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root/OpenMD/trunk/src/applications/staticProps/StaticPropsCmd.c
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Comparing trunk/src/applications/staticProps/StaticPropsCmd.c (file contents):
Revision 955 by xsun, Fri May 12 21:34:43 2006 UTC vs.
Revision 1091 by chuckv, Fri Nov 10 18:45:29 2006 UTC

# Line 1 | Line 1
1   /*
2 <  File autogenerated by gengetopt version 2.16
2 >  File autogenerated by gengetopt version 2.15
3    generated with the following command:
4 <  gengetopt -F StaticPropsCmd
4 >  gengetopt -i StaticProps.ggo -F StaticPropsCmd
5  
6    The developers of gengetopt consider the fixed text that goes in all
7    gengetopt output files to be in the public domain:
# Line 43 | Line 43 | void clear_given (struct gengetopt_args_info *args_inf
43    args_info->input_given = 0 ;
44    args_info->output_given = 0 ;
45    args_info->step_given = 0 ;
46 <  args_info->nrbins_given = 0 ;
46 >  args_info->nbins_given = 0 ;
47    args_info->nbins_x_given = 0 ;
48    args_info->nbins_y_given = 0 ;
49    args_info->nanglebins_given = 0 ;
50    args_info->length_given = 0 ;
51 +  args_info->rcut_given = 0 ;
52    args_info->zoffset_given = 0 ;
53    args_info->sele1_given = 0 ;
54    args_info->sele2_given = 0 ;
# Line 56 | Line 57 | void clear_given (struct gengetopt_args_info *args_inf
57    args_info->molname_given = 0 ;
58    args_info->begin_given = 0 ;
59    args_info->end_given = 0 ;
60 +  args_info->radius_given = 0 ;
61 +  args_info->bo_given = 0 ;
62    args_info->gofr_given = 0 ;
63    args_info->r_theta_given = 0 ;
64    args_info->r_omega_given = 0 ;
65    args_info->theta_omega_given = 0 ;
66    args_info->gxyz_given = 0 ;
67    args_info->p2_given = 0 ;
68 +  args_info->rp2_given = 0 ;
69    args_info->scd_given = 0 ;
70    args_info->density_given = 0 ;
71    args_info->slab_density_given = 0 ;
72    args_info->hxy_given = 0 ;
73 +  args_info->rho_r_given = 0 ;
74    args_info->staticProps_group_counter = 0 ;
75   }
76  
# Line 78 | Line 83 | void clear_args (struct gengetopt_args_info *args_info
83    args_info->output_orig = NULL;
84    args_info->step_arg = 1;
85    args_info->step_orig = NULL;
86 <  args_info->nrbins_arg = 100;
87 <  args_info->nrbins_orig = NULL;
86 >  args_info->nbins_arg = 100;
87 >  args_info->nbins_orig = NULL;
88    args_info->nbins_x_arg = 100;
89    args_info->nbins_x_orig = NULL;
90    args_info->nbins_y_arg = 100;
# Line 87 | Line 92 | void clear_args (struct gengetopt_args_info *args_info
92    args_info->nanglebins_arg = 50;
93    args_info->nanglebins_orig = NULL;
94    args_info->length_orig = NULL;
95 +  args_info->rcut_orig = NULL;
96    args_info->zoffset_arg = 0;
97    args_info->zoffset_orig = NULL;
98    args_info->sele1_arg = NULL;
# Line 101 | Line 107 | void clear_args (struct gengetopt_args_info *args_info
107    args_info->molname_orig = NULL;
108    args_info->begin_orig = NULL;
109    args_info->end_orig = NULL;
110 +  args_info->radius_orig = NULL;
111    
112   }
113  
# Line 120 | Line 127 | cmdline_parser_print_help (void)
127    printf("%s\n","  -i, --input=filename          input dump file");
128    printf("%s\n","  -o, --output=filename         output file name");
129    printf("%s\n","  -n, --step=INT                process every n frame  (default=`1')");
130 <  printf("%s\n","  -x,  --nbins_x=INT              number of bins in x axis  (default=`100')");
131 <  printf("%s\n","  -y , --nbins_y=INT              number of bins in y axis  (default=`100')");
132 <   printf("%s\n","  -r, --nrbins=INT              number of bins for distance  (default=`100')");
130 >  printf("%s\n","  -b, --nbins=INT               number of bins (general purpose)  \n                                  (default=`100')");
131 >  printf("%s\n","  -x, --nbins_x=INT             number of bins in x axis  (default=`100')");
132 >  printf("%s\n","  -y, --nbins_y=INT             number of bins in y axis  (default=`100')");
133    printf("%s\n","  -a, --nanglebins=INT          number of bins for cos(angle)  (default=`50')");
134 <  printf("%s\n","  -l, --length=DOUBLE           maximum length (Defaults to 1/2 smallest length \n                                  of first frame)");
134 >  printf("%s\n","      --length=DOUBLE           maximum length (Defaults to 1/2 smallest length \n                                  of first frame)");
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 interanl index");
142 >  printf("%s\n","      --begin=INT               begin internal index");
143    printf("%s\n","      --end=INT                 end internal index");
144 +  printf("%s\n","      --radius=DOUBLE           nanoparticle radius");
145    printf("%s\n","\n Group: staticProps\n   an option of this group is required");
146 <  printf("%s\n","      --gofr                    g(r)");
146 >  printf("%s\n","      --bo                      bond order parameter (--rcut must be specified");
147 >  printf("%s\n","  -g, --gofr                    g(r)");
148    printf("%s\n","      --r_theta                 g(r, cos(theta))");
149    printf("%s\n","      --r_omega                 g(r, cos(omega))");
150    printf("%s\n","      --theta_omega             g(cos(theta), cos(omega))");
151    printf("%s\n","      --gxyz                    g(x, y, z)");
152 <  printf("%s\n","      --p2                      p2 order parameter (--sele1 and --sele2 must be \n                                  specified)");
153 <  printf("%s\n","      --scd                     scd order parameter(either --sele1, --sele2, \n                                  --sele3 are specified or --molname, --begin, \n                                  --end are specified)");
154 <  printf("%s\n","      --density                 density plot (--sele1 must be specified)");
155 <  printf("%s\n","      --slab_density            slab density (--sele1 must be specified)");
156 <  printf("%s\n","      --hxy            hxy (--sele1 must be specified)");
152 >  printf("%s\n","  -p, --p2                      p2 order parameter (--sele1 and --sele2 must be \n                                  specified)");
153 >  printf("%s\n","      --rp2                     rp2 order parameter (--sele1 and --sele2 must \n                                  be specified)");
154 >  printf("%s\n","  -s, --scd                     scd order parameter (either --sele1, --sele2, \n                                  --sele3 are specified or --molname, --begin, \n                                  --end are specified)");
155 >  printf("%s\n","  -d, --density                 density plot");
156 >  printf("%s\n","      --slab_density            slab density");
157 >  printf("%s\n","      --hxy                     hxy");
158 >  printf("%s\n","      --rho_r                   rho of R");
159    
160   }
161  
# Line 183 | Line 195 | cmdline_parser_release (struct gengetopt_args_info *ar
195        free (args_info->step_orig); /* free previous argument */
196        args_info->step_orig = 0;
197      }
198 <  if (args_info->nrbins_orig)
198 >  if (args_info->nbins_orig)
199      {
200 <      free (args_info->nrbins_orig); /* free previous argument */
201 <      args_info->nrbins_orig = 0;
200 >      free (args_info->nbins_orig); /* free previous argument */
201 >      args_info->nbins_orig = 0;
202      }
203 <    if (args_info->nbins_x_orig)
203 >  if (args_info->nbins_x_orig)
204      {
205        free (args_info->nbins_x_orig); /* free previous argument */
206        args_info->nbins_x_orig = 0;
# Line 198 | Line 210 | cmdline_parser_release (struct gengetopt_args_info *ar
210        free (args_info->nbins_y_orig); /* free previous argument */
211        args_info->nbins_y_orig = 0;
212      }
201 –        
213    if (args_info->nanglebins_orig)
214      {
215        free (args_info->nanglebins_orig); /* free previous argument */
# Line 209 | Line 220 | cmdline_parser_release (struct gengetopt_args_info *ar
220        free (args_info->length_orig); /* free previous argument */
221        args_info->length_orig = 0;
222      }
223 +  if (args_info->rcut_orig)
224 +    {
225 +      free (args_info->rcut_orig); /* free previous argument */
226 +      args_info->rcut_orig = 0;
227 +    }
228    if (args_info->zoffset_orig)
229      {
230        free (args_info->zoffset_orig); /* free previous argument */
# Line 274 | Line 290 | cmdline_parser_release (struct gengetopt_args_info *ar
290        free (args_info->end_orig); /* free previous argument */
291        args_info->end_orig = 0;
292      }
293 +  if (args_info->radius_orig)
294 +    {
295 +      free (args_info->radius_orig); /* free previous argument */
296 +      args_info->radius_orig = 0;
297 +    }
298    
299    clear_given (args_info);
300   }
# Line 319 | Line 340 | cmdline_parser_file_save(const char *filename, struct
340        fprintf(outfile, "%s\n", "step");
341      }
342    }
343 <  if (args_info->nrbins_given) {
344 <    if (args_info->nrbins_orig) {
345 <      fprintf(outfile, "%s=\"%s\"\n", "nrbins", args_info->nrbins_orig);
343 >  if (args_info->nbins_given) {
344 >    if (args_info->nbins_orig) {
345 >      fprintf(outfile, "%s=\"%s\"\n", "nbins", args_info->nbins_orig);
346      } else {
347 <      fprintf(outfile, "%s\n", "nrbins");
347 >      fprintf(outfile, "%s\n", "nbins");
348      }
349    }
350    if (args_info->nbins_x_given) {
# Line 354 | Line 375 | cmdline_parser_file_save(const char *filename, struct
375        fprintf(outfile, "%s\n", "length");
376      }
377    }
378 +  if (args_info->rcut_given) {
379 +    if (args_info->rcut_orig) {
380 +      fprintf(outfile, "%s=\"%s\"\n", "rcut", args_info->rcut_orig);
381 +    } else {
382 +      fprintf(outfile, "%s\n", "rcut");
383 +    }
384 +  }
385    if (args_info->zoffset_given) {
386      if (args_info->zoffset_orig) {
387        fprintf(outfile, "%s=\"%s\"\n", "zoffset", args_info->zoffset_orig);
# Line 410 | Line 438 | cmdline_parser_file_save(const char *filename, struct
438        fprintf(outfile, "%s\n", "end");
439      }
440    }
441 +  if (args_info->radius_given) {
442 +    if (args_info->radius_orig) {
443 +      fprintf(outfile, "%s=\"%s\"\n", "radius", args_info->radius_orig);
444 +    } else {
445 +      fprintf(outfile, "%s\n", "radius");
446 +    }
447 +  }
448 +  if (args_info->bo_given) {
449 +    fprintf(outfile, "%s\n", "bo");
450 +  }
451    if (args_info->gofr_given) {
452      fprintf(outfile, "%s\n", "gofr");
453    }
# Line 428 | Line 466 | cmdline_parser_file_save(const char *filename, struct
466    if (args_info->p2_given) {
467      fprintf(outfile, "%s\n", "p2");
468    }
469 +  if (args_info->rp2_given) {
470 +    fprintf(outfile, "%s\n", "rp2");
471 +  }
472    if (args_info->scd_given) {
473      fprintf(outfile, "%s\n", "scd");
474    }
# Line 440 | Line 481 | cmdline_parser_file_save(const char *filename, struct
481    if (args_info->hxy_given) {
482      fprintf(outfile, "%s\n", "hxy");
483    }
484 +  if (args_info->rho_r_given) {
485 +    fprintf(outfile, "%s\n", "rho_r");
486 +  }
487 +  
488    fclose (outfile);
489  
490    i = EXIT_SUCCESS;
# Line 478 | Line 523 | reset_group_staticProps(struct gengetopt_args_info *ar
523    if (! args_info->staticProps_group_counter)
524      return;
525    
526 +  args_info->bo_given = 0 ;
527    args_info->gofr_given = 0 ;
528    args_info->r_theta_given = 0 ;
529    args_info->r_omega_given = 0 ;
530    args_info->theta_omega_given = 0 ;
531    args_info->gxyz_given = 0 ;
532    args_info->p2_given = 0 ;
533 +  args_info->rp2_given = 0 ;
534    args_info->scd_given = 0 ;
535    args_info->density_given = 0 ;
536    args_info->slab_density_given = 0 ;
537 <  args_info->hxy_given= 0 ;
537 >  args_info->hxy_given = 0 ;
538 >  args_info->rho_r_given = 0 ;
539  
540    args_info->staticProps_group_counter = 0;
541   }
# Line 565 | Line 613 | cmdline_parser_internal (int argc, char * const *argv,
613    cmdline_parser_init (&local_args_info);
614  
615    optarg = 0;
616 <  optind = 0;
616 >  optind = 1;
617    opterr = 1;
618    optopt = '?';
619  
# Line 580 | Line 628 | cmdline_parser_internal (int argc, char * const *argv,
628          { "input",      1, NULL, 'i' },
629          { "output",     1, NULL, 'o' },
630          { "step",       1, NULL, 'n' },
631 <        { "nrbins",     1, NULL, 'r' },
631 >        { "nbins",      1, NULL, 'b' },
632 >        { "nbins_x",    1, NULL, 'x' },
633 >        { "nbins_y",    1, NULL, 'y' },
634          { "nanglebins", 1, NULL, 'a' },
635 <        { "length",     1, NULL, 'l' },
635 >        { "length",     1, NULL, 0 },
636 >        { "rcut",       1, NULL, 'c' },
637          { "zoffset",    1, NULL, 'z' },
638          { "sele1",      1, NULL, 0 },
639          { "sele2",      1, NULL, 0 },
# Line 591 | Line 642 | cmdline_parser_internal (int argc, char * const *argv,
642          { "molname",    1, NULL, 0 },
643          { "begin",      1, NULL, 0 },
644          { "end",        1, NULL, 0 },
645 <        { "gofr",       0, NULL, 0 },
645 >        { "radius",     1, NULL, 0 },
646 >        { "bo", 0, NULL, 0 },
647 >        { "gofr",       0, NULL, 'g' },
648          { "r_theta",    0, NULL, 0 },
649          { "r_omega",    0, NULL, 0 },
650          { "theta_omega",        0, NULL, 0 },
651          { "gxyz",       0, NULL, 0 },
652 <        { "p2", 0, NULL, 0 },
653 <        { "scd",        0, NULL, 0 },
654 <        { "density",    0, NULL, 0 },
652 >        { "p2", 0, NULL, 'p' },
653 >        { "rp2",        0, NULL, 0 },
654 >        { "scd",        0, NULL, 's' },
655 >        { "density",    0, NULL, 'd' },
656          { "slab_density",       0, NULL, 0 },
657          { "hxy",        0, NULL, 0 },
658 +        { "rho_r",      0, NULL, 0 },
659          { NULL, 0, NULL, 0 }
660        };
661  
662        stop_char = 0;
663 <      c = getopt_long (argc, argv, "hVi:o:n:r:a:l:z:", long_options, &option_index);
663 >      c = getopt_long (argc, argv, "hVi:o:n:b:x:y:a:c:z:gpsd", long_options, &option_index);
664  
665        if (c == -1) break;       /* Exit from `while (1)' loop.  */
666  
# Line 677 | Line 732 | cmdline_parser_internal (int argc, char * const *argv,
732            args_info->step_orig = gengetopt_strdup (optarg);
733            break;
734  
735 <        case 'r':       /* number of bins for distance.  */
736 <          if (local_args_info.nrbins_given)
735 >        case 'b':       /* number of bins (general purpose).  */
736 >          if (local_args_info.nbins_given)
737              {
738 <              fprintf (stderr, "%s: `--nrbins' (`-r') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
738 >              fprintf (stderr, "%s: `--nbins' (`-b') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
739                goto failure;
740              }
741 <          if (args_info->nrbins_given && ! override)
741 >          if (args_info->nbins_given && ! override)
742              continue;
743 <          local_args_info.nrbins_given = 1;
744 <          args_info->nrbins_given = 1;
745 <          args_info->nrbins_arg = strtol (optarg, &stop_char, 0);
743 >          local_args_info.nbins_given = 1;
744 >          args_info->nbins_given = 1;
745 >          args_info->nbins_arg = strtol (optarg, &stop_char, 0);
746            if (!(stop_char && *stop_char == '\0')) {
747              fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
748              goto failure;
749            }
750 <          if (args_info->nrbins_orig)
751 <            free (args_info->nrbins_orig); /* free previous string */
752 <          args_info->nrbins_orig = gengetopt_strdup (optarg);
750 >          if (args_info->nbins_orig)
751 >            free (args_info->nbins_orig); /* free previous string */
752 >          args_info->nbins_orig = gengetopt_strdup (optarg);
753            break;
754  
755          case 'x':       /* number of bins in x axis.  */
756            if (local_args_info.nbins_x_given)
757              {
758 <              fprintf (stderr, "%s: `--nbins_x' (`-r') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
758 >              fprintf (stderr, "%s: `--nbins_x' (`-x') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
759                goto failure;
760              }
761            if (args_info->nbins_x_given && ! override)
# Line 720 | Line 775 | cmdline_parser_internal (int argc, char * const *argv,
775          case 'y':       /* number of bins in y axis.  */
776            if (local_args_info.nbins_y_given)
777              {
778 <              fprintf (stderr, "%s: `--nbins_y' (`-r') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
778 >              fprintf (stderr, "%s: `--nbins_y' (`-y') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
779                goto failure;
780              }
781            if (args_info->nbins_y_given && ! override)
# Line 757 | Line 812 | cmdline_parser_internal (int argc, char * const *argv,
812            args_info->nanglebins_orig = gengetopt_strdup (optarg);
813            break;
814  
815 <        case 'l':       /* maximum length (Defaults to 1/2 smallest length of first frame).  */
816 <          if (local_args_info.length_given)
815 >        case 'c':       /* cutoff radius (rcut).  */
816 >          if (local_args_info.rcut_given)
817              {
818 <              fprintf (stderr, "%s: `--length' (`-l') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
818 >              fprintf (stderr, "%s: `--rcut' (`-c') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
819                goto failure;
820              }
821 <          if (args_info->length_given && ! override)
821 >          if (args_info->rcut_given && ! override)
822              continue;
823 <          local_args_info.length_given = 1;
824 <          args_info->length_given = 1;
825 <          args_info->length_arg = strtod (optarg, &stop_char);
823 >          local_args_info.rcut_given = 1;
824 >          args_info->rcut_given = 1;
825 >          args_info->rcut_arg = strtod (optarg, &stop_char);
826            if (!(stop_char && *stop_char == '\0')) {
827              fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
828              goto failure;
829            }
830 <          if (args_info->length_orig)
831 <            free (args_info->length_orig); /* free previous string */
832 <          args_info->length_orig = gengetopt_strdup (optarg);
830 >          if (args_info->rcut_orig)
831 >            free (args_info->rcut_orig); /* free previous string */
832 >          args_info->rcut_orig = gengetopt_strdup (optarg);
833            break;
834  
835          case 'z':       /* Where to set the zero for the slab_density calculation.  */
# Line 795 | Line 850 | cmdline_parser_internal (int argc, char * const *argv,
850            if (args_info->zoffset_orig)
851              free (args_info->zoffset_orig); /* free previous string */
852            args_info->zoffset_orig = gengetopt_strdup (optarg);
853 +          break;
854 +
855 +        case 'g':       /* g(r).  */
856 +          if (local_args_info.gofr_given)
857 +            {
858 +              fprintf (stderr, "%s: `--gofr' (`-g') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
859 +              goto failure;
860 +            }
861 +          if (args_info->gofr_given && ! override)
862 +            continue;
863 +          local_args_info.gofr_given = 1;
864 +          args_info->gofr_given = 1;
865 +          if (args_info->staticProps_group_counter && override)
866 +            reset_group_staticProps (args_info);
867 +          args_info->staticProps_group_counter += 1;
868 +          break;
869 +
870 +        case 'p':       /* p2 order parameter (--sele1 and --sele2 must be specified).  */
871 +          if (local_args_info.p2_given)
872 +            {
873 +              fprintf (stderr, "%s: `--p2' (`-p') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
874 +              goto failure;
875 +            }
876 +          if (args_info->p2_given && ! override)
877 +            continue;
878 +          local_args_info.p2_given = 1;
879 +          args_info->p2_given = 1;
880 +          if (args_info->staticProps_group_counter && override)
881 +            reset_group_staticProps (args_info);
882 +          args_info->staticProps_group_counter += 1;
883            break;
884  
885 +        case 's':       /* scd order parameter (either --sele1, --sele2, --sele3 are specified or --molname, --begin, --end are specified).  */
886 +          if (local_args_info.scd_given)
887 +            {
888 +              fprintf (stderr, "%s: `--scd' (`-s') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
889 +              goto failure;
890 +            }
891 +          if (args_info->scd_given && ! override)
892 +            continue;
893 +          local_args_info.scd_given = 1;
894 +          args_info->scd_given = 1;
895 +          if (args_info->staticProps_group_counter && override)
896 +            reset_group_staticProps (args_info);
897 +          args_info->staticProps_group_counter += 1;
898 +          break;
899  
900 +        case 'd':       /* density plot.  */
901 +          if (local_args_info.density_given)
902 +            {
903 +              fprintf (stderr, "%s: `--density' (`-d') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
904 +              goto failure;
905 +            }
906 +          if (args_info->density_given && ! override)
907 +            continue;
908 +          local_args_info.density_given = 1;
909 +          args_info->density_given = 1;
910 +          if (args_info->staticProps_group_counter && override)
911 +            reset_group_staticProps (args_info);
912 +          args_info->staticProps_group_counter += 1;
913 +          break;
914 +
915 +
916          case 0: /* Long option with no short option */
917 +          /* maximum length (Defaults to 1/2 smallest length of first frame).  */
918 +          if (strcmp (long_options[option_index].name, "length") == 0)
919 +          {
920 +            if (local_args_info.length_given)
921 +              {
922 +                fprintf (stderr, "%s: `--length' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
923 +                goto failure;
924 +              }
925 +            if (args_info->length_given && ! override)
926 +              continue;
927 +            local_args_info.length_given = 1;
928 +            args_info->length_given = 1;
929 +            args_info->length_arg = strtod (optarg, &stop_char);
930 +            if (!(stop_char && *stop_char == '\0')) {
931 +              fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
932 +              goto failure;
933 +            }
934 +            if (args_info->length_orig)
935 +              free (args_info->length_orig); /* free previous string */
936 +            args_info->length_orig = gengetopt_strdup (optarg);
937 +          }
938            /* select the first stuntdouble set.  */
939 <          if (strcmp (long_options[option_index].name, "sele1") == 0)
939 >          else if (strcmp (long_options[option_index].name, "sele1") == 0)
940            {
941              if (local_args_info.sele1_given)
942                {
# Line 894 | Line 1030 | cmdline_parser_internal (int argc, char * const *argv,
1030                free (args_info->molname_orig); /* free previous string */
1031              args_info->molname_orig = gengetopt_strdup (optarg);
1032            }
1033 <          /* begin interanl index.  */
1033 >          /* begin internal index.  */
1034            else if (strcmp (long_options[option_index].name, "begin") == 0)
1035            {
1036              if (local_args_info.begin_given)
# Line 936 | Line 1072 | cmdline_parser_internal (int argc, char * const *argv,
1072                free (args_info->end_orig); /* free previous string */
1073              args_info->end_orig = gengetopt_strdup (optarg);
1074            }
1075 <          /* g(r).  */
1076 <          else if (strcmp (long_options[option_index].name, "gofr") == 0)
1075 >          /* nanoparticle radius.  */
1076 >          else if (strcmp (long_options[option_index].name, "radius") == 0)
1077            {
1078 <            if (local_args_info.gofr_given)
1078 >            if (local_args_info.radius_given)
1079                {
1080 <                fprintf (stderr, "%s: `--gofr' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1080 >                fprintf (stderr, "%s: `--radius' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1081                  goto failure;
1082                }
1083 <            if (args_info->gofr_given && ! override)
1083 >            if (args_info->radius_given && ! override)
1084                continue;
1085 <            local_args_info.gofr_given = 1;
1086 <            args_info->gofr_given = 1;
1085 >            local_args_info.radius_given = 1;
1086 >            args_info->radius_given = 1;
1087 >            args_info->radius_arg = strtod (optarg, &stop_char);
1088 >            if (!(stop_char && *stop_char == '\0')) {
1089 >              fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
1090 >              goto failure;
1091 >            }
1092 >            if (args_info->radius_orig)
1093 >              free (args_info->radius_orig); /* free previous string */
1094 >            args_info->radius_orig = gengetopt_strdup (optarg);
1095 >          }
1096 >          /* bond order parameter (--rcut must be specified.  */
1097 >          else if (strcmp (long_options[option_index].name, "bo") == 0)
1098 >          {
1099 >            if (local_args_info.bo_given)
1100 >              {
1101 >                fprintf (stderr, "%s: `--bo' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1102 >                goto failure;
1103 >              }
1104 >            if (args_info->bo_given && ! override)
1105 >              continue;
1106 >            local_args_info.bo_given = 1;
1107 >            args_info->bo_given = 1;
1108              if (args_info->staticProps_group_counter && override)
1109                reset_group_staticProps (args_info);
1110              args_info->staticProps_group_counter += 1;
# Line 1021 | Line 1178 | cmdline_parser_internal (int argc, char * const *argv,
1178              args_info->staticProps_group_counter += 1;
1179              break;
1180            }
1181 <          /* p2 order parameter (--sele1 and --sele2 must be specified).  */
1182 <          else if (strcmp (long_options[option_index].name, "p2") == 0)
1181 >          /* rp2 order parameter (--sele1 and --sele2 must be specified).  */
1182 >          else if (strcmp (long_options[option_index].name, "rp2") == 0)
1183            {
1184 <            if (local_args_info.p2_given)
1184 >            if (local_args_info.rp2_given)
1185                {
1186 <                fprintf (stderr, "%s: `--p2' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1186 >                fprintf (stderr, "%s: `--rp2' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1187                  goto failure;
1188                }
1189 <            if (args_info->p2_given && ! override)
1189 >            if (args_info->rp2_given && ! override)
1190                continue;
1191 <            local_args_info.p2_given = 1;
1192 <            args_info->p2_given = 1;
1191 >            local_args_info.rp2_given = 1;
1192 >            args_info->rp2_given = 1;
1193              if (args_info->staticProps_group_counter && override)
1194                reset_group_staticProps (args_info);
1195              args_info->staticProps_group_counter += 1;
1196              break;
1197            }
1198 <          /* scd order parameter(either --sele1, --sele2, --sele3 are specified or --molname, --begin, --end are specified).  */
1042 <          else if (strcmp (long_options[option_index].name, "scd") == 0)
1043 <          {
1044 <            if (local_args_info.scd_given)
1045 <              {
1046 <                fprintf (stderr, "%s: `--scd' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1047 <                goto failure;
1048 <              }
1049 <            if (args_info->scd_given && ! override)
1050 <              continue;
1051 <            local_args_info.scd_given = 1;
1052 <            args_info->scd_given = 1;
1053 <            if (args_info->staticProps_group_counter && override)
1054 <              reset_group_staticProps (args_info);
1055 <            args_info->staticProps_group_counter += 1;
1056 <            break;
1057 <          }
1058 <          /* density plot (--sele1 must be specified).  */
1059 <          else if (strcmp (long_options[option_index].name, "density") == 0)
1060 <          {
1061 <            if (local_args_info.density_given)
1062 <              {
1063 <                fprintf (stderr, "%s: `--density' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1064 <                goto failure;
1065 <              }
1066 <            if (args_info->density_given && ! override)
1067 <              continue;
1068 <            local_args_info.density_given = 1;
1069 <            args_info->density_given = 1;
1070 <            if (args_info->staticProps_group_counter && override)
1071 <              reset_group_staticProps (args_info);
1072 <            args_info->staticProps_group_counter += 1;
1073 <            break;
1074 <          }
1075 <          /* slab density (--sele1 must be specified).  */
1198 >          /* slab density.  */
1199            else if (strcmp (long_options[option_index].name, "slab_density") == 0)
1200            {
1201              if (local_args_info.slab_density_given)
# Line 1089 | Line 1212 | cmdline_parser_internal (int argc, char * const *argv,
1212              args_info->staticProps_group_counter += 1;
1213              break;
1214            }
1215 <          /* hxy (--sele1 must be specified).  */
1215 >          /* hxy.  */
1216            else if (strcmp (long_options[option_index].name, "hxy") == 0)
1217            {
1218              if (local_args_info.hxy_given)
# Line 1106 | Line 1229 | cmdline_parser_internal (int argc, char * const *argv,
1229              args_info->staticProps_group_counter += 1;
1230              break;
1231            }
1232 +          /* rho of R.  */
1233 +          else if (strcmp (long_options[option_index].name, "rho_r") == 0)
1234 +          {
1235 +            if (local_args_info.rho_r_given)
1236 +              {
1237 +                fprintf (stderr, "%s: `--rho_r' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1238 +                goto failure;
1239 +              }
1240 +            if (args_info->rho_r_given && ! override)
1241 +              continue;
1242 +            local_args_info.rho_r_given = 1;
1243 +            args_info->rho_r_given = 1;
1244 +            if (args_info->staticProps_group_counter && override)
1245 +              reset_group_staticProps (args_info);
1246 +            args_info->staticProps_group_counter += 1;
1247 +            break;
1248 +          }
1249            
1250            break;
1251          case '?':       /* Invalid option.  */

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