--- trunk/src/applications/staticProps/StaticPropsCmd.c	2005/05/27 21:11:24	545
+++ trunk/src/applications/staticProps/StaticPropsCmd.c	2007/09/17 20:05:51	1180
@@ -1,27 +1,208 @@
 /*
-  File autogenerated by gengetopt version 2.11
+  File autogenerated by gengetopt version 2.19.1
   generated with the following command:
-  /home/maul/gezelter/tim/bin/gengetopt -i StaticProps.ggo -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:
   we make no copyright claims on it.
 */
 
-
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-
 /* If we use autoconf.  */
 #ifdef HAVE_CONFIG_H
 #include "config.h"
 #endif
 
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+
 #include "getopt.h"
 
 #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)",
+  "      --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
+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);
+
+static int
+cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error);
+
+static char *
+gengetopt_strdup (const char *s);
+
+static
+void clear_given (struct gengetopt_args_info *args_info)
+{
+  args_info->help_given = 0 ;
+  args_info->version_given = 0 ;
+  args_info->input_given = 0 ;
+  args_info->output_given = 0 ;
+  args_info->step_given = 0 ;
+  args_info->nbins_given = 0 ;
+  args_info->nbins_x_given = 0 ;
+  args_info->nbins_y_given = 0 ;
+  args_info->nanglebins_given = 0 ;
+  args_info->length_given = 0 ;
+  args_info->rcut_given = 0 ;
+  args_info->zoffset_given = 0 ;
+  args_info->sele1_given = 0 ;
+  args_info->sele2_given = 0 ;
+  args_info->sele3_given = 0 ;
+  args_info->refsele_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->r_theta_given = 0 ;
+  args_info->r_omega_given = 0 ;
+  args_info->theta_omega_given = 0 ;
+  args_info->gxyz_given = 0 ;
+  args_info->p2_given = 0 ;
+  args_info->rp2_given = 0 ;
+  args_info->scd_given = 0 ;
+  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 ;
+}
+
+static
+void clear_args (struct gengetopt_args_info *args_info)
+{
+  args_info->input_arg = NULL;
+  args_info->input_orig = NULL;
+  args_info->output_arg = NULL;
+  args_info->output_orig = NULL;
+  args_info->step_arg = 1;
+  args_info->step_orig = NULL;
+  args_info->nbins_arg = 100;
+  args_info->nbins_orig = NULL;
+  args_info->nbins_x_arg = 100;
+  args_info->nbins_x_orig = NULL;
+  args_info->nbins_y_arg = 100;
+  args_info->nbins_y_orig = NULL;
+  args_info->nanglebins_arg = 50;
+  args_info->nanglebins_orig = NULL;
+  args_info->length_orig = NULL;
+  args_info->rcut_orig = NULL;
+  args_info->zoffset_arg = 0;
+  args_info->zoffset_orig = NULL;
+  args_info->sele1_arg = NULL;
+  args_info->sele1_orig = NULL;
+  args_info->sele2_arg = NULL;
+  args_info->sele2_orig = NULL;
+  args_info->sele3_arg = NULL;
+  args_info->sele3_orig = NULL;
+  args_info->refsele_arg = NULL;
+  args_info->refsele_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->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->r_theta_help = gengetopt_args_info_help[24] ;
+  args_info->r_omega_help = gengetopt_args_info_help[25] ;
+  args_info->theta_omega_help = gengetopt_args_info_help[26] ;
+  args_info->gxyz_help = gengetopt_args_info_help[27] ;
+  args_info->p2_help = gengetopt_args_info_help[28] ;
+  args_info->rp2_help = gengetopt_args_info_help[29] ;
+  args_info->scd_help = gengetopt_args_info_help[30] ;
+  args_info->density_help = gengetopt_args_info_help[31] ;
+  args_info->slab_density_help = gengetopt_args_info_help[32] ;
+  args_info->hxy_help = gengetopt_args_info_help[33] ;
+  args_info->rho_r_help = gengetopt_args_info_help[34] ;
+  args_info->hullvol_help = gengetopt_args_info_help[35] ;
+  
+}
+
 void
 cmdline_parser_print_version (void)
 {
@@ -31,100 +212,503 @@ cmdline_parser_print_help (void)
 void
 cmdline_parser_print_help (void)
 {
+  int i = 0;
   cmdline_parser_print_version ();
-  printf("\n"
-  "Usage: %s [OPTIONS]...\n", CMDLINE_PARSER_PACKAGE);
-  printf("\n");
-  printf("  -h, --help                      Print help and exit\n");
-  printf("  -V, --version                   Print version and exit\n");
-  printf("  -i, --input=filename            input dump file\n");
-  printf("  -o, --output=filename           output file name\n");
-  printf("  -n, --step=INT                  process every n frame  (default=`1')\n");
-  printf("  -r, --nrbins=INT                number of bins for distance  (default=`100')\n");
-  printf("  -a, --nanglebins=INT            number of bins for cos(angle)  (default=\n                                    `50')\n");
-  printf("  -l, --length=DOUBLE             maximum length (Defaults to 1/2 smallest \n                                    length of first frame)\n");
-  printf("      --sele1=selection script    select the first stuntdouble set\n");
-  printf("      --sele2=selection script    select the second stuntdouble set\n");
-  printf("      --sele3=selection script    select the third stuntdouble set\n");
-  printf("      --refsele=selection script  select reference (use and only use with \n                                    --gxyz)\n");
-  printf("      --molname=STRING            molecule name\n");
-  printf("      --begin=INT                 begin interanl index\n");
-  printf("      --end=INT                   end internal index\n");
-  printf("\n");
-  printf(" Group: staticProps  an option of this group is required\n");
-  printf("      --gofr                      g(r)\n");
-  printf("      --r_theta                   g(r, cos(theta))\n");
-  printf("      --r_omega                   g(r, cos(omega))\n");
-  printf("      --theta_omega               g(cos(theta), cos(omega))\n");
-  printf("      --gxyz                      g(x, y, z)\n");
-  printf("      --p2                        p2 order parameter (--sele1 and --sele2 must \n                                    be specified)\n");
-  printf("      --scd                       scd order parameter(either --sele1, --sele2, \n                                    --sele3 are specified or --molname, \n                                    --begin, --end are specified)\n");
-  printf("      --density                   density plot (--sele1 must be specified)\n");
+
+  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
+cmdline_parser_init (struct gengetopt_args_info *args_info)
+{
+  clear_given (args_info);
+  clear_args (args_info);
+  init_args_info (args_info);
 
-static char *gengetopt_strdup (const char *s);
+  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 */
+      args_info->input_arg = 0;
+    }
+  if (args_info->input_orig)
+    {
+      free (args_info->input_orig); /* free previous argument */
+      args_info->input_orig = 0;
+    }
+  if (args_info->output_arg)
+    {
+      free (args_info->output_arg); /* free previous argument */
+      args_info->output_arg = 0;
+    }
+  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->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);
+}
+
+int
+cmdline_parser_file_save(const char *filename, struct gengetopt_args_info *args_info)
+{
+  FILE *outfile;
+  int i = 0;
+
+  outfile = fopen(filename, "w");
+
+  if (!outfile)
+    {
+      fprintf (stderr, "%s: cannot open file for writing: %s\n", CMDLINE_PARSER_PACKAGE, filename);
+      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->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->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");
+  }
+  if (args_info->rho_r_given) {
+    fprintf(outfile, "%s\n", "rho_r");
+  }
+  if (args_info->hullvol_given) {
+    fprintf(outfile, "%s\n", "hullvol");
+  }
+  
+  fclose (outfile);
 
+  i = EXIT_SUCCESS;
+  return i;
+}
+
+void
+cmdline_parser_free (struct gengetopt_args_info *args_info)
+{
+  cmdline_parser_release (args_info);
+}
+
+
 /* gengetopt_strdup() */
 /* strdup.c replacement of strdup, which is not standard */
 char *
 gengetopt_strdup (const char *s)
 {
-  char *result = (char*)malloc(strlen(s) + 1);
+  char *result = NULL;
+  if (!s)
+    return result;
+
+  result = (char*)malloc(strlen(s) + 1);
   if (result == (char*)0)
     return (char*)0;
   strcpy(result, s);
   return result;
 }
 
-int
-cmdline_parser (int argc, char * const *argv, struct gengetopt_args_info *args_info)
+static void
+reset_group_staticProps(struct gengetopt_args_info *args_info);
+
+static void
+reset_group_staticProps(struct gengetopt_args_info *args_info)
 {
-  int c;	/* Character of the parsed option.  */
-  int missing_required_options = 0;
-  int staticProps_group_counter = 0;
+  if (! args_info->staticProps_group_counter)
+    return;
   
-
-  args_info->help_given = 0 ;
-  args_info->version_given = 0 ;
-  args_info->input_given = 0 ;
-  args_info->output_given = 0 ;
-  args_info->step_given = 0 ;
-  args_info->nrbins_given = 0 ;
-  args_info->nanglebins_given = 0 ;
-  args_info->length_given = 0 ;
-  args_info->sele1_given = 0 ;
-  args_info->sele2_given = 0 ;
-  args_info->sele3_given = 0 ;
-  args_info->refsele_given = 0 ;
-  args_info->molname_given = 0 ;
-  args_info->begin_given = 0 ;
-  args_info->end_given = 0 ;
+  args_info->bo_given = 0 ;
+  args_info->bor_given = 0 ;
+  args_info->bad_given = 0 ;
   args_info->gofr_given = 0 ;
   args_info->r_theta_given = 0 ;
   args_info->r_omega_given = 0 ;
   args_info->theta_omega_given = 0 ;
   args_info->gxyz_given = 0 ;
   args_info->p2_given = 0 ;
+  args_info->rp2_given = 0 ;
   args_info->scd_given = 0 ;
   args_info->density_given = 0 ;
-#define clear_args() { \
-  args_info->input_arg = NULL; \
-  args_info->output_arg = NULL; \
-  args_info->step_arg = 1 ;\
-  args_info->nrbins_arg = 100 ;\
-  args_info->nanglebins_arg = 50 ;\
-  args_info->sele1_arg = NULL; \
-  args_info->sele2_arg = NULL; \
-  args_info->sele3_arg = NULL; \
-  args_info->refsele_arg = NULL; \
-  args_info->molname_arg = NULL; \
+  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;
 }
 
-  clear_args();
+int
+cmdline_parser (int argc, char * const *argv, struct gengetopt_args_info *args_info)
+{
+  return cmdline_parser2 (argc, argv, args_info, 0, 1, 1);
+}
 
+int
+cmdline_parser2 (int argc, char * const *argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required)
+{
+  int result;
+
+  result = cmdline_parser_internal (argc, argv, args_info, override, initialize, check_required, NULL);
+
+  if (result == EXIT_FAILURE)
+    {
+      cmdline_parser_free (args_info);
+      exit (EXIT_FAILURE);
+    }
+  
+  return result;
+}
+
+int
+cmdline_parser_required (struct gengetopt_args_info *args_info, const char *prog_name)
+{
+  int result = EXIT_SUCCESS;
+
+  if (cmdline_parser_required2(args_info, prog_name, NULL) > 0)
+    result = EXIT_FAILURE;
+
+  if (result == EXIT_FAILURE)
+    {
+      cmdline_parser_free (args_info);
+      exit (EXIT_FAILURE);
+    }
+  
+  return result;
+}
+
+int
+cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error)
+{
+  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;
+}
+
+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)
+{
+  int c;	/* Character of the parsed option.  */
+
+  int error = 0;
+  struct gengetopt_args_info local_args_info;
+
+  if (initialize)
+    cmdline_parser_init (args_info);
+
+  cmdline_parser_init (&local_args_info);
+
   optarg = 0;
-  optind = 1;
+  optind = 0;
   opterr = 1;
   optopt = '?';
 
@@ -139,9 +723,13 @@ cmdline_parser (int argc, char * const *argv, struct g
         { "input",	1, NULL, 'i' },
         { "output",	1, NULL, 'o' },
         { "step",	1, NULL, 'n' },
-        { "nrbins",	1, NULL, 'r' },
+        { "nbins",	1, NULL, 'b' },
+        { "nbins_x",	1, NULL, 'x' },
+        { "nbins_y",	1, NULL, 'y' },
         { "nanglebins",	1, NULL, 'a' },
-        { "length",	1, NULL, 'l' },
+        { "length",	1, NULL, 0 },
+        { "rcut",	1, NULL, 'c' },
+        { "zoffset",	1, NULL, 'z' },
         { "sele1",	1, NULL, 0 },
         { "sele2",	1, NULL, 0 },
         { "sele3",	1, NULL, 0 },
@@ -149,337 +737,722 @@ cmdline_parser (int argc, char * const *argv, struct g
         { "molname",	1, NULL, 0 },
         { "begin",	1, NULL, 0 },
         { "end",	1, NULL, 0 },
-        { "gofr",	0, NULL, 0 },
+        { "radius",	1, NULL, 0 },
+        { "bo",	0, NULL, 0 },
+        { "bor",	0, NULL, 0 },
+        { "bad",	0, NULL, 0 },
+        { "gofr",	0, NULL, 'g' },
         { "r_theta",	0, NULL, 0 },
         { "r_omega",	0, NULL, 0 },
         { "theta_omega",	0, NULL, 0 },
         { "gxyz",	0, NULL, 0 },
-        { "p2",	0, NULL, 0 },
-        { "scd",	0, NULL, 0 },
-        { "density",	0, NULL, 0 },
+        { "p2",	0, NULL, 'p' },
+        { "rp2",	0, NULL, 0 },
+        { "scd",	0, NULL, 's' },
+        { "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:r:a:l:", 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.  */
 
       switch (c)
         {
         case 'h':	/* Print help and exit.  */
-          clear_args ();
           cmdline_parser_print_help ();
+          cmdline_parser_free (&local_args_info);
           exit (EXIT_SUCCESS);
 
         case 'V':	/* Print version and exit.  */
-          clear_args ();
           cmdline_parser_print_version ();
+          cmdline_parser_free (&local_args_info);
           exit (EXIT_SUCCESS);
 
         case 'i':	/* input dump file.  */
-          if (args_info->input_given)
+          if (local_args_info.input_given)
             {
-              fprintf (stderr, "%s: `--input' (`-i') option given more than once\n", CMDLINE_PARSER_PACKAGE);
-              clear_args ();
-              exit (EXIT_FAILURE);
+              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);
           break;
 
         case 'o':	/* output file name.  */
-          if (args_info->output_given)
+          if (local_args_info.output_given)
             {
-              fprintf (stderr, "%s: `--output' (`-o') option given more than once\n", CMDLINE_PARSER_PACKAGE);
-              clear_args ();
-              exit (EXIT_FAILURE);
+              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;
 
         case 'n':	/* process every n frame.  */
-          if (args_info->step_given)
+          if (local_args_info.step_given)
             {
-              fprintf (stderr, "%s: `--step' (`-n') option given more than once\n", CMDLINE_PARSER_PACKAGE);
-              clear_args ();
-              exit (EXIT_FAILURE);
+              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);
+          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);
+            goto failure;
+          }
+          if (args_info->step_orig)
+            free (args_info->step_orig); /* free previous string */
+          args_info->step_orig = gengetopt_strdup (optarg);
           break;
 
-        case 'r':	/* number of bins for distance.  */
-          if (args_info->nrbins_given)
+        case 'b':	/* number of bins (general purpose).  */
+          if (local_args_info.nbins_given)
             {
-              fprintf (stderr, "%s: `--nrbins' (`-r') option given more than once\n", CMDLINE_PARSER_PACKAGE);
-              clear_args ();
-              exit (EXIT_FAILURE);
+              fprintf (stderr, "%s: `--nbins' (`-b') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
+              goto failure;
             }
-          args_info->nrbins_given = 1;
-          args_info->nrbins_arg = strtol (optarg,&stop_char,0);
+          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);
+            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);
+            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);
+            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 (args_info->nanglebins_given)
+          if (local_args_info.nanglebins_given)
             {
-              fprintf (stderr, "%s: `--nanglebins' (`-a') option given more than once\n", CMDLINE_PARSER_PACKAGE);
-              clear_args ();
-              exit (EXIT_FAILURE);
+              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);
+          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);
+            goto failure;
+          }
+          if (args_info->nanglebins_orig)
+            free (args_info->nanglebins_orig); /* free previous string */
+          args_info->nanglebins_orig = gengetopt_strdup (optarg);
           break;
 
-        case 'l':	/* maximum length (Defaults to 1/2 smallest length of first frame).  */
-          if (args_info->length_given)
+        case 'c':	/* cutoff radius (rcut).  */
+          if (local_args_info.rcut_given)
             {
-              fprintf (stderr, "%s: `--length' (`-l') option given more than once\n", CMDLINE_PARSER_PACKAGE);
-              clear_args ();
-              exit (EXIT_FAILURE);
+              fprintf (stderr, "%s: `--rcut' (`-c') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
+              goto failure;
             }
-          args_info->length_given = 1;
-          args_info->length_arg = strtod (optarg, NULL);
+          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);
+            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);
+            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;
+          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;
+          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;
+          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;
+          break;
+
+
         case 0:	/* Long option with no short option */
+          /* maximum length (Defaults to 1/2 smallest length of first frame).  */
+          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);
+              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.  */
-          if (strcmp (long_options[option_index].name, "sele1") == 0)
+          else if (strcmp (long_options[option_index].name, "sele1") == 0)
           {
-            if (args_info->sele1_given)
+            if (local_args_info.sele1_given)
               {
-                fprintf (stderr, "%s: `--sele1' option given more than once\n", CMDLINE_PARSER_PACKAGE);
-                clear_args ();
-                exit (EXIT_FAILURE);
+                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);
-            break;
+            if (args_info->sele1_orig)
+              free (args_info->sele1_orig); /* free previous string */
+            args_info->sele1_orig = gengetopt_strdup (optarg);
           }
-          
           /* select the second stuntdouble set.  */
           else if (strcmp (long_options[option_index].name, "sele2") == 0)
           {
-            if (args_info->sele2_given)
+            if (local_args_info.sele2_given)
               {
-                fprintf (stderr, "%s: `--sele2' option given more than once\n", CMDLINE_PARSER_PACKAGE);
-                clear_args ();
-                exit (EXIT_FAILURE);
+                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);
-            break;
+            if (args_info->sele2_orig)
+              free (args_info->sele2_orig); /* free previous string */
+            args_info->sele2_orig = gengetopt_strdup (optarg);
           }
-          
           /* select the third stuntdouble set.  */
           else if (strcmp (long_options[option_index].name, "sele3") == 0)
           {
-            if (args_info->sele3_given)
+            if (local_args_info.sele3_given)
               {
-                fprintf (stderr, "%s: `--sele3' option given more than once\n", CMDLINE_PARSER_PACKAGE);
-                clear_args ();
-                exit (EXIT_FAILURE);
+                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);
-            break;
+            if (args_info->sele3_orig)
+              free (args_info->sele3_orig); /* free previous string */
+            args_info->sele3_orig = gengetopt_strdup (optarg);
           }
-          
           /* select reference (use and only use with --gxyz).  */
           else if (strcmp (long_options[option_index].name, "refsele") == 0)
           {
-            if (args_info->refsele_given)
+            if (local_args_info.refsele_given)
               {
-                fprintf (stderr, "%s: `--refsele' option given more than once\n", CMDLINE_PARSER_PACKAGE);
-                clear_args ();
-                exit (EXIT_FAILURE);
+                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);
-            break;
+            if (args_info->refsele_orig)
+              free (args_info->refsele_orig); /* free previous string */
+            args_info->refsele_orig = gengetopt_strdup (optarg);
           }
-          
           /* molecule name.  */
           else if (strcmp (long_options[option_index].name, "molname") == 0)
           {
-            if (args_info->molname_given)
+            if (local_args_info.molname_given)
               {
-                fprintf (stderr, "%s: `--molname' option given more than once\n", CMDLINE_PARSER_PACKAGE);
-                clear_args ();
-                exit (EXIT_FAILURE);
+                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);
-            break;
+            if (args_info->molname_orig)
+              free (args_info->molname_orig); /* free previous string */
+            args_info->molname_orig = gengetopt_strdup (optarg);
           }
-          
-          /* begin interanl index.  */
+          /* begin internal index.  */
           else if (strcmp (long_options[option_index].name, "begin") == 0)
           {
-            if (args_info->begin_given)
+            if (local_args_info.begin_given)
               {
-                fprintf (stderr, "%s: `--begin' option given more than once\n", CMDLINE_PARSER_PACKAGE);
-                clear_args ();
-                exit (EXIT_FAILURE);
+                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);
-            break;
+            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);
+              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 (args_info->end_given)
+            if (local_args_info.end_given)
               {
-                fprintf (stderr, "%s: `--end' option given more than once\n", CMDLINE_PARSER_PACKAGE);
-                clear_args ();
-                exit (EXIT_FAILURE);
+                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);
+            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);
+              goto failure;
+            }
+            if (args_info->end_orig)
+              free (args_info->end_orig); /* free previous string */
+            args_info->end_orig = gengetopt_strdup (optarg);
+          }
+          /* 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)
+              {
+                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;
           }
-          
-          /* g(r).  */
-          else if (strcmp (long_options[option_index].name, "gofr") == 0)
+          /* 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->gofr_given)
+            if (local_args_info.bor_given)
               {
-                fprintf (stderr, "%s: `--gofr' option given more than once\n", CMDLINE_PARSER_PACKAGE);
-                clear_args ();
-                exit (EXIT_FAILURE);
+                fprintf (stderr, "%s: `--bor' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
+                goto failure;
               }
-            args_info->gofr_given = 1; staticProps_group_counter += 1;
-          
+            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(r, cos(theta)).  */
           else if (strcmp (long_options[option_index].name, "r_theta") == 0)
           {
-            if (args_info->r_theta_given)
+            if (local_args_info.r_theta_given)
               {
-                fprintf (stderr, "%s: `--r_theta' option given more than once\n", CMDLINE_PARSER_PACKAGE);
-                clear_args ();
-                exit (EXIT_FAILURE);
+                fprintf (stderr, "%s: `--r_theta' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
+                goto failure;
               }
-            args_info->r_theta_given = 1; staticProps_group_counter += 1;
-          
+            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;
           }
-          
           /* g(r, cos(omega)).  */
           else if (strcmp (long_options[option_index].name, "r_omega") == 0)
           {
-            if (args_info->r_omega_given)
+            if (local_args_info.r_omega_given)
               {
-                fprintf (stderr, "%s: `--r_omega' option given more than once\n", CMDLINE_PARSER_PACKAGE);
-                clear_args ();
-                exit (EXIT_FAILURE);
+                fprintf (stderr, "%s: `--r_omega' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
+                goto failure;
               }
-            args_info->r_omega_given = 1; staticProps_group_counter += 1;
-          
+            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;
           }
-          
           /* g(cos(theta), cos(omega)).  */
           else if (strcmp (long_options[option_index].name, "theta_omega") == 0)
           {
-            if (args_info->theta_omega_given)
+            if (local_args_info.theta_omega_given)
               {
-                fprintf (stderr, "%s: `--theta_omega' option given more than once\n", CMDLINE_PARSER_PACKAGE);
-                clear_args ();
-                exit (EXIT_FAILURE);
+                fprintf (stderr, "%s: `--theta_omega' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
+                goto failure;
               }
-            args_info->theta_omega_given = 1; staticProps_group_counter += 1;
-          
+            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;
           }
-          
           /* g(x, y, z).  */
           else if (strcmp (long_options[option_index].name, "gxyz") == 0)
           {
-            if (args_info->gxyz_given)
+            if (local_args_info.gxyz_given)
               {
-                fprintf (stderr, "%s: `--gxyz' option given more than once\n", CMDLINE_PARSER_PACKAGE);
-                clear_args ();
-                exit (EXIT_FAILURE);
+                fprintf (stderr, "%s: `--gxyz' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
+                goto failure;
               }
-            args_info->gxyz_given = 1; staticProps_group_counter += 1;
-          
+            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;
           }
-          
-          /* p2 order parameter (--sele1 and --sele2 must be specified).  */
-          else if (strcmp (long_options[option_index].name, "p2") == 0)
+          /* rp2 order parameter (--sele1 and --sele2 must be specified).  */
+          else if (strcmp (long_options[option_index].name, "rp2") == 0)
           {
-            if (args_info->p2_given)
+            if (local_args_info.rp2_given)
               {
-                fprintf (stderr, "%s: `--p2' option given more than once\n", CMDLINE_PARSER_PACKAGE);
-                clear_args ();
-                exit (EXIT_FAILURE);
+                fprintf (stderr, "%s: `--rp2' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
+                goto failure;
               }
-            args_info->p2_given = 1; staticProps_group_counter += 1;
-          
+            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;
           }
-          
-          /* scd order parameter(either --sele1, --sele2, --sele3 are specified or --molname, --begin, --end are specified).  */
-          else if (strcmp (long_options[option_index].name, "scd") == 0)
+          /* slab density.  */
+          else if (strcmp (long_options[option_index].name, "slab_density") == 0)
           {
-            if (args_info->scd_given)
+            if (local_args_info.slab_density_given)
               {
-                fprintf (stderr, "%s: `--scd' option given more than once\n", CMDLINE_PARSER_PACKAGE);
-                clear_args ();
-                exit (EXIT_FAILURE);
+                fprintf (stderr, "%s: `--slab_density' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
+                goto failure;
               }
-            args_info->scd_given = 1; staticProps_group_counter += 1;
-          
+            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;
           }
-          
-          /* density plot (--sele1 must be specified).  */
-          else if (strcmp (long_options[option_index].name, "density") == 0)
+          /* hxy.  */
+          else if (strcmp (long_options[option_index].name, "hxy") == 0)
           {
-            if (args_info->density_given)
+            if (local_args_info.hxy_given)
               {
-                fprintf (stderr, "%s: `--density' option given more than once\n", CMDLINE_PARSER_PACKAGE);
-                clear_args ();
-                exit (EXIT_FAILURE);
+                fprintf (stderr, "%s: `--hxy' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
+                goto failure;
               }
-            args_info->density_given = 1; staticProps_group_counter += 1;
-          
+            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;
           }
+          /* 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.  */
           /* `getopt_long' already printed an error message.  */
-          exit (EXIT_FAILURE);
+          goto failure;
 
         default:	/* bug: option not considered.  */
-          fprintf (stderr, "%s: option unknown: %c\n", CMDLINE_PARSER_PACKAGE, c);
+          fprintf (stderr, "%s: option unknown: %c%s\n", CMDLINE_PARSER_PACKAGE, c, (additional_error ? additional_error : ""));
           abort ();
         } /* switch */
     } /* while */
 
-  if ( staticProps_group_counter != 1)
+  if (args_info->staticProps_group_counter > 1)
     {
-      fprintf (stderr, "%s: %d options of group staticProps were given. One is required\n", CMDLINE_PARSER_PACKAGE, staticProps_group_counter);
-      missing_required_options = 1;
+      fprintf (stderr, "%s: %d options of group staticProps were given. One is required.%s\n", argv[0], args_info->staticProps_group_counter, (additional_error ? additional_error : ""));
+      error = 1;
     }
   
 
-  if (! args_info->input_given)
+
+  if (check_required)
     {
-      fprintf (stderr, "%s: '--input' ('-i') option required\n", CMDLINE_PARSER_PACKAGE);
-      missing_required_options = 1;
+      error += cmdline_parser_required2 (args_info, argv[0], additional_error);
     }
-  if ( missing_required_options )
-    exit (EXIT_FAILURE);
 
+  cmdline_parser_release (&local_args_info);
+
+  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:
+  
+  cmdline_parser_release (&local_args_info);
+  return (EXIT_FAILURE);
 }