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root/OpenMD/trunk/src/applications/staticProps/StaticPropsCmd.cpp
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Comparing trunk/src/applications/staticProps/StaticPropsCmd.c (file contents):
Revision 310 by tim, Thu Feb 10 18:14:03 2005 UTC vs.
Revision 980 by xsun, Thu Jun 1 18:06:33 2006 UTC

# Line 1 | Line 1
1   /*
2 <  File autogenerated by gengetopt version 2.11
2 >  File autogenerated by gengetopt version 2.16
3    generated with the following command:
4 <  /home/maul/gezelter/tim/bin/gengetopt -F staticPropsCmd
4 >  gengetopt -F StaticPropsCmd
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 "staticPropsCmd.h"
22 > #include "StaticPropsCmd.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->step_given = 0 ;
46 +  args_info->nrbins_given = 0 ;
47 +  args_info->nbins_x_given = 0 ;
48 +  args_info->nbins_y_given = 0 ;
49 +  args_info->nanglebins_given = 0 ;
50 +  args_info->length_given = 0 ;
51 +  args_info->zoffset_given = 0 ;
52 +  args_info->sele1_given = 0 ;
53 +  args_info->sele2_given = 0 ;
54 +  args_info->sele3_given = 0 ;
55 +  args_info->refsele_given = 0 ;
56 +  args_info->molname_given = 0 ;
57 +  args_info->begin_given = 0 ;
58 +  args_info->end_given = 0 ;
59 +  args_info->gofr_given = 0 ;
60 +  args_info->r_theta_given = 0 ;
61 +  args_info->r_omega_given = 0 ;
62 +  args_info->theta_omega_given = 0 ;
63 +  args_info->gxyz_given = 0 ;
64 +  args_info->p2_given = 0 ;
65 +  args_info->rp2_given = 0 ;
66 +  args_info->scd_given = 0 ;
67 +  args_info->density_given = 0 ;
68 +  args_info->slab_density_given = 0 ;
69 +  args_info->hxy_given = 0 ;
70 +  args_info->staticProps_group_counter = 0 ;
71 + }
72 +
73 + static
74 + void clear_args (struct gengetopt_args_info *args_info)
75 + {
76 +  args_info->input_arg = NULL;
77 +  args_info->input_orig = NULL;
78 +  args_info->output_arg = NULL;
79 +  args_info->output_orig = NULL;
80 +  args_info->step_arg = 1;
81 +  args_info->step_orig = NULL;
82 +  args_info->nrbins_arg = 100;
83 +  args_info->nrbins_orig = NULL;
84 +  args_info->nbins_x_arg = 100;
85 +  args_info->nbins_x_orig = NULL;
86 +  args_info->nbins_y_arg = 100;
87 +  args_info->nbins_y_orig = NULL;
88 +  args_info->nanglebins_arg = 50;
89 +  args_info->nanglebins_orig = NULL;
90 +  args_info->length_orig = NULL;
91 +  args_info->zoffset_arg = 0;
92 +  args_info->zoffset_orig = NULL;
93 +  args_info->sele1_arg = NULL;
94 +  args_info->sele1_orig = NULL;
95 +  args_info->sele2_arg = NULL;
96 +  args_info->sele2_orig = NULL;
97 +  args_info->sele3_arg = NULL;
98 +  args_info->sele3_orig = NULL;
99 +  args_info->refsele_arg = NULL;
100 +  args_info->refsele_orig = NULL;
101 +  args_info->molname_arg = NULL;
102 +  args_info->molname_orig = NULL;
103 +  args_info->begin_orig = NULL;
104 +  args_info->end_orig = NULL;
105 +  
106 + }
107 +
108   void
109   cmdline_parser_print_version (void)
110   {
# Line 32 | Line 115 | cmdline_parser_print_help (void)
115   cmdline_parser_print_help (void)
116   {
117    cmdline_parser_print_version ();
118 <  printf("\n"
119 <  "Usage: %s [OPTIONS]...\n", CMDLINE_PARSER_PACKAGE);
120 <  printf("\n");
121 <  printf("  -h, --help                    Print help and exit\n");
122 <  printf("  -V, --version                 Print version and exit\n");
123 <  printf("  -i, --input=filename          input dump file\n");
124 <  printf("  -o, --output=filename         output file name\n");
125 <  printf("  -n, --frame=INT               print every n frame  (default=`1')\n");
126 <  printf("  -d, --ndistebins=INT          number of bins for distance  (default=`50')\n");
127 <  printf("  -a, --nanglebins=INT          number of bins for cos(angle)  (default=`50')\n");
128 <  printf("  -l, --length=DOUBLE           maximum length\n");
129 <  printf("      --sele1=selection script  select first stuntdouble set\n");
130 <  printf("      --sele2=selection script  select second stuntdouble set\n");
131 <  printf("\n");
132 <  printf(" Group: staticProps  an option of this group is required\n");
133 <  printf("      --gofr                    g(r)\n");
134 <  printf("      --r_theta                 g(r, cos(theta))\n");
135 <  printf("      --r_omega                 g(r, cos(omega))\n");
136 <  printf("      --theta_omega             g(cos(theta), cos(omega))\n");
137 <  printf("      --xyz                     g(x, y, z)\n");
118 >  printf("\nUsage: StaticProps [OPTIONS]...\n\n");
119 >  printf("%s\n","  -h, --help                    Print help and exit");
120 >  printf("%s\n","  -V, --version                 Print version and exit");
121 >  printf("%s\n","  -i, --input=filename          input dump file");
122 >  printf("%s\n","  -o, --output=filename         output file name");
123 >  printf("%s\n","  -n, --step=INT                process every n frame  (default=`1')");
124 >  printf("%s\n","  -r, --nrbins=INT              number of bins for distance  (default=`100')");
125 >  printf("%s\n","  -x, --nbins_x=INT             number of bins in x axis  (default=`100')");
126 >  printf("%s\n","  -y, --nbins_y=INT             number of bins in y axis  (default=`100')");
127 >  printf("%s\n","  -a, --nanglebins=INT          number of bins for cos(angle)  (default=`50')");
128 >  printf("%s\n","  -l, --length=DOUBLE           maximum length (Defaults to 1/2 smallest length \n                                  of first frame)");
129 >  printf("%s\n","  -z, --zoffset=DOUBLE          Where to set the zero for the slab_density \n                                  calculation  (default=`0')");
130 >  printf("%s\n","      --sele1=selection script  select the first stuntdouble set");
131 >  printf("%s\n","      --sele2=selection script  select the second stuntdouble set");
132 >  printf("%s\n","      --sele3=selection script  select the third stuntdouble set");
133 >  printf("%s\n","      --refsele=selection script\n                                select reference (use and only use with --gxyz)");
134 >  printf("%s\n","      --molname=STRING          molecule name");
135 >  printf("%s\n","      --begin=INT               begin interanl index");
136 >  printf("%s\n","      --end=INT                 end internal index");
137 >  printf("%s\n","\n Group: staticProps\n   an option of this group is required");
138 >  printf("%s\n","      --gofr                    g(r)");
139 >  printf("%s\n","      --r_theta                 g(r, cos(theta))");
140 >  printf("%s\n","      --r_omega                 g(r, cos(omega))");
141 >  printf("%s\n","      --theta_omega             g(cos(theta), cos(omega))");
142 >  printf("%s\n","      --gxyz                    g(x, y, z)");
143 >  printf("%s\n","      --p2                      p2 order parameter (--sele1 and --sele2 must be \n                                  specified)");
144 >  printf("%s\n","      --rp2                     rp2 order parameter (--sele1 and --sele2 must \n                                  be specified)");
145 >  printf("%s\n","      --scd                     scd order parameter(either --sele1, --sele2, \n                                  --sele3 are specified or --molname, --begin, \n                                  --end are specified)");
146 >  printf("%s\n","      --density                 density plot (--sele1 must be specified)");
147 >  printf("%s\n","      --slab_density            slab density (--sele1 must be specified)");
148 >  printf("%s\n","      --hxy                     hxy (--sele1 must be specified)");
149 >  
150   }
151  
152 + void
153 + cmdline_parser_init (struct gengetopt_args_info *args_info)
154 + {
155 +  clear_given (args_info);
156 +  clear_args (args_info);
157 + }
158  
159 < static char *gengetopt_strdup (const char *s);
159 > static void
160 > cmdline_parser_release (struct gengetopt_args_info *args_info)
161 > {
162 >  
163 >  if (args_info->input_arg)
164 >    {
165 >      free (args_info->input_arg); /* free previous argument */
166 >      args_info->input_arg = 0;
167 >    }
168 >  if (args_info->input_orig)
169 >    {
170 >      free (args_info->input_orig); /* free previous argument */
171 >      args_info->input_orig = 0;
172 >    }
173 >  if (args_info->output_arg)
174 >    {
175 >      free (args_info->output_arg); /* free previous argument */
176 >      args_info->output_arg = 0;
177 >    }
178 >  if (args_info->output_orig)
179 >    {
180 >      free (args_info->output_orig); /* free previous argument */
181 >      args_info->output_orig = 0;
182 >    }
183 >  if (args_info->step_orig)
184 >    {
185 >      free (args_info->step_orig); /* free previous argument */
186 >      args_info->step_orig = 0;
187 >    }
188 >  if (args_info->nrbins_orig)
189 >    {
190 >      free (args_info->nrbins_orig); /* free previous argument */
191 >      args_info->nrbins_orig = 0;
192 >    }
193 >  if (args_info->nbins_x_orig)
194 >    {
195 >      free (args_info->nbins_x_orig); /* free previous argument */
196 >      args_info->nbins_x_orig = 0;
197 >    }
198 >  if (args_info->nbins_y_orig)
199 >    {
200 >      free (args_info->nbins_y_orig); /* free previous argument */
201 >      args_info->nbins_y_orig = 0;
202 >    }
203 >  if (args_info->nanglebins_orig)
204 >    {
205 >      free (args_info->nanglebins_orig); /* free previous argument */
206 >      args_info->nanglebins_orig = 0;
207 >    }
208 >  if (args_info->length_orig)
209 >    {
210 >      free (args_info->length_orig); /* free previous argument */
211 >      args_info->length_orig = 0;
212 >    }
213 >  if (args_info->zoffset_orig)
214 >    {
215 >      free (args_info->zoffset_orig); /* free previous argument */
216 >      args_info->zoffset_orig = 0;
217 >    }
218 >  if (args_info->sele1_arg)
219 >    {
220 >      free (args_info->sele1_arg); /* free previous argument */
221 >      args_info->sele1_arg = 0;
222 >    }
223 >  if (args_info->sele1_orig)
224 >    {
225 >      free (args_info->sele1_orig); /* free previous argument */
226 >      args_info->sele1_orig = 0;
227 >    }
228 >  if (args_info->sele2_arg)
229 >    {
230 >      free (args_info->sele2_arg); /* free previous argument */
231 >      args_info->sele2_arg = 0;
232 >    }
233 >  if (args_info->sele2_orig)
234 >    {
235 >      free (args_info->sele2_orig); /* free previous argument */
236 >      args_info->sele2_orig = 0;
237 >    }
238 >  if (args_info->sele3_arg)
239 >    {
240 >      free (args_info->sele3_arg); /* free previous argument */
241 >      args_info->sele3_arg = 0;
242 >    }
243 >  if (args_info->sele3_orig)
244 >    {
245 >      free (args_info->sele3_orig); /* free previous argument */
246 >      args_info->sele3_orig = 0;
247 >    }
248 >  if (args_info->refsele_arg)
249 >    {
250 >      free (args_info->refsele_arg); /* free previous argument */
251 >      args_info->refsele_arg = 0;
252 >    }
253 >  if (args_info->refsele_orig)
254 >    {
255 >      free (args_info->refsele_orig); /* free previous argument */
256 >      args_info->refsele_orig = 0;
257 >    }
258 >  if (args_info->molname_arg)
259 >    {
260 >      free (args_info->molname_arg); /* free previous argument */
261 >      args_info->molname_arg = 0;
262 >    }
263 >  if (args_info->molname_orig)
264 >    {
265 >      free (args_info->molname_orig); /* free previous argument */
266 >      args_info->molname_orig = 0;
267 >    }
268 >  if (args_info->begin_orig)
269 >    {
270 >      free (args_info->begin_orig); /* free previous argument */
271 >      args_info->begin_orig = 0;
272 >    }
273 >  if (args_info->end_orig)
274 >    {
275 >      free (args_info->end_orig); /* free previous argument */
276 >      args_info->end_orig = 0;
277 >    }
278 >  
279 >  clear_given (args_info);
280 > }
281 >
282 > int
283 > cmdline_parser_file_save(const char *filename, struct gengetopt_args_info *args_info)
284 > {
285 >  FILE *outfile;
286 >  int i = 0;
287 >
288 >  outfile = fopen(filename, "w");
289 >
290 >  if (!outfile)
291 >    {
292 >      fprintf (stderr, "%s: cannot open file for writing: %s\n", CMDLINE_PARSER_PACKAGE, filename);
293 >      return EXIT_FAILURE;
294 >    }
295 >
296 >  if (args_info->help_given) {
297 >    fprintf(outfile, "%s\n", "help");
298 >  }
299 >  if (args_info->version_given) {
300 >    fprintf(outfile, "%s\n", "version");
301 >  }
302 >  if (args_info->input_given) {
303 >    if (args_info->input_orig) {
304 >      fprintf(outfile, "%s=\"%s\"\n", "input", args_info->input_orig);
305 >    } else {
306 >      fprintf(outfile, "%s\n", "input");
307 >    }
308 >  }
309 >  if (args_info->output_given) {
310 >    if (args_info->output_orig) {
311 >      fprintf(outfile, "%s=\"%s\"\n", "output", args_info->output_orig);
312 >    } else {
313 >      fprintf(outfile, "%s\n", "output");
314 >    }
315 >  }
316 >  if (args_info->step_given) {
317 >    if (args_info->step_orig) {
318 >      fprintf(outfile, "%s=\"%s\"\n", "step", args_info->step_orig);
319 >    } else {
320 >      fprintf(outfile, "%s\n", "step");
321 >    }
322 >  }
323 >  if (args_info->nrbins_given) {
324 >    if (args_info->nrbins_orig) {
325 >      fprintf(outfile, "%s=\"%s\"\n", "nrbins", args_info->nrbins_orig);
326 >    } else {
327 >      fprintf(outfile, "%s\n", "nrbins");
328 >    }
329 >  }
330 >  if (args_info->nbins_x_given) {
331 >    if (args_info->nbins_x_orig) {
332 >      fprintf(outfile, "%s=\"%s\"\n", "nbins_x", args_info->nbins_x_orig);
333 >    } else {
334 >      fprintf(outfile, "%s\n", "nbins_x");
335 >    }
336 >  }
337 >  if (args_info->nbins_y_given) {
338 >    if (args_info->nbins_y_orig) {
339 >      fprintf(outfile, "%s=\"%s\"\n", "nbins_y", args_info->nbins_y_orig);
340 >    } else {
341 >      fprintf(outfile, "%s\n", "nbins_y");
342 >    }
343 >  }
344 >  if (args_info->nanglebins_given) {
345 >    if (args_info->nanglebins_orig) {
346 >      fprintf(outfile, "%s=\"%s\"\n", "nanglebins", args_info->nanglebins_orig);
347 >    } else {
348 >      fprintf(outfile, "%s\n", "nanglebins");
349 >    }
350 >  }
351 >  if (args_info->length_given) {
352 >    if (args_info->length_orig) {
353 >      fprintf(outfile, "%s=\"%s\"\n", "length", args_info->length_orig);
354 >    } else {
355 >      fprintf(outfile, "%s\n", "length");
356 >    }
357 >  }
358 >  if (args_info->zoffset_given) {
359 >    if (args_info->zoffset_orig) {
360 >      fprintf(outfile, "%s=\"%s\"\n", "zoffset", args_info->zoffset_orig);
361 >    } else {
362 >      fprintf(outfile, "%s\n", "zoffset");
363 >    }
364 >  }
365 >  if (args_info->sele1_given) {
366 >    if (args_info->sele1_orig) {
367 >      fprintf(outfile, "%s=\"%s\"\n", "sele1", args_info->sele1_orig);
368 >    } else {
369 >      fprintf(outfile, "%s\n", "sele1");
370 >    }
371 >  }
372 >  if (args_info->sele2_given) {
373 >    if (args_info->sele2_orig) {
374 >      fprintf(outfile, "%s=\"%s\"\n", "sele2", args_info->sele2_orig);
375 >    } else {
376 >      fprintf(outfile, "%s\n", "sele2");
377 >    }
378 >  }
379 >  if (args_info->sele3_given) {
380 >    if (args_info->sele3_orig) {
381 >      fprintf(outfile, "%s=\"%s\"\n", "sele3", args_info->sele3_orig);
382 >    } else {
383 >      fprintf(outfile, "%s\n", "sele3");
384 >    }
385 >  }
386 >  if (args_info->refsele_given) {
387 >    if (args_info->refsele_orig) {
388 >      fprintf(outfile, "%s=\"%s\"\n", "refsele", args_info->refsele_orig);
389 >    } else {
390 >      fprintf(outfile, "%s\n", "refsele");
391 >    }
392 >  }
393 >  if (args_info->molname_given) {
394 >    if (args_info->molname_orig) {
395 >      fprintf(outfile, "%s=\"%s\"\n", "molname", args_info->molname_orig);
396 >    } else {
397 >      fprintf(outfile, "%s\n", "molname");
398 >    }
399 >  }
400 >  if (args_info->begin_given) {
401 >    if (args_info->begin_orig) {
402 >      fprintf(outfile, "%s=\"%s\"\n", "begin", args_info->begin_orig);
403 >    } else {
404 >      fprintf(outfile, "%s\n", "begin");
405 >    }
406 >  }
407 >  if (args_info->end_given) {
408 >    if (args_info->end_orig) {
409 >      fprintf(outfile, "%s=\"%s\"\n", "end", args_info->end_orig);
410 >    } else {
411 >      fprintf(outfile, "%s\n", "end");
412 >    }
413 >  }
414 >  if (args_info->gofr_given) {
415 >    fprintf(outfile, "%s\n", "gofr");
416 >  }
417 >  if (args_info->r_theta_given) {
418 >    fprintf(outfile, "%s\n", "r_theta");
419 >  }
420 >  if (args_info->r_omega_given) {
421 >    fprintf(outfile, "%s\n", "r_omega");
422 >  }
423 >  if (args_info->theta_omega_given) {
424 >    fprintf(outfile, "%s\n", "theta_omega");
425 >  }
426 >  if (args_info->gxyz_given) {
427 >    fprintf(outfile, "%s\n", "gxyz");
428 >  }
429 >  if (args_info->p2_given) {
430 >    fprintf(outfile, "%s\n", "p2");
431 >  }
432 >  if (args_info->rp2_given) {
433 >    fprintf(outfile, "%s\n", "rp2");
434 >  }
435 >  if (args_info->scd_given) {
436 >    fprintf(outfile, "%s\n", "scd");
437 >  }
438 >  if (args_info->density_given) {
439 >    fprintf(outfile, "%s\n", "density");
440 >  }
441 >  if (args_info->slab_density_given) {
442 >    fprintf(outfile, "%s\n", "slab_density");
443 >  }
444 >  if (args_info->hxy_given) {
445 >    fprintf(outfile, "%s\n", "hxy");
446 >  }
447 >  
448 >  fclose (outfile);
449  
450 +  i = EXIT_SUCCESS;
451 +  return i;
452 + }
453 +
454 + void
455 + cmdline_parser_free (struct gengetopt_args_info *args_info)
456 + {
457 +  cmdline_parser_release (args_info);
458 + }
459 +
460 +
461   /* gengetopt_strdup() */
462   /* strdup.c replacement of strdup, which is not standard */
463   char *
464   gengetopt_strdup (const char *s)
465   {
466 <  char *result = (char*)malloc(strlen(s) + 1);
466 >  char *result = NULL;
467 >  if (!s)
468 >    return result;
469 >
470 >  result = (char*)malloc(strlen(s) + 1);
471    if (result == (char*)0)
472      return (char*)0;
473    strcpy(result, s);
474    return result;
475   }
476  
477 < int
478 < cmdline_parser (int argc, char * const *argv, struct gengetopt_args_info *args_info)
477 > static void
478 > reset_group_staticProps(struct gengetopt_args_info *args_info);
479 >
480 > static void
481 > reset_group_staticProps(struct gengetopt_args_info *args_info)
482   {
483 <  int c;        /* Character of the parsed option.  */
484 <  int missing_required_options = 0;
77 <  int staticProps_group_counter = 0;
483 >  if (! args_info->staticProps_group_counter)
484 >    return;
485    
79 –
80 –  args_info->help_given = 0 ;
81 –  args_info->version_given = 0 ;
82 –  args_info->input_given = 0 ;
83 –  args_info->output_given = 0 ;
84 –  args_info->frame_given = 0 ;
85 –  args_info->ndistebins_given = 0 ;
86 –  args_info->nanglebins_given = 0 ;
87 –  args_info->length_given = 0 ;
88 –  args_info->sele1_given = 0 ;
89 –  args_info->sele2_given = 0 ;
486    args_info->gofr_given = 0 ;
487    args_info->r_theta_given = 0 ;
488    args_info->r_omega_given = 0 ;
489    args_info->theta_omega_given = 0 ;
490 <  args_info->xyz_given = 0 ;
491 < #define clear_args() { \
492 <  args_info->input_arg = NULL; \
493 <  args_info->output_arg = NULL; \
494 <  args_info->frame_arg = 1 ;\
495 <  args_info->ndistebins_arg = 50 ;\
496 <  args_info->nanglebins_arg = 50 ;\
497 <  args_info->sele1_arg = NULL; \
498 <  args_info->sele2_arg = NULL; \
490 >  args_info->gxyz_given = 0 ;
491 >  args_info->p2_given = 0 ;
492 >  args_info->rp2_given = 0 ;
493 >  args_info->scd_given = 0 ;
494 >  args_info->density_given = 0 ;
495 >  args_info->slab_density_given = 0 ;
496 >  args_info->hxy_given = 0 ;
497 >
498 >  args_info->staticProps_group_counter = 0;
499   }
500  
501 <  clear_args();
501 > int
502 > cmdline_parser (int argc, char * const *argv, struct gengetopt_args_info *args_info)
503 > {
504 >  return cmdline_parser2 (argc, argv, args_info, 0, 1, 1);
505 > }
506  
507 + int
508 + cmdline_parser2 (int argc, char * const *argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required)
509 + {
510 +  int result;
511 +
512 +  result = cmdline_parser_internal (argc, argv, args_info, override, initialize, check_required, NULL);
513 +
514 +  if (result == EXIT_FAILURE)
515 +    {
516 +      cmdline_parser_free (args_info);
517 +      exit (EXIT_FAILURE);
518 +    }
519 +  
520 +  return result;
521 + }
522 +
523 + int
524 + cmdline_parser_required (struct gengetopt_args_info *args_info, const char *prog_name)
525 + {
526 +  int result = EXIT_SUCCESS;
527 +
528 +  if (cmdline_parser_required2(args_info, prog_name, NULL) > 0)
529 +    result = EXIT_FAILURE;
530 +
531 +  if (result == EXIT_FAILURE)
532 +    {
533 +      cmdline_parser_free (args_info);
534 +      exit (EXIT_FAILURE);
535 +    }
536 +  
537 +  return result;
538 + }
539 +
540 + int
541 + cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error)
542 + {
543 +  int error = 0;
544 +
545 +  if (! args_info->input_given)
546 +    {
547 +      fprintf (stderr, "%s: '--input' ('-i') option required%s\n", prog_name, (additional_error ? additional_error : ""));
548 +      error = 1;
549 +    }
550 +  if (args_info->staticProps_group_counter == 0)
551 +    {
552 +      fprintf (stderr, "%s: %d options of group staticProps were given. One is required.%s\n", prog_name, args_info->staticProps_group_counter, (additional_error ? additional_error : ""));
553 +      error = 1;
554 +    }
555 +  
556 +
557 +  return error;
558 + }
559 +
560 + int
561 + 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)
562 + {
563 +  int c;        /* Character of the parsed option.  */
564 +
565 +  int error = 0;
566 +  struct gengetopt_args_info local_args_info;
567 +
568 +  if (initialize)
569 +    cmdline_parser_init (args_info);
570 +
571 +  cmdline_parser_init (&local_args_info);
572 +
573    optarg = 0;
574 <  optind = 1;
574 >  optind = 0;
575    opterr = 1;
576    optopt = '?';
577  
# Line 119 | Line 585 | cmdline_parser (int argc, char * const *argv, struct g
585          { "version",    0, NULL, 'V' },
586          { "input",      1, NULL, 'i' },
587          { "output",     1, NULL, 'o' },
588 <        { "frame",      1, NULL, 'n' },
589 <        { "ndistebins", 1, NULL, 'd' },
588 >        { "step",       1, NULL, 'n' },
589 >        { "nrbins",     1, NULL, 'r' },
590 >        { "nbins_x",    1, NULL, 'x' },
591 >        { "nbins_y",    1, NULL, 'y' },
592          { "nanglebins", 1, NULL, 'a' },
593          { "length",     1, NULL, 'l' },
594 +        { "zoffset",    1, NULL, 'z' },
595          { "sele1",      1, NULL, 0 },
596          { "sele2",      1, NULL, 0 },
597 +        { "sele3",      1, NULL, 0 },
598 +        { "refsele",    1, NULL, 0 },
599 +        { "molname",    1, NULL, 0 },
600 +        { "begin",      1, NULL, 0 },
601 +        { "end",        1, NULL, 0 },
602          { "gofr",       0, NULL, 0 },
603          { "r_theta",    0, NULL, 0 },
604          { "r_omega",    0, NULL, 0 },
605          { "theta_omega",        0, NULL, 0 },
606 <        { "xyz",        0, NULL, 0 },
606 >        { "gxyz",       0, NULL, 0 },
607 >        { "p2", 0, NULL, 0 },
608 >        { "rp2",        0, NULL, 0 },
609 >        { "scd",        0, NULL, 0 },
610 >        { "density",    0, NULL, 0 },
611 >        { "slab_density",       0, NULL, 0 },
612 >        { "hxy",        0, NULL, 0 },
613          { NULL, 0, NULL, 0 }
614        };
615  
616        stop_char = 0;
617 <      c = getopt_long (argc, argv, "hVi:o:n:d:a:l:", long_options, &option_index);
617 >      c = getopt_long (argc, argv, "hVi:o:n:r:x:y:a:l:z:", long_options, &option_index);
618  
619        if (c == -1) break;       /* Exit from `while (1)' loop.  */
620  
621        switch (c)
622          {
623          case 'h':       /* Print help and exit.  */
144 –          clear_args ();
624            cmdline_parser_print_help ();
625 +          cmdline_parser_free (&local_args_info);
626            exit (EXIT_SUCCESS);
627  
628          case 'V':       /* Print version and exit.  */
149 –          clear_args ();
629            cmdline_parser_print_version ();
630 +          cmdline_parser_free (&local_args_info);
631            exit (EXIT_SUCCESS);
632  
633          case 'i':       /* input dump file.  */
634 <          if (args_info->input_given)
634 >          if (local_args_info.input_given)
635              {
636 <              fprintf (stderr, "%s: `--input' (`-i') option given more than once\n", CMDLINE_PARSER_PACKAGE);
637 <              clear_args ();
158 <              exit (EXIT_FAILURE);
636 >              fprintf (stderr, "%s: `--input' (`-i') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
637 >              goto failure;
638              }
639 +          if (args_info->input_given && ! override)
640 +            continue;
641 +          local_args_info.input_given = 1;
642            args_info->input_given = 1;
643 +          if (args_info->input_arg)
644 +            free (args_info->input_arg); /* free previous string */
645            args_info->input_arg = gengetopt_strdup (optarg);
646 +          if (args_info->input_orig)
647 +            free (args_info->input_orig); /* free previous string */
648 +          args_info->input_orig = gengetopt_strdup (optarg);
649            break;
650  
651          case 'o':       /* output file name.  */
652 <          if (args_info->output_given)
652 >          if (local_args_info.output_given)
653              {
654 <              fprintf (stderr, "%s: `--output' (`-o') option given more than once\n", CMDLINE_PARSER_PACKAGE);
655 <              clear_args ();
169 <              exit (EXIT_FAILURE);
654 >              fprintf (stderr, "%s: `--output' (`-o') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
655 >              goto failure;
656              }
657 +          if (args_info->output_given && ! override)
658 +            continue;
659 +          local_args_info.output_given = 1;
660            args_info->output_given = 1;
661 +          if (args_info->output_arg)
662 +            free (args_info->output_arg); /* free previous string */
663            args_info->output_arg = gengetopt_strdup (optarg);
664 +          if (args_info->output_orig)
665 +            free (args_info->output_orig); /* free previous string */
666 +          args_info->output_orig = gengetopt_strdup (optarg);
667            break;
668  
669 <        case 'n':       /* print every n frame.  */
670 <          if (args_info->frame_given)
669 >        case 'n':       /* process every n frame.  */
670 >          if (local_args_info.step_given)
671              {
672 <              fprintf (stderr, "%s: `--frame' (`-n') option given more than once\n", CMDLINE_PARSER_PACKAGE);
673 <              clear_args ();
180 <              exit (EXIT_FAILURE);
672 >              fprintf (stderr, "%s: `--step' (`-n') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
673 >              goto failure;
674              }
675 <          args_info->frame_given = 1;
676 <          args_info->frame_arg = strtol (optarg,&stop_char,0);
675 >          if (args_info->step_given && ! override)
676 >            continue;
677 >          local_args_info.step_given = 1;
678 >          args_info->step_given = 1;
679 >          args_info->step_arg = strtol (optarg, &stop_char, 0);
680 >          if (!(stop_char && *stop_char == '\0')) {
681 >            fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
682 >            goto failure;
683 >          }
684 >          if (args_info->step_orig)
685 >            free (args_info->step_orig); /* free previous string */
686 >          args_info->step_orig = gengetopt_strdup (optarg);
687            break;
688  
689 <        case 'd':       /* number of bins for distance.  */
690 <          if (args_info->ndistebins_given)
689 >        case 'r':       /* number of bins for distance.  */
690 >          if (local_args_info.nrbins_given)
691              {
692 <              fprintf (stderr, "%s: `--ndistebins' (`-d') option given more than once\n", CMDLINE_PARSER_PACKAGE);
693 <              clear_args ();
191 <              exit (EXIT_FAILURE);
692 >              fprintf (stderr, "%s: `--nrbins' (`-r') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
693 >              goto failure;
694              }
695 <          args_info->ndistebins_given = 1;
696 <          args_info->ndistebins_arg = strtol (optarg,&stop_char,0);
695 >          if (args_info->nrbins_given && ! override)
696 >            continue;
697 >          local_args_info.nrbins_given = 1;
698 >          args_info->nrbins_given = 1;
699 >          args_info->nrbins_arg = strtol (optarg, &stop_char, 0);
700 >          if (!(stop_char && *stop_char == '\0')) {
701 >            fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
702 >            goto failure;
703 >          }
704 >          if (args_info->nrbins_orig)
705 >            free (args_info->nrbins_orig); /* free previous string */
706 >          args_info->nrbins_orig = gengetopt_strdup (optarg);
707            break;
708  
709 +        case 'x':       /* number of bins in x axis.  */
710 +          if (local_args_info.nbins_x_given)
711 +            {
712 +              fprintf (stderr, "%s: `--nbins_x' (`-x') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
713 +              goto failure;
714 +            }
715 +          if (args_info->nbins_x_given && ! override)
716 +            continue;
717 +          local_args_info.nbins_x_given = 1;
718 +          args_info->nbins_x_given = 1;
719 +          args_info->nbins_x_arg = strtol (optarg, &stop_char, 0);
720 +          if (!(stop_char && *stop_char == '\0')) {
721 +            fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
722 +            goto failure;
723 +          }
724 +          if (args_info->nbins_x_orig)
725 +            free (args_info->nbins_x_orig); /* free previous string */
726 +          args_info->nbins_x_orig = gengetopt_strdup (optarg);
727 +          break;
728 +
729 +        case 'y':       /* number of bins in y axis.  */
730 +          if (local_args_info.nbins_y_given)
731 +            {
732 +              fprintf (stderr, "%s: `--nbins_y' (`-y') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
733 +              goto failure;
734 +            }
735 +          if (args_info->nbins_y_given && ! override)
736 +            continue;
737 +          local_args_info.nbins_y_given = 1;
738 +          args_info->nbins_y_given = 1;
739 +          args_info->nbins_y_arg = strtol (optarg, &stop_char, 0);
740 +          if (!(stop_char && *stop_char == '\0')) {
741 +            fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
742 +            goto failure;
743 +          }
744 +          if (args_info->nbins_y_orig)
745 +            free (args_info->nbins_y_orig); /* free previous string */
746 +          args_info->nbins_y_orig = gengetopt_strdup (optarg);
747 +          break;
748 +
749          case 'a':       /* number of bins for cos(angle).  */
750 <          if (args_info->nanglebins_given)
750 >          if (local_args_info.nanglebins_given)
751              {
752 <              fprintf (stderr, "%s: `--nanglebins' (`-a') option given more than once\n", CMDLINE_PARSER_PACKAGE);
753 <              clear_args ();
202 <              exit (EXIT_FAILURE);
752 >              fprintf (stderr, "%s: `--nanglebins' (`-a') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
753 >              goto failure;
754              }
755 +          if (args_info->nanglebins_given && ! override)
756 +            continue;
757 +          local_args_info.nanglebins_given = 1;
758            args_info->nanglebins_given = 1;
759 <          args_info->nanglebins_arg = strtol (optarg,&stop_char,0);
759 >          args_info->nanglebins_arg = strtol (optarg, &stop_char, 0);
760 >          if (!(stop_char && *stop_char == '\0')) {
761 >            fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
762 >            goto failure;
763 >          }
764 >          if (args_info->nanglebins_orig)
765 >            free (args_info->nanglebins_orig); /* free previous string */
766 >          args_info->nanglebins_orig = gengetopt_strdup (optarg);
767            break;
768  
769 <        case 'l':       /* maximum length.  */
770 <          if (args_info->length_given)
769 >        case 'l':       /* maximum length (Defaults to 1/2 smallest length of first frame).  */
770 >          if (local_args_info.length_given)
771              {
772 <              fprintf (stderr, "%s: `--length' (`-l') option given more than once\n", CMDLINE_PARSER_PACKAGE);
773 <              clear_args ();
213 <              exit (EXIT_FAILURE);
772 >              fprintf (stderr, "%s: `--length' (`-l') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
773 >              goto failure;
774              }
775 +          if (args_info->length_given && ! override)
776 +            continue;
777 +          local_args_info.length_given = 1;
778            args_info->length_given = 1;
779 <          args_info->length_arg = strtod (optarg, NULL);
779 >          args_info->length_arg = strtod (optarg, &stop_char);
780 >          if (!(stop_char && *stop_char == '\0')) {
781 >            fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
782 >            goto failure;
783 >          }
784 >          if (args_info->length_orig)
785 >            free (args_info->length_orig); /* free previous string */
786 >          args_info->length_orig = gengetopt_strdup (optarg);
787            break;
788  
789 +        case 'z':       /* Where to set the zero for the slab_density calculation.  */
790 +          if (local_args_info.zoffset_given)
791 +            {
792 +              fprintf (stderr, "%s: `--zoffset' (`-z') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
793 +              goto failure;
794 +            }
795 +          if (args_info->zoffset_given && ! override)
796 +            continue;
797 +          local_args_info.zoffset_given = 1;
798 +          args_info->zoffset_given = 1;
799 +          args_info->zoffset_arg = strtod (optarg, &stop_char);
800 +          if (!(stop_char && *stop_char == '\0')) {
801 +            fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
802 +            goto failure;
803 +          }
804 +          if (args_info->zoffset_orig)
805 +            free (args_info->zoffset_orig); /* free previous string */
806 +          args_info->zoffset_orig = gengetopt_strdup (optarg);
807 +          break;
808  
809 +
810          case 0: /* Long option with no short option */
811 <          /* select first stuntdouble set.  */
811 >          /* select the first stuntdouble set.  */
812            if (strcmp (long_options[option_index].name, "sele1") == 0)
813            {
814 <            if (args_info->sele1_given)
814 >            if (local_args_info.sele1_given)
815                {
816 <                fprintf (stderr, "%s: `--sele1' option given more than once\n", CMDLINE_PARSER_PACKAGE);
817 <                clear_args ();
228 <                exit (EXIT_FAILURE);
816 >                fprintf (stderr, "%s: `--sele1' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
817 >                goto failure;
818                }
819 +            if (args_info->sele1_given && ! override)
820 +              continue;
821 +            local_args_info.sele1_given = 1;
822              args_info->sele1_given = 1;
823 +            if (args_info->sele1_arg)
824 +              free (args_info->sele1_arg); /* free previous string */
825              args_info->sele1_arg = gengetopt_strdup (optarg);
826 <            break;
826 >            if (args_info->sele1_orig)
827 >              free (args_info->sele1_orig); /* free previous string */
828 >            args_info->sele1_orig = gengetopt_strdup (optarg);
829            }
830 <          
235 <          /* select second stuntdouble set.  */
830 >          /* select the second stuntdouble set.  */
831            else if (strcmp (long_options[option_index].name, "sele2") == 0)
832            {
833 <            if (args_info->sele2_given)
833 >            if (local_args_info.sele2_given)
834                {
835 <                fprintf (stderr, "%s: `--sele2' option given more than once\n", CMDLINE_PARSER_PACKAGE);
836 <                clear_args ();
242 <                exit (EXIT_FAILURE);
835 >                fprintf (stderr, "%s: `--sele2' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
836 >                goto failure;
837                }
838 +            if (args_info->sele2_given && ! override)
839 +              continue;
840 +            local_args_info.sele2_given = 1;
841              args_info->sele2_given = 1;
842 +            if (args_info->sele2_arg)
843 +              free (args_info->sele2_arg); /* free previous string */
844              args_info->sele2_arg = gengetopt_strdup (optarg);
845 <            break;
845 >            if (args_info->sele2_orig)
846 >              free (args_info->sele2_orig); /* free previous string */
847 >            args_info->sele2_orig = gengetopt_strdup (optarg);
848            }
849 <          
850 <          /* g(r).  */
250 <          else if (strcmp (long_options[option_index].name, "gofr") == 0)
849 >          /* select the third stuntdouble set.  */
850 >          else if (strcmp (long_options[option_index].name, "sele3") == 0)
851            {
852 <            if (args_info->gofr_given)
852 >            if (local_args_info.sele3_given)
853                {
854 <                fprintf (stderr, "%s: `--gofr' option given more than once\n", CMDLINE_PARSER_PACKAGE);
855 <                clear_args ();
256 <                exit (EXIT_FAILURE);
854 >                fprintf (stderr, "%s: `--sele3' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
855 >                goto failure;
856                }
857 <            args_info->gofr_given = 1; staticProps_group_counter += 1;
858 <          
857 >            if (args_info->sele3_given && ! override)
858 >              continue;
859 >            local_args_info.sele3_given = 1;
860 >            args_info->sele3_given = 1;
861 >            if (args_info->sele3_arg)
862 >              free (args_info->sele3_arg); /* free previous string */
863 >            args_info->sele3_arg = gengetopt_strdup (optarg);
864 >            if (args_info->sele3_orig)
865 >              free (args_info->sele3_orig); /* free previous string */
866 >            args_info->sele3_orig = gengetopt_strdup (optarg);
867 >          }
868 >          /* select reference (use and only use with --gxyz).  */
869 >          else if (strcmp (long_options[option_index].name, "refsele") == 0)
870 >          {
871 >            if (local_args_info.refsele_given)
872 >              {
873 >                fprintf (stderr, "%s: `--refsele' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
874 >                goto failure;
875 >              }
876 >            if (args_info->refsele_given && ! override)
877 >              continue;
878 >            local_args_info.refsele_given = 1;
879 >            args_info->refsele_given = 1;
880 >            if (args_info->refsele_arg)
881 >              free (args_info->refsele_arg); /* free previous string */
882 >            args_info->refsele_arg = gengetopt_strdup (optarg);
883 >            if (args_info->refsele_orig)
884 >              free (args_info->refsele_orig); /* free previous string */
885 >            args_info->refsele_orig = gengetopt_strdup (optarg);
886 >          }
887 >          /* molecule name.  */
888 >          else if (strcmp (long_options[option_index].name, "molname") == 0)
889 >          {
890 >            if (local_args_info.molname_given)
891 >              {
892 >                fprintf (stderr, "%s: `--molname' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
893 >                goto failure;
894 >              }
895 >            if (args_info->molname_given && ! override)
896 >              continue;
897 >            local_args_info.molname_given = 1;
898 >            args_info->molname_given = 1;
899 >            if (args_info->molname_arg)
900 >              free (args_info->molname_arg); /* free previous string */
901 >            args_info->molname_arg = gengetopt_strdup (optarg);
902 >            if (args_info->molname_orig)
903 >              free (args_info->molname_orig); /* free previous string */
904 >            args_info->molname_orig = gengetopt_strdup (optarg);
905 >          }
906 >          /* begin interanl index.  */
907 >          else if (strcmp (long_options[option_index].name, "begin") == 0)
908 >          {
909 >            if (local_args_info.begin_given)
910 >              {
911 >                fprintf (stderr, "%s: `--begin' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
912 >                goto failure;
913 >              }
914 >            if (args_info->begin_given && ! override)
915 >              continue;
916 >            local_args_info.begin_given = 1;
917 >            args_info->begin_given = 1;
918 >            args_info->begin_arg = strtol (optarg, &stop_char, 0);
919 >            if (!(stop_char && *stop_char == '\0')) {
920 >              fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
921 >              goto failure;
922 >            }
923 >            if (args_info->begin_orig)
924 >              free (args_info->begin_orig); /* free previous string */
925 >            args_info->begin_orig = gengetopt_strdup (optarg);
926 >          }
927 >          /* end internal index.  */
928 >          else if (strcmp (long_options[option_index].name, "end") == 0)
929 >          {
930 >            if (local_args_info.end_given)
931 >              {
932 >                fprintf (stderr, "%s: `--end' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
933 >                goto failure;
934 >              }
935 >            if (args_info->end_given && ! override)
936 >              continue;
937 >            local_args_info.end_given = 1;
938 >            args_info->end_given = 1;
939 >            args_info->end_arg = strtol (optarg, &stop_char, 0);
940 >            if (!(stop_char && *stop_char == '\0')) {
941 >              fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
942 >              goto failure;
943 >            }
944 >            if (args_info->end_orig)
945 >              free (args_info->end_orig); /* free previous string */
946 >            args_info->end_orig = gengetopt_strdup (optarg);
947 >          }
948 >          /* g(r).  */
949 >          else if (strcmp (long_options[option_index].name, "gofr") == 0)
950 >          {
951 >            if (local_args_info.gofr_given)
952 >              {
953 >                fprintf (stderr, "%s: `--gofr' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
954 >                goto failure;
955 >              }
956 >            if (args_info->gofr_given && ! override)
957 >              continue;
958 >            local_args_info.gofr_given = 1;
959 >            args_info->gofr_given = 1;
960 >            if (args_info->staticProps_group_counter && override)
961 >              reset_group_staticProps (args_info);
962 >            args_info->staticProps_group_counter += 1;
963              break;
964            }
262 –          
965            /* g(r, cos(theta)).  */
966            else if (strcmp (long_options[option_index].name, "r_theta") == 0)
967            {
968 <            if (args_info->r_theta_given)
968 >            if (local_args_info.r_theta_given)
969                {
970 <                fprintf (stderr, "%s: `--r_theta' option given more than once\n", CMDLINE_PARSER_PACKAGE);
971 <                clear_args ();
270 <                exit (EXIT_FAILURE);
970 >                fprintf (stderr, "%s: `--r_theta' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
971 >                goto failure;
972                }
973 <            args_info->r_theta_given = 1; staticProps_group_counter += 1;
974 <          
973 >            if (args_info->r_theta_given && ! override)
974 >              continue;
975 >            local_args_info.r_theta_given = 1;
976 >            args_info->r_theta_given = 1;
977 >            if (args_info->staticProps_group_counter && override)
978 >              reset_group_staticProps (args_info);
979 >            args_info->staticProps_group_counter += 1;
980              break;
981            }
276 –          
982            /* g(r, cos(omega)).  */
983            else if (strcmp (long_options[option_index].name, "r_omega") == 0)
984            {
985 <            if (args_info->r_omega_given)
985 >            if (local_args_info.r_omega_given)
986                {
987 <                fprintf (stderr, "%s: `--r_omega' option given more than once\n", CMDLINE_PARSER_PACKAGE);
988 <                clear_args ();
284 <                exit (EXIT_FAILURE);
987 >                fprintf (stderr, "%s: `--r_omega' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
988 >                goto failure;
989                }
990 <            args_info->r_omega_given = 1; staticProps_group_counter += 1;
991 <          
990 >            if (args_info->r_omega_given && ! override)
991 >              continue;
992 >            local_args_info.r_omega_given = 1;
993 >            args_info->r_omega_given = 1;
994 >            if (args_info->staticProps_group_counter && override)
995 >              reset_group_staticProps (args_info);
996 >            args_info->staticProps_group_counter += 1;
997              break;
998            }
290 –          
999            /* g(cos(theta), cos(omega)).  */
1000            else if (strcmp (long_options[option_index].name, "theta_omega") == 0)
1001            {
1002 <            if (args_info->theta_omega_given)
1002 >            if (local_args_info.theta_omega_given)
1003                {
1004 <                fprintf (stderr, "%s: `--theta_omega' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1005 <                clear_args ();
298 <                exit (EXIT_FAILURE);
1004 >                fprintf (stderr, "%s: `--theta_omega' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1005 >                goto failure;
1006                }
1007 <            args_info->theta_omega_given = 1; staticProps_group_counter += 1;
1008 <          
1007 >            if (args_info->theta_omega_given && ! override)
1008 >              continue;
1009 >            local_args_info.theta_omega_given = 1;
1010 >            args_info->theta_omega_given = 1;
1011 >            if (args_info->staticProps_group_counter && override)
1012 >              reset_group_staticProps (args_info);
1013 >            args_info->staticProps_group_counter += 1;
1014              break;
1015            }
304 –          
1016            /* g(x, y, z).  */
1017 <          else if (strcmp (long_options[option_index].name, "xyz") == 0)
1017 >          else if (strcmp (long_options[option_index].name, "gxyz") == 0)
1018            {
1019 <            if (args_info->xyz_given)
1019 >            if (local_args_info.gxyz_given)
1020                {
1021 <                fprintf (stderr, "%s: `--xyz' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1022 <                clear_args ();
312 <                exit (EXIT_FAILURE);
1021 >                fprintf (stderr, "%s: `--gxyz' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1022 >                goto failure;
1023                }
1024 <            args_info->xyz_given = 1; staticProps_group_counter += 1;
1025 <          
1024 >            if (args_info->gxyz_given && ! override)
1025 >              continue;
1026 >            local_args_info.gxyz_given = 1;
1027 >            args_info->gxyz_given = 1;
1028 >            if (args_info->staticProps_group_counter && override)
1029 >              reset_group_staticProps (args_info);
1030 >            args_info->staticProps_group_counter += 1;
1031              break;
1032            }
1033 +          /* p2 order parameter (--sele1 and --sele2 must be specified).  */
1034 +          else if (strcmp (long_options[option_index].name, "p2") == 0)
1035 +          {
1036 +            if (local_args_info.p2_given)
1037 +              {
1038 +                fprintf (stderr, "%s: `--p2' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1039 +                goto failure;
1040 +              }
1041 +            if (args_info->p2_given && ! override)
1042 +              continue;
1043 +            local_args_info.p2_given = 1;
1044 +            args_info->p2_given = 1;
1045 +            if (args_info->staticProps_group_counter && override)
1046 +              reset_group_staticProps (args_info);
1047 +            args_info->staticProps_group_counter += 1;
1048 +            break;
1049 +          }
1050 +          /* rp2 order parameter (--sele1 and --sele2 must be specified).  */
1051 +          else if (strcmp (long_options[option_index].name, "rp2") == 0)
1052 +          {
1053 +            if (local_args_info.rp2_given)
1054 +              {
1055 +                fprintf (stderr, "%s: `--rp2' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1056 +                goto failure;
1057 +              }
1058 +            if (args_info->rp2_given && ! override)
1059 +              continue;
1060 +            local_args_info.rp2_given = 1;
1061 +            args_info->rp2_given = 1;
1062 +            if (args_info->staticProps_group_counter && override)
1063 +              reset_group_staticProps (args_info);
1064 +            args_info->staticProps_group_counter += 1;
1065 +            break;
1066 +          }
1067 +          /* scd order parameter(either --sele1, --sele2, --sele3 are specified or --molname, --begin, --end are specified).  */
1068 +          else if (strcmp (long_options[option_index].name, "scd") == 0)
1069 +          {
1070 +            if (local_args_info.scd_given)
1071 +              {
1072 +                fprintf (stderr, "%s: `--scd' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1073 +                goto failure;
1074 +              }
1075 +            if (args_info->scd_given && ! override)
1076 +              continue;
1077 +            local_args_info.scd_given = 1;
1078 +            args_info->scd_given = 1;
1079 +            if (args_info->staticProps_group_counter && override)
1080 +              reset_group_staticProps (args_info);
1081 +            args_info->staticProps_group_counter += 1;
1082 +            break;
1083 +          }
1084 +          /* density plot (--sele1 must be specified).  */
1085 +          else if (strcmp (long_options[option_index].name, "density") == 0)
1086 +          {
1087 +            if (local_args_info.density_given)
1088 +              {
1089 +                fprintf (stderr, "%s: `--density' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1090 +                goto failure;
1091 +              }
1092 +            if (args_info->density_given && ! override)
1093 +              continue;
1094 +            local_args_info.density_given = 1;
1095 +            args_info->density_given = 1;
1096 +            if (args_info->staticProps_group_counter && override)
1097 +              reset_group_staticProps (args_info);
1098 +            args_info->staticProps_group_counter += 1;
1099 +            break;
1100 +          }
1101 +          /* slab density (--sele1 must be specified).  */
1102 +          else if (strcmp (long_options[option_index].name, "slab_density") == 0)
1103 +          {
1104 +            if (local_args_info.slab_density_given)
1105 +              {
1106 +                fprintf (stderr, "%s: `--slab_density' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1107 +                goto failure;
1108 +              }
1109 +            if (args_info->slab_density_given && ! override)
1110 +              continue;
1111 +            local_args_info.slab_density_given = 1;
1112 +            args_info->slab_density_given = 1;
1113 +            if (args_info->staticProps_group_counter && override)
1114 +              reset_group_staticProps (args_info);
1115 +            args_info->staticProps_group_counter += 1;
1116 +            break;
1117 +          }
1118 +          /* hxy (--sele1 must be specified).  */
1119 +          else if (strcmp (long_options[option_index].name, "hxy") == 0)
1120 +          {
1121 +            if (local_args_info.hxy_given)
1122 +              {
1123 +                fprintf (stderr, "%s: `--hxy' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1124 +                goto failure;
1125 +              }
1126 +            if (args_info->hxy_given && ! override)
1127 +              continue;
1128 +            local_args_info.hxy_given = 1;
1129 +            args_info->hxy_given = 1;
1130 +            if (args_info->staticProps_group_counter && override)
1131 +              reset_group_staticProps (args_info);
1132 +            args_info->staticProps_group_counter += 1;
1133 +            break;
1134 +          }
1135            
1136 <
1136 >          break;
1137          case '?':       /* Invalid option.  */
1138            /* `getopt_long' already printed an error message.  */
1139 <          exit (EXIT_FAILURE);
1139 >          goto failure;
1140  
1141          default:        /* bug: option not considered.  */
1142 <          fprintf (stderr, "%s: option unknown: %c\n", CMDLINE_PARSER_PACKAGE, c);
1142 >          fprintf (stderr, "%s: option unknown: %c%s\n", CMDLINE_PARSER_PACKAGE, c, (additional_error ? additional_error : ""));
1143            abort ();
1144          } /* switch */
1145      } /* while */
1146  
1147 <  if ( staticProps_group_counter != 1)
1147 >  if (args_info->staticProps_group_counter > 1)
1148      {
1149 <      fprintf (stderr, "%s: %d options of group staticProps were given. One is required\n", CMDLINE_PARSER_PACKAGE, staticProps_group_counter);
1150 <      missing_required_options = 1;
1149 >      fprintf (stderr, "%s: %d options of group staticProps were given. One is required.%s\n", argv[0], args_info->staticProps_group_counter, (additional_error ? additional_error : ""));
1150 >      error = 1;
1151      }
1152    
1153  
1154 <  if (! args_info->input_given)
1154 >
1155 >  if (check_required)
1156      {
1157 <      fprintf (stderr, "%s: '--input' ('-i') option required\n", CMDLINE_PARSER_PACKAGE);
340 <      missing_required_options = 1;
1157 >      error += cmdline_parser_required2 (args_info, argv[0], additional_error);
1158      }
342 –  if (! args_info->length_given)
343 –    {
344 –      fprintf (stderr, "%s: '--length' ('-l') option required\n", CMDLINE_PARSER_PACKAGE);
345 –      missing_required_options = 1;
346 –    }
347 –  if ( missing_required_options )
348 –    exit (EXIT_FAILURE);
1159  
1160 +  cmdline_parser_release (&local_args_info);
1161 +
1162 +  if ( error )
1163 +    return (EXIT_FAILURE);
1164 +
1165    return 0;
1166 +
1167 + failure:
1168 +  
1169 +  cmdline_parser_release (&local_args_info);
1170 +  return (EXIT_FAILURE);
1171   }

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