <            args_info->vacancyPCT_arg = strtod (optarg, NULL);
998 >          
999 >          
1000 >            if (update_arg( (void *)&(args_info->vacancyInnerRadius_arg),
1001 >                 &(args_info->vacancyInnerRadius_orig), &(args_info->vacancyInnerRadius_given),
1002 >                &(local_args_info.vacancyInnerRadius_given), optarg, 0, 0, ARG_DOUBLE,
1003 >                check_ambiguity, override, 0, 0,
1004 >                "vacancyInnerRadius", '-',
1005 >                additional_error))
1006 >              goto failure;
1007 >          
1008            }
1009            /* Radius arround core-shell where vacancies should be located..  */
1010 <          else if (strcmp (long_options[option_index].name, "vacancyRadius") == 0)
1010 >          else if (strcmp (long_options[option_index].name, "vacancyOuterRadius") == 0)
1011            {
459            local_args_info.vacancyRadius_given++;
1012            
461            multi_token = get_multiple_arg_token(optarg);
462            multi_next = get_multiple_arg_token_next (optarg);
1013            
1014 <            while (1)
1015 <              {
1016 <                vacancyRadius_new = (struct vacancyRadius_list *) malloc (sizeof (struct vacancyRadius_list));
1017 <                vacancyRadius_new->next = vacancyRadius_list;
1018 <                vacancyRadius_list = vacancyRadius_new;
1019 <                vacancyRadius_new->vacancyRadius_arg = strtod (multi_token, NULL);
1020 <                free (multi_token);
1014 >            if (update_arg( (void *)&(args_info->vacancyOuterRadius_arg),
1015 >                 &(args_info->vacancyOuterRadius_orig), &(args_info->vacancyOuterRadius_given),
1016 >                &(local_args_info.vacancyOuterRadius_given), optarg, 0, 0, ARG_DOUBLE,
1017 >                check_ambiguity, override, 0, 0,
1018 >                "vacancyOuterRadius", '-',
1019 >                additional_error))
1020 >              goto failure;
1021            
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;
1022            }
1023            
1024            break;
# Line 493 | Line 1033 | cmdline_parser_internal (int argc, char * const *argv,
1033      } /* while */
1034  
1035  
1036 <  if (local_args_info.ShellRadius_given && ShellRadius_list)
1037 <    {
1038 <      struct ShellRadius_list *tmp;
1039 <      args_info->ShellRadius_arg = (double *) realloc (args_info->ShellRadius_arg, (args_info->ShellRadius_given + local_args_info.ShellRadius_given) * sizeof (double));
1040 <      for (i = (local_args_info.ShellRadius_given - 1); i >= 0; --i)
1041 <        {
1042 <          tmp = ShellRadius_list;
1043 <          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 <  
1036 >  update_multiple_arg((void *)&(args_info->shellRadius_arg),
1037 >    &(args_info->shellRadius_orig), args_info->shellRadius_given,
1038 >    local_args_info.shellRadius_given, 0,
1039 >    ARG_DOUBLE, shellRadius_list);
1040 >  update_multiple_arg((void *)&(args_info->molFraction_arg),
1041 >    &(args_info->molFraction_orig), args_info->molFraction_given,
1042 >    local_args_info.molFraction_given, 0,
1043 >    ARG_DOUBLE, molFraction_list);
1044  
1045 <  args_info->ShellRadius_given += local_args_info.ShellRadius_given;
1046 <  local_args_info.ShellRadius_given = 0;
1045 >  args_info->shellRadius_given += local_args_info.shellRadius_given;
1046 >  local_args_info.shellRadius_given = 0;
1047    args_info->molFraction_given += local_args_info.molFraction_given;
1048    local_args_info.molFraction_given = 0;
540  args_info->vacancyRadius_given += local_args_info.vacancyRadius_given;
541  local_args_info.vacancyRadius_given = 0;
1049    
1050    if (check_required)
1051      {
1052        error += cmdline_parser_required2 (args_info, argv[0], additional_error);
1053      }
1054  
1055 <  cmdline_parser_free (&local_args_info);
1055 >  cmdline_parser_release (&local_args_info);
1056  
1057    if ( error )
1058      return (EXIT_FAILURE);
# Line 553 | Line 1060 | cmdline_parser_internal (int argc, char * const *argv,
1060    if (optind < argc)
1061      {
1062        int i = 0 ;
1063 +      int found_prog_name = 0;
1064 +      /* whether program name, i.e., argv[0], is in the remaining args
1065 +         (this may happen with some implementations of getopt,
1066 +          but surely not with the one included by gengetopt) */
1067  
1068 <      args_info->inputs_num = argc - optind ;
1068 >      i = optind;
1069 >      while (i < argc)
1070 >        if (argv[i++] == argv[0]) {
1071 >          found_prog_name = 1;
1072 >          break;
1073 >        }
1074 >      i = 0;
1075 >
1076 >      args_info->inputs_num = argc - optind - found_prog_name;
1077        args_info->inputs =
1078          (char **)(malloc ((args_info->inputs_num)*sizeof(char *))) ;
1079        while (optind < argc)
1080 <        args_info->inputs[ i++ ] = gengetopt_strdup (argv[optind++]) ;
1080 >        if (argv[optind++] != argv[0])
1081 >          args_info->inputs[ i++ ] = gengetopt_strdup (argv[optind-1]) ;
1082      }
1083  
1084    return 0;
1085  
1086   failure:
1087 <  if (ShellRadius_list)
1088 <    {
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 <    }
1087 >  free_list (shellRadius_list, 0 );
1088 >  free_list (molFraction_list, 0 );
1089    
1090 <  cmdline_parser_free (&local_args_info);
1090 >  cmdline_parser_release (&local_args_info);
1091    return (EXIT_FAILURE);
1092   }

Comparing:
trunk/src/applications/nanoparticleBuilder/nanoparticleBuilderCmd.c (property svn:keywords), Revision 653 by chuckv, Tue Oct 11 21:57:22 2005 UTC vs.
trunk/src/applications/nanoparticleBuilder/nanoparticleBuilderCmd.cpp (property svn:keywords), Revision 1795 by gezelter, Fri Sep 7 18:13:55 2012 UTC

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