--- trunk/src/applications/dynamicProps/DynamicPropsCmd.c	2007/10/02 12:05:25	1183
+++ branches/development/src/applications/dynamicProps/DynamicPropsCmd.c	2010/07/09 23:08:25	1465
@@ -1,7 +1,7 @@
 /*
-  File autogenerated by gengetopt version 2.16
+  File autogenerated by gengetopt version 2.14
   generated with the following command:
-  gengetopt -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:
@@ -51,8 +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->actioncorr_given = 0 ;
   args_info->drcorr_given = 0 ;
+  args_info->helfandEcorr_given = 0 ;
   args_info->dynamicProps_group_counter = 0 ;
 }
 
@@ -96,8 +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","      --actioncorr              Action correlation function");
   printf("%s\n","      --drcorr                  Directional rmsd for particles with unit \n                                  vectors");
+  printf("%s\n","      --helfandEcorr            Helfand moment for thermal conductvity");
   
 }
 
@@ -233,13 +233,13 @@ cmdline_parser_file_save(const char *filename, struct 
   }
   if (args_info->thetacorr_given) {
     fprintf(outfile, "%s\n", "thetacorr");
-  }
-  if (args_info->actioncorr_given) {
-    fprintf(outfile, "%s\n", "actioncorr");
   }
   if (args_info->drcorr_given) {
     fprintf(outfile, "%s\n", "drcorr");
   }
+  if (args_info->helfandEcorr_given) {
+    fprintf(outfile, "%s\n", "helfandEcorr");
+  }
   
   fclose (outfile);
 
@@ -285,8 +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->actioncorr_given = 0 ;
   args_info->drcorr_given = 0 ;
+  args_info->helfandEcorr_given = 0 ;
 
   args_info->dynamicProps_group_counter = 0;
 }
@@ -364,7 +364,7 @@ cmdline_parser_internal (int argc, char * const *argv,
   cmdline_parser_init (&local_args_info);
 
   optarg = 0;
-  optind = 0;
+  optind = 1;
   opterr = 1;
   optopt = '?';
 
@@ -387,8 +387,8 @@ cmdline_parser_internal (int argc, char * const *argv,
         { "lcorr",	0, NULL, 'l' },
         { "r_rcorr",	0, NULL, 0 },
         { "thetacorr",	0, NULL, 0 },
-        { "actioncorr",	0, NULL, 0 },
         { "drcorr",	0, NULL, 0 },
+        { "helfandEcorr",	0, NULL, 0 },
         { NULL,	0, NULL, 0 }
       };
 
@@ -557,11 +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);
@@ -595,23 +591,6 @@ cmdline_parser_internal (int argc, char * const *argv,
               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;
-          }
-          /* Action correlation function.  */
-          else if (strcmp (long_options[option_index].name, "actioncorr") == 0)
-          {
-            if (local_args_info.actioncorr_given)
-              {
-                fprintf (stderr, "%s: `--actioncorr' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
-                goto failure;
-              }
-            if (args_info->actioncorr_given && ! override)
-              continue;
-            local_args_info.actioncorr_given = 1;
-            args_info->actioncorr_given = 1;
             if (args_info->dynamicProps_group_counter && override)
               reset_group_dynamicProps (args_info);
             args_info->dynamicProps_group_counter += 1;
@@ -634,6 +613,23 @@ cmdline_parser_internal (int argc, char * const *argv,
             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.  */