| 48 | 
  | 
  args_info->nbins_y_given = 0 ; | 
| 49 | 
  | 
  args_info->nanglebins_given = 0 ; | 
| 50 | 
  | 
  args_info->length_given = 0 ; | 
| 51 | 
– | 
  args_info->LegendreL_given = 0 ; | 
| 51 | 
  | 
  args_info->rcut_given = 0 ; | 
| 52 | 
  | 
  args_info->zoffset_given = 0 ; | 
| 53 | 
  | 
  args_info->sele1_given = 0 ; | 
| 90 | 
  | 
  args_info->nanglebins_arg = 50; | 
| 91 | 
  | 
  args_info->nanglebins_orig = NULL; | 
| 92 | 
  | 
  args_info->length_orig = NULL; | 
| 94 | 
– | 
  args_info->LegendreL_orig = NULL; | 
| 93 | 
  | 
  args_info->rcut_orig = NULL; | 
| 94 | 
  | 
  args_info->zoffset_arg = 0; | 
| 95 | 
  | 
  args_info->zoffset_orig = NULL; | 
| 129 | 
  | 
  printf("%s\n","  -y, --nbins_y=INT             number of bins in y axis  (default=`100')"); | 
| 130 | 
  | 
  printf("%s\n","  -a, --nanglebins=INT          number of bins for cos(angle)  (default=`50')"); | 
| 131 | 
  | 
  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)"); | 
| 132 | 
  | 
  printf("%s\n","  -c, --rcut=DOUBLE             cutoff radius (rcut)"); | 
| 133 | 
  | 
  printf("%s\n","  -z, --zoffset=DOUBLE          Where to set the zero for the slab_density \n                                  calculation  (default=`0')"); | 
| 134 | 
  | 
  printf("%s\n","      --sele1=selection script  select the first stuntdouble set"); | 
| 139 | 
  | 
  printf("%s\n","      --begin=INT               begin internal index"); | 
| 140 | 
  | 
  printf("%s\n","      --end=INT                 end internal index"); | 
| 141 | 
  | 
  printf("%s\n","\n Group: staticProps\n   an option of this group is required"); | 
| 142 | 
< | 
  printf("%s\n","      --bo                      bond order parameter (--rcut and --LegendreL \n                                  must be specified"); | 
| 142 | 
> | 
  printf("%s\n","      --bo                      bond order parameter (--rcut must be specified"); | 
| 143 | 
  | 
  printf("%s\n","  -g, --gofr                    g(r)"); | 
| 144 | 
  | 
  printf("%s\n","      --r_theta                 g(r, cos(theta))"); | 
| 145 | 
  | 
  printf("%s\n","      --r_omega                 g(r, cos(omega))"); | 
| 215 | 
  | 
      free (args_info->length_orig); /* free previous argument */ | 
| 216 | 
  | 
      args_info->length_orig = 0; | 
| 217 | 
  | 
    } | 
| 221 | 
– | 
  if (args_info->LegendreL_orig) | 
| 222 | 
– | 
    { | 
| 223 | 
– | 
      free (args_info->LegendreL_orig); /* free previous argument */ | 
| 224 | 
– | 
      args_info->LegendreL_orig = 0; | 
| 225 | 
– | 
    } | 
| 218 | 
  | 
  if (args_info->rcut_orig) | 
| 219 | 
  | 
    { | 
| 220 | 
  | 
      free (args_info->rcut_orig); /* free previous argument */ | 
| 365 | 
  | 
      fprintf(outfile, "%s\n", "length"); | 
| 366 | 
  | 
    } | 
| 367 | 
  | 
  } | 
| 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"); | 
| 381 | 
– | 
    } | 
| 382 | 
– | 
  } | 
| 368 | 
  | 
  if (args_info->rcut_given) { | 
| 369 | 
  | 
    if (args_info->rcut_orig) { | 
| 370 | 
  | 
      fprintf(outfile, "%s=\"%s\"\n", "rcut", args_info->rcut_orig); | 
| 612 | 
  | 
        { "nbins_y",    1, NULL, 'y' }, | 
| 613 | 
  | 
        { "nanglebins", 1, NULL, 'a' }, | 
| 614 | 
  | 
        { "length",     1, NULL, 0 }, | 
| 630 | 
– | 
        { "LegendreL",  1, NULL, 'l' }, | 
| 615 | 
  | 
        { "rcut",       1, NULL, 'c' }, | 
| 616 | 
  | 
        { "zoffset",    1, NULL, 'z' }, | 
| 617 | 
  | 
        { "sele1",      1, NULL, 0 }, | 
| 637 | 
  | 
      }; | 
| 638 | 
  | 
 | 
| 639 | 
  | 
      stop_char = 0; | 
| 640 | 
< | 
      c = getopt_long (argc, argv, "hVi:o:n:b:x:y:a:l:c:z:gpsd", long_options, &option_index); | 
| 640 | 
> | 
      c = getopt_long (argc, argv, "hVi:o:n:b:x:y:a:c:z:gpsd", long_options, &option_index); | 
| 641 | 
  | 
 | 
| 642 | 
  | 
      if (c == -1) break;       /* Exit from `while (1)' loop.  */ | 
| 643 | 
  | 
 | 
| 787 | 
  | 
          if (args_info->nanglebins_orig) | 
| 788 | 
  | 
            free (args_info->nanglebins_orig); /* free previous string */ | 
| 789 | 
  | 
          args_info->nanglebins_orig = gengetopt_strdup (optarg); | 
| 806 | 
– | 
          break; | 
| 807 | 
– | 
 | 
| 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); | 
| 790 | 
  | 
          break; | 
| 791 | 
  | 
 | 
| 792 | 
  | 
        case 'c':       /* cutoff radius (rcut).  */ | 
| 1049 | 
  | 
              free (args_info->end_orig); /* free previous string */ | 
| 1050 | 
  | 
            args_info->end_orig = gengetopt_strdup (optarg); | 
| 1051 | 
  | 
          } | 
| 1052 | 
< | 
          /* bond order parameter (--rcut and --LegendreL must be specified.  */ | 
| 1052 | 
> | 
          /* bond order parameter (--rcut must be specified.  */ | 
| 1053 | 
  | 
          else if (strcmp (long_options[option_index].name, "bo") == 0) | 
| 1054 | 
  | 
          { | 
| 1055 | 
  | 
            if (local_args_info.bo_given) |