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root/OpenMD/trunk/src/applications/dynamicProps/DynamicPropsCmd.cpp
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Comparing:
branches/development/src/applications/dynamicProps/DynamicPropsCmd.c (file contents), Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC vs.
trunk/src/applications/dynamicProps/DynamicPropsCmd.cpp (file contents), Revision 2003 by gezelter, Sun Jun 1 19:28:44 2014 UTC

# Line 1 | Line 1
1   /*
2 <  File autogenerated by gengetopt version 2.14
2 >  File autogenerated by gengetopt version 2.22.4
3    generated with the following command:
4 <  gengetopt -i DynamicProps.ggo -F DynamicPropsCmd
4 >  gengetopt --file-name=DynamicPropsCmd --unamed-opts
5  
6    The developers of gengetopt consider the fixed text that goes in all
7    gengetopt output files to be in the public domain:
# Line 17 | Line 17
17   #include <stdlib.h>
18   #include <string.h>
19  
20 < #include "getopt.h"
20 > #ifndef FIX_UNUSED
21 > #define FIX_UNUSED(X) (void) (X) /* avoid warnings for unused params */
22 > #endif
23  
24 + #ifdef WIN32
25 + #include "utils/wingetopt.h"
26 + #else
27 + #include <getopt.h>
28 + #endif
29 +
30   #include "DynamicPropsCmd.h"
31  
32 + const char *gengetopt_args_info_purpose = "";
33 +
34 + const char *gengetopt_args_info_usage = "Usage: DynamicProps [OPTIONS]... [FILES]...";
35 +
36 + const char *gengetopt_args_info_description = "";
37 +
38 + const char *gengetopt_args_info_help[] = {
39 +  "  -h, --help                    Print help and exit",
40 +  "  -V, --version                 Print version and exit",
41 +  "  -i, --input=filename          input dump file",
42 +  "  -o, --output=filename         output file name",
43 +  "      --sele1=selection script  select first stuntdouble set",
44 +  "      --sele2=selection script  select second stuntdouble set (if sele2 is not \n                                  set, use script from sele1)",
45 +  "      --order=INT               Lengendre Polynomial Order",
46 +  "  -z, --nzbins=INT              Number of Z bins  (default=`100')",
47 +  "  -m, --memory=memory specification\n                                Available memory (defaults to 2G)  \n                                  (default=`2G')",
48 +  "\n Group: dynamicProps\n   an option of this group is required",
49 +  "  -s, --selecorr                selection correlation function",
50 +  "  -r, --rcorr                   rmsd",
51 +  "  -v, --vcorr                   velocity correlation function",
52 +  "  -d, --dcorr                   dipole correlation function",
53 +  "  -l, --lcorr                   Lengendre correlation function",
54 +  "      --lcorrZ                  Lengendre correlation function binned by Z",
55 +  "      --cohZ                    Lengendre correlation function for OH bond \n                                  vectors binned by Z",
56 +  "  -M, --sdcorr                  System dipole correlation function",
57 +  "      --r_rcorr                 Radial rmsd",
58 +  "      --thetacorr               Angular rmsd",
59 +  "      --drcorr                  Directional rmsd for particles with unit \n                                  vectors",
60 +  "      --helfandEcorr            Helfand moment for thermal conductvity",
61 +  "  -p, --momentum                Helfand momentum for viscosity",
62 +  "      --stresscorr              Stress tensor correlation function",
63 +  "  -b, --bondcorr                Bond extension correlation function",
64 +  "  -f, --freqfluccorr            Frequency Fluctuation correlation function",
65 +    0
66 + };
67 +
68 + typedef enum {ARG_NO
69 +  , ARG_STRING
70 +  , ARG_INT
71 + } cmdline_parser_arg_type;
72 +
73   static
74   void clear_given (struct gengetopt_args_info *args_info);
75   static
76   void clear_args (struct gengetopt_args_info *args_info);
77  
78   static int
79 < 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);
79 > cmdline_parser_internal (int argc, char **argv, struct gengetopt_args_info *args_info,
80 >                        struct cmdline_parser_params *params, const char *additional_error);
81  
82   static int
83   cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error);
# Line 45 | Line 95 | void clear_given (struct gengetopt_args_info *args_inf
95    args_info->sele1_given = 0 ;
96    args_info->sele2_given = 0 ;
97    args_info->order_given = 0 ;
98 +  args_info->nzbins_given = 0 ;
99 +  args_info->memory_given = 0 ;
100 +  args_info->selecorr_given = 0 ;
101    args_info->rcorr_given = 0 ;
102    args_info->vcorr_given = 0 ;
103    args_info->dcorr_given = 0 ;
104    args_info->lcorr_given = 0 ;
105 +  args_info->lcorrZ_given = 0 ;
106 +  args_info->cohZ_given = 0 ;
107 +  args_info->sdcorr_given = 0 ;
108    args_info->r_rcorr_given = 0 ;
109    args_info->thetacorr_given = 0 ;
110    args_info->drcorr_given = 0 ;
111    args_info->helfandEcorr_given = 0 ;
112 +  args_info->momentum_given = 0 ;
113 +  args_info->stresscorr_given = 0 ;
114 +  args_info->bondcorr_given = 0 ;
115 +  args_info->freqfluccorr_given = 0 ;
116    args_info->dynamicProps_group_counter = 0 ;
117   }
118  
119   static
120   void clear_args (struct gengetopt_args_info *args_info)
121   {
122 +  FIX_UNUSED (args_info);
123    args_info->input_arg = NULL;
124    args_info->input_orig = NULL;
125    args_info->output_arg = NULL;
# Line 68 | Line 129 | void clear_args (struct gengetopt_args_info *args_info
129    args_info->sele2_arg = NULL;
130    args_info->sele2_orig = NULL;
131    args_info->order_orig = NULL;
132 +  args_info->nzbins_arg = 100;
133 +  args_info->nzbins_orig = NULL;
134 +  args_info->memory_arg = gengetopt_strdup ("2G");
135 +  args_info->memory_orig = NULL;
136    
137   }
138  
139 + static
140 + void init_args_info(struct gengetopt_args_info *args_info)
141 + {
142 +
143 +
144 +  args_info->help_help = gengetopt_args_info_help[0] ;
145 +  args_info->version_help = gengetopt_args_info_help[1] ;
146 +  args_info->input_help = gengetopt_args_info_help[2] ;
147 +  args_info->output_help = gengetopt_args_info_help[3] ;
148 +  args_info->sele1_help = gengetopt_args_info_help[4] ;
149 +  args_info->sele2_help = gengetopt_args_info_help[5] ;
150 +  args_info->order_help = gengetopt_args_info_help[6] ;
151 +  args_info->nzbins_help = gengetopt_args_info_help[7] ;
152 +  args_info->memory_help = gengetopt_args_info_help[8] ;
153 +  args_info->selecorr_help = gengetopt_args_info_help[10] ;
154 +  args_info->rcorr_help = gengetopt_args_info_help[11] ;
155 +  args_info->vcorr_help = gengetopt_args_info_help[12] ;
156 +  args_info->dcorr_help = gengetopt_args_info_help[13] ;
157 +  args_info->lcorr_help = gengetopt_args_info_help[14] ;
158 +  args_info->lcorrZ_help = gengetopt_args_info_help[15] ;
159 +  args_info->cohZ_help = gengetopt_args_info_help[16] ;
160 +  args_info->sdcorr_help = gengetopt_args_info_help[17] ;
161 +  args_info->r_rcorr_help = gengetopt_args_info_help[18] ;
162 +  args_info->thetacorr_help = gengetopt_args_info_help[19] ;
163 +  args_info->drcorr_help = gengetopt_args_info_help[20] ;
164 +  args_info->helfandEcorr_help = gengetopt_args_info_help[21] ;
165 +  args_info->momentum_help = gengetopt_args_info_help[22] ;
166 +  args_info->stresscorr_help = gengetopt_args_info_help[23] ;
167 +  args_info->bondcorr_help = gengetopt_args_info_help[24] ;
168 +  args_info->freqfluccorr_help = gengetopt_args_info_help[25] ;
169 +  
170 + }
171 +
172   void
173   cmdline_parser_print_version (void)
174   {
175 <  printf ("%s %s\n", CMDLINE_PARSER_PACKAGE, CMDLINE_PARSER_VERSION);
175 >  printf ("%s %s\n",
176 >     (strlen(CMDLINE_PARSER_PACKAGE_NAME) ? CMDLINE_PARSER_PACKAGE_NAME : CMDLINE_PARSER_PACKAGE),
177 >     CMDLINE_PARSER_VERSION);
178   }
179  
180 + static void print_help_common(void) {
181 +  cmdline_parser_print_version ();
182 +
183 +  if (strlen(gengetopt_args_info_purpose) > 0)
184 +    printf("\n%s\n", gengetopt_args_info_purpose);
185 +
186 +  if (strlen(gengetopt_args_info_usage) > 0)
187 +    printf("\n%s\n", gengetopt_args_info_usage);
188 +
189 +  printf("\n");
190 +
191 +  if (strlen(gengetopt_args_info_description) > 0)
192 +    printf("%s\n\n", gengetopt_args_info_description);
193 + }
194 +
195   void
196   cmdline_parser_print_help (void)
197   {
198 <  cmdline_parser_print_version ();
199 <  printf("\nUsage: DynamicProps [OPTIONS]...\n\n");
200 <  printf("%s\n","  -h, --help                    Print help and exit");
201 <  printf("%s\n","  -V, --version                 Print version and exit");
87 <  printf("%s\n","  -i, --input=filename          input dump file");
88 <  printf("%s\n","  -o, --output=filename         output file name");
89 <  printf("%s\n","      --sele1=selection script  select first stuntdouble set");
90 <  printf("%s\n","      --sele2=selection script  select second stuntdouble set (if sele2 is not \n                                  set, use script from sele1)");
91 <  printf("%s\n","      --order=INT               Lengendre Polynomial Order");
92 <  printf("%s\n","\n Group: dynamicProps\n   an option of this group is required");
93 <  printf("%s\n","  -r, --rcorr                   rmsd");
94 <  printf("%s\n","  -v, --vcorr                   velocity correlation function");
95 <  printf("%s\n","  -d, --dcorr                   dipole correlation function");
96 <  printf("%s\n","  -l, --lcorr                   Lengendre correlation function");
97 <  printf("%s\n","      --r_rcorr                 Radial rmsd");
98 <  printf("%s\n","      --thetacorr               Angular rmsd");
99 <  printf("%s\n","      --drcorr                  Directional rmsd for particles with unit \n                                  vectors");
100 <  printf("%s\n","      --helfandEcorr            Helfand moment for thermal conductvity");
101 <  
198 >  int i = 0;
199 >  print_help_common();
200 >  while (gengetopt_args_info_help[i])
201 >    printf("%s\n", gengetopt_args_info_help[i++]);
202   }
203  
204   void
# Line 106 | Line 206 | cmdline_parser_init (struct gengetopt_args_info *args_
206   {
207    clear_given (args_info);
208    clear_args (args_info);
209 +  init_args_info (args_info);
210 +
211 +  args_info->inputs = 0;
212 +  args_info->inputs_num = 0;
213   }
214  
215 + void
216 + cmdline_parser_params_init(struct cmdline_parser_params *params)
217 + {
218 +  if (params)
219 +    {
220 +      params->override = 0;
221 +      params->initialize = 1;
222 +      params->check_required = 1;
223 +      params->check_ambiguity = 0;
224 +      params->print_errors = 1;
225 +    }
226 + }
227 +
228 + struct cmdline_parser_params *
229 + cmdline_parser_params_create(void)
230 + {
231 +  struct cmdline_parser_params *params =
232 +    (struct cmdline_parser_params *)malloc(sizeof(struct cmdline_parser_params));
233 +  cmdline_parser_params_init(params);  
234 +  return params;
235 + }
236 +
237   static void
238 + free_string_field (char **s)
239 + {
240 +  if (*s)
241 +    {
242 +      free (*s);
243 +      *s = 0;
244 +    }
245 + }
246 +
247 +
248 + static void
249   cmdline_parser_release (struct gengetopt_args_info *args_info)
250   {
251 +  unsigned int i;
252 +  free_string_field (&(args_info->input_arg));
253 +  free_string_field (&(args_info->input_orig));
254 +  free_string_field (&(args_info->output_arg));
255 +  free_string_field (&(args_info->output_orig));
256 +  free_string_field (&(args_info->sele1_arg));
257 +  free_string_field (&(args_info->sele1_orig));
258 +  free_string_field (&(args_info->sele2_arg));
259 +  free_string_field (&(args_info->sele2_orig));
260 +  free_string_field (&(args_info->order_orig));
261 +  free_string_field (&(args_info->nzbins_orig));
262 +  free_string_field (&(args_info->memory_arg));
263 +  free_string_field (&(args_info->memory_orig));
264    
265 <  if (args_info->input_arg)
265 >  
266 >  for (i = 0; i < args_info->inputs_num; ++i)
267 >    free (args_info->inputs [i]);
268 >
269 >  if (args_info->inputs_num)
270 >    free (args_info->inputs);
271 >
272 >  clear_given (args_info);
273 > }
274 >
275 >
276 > static void
277 > write_into_file(FILE *outfile, const char *opt, const char *arg, const char *values[])
278 > {
279 >  FIX_UNUSED (values);
280 >  if (arg) {
281 >    fprintf(outfile, "%s=\"%s\"\n", opt, arg);
282 >  } else {
283 >    fprintf(outfile, "%s\n", opt);
284 >  }
285 > }
286 >
287 >
288 > int
289 > cmdline_parser_dump(FILE *outfile, struct gengetopt_args_info *args_info)
290 > {
291 >  int i = 0;
292 >
293 >  if (!outfile)
294      {
295 <      free (args_info->input_arg); /* free previous argument */
296 <      args_info->input_arg = 0;
119 <    }
120 <  if (args_info->input_orig)
121 <    {
122 <      free (args_info->input_orig); /* free previous argument */
123 <      args_info->input_orig = 0;
124 <    }
125 <  if (args_info->output_arg)
126 <    {
127 <      free (args_info->output_arg); /* free previous argument */
128 <      args_info->output_arg = 0;
129 <    }
130 <  if (args_info->output_orig)
131 <    {
132 <      free (args_info->output_orig); /* free previous argument */
133 <      args_info->output_orig = 0;
134 <    }
135 <  if (args_info->sele1_arg)
136 <    {
137 <      free (args_info->sele1_arg); /* free previous argument */
138 <      args_info->sele1_arg = 0;
139 <    }
140 <  if (args_info->sele1_orig)
141 <    {
142 <      free (args_info->sele1_orig); /* free previous argument */
143 <      args_info->sele1_orig = 0;
144 <    }
145 <  if (args_info->sele2_arg)
146 <    {
147 <      free (args_info->sele2_arg); /* free previous argument */
148 <      args_info->sele2_arg = 0;
149 <    }
150 <  if (args_info->sele2_orig)
151 <    {
152 <      free (args_info->sele2_orig); /* free previous argument */
153 <      args_info->sele2_orig = 0;
154 <    }
155 <  if (args_info->order_orig)
156 <    {
157 <      free (args_info->order_orig); /* free previous argument */
158 <      args_info->order_orig = 0;
295 >      fprintf (stderr, "%s: cannot dump options to stream\n", CMDLINE_PARSER_PACKAGE);
296 >      return EXIT_FAILURE;
297      }
298 +
299 +  if (args_info->help_given)
300 +    write_into_file(outfile, "help", 0, 0 );
301 +  if (args_info->version_given)
302 +    write_into_file(outfile, "version", 0, 0 );
303 +  if (args_info->input_given)
304 +    write_into_file(outfile, "input", args_info->input_orig, 0);
305 +  if (args_info->output_given)
306 +    write_into_file(outfile, "output", args_info->output_orig, 0);
307 +  if (args_info->sele1_given)
308 +    write_into_file(outfile, "sele1", args_info->sele1_orig, 0);
309 +  if (args_info->sele2_given)
310 +    write_into_file(outfile, "sele2", args_info->sele2_orig, 0);
311 +  if (args_info->order_given)
312 +    write_into_file(outfile, "order", args_info->order_orig, 0);
313 +  if (args_info->nzbins_given)
314 +    write_into_file(outfile, "nzbins", args_info->nzbins_orig, 0);
315 +  if (args_info->memory_given)
316 +    write_into_file(outfile, "memory", args_info->memory_orig, 0);
317 +  if (args_info->selecorr_given)
318 +    write_into_file(outfile, "selecorr", 0, 0 );
319 +  if (args_info->rcorr_given)
320 +    write_into_file(outfile, "rcorr", 0, 0 );
321 +  if (args_info->vcorr_given)
322 +    write_into_file(outfile, "vcorr", 0, 0 );
323 +  if (args_info->dcorr_given)
324 +    write_into_file(outfile, "dcorr", 0, 0 );
325 +  if (args_info->lcorr_given)
326 +    write_into_file(outfile, "lcorr", 0, 0 );
327 +  if (args_info->lcorrZ_given)
328 +    write_into_file(outfile, "lcorrZ", 0, 0 );
329 +  if (args_info->cohZ_given)
330 +    write_into_file(outfile, "cohZ", 0, 0 );
331 +  if (args_info->sdcorr_given)
332 +    write_into_file(outfile, "sdcorr", 0, 0 );
333 +  if (args_info->r_rcorr_given)
334 +    write_into_file(outfile, "r_rcorr", 0, 0 );
335 +  if (args_info->thetacorr_given)
336 +    write_into_file(outfile, "thetacorr", 0, 0 );
337 +  if (args_info->drcorr_given)
338 +    write_into_file(outfile, "drcorr", 0, 0 );
339 +  if (args_info->helfandEcorr_given)
340 +    write_into_file(outfile, "helfandEcorr", 0, 0 );
341 +  if (args_info->momentum_given)
342 +    write_into_file(outfile, "momentum", 0, 0 );
343 +  if (args_info->stresscorr_given)
344 +    write_into_file(outfile, "stresscorr", 0, 0 );
345 +  if (args_info->bondcorr_given)
346 +    write_into_file(outfile, "bondcorr", 0, 0 );
347 +  if (args_info->freqfluccorr_given)
348 +    write_into_file(outfile, "freqfluccorr", 0, 0 );
349    
350 <  clear_given (args_info);
350 >
351 >  i = EXIT_SUCCESS;
352 >  return i;
353   }
354  
355   int
# Line 175 | Line 366 | cmdline_parser_file_save(const char *filename, struct
366        return EXIT_FAILURE;
367      }
368  
369 <  if (args_info->help_given) {
179 <    fprintf(outfile, "%s\n", "help");
180 <  }
181 <  if (args_info->version_given) {
182 <    fprintf(outfile, "%s\n", "version");
183 <  }
184 <  if (args_info->input_given) {
185 <    if (args_info->input_orig) {
186 <      fprintf(outfile, "%s=\"%s\"\n", "input", args_info->input_orig);
187 <    } else {
188 <      fprintf(outfile, "%s\n", "input");
189 <    }
190 <  }
191 <  if (args_info->output_given) {
192 <    if (args_info->output_orig) {
193 <      fprintf(outfile, "%s=\"%s\"\n", "output", args_info->output_orig);
194 <    } else {
195 <      fprintf(outfile, "%s\n", "output");
196 <    }
197 <  }
198 <  if (args_info->sele1_given) {
199 <    if (args_info->sele1_orig) {
200 <      fprintf(outfile, "%s=\"%s\"\n", "sele1", args_info->sele1_orig);
201 <    } else {
202 <      fprintf(outfile, "%s\n", "sele1");
203 <    }
204 <  }
205 <  if (args_info->sele2_given) {
206 <    if (args_info->sele2_orig) {
207 <      fprintf(outfile, "%s=\"%s\"\n", "sele2", args_info->sele2_orig);
208 <    } else {
209 <      fprintf(outfile, "%s\n", "sele2");
210 <    }
211 <  }
212 <  if (args_info->order_given) {
213 <    if (args_info->order_orig) {
214 <      fprintf(outfile, "%s=\"%s\"\n", "order", args_info->order_orig);
215 <    } else {
216 <      fprintf(outfile, "%s\n", "order");
217 <    }
218 <  }
219 <  if (args_info->rcorr_given) {
220 <    fprintf(outfile, "%s\n", "rcorr");
221 <  }
222 <  if (args_info->vcorr_given) {
223 <    fprintf(outfile, "%s\n", "vcorr");
224 <  }
225 <  if (args_info->dcorr_given) {
226 <    fprintf(outfile, "%s\n", "dcorr");
227 <  }
228 <  if (args_info->lcorr_given) {
229 <    fprintf(outfile, "%s\n", "lcorr");
230 <  }
231 <  if (args_info->r_rcorr_given) {
232 <    fprintf(outfile, "%s\n", "r_rcorr");
233 <  }
234 <  if (args_info->thetacorr_given) {
235 <    fprintf(outfile, "%s\n", "thetacorr");
236 <  }
237 <  if (args_info->drcorr_given) {
238 <    fprintf(outfile, "%s\n", "drcorr");
239 <  }
240 <  if (args_info->helfandEcorr_given) {
241 <    fprintf(outfile, "%s\n", "helfandEcorr");
242 <  }
243 <  
369 >  i = cmdline_parser_dump(outfile, args_info);
370    fclose (outfile);
371  
246 –  i = EXIT_SUCCESS;
372    return i;
373   }
374  
# Line 253 | Line 378 | cmdline_parser_free (struct gengetopt_args_info *args_
378    cmdline_parser_release (args_info);
379   }
380  
381 <
257 < /* gengetopt_strdup() */
258 < /* strdup.c replacement of strdup, which is not standard */
381 > /** @brief replacement of strdup, which is not standard */
382   char *
383   gengetopt_strdup (const char *s)
384   {
385 <  char *result = NULL;
385 >  char *result = 0;
386    if (!s)
387      return result;
388  
# Line 271 | Line 394 | static void
394   }
395  
396   static void
274 – reset_group_dynamicProps(struct gengetopt_args_info *args_info);
275 –
276 – static void
397   reset_group_dynamicProps(struct gengetopt_args_info *args_info)
398   {
399    if (! args_info->dynamicProps_group_counter)
400      return;
401    
402 +  args_info->selecorr_given = 0 ;
403    args_info->rcorr_given = 0 ;
404    args_info->vcorr_given = 0 ;
405    args_info->dcorr_given = 0 ;
406    args_info->lcorr_given = 0 ;
407 +  args_info->lcorrZ_given = 0 ;
408 +  args_info->cohZ_given = 0 ;
409 +  args_info->sdcorr_given = 0 ;
410    args_info->r_rcorr_given = 0 ;
411    args_info->thetacorr_given = 0 ;
412    args_info->drcorr_given = 0 ;
413    args_info->helfandEcorr_given = 0 ;
414 +  args_info->momentum_given = 0 ;
415 +  args_info->stresscorr_given = 0 ;
416 +  args_info->bondcorr_given = 0 ;
417 +  args_info->freqfluccorr_given = 0 ;
418  
419    args_info->dynamicProps_group_counter = 0;
420   }
421  
422   int
423 < cmdline_parser (int argc, char * const *argv, struct gengetopt_args_info *args_info)
423 > cmdline_parser (int argc, char **argv, struct gengetopt_args_info *args_info)
424   {
425    return cmdline_parser2 (argc, argv, args_info, 0, 1, 1);
426   }
427  
428   int
429 < cmdline_parser2 (int argc, char * const *argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required)
429 > cmdline_parser_ext (int argc, char **argv, struct gengetopt_args_info *args_info,
430 >                   struct cmdline_parser_params *params)
431   {
432    int result;
433 +  result = cmdline_parser_internal (argc, argv, args_info, params, 0);
434  
435 <  result = cmdline_parser_internal (argc, argv, args_info, override, initialize, check_required, NULL);
435 >  if (result == EXIT_FAILURE)
436 >    {
437 >      cmdline_parser_free (args_info);
438 >      exit (EXIT_FAILURE);
439 >    }
440 >  
441 >  return result;
442 > }
443  
444 + int
445 + cmdline_parser2 (int argc, char **argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required)
446 + {
447 +  int result;
448 +  struct cmdline_parser_params params;
449 +  
450 +  params.override = override;
451 +  params.initialize = initialize;
452 +  params.check_required = check_required;
453 +  params.check_ambiguity = 0;
454 +  params.print_errors = 1;
455 +
456 +  result = cmdline_parser_internal (argc, argv, args_info, &params, 0);
457 +
458    if (result == EXIT_FAILURE)
459      {
460        cmdline_parser_free (args_info);
# Line 318 | Line 469 | cmdline_parser_required (struct gengetopt_args_info *a
469   {
470    int result = EXIT_SUCCESS;
471  
472 <  if (cmdline_parser_required2(args_info, prog_name, NULL) > 0)
472 >  if (cmdline_parser_required2(args_info, prog_name, 0) > 0)
473      result = EXIT_FAILURE;
474  
475    if (result == EXIT_FAILURE)
# Line 334 | Line 485 | cmdline_parser_required2 (struct gengetopt_args_info *
485   cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error)
486   {
487    int error = 0;
488 +  FIX_UNUSED (additional_error);
489  
490 +  /* checks for required options */
491    if (! args_info->input_given)
492      {
493        fprintf (stderr, "%s: '--input' ('-i') option required%s\n", prog_name, (additional_error ? additional_error : ""));
494        error = 1;
495      }
496 +  
497    if (args_info->dynamicProps_group_counter == 0)
498      {
499 <      fprintf (stderr, "%s: %d options of group dynamicProps were given. One is required.%s\n", prog_name, args_info->dynamicProps_group_counter, (additional_error ? additional_error : ""));
499 >      fprintf (stderr, "%s: %d options of group dynamicProps were given. One is required%s.\n", prog_name, args_info->dynamicProps_group_counter, (additional_error ? additional_error : ""));
500        error = 1;
501      }
502    
503  
504 +  /* checks for dependences among options */
505 +
506    return error;
507 + }
508 +
509 +
510 + static char *package_name = 0;
511 +
512 + /**
513 + * @brief updates an option
514 + * @param field the generic pointer to the field to update
515 + * @param orig_field the pointer to the orig field
516 + * @param field_given the pointer to the number of occurrence of this option
517 + * @param prev_given the pointer to the number of occurrence already seen
518 + * @param value the argument for this option (if null no arg was specified)
519 + * @param possible_values the possible values for this option (if specified)
520 + * @param default_value the default value (in case the option only accepts fixed values)
521 + * @param arg_type the type of this option
522 + * @param check_ambiguity @see cmdline_parser_params.check_ambiguity
523 + * @param override @see cmdline_parser_params.override
524 + * @param no_free whether to free a possible previous value
525 + * @param multiple_option whether this is a multiple option
526 + * @param long_opt the corresponding long option
527 + * @param short_opt the corresponding short option (or '-' if none)
528 + * @param additional_error possible further error specification
529 + */
530 + static
531 + int update_arg(void *field, char **orig_field,
532 +               unsigned int *field_given, unsigned int *prev_given,
533 +               char *value, const char *possible_values[],
534 +               const char *default_value,
535 +               cmdline_parser_arg_type arg_type,
536 +               int check_ambiguity, int override,
537 +               int no_free, int multiple_option,
538 +               const char *long_opt, char short_opt,
539 +               const char *additional_error)
540 + {
541 +  char *stop_char = 0;
542 +  const char *val = value;
543 +  int found;
544 +  char **string_field;
545 +  FIX_UNUSED (field);
546 +
547 +  stop_char = 0;
548 +  found = 0;
549 +
550 +  if (!multiple_option && prev_given && (*prev_given || (check_ambiguity && *field_given)))
551 +    {
552 +      if (short_opt != '-')
553 +        fprintf (stderr, "%s: `--%s' (`-%c') option given more than once%s\n",
554 +               package_name, long_opt, short_opt,
555 +               (additional_error ? additional_error : ""));
556 +      else
557 +        fprintf (stderr, "%s: `--%s' option given more than once%s\n",
558 +               package_name, long_opt,
559 +               (additional_error ? additional_error : ""));
560 +      return 1; /* failure */
561 +    }
562 +
563 +  FIX_UNUSED (default_value);
564 +    
565 +  if (field_given && *field_given && ! override)
566 +    return 0;
567 +  if (prev_given)
568 +    (*prev_given)++;
569 +  if (field_given)
570 +    (*field_given)++;
571 +  if (possible_values)
572 +    val = possible_values[found];
573 +
574 +  switch(arg_type) {
575 +  case ARG_INT:
576 +    if (val) *((int *)field) = strtol (val, &stop_char, 0);
577 +    break;
578 +  case ARG_STRING:
579 +    if (val) {
580 +      string_field = (char **)field;
581 +      if (!no_free && *string_field)
582 +        free (*string_field); /* free previous string */
583 +      *string_field = gengetopt_strdup (val);
584 +    }
585 +    break;
586 +  default:
587 +    break;
588 +  };
589 +
590 +  /* check numeric conversion */
591 +  switch(arg_type) {
592 +  case ARG_INT:
593 +    if (val && !(stop_char && *stop_char == '\0')) {
594 +      fprintf(stderr, "%s: invalid numeric value: %s\n", package_name, val);
595 +      return 1; /* failure */
596 +    }
597 +    break;
598 +  default:
599 +    ;
600 +  };
601 +
602 +  /* store the original value */
603 +  switch(arg_type) {
604 +  case ARG_NO:
605 +    break;
606 +  default:
607 +    if (value && orig_field) {
608 +      if (no_free) {
609 +        *orig_field = value;
610 +      } else {
611 +        if (*orig_field)
612 +          free (*orig_field); /* free previous string */
613 +        *orig_field = gengetopt_strdup (value);
614 +      }
615 +    }
616 +  };
617 +
618 +  return 0; /* OK */
619   }
620  
621 +
622   int
623 < 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)
623 > cmdline_parser_internal (
624 >  int argc, char **argv, struct gengetopt_args_info *args_info,
625 >                        struct cmdline_parser_params *params, const char *additional_error)
626   {
627    int c;        /* Character of the parsed option.  */
628  
629    int error = 0;
630    struct gengetopt_args_info local_args_info;
631 +  
632 +  int override;
633 +  int initialize;
634 +  int check_required;
635 +  int check_ambiguity;
636 +  
637 +  package_name = argv[0];
638 +  
639 +  override = params->override;
640 +  initialize = params->initialize;
641 +  check_required = params->check_required;
642 +  check_ambiguity = params->check_ambiguity;
643  
644    if (initialize)
645      cmdline_parser_init (args_info);
# Line 364 | Line 647 | cmdline_parser_internal (int argc, char * const *argv,
647    cmdline_parser_init (&local_args_info);
648  
649    optarg = 0;
650 <  optind = 1;
651 <  opterr = 1;
650 >  optind = 0;
651 >  opterr = params->print_errors;
652    optopt = '?';
653  
654    while (1)
655      {
656        int option_index = 0;
374 –      char *stop_char;
657  
658        static struct option long_options[] = {
659          { "help",       0, NULL, 'h' },
# Line 381 | Line 663 | cmdline_parser_internal (int argc, char * const *argv,
663          { "sele1",      1, NULL, 0 },
664          { "sele2",      1, NULL, 0 },
665          { "order",      1, NULL, 0 },
666 +        { "nzbins",     1, NULL, 'z' },
667 +        { "memory",     1, NULL, 'm' },
668 +        { "selecorr",   0, NULL, 's' },
669          { "rcorr",      0, NULL, 'r' },
670          { "vcorr",      0, NULL, 'v' },
671          { "dcorr",      0, NULL, 'd' },
672          { "lcorr",      0, NULL, 'l' },
673 +        { "lcorrZ",     0, NULL, 0 },
674 +        { "cohZ",       0, NULL, 0 },
675 +        { "sdcorr",     0, NULL, 'M' },
676          { "r_rcorr",    0, NULL, 0 },
677          { "thetacorr",  0, NULL, 0 },
678          { "drcorr",     0, NULL, 0 },
679          { "helfandEcorr",       0, NULL, 0 },
680 <        { NULL, 0, NULL, 0 }
680 >        { "momentum",   0, NULL, 'p' },
681 >        { "stresscorr", 0, NULL, 0 },
682 >        { "bondcorr",   0, NULL, 'b' },
683 >        { "freqfluccorr",       0, NULL, 'f' },
684 >        { 0,  0, 0, 0 }
685        };
686  
687 <      stop_char = 0;
396 <      c = getopt_long (argc, argv, "hVi:o:rvdl", long_options, &option_index);
687 >      c = getopt_long (argc, argv, "hVi:o:z:m:srvdlMpbf", long_options, &option_index);
688  
689        if (c == -1) break;       /* Exit from `while (1)' loop.  */
690  
# Line 410 | Line 701 | cmdline_parser_internal (int argc, char * const *argv,
701            exit (EXIT_SUCCESS);
702  
703          case 'i':       /* input dump file.  */
704 <          if (local_args_info.input_given)
705 <            {
706 <              fprintf (stderr, "%s: `--input' (`-i') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
707 <              goto failure;
708 <            }
709 <          if (args_info->input_given && ! override)
710 <            continue;
711 <          local_args_info.input_given = 1;
712 <          args_info->input_given = 1;
713 <          if (args_info->input_arg)
423 <            free (args_info->input_arg); /* free previous string */
424 <          args_info->input_arg = gengetopt_strdup (optarg);
425 <          if (args_info->input_orig)
426 <            free (args_info->input_orig); /* free previous string */
427 <          args_info->input_orig = gengetopt_strdup (optarg);
704 >        
705 >        
706 >          if (update_arg( (void *)&(args_info->input_arg),
707 >               &(args_info->input_orig), &(args_info->input_given),
708 >              &(local_args_info.input_given), optarg, 0, 0, ARG_STRING,
709 >              check_ambiguity, override, 0, 0,
710 >              "input", 'i',
711 >              additional_error))
712 >            goto failure;
713 >        
714            break;
429 –
715          case 'o':       /* output file name.  */
716 <          if (local_args_info.output_given)
717 <            {
718 <              fprintf (stderr, "%s: `--output' (`-o') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
719 <              goto failure;
720 <            }
721 <          if (args_info->output_given && ! override)
722 <            continue;
723 <          local_args_info.output_given = 1;
724 <          args_info->output_given = 1;
725 <          if (args_info->output_arg)
441 <            free (args_info->output_arg); /* free previous string */
442 <          args_info->output_arg = gengetopt_strdup (optarg);
443 <          if (args_info->output_orig)
444 <            free (args_info->output_orig); /* free previous string */
445 <          args_info->output_orig = gengetopt_strdup (optarg);
716 >        
717 >        
718 >          if (update_arg( (void *)&(args_info->output_arg),
719 >               &(args_info->output_orig), &(args_info->output_given),
720 >              &(local_args_info.output_given), optarg, 0, 0, ARG_STRING,
721 >              check_ambiguity, override, 0, 0,
722 >              "output", 'o',
723 >              additional_error))
724 >            goto failure;
725 >        
726            break;
727 <
727 >        case 'z':       /* Number of Z bins.  */
728 >        
729 >        
730 >          if (update_arg( (void *)&(args_info->nzbins_arg),
731 >               &(args_info->nzbins_orig), &(args_info->nzbins_given),
732 >              &(local_args_info.nzbins_given), optarg, 0, "100", ARG_INT,
733 >              check_ambiguity, override, 0, 0,
734 >              "nzbins", 'z',
735 >              additional_error))
736 >            goto failure;
737 >        
738 >          break;
739 >        case 'm':       /* Available memory (defaults to 2G).  */
740 >        
741 >        
742 >          if (update_arg( (void *)&(args_info->memory_arg),
743 >               &(args_info->memory_orig), &(args_info->memory_given),
744 >              &(local_args_info.memory_given), optarg, 0, "2G", ARG_STRING,
745 >              check_ambiguity, override, 0, 0,
746 >              "memory", 'm',
747 >              additional_error))
748 >            goto failure;
749 >        
750 >          break;
751 >        case 's':       /* selection correlation function.  */
752 >        
753 >          if (args_info->dynamicProps_group_counter && override)
754 >            reset_group_dynamicProps (args_info);
755 >          args_info->dynamicProps_group_counter += 1;
756 >        
757 >          if (update_arg( 0 ,
758 >               0 , &(args_info->selecorr_given),
759 >              &(local_args_info.selecorr_given), optarg, 0, 0, ARG_NO,
760 >              check_ambiguity, override, 0, 0,
761 >              "selecorr", 's',
762 >              additional_error))
763 >            goto failure;
764 >        
765 >          break;
766          case 'r':       /* rmsd.  */
767 <          if (local_args_info.rcorr_given)
450 <            {
451 <              fprintf (stderr, "%s: `--rcorr' (`-r') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
452 <              goto failure;
453 <            }
454 <          if (args_info->rcorr_given && ! override)
455 <            continue;
456 <          local_args_info.rcorr_given = 1;
457 <          args_info->rcorr_given = 1;
767 >        
768            if (args_info->dynamicProps_group_counter && override)
769              reset_group_dynamicProps (args_info);
770            args_info->dynamicProps_group_counter += 1;
771 +        
772 +          if (update_arg( 0 ,
773 +               0 , &(args_info->rcorr_given),
774 +              &(local_args_info.rcorr_given), optarg, 0, 0, ARG_NO,
775 +              check_ambiguity, override, 0, 0,
776 +              "rcorr", 'r',
777 +              additional_error))
778 +            goto failure;
779 +        
780            break;
462 –
781          case 'v':       /* velocity correlation function.  */
782 <          if (local_args_info.vcorr_given)
465 <            {
466 <              fprintf (stderr, "%s: `--vcorr' (`-v') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
467 <              goto failure;
468 <            }
469 <          if (args_info->vcorr_given && ! override)
470 <            continue;
471 <          local_args_info.vcorr_given = 1;
472 <          args_info->vcorr_given = 1;
782 >        
783            if (args_info->dynamicProps_group_counter && override)
784              reset_group_dynamicProps (args_info);
785            args_info->dynamicProps_group_counter += 1;
786 +        
787 +          if (update_arg( 0 ,
788 +               0 , &(args_info->vcorr_given),
789 +              &(local_args_info.vcorr_given), optarg, 0, 0, ARG_NO,
790 +              check_ambiguity, override, 0, 0,
791 +              "vcorr", 'v',
792 +              additional_error))
793 +            goto failure;
794 +        
795            break;
477 –
796          case 'd':       /* dipole correlation function.  */
797 <          if (local_args_info.dcorr_given)
480 <            {
481 <              fprintf (stderr, "%s: `--dcorr' (`-d') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
482 <              goto failure;
483 <            }
484 <          if (args_info->dcorr_given && ! override)
485 <            continue;
486 <          local_args_info.dcorr_given = 1;
487 <          args_info->dcorr_given = 1;
797 >        
798            if (args_info->dynamicProps_group_counter && override)
799              reset_group_dynamicProps (args_info);
800            args_info->dynamicProps_group_counter += 1;
801 +        
802 +          if (update_arg( 0 ,
803 +               0 , &(args_info->dcorr_given),
804 +              &(local_args_info.dcorr_given), optarg, 0, 0, ARG_NO,
805 +              check_ambiguity, override, 0, 0,
806 +              "dcorr", 'd',
807 +              additional_error))
808 +            goto failure;
809 +        
810            break;
492 –
811          case 'l':       /* Lengendre correlation function.  */
812 <          if (local_args_info.lcorr_given)
495 <            {
496 <              fprintf (stderr, "%s: `--lcorr' (`-l') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
497 <              goto failure;
498 <            }
499 <          if (args_info->lcorr_given && ! override)
500 <            continue;
501 <          local_args_info.lcorr_given = 1;
502 <          args_info->lcorr_given = 1;
812 >        
813            if (args_info->dynamicProps_group_counter && override)
814              reset_group_dynamicProps (args_info);
815            args_info->dynamicProps_group_counter += 1;
816 +        
817 +          if (update_arg( 0 ,
818 +               0 , &(args_info->lcorr_given),
819 +              &(local_args_info.lcorr_given), optarg, 0, 0, ARG_NO,
820 +              check_ambiguity, override, 0, 0,
821 +              "lcorr", 'l',
822 +              additional_error))
823 +            goto failure;
824 +        
825            break;
826 <
826 >        case 'M':       /* System dipole correlation function.  */
827 >        
828 >          if (args_info->dynamicProps_group_counter && override)
829 >            reset_group_dynamicProps (args_info);
830 >          args_info->dynamicProps_group_counter += 1;
831 >        
832 >          if (update_arg( 0 ,
833 >               0 , &(args_info->sdcorr_given),
834 >              &(local_args_info.sdcorr_given), optarg, 0, 0, ARG_NO,
835 >              check_ambiguity, override, 0, 0,
836 >              "sdcorr", 'M',
837 >              additional_error))
838 >            goto failure;
839 >        
840 >          break;
841 >        case 'p':       /* Helfand momentum for viscosity.  */
842 >        
843 >          if (args_info->dynamicProps_group_counter && override)
844 >            reset_group_dynamicProps (args_info);
845 >          args_info->dynamicProps_group_counter += 1;
846 >        
847 >          if (update_arg( 0 ,
848 >               0 , &(args_info->momentum_given),
849 >              &(local_args_info.momentum_given), optarg, 0, 0, ARG_NO,
850 >              check_ambiguity, override, 0, 0,
851 >              "momentum", 'p',
852 >              additional_error))
853 >            goto failure;
854 >        
855 >          break;
856 >        case 'b':       /* Bond extension correlation function.  */
857 >        
858 >          if (args_info->dynamicProps_group_counter && override)
859 >            reset_group_dynamicProps (args_info);
860 >          args_info->dynamicProps_group_counter += 1;
861 >        
862 >          if (update_arg( 0 ,
863 >               0 , &(args_info->bondcorr_given),
864 >              &(local_args_info.bondcorr_given), optarg, 0, 0, ARG_NO,
865 >              check_ambiguity, override, 0, 0,
866 >              "bondcorr", 'b',
867 >              additional_error))
868 >            goto failure;
869 >        
870 >          break;
871 >        case 'f':       /* Frequency Fluctuation correlation function.  */
872 >        
873 >          if (args_info->dynamicProps_group_counter && override)
874 >            reset_group_dynamicProps (args_info);
875 >          args_info->dynamicProps_group_counter += 1;
876 >        
877 >          if (update_arg( 0 ,
878 >               0 , &(args_info->freqfluccorr_given),
879 >              &(local_args_info.freqfluccorr_given), optarg, 0, 0, ARG_NO,
880 >              check_ambiguity, override, 0, 0,
881 >              "freqfluccorr", 'f',
882 >              additional_error))
883 >            goto failure;
884 >        
885 >          break;
886  
887          case 0: /* Long option with no short option */
888            /* select first stuntdouble set.  */
889            if (strcmp (long_options[option_index].name, "sele1") == 0)
890            {
891 <            if (local_args_info.sele1_given)
892 <              {
893 <                fprintf (stderr, "%s: `--sele1' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
894 <                goto failure;
895 <              }
896 <            if (args_info->sele1_given && ! override)
897 <              continue;
898 <            local_args_info.sele1_given = 1;
899 <            args_info->sele1_given = 1;
900 <            if (args_info->sele1_arg)
523 <              free (args_info->sele1_arg); /* free previous string */
524 <            args_info->sele1_arg = gengetopt_strdup (optarg);
525 <            if (args_info->sele1_orig)
526 <              free (args_info->sele1_orig); /* free previous string */
527 <            args_info->sele1_orig = gengetopt_strdup (optarg);
891 >          
892 >          
893 >            if (update_arg( (void *)&(args_info->sele1_arg),
894 >                 &(args_info->sele1_orig), &(args_info->sele1_given),
895 >                &(local_args_info.sele1_given), optarg, 0, 0, ARG_STRING,
896 >                check_ambiguity, override, 0, 0,
897 >                "sele1", '-',
898 >                additional_error))
899 >              goto failure;
900 >          
901            }
902            /* select second stuntdouble set (if sele2 is not set, use script from sele1).  */
903            else if (strcmp (long_options[option_index].name, "sele2") == 0)
904            {
905 <            if (local_args_info.sele2_given)
906 <              {
907 <                fprintf (stderr, "%s: `--sele2' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
908 <                goto failure;
909 <              }
910 <            if (args_info->sele2_given && ! override)
911 <              continue;
912 <            local_args_info.sele2_given = 1;
913 <            args_info->sele2_given = 1;
914 <            if (args_info->sele2_arg)
542 <              free (args_info->sele2_arg); /* free previous string */
543 <            args_info->sele2_arg = gengetopt_strdup (optarg);
544 <            if (args_info->sele2_orig)
545 <              free (args_info->sele2_orig); /* free previous string */
546 <            args_info->sele2_orig = gengetopt_strdup (optarg);
905 >          
906 >          
907 >            if (update_arg( (void *)&(args_info->sele2_arg),
908 >                 &(args_info->sele2_orig), &(args_info->sele2_given),
909 >                &(local_args_info.sele2_given), optarg, 0, 0, ARG_STRING,
910 >                check_ambiguity, override, 0, 0,
911 >                "sele2", '-',
912 >                additional_error))
913 >              goto failure;
914 >          
915            }
916            /* Lengendre Polynomial Order.  */
917            else if (strcmp (long_options[option_index].name, "order") == 0)
918            {
919 <            if (local_args_info.order_given)
920 <              {
921 <                fprintf (stderr, "%s: `--order' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
922 <                goto failure;
923 <              }
924 <            if (args_info->order_given && ! override)
925 <              continue;
926 <            local_args_info.order_given = 1;
927 <            args_info->order_given = 1;
928 <            args_info->order_arg = strtol (optarg,&stop_char,0);
561 <            if (args_info->order_orig)
562 <              free (args_info->order_orig); /* free previous string */
563 <            args_info->order_orig = gengetopt_strdup (optarg);
919 >          
920 >          
921 >            if (update_arg( (void *)&(args_info->order_arg),
922 >                 &(args_info->order_orig), &(args_info->order_given),
923 >                &(local_args_info.order_given), optarg, 0, 0, ARG_INT,
924 >                check_ambiguity, override, 0, 0,
925 >                "order", '-',
926 >                additional_error))
927 >              goto failure;
928 >          
929            }
930 +          /* Lengendre correlation function binned by Z.  */
931 +          else if (strcmp (long_options[option_index].name, "lcorrZ") == 0)
932 +          {
933 +          
934 +            if (args_info->dynamicProps_group_counter && override)
935 +              reset_group_dynamicProps (args_info);
936 +            args_info->dynamicProps_group_counter += 1;
937 +          
938 +            if (update_arg( 0 ,
939 +                 0 , &(args_info->lcorrZ_given),
940 +                &(local_args_info.lcorrZ_given), optarg, 0, 0, ARG_NO,
941 +                check_ambiguity, override, 0, 0,
942 +                "lcorrZ", '-',
943 +                additional_error))
944 +              goto failure;
945 +          
946 +          }
947 +          /* Lengendre correlation function for OH bond vectors binned by Z.  */
948 +          else if (strcmp (long_options[option_index].name, "cohZ") == 0)
949 +          {
950 +          
951 +            if (args_info->dynamicProps_group_counter && override)
952 +              reset_group_dynamicProps (args_info);
953 +            args_info->dynamicProps_group_counter += 1;
954 +          
955 +            if (update_arg( 0 ,
956 +                 0 , &(args_info->cohZ_given),
957 +                &(local_args_info.cohZ_given), optarg, 0, 0, ARG_NO,
958 +                check_ambiguity, override, 0, 0,
959 +                "cohZ", '-',
960 +                additional_error))
961 +              goto failure;
962 +          
963 +          }
964            /* Radial rmsd.  */
965            else if (strcmp (long_options[option_index].name, "r_rcorr") == 0)
966            {
967 <            if (local_args_info.r_rcorr_given)
569 <              {
570 <                fprintf (stderr, "%s: `--r_rcorr' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
571 <                goto failure;
572 <              }
573 <            if (args_info->r_rcorr_given && ! override)
574 <              continue;
575 <            local_args_info.r_rcorr_given = 1;
576 <            args_info->r_rcorr_given = 1;
967 >          
968              if (args_info->dynamicProps_group_counter && override)
969                reset_group_dynamicProps (args_info);
970              args_info->dynamicProps_group_counter += 1;
971 <            break;
971 >          
972 >            if (update_arg( 0 ,
973 >                 0 , &(args_info->r_rcorr_given),
974 >                &(local_args_info.r_rcorr_given), optarg, 0, 0, ARG_NO,
975 >                check_ambiguity, override, 0, 0,
976 >                "r_rcorr", '-',
977 >                additional_error))
978 >              goto failure;
979 >          
980            }
981            /* Angular rmsd.  */
982            else if (strcmp (long_options[option_index].name, "thetacorr") == 0)
983            {
984 <            if (local_args_info.thetacorr_given)
586 <              {
587 <                fprintf (stderr, "%s: `--thetacorr' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
588 <                goto failure;
589 <              }
590 <            if (args_info->thetacorr_given && ! override)
591 <              continue;
592 <            local_args_info.thetacorr_given = 1;
593 <            args_info->thetacorr_given = 1;
984 >          
985              if (args_info->dynamicProps_group_counter && override)
986                reset_group_dynamicProps (args_info);
987              args_info->dynamicProps_group_counter += 1;
988 <            break;
988 >          
989 >            if (update_arg( 0 ,
990 >                 0 , &(args_info->thetacorr_given),
991 >                &(local_args_info.thetacorr_given), optarg, 0, 0, ARG_NO,
992 >                check_ambiguity, override, 0, 0,
993 >                "thetacorr", '-',
994 >                additional_error))
995 >              goto failure;
996 >          
997            }
998            /* Directional rmsd for particles with unit vectors.  */
999            else if (strcmp (long_options[option_index].name, "drcorr") == 0)
1000            {
1001 <            if (local_args_info.drcorr_given)
603 <              {
604 <                fprintf (stderr, "%s: `--drcorr' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
605 <                goto failure;
606 <              }
607 <            if (args_info->drcorr_given && ! override)
608 <              continue;
609 <            local_args_info.drcorr_given = 1;
610 <            args_info->drcorr_given = 1;
1001 >          
1002              if (args_info->dynamicProps_group_counter && override)
1003                reset_group_dynamicProps (args_info);
1004              args_info->dynamicProps_group_counter += 1;
1005 <            break;
1005 >          
1006 >            if (update_arg( 0 ,
1007 >                 0 , &(args_info->drcorr_given),
1008 >                &(local_args_info.drcorr_given), optarg, 0, 0, ARG_NO,
1009 >                check_ambiguity, override, 0, 0,
1010 >                "drcorr", '-',
1011 >                additional_error))
1012 >              goto failure;
1013 >          
1014            }
1015            /* Helfand moment for thermal conductvity.  */
1016            else if (strcmp (long_options[option_index].name, "helfandEcorr") == 0)
1017            {
1018 <            if (local_args_info.helfandEcorr_given)
620 <              {
621 <                fprintf (stderr, "%s: `--helfandEcorr' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
622 <                goto failure;
623 <              }
624 <            if (args_info->helfandEcorr_given && ! override)
625 <              continue;
626 <            local_args_info.helfandEcorr_given = 1;
627 <            args_info->helfandEcorr_given = 1;
1018 >          
1019              if (args_info->dynamicProps_group_counter && override)
1020                reset_group_dynamicProps (args_info);
1021              args_info->dynamicProps_group_counter += 1;
1022 <            break;
1022 >          
1023 >            if (update_arg( 0 ,
1024 >                 0 , &(args_info->helfandEcorr_given),
1025 >                &(local_args_info.helfandEcorr_given), optarg, 0, 0, ARG_NO,
1026 >                check_ambiguity, override, 0, 0,
1027 >                "helfandEcorr", '-',
1028 >                additional_error))
1029 >              goto failure;
1030 >          
1031            }
1032 +          /* Stress tensor correlation function.  */
1033 +          else if (strcmp (long_options[option_index].name, "stresscorr") == 0)
1034 +          {
1035            
1036 +            if (args_info->dynamicProps_group_counter && override)
1037 +              reset_group_dynamicProps (args_info);
1038 +            args_info->dynamicProps_group_counter += 1;
1039 +          
1040 +            if (update_arg( 0 ,
1041 +                 0 , &(args_info->stresscorr_given),
1042 +                &(local_args_info.stresscorr_given), optarg, 0, 0, ARG_NO,
1043 +                check_ambiguity, override, 0, 0,
1044 +                "stresscorr", '-',
1045 +                additional_error))
1046 +              goto failure;
1047 +          
1048 +          }
1049 +          
1050            break;
1051          case '?':       /* Invalid option.  */
1052            /* `getopt_long' already printed an error message.  */
# Line 644 | Line 1060 | cmdline_parser_internal (int argc, char * const *argv,
1060  
1061    if (args_info->dynamicProps_group_counter > 1)
1062      {
1063 <      fprintf (stderr, "%s: %d options of group dynamicProps were given. One is required.%s\n", argv[0], args_info->dynamicProps_group_counter, (additional_error ? additional_error : ""));
1063 >      fprintf (stderr, "%s: %d options of group dynamicProps were given. One is required%s.\n", argv[0], args_info->dynamicProps_group_counter, (additional_error ? additional_error : ""));
1064        error = 1;
1065      }
1066    
# Line 660 | Line 1076 | cmdline_parser_internal (int argc, char * const *argv,
1076    if ( error )
1077      return (EXIT_FAILURE);
1078  
1079 +  if (optind < argc)
1080 +    {
1081 +      int i = 0 ;
1082 +      int found_prog_name = 0;
1083 +      /* whether program name, i.e., argv[0], is in the remaining args
1084 +         (this may happen with some implementations of getopt,
1085 +          but surely not with the one included by gengetopt) */
1086 +
1087 +      i = optind;
1088 +      while (i < argc)
1089 +        if (argv[i++] == argv[0]) {
1090 +          found_prog_name = 1;
1091 +          break;
1092 +        }
1093 +      i = 0;
1094 +
1095 +      args_info->inputs_num = argc - optind - found_prog_name;
1096 +      args_info->inputs =
1097 +        (char **)(malloc ((args_info->inputs_num)*sizeof(char *))) ;
1098 +      while (optind < argc)
1099 +        if (argv[optind++] != argv[0])
1100 +          args_info->inputs[ i++ ] = gengetopt_strdup (argv[optind-1]) ;
1101 +    }
1102 +
1103    return 0;
1104  
1105   failure:

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