--- trunk/src/applications/dynamicProps/DynamicPropsCmd.c	2007/01/03 20:47:00	1112
+++ branches/development/src/applications/dynamicProps/DynamicPropsCmd.c	2010/07/09 23:08:25	1465
@@ -1,7 +1,7 @@
 /*
-  File autogenerated by gengetopt version 2.15
+  File autogenerated by gengetopt version 2.14
   generated with the following command:
-  gengetopt -u -i DynamicProps.ggo -F DynamicPropsCmd 
+  gengetopt -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:
@@ -51,6 +51,8 @@ void clear_given (struct gengetopt_args_info *args_inf
   args_info->lcorr_given = 0 ;
   args_info->r_rcorr_given = 0 ;
   args_info->thetacorr_given = 0 ;
+  args_info->drcorr_given = 0 ;
+  args_info->helfandEcorr_given = 0 ;
   args_info->dynamicProps_group_counter = 0 ;
 }
 
@@ -79,7 +81,7 @@ cmdline_parser_print_help (void)
 cmdline_parser_print_help (void)
 {
   cmdline_parser_print_version ();
-  printf("\nUsage: DynamicProps [OPTIONS]... [FILES]...\n\n");
+  printf("\nUsage: DynamicProps [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");
@@ -94,6 +96,8 @@ cmdline_parser_print_help (void)
   printf("%s\n","  -l, --lcorr                   Lengendre correlation function");
   printf("%s\n","      --r_rcorr                 Radial rmsd");
   printf("%s\n","      --thetacorr               Angular rmsd");
+  printf("%s\n","      --drcorr                  Directional rmsd for particles with unit \n                                  vectors");
+  printf("%s\n","      --helfandEcorr            Helfand moment for thermal conductvity");
   
 }
 
@@ -102,16 +106,12 @@ 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 */
@@ -157,12 +157,6 @@ 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);
 }
@@ -240,6 +234,12 @@ cmdline_parser_file_save(const char *filename, struct 
   if (args_info->thetacorr_given) {
     fprintf(outfile, "%s\n", "thetacorr");
   }
+  if (args_info->drcorr_given) {
+    fprintf(outfile, "%s\n", "drcorr");
+  }
+  if (args_info->helfandEcorr_given) {
+    fprintf(outfile, "%s\n", "helfandEcorr");
+  }
   
   fclose (outfile);
 
@@ -285,6 +285,8 @@ reset_group_dynamicProps(struct gengetopt_args_info *a
   args_info->lcorr_given = 0 ;
   args_info->r_rcorr_given = 0 ;
   args_info->thetacorr_given = 0 ;
+  args_info->drcorr_given = 0 ;
+  args_info->helfandEcorr_given = 0 ;
 
   args_info->dynamicProps_group_counter = 0;
 }
@@ -385,6 +387,8 @@ cmdline_parser_internal (int argc, char * const *argv,
         { "lcorr",	0, NULL, 'l' },
         { "r_rcorr",	0, NULL, 0 },
         { "thetacorr",	0, NULL, 0 },
+        { "drcorr",	0, NULL, 0 },
+        { "helfandEcorr",	0, NULL, 0 },
         { NULL,	0, NULL, 0 }
       };
 
@@ -553,11 +557,7 @@ cmdline_parser_internal (int argc, char * const *argv,
               continue;
             local_args_info.order_given = 1;
             args_info->order_given = 1;
-            args_info->order_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;
-            }
+            args_info->order_arg = strtol (optarg,&stop_char,0);
             if (args_info->order_orig)
               free (args_info->order_orig); /* free previous string */
             args_info->order_orig = gengetopt_strdup (optarg);
@@ -596,6 +596,40 @@ cmdline_parser_internal (int argc, char * const *argv,
             args_info->dynamicProps_group_counter += 1;
             break;
           }
+          /* Directional rmsd for particles with unit vectors.  */
+          else if (strcmp (long_options[option_index].name, "drcorr") == 0)
+          {
+            if (local_args_info.drcorr_given)
+              {
+                fprintf (stderr, "%s: `--drcorr' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
+                goto failure;
+              }
+            if (args_info->drcorr_given && ! override)
+              continue;
+            local_args_info.drcorr_given = 1;
+            args_info->drcorr_given = 1;
+            if (args_info->dynamicProps_group_counter && override)
+              reset_group_dynamicProps (args_info);
+            args_info->dynamicProps_group_counter += 1;
+            break;
+          }
+          /* Helfand moment for thermal conductvity.  */
+          else if (strcmp (long_options[option_index].name, "helfandEcorr") == 0)
+          {
+            if (local_args_info.helfandEcorr_given)
+              {
+                fprintf (stderr, "%s: `--helfandEcorr' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
+                goto failure;
+              }
+            if (args_info->helfandEcorr_given && ! override)
+              continue;
+            local_args_info.helfandEcorr_given = 1;
+            args_info->helfandEcorr_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.  */
@@ -626,17 +660,6 @@ 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: