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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 929 by gezelter, Tue Apr 11 15:33:27 2006 UTC vs.
Revision 1052 by gezelter, Tue Sep 26 01:30:32 2006 UTC

# 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 54 | 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->bo_given = 0 ;
61    args_info->gofr_given = 0 ;
62    args_info->r_theta_given = 0 ;
63    args_info->r_omega_given = 0 ;
64    args_info->theta_omega_given = 0 ;
65    args_info->gxyz_given = 0 ;
66    args_info->p2_given = 0 ;
67 +  args_info->rp2_given = 0 ;
68    args_info->scd_given = 0 ;
69    args_info->density_given = 0 ;
70    args_info->slab_density_given = 0 ;
71 +  args_info->hxy_given = 0 ;
72    args_info->staticProps_group_counter = 0 ;
73   }
74  
# Line 75 | Line 81 | void clear_args (struct gengetopt_args_info *args_info
81    args_info->output_orig = NULL;
82    args_info->step_arg = 1;
83    args_info->step_orig = NULL;
84 <  args_info->nrbins_arg = 100;
85 <  args_info->nrbins_orig = NULL;
84 >  args_info->nbins_arg = 100;
85 >  args_info->nbins_orig = NULL;
86 >  args_info->nbins_x_arg = 100;
87 >  args_info->nbins_x_orig = NULL;
88 >  args_info->nbins_y_arg = 100;
89 >  args_info->nbins_y_orig = NULL;
90    args_info->nanglebins_arg = 50;
91    args_info->nanglebins_orig = NULL;
92    args_info->length_orig = NULL;
93 +  args_info->rcut_orig = NULL;
94    args_info->zoffset_arg = 0;
95    args_info->zoffset_orig = NULL;
96    args_info->sele1_arg = NULL;
# Line 113 | Line 124 | cmdline_parser_print_help (void)
124    printf("%s\n","  -i, --input=filename          input dump file");
125    printf("%s\n","  -o, --output=filename         output file name");
126    printf("%s\n","  -n, --step=INT                process every n frame  (default=`1')");
127 <  printf("%s\n","  -r, --nrbins=INT              number of bins for distance  (default=`100')");
127 >  printf("%s\n","  -b, --nbins=INT               number of bins (general purpose)  \n                                  (default=`100')");
128 >  printf("%s\n","  -x, --nbins_x=INT             number of bins in x axis  (default=`100')");
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","  -l, --length=DOUBLE           maximum length (Defaults to 1/2 smallest length \n                                  of first frame)");
131 >  printf("%s\n","      --length=DOUBLE           maximum length (Defaults to 1/2 smallest length \n                                  of first frame)");
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");
135    printf("%s\n","      --sele2=selection script  select the second stuntdouble set");
136    printf("%s\n","      --sele3=selection script  select the third stuntdouble set");
137    printf("%s\n","      --refsele=selection script\n                                select reference (use and only use with --gxyz)");
138    printf("%s\n","      --molname=STRING          molecule name");
139 <  printf("%s\n","      --begin=INT               begin interanl index");
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","      --gofr                    g(r)");
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))");
146    printf("%s\n","      --theta_omega             g(cos(theta), cos(omega))");
147    printf("%s\n","      --gxyz                    g(x, y, z)");
148 <  printf("%s\n","      --p2                      p2 order parameter (--sele1 and --sele2 must be \n                                  specified)");
149 <  printf("%s\n","      --scd                     scd order parameter(either --sele1, --sele2, \n                                  --sele3 are specified or --molname, --begin, \n                                  --end are specified)");
150 <  printf("%s\n","      --density                 density plot (--sele1 must be specified)");
151 <  printf("%s\n","      --slab_density            slab density (--sele1 must be specified)");
148 >  printf("%s\n","  -p, --p2                      p2 order parameter (--sele1 and --sele2 must be \n                                  specified)");
149 >  printf("%s\n","      --rp2                     rp2 order parameter (--sele1 and --sele2 must \n                                  be specified)");
150 >  printf("%s\n","  -s, --scd                     scd order parameter (either --sele1, --sele2, \n                                  --sele3 are specified or --molname, --begin, \n                                  --end are specified)");
151 >  printf("%s\n","  -d, --density                 density plot");
152 >  printf("%s\n","      --slab_density            slab density");
153 >  printf("%s\n","      --hxy                     hxy");
154    
155   }
156  
# Line 173 | Line 190 | cmdline_parser_release (struct gengetopt_args_info *ar
190        free (args_info->step_orig); /* free previous argument */
191        args_info->step_orig = 0;
192      }
193 <  if (args_info->nrbins_orig)
193 >  if (args_info->nbins_orig)
194      {
195 <      free (args_info->nrbins_orig); /* free previous argument */
196 <      args_info->nrbins_orig = 0;
195 >      free (args_info->nbins_orig); /* free previous argument */
196 >      args_info->nbins_orig = 0;
197 >    }
198 >  if (args_info->nbins_x_orig)
199 >    {
200 >      free (args_info->nbins_x_orig); /* free previous argument */
201 >      args_info->nbins_x_orig = 0;
202 >    }
203 >  if (args_info->nbins_y_orig)
204 >    {
205 >      free (args_info->nbins_y_orig); /* free previous argument */
206 >      args_info->nbins_y_orig = 0;
207      }
208    if (args_info->nanglebins_orig)
209      {
# Line 188 | Line 215 | cmdline_parser_release (struct gengetopt_args_info *ar
215        free (args_info->length_orig); /* free previous argument */
216        args_info->length_orig = 0;
217      }
218 +  if (args_info->rcut_orig)
219 +    {
220 +      free (args_info->rcut_orig); /* free previous argument */
221 +      args_info->rcut_orig = 0;
222 +    }
223    if (args_info->zoffset_orig)
224      {
225        free (args_info->zoffset_orig); /* free previous argument */
# Line 298 | Line 330 | cmdline_parser_file_save(const char *filename, struct
330        fprintf(outfile, "%s\n", "step");
331      }
332    }
333 <  if (args_info->nrbins_given) {
334 <    if (args_info->nrbins_orig) {
335 <      fprintf(outfile, "%s=\"%s\"\n", "nrbins", args_info->nrbins_orig);
333 >  if (args_info->nbins_given) {
334 >    if (args_info->nbins_orig) {
335 >      fprintf(outfile, "%s=\"%s\"\n", "nbins", args_info->nbins_orig);
336      } else {
337 <      fprintf(outfile, "%s\n", "nrbins");
337 >      fprintf(outfile, "%s\n", "nbins");
338 >    }
339 >  }
340 >  if (args_info->nbins_x_given) {
341 >    if (args_info->nbins_x_orig) {
342 >      fprintf(outfile, "%s=\"%s\"\n", "nbins_x", args_info->nbins_x_orig);
343 >    } else {
344 >      fprintf(outfile, "%s\n", "nbins_x");
345 >    }
346 >  }
347 >  if (args_info->nbins_y_given) {
348 >    if (args_info->nbins_y_orig) {
349 >      fprintf(outfile, "%s=\"%s\"\n", "nbins_y", args_info->nbins_y_orig);
350 >    } else {
351 >      fprintf(outfile, "%s\n", "nbins_y");
352      }
353    }
354    if (args_info->nanglebins_given) {
# Line 319 | Line 365 | cmdline_parser_file_save(const char *filename, struct
365        fprintf(outfile, "%s\n", "length");
366      }
367    }
368 +  if (args_info->rcut_given) {
369 +    if (args_info->rcut_orig) {
370 +      fprintf(outfile, "%s=\"%s\"\n", "rcut", args_info->rcut_orig);
371 +    } else {
372 +      fprintf(outfile, "%s\n", "rcut");
373 +    }
374 +  }
375    if (args_info->zoffset_given) {
376      if (args_info->zoffset_orig) {
377        fprintf(outfile, "%s=\"%s\"\n", "zoffset", args_info->zoffset_orig);
# Line 375 | Line 428 | cmdline_parser_file_save(const char *filename, struct
428        fprintf(outfile, "%s\n", "end");
429      }
430    }
431 +  if (args_info->bo_given) {
432 +    fprintf(outfile, "%s\n", "bo");
433 +  }
434    if (args_info->gofr_given) {
435      fprintf(outfile, "%s\n", "gofr");
436    }
# Line 393 | Line 449 | cmdline_parser_file_save(const char *filename, struct
449    if (args_info->p2_given) {
450      fprintf(outfile, "%s\n", "p2");
451    }
452 +  if (args_info->rp2_given) {
453 +    fprintf(outfile, "%s\n", "rp2");
454 +  }
455    if (args_info->scd_given) {
456      fprintf(outfile, "%s\n", "scd");
457    }
# Line 402 | Line 461 | cmdline_parser_file_save(const char *filename, struct
461    if (args_info->slab_density_given) {
462      fprintf(outfile, "%s\n", "slab_density");
463    }
464 +  if (args_info->hxy_given) {
465 +    fprintf(outfile, "%s\n", "hxy");
466 +  }
467    
468    fclose (outfile);
469  
# Line 441 | Line 503 | reset_group_staticProps(struct gengetopt_args_info *ar
503    if (! args_info->staticProps_group_counter)
504      return;
505    
506 +  args_info->bo_given = 0 ;
507    args_info->gofr_given = 0 ;
508    args_info->r_theta_given = 0 ;
509    args_info->r_omega_given = 0 ;
510    args_info->theta_omega_given = 0 ;
511    args_info->gxyz_given = 0 ;
512    args_info->p2_given = 0 ;
513 +  args_info->rp2_given = 0 ;
514    args_info->scd_given = 0 ;
515    args_info->density_given = 0 ;
516    args_info->slab_density_given = 0 ;
517 +  args_info->hxy_given = 0 ;
518  
519    args_info->staticProps_group_counter = 0;
520   }
# Line 542 | Line 607 | cmdline_parser_internal (int argc, char * const *argv,
607          { "input",      1, NULL, 'i' },
608          { "output",     1, NULL, 'o' },
609          { "step",       1, NULL, 'n' },
610 <        { "nrbins",     1, NULL, 'r' },
610 >        { "nbins",      1, NULL, 'b' },
611 >        { "nbins_x",    1, NULL, 'x' },
612 >        { "nbins_y",    1, NULL, 'y' },
613          { "nanglebins", 1, NULL, 'a' },
614 <        { "length",     1, NULL, 'l' },
614 >        { "length",     1, NULL, 0 },
615 >        { "rcut",       1, NULL, 'c' },
616          { "zoffset",    1, NULL, 'z' },
617          { "sele1",      1, NULL, 0 },
618          { "sele2",      1, NULL, 0 },
# Line 553 | Line 621 | cmdline_parser_internal (int argc, char * const *argv,
621          { "molname",    1, NULL, 0 },
622          { "begin",      1, NULL, 0 },
623          { "end",        1, NULL, 0 },
624 <        { "gofr",       0, NULL, 0 },
624 >        { "bo", 0, NULL, 0 },
625 >        { "gofr",       0, NULL, 'g' },
626          { "r_theta",    0, NULL, 0 },
627          { "r_omega",    0, NULL, 0 },
628          { "theta_omega",        0, NULL, 0 },
629          { "gxyz",       0, NULL, 0 },
630 <        { "p2", 0, NULL, 0 },
631 <        { "scd",        0, NULL, 0 },
632 <        { "density",    0, NULL, 0 },
630 >        { "p2", 0, NULL, 'p' },
631 >        { "rp2",        0, NULL, 0 },
632 >        { "scd",        0, NULL, 's' },
633 >        { "density",    0, NULL, 'd' },
634          { "slab_density",       0, NULL, 0 },
635 +        { "hxy",        0, NULL, 0 },
636          { NULL, 0, NULL, 0 }
637        };
638  
639        stop_char = 0;
640 <      c = getopt_long (argc, argv, "hVi:o:n:r:a:l:z:", 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  
# Line 638 | Line 709 | cmdline_parser_internal (int argc, char * const *argv,
709            args_info->step_orig = gengetopt_strdup (optarg);
710            break;
711  
712 <        case 'r':       /* number of bins for distance.  */
713 <          if (local_args_info.nrbins_given)
712 >        case 'b':       /* number of bins (general purpose).  */
713 >          if (local_args_info.nbins_given)
714              {
715 <              fprintf (stderr, "%s: `--nrbins' (`-r') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
715 >              fprintf (stderr, "%s: `--nbins' (`-b') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
716                goto failure;
717              }
718 <          if (args_info->nrbins_given && ! override)
718 >          if (args_info->nbins_given && ! override)
719              continue;
720 <          local_args_info.nrbins_given = 1;
721 <          args_info->nrbins_given = 1;
722 <          args_info->nrbins_arg = strtol (optarg, &stop_char, 0);
720 >          local_args_info.nbins_given = 1;
721 >          args_info->nbins_given = 1;
722 >          args_info->nbins_arg = strtol (optarg, &stop_char, 0);
723            if (!(stop_char && *stop_char == '\0')) {
724              fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
725              goto failure;
726            }
727 <          if (args_info->nrbins_orig)
728 <            free (args_info->nrbins_orig); /* free previous string */
729 <          args_info->nrbins_orig = gengetopt_strdup (optarg);
727 >          if (args_info->nbins_orig)
728 >            free (args_info->nbins_orig); /* free previous string */
729 >          args_info->nbins_orig = gengetopt_strdup (optarg);
730            break;
731  
732 +        case 'x':       /* number of bins in x axis.  */
733 +          if (local_args_info.nbins_x_given)
734 +            {
735 +              fprintf (stderr, "%s: `--nbins_x' (`-x') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
736 +              goto failure;
737 +            }
738 +          if (args_info->nbins_x_given && ! override)
739 +            continue;
740 +          local_args_info.nbins_x_given = 1;
741 +          args_info->nbins_x_given = 1;
742 +          args_info->nbins_x_arg = strtol (optarg, &stop_char, 0);
743 +          if (!(stop_char && *stop_char == '\0')) {
744 +            fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
745 +            goto failure;
746 +          }
747 +          if (args_info->nbins_x_orig)
748 +            free (args_info->nbins_x_orig); /* free previous string */
749 +          args_info->nbins_x_orig = gengetopt_strdup (optarg);
750 +          break;
751 +
752 +        case 'y':       /* number of bins in y axis.  */
753 +          if (local_args_info.nbins_y_given)
754 +            {
755 +              fprintf (stderr, "%s: `--nbins_y' (`-y') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
756 +              goto failure;
757 +            }
758 +          if (args_info->nbins_y_given && ! override)
759 +            continue;
760 +          local_args_info.nbins_y_given = 1;
761 +          args_info->nbins_y_given = 1;
762 +          args_info->nbins_y_arg = strtol (optarg, &stop_char, 0);
763 +          if (!(stop_char && *stop_char == '\0')) {
764 +            fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
765 +            goto failure;
766 +          }
767 +          if (args_info->nbins_y_orig)
768 +            free (args_info->nbins_y_orig); /* free previous string */
769 +          args_info->nbins_y_orig = gengetopt_strdup (optarg);
770 +          break;
771 +
772          case 'a':       /* number of bins for cos(angle).  */
773            if (local_args_info.nanglebins_given)
774              {
# Line 678 | Line 789 | cmdline_parser_internal (int argc, char * const *argv,
789            args_info->nanglebins_orig = gengetopt_strdup (optarg);
790            break;
791  
792 <        case 'l':       /* maximum length (Defaults to 1/2 smallest length of first frame).  */
793 <          if (local_args_info.length_given)
792 >        case 'c':       /* cutoff radius (rcut).  */
793 >          if (local_args_info.rcut_given)
794              {
795 <              fprintf (stderr, "%s: `--length' (`-l') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
795 >              fprintf (stderr, "%s: `--rcut' (`-c') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
796                goto failure;
797              }
798 <          if (args_info->length_given && ! override)
798 >          if (args_info->rcut_given && ! override)
799              continue;
800 <          local_args_info.length_given = 1;
801 <          args_info->length_given = 1;
802 <          args_info->length_arg = strtod (optarg, &stop_char);
800 >          local_args_info.rcut_given = 1;
801 >          args_info->rcut_given = 1;
802 >          args_info->rcut_arg = strtod (optarg, &stop_char);
803            if (!(stop_char && *stop_char == '\0')) {
804              fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
805              goto failure;
806            }
807 <          if (args_info->length_orig)
808 <            free (args_info->length_orig); /* free previous string */
809 <          args_info->length_orig = gengetopt_strdup (optarg);
807 >          if (args_info->rcut_orig)
808 >            free (args_info->rcut_orig); /* free previous string */
809 >          args_info->rcut_orig = gengetopt_strdup (optarg);
810            break;
811  
812          case 'z':       /* Where to set the zero for the slab_density calculation.  */
# Line 718 | Line 829 | cmdline_parser_internal (int argc, char * const *argv,
829            args_info->zoffset_orig = gengetopt_strdup (optarg);
830            break;
831  
832 +        case 'g':       /* g(r).  */
833 +          if (local_args_info.gofr_given)
834 +            {
835 +              fprintf (stderr, "%s: `--gofr' (`-g') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
836 +              goto failure;
837 +            }
838 +          if (args_info->gofr_given && ! override)
839 +            continue;
840 +          local_args_info.gofr_given = 1;
841 +          args_info->gofr_given = 1;
842 +          if (args_info->staticProps_group_counter && override)
843 +            reset_group_staticProps (args_info);
844 +          args_info->staticProps_group_counter += 1;
845 +          break;
846  
847 +        case 'p':       /* p2 order parameter (--sele1 and --sele2 must be specified).  */
848 +          if (local_args_info.p2_given)
849 +            {
850 +              fprintf (stderr, "%s: `--p2' (`-p') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
851 +              goto failure;
852 +            }
853 +          if (args_info->p2_given && ! override)
854 +            continue;
855 +          local_args_info.p2_given = 1;
856 +          args_info->p2_given = 1;
857 +          if (args_info->staticProps_group_counter && override)
858 +            reset_group_staticProps (args_info);
859 +          args_info->staticProps_group_counter += 1;
860 +          break;
861 +
862 +        case 's':       /* scd order parameter (either --sele1, --sele2, --sele3 are specified or --molname, --begin, --end are specified).  */
863 +          if (local_args_info.scd_given)
864 +            {
865 +              fprintf (stderr, "%s: `--scd' (`-s') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
866 +              goto failure;
867 +            }
868 +          if (args_info->scd_given && ! override)
869 +            continue;
870 +          local_args_info.scd_given = 1;
871 +          args_info->scd_given = 1;
872 +          if (args_info->staticProps_group_counter && override)
873 +            reset_group_staticProps (args_info);
874 +          args_info->staticProps_group_counter += 1;
875 +          break;
876 +
877 +        case 'd':       /* density plot.  */
878 +          if (local_args_info.density_given)
879 +            {
880 +              fprintf (stderr, "%s: `--density' (`-d') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
881 +              goto failure;
882 +            }
883 +          if (args_info->density_given && ! override)
884 +            continue;
885 +          local_args_info.density_given = 1;
886 +          args_info->density_given = 1;
887 +          if (args_info->staticProps_group_counter && override)
888 +            reset_group_staticProps (args_info);
889 +          args_info->staticProps_group_counter += 1;
890 +          break;
891 +
892 +
893          case 0: /* Long option with no short option */
894 +          /* maximum length (Defaults to 1/2 smallest length of first frame).  */
895 +          if (strcmp (long_options[option_index].name, "length") == 0)
896 +          {
897 +            if (local_args_info.length_given)
898 +              {
899 +                fprintf (stderr, "%s: `--length' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
900 +                goto failure;
901 +              }
902 +            if (args_info->length_given && ! override)
903 +              continue;
904 +            local_args_info.length_given = 1;
905 +            args_info->length_given = 1;
906 +            args_info->length_arg = strtod (optarg, &stop_char);
907 +            if (!(stop_char && *stop_char == '\0')) {
908 +              fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
909 +              goto failure;
910 +            }
911 +            if (args_info->length_orig)
912 +              free (args_info->length_orig); /* free previous string */
913 +            args_info->length_orig = gengetopt_strdup (optarg);
914 +          }
915            /* select the first stuntdouble set.  */
916 <          if (strcmp (long_options[option_index].name, "sele1") == 0)
916 >          else if (strcmp (long_options[option_index].name, "sele1") == 0)
917            {
918              if (local_args_info.sele1_given)
919                {
# Line 815 | Line 1007 | cmdline_parser_internal (int argc, char * const *argv,
1007                free (args_info->molname_orig); /* free previous string */
1008              args_info->molname_orig = gengetopt_strdup (optarg);
1009            }
1010 <          /* begin interanl index.  */
1010 >          /* begin internal index.  */
1011            else if (strcmp (long_options[option_index].name, "begin") == 0)
1012            {
1013              if (local_args_info.begin_given)
# Line 857 | Line 1049 | cmdline_parser_internal (int argc, char * const *argv,
1049                free (args_info->end_orig); /* free previous string */
1050              args_info->end_orig = gengetopt_strdup (optarg);
1051            }
1052 <          /* g(r).  */
1053 <          else if (strcmp (long_options[option_index].name, "gofr") == 0)
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.gofr_given)
1055 >            if (local_args_info.bo_given)
1056                {
1057 <                fprintf (stderr, "%s: `--gofr' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1057 >                fprintf (stderr, "%s: `--bo' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1058                  goto failure;
1059                }
1060 <            if (args_info->gofr_given && ! override)
1060 >            if (args_info->bo_given && ! override)
1061                continue;
1062 <            local_args_info.gofr_given = 1;
1063 <            args_info->gofr_given = 1;
1062 >            local_args_info.bo_given = 1;
1063 >            args_info->bo_given = 1;
1064              if (args_info->staticProps_group_counter && override)
1065                reset_group_staticProps (args_info);
1066              args_info->staticProps_group_counter += 1;
# Line 942 | Line 1134 | cmdline_parser_internal (int argc, char * const *argv,
1134              args_info->staticProps_group_counter += 1;
1135              break;
1136            }
1137 <          /* p2 order parameter (--sele1 and --sele2 must be specified).  */
1138 <          else if (strcmp (long_options[option_index].name, "p2") == 0)
1137 >          /* rp2 order parameter (--sele1 and --sele2 must be specified).  */
1138 >          else if (strcmp (long_options[option_index].name, "rp2") == 0)
1139            {
1140 <            if (local_args_info.p2_given)
1140 >            if (local_args_info.rp2_given)
1141                {
1142 <                fprintf (stderr, "%s: `--p2' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1142 >                fprintf (stderr, "%s: `--rp2' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1143                  goto failure;
1144                }
1145 <            if (args_info->p2_given && ! override)
1145 >            if (args_info->rp2_given && ! override)
1146                continue;
1147 <            local_args_info.p2_given = 1;
1148 <            args_info->p2_given = 1;
1147 >            local_args_info.rp2_given = 1;
1148 >            args_info->rp2_given = 1;
1149              if (args_info->staticProps_group_counter && override)
1150                reset_group_staticProps (args_info);
1151              args_info->staticProps_group_counter += 1;
1152              break;
1153            }
1154 <          /* scd order parameter(either --sele1, --sele2, --sele3 are specified or --molname, --begin, --end are specified).  */
1155 <          else if (strcmp (long_options[option_index].name, "scd") == 0)
1154 >          /* slab density.  */
1155 >          else if (strcmp (long_options[option_index].name, "slab_density") == 0)
1156            {
1157 <            if (local_args_info.scd_given)
1157 >            if (local_args_info.slab_density_given)
1158                {
1159 <                fprintf (stderr, "%s: `--scd' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1159 >                fprintf (stderr, "%s: `--slab_density' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1160                  goto failure;
1161                }
1162 <            if (args_info->scd_given && ! override)
1162 >            if (args_info->slab_density_given && ! override)
1163                continue;
1164 <            local_args_info.scd_given = 1;
1165 <            args_info->scd_given = 1;
1164 >            local_args_info.slab_density_given = 1;
1165 >            args_info->slab_density_given = 1;
1166              if (args_info->staticProps_group_counter && override)
1167                reset_group_staticProps (args_info);
1168              args_info->staticProps_group_counter += 1;
1169              break;
1170            }
1171 <          /* density plot (--sele1 must be specified).  */
1172 <          else if (strcmp (long_options[option_index].name, "density") == 0)
1171 >          /* hxy.  */
1172 >          else if (strcmp (long_options[option_index].name, "hxy") == 0)
1173            {
1174 <            if (local_args_info.density_given)
1174 >            if (local_args_info.hxy_given)
1175                {
1176 <                fprintf (stderr, "%s: `--density' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1176 >                fprintf (stderr, "%s: `--hxy' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1177                  goto failure;
1178                }
1179 <            if (args_info->density_given && ! override)
1179 >            if (args_info->hxy_given && ! override)
1180                continue;
1181 <            local_args_info.density_given = 1;
1182 <            args_info->density_given = 1;
1181 >            local_args_info.hxy_given = 1;
1182 >            args_info->hxy_given = 1;
1183              if (args_info->staticProps_group_counter && override)
1184                reset_group_staticProps (args_info);
1185              args_info->staticProps_group_counter += 1;
1186              break;
1187            }
996 –          /* slab density (--sele1 must be specified).  */
997 –          else if (strcmp (long_options[option_index].name, "slab_density") == 0)
998 –          {
999 –            if (local_args_info.slab_density_given)
1000 –              {
1001 –                fprintf (stderr, "%s: `--slab_density' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
1002 –                goto failure;
1003 –              }
1004 –            if (args_info->slab_density_given && ! override)
1005 –              continue;
1006 –            local_args_info.slab_density_given = 1;
1007 –            args_info->slab_density_given = 1;
1008 –            if (args_info->staticProps_group_counter && override)
1009 –              reset_group_staticProps (args_info);
1010 –            args_info->staticProps_group_counter += 1;
1011 –            break;
1012 –          }
1188            
1189            break;
1190          case '?':       /* Invalid option.  */

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