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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 1039 by gezelter, Tue Sep 19 21:14:11 2006 UTC vs.
Revision 1128 by chuckv, Wed Apr 11 23:27:20 2007 UTC

# Line 1 | Line 1
1   /*
2 <  File autogenerated by gengetopt version 2.16
2 >  File autogenerated by gengetopt version 2.19.1
3    generated with the following command:
4 <  gengetopt -F StaticPropsCmd
4 >  gengetopt -i StaticProps.ggo -F StaticPropsCmd -u
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 21 | Line 21
21  
22   #include "StaticPropsCmd.h"
23  
24 + const char *gengetopt_args_info_purpose = "";
25 +
26 + const char *gengetopt_args_info_usage = "Usage: StaticProps [OPTIONS]... [FILES]...";
27 +
28 + const char *gengetopt_args_info_description = "";
29 +
30 + const char *gengetopt_args_info_help[] = {
31 +  "  -h, --help                    Print help and exit",
32 +  "  -V, --version                 Print version and exit",
33 +  "  -i, --input=filename          input dump file",
34 +  "  -o, --output=filename         output file name",
35 +  "  -n, --step=INT                process every n frame  (default=`1')",
36 +  "  -b, --nbins=INT               number of bins (general purpose)  \n                                  (default=`100')",
37 +  "  -x, --nbins_x=INT             number of bins in x axis  (default=`100')",
38 +  "  -y, --nbins_y=INT             number of bins in y axis  (default=`100')",
39 +  "  -a, --nanglebins=INT          number of bins for cos(angle)  (default=`50')",
40 +  "      --length=DOUBLE           maximum length (Defaults to 1/2 smallest length \n                                  of first frame)",
41 +  "  -c, --rcut=DOUBLE             cutoff radius (rcut)",
42 +  "  -z, --zoffset=DOUBLE          Where to set the zero for the slab_density \n                                  calculation  (default=`0')",
43 +  "      --sele1=selection script  select the first stuntdouble set",
44 +  "      --sele2=selection script  select the second stuntdouble set",
45 +  "      --sele3=selection script  select the third stuntdouble set",
46 +  "      --refsele=selection script\n                                select reference (use and only use with --gxyz)",
47 +  "      --molname=STRING          molecule name",
48 +  "      --begin=INT               begin internal index",
49 +  "      --end=INT                 end internal index",
50 +  "      --radius=DOUBLE           nanoparticle radius",
51 +  "\n Group: staticProps\n   an option of this group is required",
52 +  "      --bo                      bond order parameter (--rcut must be specified)",
53 +  "      --bor                     bond order parameter as a function of radius \n                                  (--rcut must be specified)",
54 +  "  -g, --gofr                    g(r)",
55 +  "      --r_theta                 g(r, cos(theta))",
56 +  "      --r_omega                 g(r, cos(omega))",
57 +  "      --theta_omega             g(cos(theta), cos(omega))",
58 +  "      --gxyz                    g(x, y, z)",
59 +  "  -p, --p2                      p2 order parameter (--sele1 and --sele2 must be \n                                  specified)",
60 +  "      --rp2                     rp2 order parameter (--sele1 and --sele2 must \n                                  be specified)",
61 +  "  -s, --scd                     scd order parameter (either --sele1, --sele2, \n                                  --sele3 are specified or --molname, --begin, \n                                  --end are specified)",
62 +  "  -d, --density                 density plot",
63 +  "      --slab_density            slab density",
64 +  "      --hxy                     hxy",
65 +  "      --rho_r                   rho of R",
66 +    0
67 + };
68 +
69   static
70   void clear_given (struct gengetopt_args_info *args_info);
71   static
# Line 43 | Line 88 | void clear_given (struct gengetopt_args_info *args_inf
88    args_info->input_given = 0 ;
89    args_info->output_given = 0 ;
90    args_info->step_given = 0 ;
91 <  args_info->nrbins_given = 0 ;
91 >  args_info->nbins_given = 0 ;
92    args_info->nbins_x_given = 0 ;
93    args_info->nbins_y_given = 0 ;
94    args_info->nanglebins_given = 0 ;
95    args_info->length_given = 0 ;
51 –  args_info->LegendreL_given = 0 ;
96    args_info->rcut_given = 0 ;
97    args_info->zoffset_given = 0 ;
98    args_info->sele1_given = 0 ;
# Line 58 | Line 102 | void clear_given (struct gengetopt_args_info *args_inf
102    args_info->molname_given = 0 ;
103    args_info->begin_given = 0 ;
104    args_info->end_given = 0 ;
105 +  args_info->radius_given = 0 ;
106    args_info->bo_given = 0 ;
107 +  args_info->bor_given = 0 ;
108    args_info->gofr_given = 0 ;
109    args_info->r_theta_given = 0 ;
110    args_info->r_omega_given = 0 ;
# Line 70 | Line 116 | void clear_given (struct gengetopt_args_info *args_inf
116    args_info->density_given = 0 ;
117    args_info->slab_density_given = 0 ;
118    args_info->hxy_given = 0 ;
119 +  args_info->rho_r_given = 0 ;
120    args_info->staticProps_group_counter = 0 ;
121   }
122  
# Line 82 | Line 129 | void clear_args (struct gengetopt_args_info *args_info
129    args_info->output_orig = NULL;
130    args_info->step_arg = 1;
131    args_info->step_orig = NULL;
132 <  args_info->nrbins_arg = 100;
133 <  args_info->nrbins_orig = NULL;
132 >  args_info->nbins_arg = 100;
133 >  args_info->nbins_orig = NULL;
134    args_info->nbins_x_arg = 100;
135    args_info->nbins_x_orig = NULL;
136    args_info->nbins_y_arg = 100;
# Line 91 | Line 138 | void clear_args (struct gengetopt_args_info *args_info
138    args_info->nanglebins_arg = 50;
139    args_info->nanglebins_orig = NULL;
140    args_info->length_orig = NULL;
94 –  args_info->LegendreL_orig = NULL;
141    args_info->rcut_orig = NULL;
142    args_info->zoffset_arg = 0;
143    args_info->zoffset_orig = NULL;
# Line 107 | Line 153 | void clear_args (struct gengetopt_args_info *args_info
153    args_info->molname_orig = NULL;
154    args_info->begin_orig = NULL;
155    args_info->end_orig = NULL;
156 +  args_info->radius_orig = NULL;
157    
158   }
159  
160 + static
161 + void init_args_info(struct gengetopt_args_info *args_info)
162 + {
163 +  args_info->help_help = gengetopt_args_info_help[0] ;
164 +  args_info->version_help = gengetopt_args_info_help[1] ;
165 +  args_info->input_help = gengetopt_args_info_help[2] ;
166 +  args_info->output_help = gengetopt_args_info_help[3] ;
167 +  args_info->step_help = gengetopt_args_info_help[4] ;
168 +  args_info->nbins_help = gengetopt_args_info_help[5] ;
169 +  args_info->nbins_x_help = gengetopt_args_info_help[6] ;
170 +  args_info->nbins_y_help = gengetopt_args_info_help[7] ;
171 +  args_info->nanglebins_help = gengetopt_args_info_help[8] ;
172 +  args_info->length_help = gengetopt_args_info_help[9] ;
173 +  args_info->rcut_help = gengetopt_args_info_help[10] ;
174 +  args_info->zoffset_help = gengetopt_args_info_help[11] ;
175 +  args_info->sele1_help = gengetopt_args_info_help[12] ;
176 +  args_info->sele2_help = gengetopt_args_info_help[13] ;
177 +  args_info->sele3_help = gengetopt_args_info_help[14] ;
178 +  args_info->refsele_help = gengetopt_args_info_help[15] ;
179 +  args_info->molname_help = gengetopt_args_info_help[16] ;
180 +  args_info->begin_help = gengetopt_args_info_help[17] ;
181 +  args_info->end_help = gengetopt_args_info_help[18] ;
182 +  args_info->radius_help = gengetopt_args_info_help[19] ;
183 +  args_info->bo_help = gengetopt_args_info_help[20] ;
184 +  args_info->bor_help = gengetopt_args_info_help[21] ;
185 +  args_info->gofr_help = gengetopt_args_info_help[22] ;
186 +  args_info->r_theta_help = gengetopt_args_info_help[23] ;
187 +  args_info->r_omega_help = gengetopt_args_info_help[24] ;
188 +  args_info->theta_omega_help = gengetopt_args_info_help[25] ;
189 +  args_info->gxyz_help = gengetopt_args_info_help[26] ;
190 +  args_info->p2_help = gengetopt_args_info_help[27] ;
191 +  args_info->rp2_help = gengetopt_args_info_help[28] ;
192 +  args_info->scd_help = gengetopt_args_info_help[29] ;
193 +  args_info->density_help = gengetopt_args_info_help[30] ;
194 +  args_info->slab_density_help = gengetopt_args_info_help[31] ;
195 +  args_info->hxy_help = gengetopt_args_info_help[32] ;
196 +  args_info->rho_r_help = gengetopt_args_info_help[33] ;
197 +  
198 + }
199 +
200   void
201   cmdline_parser_print_version (void)
202   {
# Line 119 | Line 206 | cmdline_parser_print_help (void)
206   void
207   cmdline_parser_print_help (void)
208   {
209 +  int i = 0;
210    cmdline_parser_print_version ();
211 <  printf("\nUsage: StaticProps [OPTIONS]...\n\n");
212 <  printf("%s\n","  -h, --help                    Print help and exit");
213 <  printf("%s\n","  -V, --version                 Print version and exit");
214 <  printf("%s\n","  -i, --input=filename          input dump file");
215 <  printf("%s\n","  -o, --output=filename         output file name");
216 <  printf("%s\n","  -n, --step=INT                process every n frame  (default=`1')");
217 <  printf("%s\n","  -r, --nrbins=INT              number of bins for distance  (default=`100')");
218 <  printf("%s\n","  -x, --nbins_x=INT             number of bins in x axis  (default=`100')");
219 <  printf("%s\n","  -y, --nbins_y=INT             number of bins in y axis  (default=`100')");
220 <  printf("%s\n","  -a, --nanglebins=INT          number of bins for cos(angle)  (default=`50')");
221 <  printf("%s\n","      --length=DOUBLE           maximum length (Defaults to 1/2 smallest length \n                                  of first frame)");
134 <  printf("%s\n","  -l, --LegendreL=INT           Order of Legendre Polynomial (used for Bond \n                                  Order calculations)");
135 <  printf("%s\n","  -c, --rcut=DOUBLE             cutoff radius (rcut)");
136 <  printf("%s\n","  -z, --zoffset=DOUBLE          Where to set the zero for the slab_density \n                                  calculation  (default=`0')");
137 <  printf("%s\n","      --sele1=selection script  select the first stuntdouble set");
138 <  printf("%s\n","      --sele2=selection script  select the second stuntdouble set");
139 <  printf("%s\n","      --sele3=selection script  select the third stuntdouble set");
140 <  printf("%s\n","      --refsele=selection script\n                                select reference (use and only use with --gxyz)");
141 <  printf("%s\n","      --molname=STRING          molecule name");
142 <  printf("%s\n","      --begin=INT               begin internal index");
143 <  printf("%s\n","      --end=INT                 end internal index");
144 <  printf("%s\n","\n Group: staticProps\n   an option of this group is required");
145 <  printf("%s\n","  -b, --bo                      bond order parameter (--rcut and --LegendreL \n                                  must be specified");
146 <  printf("%s\n","  -g, --gofr                    g(r)");
147 <  printf("%s\n","      --r_theta                 g(r, cos(theta))");
148 <  printf("%s\n","      --r_omega                 g(r, cos(omega))");
149 <  printf("%s\n","      --theta_omega             g(cos(theta), cos(omega))");
150 <  printf("%s\n","      --gxyz                    g(x, y, z)");
151 <  printf("%s\n","  -p, --p2                      p2 order parameter (--sele1 and --sele2 must be \n                                  specified)");
152 <  printf("%s\n","      --rp2                     rp2 order parameter (--sele1 and --sele2 must \n                                  be specified)");
153 <  printf("%s\n","  -s, --scd                     scd order parameter (either --sele1, --sele2, \n                                  --sele3 are specified or --molname, --begin, \n                                  --end are specified)");
154 <  printf("%s\n","  -d, --density                 density plot");
155 <  printf("%s\n","      --slab_density            slab density");
156 <  printf("%s\n","      --hxy                     hxy");
157 <  
211 >
212 >  if (strlen(gengetopt_args_info_purpose) > 0)
213 >    printf("\n%s\n", gengetopt_args_info_purpose);
214 >
215 >  printf("\n%s\n\n", gengetopt_args_info_usage);
216 >
217 >  if (strlen(gengetopt_args_info_description) > 0)
218 >    printf("%s\n", gengetopt_args_info_description);
219 >
220 >  while (gengetopt_args_info_help[i])
221 >    printf("%s\n", gengetopt_args_info_help[i++]);
222   }
223  
224   void
# Line 162 | Line 226 | cmdline_parser_init (struct gengetopt_args_info *args_
226   {
227    clear_given (args_info);
228    clear_args (args_info);
229 +  init_args_info (args_info);
230 +
231 +  args_info->inputs = NULL;
232 +  args_info->inputs_num = 0;
233   }
234  
235   static void
236   cmdline_parser_release (struct gengetopt_args_info *args_info)
237   {
238    
239 +  unsigned int i;
240    if (args_info->input_arg)
241      {
242        free (args_info->input_arg); /* free previous argument */
# Line 193 | Line 262 | cmdline_parser_release (struct gengetopt_args_info *ar
262        free (args_info->step_orig); /* free previous argument */
263        args_info->step_orig = 0;
264      }
265 <  if (args_info->nrbins_orig)
265 >  if (args_info->nbins_orig)
266      {
267 <      free (args_info->nrbins_orig); /* free previous argument */
268 <      args_info->nrbins_orig = 0;
267 >      free (args_info->nbins_orig); /* free previous argument */
268 >      args_info->nbins_orig = 0;
269      }
270    if (args_info->nbins_x_orig)
271      {
# Line 218 | Line 287 | cmdline_parser_release (struct gengetopt_args_info *ar
287        free (args_info->length_orig); /* free previous argument */
288        args_info->length_orig = 0;
289      }
221 –  if (args_info->LegendreL_orig)
222 –    {
223 –      free (args_info->LegendreL_orig); /* free previous argument */
224 –      args_info->LegendreL_orig = 0;
225 –    }
290    if (args_info->rcut_orig)
291      {
292        free (args_info->rcut_orig); /* free previous argument */
# Line 293 | Line 357 | cmdline_parser_release (struct gengetopt_args_info *ar
357        free (args_info->end_orig); /* free previous argument */
358        args_info->end_orig = 0;
359      }
360 +  if (args_info->radius_orig)
361 +    {
362 +      free (args_info->radius_orig); /* free previous argument */
363 +      args_info->radius_orig = 0;
364 +    }
365    
366 +  for (i = 0; i < args_info->inputs_num; ++i)
367 +    free (args_info->inputs [i]);
368 +  
369 +  if (args_info->inputs_num)
370 +    free (args_info->inputs);
371 +  
372    clear_given (args_info);
373   }
374  
# Line 338 | Line 413 | cmdline_parser_file_save(const char *filename, struct
413        fprintf(outfile, "%s\n", "step");
414      }
415    }
416 <  if (args_info->nrbins_given) {
417 <    if (args_info->nrbins_orig) {
418 <      fprintf(outfile, "%s=\"%s\"\n", "nrbins", args_info->nrbins_orig);
416 >  if (args_info->nbins_given) {
417 >    if (args_info->nbins_orig) {
418 >      fprintf(outfile, "%s=\"%s\"\n", "nbins", args_info->nbins_orig);
419      } else {
420 <      fprintf(outfile, "%s\n", "nrbins");
420 >      fprintf(outfile, "%s\n", "nbins");
421      }
422    }
423    if (args_info->nbins_x_given) {
# Line 371 | Line 446 | cmdline_parser_file_save(const char *filename, struct
446        fprintf(outfile, "%s=\"%s\"\n", "length", args_info->length_orig);
447      } else {
448        fprintf(outfile, "%s\n", "length");
374 –    }
375 –  }
376 –  if (args_info->LegendreL_given) {
377 –    if (args_info->LegendreL_orig) {
378 –      fprintf(outfile, "%s=\"%s\"\n", "LegendreL", args_info->LegendreL_orig);
379 –    } else {
380 –      fprintf(outfile, "%s\n", "LegendreL");
449      }
450    }
451    if (args_info->rcut_given) {
# Line 443 | Line 511 | cmdline_parser_file_save(const char *filename, struct
511        fprintf(outfile, "%s\n", "end");
512      }
513    }
514 +  if (args_info->radius_given) {
515 +    if (args_info->radius_orig) {
516 +      fprintf(outfile, "%s=\"%s\"\n", "radius", args_info->radius_orig);
517 +    } else {
518 +      fprintf(outfile, "%s\n", "radius");
519 +    }
520 +  }
521    if (args_info->bo_given) {
522      fprintf(outfile, "%s\n", "bo");
523 +  }
524 +  if (args_info->bor_given) {
525 +    fprintf(outfile, "%s\n", "bor");
526    }
527    if (args_info->gofr_given) {
528      fprintf(outfile, "%s\n", "gofr");
# Line 479 | Line 557 | cmdline_parser_file_save(const char *filename, struct
557    if (args_info->hxy_given) {
558      fprintf(outfile, "%s\n", "hxy");
559    }
560 +  if (args_info->rho_r_given) {
561 +    fprintf(outfile, "%s\n", "rho_r");
562 +  }
563    
564    fclose (outfile);
565  
# Line 519 | Line 600 | reset_group_staticProps(struct gengetopt_args_info *ar
600      return;
601    
602    args_info->bo_given = 0 ;
603 +  args_info->bor_given = 0 ;
604    args_info->gofr_given = 0 ;
605    args_info->r_theta_given = 0 ;
606    args_info->r_omega_given = 0 ;
# Line 530 | Line 612 | reset_group_staticProps(struct gengetopt_args_info *ar
612    args_info->density_given = 0 ;
613    args_info->slab_density_given = 0 ;
614    args_info->hxy_given = 0 ;
615 +  args_info->rho_r_given = 0 ;
616  
617    args_info->staticProps_group_counter = 0;
618   }
# Line 578 | Line 661 | cmdline_parser_required2 (struct gengetopt_args_info *
661   {
662    int error = 0;
663  
664 +  /* checks for required options */
665    if (! args_info->input_given)
666      {
667        fprintf (stderr, "%s: '--input' ('-i') option required%s\n", prog_name, (additional_error ? additional_error : ""));
668        error = 1;
669      }
670 +  
671    if (args_info->staticProps_group_counter == 0)
672      {
673        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 : ""));
# Line 590 | Line 675 | cmdline_parser_required2 (struct gengetopt_args_info *
675      }
676    
677  
678 +  /* checks for dependences among options */
679 +
680    return error;
681   }
682  
# Line 622 | Line 709 | cmdline_parser_internal (int argc, char * const *argv,
709          { "input",      1, NULL, 'i' },
710          { "output",     1, NULL, 'o' },
711          { "step",       1, NULL, 'n' },
712 <        { "nrbins",     1, NULL, 'r' },
712 >        { "nbins",      1, NULL, 'b' },
713          { "nbins_x",    1, NULL, 'x' },
714          { "nbins_y",    1, NULL, 'y' },
715          { "nanglebins", 1, NULL, 'a' },
716          { "length",     1, NULL, 0 },
630 –        { "LegendreL",  1, NULL, 'l' },
717          { "rcut",       1, NULL, 'c' },
718          { "zoffset",    1, NULL, 'z' },
719          { "sele1",      1, NULL, 0 },
# Line 637 | Line 723 | cmdline_parser_internal (int argc, char * const *argv,
723          { "molname",    1, NULL, 0 },
724          { "begin",      1, NULL, 0 },
725          { "end",        1, NULL, 0 },
726 <        { "bo", 0, NULL, 'b' },
726 >        { "radius",     1, NULL, 0 },
727 >        { "bo", 0, NULL, 0 },
728 >        { "bor",        0, NULL, 0 },
729          { "gofr",       0, NULL, 'g' },
730          { "r_theta",    0, NULL, 0 },
731          { "r_omega",    0, NULL, 0 },
# Line 649 | Line 737 | cmdline_parser_internal (int argc, char * const *argv,
737          { "density",    0, NULL, 'd' },
738          { "slab_density",       0, NULL, 0 },
739          { "hxy",        0, NULL, 0 },
740 +        { "rho_r",      0, NULL, 0 },
741          { NULL, 0, NULL, 0 }
742        };
743  
744        stop_char = 0;
745 <      c = getopt_long (argc, argv, "hVi:o:n:r:x:y:a:l:c:z:bgpsd", long_options, &option_index);
745 >      c = getopt_long (argc, argv, "hVi:o:n:b:x:y:a:c:z:gpsd", long_options, &option_index);
746  
747        if (c == -1) break;       /* Exit from `while (1)' loop.  */
748  
# Line 725 | Line 814 | cmdline_parser_internal (int argc, char * const *argv,
814            args_info->step_orig = gengetopt_strdup (optarg);
815            break;
816  
817 <        case 'r':       /* number of bins for distance.  */
818 <          if (local_args_info.nrbins_given)
817 >        case 'b':       /* number of bins (general purpose).  */
818 >          if (local_args_info.nbins_given)
819              {
820 <              fprintf (stderr, "%s: `--nrbins' (`-r') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
820 >              fprintf (stderr, "%s: `--nbins' (`-b') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
821                goto failure;
822              }
823 <          if (args_info->nrbins_given && ! override)
823 >          if (args_info->nbins_given && ! override)
824              continue;
825 <          local_args_info.nrbins_given = 1;
826 <          args_info->nrbins_given = 1;
827 <          args_info->nrbins_arg = strtol (optarg, &stop_char, 0);
825 >          local_args_info.nbins_given = 1;
826 >          args_info->nbins_given = 1;
827 >          args_info->nbins_arg = strtol (optarg, &stop_char, 0);
828            if (!(stop_char && *stop_char == '\0')) {
829              fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
830              goto failure;
831            }
832 <          if (args_info->nrbins_orig)
833 <            free (args_info->nrbins_orig); /* free previous string */
834 <          args_info->nrbins_orig = gengetopt_strdup (optarg);
832 >          if (args_info->nbins_orig)
833 >            free (args_info->nbins_orig); /* free previous string */
834 >          args_info->nbins_orig = gengetopt_strdup (optarg);
835            break;
836  
837          case 'x':       /* number of bins in x axis.  */
# Line 805 | Line 894 | cmdline_parser_internal (int argc, char * const *argv,
894            args_info->nanglebins_orig = gengetopt_strdup (optarg);
895            break;
896  
808 –        case 'l':       /* Order of Legendre Polynomial (used for Bond Order calculations).  */
809 –          if (local_args_info.LegendreL_given)
810 –            {
811 –              fprintf (stderr, "%s: `--LegendreL' (`-l') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
812 –              goto failure;
813 –            }
814 –          if (args_info->LegendreL_given && ! override)
815 –            continue;
816 –          local_args_info.LegendreL_given = 1;
817 –          args_info->LegendreL_given = 1;
818 –          args_info->LegendreL_arg = strtol (optarg, &stop_char, 0);
819 –          if (!(stop_char && *stop_char == '\0')) {
820 –            fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
821 –            goto failure;
822 –          }
823 –          if (args_info->LegendreL_orig)
824 –            free (args_info->LegendreL_orig); /* free previous string */
825 –          args_info->LegendreL_orig = gengetopt_strdup (optarg);
826 –          break;
827 –
897          case 'c':       /* cutoff radius (rcut).  */
898            if (local_args_info.rcut_given)
899              {
# Line 863 | Line 932 | cmdline_parser_internal (int argc, char * const *argv,
932            if (args_info->zoffset_orig)
933              free (args_info->zoffset_orig); /* free previous string */
934            args_info->zoffset_orig = gengetopt_strdup (optarg);
866 –          break;
867 –
868 –        case 'b':       /* bond order parameter (--rcut and --LegendreL must be specified.  */
869 –          if (local_args_info.bo_given)
870 –            {
871 –              fprintf (stderr, "%s: `--bo' (`-b') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
872 –              goto failure;
873 –            }
874 –          if (args_info->bo_given && ! override)
875 –            continue;
876 –          local_args_info.bo_given = 1;
877 –          args_info->bo_given = 1;
878 –          if (args_info->staticProps_group_counter && override)
879 –            reset_group_staticProps (args_info);
880 –          args_info->staticProps_group_counter += 1;
935            break;
936  
937          case 'g':       /* g(r).  */
# Line 1099 | Line 1153 | cmdline_parser_internal (int argc, char * const *argv,
1153              if (args_info->end_orig)
1154                free (args_info->end_orig); /* free previous string */
1155              args_info->end_orig = gengetopt_strdup (optarg);
1156 +          }
1157 +          /* nanoparticle radius.  */
1158 +          else if (strcmp (long_options[option_index].name, "radius") == 0)
1159 +          {
1160 +            if (local_args_info.radius_given)
1161 +              {
1162 +                fprintf (stderr, "%s: `--radius' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1163 +                goto failure;
1164 +              }
1165 +            if (args_info->radius_given && ! override)
1166 +              continue;
1167 +            local_args_info.radius_given = 1;
1168 +            args_info->radius_given = 1;
1169 +            args_info->radius_arg = strtod (optarg, &stop_char);
1170 +            if (!(stop_char && *stop_char == '\0')) {
1171 +              fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
1172 +              goto failure;
1173 +            }
1174 +            if (args_info->radius_orig)
1175 +              free (args_info->radius_orig); /* free previous string */
1176 +            args_info->radius_orig = gengetopt_strdup (optarg);
1177            }
1178 +          /* bond order parameter (--rcut must be specified).  */
1179 +          else if (strcmp (long_options[option_index].name, "bo") == 0)
1180 +          {
1181 +            if (local_args_info.bo_given)
1182 +              {
1183 +                fprintf (stderr, "%s: `--bo' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1184 +                goto failure;
1185 +              }
1186 +            if (args_info->bo_given && ! override)
1187 +              continue;
1188 +            local_args_info.bo_given = 1;
1189 +            args_info->bo_given = 1;
1190 +            if (args_info->staticProps_group_counter && override)
1191 +              reset_group_staticProps (args_info);
1192 +            args_info->staticProps_group_counter += 1;
1193 +            break;
1194 +          }
1195 +          /* bond order parameter as a function of radius (--rcut must be specified).  */
1196 +          else if (strcmp (long_options[option_index].name, "bor") == 0)
1197 +          {
1198 +            if (local_args_info.bor_given)
1199 +              {
1200 +                fprintf (stderr, "%s: `--bor' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1201 +                goto failure;
1202 +              }
1203 +            if (args_info->bor_given && ! override)
1204 +              continue;
1205 +            local_args_info.bor_given = 1;
1206 +            args_info->bor_given = 1;
1207 +            if (args_info->staticProps_group_counter && override)
1208 +              reset_group_staticProps (args_info);
1209 +            args_info->staticProps_group_counter += 1;
1210 +            break;
1211 +          }
1212            /* g(r, cos(theta)).  */
1213            else if (strcmp (long_options[option_index].name, "r_theta") == 0)
1214            {
# Line 1219 | Line 1328 | cmdline_parser_internal (int argc, char * const *argv,
1328              args_info->staticProps_group_counter += 1;
1329              break;
1330            }
1331 +          /* rho of R.  */
1332 +          else if (strcmp (long_options[option_index].name, "rho_r") == 0)
1333 +          {
1334 +            if (local_args_info.rho_r_given)
1335 +              {
1336 +                fprintf (stderr, "%s: `--rho_r' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1337 +                goto failure;
1338 +              }
1339 +            if (args_info->rho_r_given && ! override)
1340 +              continue;
1341 +            local_args_info.rho_r_given = 1;
1342 +            args_info->rho_r_given = 1;
1343 +            if (args_info->staticProps_group_counter && override)
1344 +              reset_group_staticProps (args_info);
1345 +            args_info->staticProps_group_counter += 1;
1346 +            break;
1347 +          }
1348            
1349            break;
1350          case '?':       /* Invalid option.  */
# Line 1249 | Line 1375 | cmdline_parser_internal (int argc, char * const *argv,
1375    if ( error )
1376      return (EXIT_FAILURE);
1377  
1378 +  if (optind < argc)
1379 +    {
1380 +      int i = 0 ;
1381 +      int found_prog_name = 0;
1382 +      /* whether program name, i.e., argv[0], is in the remaining args
1383 +         (this may happen with some implementations of getopt,
1384 +          but surely not with the one included by gengetopt) */
1385 +
1386 +      i = optind;
1387 +      while (i < argc)
1388 +        if (argv[i++] == argv[0]) {
1389 +          found_prog_name = 1;
1390 +          break;
1391 +        }
1392 +      i = 0;
1393 +
1394 +      args_info->inputs_num = argc - optind - found_prog_name;
1395 +      args_info->inputs =
1396 +        (char **)(malloc ((args_info->inputs_num)*sizeof(char *))) ;
1397 +      while (optind < argc)
1398 +        if (argv[optind++] != argv[0])
1399 +          args_info->inputs[ i++ ] = gengetopt_strdup (argv[optind-1]) ;
1400 +    }
1401 +
1402    return 0;
1403  
1404   failure:

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