--- trunk/src/applications/dynamicProps/DynamicPropsCmd.c	2006/12/14 19:38:56	1098
+++ trunk/src/applications/dynamicProps/DynamicPropsCmd.c	2007/01/03 20:47:00	1112
@@ -1,7 +1,7 @@
 /*
   File autogenerated by gengetopt version 2.15
   generated with the following command:
-  gengetopt -i DynamicProps.ggo --file-name=DynamicPropsCmd 
+  gengetopt -u -i DynamicProps.ggo -F DynamicPropsCmd 
 
   The developers of gengetopt consider the fixed text that goes in all
   gengetopt output files to be in the public domain:
@@ -50,6 +50,7 @@ void clear_given (struct gengetopt_args_info *args_inf
   args_info->dcorr_given = 0 ;
   args_info->lcorr_given = 0 ;
   args_info->r_rcorr_given = 0 ;
+  args_info->thetacorr_given = 0 ;
   args_info->dynamicProps_group_counter = 0 ;
 }
 
@@ -78,7 +79,7 @@ cmdline_parser_print_help (void)
 cmdline_parser_print_help (void)
 {
   cmdline_parser_print_version ();
-  printf("\nUsage: DynamicProps [OPTIONS]...\n\n");
+  printf("\nUsage: DynamicProps [OPTIONS]... [FILES]...\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");
@@ -92,6 +93,7 @@ cmdline_parser_print_help (void)
   printf("%s\n","  -d, --dcorr                   dipole correlation function");
   printf("%s\n","  -l, --lcorr                   Lengendre correlation function");
   printf("%s\n","      --r_rcorr                 Radial rmsd");
+  printf("%s\n","      --thetacorr               Angular rmsd");
   
 }
 
@@ -100,12 +102,16 @@ cmdline_parser_init (struct gengetopt_args_info *args_
 {
   clear_given (args_info);
   clear_args (args_info);
+
+  args_info->inputs = NULL;
+  args_info->inputs_num = 0;
 }
 
 static void
 cmdline_parser_release (struct gengetopt_args_info *args_info)
 {
   
+  unsigned int i;
   if (args_info->input_arg)
     {
       free (args_info->input_arg); /* free previous argument */
@@ -151,7 +157,13 @@ cmdline_parser_release (struct gengetopt_args_info *ar
       free (args_info->order_orig); /* free previous argument */
       args_info->order_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);
 }
 
@@ -225,6 +237,9 @@ cmdline_parser_file_save(const char *filename, struct 
   if (args_info->r_rcorr_given) {
     fprintf(outfile, "%s\n", "r_rcorr");
   }
+  if (args_info->thetacorr_given) {
+    fprintf(outfile, "%s\n", "thetacorr");
+  }
   
   fclose (outfile);
 
@@ -269,6 +284,7 @@ reset_group_dynamicProps(struct gengetopt_args_info *a
   args_info->dcorr_given = 0 ;
   args_info->lcorr_given = 0 ;
   args_info->r_rcorr_given = 0 ;
+  args_info->thetacorr_given = 0 ;
 
   args_info->dynamicProps_group_counter = 0;
 }
@@ -368,6 +384,7 @@ cmdline_parser_internal (int argc, char * const *argv,
         { "dcorr",	0, NULL, 'd' },
         { "lcorr",	0, NULL, 'l' },
         { "r_rcorr",	0, NULL, 0 },
+        { "thetacorr",	0, NULL, 0 },
         { NULL,	0, NULL, 0 }
       };
 
@@ -562,6 +579,23 @@ cmdline_parser_internal (int argc, char * const *argv,
             args_info->dynamicProps_group_counter += 1;
             break;
           }
+          /* Angular rmsd.  */
+          else if (strcmp (long_options[option_index].name, "thetacorr") == 0)
+          {
+            if (local_args_info.thetacorr_given)
+              {
+                fprintf (stderr, "%s: `--thetacorr' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
+                goto failure;
+              }
+            if (args_info->thetacorr_given && ! override)
+              continue;
+            local_args_info.thetacorr_given = 1;
+            args_info->thetacorr_given = 1;
+            if (args_info->dynamicProps_group_counter && override)
+              reset_group_dynamicProps (args_info);
+            args_info->dynamicProps_group_counter += 1;
+            break;
+          }
           
           break;
         case '?':	/* Invalid option.  */
@@ -592,6 +626,17 @@ cmdline_parser_internal (int argc, char * const *argv,
   if ( error )
     return (EXIT_FAILURE);
 
+  if (optind < argc)
+    {
+      int i = 0 ;
+
+      args_info->inputs_num = argc - optind ;
+      args_info->inputs =
+        (char **)(malloc ((args_info->inputs_num)*sizeof(char *))) ;
+      while (optind < argc)
+        args_info->inputs[ i++ ] = gengetopt_strdup (argv[optind++]) ;
+    }
+
   return 0;
 
 failure: