--- trunk/src/applications/staticProps/StaticPropsCmd.c	2006/09/20 20:13:40	1041
+++ trunk/src/applications/staticProps/StaticPropsCmd.c	2008/01/23 21:21:50	1213
@@ -1,7 +1,7 @@
 /*
-  File autogenerated by gengetopt version 2.16
+  File autogenerated by gengetopt version 2.19.1
   generated with the following command:
-  gengetopt -F StaticPropsCmd 
+  gengetopt --file-name=StaticPropsCmd -u 
 
   The developers of gengetopt consider the fixed text that goes in all
   gengetopt output files to be in the public domain:
@@ -21,6 +21,54 @@
 
 #include "StaticPropsCmd.h"
 
+const char *gengetopt_args_info_purpose = "";
+
+const char *gengetopt_args_info_usage = "Usage: StaticProps [OPTIONS]... [FILES]...";
+
+const char *gengetopt_args_info_description = "";
+
+const char *gengetopt_args_info_help[] = {
+  "  -h, --help                    Print help and exit",
+  "  -V, --version                 Print version and exit",
+  "  -i, --input=filename          input dump file",
+  "  -o, --output=filename         output file name",
+  "  -n, --step=INT                process every n frame  (default=`1')",
+  "  -b, --nbins=INT               number of bins (general purpose)  \n                                  (default=`100')",
+  "  -x, --nbins_x=INT             number of bins in x axis  (default=`100')",
+  "  -y, --nbins_y=INT             number of bins in y axis  (default=`100')",
+  "  -a, --nanglebins=INT          number of bins for cos(angle)  (default=`50')",
+  "      --length=DOUBLE           maximum length (Defaults to 1/2 smallest length \n                                  of first frame)",
+  "  -c, --rcut=DOUBLE             cutoff radius (rcut)",
+  "  -z, --zoffset=DOUBLE          Where to set the zero for the slab_density \n                                  calculation  (default=`0')",
+  "      --sele1=selection script  select the first stuntdouble set",
+  "      --sele2=selection script  select the second stuntdouble set",
+  "      --sele3=selection script  select the third stuntdouble set",
+  "      --refsele=selection script\n                                select reference (use and only use with --gxyz)",
+  "      --molname=STRING          molecule name",
+  "      --begin=INT               begin internal index",
+  "      --end=INT                 end internal index",
+  "      --radius=DOUBLE           nanoparticle radius",
+  "\n Group: staticProps\n   an option of this group is required",
+  "      --bo                      bond order parameter (--rcut must be specified)",
+  "      --bor                     bond order parameter as a function of radius \n                                  (--rcut must be specified)",
+  "      --bad                     N(theta) bond angle density within (--rcut must \n                                  be specified)",
+  "  -g, --gofr                    g(r)",
+  "      --gofz                    g(z)",
+  "      --r_theta                 g(r, cos(theta))",
+  "      --r_omega                 g(r, cos(omega))",
+  "      --theta_omega             g(cos(theta), cos(omega))",
+  "      --gxyz                    g(x, y, z)",
+  "  -p, --p2                      p2 order parameter (--sele1 and --sele2 must be \n                                  specified)",
+  "      --rp2                     rp2 order parameter (--sele1 and --sele2 must \n                                  be specified)",
+  "  -s, --scd                     scd order parameter (either --sele1, --sele2, \n                                  --sele3 are specified or --molname, --begin, \n                                  --end are specified)",
+  "  -d, --density                 density plot",
+  "      --slab_density            slab density",
+  "      --hxy                     hxy",
+  "      --rho_r                   rho of R",
+  "      --hullvol                 hull volume of nanoparticle",
+    0
+};
+
 static
 void clear_given (struct gengetopt_args_info *args_info);
 static
@@ -48,7 +96,6 @@ void clear_given (struct gengetopt_args_info *args_inf
   args_info->nbins_y_given = 0 ;
   args_info->nanglebins_given = 0 ;
   args_info->length_given = 0 ;
-  args_info->LegendreL_given = 0 ;
   args_info->rcut_given = 0 ;
   args_info->zoffset_given = 0 ;
   args_info->sele1_given = 0 ;
@@ -58,8 +105,12 @@ void clear_given (struct gengetopt_args_info *args_inf
   args_info->molname_given = 0 ;
   args_info->begin_given = 0 ;
   args_info->end_given = 0 ;
+  args_info->radius_given = 0 ;
   args_info->bo_given = 0 ;
+  args_info->bor_given = 0 ;
+  args_info->bad_given = 0 ;
   args_info->gofr_given = 0 ;
+  args_info->gofz_given = 0 ;
   args_info->r_theta_given = 0 ;
   args_info->r_omega_given = 0 ;
   args_info->theta_omega_given = 0 ;
@@ -70,6 +121,8 @@ void clear_given (struct gengetopt_args_info *args_inf
   args_info->density_given = 0 ;
   args_info->slab_density_given = 0 ;
   args_info->hxy_given = 0 ;
+  args_info->rho_r_given = 0 ;
+  args_info->hullvol_given = 0 ;
   args_info->staticProps_group_counter = 0 ;
 }
 
@@ -91,7 +144,6 @@ void clear_args (struct gengetopt_args_info *args_info
   args_info->nanglebins_arg = 50;
   args_info->nanglebins_orig = NULL;
   args_info->length_orig = NULL;
-  args_info->LegendreL_orig = NULL;
   args_info->rcut_orig = NULL;
   args_info->zoffset_arg = 0;
   args_info->zoffset_orig = NULL;
@@ -107,6 +159,50 @@ void clear_args (struct gengetopt_args_info *args_info
   args_info->molname_orig = NULL;
   args_info->begin_orig = NULL;
   args_info->end_orig = NULL;
+  args_info->radius_orig = NULL;
+  
+}
+
+static
+void init_args_info(struct gengetopt_args_info *args_info)
+{
+  args_info->help_help = gengetopt_args_info_help[0] ;
+  args_info->version_help = gengetopt_args_info_help[1] ;
+  args_info->input_help = gengetopt_args_info_help[2] ;
+  args_info->output_help = gengetopt_args_info_help[3] ;
+  args_info->step_help = gengetopt_args_info_help[4] ;
+  args_info->nbins_help = gengetopt_args_info_help[5] ;
+  args_info->nbins_x_help = gengetopt_args_info_help[6] ;
+  args_info->nbins_y_help = gengetopt_args_info_help[7] ;
+  args_info->nanglebins_help = gengetopt_args_info_help[8] ;
+  args_info->length_help = gengetopt_args_info_help[9] ;
+  args_info->rcut_help = gengetopt_args_info_help[10] ;
+  args_info->zoffset_help = gengetopt_args_info_help[11] ;
+  args_info->sele1_help = gengetopt_args_info_help[12] ;
+  args_info->sele2_help = gengetopt_args_info_help[13] ;
+  args_info->sele3_help = gengetopt_args_info_help[14] ;
+  args_info->refsele_help = gengetopt_args_info_help[15] ;
+  args_info->molname_help = gengetopt_args_info_help[16] ;
+  args_info->begin_help = gengetopt_args_info_help[17] ;
+  args_info->end_help = gengetopt_args_info_help[18] ;
+  args_info->radius_help = gengetopt_args_info_help[19] ;
+  args_info->bo_help = gengetopt_args_info_help[20] ;
+  args_info->bor_help = gengetopt_args_info_help[21] ;
+  args_info->bad_help = gengetopt_args_info_help[22] ;
+  args_info->gofr_help = gengetopt_args_info_help[23] ;
+  args_info->gofz_help = gengetopt_args_info_help[24] ;
+  args_info->r_theta_help = gengetopt_args_info_help[25] ;
+  args_info->r_omega_help = gengetopt_args_info_help[26] ;
+  args_info->theta_omega_help = gengetopt_args_info_help[27] ;
+  args_info->gxyz_help = gengetopt_args_info_help[28] ;
+  args_info->p2_help = gengetopt_args_info_help[29] ;
+  args_info->rp2_help = gengetopt_args_info_help[30] ;
+  args_info->scd_help = gengetopt_args_info_help[31] ;
+  args_info->density_help = gengetopt_args_info_help[32] ;
+  args_info->slab_density_help = gengetopt_args_info_help[33] ;
+  args_info->hxy_help = gengetopt_args_info_help[34] ;
+  args_info->rho_r_help = gengetopt_args_info_help[35] ;
+  args_info->hullvol_help = gengetopt_args_info_help[36] ;
   
 }
 
@@ -119,42 +215,19 @@ cmdline_parser_print_help (void)
 void
 cmdline_parser_print_help (void)
 {
+  int i = 0;
   cmdline_parser_print_version ();
-  printf("\nUsage: StaticProps [OPTIONS]...\n\n");
-  printf("%s\n","  -h, --help                    Print help and exit");
-  printf("%s\n","  -V, --version                 Print version and exit");
-  printf("%s\n","  -i, --input=filename          input dump file");
-  printf("%s\n","  -o, --output=filename         output file name");
-  printf("%s\n","  -n, --step=INT                process every n frame  (default=`1')");
-  printf("%s\n","  -b, --nbins=INT               number of bins (general purpose)  \n                                  (default=`100')");
-  printf("%s\n","  -x, --nbins_x=INT             number of bins in x axis  (default=`100')");
-  printf("%s\n","  -y, --nbins_y=INT             number of bins in y axis  (default=`100')");
-  printf("%s\n","  -a, --nanglebins=INT          number of bins for cos(angle)  (default=`50')");
-  printf("%s\n","      --length=DOUBLE           maximum length (Defaults to 1/2 smallest length \n                                  of first frame)");
-  printf("%s\n","  -l, --LegendreL=INT           Order of Legendre Polynomial (used for Bond \n                                  Order calculations)");
-  printf("%s\n","  -c, --rcut=DOUBLE             cutoff radius (rcut)");
-  printf("%s\n","  -z, --zoffset=DOUBLE          Where to set the zero for the slab_density \n                                  calculation  (default=`0')");
-  printf("%s\n","      --sele1=selection script  select the first stuntdouble set");
-  printf("%s\n","      --sele2=selection script  select the second stuntdouble set");
-  printf("%s\n","      --sele3=selection script  select the third stuntdouble set");
-  printf("%s\n","      --refsele=selection script\n                                select reference (use and only use with --gxyz)");
-  printf("%s\n","      --molname=STRING          molecule name");
-  printf("%s\n","      --begin=INT               begin internal index");
-  printf("%s\n","      --end=INT                 end internal index");
-  printf("%s\n","\n Group: staticProps\n   an option of this group is required");
-  printf("%s\n","      --bo                      bond order parameter (--rcut and --LegendreL \n                                  must be specified");
-  printf("%s\n","  -g, --gofr                    g(r)");
-  printf("%s\n","      --r_theta                 g(r, cos(theta))");
-  printf("%s\n","      --r_omega                 g(r, cos(omega))");
-  printf("%s\n","      --theta_omega             g(cos(theta), cos(omega))");
-  printf("%s\n","      --gxyz                    g(x, y, z)");
-  printf("%s\n","  -p, --p2                      p2 order parameter (--sele1 and --sele2 must be \n                                  specified)");
-  printf("%s\n","      --rp2                     rp2 order parameter (--sele1 and --sele2 must \n                                  be specified)");
-  printf("%s\n","  -s, --scd                     scd order parameter (either --sele1, --sele2, \n                                  --sele3 are specified or --molname, --begin, \n                                  --end are specified)");
-  printf("%s\n","  -d, --density                 density plot");
-  printf("%s\n","      --slab_density            slab density");
-  printf("%s\n","      --hxy                     hxy");
-  
+
+  if (strlen(gengetopt_args_info_purpose) > 0)
+    printf("\n%s\n", gengetopt_args_info_purpose);
+
+  printf("\n%s\n\n", gengetopt_args_info_usage);
+
+  if (strlen(gengetopt_args_info_description) > 0)
+    printf("%s\n", gengetopt_args_info_description);
+
+  while (gengetopt_args_info_help[i])
+    printf("%s\n", gengetopt_args_info_help[i++]);
 }
 
 void
@@ -162,12 +235,17 @@ cmdline_parser_init (struct gengetopt_args_info *args_
 {
   clear_given (args_info);
   clear_args (args_info);
+  init_args_info (args_info);
+
+  args_info->inputs = NULL;
+  args_info->inputs_num = 0;
 }
 
 static void
 cmdline_parser_release (struct gengetopt_args_info *args_info)
 {
   
+  unsigned int i;
   if (args_info->input_arg)
     {
       free (args_info->input_arg); /* free previous argument */
@@ -218,11 +296,6 @@ cmdline_parser_release (struct gengetopt_args_info *ar
       free (args_info->length_orig); /* free previous argument */
       args_info->length_orig = 0;
     }
-  if (args_info->LegendreL_orig)
-    {
-      free (args_info->LegendreL_orig); /* free previous argument */
-      args_info->LegendreL_orig = 0;
-    }
   if (args_info->rcut_orig)
     {
       free (args_info->rcut_orig); /* free previous argument */
@@ -293,7 +366,18 @@ cmdline_parser_release (struct gengetopt_args_info *ar
       free (args_info->end_orig); /* free previous argument */
       args_info->end_orig = 0;
     }
+  if (args_info->radius_orig)
+    {
+      free (args_info->radius_orig); /* free previous argument */
+      args_info->radius_orig = 0;
+    }
   
+  for (i = 0; i < args_info->inputs_num; ++i)
+    free (args_info->inputs [i]);
+  
+  if (args_info->inputs_num)
+    free (args_info->inputs);
+  
   clear_given (args_info);
 }
 
@@ -373,13 +457,6 @@ cmdline_parser_file_save(const char *filename, struct 
       fprintf(outfile, "%s\n", "length");
     }
   }
-  if (args_info->LegendreL_given) {
-    if (args_info->LegendreL_orig) {
-      fprintf(outfile, "%s=\"%s\"\n", "LegendreL", args_info->LegendreL_orig);
-    } else {
-      fprintf(outfile, "%s\n", "LegendreL");
-    }
-  }
   if (args_info->rcut_given) {
     if (args_info->rcut_orig) {
       fprintf(outfile, "%s=\"%s\"\n", "rcut", args_info->rcut_orig);
@@ -443,12 +520,28 @@ cmdline_parser_file_save(const char *filename, struct 
       fprintf(outfile, "%s\n", "end");
     }
   }
+  if (args_info->radius_given) {
+    if (args_info->radius_orig) {
+      fprintf(outfile, "%s=\"%s\"\n", "radius", args_info->radius_orig);
+    } else {
+      fprintf(outfile, "%s\n", "radius");
+    }
+  }
   if (args_info->bo_given) {
     fprintf(outfile, "%s\n", "bo");
   }
+  if (args_info->bor_given) {
+    fprintf(outfile, "%s\n", "bor");
+  }
+  if (args_info->bad_given) {
+    fprintf(outfile, "%s\n", "bad");
+  }
   if (args_info->gofr_given) {
     fprintf(outfile, "%s\n", "gofr");
   }
+  if (args_info->gofz_given) {
+    fprintf(outfile, "%s\n", "gofz");
+  }
   if (args_info->r_theta_given) {
     fprintf(outfile, "%s\n", "r_theta");
   }
@@ -479,6 +572,12 @@ cmdline_parser_file_save(const char *filename, struct 
   if (args_info->hxy_given) {
     fprintf(outfile, "%s\n", "hxy");
   }
+  if (args_info->rho_r_given) {
+    fprintf(outfile, "%s\n", "rho_r");
+  }
+  if (args_info->hullvol_given) {
+    fprintf(outfile, "%s\n", "hullvol");
+  }
   
   fclose (outfile);
 
@@ -519,7 +618,10 @@ reset_group_staticProps(struct gengetopt_args_info *ar
     return;
   
   args_info->bo_given = 0 ;
+  args_info->bor_given = 0 ;
+  args_info->bad_given = 0 ;
   args_info->gofr_given = 0 ;
+  args_info->gofz_given = 0 ;
   args_info->r_theta_given = 0 ;
   args_info->r_omega_given = 0 ;
   args_info->theta_omega_given = 0 ;
@@ -530,6 +632,8 @@ reset_group_staticProps(struct gengetopt_args_info *ar
   args_info->density_given = 0 ;
   args_info->slab_density_given = 0 ;
   args_info->hxy_given = 0 ;
+  args_info->rho_r_given = 0 ;
+  args_info->hullvol_given = 0 ;
 
   args_info->staticProps_group_counter = 0;
 }
@@ -578,17 +682,21 @@ cmdline_parser_required2 (struct gengetopt_args_info *
 {
   int error = 0;
 
+  /* checks for required options */
   if (! args_info->input_given)
     {
       fprintf (stderr, "%s: '--input' ('-i') option required%s\n", prog_name, (additional_error ? additional_error : ""));
       error = 1;
     }
+  
   if (args_info->staticProps_group_counter == 0)
     {
       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 : ""));
       error = 1;
     }
   
+
+  /* checks for dependences among options */
 
   return error;
 }
@@ -627,7 +735,6 @@ cmdline_parser_internal (int argc, char * const *argv,
         { "nbins_y",	1, NULL, 'y' },
         { "nanglebins",	1, NULL, 'a' },
         { "length",	1, NULL, 0 },
-        { "LegendreL",	1, NULL, 'l' },
         { "rcut",	1, NULL, 'c' },
         { "zoffset",	1, NULL, 'z' },
         { "sele1",	1, NULL, 0 },
@@ -637,8 +744,12 @@ cmdline_parser_internal (int argc, char * const *argv,
         { "molname",	1, NULL, 0 },
         { "begin",	1, NULL, 0 },
         { "end",	1, NULL, 0 },
+        { "radius",	1, NULL, 0 },
         { "bo",	0, NULL, 0 },
+        { "bor",	0, NULL, 0 },
+        { "bad",	0, NULL, 0 },
         { "gofr",	0, NULL, 'g' },
+        { "gofz",	0, NULL, 0 },
         { "r_theta",	0, NULL, 0 },
         { "r_omega",	0, NULL, 0 },
         { "theta_omega",	0, NULL, 0 },
@@ -649,11 +760,13 @@ cmdline_parser_internal (int argc, char * const *argv,
         { "density",	0, NULL, 'd' },
         { "slab_density",	0, NULL, 0 },
         { "hxy",	0, NULL, 0 },
+        { "rho_r",	0, NULL, 0 },
+        { "hullvol",	0, NULL, 0 },
         { NULL,	0, NULL, 0 }
       };
 
       stop_char = 0;
-      c = getopt_long (argc, argv, "hVi:o:n:b:x:y:a:l:c:z:gpsd", long_options, &option_index);
+      c = getopt_long (argc, argv, "hVi:o:n:b:x:y:a:c:z:gpsd", long_options, &option_index);
 
       if (c == -1) break;	/* Exit from `while (1)' loop.  */
 
@@ -803,26 +916,6 @@ cmdline_parser_internal (int argc, char * const *argv,
           if (args_info->nanglebins_orig)
             free (args_info->nanglebins_orig); /* free previous string */
           args_info->nanglebins_orig = gengetopt_strdup (optarg);
-          break;
-
-        case 'l':	/* Order of Legendre Polynomial (used for Bond Order calculations).  */
-          if (local_args_info.LegendreL_given)
-            {
-              fprintf (stderr, "%s: `--LegendreL' (`-l') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
-              goto failure;
-            }
-          if (args_info->LegendreL_given && ! override)
-            continue;
-          local_args_info.LegendreL_given = 1;
-          args_info->LegendreL_given = 1;
-          args_info->LegendreL_arg = strtol (optarg, &stop_char, 0);
-          if (!(stop_char && *stop_char == '\0')) {
-            fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
-            goto failure;
-          }
-          if (args_info->LegendreL_orig)
-            free (args_info->LegendreL_orig); /* free previous string */
-          args_info->LegendreL_orig = gengetopt_strdup (optarg);
           break;
 
         case 'c':	/* cutoff radius (rcut).  */
@@ -1085,7 +1178,28 @@ cmdline_parser_internal (int argc, char * const *argv,
               free (args_info->end_orig); /* free previous string */
             args_info->end_orig = gengetopt_strdup (optarg);
           }
-          /* bond order parameter (--rcut and --LegendreL must be specified.  */
+          /* nanoparticle radius.  */
+          else if (strcmp (long_options[option_index].name, "radius") == 0)
+          {
+            if (local_args_info.radius_given)
+              {
+                fprintf (stderr, "%s: `--radius' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
+                goto failure;
+              }
+            if (args_info->radius_given && ! override)
+              continue;
+            local_args_info.radius_given = 1;
+            args_info->radius_given = 1;
+            args_info->radius_arg = strtod (optarg, &stop_char);
+            if (!(stop_char && *stop_char == '\0')) {
+              fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
+              goto failure;
+            }
+            if (args_info->radius_orig)
+              free (args_info->radius_orig); /* free previous string */
+            args_info->radius_orig = gengetopt_strdup (optarg);
+          }
+          /* bond order parameter (--rcut must be specified).  */
           else if (strcmp (long_options[option_index].name, "bo") == 0)
           {
             if (local_args_info.bo_given)
@@ -1102,6 +1216,57 @@ cmdline_parser_internal (int argc, char * const *argv,
             args_info->staticProps_group_counter += 1;
             break;
           }
+          /* bond order parameter as a function of radius (--rcut must be specified).  */
+          else if (strcmp (long_options[option_index].name, "bor") == 0)
+          {
+            if (local_args_info.bor_given)
+              {
+                fprintf (stderr, "%s: `--bor' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
+                goto failure;
+              }
+            if (args_info->bor_given && ! override)
+              continue;
+            local_args_info.bor_given = 1;
+            args_info->bor_given = 1;
+            if (args_info->staticProps_group_counter && override)
+              reset_group_staticProps (args_info);
+            args_info->staticProps_group_counter += 1;
+            break;
+          }
+          /* N(theta) bond angle density within (--rcut must be specified).  */
+          else if (strcmp (long_options[option_index].name, "bad") == 0)
+          {
+            if (local_args_info.bad_given)
+              {
+                fprintf (stderr, "%s: `--bad' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
+                goto failure;
+              }
+            if (args_info->bad_given && ! override)
+              continue;
+            local_args_info.bad_given = 1;
+            args_info->bad_given = 1;
+            if (args_info->staticProps_group_counter && override)
+              reset_group_staticProps (args_info);
+            args_info->staticProps_group_counter += 1;
+            break;
+          }
+          /* g(z).  */
+          else if (strcmp (long_options[option_index].name, "gofz") == 0)
+          {
+            if (local_args_info.gofz_given)
+              {
+                fprintf (stderr, "%s: `--gofz' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
+                goto failure;
+              }
+            if (args_info->gofz_given && ! override)
+              continue;
+            local_args_info.gofz_given = 1;
+            args_info->gofz_given = 1;
+            if (args_info->staticProps_group_counter && override)
+              reset_group_staticProps (args_info);
+            args_info->staticProps_group_counter += 1;
+            break;
+          }
           /* g(r, cos(theta)).  */
           else if (strcmp (long_options[option_index].name, "r_theta") == 0)
           {
@@ -1221,6 +1386,40 @@ cmdline_parser_internal (int argc, char * const *argv,
             args_info->staticProps_group_counter += 1;
             break;
           }
+          /* rho of R.  */
+          else if (strcmp (long_options[option_index].name, "rho_r") == 0)
+          {
+            if (local_args_info.rho_r_given)
+              {
+                fprintf (stderr, "%s: `--rho_r' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
+                goto failure;
+              }
+            if (args_info->rho_r_given && ! override)
+              continue;
+            local_args_info.rho_r_given = 1;
+            args_info->rho_r_given = 1;
+            if (args_info->staticProps_group_counter && override)
+              reset_group_staticProps (args_info);
+            args_info->staticProps_group_counter += 1;
+            break;
+          }
+          /* hull volume of nanoparticle.  */
+          else if (strcmp (long_options[option_index].name, "hullvol") == 0)
+          {
+            if (local_args_info.hullvol_given)
+              {
+                fprintf (stderr, "%s: `--hullvol' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
+                goto failure;
+              }
+            if (args_info->hullvol_given && ! override)
+              continue;
+            local_args_info.hullvol_given = 1;
+            args_info->hullvol_given = 1;
+            if (args_info->staticProps_group_counter && override)
+              reset_group_staticProps (args_info);
+            args_info->staticProps_group_counter += 1;
+            break;
+          }
           
           break;
         case '?':	/* Invalid option.  */
@@ -1251,6 +1450,30 @@ cmdline_parser_internal (int argc, char * const *argv,
   if ( error )
     return (EXIT_FAILURE);
 
+  if (optind < argc)
+    {
+      int i = 0 ;
+      int found_prog_name = 0;
+      /* whether program name, i.e., argv[0], is in the remaining args
+         (this may happen with some implementations of getopt,
+          but surely not with the one included by gengetopt) */
+
+      i = optind;
+      while (i < argc)
+        if (argv[i++] == argv[0]) {
+          found_prog_name = 1;
+          break;
+        }
+      i = 0;
+
+      args_info->inputs_num = argc - optind - found_prog_name;
+      args_info->inputs =
+        (char **)(malloc ((args_info->inputs_num)*sizeof(char *))) ;
+      while (optind < argc)
+        if (argv[optind++] != argv[0])
+          args_info->inputs[ i++ ] = gengetopt_strdup (argv[optind-1]) ;
+    }
+
   return 0;
 
 failure: