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root/group/trunk/OOPSE-4/src/applications/dump2Xyz/Dump2XYZCmd.c
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Comparing trunk/OOPSE-4/src/applications/dump2Xyz/Dump2XYZCmd.c (file contents):
Revision 2204 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
Revision 3115 by chuckv, Tue Jan 16 22:17:27 2007 UTC

# Line 1 | Line 1
1   /*
2 <  File autogenerated by gengetopt version 2.11
2 >  File autogenerated by gengetopt version 2.15
3    generated with the following command:
4 <  /home/maul/gezelter/tim/bin/gengetopt -F Dump2XYZCmd
4 >  gengetopt -i Dump2XYZ.ggo -F Dump2XYZCmd
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 –
12 – #include <stdio.h>
13 – #include <stdlib.h>
14 – #include <string.h>
15 –
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 "Dump2XYZCmd.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 + static char *
36 + gengetopt_strdup (const char *s);
37 +
38 + static
39 + void clear_given (struct gengetopt_args_info *args_info)
40 + {
41 +  args_info->help_given = 0 ;
42 +  args_info->version_given = 0 ;
43 +  args_info->input_given = 0 ;
44 +  args_info->output_given = 0 ;
45 +  args_info->frame_given = 0 ;
46 +  args_info->water_given = 0 ;
47 +  args_info->periodicBox_given = 0 ;
48 +  args_info->zconstraint_given = 0 ;
49 +  args_info->rigidbody_given = 0 ;
50 +  args_info->watertype_given = 0 ;
51 +  args_info->selection_given = 0 ;
52 +  args_info->originsele_given = 0 ;
53 +  args_info->refsele_given = 0 ;
54 +  args_info->repeatX_given = 0 ;
55 +  args_info->repeatY_given = 0 ;
56 +  args_info->repeatZ_given = 0 ;
57 +  args_info->gb_given = 0 ;
58 +  args_info->basetype_given = 0 ;
59 +  args_info->printPosOnly_given = 0 ;
60 + }
61 +
62 + static
63 + void clear_args (struct gengetopt_args_info *args_info)
64 + {
65 +  args_info->input_arg = NULL;
66 +  args_info->input_orig = NULL;
67 +  args_info->output_arg = NULL;
68 +  args_info->output_orig = NULL;
69 +  args_info->frame_arg = 1;
70 +  args_info->frame_orig = NULL;
71 +  args_info->water_flag = 0;
72 +  args_info->periodicBox_flag = 0;
73 +  args_info->zconstraint_flag = 0;
74 +  args_info->rigidbody_flag = 0;
75 +  args_info->watertype_flag = 1;
76 +  args_info->selection_arg = NULL;
77 +  args_info->selection_orig = NULL;
78 +  args_info->originsele_arg = NULL;
79 +  args_info->originsele_orig = NULL;
80 +  args_info->refsele_arg = NULL;
81 +  args_info->refsele_orig = NULL;
82 +  args_info->repeatX_arg = 0;
83 +  args_info->repeatX_orig = NULL;
84 +  args_info->repeatY_arg = 0;
85 +  args_info->repeatY_orig = NULL;
86 +  args_info->repeatZ_arg = 0;
87 +  args_info->repeatZ_orig = NULL;
88 +  args_info->gb_arg = NULL;
89 +  args_info->gb_orig = NULL;
90 +  args_info->basetype_flag = 0;
91 +  args_info->printPosOnly_flag = 0;
92 +  
93 + }
94 +
95   void
96   cmdline_parser_print_version (void)
97   {
# Line 32 | Line 102 | cmdline_parser_print_help (void)
102   cmdline_parser_print_help (void)
103   {
104    cmdline_parser_print_version ();
105 <  printf("\n"
106 <         "Usage: %s [OPTIONS]...\n", CMDLINE_PARSER_PACKAGE);
107 <  printf("\n");
108 <  printf("  -h, --help                         Print help and exit\n");
109 <  printf("  -V, --version                      Print version and exit\n");
110 <  printf("  -i, --input=filename               input dump file\n");
111 <  printf("  -o, --output=filename              output file name\n");
112 <  printf("  -n, --frame=INT                    print every n frame  (default=`1')\n");
113 <  printf("  -w, --water                        skip the the waters  (default=off)\n");
114 <  printf("  -m, --periodicBox                  map to the periodic box  (default=off)\n");
115 <  printf("  -z, --zconstraint                  replace the atom types of zconstraint \n                                       molecules  (default=off)\n");
116 <  printf("  -r, --rigidbody                    add a pseudo COM atom to rigidbody  \n                                       (default=off)\n");
117 <  printf("  -t, --watertype                    replace the atom type of water model  \n                                       (default=on)\n");
118 <  printf("  -s, --selection=selection script   general selection syntax\n");
119 <  printf("      --originsele=selection script  select origin\n");
120 <  printf("      --refsele=selection script     select reference\n");
121 <  printf("      --repeatX=INT                  The number of images to repeat in the x \n                                       direction  (default=`0')\n");
122 <  printf("      --repeatY=INT                  The number of images to repeat in the y \n                                       direction  (default=`0')\n");
123 <  printf("      --repeatZ=INT                  The number of images to repeat in the z \n                                       direction  (default=`0')\n");
105 >  printf("\nUsage: Dump2XYZ [OPTIONS]...\n\n");
106 >  printf("%s\n","  -h, --help                    Print help and exit");
107 >  printf("%s\n","  -V, --version                 Print version and exit");
108 >  printf("%s\n","  -i, --input=filename          input dump file");
109 >  printf("%s\n","  -o, --output=filename         output file name");
110 >  printf("%s\n","  -n, --frame=INT               print every n frame  (default=`1')");
111 >  printf("%s\n","  -w, --water                   skip the the waters  (default=off)");
112 >  printf("%s\n","  -m, --periodicBox             map to the periodic box  (default=off)");
113 >  printf("%s\n","  -z, --zconstraint             replace the atom types of zconstraint molecules \n                                   (default=off)");
114 >  printf("%s\n","  -r, --rigidbody               add a pseudo COM atom to rigidbody  \n                                  (default=off)");
115 >  printf("%s\n","  -t, --watertype               replace the atom type of water model  \n                                  (default=on)");
116 >  printf("%s\n","  -s, --selection=selection script\n                                general selection syntax");
117 >  printf("%s\n","      --originsele=selection script\n                                select origin");
118 >  printf("%s\n","      --refsele=selection script\n                                select reference");
119 >  printf("%s\n","      --repeatX=INT             The number of images to repeat in the x \n                                  direction  (default=`0')");
120 >  printf("%s\n","      --repeatY=INT             The number of images to repeat in the y \n                                  direction  (default=`0')");
121 >  printf("%s\n","      --repeatZ=INT             The number of images to repeat in the z \n                                  direction  (default=`0')");
122 >  printf("%s\n","      --gb=atomtype             Replace the Gay-Berne atom with four linear \n                                  atoms");
123 >  printf("%s\n","  -b, --basetype                Convert to base atom type  (default=off)");
124 >  printf("%s\n","      --printPosOnly            Print only positions in xyz file  (default=off)");
125 >  
126   }
127  
128 + void
129 + cmdline_parser_init (struct gengetopt_args_info *args_info)
130 + {
131 +  clear_given (args_info);
132 +  clear_args (args_info);
133 + }
134  
135 < static char *gengetopt_strdup (const char *s);
135 > static void
136 > cmdline_parser_release (struct gengetopt_args_info *args_info)
137 > {
138 >  
139 >  if (args_info->input_arg)
140 >    {
141 >      free (args_info->input_arg); /* free previous argument */
142 >      args_info->input_arg = 0;
143 >    }
144 >  if (args_info->input_orig)
145 >    {
146 >      free (args_info->input_orig); /* free previous argument */
147 >      args_info->input_orig = 0;
148 >    }
149 >  if (args_info->output_arg)
150 >    {
151 >      free (args_info->output_arg); /* free previous argument */
152 >      args_info->output_arg = 0;
153 >    }
154 >  if (args_info->output_orig)
155 >    {
156 >      free (args_info->output_orig); /* free previous argument */
157 >      args_info->output_orig = 0;
158 >    }
159 >  if (args_info->frame_orig)
160 >    {
161 >      free (args_info->frame_orig); /* free previous argument */
162 >      args_info->frame_orig = 0;
163 >    }
164 >  if (args_info->selection_arg)
165 >    {
166 >      free (args_info->selection_arg); /* free previous argument */
167 >      args_info->selection_arg = 0;
168 >    }
169 >  if (args_info->selection_orig)
170 >    {
171 >      free (args_info->selection_orig); /* free previous argument */
172 >      args_info->selection_orig = 0;
173 >    }
174 >  if (args_info->originsele_arg)
175 >    {
176 >      free (args_info->originsele_arg); /* free previous argument */
177 >      args_info->originsele_arg = 0;
178 >    }
179 >  if (args_info->originsele_orig)
180 >    {
181 >      free (args_info->originsele_orig); /* free previous argument */
182 >      args_info->originsele_orig = 0;
183 >    }
184 >  if (args_info->refsele_arg)
185 >    {
186 >      free (args_info->refsele_arg); /* free previous argument */
187 >      args_info->refsele_arg = 0;
188 >    }
189 >  if (args_info->refsele_orig)
190 >    {
191 >      free (args_info->refsele_orig); /* free previous argument */
192 >      args_info->refsele_orig = 0;
193 >    }
194 >  if (args_info->repeatX_orig)
195 >    {
196 >      free (args_info->repeatX_orig); /* free previous argument */
197 >      args_info->repeatX_orig = 0;
198 >    }
199 >  if (args_info->repeatY_orig)
200 >    {
201 >      free (args_info->repeatY_orig); /* free previous argument */
202 >      args_info->repeatY_orig = 0;
203 >    }
204 >  if (args_info->repeatZ_orig)
205 >    {
206 >      free (args_info->repeatZ_orig); /* free previous argument */
207 >      args_info->repeatZ_orig = 0;
208 >    }
209 >  if (args_info->gb_arg)
210 >    {
211 >      free (args_info->gb_arg); /* free previous argument */
212 >      args_info->gb_arg = 0;
213 >    }
214 >  if (args_info->gb_orig)
215 >    {
216 >      free (args_info->gb_orig); /* free previous argument */
217 >      args_info->gb_orig = 0;
218 >    }
219 >  
220 >  clear_given (args_info);
221 > }
222  
223 + int
224 + cmdline_parser_file_save(const char *filename, struct gengetopt_args_info *args_info)
225 + {
226 +  FILE *outfile;
227 +  int i = 0;
228 +
229 +  outfile = fopen(filename, "w");
230 +
231 +  if (!outfile)
232 +    {
233 +      fprintf (stderr, "%s: cannot open file for writing: %s\n", CMDLINE_PARSER_PACKAGE, filename);
234 +      return EXIT_FAILURE;
235 +    }
236 +
237 +  if (args_info->help_given) {
238 +    fprintf(outfile, "%s\n", "help");
239 +  }
240 +  if (args_info->version_given) {
241 +    fprintf(outfile, "%s\n", "version");
242 +  }
243 +  if (args_info->input_given) {
244 +    if (args_info->input_orig) {
245 +      fprintf(outfile, "%s=\"%s\"\n", "input", args_info->input_orig);
246 +    } else {
247 +      fprintf(outfile, "%s\n", "input");
248 +    }
249 +  }
250 +  if (args_info->output_given) {
251 +    if (args_info->output_orig) {
252 +      fprintf(outfile, "%s=\"%s\"\n", "output", args_info->output_orig);
253 +    } else {
254 +      fprintf(outfile, "%s\n", "output");
255 +    }
256 +  }
257 +  if (args_info->frame_given) {
258 +    if (args_info->frame_orig) {
259 +      fprintf(outfile, "%s=\"%s\"\n", "frame", args_info->frame_orig);
260 +    } else {
261 +      fprintf(outfile, "%s\n", "frame");
262 +    }
263 +  }
264 +  if (args_info->water_given) {
265 +    fprintf(outfile, "%s\n", "water");
266 +  }
267 +  if (args_info->periodicBox_given) {
268 +    fprintf(outfile, "%s\n", "periodicBox");
269 +  }
270 +  if (args_info->zconstraint_given) {
271 +    fprintf(outfile, "%s\n", "zconstraint");
272 +  }
273 +  if (args_info->rigidbody_given) {
274 +    fprintf(outfile, "%s\n", "rigidbody");
275 +  }
276 +  if (args_info->watertype_given) {
277 +    fprintf(outfile, "%s\n", "watertype");
278 +  }
279 +  if (args_info->selection_given) {
280 +    if (args_info->selection_orig) {
281 +      fprintf(outfile, "%s=\"%s\"\n", "selection", args_info->selection_orig);
282 +    } else {
283 +      fprintf(outfile, "%s\n", "selection");
284 +    }
285 +  }
286 +  if (args_info->originsele_given) {
287 +    if (args_info->originsele_orig) {
288 +      fprintf(outfile, "%s=\"%s\"\n", "originsele", args_info->originsele_orig);
289 +    } else {
290 +      fprintf(outfile, "%s\n", "originsele");
291 +    }
292 +  }
293 +  if (args_info->refsele_given) {
294 +    if (args_info->refsele_orig) {
295 +      fprintf(outfile, "%s=\"%s\"\n", "refsele", args_info->refsele_orig);
296 +    } else {
297 +      fprintf(outfile, "%s\n", "refsele");
298 +    }
299 +  }
300 +  if (args_info->repeatX_given) {
301 +    if (args_info->repeatX_orig) {
302 +      fprintf(outfile, "%s=\"%s\"\n", "repeatX", args_info->repeatX_orig);
303 +    } else {
304 +      fprintf(outfile, "%s\n", "repeatX");
305 +    }
306 +  }
307 +  if (args_info->repeatY_given) {
308 +    if (args_info->repeatY_orig) {
309 +      fprintf(outfile, "%s=\"%s\"\n", "repeatY", args_info->repeatY_orig);
310 +    } else {
311 +      fprintf(outfile, "%s\n", "repeatY");
312 +    }
313 +  }
314 +  if (args_info->repeatZ_given) {
315 +    if (args_info->repeatZ_orig) {
316 +      fprintf(outfile, "%s=\"%s\"\n", "repeatZ", args_info->repeatZ_orig);
317 +    } else {
318 +      fprintf(outfile, "%s\n", "repeatZ");
319 +    }
320 +  }
321 +  if (args_info->gb_given) {
322 +    if (args_info->gb_orig) {
323 +      fprintf(outfile, "%s=\"%s\"\n", "gb", args_info->gb_orig);
324 +    } else {
325 +      fprintf(outfile, "%s\n", "gb");
326 +    }
327 +  }
328 +  if (args_info->basetype_given) {
329 +    fprintf(outfile, "%s\n", "basetype");
330 +  }
331 +  if (args_info->printPosOnly_given) {
332 +    fprintf(outfile, "%s\n", "printPosOnly");
333 +  }
334 +  
335 +  fclose (outfile);
336 +
337 +  i = EXIT_SUCCESS;
338 +  return i;
339 + }
340 +
341 + void
342 + cmdline_parser_free (struct gengetopt_args_info *args_info)
343 + {
344 +  cmdline_parser_release (args_info);
345 + }
346 +
347 +
348   /* gengetopt_strdup() */
349   /* strdup.c replacement of strdup, which is not standard */
350   char *
351   gengetopt_strdup (const char *s)
352   {
353 <  char *result = (char*)malloc(strlen(s) + 1);
353 >  char *result = NULL;
354 >  if (!s)
355 >    return result;
356 >
357 >  result = (char*)malloc(strlen(s) + 1);
358    if (result == (char*)0)
359      return (char*)0;
360    strcpy(result, s);
# Line 71 | Line 364 | cmdline_parser (int argc, char * const *argv, struct g
364   int
365   cmdline_parser (int argc, char * const *argv, struct gengetopt_args_info *args_info)
366   {
367 <  int c;        /* Character of the parsed option.  */
368 <  int missing_required_options = 0;
367 >  return cmdline_parser2 (argc, argv, args_info, 0, 1, 1);
368 > }
369  
370 <  args_info->help_given = 0 ;
371 <  args_info->version_given = 0 ;
372 <  args_info->input_given = 0 ;
373 <  args_info->output_given = 0 ;
81 <  args_info->frame_given = 0 ;
82 <  args_info->water_given = 0 ;
83 <  args_info->periodicBox_given = 0 ;
84 <  args_info->zconstraint_given = 0 ;
85 <  args_info->rigidbody_given = 0 ;
86 <  args_info->watertype_given = 0 ;
87 <  args_info->selection_given = 0 ;
88 <  args_info->originsele_given = 0 ;
89 <  args_info->refsele_given = 0 ;
90 <  args_info->repeatX_given = 0 ;
91 <  args_info->repeatY_given = 0 ;
92 <  args_info->repeatZ_given = 0 ;
93 < #define clear_args() {                          \
94 <    args_info->input_arg = NULL;                \
95 <    args_info->output_arg = NULL;               \
96 <    args_info->frame_arg = 1 ;                  \
97 <    args_info->water_flag = 0;                  \
98 <    args_info->periodicBox_flag = 0;            \
99 <    args_info->zconstraint_flag = 0;            \
100 <    args_info->rigidbody_flag = 0;              \
101 <    args_info->watertype_flag = 1;              \
102 <    args_info->selection_arg = NULL;            \
103 <    args_info->originsele_arg = NULL;           \
104 <    args_info->refsele_arg = NULL;              \
105 <    args_info->repeatX_arg = 0 ;                \
106 <    args_info->repeatY_arg = 0 ;                \
107 <    args_info->repeatZ_arg = 0 ;                \
108 <  }
370 > int
371 > cmdline_parser2 (int argc, char * const *argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required)
372 > {
373 >  int result;
374  
375 <  clear_args();
375 >  result = cmdline_parser_internal (argc, argv, args_info, override, initialize, check_required, NULL);
376  
377 +  if (result == EXIT_FAILURE)
378 +    {
379 +      cmdline_parser_free (args_info);
380 +      exit (EXIT_FAILURE);
381 +    }
382 +  
383 +  return result;
384 + }
385 +
386 + int
387 + cmdline_parser_required (struct gengetopt_args_info *args_info, const char *prog_name)
388 + {
389 +  int result = EXIT_SUCCESS;
390 +
391 +  if (cmdline_parser_required2(args_info, prog_name, NULL) > 0)
392 +    result = EXIT_FAILURE;
393 +
394 +  if (result == EXIT_FAILURE)
395 +    {
396 +      cmdline_parser_free (args_info);
397 +      exit (EXIT_FAILURE);
398 +    }
399 +  
400 +  return result;
401 + }
402 +
403 + int
404 + cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error)
405 + {
406 +  int error = 0;
407 +
408 +  if (! args_info->input_given)
409 +    {
410 +      fprintf (stderr, "%s: '--input' ('-i') option required%s\n", prog_name, (additional_error ? additional_error : ""));
411 +      error = 1;
412 +    }
413 +
414 +  return error;
415 + }
416 +
417 + int
418 + 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)
419 + {
420 +  int c;        /* Character of the parsed option.  */
421 +
422 +  int error = 0;
423 +  struct gengetopt_args_info local_args_info;
424 +
425 +  if (initialize)
426 +    cmdline_parser_init (args_info);
427 +
428 +  cmdline_parser_init (&local_args_info);
429 +
430    optarg = 0;
431    optind = 1;
432    opterr = 1;
# Line 136 | Line 454 | cmdline_parser (int argc, char * const *argv, struct g
454          { "repeatX",    1, NULL, 0 },
455          { "repeatY",    1, NULL, 0 },
456          { "repeatZ",    1, NULL, 0 },
457 +        { "gb", 1, NULL, 0 },
458 +        { "basetype",   0, NULL, 'b' },
459 +        { "printPosOnly",       0, NULL, 0 },
460          { NULL, 0, NULL, 0 }
461        };
462  
463        stop_char = 0;
464 <      c = getopt_long (argc, argv, "hVi:o:n:wmzrts:", long_options, &option_index);
464 >      c = getopt_long (argc, argv, "hVi:o:n:wmzrts:b", long_options, &option_index);
465  
466        if (c == -1) break;       /* Exit from `while (1)' loop.  */
467  
468        switch (c)
469          {
470          case 'h':       /* Print help and exit.  */
150 –          clear_args ();
471            cmdline_parser_print_help ();
472 +          cmdline_parser_free (&local_args_info);
473            exit (EXIT_SUCCESS);
474  
475          case 'V':       /* Print version and exit.  */
155 –          clear_args ();
476            cmdline_parser_print_version ();
477 +          cmdline_parser_free (&local_args_info);
478            exit (EXIT_SUCCESS);
479  
480          case 'i':       /* input dump file.  */
481 <          if (args_info->input_given)
481 >          if (local_args_info.input_given)
482              {
483 <              fprintf (stderr, "%s: `--input' (`-i') option given more than once\n", CMDLINE_PARSER_PACKAGE);
484 <              clear_args ();
164 <              exit (EXIT_FAILURE);
483 >              fprintf (stderr, "%s: `--input' (`-i') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
484 >              goto failure;
485              }
486 +          if (args_info->input_given && ! override)
487 +            continue;
488 +          local_args_info.input_given = 1;
489            args_info->input_given = 1;
490 +          if (args_info->input_arg)
491 +            free (args_info->input_arg); /* free previous string */
492            args_info->input_arg = gengetopt_strdup (optarg);
493 +          if (args_info->input_orig)
494 +            free (args_info->input_orig); /* free previous string */
495 +          args_info->input_orig = gengetopt_strdup (optarg);
496            break;
497  
498          case 'o':       /* output file name.  */
499 <          if (args_info->output_given)
499 >          if (local_args_info.output_given)
500              {
501 <              fprintf (stderr, "%s: `--output' (`-o') option given more than once\n", CMDLINE_PARSER_PACKAGE);
502 <              clear_args ();
175 <              exit (EXIT_FAILURE);
501 >              fprintf (stderr, "%s: `--output' (`-o') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
502 >              goto failure;
503              }
504 +          if (args_info->output_given && ! override)
505 +            continue;
506 +          local_args_info.output_given = 1;
507            args_info->output_given = 1;
508 +          if (args_info->output_arg)
509 +            free (args_info->output_arg); /* free previous string */
510            args_info->output_arg = gengetopt_strdup (optarg);
511 +          if (args_info->output_orig)
512 +            free (args_info->output_orig); /* free previous string */
513 +          args_info->output_orig = gengetopt_strdup (optarg);
514            break;
515  
516          case 'n':       /* print every n frame.  */
517 <          if (args_info->frame_given)
517 >          if (local_args_info.frame_given)
518              {
519 <              fprintf (stderr, "%s: `--frame' (`-n') option given more than once\n", CMDLINE_PARSER_PACKAGE);
520 <              clear_args ();
186 <              exit (EXIT_FAILURE);
519 >              fprintf (stderr, "%s: `--frame' (`-n') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
520 >              goto failure;
521              }
522 +          if (args_info->frame_given && ! override)
523 +            continue;
524 +          local_args_info.frame_given = 1;
525            args_info->frame_given = 1;
526 <          args_info->frame_arg = strtol (optarg,&stop_char,0);
526 >          args_info->frame_arg = strtol (optarg, &stop_char, 0);
527 >          if (!(stop_char && *stop_char == '\0')) {
528 >            fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
529 >            goto failure;
530 >          }
531 >          if (args_info->frame_orig)
532 >            free (args_info->frame_orig); /* free previous string */
533 >          args_info->frame_orig = gengetopt_strdup (optarg);
534            break;
535  
536          case 'w':       /* skip the the waters.  */
537 <          if (args_info->water_given)
537 >          if (local_args_info.water_given)
538              {
539 <              fprintf (stderr, "%s: `--water' (`-w') option given more than once\n", CMDLINE_PARSER_PACKAGE);
540 <              clear_args ();
197 <              exit (EXIT_FAILURE);
539 >              fprintf (stderr, "%s: `--water' (`-w') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
540 >              goto failure;
541              }
542 +          if (args_info->water_given && ! override)
543 +            continue;
544 +          local_args_info.water_given = 1;
545            args_info->water_given = 1;
546            args_info->water_flag = !(args_info->water_flag);
547            break;
548  
549          case 'm':       /* map to the periodic box.  */
550 <          if (args_info->periodicBox_given)
550 >          if (local_args_info.periodicBox_given)
551              {
552 <              fprintf (stderr, "%s: `--periodicBox' (`-m') option given more than once\n", CMDLINE_PARSER_PACKAGE);
553 <              clear_args ();
208 <              exit (EXIT_FAILURE);
552 >              fprintf (stderr, "%s: `--periodicBox' (`-m') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
553 >              goto failure;
554              }
555 +          if (args_info->periodicBox_given && ! override)
556 +            continue;
557 +          local_args_info.periodicBox_given = 1;
558            args_info->periodicBox_given = 1;
559            args_info->periodicBox_flag = !(args_info->periodicBox_flag);
560            break;
561  
562          case 'z':       /* replace the atom types of zconstraint molecules.  */
563 <          if (args_info->zconstraint_given)
563 >          if (local_args_info.zconstraint_given)
564              {
565 <              fprintf (stderr, "%s: `--zconstraint' (`-z') option given more than once\n", CMDLINE_PARSER_PACKAGE);
566 <              clear_args ();
219 <              exit (EXIT_FAILURE);
565 >              fprintf (stderr, "%s: `--zconstraint' (`-z') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
566 >              goto failure;
567              }
568 +          if (args_info->zconstraint_given && ! override)
569 +            continue;
570 +          local_args_info.zconstraint_given = 1;
571            args_info->zconstraint_given = 1;
572            args_info->zconstraint_flag = !(args_info->zconstraint_flag);
573            break;
574  
575          case 'r':       /* add a pseudo COM atom to rigidbody.  */
576 <          if (args_info->rigidbody_given)
576 >          if (local_args_info.rigidbody_given)
577              {
578 <              fprintf (stderr, "%s: `--rigidbody' (`-r') option given more than once\n", CMDLINE_PARSER_PACKAGE);
579 <              clear_args ();
230 <              exit (EXIT_FAILURE);
578 >              fprintf (stderr, "%s: `--rigidbody' (`-r') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
579 >              goto failure;
580              }
581 +          if (args_info->rigidbody_given && ! override)
582 +            continue;
583 +          local_args_info.rigidbody_given = 1;
584            args_info->rigidbody_given = 1;
585            args_info->rigidbody_flag = !(args_info->rigidbody_flag);
586            break;
587  
588          case 't':       /* replace the atom type of water model.  */
589 <          if (args_info->watertype_given)
589 >          if (local_args_info.watertype_given)
590              {
591 <              fprintf (stderr, "%s: `--watertype' (`-t') option given more than once\n", CMDLINE_PARSER_PACKAGE);
592 <              clear_args ();
241 <              exit (EXIT_FAILURE);
591 >              fprintf (stderr, "%s: `--watertype' (`-t') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
592 >              goto failure;
593              }
594 +          if (args_info->watertype_given && ! override)
595 +            continue;
596 +          local_args_info.watertype_given = 1;
597            args_info->watertype_given = 1;
598            args_info->watertype_flag = !(args_info->watertype_flag);
599            break;
600  
601          case 's':       /* general selection syntax.  */
602 <          if (args_info->selection_given)
602 >          if (local_args_info.selection_given)
603              {
604 <              fprintf (stderr, "%s: `--selection' (`-s') option given more than once\n", CMDLINE_PARSER_PACKAGE);
605 <              clear_args ();
252 <              exit (EXIT_FAILURE);
604 >              fprintf (stderr, "%s: `--selection' (`-s') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
605 >              goto failure;
606              }
607 +          if (args_info->selection_given && ! override)
608 +            continue;
609 +          local_args_info.selection_given = 1;
610            args_info->selection_given = 1;
611 +          if (args_info->selection_arg)
612 +            free (args_info->selection_arg); /* free previous string */
613            args_info->selection_arg = gengetopt_strdup (optarg);
614 +          if (args_info->selection_orig)
615 +            free (args_info->selection_orig); /* free previous string */
616 +          args_info->selection_orig = gengetopt_strdup (optarg);
617            break;
618  
619 +        case 'b':       /* Convert to base atom type.  */
620 +          if (local_args_info.basetype_given)
621 +            {
622 +              fprintf (stderr, "%s: `--basetype' (`-b') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
623 +              goto failure;
624 +            }
625 +          if (args_info->basetype_given && ! override)
626 +            continue;
627 +          local_args_info.basetype_given = 1;
628 +          args_info->basetype_given = 1;
629 +          args_info->basetype_flag = !(args_info->basetype_flag);
630 +          break;
631  
632 +
633          case 0: /* Long option with no short option */
634            /* select origin.  */
635            if (strcmp (long_options[option_index].name, "originsele") == 0)
636 <            {
637 <              if (args_info->originsele_given)
638 <                {
639 <                  fprintf (stderr, "%s: `--originsele' option given more than once\n", CMDLINE_PARSER_PACKAGE);
640 <                  clear_args ();
641 <                  exit (EXIT_FAILURE);
642 <                }
643 <              args_info->originsele_given = 1;
644 <              args_info->originsele_arg = gengetopt_strdup (optarg);
645 <              break;
646 <            }
647 <          
648 <          /* select reference.  */
649 <          else if (strcmp (long_options[option_index].name, "refsele") == 0)
650 <            {
651 <              if (args_info->refsele_given)
652 <                {
653 <                  fprintf (stderr, "%s: `--refsele' option given more than once\n", CMDLINE_PARSER_PACKAGE);
654 <                  clear_args ();
655 <                  exit (EXIT_FAILURE);
656 <                }
657 <              args_info->refsele_given = 1;
658 <              args_info->refsele_arg = gengetopt_strdup (optarg);
659 <              break;
660 <            }
661 <          
662 <          /* The number of images to repeat in the x direction.  */
663 <          else if (strcmp (long_options[option_index].name, "repeatX") == 0)
664 <            {
665 <              if (args_info->repeatX_given)
666 <                {
667 <                  fprintf (stderr, "%s: `--repeatX' option given more than once\n", CMDLINE_PARSER_PACKAGE);
668 <                  clear_args ();
669 <                  exit (EXIT_FAILURE);
670 <                }
671 <              args_info->repeatX_given = 1;
672 <              args_info->repeatX_arg = strtol (optarg,&stop_char,0);
673 <              break;
674 <            }
675 <          
636 >          {
637 >            if (local_args_info.originsele_given)
638 >              {
639 >                fprintf (stderr, "%s: `--originsele' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
640 >                goto failure;
641 >              }
642 >            if (args_info->originsele_given && ! override)
643 >              continue;
644 >            local_args_info.originsele_given = 1;
645 >            args_info->originsele_given = 1;
646 >            if (args_info->originsele_arg)
647 >              free (args_info->originsele_arg); /* free previous string */
648 >            args_info->originsele_arg = gengetopt_strdup (optarg);
649 >            if (args_info->originsele_orig)
650 >              free (args_info->originsele_orig); /* free previous string */
651 >            args_info->originsele_orig = gengetopt_strdup (optarg);
652 >          }
653 >          /* select reference.  */
654 >          else if (strcmp (long_options[option_index].name, "refsele") == 0)
655 >          {
656 >            if (local_args_info.refsele_given)
657 >              {
658 >                fprintf (stderr, "%s: `--refsele' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
659 >                goto failure;
660 >              }
661 >            if (args_info->refsele_given && ! override)
662 >              continue;
663 >            local_args_info.refsele_given = 1;
664 >            args_info->refsele_given = 1;
665 >            if (args_info->refsele_arg)
666 >              free (args_info->refsele_arg); /* free previous string */
667 >            args_info->refsele_arg = gengetopt_strdup (optarg);
668 >            if (args_info->refsele_orig)
669 >              free (args_info->refsele_orig); /* free previous string */
670 >            args_info->refsele_orig = gengetopt_strdup (optarg);
671 >          }
672 >          /* The number of images to repeat in the x direction.  */
673 >          else if (strcmp (long_options[option_index].name, "repeatX") == 0)
674 >          {
675 >            if (local_args_info.repeatX_given)
676 >              {
677 >                fprintf (stderr, "%s: `--repeatX' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
678 >                goto failure;
679 >              }
680 >            if (args_info->repeatX_given && ! override)
681 >              continue;
682 >            local_args_info.repeatX_given = 1;
683 >            args_info->repeatX_given = 1;
684 >            args_info->repeatX_arg = strtol (optarg, &stop_char, 0);
685 >            if (!(stop_char && *stop_char == '\0')) {
686 >              fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
687 >              goto failure;
688 >            }
689 >            if (args_info->repeatX_orig)
690 >              free (args_info->repeatX_orig); /* free previous string */
691 >            args_info->repeatX_orig = gengetopt_strdup (optarg);
692 >          }
693            /* The number of images to repeat in the y direction.  */
694            else if (strcmp (long_options[option_index].name, "repeatY") == 0)
695 <            {
696 <              if (args_info->repeatY_given)
697 <                {
698 <                  fprintf (stderr, "%s: `--repeatY' option given more than once\n", CMDLINE_PARSER_PACKAGE);
699 <                  clear_args ();
700 <                  exit (EXIT_FAILURE);
701 <                }
702 <              args_info->repeatY_given = 1;
703 <              args_info->repeatY_arg = strtol (optarg,&stop_char,0);
704 <              break;
705 <            }
706 <          
695 >          {
696 >            if (local_args_info.repeatY_given)
697 >              {
698 >                fprintf (stderr, "%s: `--repeatY' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
699 >                goto failure;
700 >              }
701 >            if (args_info->repeatY_given && ! override)
702 >              continue;
703 >            local_args_info.repeatY_given = 1;
704 >            args_info->repeatY_given = 1;
705 >            args_info->repeatY_arg = strtol (optarg, &stop_char, 0);
706 >            if (!(stop_char && *stop_char == '\0')) {
707 >              fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
708 >              goto failure;
709 >            }
710 >            if (args_info->repeatY_orig)
711 >              free (args_info->repeatY_orig); /* free previous string */
712 >            args_info->repeatY_orig = gengetopt_strdup (optarg);
713 >          }
714            /* The number of images to repeat in the z direction.  */
715            else if (strcmp (long_options[option_index].name, "repeatZ") == 0)
716 <            {
717 <              if (args_info->repeatZ_given)
718 <                {
719 <                  fprintf (stderr, "%s: `--repeatZ' option given more than once\n", CMDLINE_PARSER_PACKAGE);
720 <                  clear_args ();
721 <                  exit (EXIT_FAILURE);
722 <                }
723 <              args_info->repeatZ_given = 1;
724 <              args_info->repeatZ_arg = strtol (optarg,&stop_char,0);
725 <              break;
726 <            }
716 >          {
717 >            if (local_args_info.repeatZ_given)
718 >              {
719 >                fprintf (stderr, "%s: `--repeatZ' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
720 >                goto failure;
721 >              }
722 >            if (args_info->repeatZ_given && ! override)
723 >              continue;
724 >            local_args_info.repeatZ_given = 1;
725 >            args_info->repeatZ_given = 1;
726 >            args_info->repeatZ_arg = strtol (optarg, &stop_char, 0);
727 >            if (!(stop_char && *stop_char == '\0')) {
728 >              fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
729 >              goto failure;
730 >            }
731 >            if (args_info->repeatZ_orig)
732 >              free (args_info->repeatZ_orig); /* free previous string */
733 >            args_info->repeatZ_orig = gengetopt_strdup (optarg);
734 >          }
735 >          /* Replace the Gay-Berne atom with four linear atoms.  */
736 >          else if (strcmp (long_options[option_index].name, "gb") == 0)
737 >          {
738 >            if (local_args_info.gb_given)
739 >              {
740 >                fprintf (stderr, "%s: `--gb' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
741 >                goto failure;
742 >              }
743 >            if (args_info->gb_given && ! override)
744 >              continue;
745 >            local_args_info.gb_given = 1;
746 >            args_info->gb_given = 1;
747 >            if (args_info->gb_arg)
748 >              free (args_info->gb_arg); /* free previous string */
749 >            args_info->gb_arg = gengetopt_strdup (optarg);
750 >            if (args_info->gb_orig)
751 >              free (args_info->gb_orig); /* free previous string */
752 >            args_info->gb_orig = gengetopt_strdup (optarg);
753 >          }
754 >          /* Print only positions in xyz file.  */
755 >          else if (strcmp (long_options[option_index].name, "printPosOnly") == 0)
756 >          {
757 >            if (local_args_info.printPosOnly_given)
758 >              {
759 >                fprintf (stderr, "%s: `--printPosOnly' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
760 >                goto failure;
761 >              }
762 >            if (args_info->printPosOnly_given && ! override)
763 >              continue;
764 >            local_args_info.printPosOnly_given = 1;
765 >            args_info->printPosOnly_given = 1;
766 >            args_info->printPosOnly_flag = !(args_info->printPosOnly_flag);
767 >          }
768            
769 <
769 >          break;
770          case '?':       /* Invalid option.  */
771            /* `getopt_long' already printed an error message.  */
772 <          exit (EXIT_FAILURE);
772 >          goto failure;
773  
774          default:        /* bug: option not considered.  */
775 <          fprintf (stderr, "%s: option unknown: %c\n", CMDLINE_PARSER_PACKAGE, c);
775 >          fprintf (stderr, "%s: option unknown: %c%s\n", CMDLINE_PARSER_PACKAGE, c, (additional_error ? additional_error : ""));
776            abort ();
777          } /* switch */
778      } /* while */
779  
780  
781 <  if (! args_info->input_given)
781 >
782 >  if (check_required)
783      {
784 <      fprintf (stderr, "%s: '--input' ('-i') option required\n", CMDLINE_PARSER_PACKAGE);
345 <      missing_required_options = 1;
784 >      error += cmdline_parser_required2 (args_info, argv[0], additional_error);
785      }
347 –  if ( missing_required_options )
348 –    exit (EXIT_FAILURE);
786  
787 +  cmdline_parser_release (&local_args_info);
788 +
789 +  if ( error )
790 +    return (EXIT_FAILURE);
791 +
792    return 0;
793 +
794 + failure:
795 +  
796 +  cmdline_parser_release (&local_args_info);
797 +  return (EXIT_FAILURE);
798   }

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