| 44 | 
  | 
  args_info->output_given = 0 ; | 
| 45 | 
  | 
  args_info->step_given = 0 ; | 
| 46 | 
  | 
  args_info->nrbins_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->zoffset_given = 0 ; | 
| 62 | 
  | 
  args_info->theta_omega_given = 0 ; | 
| 63 | 
  | 
  args_info->gxyz_given = 0 ; | 
| 64 | 
  | 
  args_info->p2_given = 0 ; | 
| 65 | 
+ | 
  args_info->rp2_given = 0 ; | 
| 66 | 
  | 
  args_info->scd_given = 0 ; | 
| 67 | 
  | 
  args_info->density_given = 0 ; | 
| 68 | 
  | 
  args_info->slab_density_given = 0 ; | 
| 69 | 
+ | 
  args_info->hxy_given = 0 ; | 
| 70 | 
  | 
  args_info->staticProps_group_counter = 0 ; | 
| 71 | 
  | 
} | 
| 72 | 
  | 
 | 
| 81 | 
  | 
  args_info->step_orig = NULL; | 
| 82 | 
  | 
  args_info->nrbins_arg = 100; | 
| 83 | 
  | 
  args_info->nrbins_orig = NULL; | 
| 84 | 
+ | 
  args_info->nbins_x_arg = 100; | 
| 85 | 
+ | 
  args_info->nbins_x_orig = NULL; | 
| 86 | 
+ | 
  args_info->nbins_y_arg = 100; | 
| 87 | 
+ | 
  args_info->nbins_y_orig = NULL; | 
| 88 | 
  | 
  args_info->nanglebins_arg = 50; | 
| 89 | 
  | 
  args_info->nanglebins_orig = NULL; | 
| 90 | 
  | 
  args_info->length_orig = NULL; | 
| 122 | 
  | 
  printf("%s\n","  -o, --output=filename         output file name"); | 
| 123 | 
  | 
  printf("%s\n","  -n, --step=INT                process every n frame  (default=`1')"); | 
| 124 | 
  | 
  printf("%s\n","  -r, --nrbins=INT              number of bins for distance  (default=`100')"); | 
| 125 | 
+ | 
  printf("%s\n","  -x, --nbins_x=INT             number of bins in x axis  (default=`100')"); | 
| 126 | 
+ | 
  printf("%s\n","  -y, --nbins_y=INT             number of bins in y axis  (default=`100')"); | 
| 127 | 
  | 
  printf("%s\n","  -a, --nanglebins=INT          number of bins for cos(angle)  (default=`50')"); | 
| 128 | 
  | 
  printf("%s\n","  -l, --length=DOUBLE           maximum length (Defaults to 1/2 smallest length \n                                  of first frame)"); | 
| 129 | 
  | 
  printf("%s\n","  -z, --zoffset=DOUBLE          Where to set the zero for the slab_density \n                                  calculation  (default=`0')"); | 
| 141 | 
  | 
  printf("%s\n","      --theta_omega             g(cos(theta), cos(omega))"); | 
| 142 | 
  | 
  printf("%s\n","      --gxyz                    g(x, y, z)"); | 
| 143 | 
  | 
  printf("%s\n","      --p2                      p2 order parameter (--sele1 and --sele2 must be \n                                  specified)"); | 
| 144 | 
+ | 
  printf("%s\n","      --rp2                     rp2 order parameter (--sele1 and --sele2 must \n                                  be specified)"); | 
| 145 | 
  | 
  printf("%s\n","      --scd                     scd order parameter(either --sele1, --sele2, \n                                  --sele3 are specified or --molname, --begin, \n                                  --end are specified)"); | 
| 146 | 
  | 
  printf("%s\n","      --density                 density plot (--sele1 must be specified)"); | 
| 147 | 
  | 
  printf("%s\n","      --slab_density            slab density (--sele1 must be specified)"); | 
| 148 | 
+ | 
  printf("%s\n","      --hxy                     hxy (--sele1 must be specified)"); | 
| 149 | 
  | 
   | 
| 150 | 
  | 
} | 
| 151 | 
  | 
 | 
| 190 | 
  | 
      free (args_info->nrbins_orig); /* free previous argument */ | 
| 191 | 
  | 
      args_info->nrbins_orig = 0; | 
| 192 | 
  | 
    } | 
| 193 | 
+ | 
  if (args_info->nbins_x_orig) | 
| 194 | 
+ | 
    { | 
| 195 | 
+ | 
      free (args_info->nbins_x_orig); /* free previous argument */ | 
| 196 | 
+ | 
      args_info->nbins_x_orig = 0; | 
| 197 | 
+ | 
    } | 
| 198 | 
+ | 
  if (args_info->nbins_y_orig) | 
| 199 | 
+ | 
    { | 
| 200 | 
+ | 
      free (args_info->nbins_y_orig); /* free previous argument */ | 
| 201 | 
+ | 
      args_info->nbins_y_orig = 0; | 
| 202 | 
+ | 
    } | 
| 203 | 
  | 
  if (args_info->nanglebins_orig) | 
| 204 | 
  | 
    { | 
| 205 | 
  | 
      free (args_info->nanglebins_orig); /* free previous argument */ | 
| 325 | 
  | 
      fprintf(outfile, "%s=\"%s\"\n", "nrbins", args_info->nrbins_orig); | 
| 326 | 
  | 
    } else { | 
| 327 | 
  | 
      fprintf(outfile, "%s\n", "nrbins"); | 
| 328 | 
+ | 
    } | 
| 329 | 
+ | 
  } | 
| 330 | 
+ | 
  if (args_info->nbins_x_given) { | 
| 331 | 
+ | 
    if (args_info->nbins_x_orig) { | 
| 332 | 
+ | 
      fprintf(outfile, "%s=\"%s\"\n", "nbins_x", args_info->nbins_x_orig); | 
| 333 | 
+ | 
    } else { | 
| 334 | 
+ | 
      fprintf(outfile, "%s\n", "nbins_x"); | 
| 335 | 
+ | 
    } | 
| 336 | 
+ | 
  } | 
| 337 | 
+ | 
  if (args_info->nbins_y_given) { | 
| 338 | 
+ | 
    if (args_info->nbins_y_orig) { | 
| 339 | 
+ | 
      fprintf(outfile, "%s=\"%s\"\n", "nbins_y", args_info->nbins_y_orig); | 
| 340 | 
+ | 
    } else { | 
| 341 | 
+ | 
      fprintf(outfile, "%s\n", "nbins_y"); | 
| 342 | 
  | 
    } | 
| 343 | 
  | 
  } | 
| 344 | 
  | 
  if (args_info->nanglebins_given) { | 
| 429 | 
  | 
  if (args_info->p2_given) { | 
| 430 | 
  | 
    fprintf(outfile, "%s\n", "p2"); | 
| 431 | 
  | 
  } | 
| 432 | 
+ | 
  if (args_info->rp2_given) { | 
| 433 | 
+ | 
    fprintf(outfile, "%s\n", "rp2"); | 
| 434 | 
+ | 
  } | 
| 435 | 
  | 
  if (args_info->scd_given) { | 
| 436 | 
  | 
    fprintf(outfile, "%s\n", "scd"); | 
| 437 | 
  | 
  } | 
| 441 | 
  | 
  if (args_info->slab_density_given) { | 
| 442 | 
  | 
    fprintf(outfile, "%s\n", "slab_density"); | 
| 443 | 
  | 
  } | 
| 444 | 
+ | 
  if (args_info->hxy_given) { | 
| 445 | 
+ | 
    fprintf(outfile, "%s\n", "hxy"); | 
| 446 | 
+ | 
  } | 
| 447 | 
  | 
   | 
| 448 | 
  | 
  fclose (outfile); | 
| 449 | 
  | 
 | 
| 489 | 
  | 
  args_info->theta_omega_given = 0 ; | 
| 490 | 
  | 
  args_info->gxyz_given = 0 ; | 
| 491 | 
  | 
  args_info->p2_given = 0 ; | 
| 492 | 
+ | 
  args_info->rp2_given = 0 ; | 
| 493 | 
  | 
  args_info->scd_given = 0 ; | 
| 494 | 
  | 
  args_info->density_given = 0 ; | 
| 495 | 
  | 
  args_info->slab_density_given = 0 ; | 
| 496 | 
+ | 
  args_info->hxy_given = 0 ; | 
| 497 | 
  | 
 | 
| 498 | 
  | 
  args_info->staticProps_group_counter = 0; | 
| 499 | 
  | 
} | 
| 587 | 
  | 
        { "output",     1, NULL, 'o' }, | 
| 588 | 
  | 
        { "step",       1, NULL, 'n' }, | 
| 589 | 
  | 
        { "nrbins",     1, NULL, 'r' }, | 
| 590 | 
+ | 
        { "nbins_x",    1, NULL, 'x' }, | 
| 591 | 
+ | 
        { "nbins_y",    1, NULL, 'y' }, | 
| 592 | 
  | 
        { "nanglebins", 1, NULL, 'a' }, | 
| 593 | 
  | 
        { "length",     1, NULL, 'l' }, | 
| 594 | 
  | 
        { "zoffset",    1, NULL, 'z' }, | 
| 605 | 
  | 
        { "theta_omega",        0, NULL, 0 }, | 
| 606 | 
  | 
        { "gxyz",       0, NULL, 0 }, | 
| 607 | 
  | 
        { "p2", 0, NULL, 0 }, | 
| 608 | 
+ | 
        { "rp2",        0, NULL, 0 }, | 
| 609 | 
  | 
        { "scd",        0, NULL, 0 }, | 
| 610 | 
  | 
        { "density",    0, NULL, 0 }, | 
| 611 | 
  | 
        { "slab_density",       0, NULL, 0 }, | 
| 612 | 
+ | 
        { "hxy",        0, NULL, 0 }, | 
| 613 | 
  | 
        { NULL, 0, NULL, 0 } | 
| 614 | 
  | 
      }; | 
| 615 | 
  | 
 | 
| 616 | 
  | 
      stop_char = 0; | 
| 617 | 
< | 
      c = getopt_long (argc, argv, "hVi:o:n:r:a:l:z:", long_options, &option_index); | 
| 617 | 
> | 
      c = getopt_long (argc, argv, "hVi:o:n:r:x:y:a:l:z:", long_options, &option_index); | 
| 618 | 
  | 
 | 
| 619 | 
  | 
      if (c == -1) break;       /* Exit from `while (1)' loop.  */ | 
| 620 | 
  | 
 | 
| 704 | 
  | 
          if (args_info->nrbins_orig) | 
| 705 | 
  | 
            free (args_info->nrbins_orig); /* free previous string */ | 
| 706 | 
  | 
          args_info->nrbins_orig = gengetopt_strdup (optarg); | 
| 707 | 
+ | 
          break; | 
| 708 | 
+ | 
 | 
| 709 | 
+ | 
        case 'x':       /* number of bins in x axis.  */ | 
| 710 | 
+ | 
          if (local_args_info.nbins_x_given) | 
| 711 | 
+ | 
            { | 
| 712 | 
+ | 
              fprintf (stderr, "%s: `--nbins_x' (`-x') option given more than once%s\n", argv[0], (additional_error ? additional_error : "")); | 
| 713 | 
+ | 
              goto failure; | 
| 714 | 
+ | 
            } | 
| 715 | 
+ | 
          if (args_info->nbins_x_given && ! override) | 
| 716 | 
+ | 
            continue; | 
| 717 | 
+ | 
          local_args_info.nbins_x_given = 1; | 
| 718 | 
+ | 
          args_info->nbins_x_given = 1; | 
| 719 | 
+ | 
          args_info->nbins_x_arg = strtol (optarg, &stop_char, 0); | 
| 720 | 
+ | 
          if (!(stop_char && *stop_char == '\0')) { | 
| 721 | 
+ | 
            fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg); | 
| 722 | 
+ | 
            goto failure; | 
| 723 | 
+ | 
          } | 
| 724 | 
+ | 
          if (args_info->nbins_x_orig) | 
| 725 | 
+ | 
            free (args_info->nbins_x_orig); /* free previous string */ | 
| 726 | 
+ | 
          args_info->nbins_x_orig = gengetopt_strdup (optarg); | 
| 727 | 
+ | 
          break; | 
| 728 | 
+ | 
 | 
| 729 | 
+ | 
        case 'y':       /* number of bins in y axis.  */ | 
| 730 | 
+ | 
          if (local_args_info.nbins_y_given) | 
| 731 | 
+ | 
            { | 
| 732 | 
+ | 
              fprintf (stderr, "%s: `--nbins_y' (`-y') option given more than once%s\n", argv[0], (additional_error ? additional_error : "")); | 
| 733 | 
+ | 
              goto failure; | 
| 734 | 
+ | 
            } | 
| 735 | 
+ | 
          if (args_info->nbins_y_given && ! override) | 
| 736 | 
+ | 
            continue; | 
| 737 | 
+ | 
          local_args_info.nbins_y_given = 1; | 
| 738 | 
+ | 
          args_info->nbins_y_given = 1; | 
| 739 | 
+ | 
          args_info->nbins_y_arg = strtol (optarg, &stop_char, 0); | 
| 740 | 
+ | 
          if (!(stop_char && *stop_char == '\0')) { | 
| 741 | 
+ | 
            fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg); | 
| 742 | 
+ | 
            goto failure; | 
| 743 | 
+ | 
          } | 
| 744 | 
+ | 
          if (args_info->nbins_y_orig) | 
| 745 | 
+ | 
            free (args_info->nbins_y_orig); /* free previous string */ | 
| 746 | 
+ | 
          args_info->nbins_y_orig = gengetopt_strdup (optarg); | 
| 747 | 
  | 
          break; | 
| 748 | 
  | 
 | 
| 749 | 
  | 
        case 'a':       /* number of bins for cos(angle).  */ | 
| 1047 | 
  | 
            args_info->staticProps_group_counter += 1; | 
| 1048 | 
  | 
            break; | 
| 1049 | 
  | 
          } | 
| 1050 | 
+ | 
          /* rp2 order parameter (--sele1 and --sele2 must be specified).  */ | 
| 1051 | 
+ | 
          else if (strcmp (long_options[option_index].name, "rp2") == 0) | 
| 1052 | 
+ | 
          { | 
| 1053 | 
+ | 
            if (local_args_info.rp2_given) | 
| 1054 | 
+ | 
              { | 
| 1055 | 
+ | 
                fprintf (stderr, "%s: `--rp2' option given more than once%s\n", argv[0], (additional_error ? additional_error : "")); | 
| 1056 | 
+ | 
                goto failure; | 
| 1057 | 
+ | 
              } | 
| 1058 | 
+ | 
            if (args_info->rp2_given && ! override) | 
| 1059 | 
+ | 
              continue; | 
| 1060 | 
+ | 
            local_args_info.rp2_given = 1; | 
| 1061 | 
+ | 
            args_info->rp2_given = 1; | 
| 1062 | 
+ | 
            if (args_info->staticProps_group_counter && override) | 
| 1063 | 
+ | 
              reset_group_staticProps (args_info); | 
| 1064 | 
+ | 
            args_info->staticProps_group_counter += 1; | 
| 1065 | 
+ | 
            break; | 
| 1066 | 
+ | 
          } | 
| 1067 | 
  | 
          /* scd order parameter(either --sele1, --sele2, --sele3 are specified or --molname, --begin, --end are specified).  */ | 
| 1068 | 
  | 
          else if (strcmp (long_options[option_index].name, "scd") == 0) | 
| 1069 | 
  | 
          { | 
| 1115 | 
  | 
            args_info->staticProps_group_counter += 1; | 
| 1116 | 
  | 
            break; | 
| 1117 | 
  | 
          } | 
| 1118 | 
+ | 
          /* hxy (--sele1 must be specified).  */ | 
| 1119 | 
+ | 
          else if (strcmp (long_options[option_index].name, "hxy") == 0) | 
| 1120 | 
+ | 
          { | 
| 1121 | 
+ | 
            if (local_args_info.hxy_given) | 
| 1122 | 
+ | 
              { | 
| 1123 | 
+ | 
                fprintf (stderr, "%s: `--hxy' option given more than once%s\n", argv[0], (additional_error ? additional_error : "")); | 
| 1124 | 
+ | 
                goto failure; | 
| 1125 | 
+ | 
              } | 
| 1126 | 
+ | 
            if (args_info->hxy_given && ! override) | 
| 1127 | 
+ | 
              continue; | 
| 1128 | 
+ | 
            local_args_info.hxy_given = 1; | 
| 1129 | 
+ | 
            args_info->hxy_given = 1; | 
| 1130 | 
+ | 
            if (args_info->staticProps_group_counter && override) | 
| 1131 | 
+ | 
              reset_group_staticProps (args_info); | 
| 1132 | 
+ | 
            args_info->staticProps_group_counter += 1; | 
| 1133 | 
+ | 
            break; | 
| 1134 | 
+ | 
          } | 
| 1135 | 
  | 
           | 
| 1136 | 
  | 
          break; | 
| 1137 | 
  | 
        case '?':       /* Invalid option.  */ |