--- trunk/src/applications/staticProps/StaticPropsCmd.c	2006/09/26 01:30:32	1052
+++ trunk/src/applications/staticProps/StaticPropsCmd.c	2010/05/10 17:28:26	1442
@@ -1,7 +1,7 @@
 /*
-  File autogenerated by gengetopt version 2.16
+  File autogenerated by gengetopt version 2.22
   generated with the following command:
-  gengetopt -F StaticPropsCmd 
+  gengetopt -F StaticPropsCmd -u 
 
   The developers of gengetopt consider the fixed text that goes in all
   gengetopt output files to be in the public domain:
@@ -21,13 +21,72 @@
 
 #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')",
+  "      --nbins_z=INT             number of bins in z 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)",
+  "      --comsele=selection script\n                                select stunt doubles for center-of-mass \n                                  reference point",
+  "      --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))",
+  "      --r_z                     g(r, z)",
+  "      --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",
+  "      --p_angle                 p(cos(theta))",
+  "      --hxy                     hxy",
+  "      --rho_r                   rho of R",
+  "      --hullvol                 hull volume of nanoparticle",
+    0
+};
+
+typedef enum {ARG_NO
+  , ARG_STRING
+  , ARG_INT
+  , ARG_DOUBLE
+} cmdline_parser_arg_type;
+
 static
 void clear_given (struct gengetopt_args_info *args_info);
 static
 void clear_args (struct gengetopt_args_info *args_info);
 
 static int
-cmdline_parser_internal (int argc, char * const *argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required, const char *additional_error);
+cmdline_parser_internal (int argc, char * const *argv, struct gengetopt_args_info *args_info,
+                        struct cmdline_parser_params *params, const char *additional_error);
 
 static int
 cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error);
@@ -46,6 +105,7 @@ void clear_given (struct gengetopt_args_info *args_inf
   args_info->nbins_given = 0 ;
   args_info->nbins_x_given = 0 ;
   args_info->nbins_y_given = 0 ;
+  args_info->nbins_z_given = 0 ;
   args_info->nanglebins_given = 0 ;
   args_info->length_given = 0 ;
   args_info->rcut_given = 0 ;
@@ -54,13 +114,19 @@ void clear_given (struct gengetopt_args_info *args_inf
   args_info->sele2_given = 0 ;
   args_info->sele3_given = 0 ;
   args_info->refsele_given = 0 ;
+  args_info->comsele_given = 0 ;
   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->r_z_given = 0 ;
   args_info->theta_omega_given = 0 ;
   args_info->gxyz_given = 0 ;
   args_info->p2_given = 0 ;
@@ -68,7 +134,10 @@ void clear_given (struct gengetopt_args_info *args_inf
   args_info->scd_given = 0 ;
   args_info->density_given = 0 ;
   args_info->slab_density_given = 0 ;
+  args_info->p_angle_given = 0 ;
   args_info->hxy_given = 0 ;
+  args_info->rho_r_given = 0 ;
+  args_info->hullvol_given = 0 ;
   args_info->staticProps_group_counter = 0 ;
 }
 
@@ -87,6 +156,8 @@ void clear_args (struct gengetopt_args_info *args_info
   args_info->nbins_x_orig = NULL;
   args_info->nbins_y_arg = 100;
   args_info->nbins_y_orig = NULL;
+  args_info->nbins_z_arg = 100;
+  args_info->nbins_z_orig = NULL;
   args_info->nanglebins_arg = 50;
   args_info->nanglebins_orig = NULL;
   args_info->length_orig = NULL;
@@ -101,57 +172,93 @@ void clear_args (struct gengetopt_args_info *args_info
   args_info->sele3_orig = NULL;
   args_info->refsele_arg = NULL;
   args_info->refsele_orig = NULL;
+  args_info->comsele_arg = NULL;
+  args_info->comsele_orig = NULL;
   args_info->molname_arg = NULL;
   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->nbins_z_help = gengetopt_args_info_help[8] ;
+  args_info->nanglebins_help = gengetopt_args_info_help[9] ;
+  args_info->length_help = gengetopt_args_info_help[10] ;
+  args_info->rcut_help = gengetopt_args_info_help[11] ;
+  args_info->zoffset_help = gengetopt_args_info_help[12] ;
+  args_info->sele1_help = gengetopt_args_info_help[13] ;
+  args_info->sele2_help = gengetopt_args_info_help[14] ;
+  args_info->sele3_help = gengetopt_args_info_help[15] ;
+  args_info->refsele_help = gengetopt_args_info_help[16] ;
+  args_info->comsele_help = gengetopt_args_info_help[17] ;
+  args_info->molname_help = gengetopt_args_info_help[18] ;
+  args_info->begin_help = gengetopt_args_info_help[19] ;
+  args_info->end_help = gengetopt_args_info_help[20] ;
+  args_info->radius_help = gengetopt_args_info_help[21] ;
+  args_info->bo_help = gengetopt_args_info_help[23] ;
+  args_info->bor_help = gengetopt_args_info_help[24] ;
+  args_info->bad_help = gengetopt_args_info_help[25] ;
+  args_info->gofr_help = gengetopt_args_info_help[26] ;
+  args_info->gofz_help = gengetopt_args_info_help[27] ;
+  args_info->r_theta_help = gengetopt_args_info_help[28] ;
+  args_info->r_omega_help = gengetopt_args_info_help[29] ;
+  args_info->r_z_help = gengetopt_args_info_help[30] ;
+  args_info->theta_omega_help = gengetopt_args_info_help[31] ;
+  args_info->gxyz_help = gengetopt_args_info_help[32] ;
+  args_info->p2_help = gengetopt_args_info_help[33] ;
+  args_info->rp2_help = gengetopt_args_info_help[34] ;
+  args_info->scd_help = gengetopt_args_info_help[35] ;
+  args_info->density_help = gengetopt_args_info_help[36] ;
+  args_info->slab_density_help = gengetopt_args_info_help[37] ;
+  args_info->p_angle_help = gengetopt_args_info_help[38] ;
+  args_info->hxy_help = gengetopt_args_info_help[39] ;
+  args_info->rho_r_help = gengetopt_args_info_help[40] ;
+  args_info->hullvol_help = gengetopt_args_info_help[41] ;
+  
+}
+
 void
 cmdline_parser_print_version (void)
 {
   printf ("%s %s\n", CMDLINE_PARSER_PACKAGE, CMDLINE_PARSER_VERSION);
 }
 
+static void print_help_common(void) {
+  cmdline_parser_print_version ();
+
+  if (strlen(gengetopt_args_info_purpose) > 0)
+    printf("\n%s\n", gengetopt_args_info_purpose);
+
+  if (strlen(gengetopt_args_info_usage) > 0)
+    printf("\n%s\n", gengetopt_args_info_usage);
+
+  printf("\n");
+
+  if (strlen(gengetopt_args_info_description) > 0)
+    printf("%s\n", gengetopt_args_info_description);
+}
+
 void
 cmdline_parser_print_help (void)
 {
-  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","  -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 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");
-  
+  int i = 0;
+  print_help_common();
+  while (gengetopt_args_info_help[i])
+    printf("%s\n", gengetopt_args_info_help[i++]);
 }
 
 void
@@ -159,134 +266,197 @@ 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;
 }
 
+void
+cmdline_parser_params_init(struct cmdline_parser_params *params)
+{
+  if (params)
+    { 
+      params->override = 0;
+      params->initialize = 1;
+      params->check_required = 1;
+      params->check_ambiguity = 0;
+      params->print_errors = 1;
+    }
+}
+
+struct cmdline_parser_params *
+cmdline_parser_params_create(void)
+{
+  struct cmdline_parser_params *params = 
+    (struct cmdline_parser_params *)malloc(sizeof(struct cmdline_parser_params));
+  cmdline_parser_params_init(params);  
+  return params;
+}
+
 static void
-cmdline_parser_release (struct gengetopt_args_info *args_info)
+free_string_field (char **s)
 {
-  
-  if (args_info->input_arg)
+  if (*s)
     {
-      free (args_info->input_arg); /* free previous argument */
-      args_info->input_arg = 0;
+      free (*s);
+      *s = 0;
     }
-  if (args_info->input_orig)
-    {
-      free (args_info->input_orig); /* free previous argument */
-      args_info->input_orig = 0;
-    }
-  if (args_info->output_arg)
+}
+
+
+static void
+cmdline_parser_release (struct gengetopt_args_info *args_info)
+{
+  unsigned int i;
+  free_string_field (&(args_info->input_arg));
+  free_string_field (&(args_info->input_orig));
+  free_string_field (&(args_info->output_arg));
+  free_string_field (&(args_info->output_orig));
+  free_string_field (&(args_info->step_orig));
+  free_string_field (&(args_info->nbins_orig));
+  free_string_field (&(args_info->nbins_x_orig));
+  free_string_field (&(args_info->nbins_y_orig));
+  free_string_field (&(args_info->nbins_z_orig));
+  free_string_field (&(args_info->nanglebins_orig));
+  free_string_field (&(args_info->length_orig));
+  free_string_field (&(args_info->rcut_orig));
+  free_string_field (&(args_info->zoffset_orig));
+  free_string_field (&(args_info->sele1_arg));
+  free_string_field (&(args_info->sele1_orig));
+  free_string_field (&(args_info->sele2_arg));
+  free_string_field (&(args_info->sele2_orig));
+  free_string_field (&(args_info->sele3_arg));
+  free_string_field (&(args_info->sele3_orig));
+  free_string_field (&(args_info->refsele_arg));
+  free_string_field (&(args_info->refsele_orig));
+  free_string_field (&(args_info->comsele_arg));
+  free_string_field (&(args_info->comsele_orig));
+  free_string_field (&(args_info->molname_arg));
+  free_string_field (&(args_info->molname_orig));
+  free_string_field (&(args_info->begin_orig));
+  free_string_field (&(args_info->end_orig));
+  free_string_field (&(args_info->radius_orig));
+  
+  
+  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);
+}
+
+
+static void
+write_into_file(FILE *outfile, const char *opt, const char *arg, char *values[])
+{
+  if (arg) {
+    fprintf(outfile, "%s=\"%s\"\n", opt, arg);
+  } else {
+    fprintf(outfile, "%s\n", opt);
+  }
+}
+
+
+int
+cmdline_parser_dump(FILE *outfile, struct gengetopt_args_info *args_info)
+{
+  int i = 0;
+
+  if (!outfile)
     {
-      free (args_info->output_arg); /* free previous argument */
-      args_info->output_arg = 0;
+      fprintf (stderr, "%s: cannot dump options to stream\n", CMDLINE_PARSER_PACKAGE);
+      return EXIT_FAILURE;
     }
-  if (args_info->output_orig)
-    {
-      free (args_info->output_orig); /* free previous argument */
-      args_info->output_orig = 0;
-    }
-  if (args_info->step_orig)
-    {
-      free (args_info->step_orig); /* free previous argument */
-      args_info->step_orig = 0;
-    }
-  if (args_info->nbins_orig)
-    {
-      free (args_info->nbins_orig); /* free previous argument */
-      args_info->nbins_orig = 0;
-    }
-  if (args_info->nbins_x_orig)
-    {
-      free (args_info->nbins_x_orig); /* free previous argument */
-      args_info->nbins_x_orig = 0;
-    }
-  if (args_info->nbins_y_orig)
-    {
-      free (args_info->nbins_y_orig); /* free previous argument */
-      args_info->nbins_y_orig = 0;
-    }
-  if (args_info->nanglebins_orig)
-    {
-      free (args_info->nanglebins_orig); /* free previous argument */
-      args_info->nanglebins_orig = 0;
-    }
-  if (args_info->length_orig)
-    {
-      free (args_info->length_orig); /* free previous argument */
-      args_info->length_orig = 0;
-    }
-  if (args_info->rcut_orig)
-    {
-      free (args_info->rcut_orig); /* free previous argument */
-      args_info->rcut_orig = 0;
-    }
-  if (args_info->zoffset_orig)
-    {
-      free (args_info->zoffset_orig); /* free previous argument */
-      args_info->zoffset_orig = 0;
-    }
-  if (args_info->sele1_arg)
-    {
-      free (args_info->sele1_arg); /* free previous argument */
-      args_info->sele1_arg = 0;
-    }
-  if (args_info->sele1_orig)
-    {
-      free (args_info->sele1_orig); /* free previous argument */
-      args_info->sele1_orig = 0;
-    }
-  if (args_info->sele2_arg)
-    {
-      free (args_info->sele2_arg); /* free previous argument */
-      args_info->sele2_arg = 0;
-    }
-  if (args_info->sele2_orig)
-    {
-      free (args_info->sele2_orig); /* free previous argument */
-      args_info->sele2_orig = 0;
-    }
-  if (args_info->sele3_arg)
-    {
-      free (args_info->sele3_arg); /* free previous argument */
-      args_info->sele3_arg = 0;
-    }
-  if (args_info->sele3_orig)
-    {
-      free (args_info->sele3_orig); /* free previous argument */
-      args_info->sele3_orig = 0;
-    }
-  if (args_info->refsele_arg)
-    {
-      free (args_info->refsele_arg); /* free previous argument */
-      args_info->refsele_arg = 0;
-    }
-  if (args_info->refsele_orig)
-    {
-      free (args_info->refsele_orig); /* free previous argument */
-      args_info->refsele_orig = 0;
-    }
-  if (args_info->molname_arg)
-    {
-      free (args_info->molname_arg); /* free previous argument */
-      args_info->molname_arg = 0;
-    }
-  if (args_info->molname_orig)
-    {
-      free (args_info->molname_orig); /* free previous argument */
-      args_info->molname_orig = 0;
-    }
-  if (args_info->begin_orig)
-    {
-      free (args_info->begin_orig); /* free previous argument */
-      args_info->begin_orig = 0;
-    }
-  if (args_info->end_orig)
-    {
-      free (args_info->end_orig); /* free previous argument */
-      args_info->end_orig = 0;
-    }
+
+  if (args_info->help_given)
+    write_into_file(outfile, "help", 0, 0 );
+  if (args_info->version_given)
+    write_into_file(outfile, "version", 0, 0 );
+  if (args_info->input_given)
+    write_into_file(outfile, "input", args_info->input_orig, 0);
+  if (args_info->output_given)
+    write_into_file(outfile, "output", args_info->output_orig, 0);
+  if (args_info->step_given)
+    write_into_file(outfile, "step", args_info->step_orig, 0);
+  if (args_info->nbins_given)
+    write_into_file(outfile, "nbins", args_info->nbins_orig, 0);
+  if (args_info->nbins_x_given)
+    write_into_file(outfile, "nbins_x", args_info->nbins_x_orig, 0);
+  if (args_info->nbins_y_given)
+    write_into_file(outfile, "nbins_y", args_info->nbins_y_orig, 0);
+  if (args_info->nbins_z_given)
+    write_into_file(outfile, "nbins_z", args_info->nbins_z_orig, 0);
+  if (args_info->nanglebins_given)
+    write_into_file(outfile, "nanglebins", args_info->nanglebins_orig, 0);
+  if (args_info->length_given)
+    write_into_file(outfile, "length", args_info->length_orig, 0);
+  if (args_info->rcut_given)
+    write_into_file(outfile, "rcut", args_info->rcut_orig, 0);
+  if (args_info->zoffset_given)
+    write_into_file(outfile, "zoffset", args_info->zoffset_orig, 0);
+  if (args_info->sele1_given)
+    write_into_file(outfile, "sele1", args_info->sele1_orig, 0);
+  if (args_info->sele2_given)
+    write_into_file(outfile, "sele2", args_info->sele2_orig, 0);
+  if (args_info->sele3_given)
+    write_into_file(outfile, "sele3", args_info->sele3_orig, 0);
+  if (args_info->refsele_given)
+    write_into_file(outfile, "refsele", args_info->refsele_orig, 0);
+  if (args_info->comsele_given)
+    write_into_file(outfile, "comsele", args_info->comsele_orig, 0);
+  if (args_info->molname_given)
+    write_into_file(outfile, "molname", args_info->molname_orig, 0);
+  if (args_info->begin_given)
+    write_into_file(outfile, "begin", args_info->begin_orig, 0);
+  if (args_info->end_given)
+    write_into_file(outfile, "end", args_info->end_orig, 0);
+  if (args_info->radius_given)
+    write_into_file(outfile, "radius", args_info->radius_orig, 0);
+  if (args_info->bo_given)
+    write_into_file(outfile, "bo", 0, 0 );
+  if (args_info->bor_given)
+    write_into_file(outfile, "bor", 0, 0 );
+  if (args_info->bad_given)
+    write_into_file(outfile, "bad", 0, 0 );
+  if (args_info->gofr_given)
+    write_into_file(outfile, "gofr", 0, 0 );
+  if (args_info->gofz_given)
+    write_into_file(outfile, "gofz", 0, 0 );
+  if (args_info->r_theta_given)
+    write_into_file(outfile, "r_theta", 0, 0 );
+  if (args_info->r_omega_given)
+    write_into_file(outfile, "r_omega", 0, 0 );
+  if (args_info->r_z_given)
+    write_into_file(outfile, "r_z", 0, 0 );
+  if (args_info->theta_omega_given)
+    write_into_file(outfile, "theta_omega", 0, 0 );
+  if (args_info->gxyz_given)
+    write_into_file(outfile, "gxyz", 0, 0 );
+  if (args_info->p2_given)
+    write_into_file(outfile, "p2", 0, 0 );
+  if (args_info->rp2_given)
+    write_into_file(outfile, "rp2", 0, 0 );
+  if (args_info->scd_given)
+    write_into_file(outfile, "scd", 0, 0 );
+  if (args_info->density_given)
+    write_into_file(outfile, "density", 0, 0 );
+  if (args_info->slab_density_given)
+    write_into_file(outfile, "slab_density", 0, 0 );
+  if (args_info->p_angle_given)
+    write_into_file(outfile, "p_angle", 0, 0 );
+  if (args_info->hxy_given)
+    write_into_file(outfile, "hxy", 0, 0 );
+  if (args_info->rho_r_given)
+    write_into_file(outfile, "rho_r", 0, 0 );
+  if (args_info->hullvol_given)
+    write_into_file(outfile, "hullvol", 0, 0 );
   
-  clear_given (args_info);
+
+  i = EXIT_SUCCESS;
+  return i;
 }
 
 int
@@ -303,171 +473,9 @@ cmdline_parser_file_save(const char *filename, struct 
       return EXIT_FAILURE;
     }
 
-  if (args_info->help_given) {
-    fprintf(outfile, "%s\n", "help");
-  }
-  if (args_info->version_given) {
-    fprintf(outfile, "%s\n", "version");
-  }
-  if (args_info->input_given) {
-    if (args_info->input_orig) {
-      fprintf(outfile, "%s=\"%s\"\n", "input", args_info->input_orig);
-    } else {
-      fprintf(outfile, "%s\n", "input");
-    }
-  }
-  if (args_info->output_given) {
-    if (args_info->output_orig) {
-      fprintf(outfile, "%s=\"%s\"\n", "output", args_info->output_orig);
-    } else {
-      fprintf(outfile, "%s\n", "output");
-    }
-  }
-  if (args_info->step_given) {
-    if (args_info->step_orig) {
-      fprintf(outfile, "%s=\"%s\"\n", "step", args_info->step_orig);
-    } else {
-      fprintf(outfile, "%s\n", "step");
-    }
-  }
-  if (args_info->nbins_given) {
-    if (args_info->nbins_orig) {
-      fprintf(outfile, "%s=\"%s\"\n", "nbins", args_info->nbins_orig);
-    } else {
-      fprintf(outfile, "%s\n", "nbins");
-    }
-  }
-  if (args_info->nbins_x_given) {
-    if (args_info->nbins_x_orig) {
-      fprintf(outfile, "%s=\"%s\"\n", "nbins_x", args_info->nbins_x_orig);
-    } else {
-      fprintf(outfile, "%s\n", "nbins_x");
-    }
-  }
-  if (args_info->nbins_y_given) {
-    if (args_info->nbins_y_orig) {
-      fprintf(outfile, "%s=\"%s\"\n", "nbins_y", args_info->nbins_y_orig);
-    } else {
-      fprintf(outfile, "%s\n", "nbins_y");
-    }
-  }
-  if (args_info->nanglebins_given) {
-    if (args_info->nanglebins_orig) {
-      fprintf(outfile, "%s=\"%s\"\n", "nanglebins", args_info->nanglebins_orig);
-    } else {
-      fprintf(outfile, "%s\n", "nanglebins");
-    }
-  }
-  if (args_info->length_given) {
-    if (args_info->length_orig) {
-      fprintf(outfile, "%s=\"%s\"\n", "length", args_info->length_orig);
-    } else {
-      fprintf(outfile, "%s\n", "length");
-    }
-  }
-  if (args_info->rcut_given) {
-    if (args_info->rcut_orig) {
-      fprintf(outfile, "%s=\"%s\"\n", "rcut", args_info->rcut_orig);
-    } else {
-      fprintf(outfile, "%s\n", "rcut");
-    }
-  }
-  if (args_info->zoffset_given) {
-    if (args_info->zoffset_orig) {
-      fprintf(outfile, "%s=\"%s\"\n", "zoffset", args_info->zoffset_orig);
-    } else {
-      fprintf(outfile, "%s\n", "zoffset");
-    }
-  }
-  if (args_info->sele1_given) {
-    if (args_info->sele1_orig) {
-      fprintf(outfile, "%s=\"%s\"\n", "sele1", args_info->sele1_orig);
-    } else {
-      fprintf(outfile, "%s\n", "sele1");
-    }
-  }
-  if (args_info->sele2_given) {
-    if (args_info->sele2_orig) {
-      fprintf(outfile, "%s=\"%s\"\n", "sele2", args_info->sele2_orig);
-    } else {
-      fprintf(outfile, "%s\n", "sele2");
-    }
-  }
-  if (args_info->sele3_given) {
-    if (args_info->sele3_orig) {
-      fprintf(outfile, "%s=\"%s\"\n", "sele3", args_info->sele3_orig);
-    } else {
-      fprintf(outfile, "%s\n", "sele3");
-    }
-  }
-  if (args_info->refsele_given) {
-    if (args_info->refsele_orig) {
-      fprintf(outfile, "%s=\"%s\"\n", "refsele", args_info->refsele_orig);
-    } else {
-      fprintf(outfile, "%s\n", "refsele");
-    }
-  }
-  if (args_info->molname_given) {
-    if (args_info->molname_orig) {
-      fprintf(outfile, "%s=\"%s\"\n", "molname", args_info->molname_orig);
-    } else {
-      fprintf(outfile, "%s\n", "molname");
-    }
-  }
-  if (args_info->begin_given) {
-    if (args_info->begin_orig) {
-      fprintf(outfile, "%s=\"%s\"\n", "begin", args_info->begin_orig);
-    } else {
-      fprintf(outfile, "%s\n", "begin");
-    }
-  }
-  if (args_info->end_given) {
-    if (args_info->end_orig) {
-      fprintf(outfile, "%s=\"%s\"\n", "end", args_info->end_orig);
-    } else {
-      fprintf(outfile, "%s\n", "end");
-    }
-  }
-  if (args_info->bo_given) {
-    fprintf(outfile, "%s\n", "bo");
-  }
-  if (args_info->gofr_given) {
-    fprintf(outfile, "%s\n", "gofr");
-  }
-  if (args_info->r_theta_given) {
-    fprintf(outfile, "%s\n", "r_theta");
-  }
-  if (args_info->r_omega_given) {
-    fprintf(outfile, "%s\n", "r_omega");
-  }
-  if (args_info->theta_omega_given) {
-    fprintf(outfile, "%s\n", "theta_omega");
-  }
-  if (args_info->gxyz_given) {
-    fprintf(outfile, "%s\n", "gxyz");
-  }
-  if (args_info->p2_given) {
-    fprintf(outfile, "%s\n", "p2");
-  }
-  if (args_info->rp2_given) {
-    fprintf(outfile, "%s\n", "rp2");
-  }
-  if (args_info->scd_given) {
-    fprintf(outfile, "%s\n", "scd");
-  }
-  if (args_info->density_given) {
-    fprintf(outfile, "%s\n", "density");
-  }
-  if (args_info->slab_density_given) {
-    fprintf(outfile, "%s\n", "slab_density");
-  }
-  if (args_info->hxy_given) {
-    fprintf(outfile, "%s\n", "hxy");
-  }
-  
+  i = cmdline_parser_dump(outfile, args_info);
   fclose (outfile);
 
-  i = EXIT_SUCCESS;
   return i;
 }
 
@@ -477,9 +485,7 @@ cmdline_parser_free (struct gengetopt_args_info *args_
   cmdline_parser_release (args_info);
 }
 
-
-/* gengetopt_strdup() */
-/* strdup.c replacement of strdup, which is not standard */
+/** @brief replacement of strdup, which is not standard */
 char *
 gengetopt_strdup (const char *s)
 {
@@ -495,18 +501,19 @@ static void
 }
 
 static void
-reset_group_staticProps(struct gengetopt_args_info *args_info);
-
-static void
 reset_group_staticProps(struct gengetopt_args_info *args_info)
 {
   if (! args_info->staticProps_group_counter)
     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->r_z_given = 0 ;
   args_info->theta_omega_given = 0 ;
   args_info->gxyz_given = 0 ;
   args_info->p2_given = 0 ;
@@ -514,7 +521,10 @@ reset_group_staticProps(struct gengetopt_args_info *ar
   args_info->scd_given = 0 ;
   args_info->density_given = 0 ;
   args_info->slab_density_given = 0 ;
+  args_info->p_angle_given = 0 ;
   args_info->hxy_given = 0 ;
+  args_info->rho_r_given = 0 ;
+  args_info->hullvol_given = 0 ;
 
   args_info->staticProps_group_counter = 0;
 }
@@ -526,11 +536,34 @@ int
 }
 
 int
+cmdline_parser_ext (int argc, char * const *argv, struct gengetopt_args_info *args_info,
+                   struct cmdline_parser_params *params)
+{
+  int result;
+  result = cmdline_parser_internal (argc, argv, args_info, params, NULL);
+
+  if (result == EXIT_FAILURE)
+    {
+      cmdline_parser_free (args_info);
+      exit (EXIT_FAILURE);
+    }
+  
+  return result;
+}
+
+int
 cmdline_parser2 (int argc, char * const *argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required)
 {
   int result;
+  struct cmdline_parser_params params;
+  
+  params.override = override;
+  params.initialize = initialize;
+  params.check_required = check_required;
+  params.check_ambiguity = 0;
+  params.print_errors = 1;
 
-  result = cmdline_parser_internal (argc, argv, args_info, override, initialize, check_required, NULL);
+  result = cmdline_parser_internal (argc, argv, args_info, &params, NULL);
 
   if (result == EXIT_FAILURE)
     {
@@ -563,11 +596,13 @@ 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 : ""));
@@ -575,16 +610,145 @@ cmdline_parser_required2 (struct gengetopt_args_info *
     }
   
 
+  /* checks for dependences among options */
+
   return error;
 }
 
+
+static char *package_name = 0;
+
+/**
+ * @brief updates an option
+ * @param field the generic pointer to the field to update
+ * @param orig_field the pointer to the orig field
+ * @param field_given the pointer to the number of occurrence of this option
+ * @param prev_given the pointer to the number of occurrence already seen
+ * @param value the argument for this option (if null no arg was specified)
+ * @param possible_values the possible values for this option (if specified)
+ * @param default_value the default value (in case the option only accepts fixed values)
+ * @param arg_type the type of this option
+ * @param check_ambiguity @see cmdline_parser_params.check_ambiguity
+ * @param override @see cmdline_parser_params.override
+ * @param no_free whether to free a possible previous value
+ * @param multiple_option whether this is a multiple option
+ * @param long_opt the corresponding long option
+ * @param short_opt the corresponding short option (or '-' if none)
+ * @param additional_error possible further error specification
+ */
+static
+int update_arg(void *field, char **orig_field,
+               unsigned int *field_given, unsigned int *prev_given, 
+               char *value, char *possible_values[], const char *default_value,
+               cmdline_parser_arg_type arg_type,
+               int check_ambiguity, int override,
+               int no_free, int multiple_option,
+               const char *long_opt, char short_opt,
+               const char *additional_error)
+{
+  char *stop_char = 0;
+  const char *val = value;
+  int found;
+  char **string_field;
+
+  stop_char = 0;
+  found = 0;
+
+  if (!multiple_option && prev_given && (*prev_given || (check_ambiguity && *field_given)))
+    {
+      if (short_opt != '-')
+        fprintf (stderr, "%s: `--%s' (`-%c') option given more than once%s\n", 
+               package_name, long_opt, short_opt,
+               (additional_error ? additional_error : ""));
+      else
+        fprintf (stderr, "%s: `--%s' option given more than once%s\n", 
+               package_name, long_opt,
+               (additional_error ? additional_error : ""));
+      return 1; /* failure */
+    }
+
+    
+  if (field_given && *field_given && ! override)
+    return 0;
+  if (prev_given)
+    (*prev_given)++;
+  if (field_given)
+    (*field_given)++;
+  if (possible_values)
+    val = possible_values[found];
+
+  switch(arg_type) {
+  case ARG_INT:
+    if (val) *((int *)field) = strtol (val, &stop_char, 0);
+    break;
+  case ARG_DOUBLE:
+    if (val) *((double *)field) = strtod (val, &stop_char);
+    break;
+  case ARG_STRING:
+    if (val) {
+      string_field = (char **)field;
+      if (!no_free && *string_field)
+        free (*string_field); /* free previous string */
+      *string_field = gengetopt_strdup (val);
+    }
+    break;
+  default:
+    break;
+  };
+
+  /* check numeric conversion */
+  switch(arg_type) {
+  case ARG_INT:
+  case ARG_DOUBLE:
+    if (val && !(stop_char && *stop_char == '\0')) {
+      fprintf(stderr, "%s: invalid numeric value: %s\n", package_name, val);
+      return 1; /* failure */
+    }
+    break;
+  default:
+    ;
+  };
+
+  /* store the original value */
+  switch(arg_type) {
+  case ARG_NO:
+    break;
+  default:
+    if (value && orig_field) {
+      if (no_free) {
+        *orig_field = value;
+      } else {
+        if (*orig_field)
+          free (*orig_field); /* free previous string */
+        *orig_field = gengetopt_strdup (value);
+      }
+    }
+  };
+
+  return 0; /* OK */
+}
+
+
 int
-cmdline_parser_internal (int argc, char * const *argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required, const char *additional_error)
+cmdline_parser_internal (int argc, char * const *argv, struct gengetopt_args_info *args_info,
+                        struct cmdline_parser_params *params, const char *additional_error)
 {
   int c;	/* Character of the parsed option.  */
 
   int error = 0;
   struct gengetopt_args_info local_args_info;
+  
+  int override;
+  int initialize;
+  int check_required;
+  int check_ambiguity;
+  
+  package_name = argv[0];
+  
+  override = params->override;
+  initialize = params->initialize;
+  check_required = params->check_required;
+  check_ambiguity = params->check_ambiguity;
 
   if (initialize)
     cmdline_parser_init (args_info);
@@ -593,13 +757,12 @@ cmdline_parser_internal (int argc, char * const *argv,
 
   optarg = 0;
   optind = 0;
-  opterr = 1;
+  opterr = params->print_errors;
   optopt = '?';
 
   while (1)
     {
       int option_index = 0;
-      char *stop_char;
 
       static struct option long_options[] = {
         { "help",	0, NULL, 'h' },
@@ -610,6 +773,7 @@ cmdline_parser_internal (int argc, char * const *argv,
         { "nbins",	1, NULL, 'b' },
         { "nbins_x",	1, NULL, 'x' },
         { "nbins_y",	1, NULL, 'y' },
+        { "nbins_z",	1, NULL, 0 },
         { "nanglebins",	1, NULL, 'a' },
         { "length",	1, NULL, 0 },
         { "rcut",	1, NULL, 'c' },
@@ -618,13 +782,19 @@ cmdline_parser_internal (int argc, char * const *argv,
         { "sele2",	1, NULL, 0 },
         { "sele3",	1, NULL, 0 },
         { "refsele",	1, NULL, 0 },
+        { "comsele",	1, NULL, 0 },
         { "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 },
+        { "r_z",	0, NULL, 0 },
         { "theta_omega",	0, NULL, 0 },
         { "gxyz",	0, NULL, 0 },
         { "p2",	0, NULL, 'p' },
@@ -632,11 +802,13 @@ cmdline_parser_internal (int argc, char * const *argv,
         { "scd",	0, NULL, 's' },
         { "density",	0, NULL, 'd' },
         { "slab_density",	0, NULL, 0 },
+        { "p_angle",	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:c:z:gpsd", long_options, &option_index);
 
       if (c == -1) break;	/* Exit from `while (1)' loop.  */
@@ -654,538 +826,585 @@ cmdline_parser_internal (int argc, char * const *argv,
           exit (EXIT_SUCCESS);
 
         case 'i':	/* input dump file.  */
-          if (local_args_info.input_given)
-            {
-              fprintf (stderr, "%s: `--input' (`-i') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
-              goto failure;
-            }
-          if (args_info->input_given && ! override)
-            continue;
-          local_args_info.input_given = 1;
-          args_info->input_given = 1;
-          if (args_info->input_arg)
-            free (args_info->input_arg); /* free previous string */
-          args_info->input_arg = gengetopt_strdup (optarg);
-          if (args_info->input_orig)
-            free (args_info->input_orig); /* free previous string */
-          args_info->input_orig = gengetopt_strdup (optarg);
+        
+        
+          if (update_arg( (void *)&(args_info->input_arg), 
+               &(args_info->input_orig), &(args_info->input_given),
+              &(local_args_info.input_given), optarg, 0, 0, ARG_STRING,
+              check_ambiguity, override, 0, 0,
+              "input", 'i',
+              additional_error))
+            goto failure;
+        
           break;
-
         case 'o':	/* output file name.  */
-          if (local_args_info.output_given)
-            {
-              fprintf (stderr, "%s: `--output' (`-o') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
-              goto failure;
-            }
-          if (args_info->output_given && ! override)
-            continue;
-          local_args_info.output_given = 1;
-          args_info->output_given = 1;
-          if (args_info->output_arg)
-            free (args_info->output_arg); /* free previous string */
-          args_info->output_arg = gengetopt_strdup (optarg);
-          if (args_info->output_orig)
-            free (args_info->output_orig); /* free previous string */
-          args_info->output_orig = gengetopt_strdup (optarg);
-          break;
-
+        
+        
+          if (update_arg( (void *)&(args_info->output_arg), 
+               &(args_info->output_orig), &(args_info->output_given),
+              &(local_args_info.output_given), optarg, 0, 0, ARG_STRING,
+              check_ambiguity, override, 0, 0,
+              "output", 'o',
+              additional_error))
+            goto failure;
+        
+          break;
         case 'n':	/* process every n frame.  */
-          if (local_args_info.step_given)
-            {
-              fprintf (stderr, "%s: `--step' (`-n') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
-              goto failure;
-            }
-          if (args_info->step_given && ! override)
-            continue;
-          local_args_info.step_given = 1;
-          args_info->step_given = 1;
-          args_info->step_arg = strtol (optarg, &stop_char, 0);
-          if (!(stop_char && *stop_char == '\0')) {
-            fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
+        
+        
+          if (update_arg( (void *)&(args_info->step_arg), 
+               &(args_info->step_orig), &(args_info->step_given),
+              &(local_args_info.step_given), optarg, 0, "1", ARG_INT,
+              check_ambiguity, override, 0, 0,
+              "step", 'n',
+              additional_error))
             goto failure;
-          }
-          if (args_info->step_orig)
-            free (args_info->step_orig); /* free previous string */
-          args_info->step_orig = gengetopt_strdup (optarg);
+        
           break;
-
         case 'b':	/* number of bins (general purpose).  */
-          if (local_args_info.nbins_given)
-            {
-              fprintf (stderr, "%s: `--nbins' (`-b') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
-              goto failure;
-            }
-          if (args_info->nbins_given && ! override)
-            continue;
-          local_args_info.nbins_given = 1;
-          args_info->nbins_given = 1;
-          args_info->nbins_arg = strtol (optarg, &stop_char, 0);
-          if (!(stop_char && *stop_char == '\0')) {
-            fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
+        
+        
+          if (update_arg( (void *)&(args_info->nbins_arg), 
+               &(args_info->nbins_orig), &(args_info->nbins_given),
+              &(local_args_info.nbins_given), optarg, 0, "100", ARG_INT,
+              check_ambiguity, override, 0, 0,
+              "nbins", 'b',
+              additional_error))
             goto failure;
-          }
-          if (args_info->nbins_orig)
-            free (args_info->nbins_orig); /* free previous string */
-          args_info->nbins_orig = gengetopt_strdup (optarg);
+        
           break;
-
         case 'x':	/* number of bins in x axis.  */
-          if (local_args_info.nbins_x_given)
-            {
-              fprintf (stderr, "%s: `--nbins_x' (`-x') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
-              goto failure;
-            }
-          if (args_info->nbins_x_given && ! override)
-            continue;
-          local_args_info.nbins_x_given = 1;
-          args_info->nbins_x_given = 1;
-          args_info->nbins_x_arg = strtol (optarg, &stop_char, 0);
-          if (!(stop_char && *stop_char == '\0')) {
-            fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
+        
+        
+          if (update_arg( (void *)&(args_info->nbins_x_arg), 
+               &(args_info->nbins_x_orig), &(args_info->nbins_x_given),
+              &(local_args_info.nbins_x_given), optarg, 0, "100", ARG_INT,
+              check_ambiguity, override, 0, 0,
+              "nbins_x", 'x',
+              additional_error))
             goto failure;
-          }
-          if (args_info->nbins_x_orig)
-            free (args_info->nbins_x_orig); /* free previous string */
-          args_info->nbins_x_orig = gengetopt_strdup (optarg);
+        
           break;
-
         case 'y':	/* number of bins in y axis.  */
-          if (local_args_info.nbins_y_given)
-            {
-              fprintf (stderr, "%s: `--nbins_y' (`-y') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
-              goto failure;
-            }
-          if (args_info->nbins_y_given && ! override)
-            continue;
-          local_args_info.nbins_y_given = 1;
-          args_info->nbins_y_given = 1;
-          args_info->nbins_y_arg = strtol (optarg, &stop_char, 0);
-          if (!(stop_char && *stop_char == '\0')) {
-            fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
+        
+        
+          if (update_arg( (void *)&(args_info->nbins_y_arg), 
+               &(args_info->nbins_y_orig), &(args_info->nbins_y_given),
+              &(local_args_info.nbins_y_given), optarg, 0, "100", ARG_INT,
+              check_ambiguity, override, 0, 0,
+              "nbins_y", 'y',
+              additional_error))
             goto failure;
-          }
-          if (args_info->nbins_y_orig)
-            free (args_info->nbins_y_orig); /* free previous string */
-          args_info->nbins_y_orig = gengetopt_strdup (optarg);
+        
           break;
-
         case 'a':	/* number of bins for cos(angle).  */
-          if (local_args_info.nanglebins_given)
-            {
-              fprintf (stderr, "%s: `--nanglebins' (`-a') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
-              goto failure;
-            }
-          if (args_info->nanglebins_given && ! override)
-            continue;
-          local_args_info.nanglebins_given = 1;
-          args_info->nanglebins_given = 1;
-          args_info->nanglebins_arg = strtol (optarg, &stop_char, 0);
-          if (!(stop_char && *stop_char == '\0')) {
-            fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
+        
+        
+          if (update_arg( (void *)&(args_info->nanglebins_arg), 
+               &(args_info->nanglebins_orig), &(args_info->nanglebins_given),
+              &(local_args_info.nanglebins_given), optarg, 0, "50", ARG_INT,
+              check_ambiguity, override, 0, 0,
+              "nanglebins", 'a',
+              additional_error))
             goto failure;
-          }
-          if (args_info->nanglebins_orig)
-            free (args_info->nanglebins_orig); /* free previous string */
-          args_info->nanglebins_orig = gengetopt_strdup (optarg);
+        
           break;
-
         case 'c':	/* cutoff radius (rcut).  */
-          if (local_args_info.rcut_given)
-            {
-              fprintf (stderr, "%s: `--rcut' (`-c') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
-              goto failure;
-            }
-          if (args_info->rcut_given && ! override)
-            continue;
-          local_args_info.rcut_given = 1;
-          args_info->rcut_given = 1;
-          args_info->rcut_arg = strtod (optarg, &stop_char);
-          if (!(stop_char && *stop_char == '\0')) {
-            fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
+        
+        
+          if (update_arg( (void *)&(args_info->rcut_arg), 
+               &(args_info->rcut_orig), &(args_info->rcut_given),
+              &(local_args_info.rcut_given), optarg, 0, 0, ARG_DOUBLE,
+              check_ambiguity, override, 0, 0,
+              "rcut", 'c',
+              additional_error))
             goto failure;
-          }
-          if (args_info->rcut_orig)
-            free (args_info->rcut_orig); /* free previous string */
-          args_info->rcut_orig = gengetopt_strdup (optarg);
+        
           break;
-
         case 'z':	/* Where to set the zero for the slab_density calculation.  */
-          if (local_args_info.zoffset_given)
-            {
-              fprintf (stderr, "%s: `--zoffset' (`-z') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
-              goto failure;
-            }
-          if (args_info->zoffset_given && ! override)
-            continue;
-          local_args_info.zoffset_given = 1;
-          args_info->zoffset_given = 1;
-          args_info->zoffset_arg = strtod (optarg, &stop_char);
-          if (!(stop_char && *stop_char == '\0')) {
-            fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
+        
+        
+          if (update_arg( (void *)&(args_info->zoffset_arg), 
+               &(args_info->zoffset_orig), &(args_info->zoffset_given),
+              &(local_args_info.zoffset_given), optarg, 0, "0", ARG_DOUBLE,
+              check_ambiguity, override, 0, 0,
+              "zoffset", 'z',
+              additional_error))
             goto failure;
-          }
-          if (args_info->zoffset_orig)
-            free (args_info->zoffset_orig); /* free previous string */
-          args_info->zoffset_orig = gengetopt_strdup (optarg);
+        
           break;
-
         case 'g':	/* g(r).  */
-          if (local_args_info.gofr_given)
-            {
-              fprintf (stderr, "%s: `--gofr' (`-g') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
-              goto failure;
-            }
-          if (args_info->gofr_given && ! override)
-            continue;
-          local_args_info.gofr_given = 1;
-          args_info->gofr_given = 1;
+        
           if (args_info->staticProps_group_counter && override)
             reset_group_staticProps (args_info);
           args_info->staticProps_group_counter += 1;
+        
+          if (update_arg( 0 , 
+               0 , &(args_info->gofr_given),
+              &(local_args_info.gofr_given), optarg, 0, 0, ARG_NO,
+              check_ambiguity, override, 0, 0,
+              "gofr", 'g',
+              additional_error))
+            goto failure;
+        
           break;
-
         case 'p':	/* p2 order parameter (--sele1 and --sele2 must be specified).  */
-          if (local_args_info.p2_given)
-            {
-              fprintf (stderr, "%s: `--p2' (`-p') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
-              goto failure;
-            }
-          if (args_info->p2_given && ! override)
-            continue;
-          local_args_info.p2_given = 1;
-          args_info->p2_given = 1;
+        
           if (args_info->staticProps_group_counter && override)
             reset_group_staticProps (args_info);
           args_info->staticProps_group_counter += 1;
+        
+          if (update_arg( 0 , 
+               0 , &(args_info->p2_given),
+              &(local_args_info.p2_given), optarg, 0, 0, ARG_NO,
+              check_ambiguity, override, 0, 0,
+              "p2", 'p',
+              additional_error))
+            goto failure;
+        
           break;
-
         case 's':	/* scd order parameter (either --sele1, --sele2, --sele3 are specified or --molname, --begin, --end are specified).  */
-          if (local_args_info.scd_given)
-            {
-              fprintf (stderr, "%s: `--scd' (`-s') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
-              goto failure;
-            }
-          if (args_info->scd_given && ! override)
-            continue;
-          local_args_info.scd_given = 1;
-          args_info->scd_given = 1;
+        
           if (args_info->staticProps_group_counter && override)
             reset_group_staticProps (args_info);
           args_info->staticProps_group_counter += 1;
+        
+          if (update_arg( 0 , 
+               0 , &(args_info->scd_given),
+              &(local_args_info.scd_given), optarg, 0, 0, ARG_NO,
+              check_ambiguity, override, 0, 0,
+              "scd", 's',
+              additional_error))
+            goto failure;
+        
           break;
-
         case 'd':	/* density plot.  */
-          if (local_args_info.density_given)
-            {
-              fprintf (stderr, "%s: `--density' (`-d') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
-              goto failure;
-            }
-          if (args_info->density_given && ! override)
-            continue;
-          local_args_info.density_given = 1;
-          args_info->density_given = 1;
+        
           if (args_info->staticProps_group_counter && override)
             reset_group_staticProps (args_info);
           args_info->staticProps_group_counter += 1;
+        
+          if (update_arg( 0 , 
+               0 , &(args_info->density_given),
+              &(local_args_info.density_given), optarg, 0, 0, ARG_NO,
+              check_ambiguity, override, 0, 0,
+              "density", 'd',
+              additional_error))
+            goto failure;
+        
           break;
 
-
         case 0:	/* Long option with no short option */
+          /* number of bins in z axis.  */
+          if (strcmp (long_options[option_index].name, "nbins_z") == 0)
+          {
+          
+          
+            if (update_arg( (void *)&(args_info->nbins_z_arg), 
+                 &(args_info->nbins_z_orig), &(args_info->nbins_z_given),
+                &(local_args_info.nbins_z_given), optarg, 0, "100", ARG_INT,
+                check_ambiguity, override, 0, 0,
+                "nbins_z", '-',
+                additional_error))
+              goto failure;
+          
+          }
           /* maximum length (Defaults to 1/2 smallest length of first frame).  */
-          if (strcmp (long_options[option_index].name, "length") == 0)
+          else if (strcmp (long_options[option_index].name, "length") == 0)
           {
-            if (local_args_info.length_given)
-              {
-                fprintf (stderr, "%s: `--length' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
-                goto failure;
-              }
-            if (args_info->length_given && ! override)
-              continue;
-            local_args_info.length_given = 1;
-            args_info->length_given = 1;
-            args_info->length_arg = strtod (optarg, &stop_char);
-            if (!(stop_char && *stop_char == '\0')) {
-              fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
+          
+          
+            if (update_arg( (void *)&(args_info->length_arg), 
+                 &(args_info->length_orig), &(args_info->length_given),
+                &(local_args_info.length_given), optarg, 0, 0, ARG_DOUBLE,
+                check_ambiguity, override, 0, 0,
+                "length", '-',
+                additional_error))
               goto failure;
-            }
-            if (args_info->length_orig)
-              free (args_info->length_orig); /* free previous string */
-            args_info->length_orig = gengetopt_strdup (optarg);
+          
           }
           /* select the first stuntdouble set.  */
           else if (strcmp (long_options[option_index].name, "sele1") == 0)
           {
-            if (local_args_info.sele1_given)
-              {
-                fprintf (stderr, "%s: `--sele1' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
-                goto failure;
-              }
-            if (args_info->sele1_given && ! override)
-              continue;
-            local_args_info.sele1_given = 1;
-            args_info->sele1_given = 1;
-            if (args_info->sele1_arg)
-              free (args_info->sele1_arg); /* free previous string */
-            args_info->sele1_arg = gengetopt_strdup (optarg);
-            if (args_info->sele1_orig)
-              free (args_info->sele1_orig); /* free previous string */
-            args_info->sele1_orig = gengetopt_strdup (optarg);
+          
+          
+            if (update_arg( (void *)&(args_info->sele1_arg), 
+                 &(args_info->sele1_orig), &(args_info->sele1_given),
+                &(local_args_info.sele1_given), optarg, 0, 0, ARG_STRING,
+                check_ambiguity, override, 0, 0,
+                "sele1", '-',
+                additional_error))
+              goto failure;
+          
           }
           /* select the second stuntdouble set.  */
           else if (strcmp (long_options[option_index].name, "sele2") == 0)
           {
-            if (local_args_info.sele2_given)
-              {
-                fprintf (stderr, "%s: `--sele2' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
-                goto failure;
-              }
-            if (args_info->sele2_given && ! override)
-              continue;
-            local_args_info.sele2_given = 1;
-            args_info->sele2_given = 1;
-            if (args_info->sele2_arg)
-              free (args_info->sele2_arg); /* free previous string */
-            args_info->sele2_arg = gengetopt_strdup (optarg);
-            if (args_info->sele2_orig)
-              free (args_info->sele2_orig); /* free previous string */
-            args_info->sele2_orig = gengetopt_strdup (optarg);
+          
+          
+            if (update_arg( (void *)&(args_info->sele2_arg), 
+                 &(args_info->sele2_orig), &(args_info->sele2_given),
+                &(local_args_info.sele2_given), optarg, 0, 0, ARG_STRING,
+                check_ambiguity, override, 0, 0,
+                "sele2", '-',
+                additional_error))
+              goto failure;
+          
           }
           /* select the third stuntdouble set.  */
           else if (strcmp (long_options[option_index].name, "sele3") == 0)
           {
-            if (local_args_info.sele3_given)
-              {
-                fprintf (stderr, "%s: `--sele3' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
-                goto failure;
-              }
-            if (args_info->sele3_given && ! override)
-              continue;
-            local_args_info.sele3_given = 1;
-            args_info->sele3_given = 1;
-            if (args_info->sele3_arg)
-              free (args_info->sele3_arg); /* free previous string */
-            args_info->sele3_arg = gengetopt_strdup (optarg);
-            if (args_info->sele3_orig)
-              free (args_info->sele3_orig); /* free previous string */
-            args_info->sele3_orig = gengetopt_strdup (optarg);
+          
+          
+            if (update_arg( (void *)&(args_info->sele3_arg), 
+                 &(args_info->sele3_orig), &(args_info->sele3_given),
+                &(local_args_info.sele3_given), optarg, 0, 0, ARG_STRING,
+                check_ambiguity, override, 0, 0,
+                "sele3", '-',
+                additional_error))
+              goto failure;
+          
           }
           /* select reference (use and only use with --gxyz).  */
           else if (strcmp (long_options[option_index].name, "refsele") == 0)
           {
-            if (local_args_info.refsele_given)
-              {
-                fprintf (stderr, "%s: `--refsele' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
-                goto failure;
-              }
-            if (args_info->refsele_given && ! override)
-              continue;
-            local_args_info.refsele_given = 1;
-            args_info->refsele_given = 1;
-            if (args_info->refsele_arg)
-              free (args_info->refsele_arg); /* free previous string */
-            args_info->refsele_arg = gengetopt_strdup (optarg);
-            if (args_info->refsele_orig)
-              free (args_info->refsele_orig); /* free previous string */
-            args_info->refsele_orig = gengetopt_strdup (optarg);
+          
+          
+            if (update_arg( (void *)&(args_info->refsele_arg), 
+                 &(args_info->refsele_orig), &(args_info->refsele_given),
+                &(local_args_info.refsele_given), optarg, 0, 0, ARG_STRING,
+                check_ambiguity, override, 0, 0,
+                "refsele", '-',
+                additional_error))
+              goto failure;
+          
+          }
+          /* select stunt doubles for center-of-mass reference point.  */
+          else if (strcmp (long_options[option_index].name, "comsele") == 0)
+          {
+          
+          
+            if (update_arg( (void *)&(args_info->comsele_arg), 
+                 &(args_info->comsele_orig), &(args_info->comsele_given),
+                &(local_args_info.comsele_given), optarg, 0, 0, ARG_STRING,
+                check_ambiguity, override, 0, 0,
+                "comsele", '-',
+                additional_error))
+              goto failure;
+          
           }
           /* molecule name.  */
           else if (strcmp (long_options[option_index].name, "molname") == 0)
           {
-            if (local_args_info.molname_given)
-              {
-                fprintf (stderr, "%s: `--molname' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
-                goto failure;
-              }
-            if (args_info->molname_given && ! override)
-              continue;
-            local_args_info.molname_given = 1;
-            args_info->molname_given = 1;
-            if (args_info->molname_arg)
-              free (args_info->molname_arg); /* free previous string */
-            args_info->molname_arg = gengetopt_strdup (optarg);
-            if (args_info->molname_orig)
-              free (args_info->molname_orig); /* free previous string */
-            args_info->molname_orig = gengetopt_strdup (optarg);
+          
+          
+            if (update_arg( (void *)&(args_info->molname_arg), 
+                 &(args_info->molname_orig), &(args_info->molname_given),
+                &(local_args_info.molname_given), optarg, 0, 0, ARG_STRING,
+                check_ambiguity, override, 0, 0,
+                "molname", '-',
+                additional_error))
+              goto failure;
+          
           }
           /* begin internal index.  */
           else if (strcmp (long_options[option_index].name, "begin") == 0)
           {
-            if (local_args_info.begin_given)
-              {
-                fprintf (stderr, "%s: `--begin' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
-                goto failure;
-              }
-            if (args_info->begin_given && ! override)
-              continue;
-            local_args_info.begin_given = 1;
-            args_info->begin_given = 1;
-            args_info->begin_arg = strtol (optarg, &stop_char, 0);
-            if (!(stop_char && *stop_char == '\0')) {
-              fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
+          
+          
+            if (update_arg( (void *)&(args_info->begin_arg), 
+                 &(args_info->begin_orig), &(args_info->begin_given),
+                &(local_args_info.begin_given), optarg, 0, 0, ARG_INT,
+                check_ambiguity, override, 0, 0,
+                "begin", '-',
+                additional_error))
               goto failure;
-            }
-            if (args_info->begin_orig)
-              free (args_info->begin_orig); /* free previous string */
-            args_info->begin_orig = gengetopt_strdup (optarg);
+          
           }
           /* end internal index.  */
           else if (strcmp (long_options[option_index].name, "end") == 0)
           {
-            if (local_args_info.end_given)
-              {
-                fprintf (stderr, "%s: `--end' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
-                goto failure;
-              }
-            if (args_info->end_given && ! override)
-              continue;
-            local_args_info.end_given = 1;
-            args_info->end_given = 1;
-            args_info->end_arg = strtol (optarg, &stop_char, 0);
-            if (!(stop_char && *stop_char == '\0')) {
-              fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
+          
+          
+            if (update_arg( (void *)&(args_info->end_arg), 
+                 &(args_info->end_orig), &(args_info->end_given),
+                &(local_args_info.end_given), optarg, 0, 0, ARG_INT,
+                check_ambiguity, override, 0, 0,
+                "end", '-',
+                additional_error))
               goto failure;
-            }
-            if (args_info->end_orig)
-              free (args_info->end_orig); /* free previous string */
-            args_info->end_orig = gengetopt_strdup (optarg);
+          
           }
-          /* bond order parameter (--rcut must be specified.  */
+          /* nanoparticle radius.  */
+          else if (strcmp (long_options[option_index].name, "radius") == 0)
+          {
+          
+          
+            if (update_arg( (void *)&(args_info->radius_arg), 
+                 &(args_info->radius_orig), &(args_info->radius_given),
+                &(local_args_info.radius_given), optarg, 0, 0, ARG_DOUBLE,
+                check_ambiguity, override, 0, 0,
+                "radius", '-',
+                additional_error))
+              goto failure;
+          
+          }
+          /* bond order parameter (--rcut must be specified).  */
           else if (strcmp (long_options[option_index].name, "bo") == 0)
           {
-            if (local_args_info.bo_given)
-              {
-                fprintf (stderr, "%s: `--bo' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
-                goto failure;
-              }
-            if (args_info->bo_given && ! override)
-              continue;
-            local_args_info.bo_given = 1;
-            args_info->bo_given = 1;
+          
             if (args_info->staticProps_group_counter && override)
               reset_group_staticProps (args_info);
             args_info->staticProps_group_counter += 1;
-            break;
+          
+            if (update_arg( 0 , 
+                 0 , &(args_info->bo_given),
+                &(local_args_info.bo_given), optarg, 0, 0, ARG_NO,
+                check_ambiguity, override, 0, 0,
+                "bo", '-',
+                additional_error))
+              goto failure;
+          
           }
+          /* bond order parameter as a function of radius (--rcut must be specified).  */
+          else if (strcmp (long_options[option_index].name, "bor") == 0)
+          {
+          
+            if (args_info->staticProps_group_counter && override)
+              reset_group_staticProps (args_info);
+            args_info->staticProps_group_counter += 1;
+          
+            if (update_arg( 0 , 
+                 0 , &(args_info->bor_given),
+                &(local_args_info.bor_given), optarg, 0, 0, ARG_NO,
+                check_ambiguity, override, 0, 0,
+                "bor", '-',
+                additional_error))
+              goto failure;
+          
+          }
+          /* N(theta) bond angle density within (--rcut must be specified).  */
+          else if (strcmp (long_options[option_index].name, "bad") == 0)
+          {
+          
+            if (args_info->staticProps_group_counter && override)
+              reset_group_staticProps (args_info);
+            args_info->staticProps_group_counter += 1;
+          
+            if (update_arg( 0 , 
+                 0 , &(args_info->bad_given),
+                &(local_args_info.bad_given), optarg, 0, 0, ARG_NO,
+                check_ambiguity, override, 0, 0,
+                "bad", '-',
+                additional_error))
+              goto failure;
+          
+          }
+          /* g(z).  */
+          else if (strcmp (long_options[option_index].name, "gofz") == 0)
+          {
+          
+            if (args_info->staticProps_group_counter && override)
+              reset_group_staticProps (args_info);
+            args_info->staticProps_group_counter += 1;
+          
+            if (update_arg( 0 , 
+                 0 , &(args_info->gofz_given),
+                &(local_args_info.gofz_given), optarg, 0, 0, ARG_NO,
+                check_ambiguity, override, 0, 0,
+                "gofz", '-',
+                additional_error))
+              goto failure;
+          
+          }
           /* g(r, cos(theta)).  */
           else if (strcmp (long_options[option_index].name, "r_theta") == 0)
           {
-            if (local_args_info.r_theta_given)
-              {
-                fprintf (stderr, "%s: `--r_theta' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
-                goto failure;
-              }
-            if (args_info->r_theta_given && ! override)
-              continue;
-            local_args_info.r_theta_given = 1;
-            args_info->r_theta_given = 1;
+          
             if (args_info->staticProps_group_counter && override)
               reset_group_staticProps (args_info);
             args_info->staticProps_group_counter += 1;
-            break;
+          
+            if (update_arg( 0 , 
+                 0 , &(args_info->r_theta_given),
+                &(local_args_info.r_theta_given), optarg, 0, 0, ARG_NO,
+                check_ambiguity, override, 0, 0,
+                "r_theta", '-',
+                additional_error))
+              goto failure;
+          
           }
           /* g(r, cos(omega)).  */
           else if (strcmp (long_options[option_index].name, "r_omega") == 0)
           {
-            if (local_args_info.r_omega_given)
-              {
-                fprintf (stderr, "%s: `--r_omega' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
-                goto failure;
-              }
-            if (args_info->r_omega_given && ! override)
-              continue;
-            local_args_info.r_omega_given = 1;
-            args_info->r_omega_given = 1;
+          
             if (args_info->staticProps_group_counter && override)
               reset_group_staticProps (args_info);
             args_info->staticProps_group_counter += 1;
-            break;
+          
+            if (update_arg( 0 , 
+                 0 , &(args_info->r_omega_given),
+                &(local_args_info.r_omega_given), optarg, 0, 0, ARG_NO,
+                check_ambiguity, override, 0, 0,
+                "r_omega", '-',
+                additional_error))
+              goto failure;
+          
           }
+          /* g(r, z).  */
+          else if (strcmp (long_options[option_index].name, "r_z") == 0)
+          {
+          
+            if (args_info->staticProps_group_counter && override)
+              reset_group_staticProps (args_info);
+            args_info->staticProps_group_counter += 1;
+          
+            if (update_arg( 0 , 
+                 0 , &(args_info->r_z_given),
+                &(local_args_info.r_z_given), optarg, 0, 0, ARG_NO,
+                check_ambiguity, override, 0, 0,
+                "r_z", '-',
+                additional_error))
+              goto failure;
+          
+          }
           /* g(cos(theta), cos(omega)).  */
           else if (strcmp (long_options[option_index].name, "theta_omega") == 0)
           {
-            if (local_args_info.theta_omega_given)
-              {
-                fprintf (stderr, "%s: `--theta_omega' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
-                goto failure;
-              }
-            if (args_info->theta_omega_given && ! override)
-              continue;
-            local_args_info.theta_omega_given = 1;
-            args_info->theta_omega_given = 1;
+          
             if (args_info->staticProps_group_counter && override)
               reset_group_staticProps (args_info);
             args_info->staticProps_group_counter += 1;
-            break;
+          
+            if (update_arg( 0 , 
+                 0 , &(args_info->theta_omega_given),
+                &(local_args_info.theta_omega_given), optarg, 0, 0, ARG_NO,
+                check_ambiguity, override, 0, 0,
+                "theta_omega", '-',
+                additional_error))
+              goto failure;
+          
           }
           /* g(x, y, z).  */
           else if (strcmp (long_options[option_index].name, "gxyz") == 0)
           {
-            if (local_args_info.gxyz_given)
-              {
-                fprintf (stderr, "%s: `--gxyz' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
-                goto failure;
-              }
-            if (args_info->gxyz_given && ! override)
-              continue;
-            local_args_info.gxyz_given = 1;
-            args_info->gxyz_given = 1;
+          
             if (args_info->staticProps_group_counter && override)
               reset_group_staticProps (args_info);
             args_info->staticProps_group_counter += 1;
-            break;
+          
+            if (update_arg( 0 , 
+                 0 , &(args_info->gxyz_given),
+                &(local_args_info.gxyz_given), optarg, 0, 0, ARG_NO,
+                check_ambiguity, override, 0, 0,
+                "gxyz", '-',
+                additional_error))
+              goto failure;
+          
           }
           /* rp2 order parameter (--sele1 and --sele2 must be specified).  */
           else if (strcmp (long_options[option_index].name, "rp2") == 0)
           {
-            if (local_args_info.rp2_given)
-              {
-                fprintf (stderr, "%s: `--rp2' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
-                goto failure;
-              }
-            if (args_info->rp2_given && ! override)
-              continue;
-            local_args_info.rp2_given = 1;
-            args_info->rp2_given = 1;
+          
             if (args_info->staticProps_group_counter && override)
               reset_group_staticProps (args_info);
             args_info->staticProps_group_counter += 1;
-            break;
+          
+            if (update_arg( 0 , 
+                 0 , &(args_info->rp2_given),
+                &(local_args_info.rp2_given), optarg, 0, 0, ARG_NO,
+                check_ambiguity, override, 0, 0,
+                "rp2", '-',
+                additional_error))
+              goto failure;
+          
           }
           /* slab density.  */
           else if (strcmp (long_options[option_index].name, "slab_density") == 0)
           {
-            if (local_args_info.slab_density_given)
-              {
-                fprintf (stderr, "%s: `--slab_density' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
-                goto failure;
-              }
-            if (args_info->slab_density_given && ! override)
-              continue;
-            local_args_info.slab_density_given = 1;
-            args_info->slab_density_given = 1;
+          
             if (args_info->staticProps_group_counter && override)
               reset_group_staticProps (args_info);
             args_info->staticProps_group_counter += 1;
-            break;
+          
+            if (update_arg( 0 , 
+                 0 , &(args_info->slab_density_given),
+                &(local_args_info.slab_density_given), optarg, 0, 0, ARG_NO,
+                check_ambiguity, override, 0, 0,
+                "slab_density", '-',
+                additional_error))
+              goto failure;
+          
           }
+          /* p(cos(theta)).  */
+          else if (strcmp (long_options[option_index].name, "p_angle") == 0)
+          {
+          
+            if (args_info->staticProps_group_counter && override)
+              reset_group_staticProps (args_info);
+            args_info->staticProps_group_counter += 1;
+          
+            if (update_arg( 0 , 
+                 0 , &(args_info->p_angle_given),
+                &(local_args_info.p_angle_given), optarg, 0, 0, ARG_NO,
+                check_ambiguity, override, 0, 0,
+                "p_angle", '-',
+                additional_error))
+              goto failure;
+          
+          }
           /* hxy.  */
           else if (strcmp (long_options[option_index].name, "hxy") == 0)
           {
-            if (local_args_info.hxy_given)
-              {
-                fprintf (stderr, "%s: `--hxy' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
-                goto failure;
-              }
-            if (args_info->hxy_given && ! override)
-              continue;
-            local_args_info.hxy_given = 1;
-            args_info->hxy_given = 1;
+          
             if (args_info->staticProps_group_counter && override)
               reset_group_staticProps (args_info);
             args_info->staticProps_group_counter += 1;
-            break;
+          
+            if (update_arg( 0 , 
+                 0 , &(args_info->hxy_given),
+                &(local_args_info.hxy_given), optarg, 0, 0, ARG_NO,
+                check_ambiguity, override, 0, 0,
+                "hxy", '-',
+                additional_error))
+              goto failure;
+          
           }
+          /* rho of R.  */
+          else if (strcmp (long_options[option_index].name, "rho_r") == 0)
+          {
           
+            if (args_info->staticProps_group_counter && override)
+              reset_group_staticProps (args_info);
+            args_info->staticProps_group_counter += 1;
+          
+            if (update_arg( 0 , 
+                 0 , &(args_info->rho_r_given),
+                &(local_args_info.rho_r_given), optarg, 0, 0, ARG_NO,
+                check_ambiguity, override, 0, 0,
+                "rho_r", '-',
+                additional_error))
+              goto failure;
+          
+          }
+          /* hull volume of nanoparticle.  */
+          else if (strcmp (long_options[option_index].name, "hullvol") == 0)
+          {
+          
+            if (args_info->staticProps_group_counter && override)
+              reset_group_staticProps (args_info);
+            args_info->staticProps_group_counter += 1;
+          
+            if (update_arg( 0 , 
+                 0 , &(args_info->hullvol_given),
+                &(local_args_info.hullvol_given), optarg, 0, 0, ARG_NO,
+                check_ambiguity, override, 0, 0,
+                "hullvol", '-',
+                additional_error))
+              goto failure;
+          
+          }
+          
           break;
         case '?':	/* Invalid option.  */
           /* `getopt_long' already printed an error message.  */
@@ -1215,6 +1434,30 @@ 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: