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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 1445 by chuckv, Tue Jun 8 20:26:50 2010 UTC vs.
trunk/src/applications/staticProps/StaticPropsCmd.cpp (file contents), Revision 1979 by gezelter, Sat Apr 5 20:56:01 2014 UTC

# Line 1 | Line 1
1   /*
2 <  File autogenerated by gengetopt version 2.22
2 >  File autogenerated by gengetopt version 2.22.4
3    generated with the following command:
4 <  gengetopt -F StaticPropsCmd
4 >  gengetopt --file-name=StaticPropsCmd --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 "StaticPropsCmd.h"
31  
32   const char *gengetopt_args_info_purpose = "";
33  
34 < const char *gengetopt_args_info_usage = "Usage: StaticProps [OPTIONS]...";
34 > const char *gengetopt_args_info_usage = "Usage: StaticProps [OPTIONS]... [FILES]...";
35  
36   const char *gengetopt_args_info_description = "";
37  
# Line 39 | Line 47 | const char *gengetopt_args_info_help[] = {
47    "      --nbins_z=INT             number of bins in z axis  (default=`100')",
48    "  -a, --nanglebins=INT          number of bins for cos(angle)  (default=`50')",
49    "  -c, --rcut=DOUBLE             cutoff radius (rcut)",
50 +  "      --dz=DOUBLE               slab width (dz)",
51    "      --length=DOUBLE           maximum length (Defaults to 1/2 smallest length \n                                  of first frame)",
52    "      --zlength=DOUBLE          maximum length (Defaults to 1/2 smallest length \n                                  of first frame)",
53    "  -z, --zoffset=DOUBLE          Where to set the zero for the slab_density \n                                  calculation  (default=`0')",
# Line 47 | Line 56 | const char *gengetopt_args_info_help[] = {
56    "      --sele3=selection script  select the third stuntdouble set",
57    "      --refsele=selection script\n                                select reference (use and only use with --gxyz)",
58    "      --comsele=selection script\n                                select stunt doubles for center-of-mass \n                                  reference point",
59 +  "      --seleoffset=INT          global index offset for a second object (used \n                                  to define a vector between sites in molecule)",
60    "      --molname=STRING          molecule name",
61    "      --begin=INT               begin internal index",
62    "      --end=INT                 end internal index",
# Line 55 | Line 65 | const char *gengetopt_args_info_help[] = {
65    "      --bo                      bond order parameter (--rcut must be specified)",
66    "      --bor                     bond order parameter as a function of radius \n                                  (--rcut must be specified)",
67    "      --bad                     N(theta) bond angle density within (--rcut must \n                                  be specified)",
68 +  "      --count                   count of molecules matching selection criteria \n                                  (and associated statistics)",
69    "  -g, --gofr                    g(r)",
70    "      --gofz                    g(z)",
71    "      --r_theta                 g(r, cos(theta))",
# Line 62 | Line 73 | const char *gengetopt_args_info_help[] = {
73    "      --r_z                     g(r, z)",
74    "      --theta_omega             g(cos(theta), cos(omega))",
75    "      --gxyz                    g(x, y, z)",
76 <  "  -p, --p2                      p2 order parameter (--sele1 and --sele2 must be \n                                  specified)",
76 >  "      --twodgofr                2D g(r) (Slab width --dz must be specified)",
77 >  "  -p, --p2                      p2 order parameter (--sele1 must be specified, \n                                  --sele2 is optional)",
78    "      --rp2                     rp2 order parameter (--sele1 and --sele2 must \n                                  be specified)",
79    "  -s, --scd                     scd order parameter (either --sele1, --sele2, \n                                  --sele3 are specified or --molname, --begin, \n                                  --end are specified)",
80    "  -d, --density                 density plot",
81    "      --slab_density            slab density",
82 <  "      --p_angle                 p(cos(theta))",
82 >  "      --p_angle                 p(cos(theta)) (--sele1 must be specified, \n                                  --sele2 is optional)",
83    "      --hxy                     hxy",
84    "      --rho_r                   rho of R",
85 +  "      --angle_r                 angle of R",
86    "      --hullvol                 hull volume of nanoparticle",
87 +  "      --rodlength               length of nanorod",
88 +  "  -Q, --tet_param               tetrahedrality order parameter (Qk)",
89 +  "      --tet_param_z             spatially-resolved tetrahedrality order \n                                  parameter Qk(z)",
90 +  "      --rnemdz                  slab-resolved RNEMD statistics (temperature, \n                                  density, velocity)",
91 +  "      --rnemdr                  shell-resolved RNEMD statistics (temperature, \n                                  density, angular velocity)",
92 +  "      --rnemdrt                 shell and angle-resolved RNEMD statistics \n                                  (temperature, density, angular velocity)",
93      0
94   };
95  
# Line 86 | Line 105 | static int
105   void clear_args (struct gengetopt_args_info *args_info);
106  
107   static int
108 < cmdline_parser_internal (int argc, char * const *argv, struct gengetopt_args_info *args_info,
108 > cmdline_parser_internal (int argc, char **argv, struct gengetopt_args_info *args_info,
109                          struct cmdline_parser_params *params, const char *additional_error);
110  
111   static int
# Line 109 | Line 128 | void clear_given (struct gengetopt_args_info *args_inf
128    args_info->nbins_z_given = 0 ;
129    args_info->nanglebins_given = 0 ;
130    args_info->rcut_given = 0 ;
131 +  args_info->dz_given = 0 ;
132    args_info->length_given = 0 ;
133    args_info->zlength_given = 0 ;
134    args_info->zoffset_given = 0 ;
# Line 117 | Line 137 | void clear_given (struct gengetopt_args_info *args_inf
137    args_info->sele3_given = 0 ;
138    args_info->refsele_given = 0 ;
139    args_info->comsele_given = 0 ;
140 +  args_info->seleoffset_given = 0 ;
141    args_info->molname_given = 0 ;
142    args_info->begin_given = 0 ;
143    args_info->end_given = 0 ;
# Line 124 | Line 145 | void clear_given (struct gengetopt_args_info *args_inf
145    args_info->bo_given = 0 ;
146    args_info->bor_given = 0 ;
147    args_info->bad_given = 0 ;
148 +  args_info->count_given = 0 ;
149    args_info->gofr_given = 0 ;
150    args_info->gofz_given = 0 ;
151    args_info->r_theta_given = 0 ;
# Line 131 | Line 153 | void clear_given (struct gengetopt_args_info *args_inf
153    args_info->r_z_given = 0 ;
154    args_info->theta_omega_given = 0 ;
155    args_info->gxyz_given = 0 ;
156 +  args_info->twodgofr_given = 0 ;
157    args_info->p2_given = 0 ;
158    args_info->rp2_given = 0 ;
159    args_info->scd_given = 0 ;
# Line 139 | Line 162 | void clear_given (struct gengetopt_args_info *args_inf
162    args_info->p_angle_given = 0 ;
163    args_info->hxy_given = 0 ;
164    args_info->rho_r_given = 0 ;
165 +  args_info->angle_r_given = 0 ;
166    args_info->hullvol_given = 0 ;
167 +  args_info->rodlength_given = 0 ;
168 +  args_info->tet_param_given = 0 ;
169 +  args_info->tet_param_z_given = 0 ;
170 +  args_info->rnemdz_given = 0 ;
171 +  args_info->rnemdr_given = 0 ;
172 +  args_info->rnemdrt_given = 0 ;
173    args_info->staticProps_group_counter = 0 ;
174   }
175  
176   static
177   void clear_args (struct gengetopt_args_info *args_info)
178   {
179 +  FIX_UNUSED (args_info);
180    args_info->input_arg = NULL;
181    args_info->input_orig = NULL;
182    args_info->output_arg = NULL;
# Line 163 | Line 194 | void clear_args (struct gengetopt_args_info *args_info
194    args_info->nanglebins_arg = 50;
195    args_info->nanglebins_orig = NULL;
196    args_info->rcut_orig = NULL;
197 +  args_info->dz_orig = NULL;
198    args_info->length_orig = NULL;
199    args_info->zlength_orig = NULL;
200    args_info->zoffset_arg = 0;
# Line 177 | Line 209 | void clear_args (struct gengetopt_args_info *args_info
209    args_info->refsele_orig = NULL;
210    args_info->comsele_arg = NULL;
211    args_info->comsele_orig = NULL;
212 +  args_info->seleoffset_orig = NULL;
213    args_info->molname_arg = NULL;
214    args_info->molname_orig = NULL;
215    args_info->begin_orig = NULL;
# Line 201 | Line 234 | void init_args_info(struct gengetopt_args_info *args_i
234    args_info->nbins_z_help = gengetopt_args_info_help[8] ;
235    args_info->nanglebins_help = gengetopt_args_info_help[9] ;
236    args_info->rcut_help = gengetopt_args_info_help[10] ;
237 <  args_info->length_help = gengetopt_args_info_help[11] ;
238 <  args_info->zlength_help = gengetopt_args_info_help[12] ;
239 <  args_info->zoffset_help = gengetopt_args_info_help[13] ;
240 <  args_info->sele1_help = gengetopt_args_info_help[14] ;
241 <  args_info->sele2_help = gengetopt_args_info_help[15] ;
242 <  args_info->sele3_help = gengetopt_args_info_help[16] ;
243 <  args_info->refsele_help = gengetopt_args_info_help[17] ;
244 <  args_info->comsele_help = gengetopt_args_info_help[18] ;
245 <  args_info->molname_help = gengetopt_args_info_help[19] ;
246 <  args_info->begin_help = gengetopt_args_info_help[20] ;
247 <  args_info->end_help = gengetopt_args_info_help[21] ;
248 <  args_info->radius_help = gengetopt_args_info_help[22] ;
249 <  args_info->bo_help = gengetopt_args_info_help[24] ;
250 <  args_info->bor_help = gengetopt_args_info_help[25] ;
251 <  args_info->bad_help = gengetopt_args_info_help[26] ;
252 <  args_info->gofr_help = gengetopt_args_info_help[27] ;
253 <  args_info->gofz_help = gengetopt_args_info_help[28] ;
254 <  args_info->r_theta_help = gengetopt_args_info_help[29] ;
255 <  args_info->r_omega_help = gengetopt_args_info_help[30] ;
256 <  args_info->r_z_help = gengetopt_args_info_help[31] ;
257 <  args_info->theta_omega_help = gengetopt_args_info_help[32] ;
258 <  args_info->gxyz_help = gengetopt_args_info_help[33] ;
259 <  args_info->p2_help = gengetopt_args_info_help[34] ;
260 <  args_info->rp2_help = gengetopt_args_info_help[35] ;
261 <  args_info->scd_help = gengetopt_args_info_help[36] ;
262 <  args_info->density_help = gengetopt_args_info_help[37] ;
263 <  args_info->slab_density_help = gengetopt_args_info_help[38] ;
264 <  args_info->p_angle_help = gengetopt_args_info_help[39] ;
265 <  args_info->hxy_help = gengetopt_args_info_help[40] ;
266 <  args_info->rho_r_help = gengetopt_args_info_help[41] ;
267 <  args_info->hullvol_help = gengetopt_args_info_help[42] ;
237 >  args_info->dz_help = gengetopt_args_info_help[11] ;
238 >  args_info->length_help = gengetopt_args_info_help[12] ;
239 >  args_info->zlength_help = gengetopt_args_info_help[13] ;
240 >  args_info->zoffset_help = gengetopt_args_info_help[14] ;
241 >  args_info->sele1_help = gengetopt_args_info_help[15] ;
242 >  args_info->sele2_help = gengetopt_args_info_help[16] ;
243 >  args_info->sele3_help = gengetopt_args_info_help[17] ;
244 >  args_info->refsele_help = gengetopt_args_info_help[18] ;
245 >  args_info->comsele_help = gengetopt_args_info_help[19] ;
246 >  args_info->seleoffset_help = gengetopt_args_info_help[20] ;
247 >  args_info->molname_help = gengetopt_args_info_help[21] ;
248 >  args_info->begin_help = gengetopt_args_info_help[22] ;
249 >  args_info->end_help = gengetopt_args_info_help[23] ;
250 >  args_info->radius_help = gengetopt_args_info_help[24] ;
251 >  args_info->bo_help = gengetopt_args_info_help[26] ;
252 >  args_info->bor_help = gengetopt_args_info_help[27] ;
253 >  args_info->bad_help = gengetopt_args_info_help[28] ;
254 >  args_info->count_help = gengetopt_args_info_help[29] ;
255 >  args_info->gofr_help = gengetopt_args_info_help[30] ;
256 >  args_info->gofz_help = gengetopt_args_info_help[31] ;
257 >  args_info->r_theta_help = gengetopt_args_info_help[32] ;
258 >  args_info->r_omega_help = gengetopt_args_info_help[33] ;
259 >  args_info->r_z_help = gengetopt_args_info_help[34] ;
260 >  args_info->theta_omega_help = gengetopt_args_info_help[35] ;
261 >  args_info->gxyz_help = gengetopt_args_info_help[36] ;
262 >  args_info->twodgofr_help = gengetopt_args_info_help[37] ;
263 >  args_info->p2_help = gengetopt_args_info_help[38] ;
264 >  args_info->rp2_help = gengetopt_args_info_help[39] ;
265 >  args_info->scd_help = gengetopt_args_info_help[40] ;
266 >  args_info->density_help = gengetopt_args_info_help[41] ;
267 >  args_info->slab_density_help = gengetopt_args_info_help[42] ;
268 >  args_info->p_angle_help = gengetopt_args_info_help[43] ;
269 >  args_info->hxy_help = gengetopt_args_info_help[44] ;
270 >  args_info->rho_r_help = gengetopt_args_info_help[45] ;
271 >  args_info->angle_r_help = gengetopt_args_info_help[46] ;
272 >  args_info->hullvol_help = gengetopt_args_info_help[47] ;
273 >  args_info->rodlength_help = gengetopt_args_info_help[48] ;
274 >  args_info->tet_param_help = gengetopt_args_info_help[49] ;
275 >  args_info->tet_param_z_help = gengetopt_args_info_help[50] ;
276 >  args_info->rnemdz_help = gengetopt_args_info_help[51] ;
277 >  args_info->rnemdr_help = gengetopt_args_info_help[52] ;
278 >  args_info->rnemdrt_help = gengetopt_args_info_help[53] ;
279    
280   }
281  
282   void
283   cmdline_parser_print_version (void)
284   {
285 <  printf ("%s %s\n", CMDLINE_PARSER_PACKAGE, CMDLINE_PARSER_VERSION);
285 >  printf ("%s %s\n",
286 >     (strlen(CMDLINE_PARSER_PACKAGE_NAME) ? CMDLINE_PARSER_PACKAGE_NAME : CMDLINE_PARSER_PACKAGE),
287 >     CMDLINE_PARSER_VERSION);
288   }
289  
290   static void print_help_common(void) {
# Line 253 | Line 299 | static void print_help_common(void) {
299    printf("\n");
300  
301    if (strlen(gengetopt_args_info_description) > 0)
302 <    printf("%s\n", gengetopt_args_info_description);
302 >    printf("%s\n\n", gengetopt_args_info_description);
303   }
304  
305   void
# Line 271 | Line 317 | cmdline_parser_init (struct gengetopt_args_info *args_
317    clear_given (args_info);
318    clear_args (args_info);
319    init_args_info (args_info);
320 +
321 +  args_info->inputs = 0;
322 +  args_info->inputs_num = 0;
323   }
324  
325   void
# Line 309 | Line 358 | cmdline_parser_release (struct gengetopt_args_info *ar
358   static void
359   cmdline_parser_release (struct gengetopt_args_info *args_info)
360   {
361 <
361 >  unsigned int i;
362    free_string_field (&(args_info->input_arg));
363    free_string_field (&(args_info->input_orig));
364    free_string_field (&(args_info->output_arg));
# Line 321 | Line 370 | cmdline_parser_release (struct gengetopt_args_info *ar
370    free_string_field (&(args_info->nbins_z_orig));
371    free_string_field (&(args_info->nanglebins_orig));
372    free_string_field (&(args_info->rcut_orig));
373 +  free_string_field (&(args_info->dz_orig));
374    free_string_field (&(args_info->length_orig));
375    free_string_field (&(args_info->zlength_orig));
376    free_string_field (&(args_info->zoffset_orig));
# Line 334 | Line 384 | cmdline_parser_release (struct gengetopt_args_info *ar
384    free_string_field (&(args_info->refsele_orig));
385    free_string_field (&(args_info->comsele_arg));
386    free_string_field (&(args_info->comsele_orig));
387 +  free_string_field (&(args_info->seleoffset_orig));
388    free_string_field (&(args_info->molname_arg));
389    free_string_field (&(args_info->molname_orig));
390    free_string_field (&(args_info->begin_orig));
# Line 341 | Line 392 | cmdline_parser_release (struct gengetopt_args_info *ar
392    free_string_field (&(args_info->radius_orig));
393    
394    
395 +  for (i = 0; i < args_info->inputs_num; ++i)
396 +    free (args_info->inputs [i]);
397  
398 +  if (args_info->inputs_num)
399 +    free (args_info->inputs);
400 +
401    clear_given (args_info);
402   }
403  
404  
405   static void
406 < write_into_file(FILE *outfile, const char *opt, const char *arg, char *values[])
406 > write_into_file(FILE *outfile, const char *opt, const char *arg, const char *values[])
407   {
408 +  FIX_UNUSED (values);
409    if (arg) {
410      fprintf(outfile, "%s=\"%s\"\n", opt, arg);
411    } else {
# Line 390 | Line 447 | cmdline_parser_dump(FILE *outfile, struct gengetopt_ar
447      write_into_file(outfile, "nanglebins", args_info->nanglebins_orig, 0);
448    if (args_info->rcut_given)
449      write_into_file(outfile, "rcut", args_info->rcut_orig, 0);
450 +  if (args_info->dz_given)
451 +    write_into_file(outfile, "dz", args_info->dz_orig, 0);
452    if (args_info->length_given)
453      write_into_file(outfile, "length", args_info->length_orig, 0);
454    if (args_info->zlength_given)
# Line 406 | Line 465 | cmdline_parser_dump(FILE *outfile, struct gengetopt_ar
465      write_into_file(outfile, "refsele", args_info->refsele_orig, 0);
466    if (args_info->comsele_given)
467      write_into_file(outfile, "comsele", args_info->comsele_orig, 0);
468 +  if (args_info->seleoffset_given)
469 +    write_into_file(outfile, "seleoffset", args_info->seleoffset_orig, 0);
470    if (args_info->molname_given)
471      write_into_file(outfile, "molname", args_info->molname_orig, 0);
472    if (args_info->begin_given)
# Line 420 | Line 481 | cmdline_parser_dump(FILE *outfile, struct gengetopt_ar
481      write_into_file(outfile, "bor", 0, 0 );
482    if (args_info->bad_given)
483      write_into_file(outfile, "bad", 0, 0 );
484 +  if (args_info->count_given)
485 +    write_into_file(outfile, "count", 0, 0 );
486    if (args_info->gofr_given)
487      write_into_file(outfile, "gofr", 0, 0 );
488    if (args_info->gofz_given)
# Line 434 | Line 497 | cmdline_parser_dump(FILE *outfile, struct gengetopt_ar
497      write_into_file(outfile, "theta_omega", 0, 0 );
498    if (args_info->gxyz_given)
499      write_into_file(outfile, "gxyz", 0, 0 );
500 +  if (args_info->twodgofr_given)
501 +    write_into_file(outfile, "twodgofr", 0, 0 );
502    if (args_info->p2_given)
503      write_into_file(outfile, "p2", 0, 0 );
504    if (args_info->rp2_given)
# Line 450 | Line 515 | cmdline_parser_dump(FILE *outfile, struct gengetopt_ar
515      write_into_file(outfile, "hxy", 0, 0 );
516    if (args_info->rho_r_given)
517      write_into_file(outfile, "rho_r", 0, 0 );
518 +  if (args_info->angle_r_given)
519 +    write_into_file(outfile, "angle_r", 0, 0 );
520    if (args_info->hullvol_given)
521      write_into_file(outfile, "hullvol", 0, 0 );
522 +  if (args_info->rodlength_given)
523 +    write_into_file(outfile, "rodlength", 0, 0 );
524 +  if (args_info->tet_param_given)
525 +    write_into_file(outfile, "tet_param", 0, 0 );
526 +  if (args_info->tet_param_z_given)
527 +    write_into_file(outfile, "tet_param_z", 0, 0 );
528 +  if (args_info->rnemdz_given)
529 +    write_into_file(outfile, "rnemdz", 0, 0 );
530 +  if (args_info->rnemdr_given)
531 +    write_into_file(outfile, "rnemdr", 0, 0 );
532 +  if (args_info->rnemdrt_given)
533 +    write_into_file(outfile, "rnemdrt", 0, 0 );
534    
535  
536    i = EXIT_SUCCESS;
# Line 488 | Line 567 | gengetopt_strdup (const char *s)
567   char *
568   gengetopt_strdup (const char *s)
569   {
570 <  char *result = NULL;
570 >  char *result = 0;
571    if (!s)
572      return result;
573  
# Line 508 | Line 587 | reset_group_staticProps(struct gengetopt_args_info *ar
587    args_info->bo_given = 0 ;
588    args_info->bor_given = 0 ;
589    args_info->bad_given = 0 ;
590 +  args_info->count_given = 0 ;
591    args_info->gofr_given = 0 ;
592    args_info->gofz_given = 0 ;
593    args_info->r_theta_given = 0 ;
# Line 515 | Line 595 | reset_group_staticProps(struct gengetopt_args_info *ar
595    args_info->r_z_given = 0 ;
596    args_info->theta_omega_given = 0 ;
597    args_info->gxyz_given = 0 ;
598 +  args_info->twodgofr_given = 0 ;
599    args_info->p2_given = 0 ;
600    args_info->rp2_given = 0 ;
601    args_info->scd_given = 0 ;
# Line 523 | Line 604 | reset_group_staticProps(struct gengetopt_args_info *ar
604    args_info->p_angle_given = 0 ;
605    args_info->hxy_given = 0 ;
606    args_info->rho_r_given = 0 ;
607 +  args_info->angle_r_given = 0 ;
608    args_info->hullvol_given = 0 ;
609 +  args_info->rodlength_given = 0 ;
610 +  args_info->tet_param_given = 0 ;
611 +  args_info->tet_param_z_given = 0 ;
612 +  args_info->rnemdz_given = 0 ;
613 +  args_info->rnemdr_given = 0 ;
614 +  args_info->rnemdrt_given = 0 ;
615  
616    args_info->staticProps_group_counter = 0;
617   }
618  
619   int
620 < cmdline_parser (int argc, char * const *argv, struct gengetopt_args_info *args_info)
620 > cmdline_parser (int argc, char **argv, struct gengetopt_args_info *args_info)
621   {
622    return cmdline_parser2 (argc, argv, args_info, 0, 1, 1);
623   }
624  
625   int
626 < cmdline_parser_ext (int argc, char * const *argv, struct gengetopt_args_info *args_info,
626 > cmdline_parser_ext (int argc, char **argv, struct gengetopt_args_info *args_info,
627                     struct cmdline_parser_params *params)
628   {
629    int result;
630 <  result = cmdline_parser_internal (argc, argv, args_info, params, NULL);
630 >  result = cmdline_parser_internal (argc, argv, args_info, params, 0);
631  
632    if (result == EXIT_FAILURE)
633      {
# Line 551 | Line 639 | int
639   }
640  
641   int
642 < cmdline_parser2 (int argc, char * const *argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required)
642 > cmdline_parser2 (int argc, char **argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required)
643   {
644    int result;
645    struct cmdline_parser_params params;
# Line 562 | Line 650 | cmdline_parser2 (int argc, char * const *argv, struct
650    params.check_ambiguity = 0;
651    params.print_errors = 1;
652  
653 <  result = cmdline_parser_internal (argc, argv, args_info, &params, NULL);
653 >  result = cmdline_parser_internal (argc, argv, args_info, &params, 0);
654  
655    if (result == EXIT_FAILURE)
656      {
# Line 578 | Line 666 | cmdline_parser_required (struct gengetopt_args_info *a
666   {
667    int result = EXIT_SUCCESS;
668  
669 <  if (cmdline_parser_required2(args_info, prog_name, NULL) > 0)
669 >  if (cmdline_parser_required2(args_info, prog_name, 0) > 0)
670      result = EXIT_FAILURE;
671  
672    if (result == EXIT_FAILURE)
# Line 594 | Line 682 | cmdline_parser_required2 (struct gengetopt_args_info *
682   cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error)
683   {
684    int error = 0;
685 +  FIX_UNUSED (additional_error);
686  
687    /* checks for required options */
688    if (! args_info->input_given)
# Line 604 | Line 693 | cmdline_parser_required2 (struct gengetopt_args_info *
693    
694    if (args_info->staticProps_group_counter == 0)
695      {
696 <      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 : ""));
696 >      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 : ""));
697        error = 1;
698      }
699    
# Line 638 | Line 727 | int update_arg(void *field, char **orig_field,
727   static
728   int update_arg(void *field, char **orig_field,
729                 unsigned int *field_given, unsigned int *prev_given,
730 <               char *value, char *possible_values[], const char *default_value,
730 >               char *value, const char *possible_values[],
731 >               const char *default_value,
732                 cmdline_parser_arg_type arg_type,
733                 int check_ambiguity, int override,
734                 int no_free, int multiple_option,
# Line 649 | Line 739 | int update_arg(void *field, char **orig_field,
739    const char *val = value;
740    int found;
741    char **string_field;
742 +  FIX_UNUSED (field);
743  
744    stop_char = 0;
745    found = 0;
# Line 666 | Line 757 | int update_arg(void *field, char **orig_field,
757        return 1; /* failure */
758      }
759  
760 +  FIX_UNUSED (default_value);
761      
762    if (field_given && *field_given && ! override)
763      return 0;
# Line 729 | Line 821 | int
821  
822  
823   int
824 < cmdline_parser_internal (int argc, char * const *argv, struct gengetopt_args_info *args_info,
824 > cmdline_parser_internal (
825 >  int argc, char **argv, struct gengetopt_args_info *args_info,
826                          struct cmdline_parser_params *params, const char *additional_error)
827   {
828    int c;        /* Character of the parsed option.  */
# Line 775 | Line 868 | cmdline_parser_internal (int argc, char * const *argv,
868          { "nbins_z",    1, NULL, 0 },
869          { "nanglebins", 1, NULL, 'a' },
870          { "rcut",       1, NULL, 'c' },
871 +        { "dz", 1, NULL, 0 },
872          { "length",     1, NULL, 0 },
873          { "zlength",    1, NULL, 0 },
874          { "zoffset",    1, NULL, 'z' },
# Line 783 | Line 877 | cmdline_parser_internal (int argc, char * const *argv,
877          { "sele3",      1, NULL, 0 },
878          { "refsele",    1, NULL, 0 },
879          { "comsele",    1, NULL, 0 },
880 +        { "seleoffset", 1, NULL, 0 },
881          { "molname",    1, NULL, 0 },
882          { "begin",      1, NULL, 0 },
883          { "end",        1, NULL, 0 },
# Line 790 | Line 885 | cmdline_parser_internal (int argc, char * const *argv,
885          { "bo", 0, NULL, 0 },
886          { "bor",        0, NULL, 0 },
887          { "bad",        0, NULL, 0 },
888 +        { "count",      0, NULL, 0 },
889          { "gofr",       0, NULL, 'g' },
890          { "gofz",       0, NULL, 0 },
891          { "r_theta",    0, NULL, 0 },
# Line 797 | Line 893 | cmdline_parser_internal (int argc, char * const *argv,
893          { "r_z",        0, NULL, 0 },
894          { "theta_omega",        0, NULL, 0 },
895          { "gxyz",       0, NULL, 0 },
896 +        { "twodgofr",   0, NULL, 0 },
897          { "p2", 0, NULL, 'p' },
898          { "rp2",        0, NULL, 0 },
899          { "scd",        0, NULL, 's' },
# Line 805 | Line 902 | cmdline_parser_internal (int argc, char * const *argv,
902          { "p_angle",    0, NULL, 0 },
903          { "hxy",        0, NULL, 0 },
904          { "rho_r",      0, NULL, 0 },
905 +        { "angle_r",    0, NULL, 0 },
906          { "hullvol",    0, NULL, 0 },
907 <        { NULL, 0, NULL, 0 }
907 >        { "rodlength",  0, NULL, 0 },
908 >        { "tet_param",  0, NULL, 'Q' },
909 >        { "tet_param_z",        0, NULL, 0 },
910 >        { "rnemdz",     0, NULL, 0 },
911 >        { "rnemdr",     0, NULL, 0 },
912 >        { "rnemdrt",    0, NULL, 0 },
913 >        { 0,  0, 0, 0 }
914        };
915  
916 <      c = getopt_long (argc, argv, "hVi:o:n:b:x:y:a:c:z:gpsd", long_options, &option_index);
916 >      c = getopt_long (argc, argv, "hVi:o:n:b:x:y:a:c:z:gpsdQ", long_options, &option_index);
917  
918        if (c == -1) break;       /* Exit from `while (1)' loop.  */
919  
# Line 948 | Line 1052 | cmdline_parser_internal (int argc, char * const *argv,
1052              goto failure;
1053          
1054            break;
1055 <        case 'p':       /* p2 order parameter (--sele1 and --sele2 must be specified).  */
1055 >        case 'p':       /* p2 order parameter (--sele1 must be specified, --sele2 is optional).  */
1056          
1057            if (args_info->staticProps_group_counter && override)
1058              reset_group_staticProps (args_info);
# Line 993 | Line 1097 | cmdline_parser_internal (int argc, char * const *argv,
1097              goto failure;
1098          
1099            break;
1100 +        case 'Q':       /* tetrahedrality order parameter (Qk).  */
1101 +        
1102 +          if (args_info->staticProps_group_counter && override)
1103 +            reset_group_staticProps (args_info);
1104 +          args_info->staticProps_group_counter += 1;
1105 +        
1106 +          if (update_arg( 0 ,
1107 +               0 , &(args_info->tet_param_given),
1108 +              &(local_args_info.tet_param_given), optarg, 0, 0, ARG_NO,
1109 +              check_ambiguity, override, 0, 0,
1110 +              "tet_param", 'Q',
1111 +              additional_error))
1112 +            goto failure;
1113 +        
1114 +          break;
1115  
1116          case 0: /* Long option with no short option */
1117            /* number of bins in z axis.  */
# Line 1005 | Line 1124 | cmdline_parser_internal (int argc, char * const *argv,
1124                  &(local_args_info.nbins_z_given), optarg, 0, "100", ARG_INT,
1125                  check_ambiguity, override, 0, 0,
1126                  "nbins_z", '-',
1127 +                additional_error))
1128 +              goto failure;
1129 +          
1130 +          }
1131 +          /* slab width (dz).  */
1132 +          else if (strcmp (long_options[option_index].name, "dz") == 0)
1133 +          {
1134 +          
1135 +          
1136 +            if (update_arg( (void *)&(args_info->dz_arg),
1137 +                 &(args_info->dz_orig), &(args_info->dz_given),
1138 +                &(local_args_info.dz_given), optarg, 0, 0, ARG_DOUBLE,
1139 +                check_ambiguity, override, 0, 0,
1140 +                "dz", '-',
1141                  additional_error))
1142                goto failure;
1143            
# Line 1107 | Line 1240 | cmdline_parser_internal (int argc, char * const *argv,
1240                goto failure;
1241            
1242            }
1243 +          /* global index offset for a second object (used to define a vector between sites in molecule).  */
1244 +          else if (strcmp (long_options[option_index].name, "seleoffset") == 0)
1245 +          {
1246 +          
1247 +          
1248 +            if (update_arg( (void *)&(args_info->seleoffset_arg),
1249 +                 &(args_info->seleoffset_orig), &(args_info->seleoffset_given),
1250 +                &(local_args_info.seleoffset_given), optarg, 0, 0, ARG_INT,
1251 +                check_ambiguity, override, 0, 0,
1252 +                "seleoffset", '-',
1253 +                additional_error))
1254 +              goto failure;
1255 +          
1256 +          }
1257            /* molecule name.  */
1258            else if (strcmp (long_options[option_index].name, "molname") == 0)
1259            {
# Line 1214 | Line 1361 | cmdline_parser_internal (int argc, char * const *argv,
1361                goto failure;
1362            
1363            }
1364 +          /* count of molecules matching selection criteria (and associated statistics).  */
1365 +          else if (strcmp (long_options[option_index].name, "count") == 0)
1366 +          {
1367 +          
1368 +            if (args_info->staticProps_group_counter && override)
1369 +              reset_group_staticProps (args_info);
1370 +            args_info->staticProps_group_counter += 1;
1371 +          
1372 +            if (update_arg( 0 ,
1373 +                 0 , &(args_info->count_given),
1374 +                &(local_args_info.count_given), optarg, 0, 0, ARG_NO,
1375 +                check_ambiguity, override, 0, 0,
1376 +                "count", '-',
1377 +                additional_error))
1378 +              goto failure;
1379 +          
1380 +          }
1381            /* g(z).  */
1382            else if (strcmp (long_options[option_index].name, "gofz") == 0)
1383            {
# Line 1316 | Line 1480 | cmdline_parser_internal (int argc, char * const *argv,
1480                goto failure;
1481            
1482            }
1483 +          /* 2D g(r) (Slab width --dz must be specified).  */
1484 +          else if (strcmp (long_options[option_index].name, "twodgofr") == 0)
1485 +          {
1486 +          
1487 +            if (args_info->staticProps_group_counter && override)
1488 +              reset_group_staticProps (args_info);
1489 +            args_info->staticProps_group_counter += 1;
1490 +          
1491 +            if (update_arg( 0 ,
1492 +                 0 , &(args_info->twodgofr_given),
1493 +                &(local_args_info.twodgofr_given), optarg, 0, 0, ARG_NO,
1494 +                check_ambiguity, override, 0, 0,
1495 +                "twodgofr", '-',
1496 +                additional_error))
1497 +              goto failure;
1498 +          
1499 +          }
1500            /* rp2 order parameter (--sele1 and --sele2 must be specified).  */
1501            else if (strcmp (long_options[option_index].name, "rp2") == 0)
1502            {
# Line 1350 | Line 1531 | cmdline_parser_internal (int argc, char * const *argv,
1531                goto failure;
1532            
1533            }
1534 <          /* p(cos(theta)).  */
1534 >          /* p(cos(theta)) (--sele1 must be specified, --sele2 is optional).  */
1535            else if (strcmp (long_options[option_index].name, "p_angle") == 0)
1536            {
1537            
# Line 1401 | Line 1582 | cmdline_parser_internal (int argc, char * const *argv,
1582                goto failure;
1583            
1584            }
1585 +          /* angle of R.  */
1586 +          else if (strcmp (long_options[option_index].name, "angle_r") == 0)
1587 +          {
1588 +          
1589 +            if (args_info->staticProps_group_counter && override)
1590 +              reset_group_staticProps (args_info);
1591 +            args_info->staticProps_group_counter += 1;
1592 +          
1593 +            if (update_arg( 0 ,
1594 +                 0 , &(args_info->angle_r_given),
1595 +                &(local_args_info.angle_r_given), optarg, 0, 0, ARG_NO,
1596 +                check_ambiguity, override, 0, 0,
1597 +                "angle_r", '-',
1598 +                additional_error))
1599 +              goto failure;
1600 +          
1601 +          }
1602            /* hull volume of nanoparticle.  */
1603            else if (strcmp (long_options[option_index].name, "hullvol") == 0)
1604            {
# Line 1414 | Line 1612 | cmdline_parser_internal (int argc, char * const *argv,
1612                  &(local_args_info.hullvol_given), optarg, 0, 0, ARG_NO,
1613                  check_ambiguity, override, 0, 0,
1614                  "hullvol", '-',
1615 +                additional_error))
1616 +              goto failure;
1617 +          
1618 +          }
1619 +          /* length of nanorod.  */
1620 +          else if (strcmp (long_options[option_index].name, "rodlength") == 0)
1621 +          {
1622 +          
1623 +            if (args_info->staticProps_group_counter && override)
1624 +              reset_group_staticProps (args_info);
1625 +            args_info->staticProps_group_counter += 1;
1626 +          
1627 +            if (update_arg( 0 ,
1628 +                 0 , &(args_info->rodlength_given),
1629 +                &(local_args_info.rodlength_given), optarg, 0, 0, ARG_NO,
1630 +                check_ambiguity, override, 0, 0,
1631 +                "rodlength", '-',
1632                  additional_error))
1633                goto failure;
1634            
1635            }
1636 +          /* spatially-resolved tetrahedrality order parameter Qk(z).  */
1637 +          else if (strcmp (long_options[option_index].name, "tet_param_z") == 0)
1638 +          {
1639            
1640 +            if (args_info->staticProps_group_counter && override)
1641 +              reset_group_staticProps (args_info);
1642 +            args_info->staticProps_group_counter += 1;
1643 +          
1644 +            if (update_arg( 0 ,
1645 +                 0 , &(args_info->tet_param_z_given),
1646 +                &(local_args_info.tet_param_z_given), optarg, 0, 0, ARG_NO,
1647 +                check_ambiguity, override, 0, 0,
1648 +                "tet_param_z", '-',
1649 +                additional_error))
1650 +              goto failure;
1651 +          
1652 +          }
1653 +          /* slab-resolved RNEMD statistics (temperature, density, velocity).  */
1654 +          else if (strcmp (long_options[option_index].name, "rnemdz") == 0)
1655 +          {
1656 +          
1657 +            if (args_info->staticProps_group_counter && override)
1658 +              reset_group_staticProps (args_info);
1659 +            args_info->staticProps_group_counter += 1;
1660 +          
1661 +            if (update_arg( 0 ,
1662 +                 0 , &(args_info->rnemdz_given),
1663 +                &(local_args_info.rnemdz_given), optarg, 0, 0, ARG_NO,
1664 +                check_ambiguity, override, 0, 0,
1665 +                "rnemdz", '-',
1666 +                additional_error))
1667 +              goto failure;
1668 +          
1669 +          }
1670 +          /* shell-resolved RNEMD statistics (temperature, density, angular velocity).  */
1671 +          else if (strcmp (long_options[option_index].name, "rnemdr") == 0)
1672 +          {
1673 +          
1674 +            if (args_info->staticProps_group_counter && override)
1675 +              reset_group_staticProps (args_info);
1676 +            args_info->staticProps_group_counter += 1;
1677 +          
1678 +            if (update_arg( 0 ,
1679 +                 0 , &(args_info->rnemdr_given),
1680 +                &(local_args_info.rnemdr_given), optarg, 0, 0, ARG_NO,
1681 +                check_ambiguity, override, 0, 0,
1682 +                "rnemdr", '-',
1683 +                additional_error))
1684 +              goto failure;
1685 +          
1686 +          }
1687 +          /* shell and angle-resolved RNEMD statistics (temperature, density, angular velocity).  */
1688 +          else if (strcmp (long_options[option_index].name, "rnemdrt") == 0)
1689 +          {
1690 +          
1691 +            if (args_info->staticProps_group_counter && override)
1692 +              reset_group_staticProps (args_info);
1693 +            args_info->staticProps_group_counter += 1;
1694 +          
1695 +            if (update_arg( 0 ,
1696 +                 0 , &(args_info->rnemdrt_given),
1697 +                &(local_args_info.rnemdrt_given), optarg, 0, 0, ARG_NO,
1698 +                check_ambiguity, override, 0, 0,
1699 +                "rnemdrt", '-',
1700 +                additional_error))
1701 +              goto failure;
1702 +          
1703 +          }
1704 +          
1705            break;
1706          case '?':       /* Invalid option.  */
1707            /* `getopt_long' already printed an error message.  */
# Line 1432 | Line 1715 | cmdline_parser_internal (int argc, char * const *argv,
1715  
1716    if (args_info->staticProps_group_counter > 1)
1717      {
1718 <      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 : ""));
1718 >      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 : ""));
1719        error = 1;
1720      }
1721    
# Line 1448 | Line 1731 | cmdline_parser_internal (int argc, char * const *argv,
1731    if ( error )
1732      return (EXIT_FAILURE);
1733  
1734 +  if (optind < argc)
1735 +    {
1736 +      int i = 0 ;
1737 +      int found_prog_name = 0;
1738 +      /* whether program name, i.e., argv[0], is in the remaining args
1739 +         (this may happen with some implementations of getopt,
1740 +          but surely not with the one included by gengetopt) */
1741 +
1742 +      i = optind;
1743 +      while (i < argc)
1744 +        if (argv[i++] == argv[0]) {
1745 +          found_prog_name = 1;
1746 +          break;
1747 +        }
1748 +      i = 0;
1749 +
1750 +      args_info->inputs_num = argc - optind - found_prog_name;
1751 +      args_info->inputs =
1752 +        (char **)(malloc ((args_info->inputs_num)*sizeof(char *))) ;
1753 +      while (optind < argc)
1754 +        if (argv[optind++] != argv[0])
1755 +          args_info->inputs[ i++ ] = gengetopt_strdup (argv[optind-1]) ;
1756 +    }
1757 +
1758    return 0;
1759  
1760   failure:

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