--- trunk/src/applications/staticProps/StaticPropsCmd.c	2009/11/25 20:02:06	1390
+++ trunk/src/applications/staticProps/StaticPropsCmd.c	2010/03/22 19:21:22	1413
@@ -1,7 +1,7 @@
 /*
   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:
@@ -23,7 +23,7 @@ const char *gengetopt_args_info_purpose = "";
 
 const char *gengetopt_args_info_purpose = "";
 
-const char *gengetopt_args_info_usage = "Usage: StaticProps [OPTIONS]...";
+const char *gengetopt_args_info_usage = "Usage: StaticProps [OPTIONS]... [FILES]...";
 
 const char *gengetopt_args_info_description = "";
 
@@ -64,6 +64,7 @@ const char *gengetopt_args_info_help[] = {
   "  -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",
@@ -129,6 +130,7 @@ 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 ;
@@ -214,9 +216,10 @@ void init_args_info(struct gengetopt_args_info *args_i
   args_info->scd_help = gengetopt_args_info_help[33] ;
   args_info->density_help = gengetopt_args_info_help[34] ;
   args_info->slab_density_help = gengetopt_args_info_help[35] ;
-  args_info->hxy_help = gengetopt_args_info_help[36] ;
-  args_info->rho_r_help = gengetopt_args_info_help[37] ;
-  args_info->hullvol_help = gengetopt_args_info_help[38] ;
+  args_info->p_angle_help = gengetopt_args_info_help[36] ;
+  args_info->hxy_help = gengetopt_args_info_help[37] ;
+  args_info->rho_r_help = gengetopt_args_info_help[38] ;
+  args_info->hullvol_help = gengetopt_args_info_help[39] ;
   
 }
 
@@ -256,6 +259,9 @@ 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
@@ -294,7 +300,7 @@ cmdline_parser_release (struct gengetopt_args_info *ar
 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));
@@ -324,7 +330,12 @@ cmdline_parser_release (struct gengetopt_args_info *ar
   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);
 }
 
@@ -421,6 +432,8 @@ cmdline_parser_dump(FILE *outfile, struct gengetopt_ar
     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)
@@ -494,6 +507,7 @@ 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 ;
@@ -772,6 +786,7 @@ 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 },
@@ -1270,6 +1285,23 @@ cmdline_parser_internal (int argc, char * const *argv,
                 &(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;
           
@@ -1355,6 +1387,30 @@ 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: