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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 1442 by gezelter, Mon May 10 17:28:26 2010 UTC vs.
trunk/src/applications/staticProps/StaticPropsCmd.cpp (file contents), Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 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 -u
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 = "";
# Line 38 | Line 46 | const char *gengetopt_args_info_help[] = {
46    "  -y, --nbins_y=INT             number of bins in y axis  (default=`100')",
47    "      --nbins_z=INT             number of bins in z axis  (default=`100')",
48    "  -a, --nanglebins=INT          number of bins for cos(angle)  (default=`50')",
41 –  "      --length=DOUBLE           maximum length (Defaults to 1/2 smallest length \n                                  of first frame)",
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')",
54    "      --sele1=selection script  select the first stuntdouble set",
55    "      --sele2=selection script  select the second stuntdouble set",
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 54 | 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 61 | 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",
# Line 69 | Line 82 | const char *gengetopt_args_info_help[] = {
82    "      --p_angle                 p(cos(theta))",
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      0
93   };
94  
# Line 85 | Line 104 | static int
104   void clear_args (struct gengetopt_args_info *args_info);
105  
106   static int
107 < cmdline_parser_internal (int argc, char * const *argv, struct gengetopt_args_info *args_info,
107 > cmdline_parser_internal (int argc, char **argv, struct gengetopt_args_info *args_info,
108                          struct cmdline_parser_params *params, const char *additional_error);
109  
110   static int
# Line 107 | Line 126 | void clear_given (struct gengetopt_args_info *args_inf
126    args_info->nbins_y_given = 0 ;
127    args_info->nbins_z_given = 0 ;
128    args_info->nanglebins_given = 0 ;
110 –  args_info->length_given = 0 ;
129    args_info->rcut_given = 0 ;
130 +  args_info->dz_given = 0 ;
131 +  args_info->length_given = 0 ;
132 +  args_info->zlength_given = 0 ;
133    args_info->zoffset_given = 0 ;
134    args_info->sele1_given = 0 ;
135    args_info->sele2_given = 0 ;
136    args_info->sele3_given = 0 ;
137    args_info->refsele_given = 0 ;
138    args_info->comsele_given = 0 ;
139 +  args_info->seleoffset_given = 0 ;
140    args_info->molname_given = 0 ;
141    args_info->begin_given = 0 ;
142    args_info->end_given = 0 ;
# Line 122 | Line 144 | void clear_given (struct gengetopt_args_info *args_inf
144    args_info->bo_given = 0 ;
145    args_info->bor_given = 0 ;
146    args_info->bad_given = 0 ;
147 +  args_info->count_given = 0 ;
148    args_info->gofr_given = 0 ;
149    args_info->gofz_given = 0 ;
150    args_info->r_theta_given = 0 ;
# Line 129 | Line 152 | void clear_given (struct gengetopt_args_info *args_inf
152    args_info->r_z_given = 0 ;
153    args_info->theta_omega_given = 0 ;
154    args_info->gxyz_given = 0 ;
155 +  args_info->twodgofr_given = 0 ;
156    args_info->p2_given = 0 ;
157    args_info->rp2_given = 0 ;
158    args_info->scd_given = 0 ;
# Line 137 | Line 161 | void clear_given (struct gengetopt_args_info *args_inf
161    args_info->p_angle_given = 0 ;
162    args_info->hxy_given = 0 ;
163    args_info->rho_r_given = 0 ;
164 +  args_info->angle_r_given = 0 ;
165    args_info->hullvol_given = 0 ;
166 +  args_info->rodlength_given = 0 ;
167 +  args_info->tet_param_given = 0 ;
168 +  args_info->tet_param_z_given = 0 ;
169 +  args_info->rnemdz_given = 0 ;
170 +  args_info->rnemdr_given = 0 ;
171    args_info->staticProps_group_counter = 0 ;
172   }
173  
174   static
175   void clear_args (struct gengetopt_args_info *args_info)
176   {
177 +  FIX_UNUSED (args_info);
178    args_info->input_arg = NULL;
179    args_info->input_orig = NULL;
180    args_info->output_arg = NULL;
# Line 160 | Line 191 | void clear_args (struct gengetopt_args_info *args_info
191    args_info->nbins_z_orig = NULL;
192    args_info->nanglebins_arg = 50;
193    args_info->nanglebins_orig = NULL;
163 –  args_info->length_orig = NULL;
194    args_info->rcut_orig = NULL;
195 +  args_info->dz_orig = NULL;
196 +  args_info->length_orig = NULL;
197 +  args_info->zlength_orig = NULL;
198    args_info->zoffset_arg = 0;
199    args_info->zoffset_orig = NULL;
200    args_info->sele1_arg = NULL;
# Line 174 | Line 207 | void clear_args (struct gengetopt_args_info *args_info
207    args_info->refsele_orig = NULL;
208    args_info->comsele_arg = NULL;
209    args_info->comsele_orig = NULL;
210 +  args_info->seleoffset_orig = NULL;
211    args_info->molname_arg = NULL;
212    args_info->molname_orig = NULL;
213    args_info->begin_orig = NULL;
# Line 197 | Line 231 | void init_args_info(struct gengetopt_args_info *args_i
231    args_info->nbins_y_help = gengetopt_args_info_help[7] ;
232    args_info->nbins_z_help = gengetopt_args_info_help[8] ;
233    args_info->nanglebins_help = gengetopt_args_info_help[9] ;
234 <  args_info->length_help = gengetopt_args_info_help[10] ;
235 <  args_info->rcut_help = gengetopt_args_info_help[11] ;
236 <  args_info->zoffset_help = gengetopt_args_info_help[12] ;
237 <  args_info->sele1_help = gengetopt_args_info_help[13] ;
238 <  args_info->sele2_help = gengetopt_args_info_help[14] ;
239 <  args_info->sele3_help = gengetopt_args_info_help[15] ;
240 <  args_info->refsele_help = gengetopt_args_info_help[16] ;
241 <  args_info->comsele_help = gengetopt_args_info_help[17] ;
242 <  args_info->molname_help = gengetopt_args_info_help[18] ;
243 <  args_info->begin_help = gengetopt_args_info_help[19] ;
244 <  args_info->end_help = gengetopt_args_info_help[20] ;
245 <  args_info->radius_help = gengetopt_args_info_help[21] ;
246 <  args_info->bo_help = gengetopt_args_info_help[23] ;
247 <  args_info->bor_help = gengetopt_args_info_help[24] ;
248 <  args_info->bad_help = gengetopt_args_info_help[25] ;
249 <  args_info->gofr_help = gengetopt_args_info_help[26] ;
250 <  args_info->gofz_help = gengetopt_args_info_help[27] ;
251 <  args_info->r_theta_help = gengetopt_args_info_help[28] ;
252 <  args_info->r_omega_help = gengetopt_args_info_help[29] ;
253 <  args_info->r_z_help = gengetopt_args_info_help[30] ;
254 <  args_info->theta_omega_help = gengetopt_args_info_help[31] ;
255 <  args_info->gxyz_help = gengetopt_args_info_help[32] ;
256 <  args_info->p2_help = gengetopt_args_info_help[33] ;
257 <  args_info->rp2_help = gengetopt_args_info_help[34] ;
258 <  args_info->scd_help = gengetopt_args_info_help[35] ;
259 <  args_info->density_help = gengetopt_args_info_help[36] ;
260 <  args_info->slab_density_help = gengetopt_args_info_help[37] ;
261 <  args_info->p_angle_help = gengetopt_args_info_help[38] ;
262 <  args_info->hxy_help = gengetopt_args_info_help[39] ;
263 <  args_info->rho_r_help = gengetopt_args_info_help[40] ;
264 <  args_info->hullvol_help = gengetopt_args_info_help[41] ;
234 >  args_info->rcut_help = gengetopt_args_info_help[10] ;
235 >  args_info->dz_help = gengetopt_args_info_help[11] ;
236 >  args_info->length_help = gengetopt_args_info_help[12] ;
237 >  args_info->zlength_help = gengetopt_args_info_help[13] ;
238 >  args_info->zoffset_help = gengetopt_args_info_help[14] ;
239 >  args_info->sele1_help = gengetopt_args_info_help[15] ;
240 >  args_info->sele2_help = gengetopt_args_info_help[16] ;
241 >  args_info->sele3_help = gengetopt_args_info_help[17] ;
242 >  args_info->refsele_help = gengetopt_args_info_help[18] ;
243 >  args_info->comsele_help = gengetopt_args_info_help[19] ;
244 >  args_info->seleoffset_help = gengetopt_args_info_help[20] ;
245 >  args_info->molname_help = gengetopt_args_info_help[21] ;
246 >  args_info->begin_help = gengetopt_args_info_help[22] ;
247 >  args_info->end_help = gengetopt_args_info_help[23] ;
248 >  args_info->radius_help = gengetopt_args_info_help[24] ;
249 >  args_info->bo_help = gengetopt_args_info_help[26] ;
250 >  args_info->bor_help = gengetopt_args_info_help[27] ;
251 >  args_info->bad_help = gengetopt_args_info_help[28] ;
252 >  args_info->count_help = gengetopt_args_info_help[29] ;
253 >  args_info->gofr_help = gengetopt_args_info_help[30] ;
254 >  args_info->gofz_help = gengetopt_args_info_help[31] ;
255 >  args_info->r_theta_help = gengetopt_args_info_help[32] ;
256 >  args_info->r_omega_help = gengetopt_args_info_help[33] ;
257 >  args_info->r_z_help = gengetopt_args_info_help[34] ;
258 >  args_info->theta_omega_help = gengetopt_args_info_help[35] ;
259 >  args_info->gxyz_help = gengetopt_args_info_help[36] ;
260 >  args_info->twodgofr_help = gengetopt_args_info_help[37] ;
261 >  args_info->p2_help = gengetopt_args_info_help[38] ;
262 >  args_info->rp2_help = gengetopt_args_info_help[39] ;
263 >  args_info->scd_help = gengetopt_args_info_help[40] ;
264 >  args_info->density_help = gengetopt_args_info_help[41] ;
265 >  args_info->slab_density_help = gengetopt_args_info_help[42] ;
266 >  args_info->p_angle_help = gengetopt_args_info_help[43] ;
267 >  args_info->hxy_help = gengetopt_args_info_help[44] ;
268 >  args_info->rho_r_help = gengetopt_args_info_help[45] ;
269 >  args_info->angle_r_help = gengetopt_args_info_help[46] ;
270 >  args_info->hullvol_help = gengetopt_args_info_help[47] ;
271 >  args_info->rodlength_help = gengetopt_args_info_help[48] ;
272 >  args_info->tet_param_help = gengetopt_args_info_help[49] ;
273 >  args_info->tet_param_z_help = gengetopt_args_info_help[50] ;
274 >  args_info->rnemdz_help = gengetopt_args_info_help[51] ;
275 >  args_info->rnemdr_help = gengetopt_args_info_help[52] ;
276    
277   }
278  
279   void
280   cmdline_parser_print_version (void)
281   {
282 <  printf ("%s %s\n", CMDLINE_PARSER_PACKAGE, CMDLINE_PARSER_VERSION);
282 >  printf ("%s %s\n",
283 >     (strlen(CMDLINE_PARSER_PACKAGE_NAME) ? CMDLINE_PARSER_PACKAGE_NAME : CMDLINE_PARSER_PACKAGE),
284 >     CMDLINE_PARSER_VERSION);
285   }
286  
287   static void print_help_common(void) {
# Line 249 | Line 296 | static void print_help_common(void) {
296    printf("\n");
297  
298    if (strlen(gengetopt_args_info_description) > 0)
299 <    printf("%s\n", gengetopt_args_info_description);
299 >    printf("%s\n\n", gengetopt_args_info_description);
300   }
301  
302   void
# Line 268 | Line 315 | cmdline_parser_init (struct gengetopt_args_info *args_
315    clear_args (args_info);
316    init_args_info (args_info);
317  
318 <  args_info->inputs = NULL;
318 >  args_info->inputs = 0;
319    args_info->inputs_num = 0;
320   }
321  
# Line 319 | Line 366 | cmdline_parser_release (struct gengetopt_args_info *ar
366    free_string_field (&(args_info->nbins_y_orig));
367    free_string_field (&(args_info->nbins_z_orig));
368    free_string_field (&(args_info->nanglebins_orig));
322 –  free_string_field (&(args_info->length_orig));
369    free_string_field (&(args_info->rcut_orig));
370 +  free_string_field (&(args_info->dz_orig));
371 +  free_string_field (&(args_info->length_orig));
372 +  free_string_field (&(args_info->zlength_orig));
373    free_string_field (&(args_info->zoffset_orig));
374    free_string_field (&(args_info->sele1_arg));
375    free_string_field (&(args_info->sele1_orig));
# Line 332 | Line 381 | cmdline_parser_release (struct gengetopt_args_info *ar
381    free_string_field (&(args_info->refsele_orig));
382    free_string_field (&(args_info->comsele_arg));
383    free_string_field (&(args_info->comsele_orig));
384 +  free_string_field (&(args_info->seleoffset_orig));
385    free_string_field (&(args_info->molname_arg));
386    free_string_field (&(args_info->molname_orig));
387    free_string_field (&(args_info->begin_orig));
# Line 350 | Line 400 | static void
400  
401  
402   static void
403 < write_into_file(FILE *outfile, const char *opt, const char *arg, char *values[])
403 > write_into_file(FILE *outfile, const char *opt, const char *arg, const char *values[])
404   {
405 +  FIX_UNUSED (values);
406    if (arg) {
407      fprintf(outfile, "%s=\"%s\"\n", opt, arg);
408    } else {
# Line 391 | Line 442 | cmdline_parser_dump(FILE *outfile, struct gengetopt_ar
442      write_into_file(outfile, "nbins_z", args_info->nbins_z_orig, 0);
443    if (args_info->nanglebins_given)
444      write_into_file(outfile, "nanglebins", args_info->nanglebins_orig, 0);
394 –  if (args_info->length_given)
395 –    write_into_file(outfile, "length", args_info->length_orig, 0);
445    if (args_info->rcut_given)
446      write_into_file(outfile, "rcut", args_info->rcut_orig, 0);
447 +  if (args_info->dz_given)
448 +    write_into_file(outfile, "dz", args_info->dz_orig, 0);
449 +  if (args_info->length_given)
450 +    write_into_file(outfile, "length", args_info->length_orig, 0);
451 +  if (args_info->zlength_given)
452 +    write_into_file(outfile, "zlength", args_info->zlength_orig, 0);
453    if (args_info->zoffset_given)
454      write_into_file(outfile, "zoffset", args_info->zoffset_orig, 0);
455    if (args_info->sele1_given)
# Line 407 | Line 462 | cmdline_parser_dump(FILE *outfile, struct gengetopt_ar
462      write_into_file(outfile, "refsele", args_info->refsele_orig, 0);
463    if (args_info->comsele_given)
464      write_into_file(outfile, "comsele", args_info->comsele_orig, 0);
465 +  if (args_info->seleoffset_given)
466 +    write_into_file(outfile, "seleoffset", args_info->seleoffset_orig, 0);
467    if (args_info->molname_given)
468      write_into_file(outfile, "molname", args_info->molname_orig, 0);
469    if (args_info->begin_given)
# Line 421 | Line 478 | cmdline_parser_dump(FILE *outfile, struct gengetopt_ar
478      write_into_file(outfile, "bor", 0, 0 );
479    if (args_info->bad_given)
480      write_into_file(outfile, "bad", 0, 0 );
481 +  if (args_info->count_given)
482 +    write_into_file(outfile, "count", 0, 0 );
483    if (args_info->gofr_given)
484      write_into_file(outfile, "gofr", 0, 0 );
485    if (args_info->gofz_given)
# Line 435 | Line 494 | cmdline_parser_dump(FILE *outfile, struct gengetopt_ar
494      write_into_file(outfile, "theta_omega", 0, 0 );
495    if (args_info->gxyz_given)
496      write_into_file(outfile, "gxyz", 0, 0 );
497 +  if (args_info->twodgofr_given)
498 +    write_into_file(outfile, "twodgofr", 0, 0 );
499    if (args_info->p2_given)
500      write_into_file(outfile, "p2", 0, 0 );
501    if (args_info->rp2_given)
# Line 451 | Line 512 | cmdline_parser_dump(FILE *outfile, struct gengetopt_ar
512      write_into_file(outfile, "hxy", 0, 0 );
513    if (args_info->rho_r_given)
514      write_into_file(outfile, "rho_r", 0, 0 );
515 +  if (args_info->angle_r_given)
516 +    write_into_file(outfile, "angle_r", 0, 0 );
517    if (args_info->hullvol_given)
518      write_into_file(outfile, "hullvol", 0, 0 );
519 +  if (args_info->rodlength_given)
520 +    write_into_file(outfile, "rodlength", 0, 0 );
521 +  if (args_info->tet_param_given)
522 +    write_into_file(outfile, "tet_param", 0, 0 );
523 +  if (args_info->tet_param_z_given)
524 +    write_into_file(outfile, "tet_param_z", 0, 0 );
525 +  if (args_info->rnemdz_given)
526 +    write_into_file(outfile, "rnemdz", 0, 0 );
527 +  if (args_info->rnemdr_given)
528 +    write_into_file(outfile, "rnemdr", 0, 0 );
529    
530  
531    i = EXIT_SUCCESS;
# Line 489 | Line 562 | gengetopt_strdup (const char *s)
562   char *
563   gengetopt_strdup (const char *s)
564   {
565 <  char *result = NULL;
565 >  char *result = 0;
566    if (!s)
567      return result;
568  
# Line 509 | Line 582 | reset_group_staticProps(struct gengetopt_args_info *ar
582    args_info->bo_given = 0 ;
583    args_info->bor_given = 0 ;
584    args_info->bad_given = 0 ;
585 +  args_info->count_given = 0 ;
586    args_info->gofr_given = 0 ;
587    args_info->gofz_given = 0 ;
588    args_info->r_theta_given = 0 ;
# Line 516 | Line 590 | reset_group_staticProps(struct gengetopt_args_info *ar
590    args_info->r_z_given = 0 ;
591    args_info->theta_omega_given = 0 ;
592    args_info->gxyz_given = 0 ;
593 +  args_info->twodgofr_given = 0 ;
594    args_info->p2_given = 0 ;
595    args_info->rp2_given = 0 ;
596    args_info->scd_given = 0 ;
# Line 524 | Line 599 | reset_group_staticProps(struct gengetopt_args_info *ar
599    args_info->p_angle_given = 0 ;
600    args_info->hxy_given = 0 ;
601    args_info->rho_r_given = 0 ;
602 +  args_info->angle_r_given = 0 ;
603    args_info->hullvol_given = 0 ;
604 +  args_info->rodlength_given = 0 ;
605 +  args_info->tet_param_given = 0 ;
606 +  args_info->tet_param_z_given = 0 ;
607 +  args_info->rnemdz_given = 0 ;
608 +  args_info->rnemdr_given = 0 ;
609  
610    args_info->staticProps_group_counter = 0;
611   }
612  
613   int
614 < cmdline_parser (int argc, char * const *argv, struct gengetopt_args_info *args_info)
614 > cmdline_parser (int argc, char **argv, struct gengetopt_args_info *args_info)
615   {
616    return cmdline_parser2 (argc, argv, args_info, 0, 1, 1);
617   }
618  
619   int
620 < cmdline_parser_ext (int argc, char * const *argv, struct gengetopt_args_info *args_info,
620 > cmdline_parser_ext (int argc, char **argv, struct gengetopt_args_info *args_info,
621                     struct cmdline_parser_params *params)
622   {
623    int result;
624 <  result = cmdline_parser_internal (argc, argv, args_info, params, NULL);
624 >  result = cmdline_parser_internal (argc, argv, args_info, params, 0);
625  
626    if (result == EXIT_FAILURE)
627      {
# Line 552 | Line 633 | int
633   }
634  
635   int
636 < cmdline_parser2 (int argc, char * const *argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required)
636 > cmdline_parser2 (int argc, char **argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required)
637   {
638    int result;
639    struct cmdline_parser_params params;
# Line 563 | Line 644 | cmdline_parser2 (int argc, char * const *argv, struct
644    params.check_ambiguity = 0;
645    params.print_errors = 1;
646  
647 <  result = cmdline_parser_internal (argc, argv, args_info, &params, NULL);
647 >  result = cmdline_parser_internal (argc, argv, args_info, &params, 0);
648  
649    if (result == EXIT_FAILURE)
650      {
# Line 579 | Line 660 | cmdline_parser_required (struct gengetopt_args_info *a
660   {
661    int result = EXIT_SUCCESS;
662  
663 <  if (cmdline_parser_required2(args_info, prog_name, NULL) > 0)
663 >  if (cmdline_parser_required2(args_info, prog_name, 0) > 0)
664      result = EXIT_FAILURE;
665  
666    if (result == EXIT_FAILURE)
# Line 595 | Line 676 | cmdline_parser_required2 (struct gengetopt_args_info *
676   cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error)
677   {
678    int error = 0;
679 +  FIX_UNUSED (additional_error);
680  
681    /* checks for required options */
682    if (! args_info->input_given)
# Line 605 | Line 687 | cmdline_parser_required2 (struct gengetopt_args_info *
687    
688    if (args_info->staticProps_group_counter == 0)
689      {
690 <      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 : ""));
690 >      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 : ""));
691        error = 1;
692      }
693    
# Line 639 | Line 721 | int update_arg(void *field, char **orig_field,
721   static
722   int update_arg(void *field, char **orig_field,
723                 unsigned int *field_given, unsigned int *prev_given,
724 <               char *value, char *possible_values[], const char *default_value,
724 >               char *value, const char *possible_values[],
725 >               const char *default_value,
726                 cmdline_parser_arg_type arg_type,
727                 int check_ambiguity, int override,
728                 int no_free, int multiple_option,
# Line 650 | Line 733 | int update_arg(void *field, char **orig_field,
733    const char *val = value;
734    int found;
735    char **string_field;
736 +  FIX_UNUSED (field);
737  
738    stop_char = 0;
739    found = 0;
# Line 667 | Line 751 | int update_arg(void *field, char **orig_field,
751        return 1; /* failure */
752      }
753  
754 +  FIX_UNUSED (default_value);
755      
756    if (field_given && *field_given && ! override)
757      return 0;
# Line 730 | Line 815 | int
815  
816  
817   int
818 < cmdline_parser_internal (int argc, char * const *argv, struct gengetopt_args_info *args_info,
818 > cmdline_parser_internal (
819 >  int argc, char **argv, struct gengetopt_args_info *args_info,
820                          struct cmdline_parser_params *params, const char *additional_error)
821   {
822    int c;        /* Character of the parsed option.  */
# Line 775 | Line 861 | cmdline_parser_internal (int argc, char * const *argv,
861          { "nbins_y",    1, NULL, 'y' },
862          { "nbins_z",    1, NULL, 0 },
863          { "nanglebins", 1, NULL, 'a' },
778 –        { "length",     1, NULL, 0 },
864          { "rcut",       1, NULL, 'c' },
865 +        { "dz", 1, NULL, 0 },
866 +        { "length",     1, NULL, 0 },
867 +        { "zlength",    1, NULL, 0 },
868          { "zoffset",    1, NULL, 'z' },
869          { "sele1",      1, NULL, 0 },
870          { "sele2",      1, NULL, 0 },
871          { "sele3",      1, NULL, 0 },
872          { "refsele",    1, NULL, 0 },
873          { "comsele",    1, NULL, 0 },
874 +        { "seleoffset", 1, NULL, 0 },
875          { "molname",    1, NULL, 0 },
876          { "begin",      1, NULL, 0 },
877          { "end",        1, NULL, 0 },
# Line 790 | Line 879 | cmdline_parser_internal (int argc, char * const *argv,
879          { "bo", 0, NULL, 0 },
880          { "bor",        0, NULL, 0 },
881          { "bad",        0, NULL, 0 },
882 +        { "count",      0, NULL, 0 },
883          { "gofr",       0, NULL, 'g' },
884          { "gofz",       0, NULL, 0 },
885          { "r_theta",    0, NULL, 0 },
# Line 797 | Line 887 | cmdline_parser_internal (int argc, char * const *argv,
887          { "r_z",        0, NULL, 0 },
888          { "theta_omega",        0, NULL, 0 },
889          { "gxyz",       0, NULL, 0 },
890 +        { "twodgofr",   0, NULL, 0 },
891          { "p2", 0, NULL, 'p' },
892          { "rp2",        0, NULL, 0 },
893          { "scd",        0, NULL, 's' },
# Line 805 | Line 896 | cmdline_parser_internal (int argc, char * const *argv,
896          { "p_angle",    0, NULL, 0 },
897          { "hxy",        0, NULL, 0 },
898          { "rho_r",      0, NULL, 0 },
899 +        { "angle_r",    0, NULL, 0 },
900          { "hullvol",    0, NULL, 0 },
901 <        { NULL, 0, NULL, 0 }
901 >        { "rodlength",  0, NULL, 0 },
902 >        { "tet_param",  0, NULL, 'Q' },
903 >        { "tet_param_z",        0, NULL, 0 },
904 >        { "rnemdz",     0, NULL, 0 },
905 >        { "rnemdr",     0, NULL, 0 },
906 >        { 0,  0, 0, 0 }
907        };
908  
909 <      c = getopt_long (argc, argv, "hVi:o:n:b:x:y:a:c:z:gpsd", long_options, &option_index);
909 >      c = getopt_long (argc, argv, "hVi:o:n:b:x:y:a:c:z:gpsdQ", long_options, &option_index);
910  
911        if (c == -1) break;       /* Exit from `while (1)' loop.  */
912  
# Line 948 | Line 1045 | cmdline_parser_internal (int argc, char * const *argv,
1045              goto failure;
1046          
1047            break;
1048 <        case 'p':       /* p2 order parameter (--sele1 and --sele2 must be specified).  */
1048 >        case 'p':       /* p2 order parameter (--sele1 must be specified, --sele2 is optional).  */
1049          
1050            if (args_info->staticProps_group_counter && override)
1051              reset_group_staticProps (args_info);
# Line 993 | Line 1090 | cmdline_parser_internal (int argc, char * const *argv,
1090              goto failure;
1091          
1092            break;
1093 +        case 'Q':       /* tetrahedrality order parameter (Qk).  */
1094 +        
1095 +          if (args_info->staticProps_group_counter && override)
1096 +            reset_group_staticProps (args_info);
1097 +          args_info->staticProps_group_counter += 1;
1098 +        
1099 +          if (update_arg( 0 ,
1100 +               0 , &(args_info->tet_param_given),
1101 +              &(local_args_info.tet_param_given), optarg, 0, 0, ARG_NO,
1102 +              check_ambiguity, override, 0, 0,
1103 +              "tet_param", 'Q',
1104 +              additional_error))
1105 +            goto failure;
1106 +        
1107 +          break;
1108  
1109          case 0: /* Long option with no short option */
1110            /* number of bins in z axis.  */
# Line 1009 | Line 1121 | cmdline_parser_internal (int argc, char * const *argv,
1121                goto failure;
1122            
1123            }
1124 +          /* slab width (dz).  */
1125 +          else if (strcmp (long_options[option_index].name, "dz") == 0)
1126 +          {
1127 +          
1128 +          
1129 +            if (update_arg( (void *)&(args_info->dz_arg),
1130 +                 &(args_info->dz_orig), &(args_info->dz_given),
1131 +                &(local_args_info.dz_given), optarg, 0, 0, ARG_DOUBLE,
1132 +                check_ambiguity, override, 0, 0,
1133 +                "dz", '-',
1134 +                additional_error))
1135 +              goto failure;
1136 +          
1137 +          }
1138            /* maximum length (Defaults to 1/2 smallest length of first frame).  */
1139            else if (strcmp (long_options[option_index].name, "length") == 0)
1140            {
# Line 1019 | Line 1145 | cmdline_parser_internal (int argc, char * const *argv,
1145                  &(local_args_info.length_given), optarg, 0, 0, ARG_DOUBLE,
1146                  check_ambiguity, override, 0, 0,
1147                  "length", '-',
1148 +                additional_error))
1149 +              goto failure;
1150 +          
1151 +          }
1152 +          /* maximum length (Defaults to 1/2 smallest length of first frame).  */
1153 +          else if (strcmp (long_options[option_index].name, "zlength") == 0)
1154 +          {
1155 +          
1156 +          
1157 +            if (update_arg( (void *)&(args_info->zlength_arg),
1158 +                 &(args_info->zlength_orig), &(args_info->zlength_given),
1159 +                &(local_args_info.zlength_given), optarg, 0, 0, ARG_DOUBLE,
1160 +                check_ambiguity, override, 0, 0,
1161 +                "zlength", '-',
1162                  additional_error))
1163                goto failure;
1164            
# Line 1089 | Line 1229 | cmdline_parser_internal (int argc, char * const *argv,
1229                  &(local_args_info.comsele_given), optarg, 0, 0, ARG_STRING,
1230                  check_ambiguity, override, 0, 0,
1231                  "comsele", '-',
1232 +                additional_error))
1233 +              goto failure;
1234 +          
1235 +          }
1236 +          /* global index offset for a second object (used to define a vector between sites in molecule).  */
1237 +          else if (strcmp (long_options[option_index].name, "seleoffset") == 0)
1238 +          {
1239 +          
1240 +          
1241 +            if (update_arg( (void *)&(args_info->seleoffset_arg),
1242 +                 &(args_info->seleoffset_orig), &(args_info->seleoffset_given),
1243 +                &(local_args_info.seleoffset_given), optarg, 0, 0, ARG_INT,
1244 +                check_ambiguity, override, 0, 0,
1245 +                "seleoffset", '-',
1246                  additional_error))
1247                goto failure;
1248            
# Line 1200 | Line 1354 | cmdline_parser_internal (int argc, char * const *argv,
1354                goto failure;
1355            
1356            }
1357 +          /* count of molecules matching selection criteria (and associated statistics).  */
1358 +          else if (strcmp (long_options[option_index].name, "count") == 0)
1359 +          {
1360 +          
1361 +            if (args_info->staticProps_group_counter && override)
1362 +              reset_group_staticProps (args_info);
1363 +            args_info->staticProps_group_counter += 1;
1364 +          
1365 +            if (update_arg( 0 ,
1366 +                 0 , &(args_info->count_given),
1367 +                &(local_args_info.count_given), optarg, 0, 0, ARG_NO,
1368 +                check_ambiguity, override, 0, 0,
1369 +                "count", '-',
1370 +                additional_error))
1371 +              goto failure;
1372 +          
1373 +          }
1374            /* g(z).  */
1375            else if (strcmp (long_options[option_index].name, "gofz") == 0)
1376            {
# Line 1302 | Line 1473 | cmdline_parser_internal (int argc, char * const *argv,
1473                goto failure;
1474            
1475            }
1476 +          /* 2D g(r) (Slab width --dz must be specified).  */
1477 +          else if (strcmp (long_options[option_index].name, "twodgofr") == 0)
1478 +          {
1479 +          
1480 +            if (args_info->staticProps_group_counter && override)
1481 +              reset_group_staticProps (args_info);
1482 +            args_info->staticProps_group_counter += 1;
1483 +          
1484 +            if (update_arg( 0 ,
1485 +                 0 , &(args_info->twodgofr_given),
1486 +                &(local_args_info.twodgofr_given), optarg, 0, 0, ARG_NO,
1487 +                check_ambiguity, override, 0, 0,
1488 +                "twodgofr", '-',
1489 +                additional_error))
1490 +              goto failure;
1491 +          
1492 +          }
1493            /* rp2 order parameter (--sele1 and --sele2 must be specified).  */
1494            else if (strcmp (long_options[option_index].name, "rp2") == 0)
1495            {
# Line 1387 | Line 1575 | cmdline_parser_internal (int argc, char * const *argv,
1575                goto failure;
1576            
1577            }
1578 +          /* angle of R.  */
1579 +          else if (strcmp (long_options[option_index].name, "angle_r") == 0)
1580 +          {
1581 +          
1582 +            if (args_info->staticProps_group_counter && override)
1583 +              reset_group_staticProps (args_info);
1584 +            args_info->staticProps_group_counter += 1;
1585 +          
1586 +            if (update_arg( 0 ,
1587 +                 0 , &(args_info->angle_r_given),
1588 +                &(local_args_info.angle_r_given), optarg, 0, 0, ARG_NO,
1589 +                check_ambiguity, override, 0, 0,
1590 +                "angle_r", '-',
1591 +                additional_error))
1592 +              goto failure;
1593 +          
1594 +          }
1595            /* hull volume of nanoparticle.  */
1596            else if (strcmp (long_options[option_index].name, "hullvol") == 0)
1597            {
# Line 1404 | Line 1609 | cmdline_parser_internal (int argc, char * const *argv,
1609                goto failure;
1610            
1611            }
1612 +          /* length of nanorod.  */
1613 +          else if (strcmp (long_options[option_index].name, "rodlength") == 0)
1614 +          {
1615            
1616 +            if (args_info->staticProps_group_counter && override)
1617 +              reset_group_staticProps (args_info);
1618 +            args_info->staticProps_group_counter += 1;
1619 +          
1620 +            if (update_arg( 0 ,
1621 +                 0 , &(args_info->rodlength_given),
1622 +                &(local_args_info.rodlength_given), optarg, 0, 0, ARG_NO,
1623 +                check_ambiguity, override, 0, 0,
1624 +                "rodlength", '-',
1625 +                additional_error))
1626 +              goto failure;
1627 +          
1628 +          }
1629 +          /* spatially-resolved tetrahedrality order parameter Qk(z).  */
1630 +          else if (strcmp (long_options[option_index].name, "tet_param_z") == 0)
1631 +          {
1632 +          
1633 +            if (args_info->staticProps_group_counter && override)
1634 +              reset_group_staticProps (args_info);
1635 +            args_info->staticProps_group_counter += 1;
1636 +          
1637 +            if (update_arg( 0 ,
1638 +                 0 , &(args_info->tet_param_z_given),
1639 +                &(local_args_info.tet_param_z_given), optarg, 0, 0, ARG_NO,
1640 +                check_ambiguity, override, 0, 0,
1641 +                "tet_param_z", '-',
1642 +                additional_error))
1643 +              goto failure;
1644 +          
1645 +          }
1646 +          /* slab-resolved RNEMD statistics (temperature, density, velocity).  */
1647 +          else if (strcmp (long_options[option_index].name, "rnemdz") == 0)
1648 +          {
1649 +          
1650 +            if (args_info->staticProps_group_counter && override)
1651 +              reset_group_staticProps (args_info);
1652 +            args_info->staticProps_group_counter += 1;
1653 +          
1654 +            if (update_arg( 0 ,
1655 +                 0 , &(args_info->rnemdz_given),
1656 +                &(local_args_info.rnemdz_given), optarg, 0, 0, ARG_NO,
1657 +                check_ambiguity, override, 0, 0,
1658 +                "rnemdz", '-',
1659 +                additional_error))
1660 +              goto failure;
1661 +          
1662 +          }
1663 +          /* shell-resolved RNEMD statistics (temperature, density, angular velocity).  */
1664 +          else if (strcmp (long_options[option_index].name, "rnemdr") == 0)
1665 +          {
1666 +          
1667 +            if (args_info->staticProps_group_counter && override)
1668 +              reset_group_staticProps (args_info);
1669 +            args_info->staticProps_group_counter += 1;
1670 +          
1671 +            if (update_arg( 0 ,
1672 +                 0 , &(args_info->rnemdr_given),
1673 +                &(local_args_info.rnemdr_given), optarg, 0, 0, ARG_NO,
1674 +                check_ambiguity, override, 0, 0,
1675 +                "rnemdr", '-',
1676 +                additional_error))
1677 +              goto failure;
1678 +          
1679 +          }
1680 +          
1681            break;
1682          case '?':       /* Invalid option.  */
1683            /* `getopt_long' already printed an error message.  */
# Line 1418 | Line 1691 | cmdline_parser_internal (int argc, char * const *argv,
1691  
1692    if (args_info->staticProps_group_counter > 1)
1693      {
1694 <      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 : ""));
1694 >      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 : ""));
1695        error = 1;
1696      }
1697    

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