--- trunk/src/applications/staticProps/StaticPropsCmd.cpp	2014/08/13 20:42:43	2015
+++ trunk/src/applications/staticProps/StaticPropsCmd.cpp	2014/10/31 18:40:40	2031
@@ -1,7 +1,7 @@
 /*
   File autogenerated by gengetopt version 2.22.4
   generated with the following command:
-  gengetopt --file-name=StaticPropsCmd --unamed-opts 
+  gengetopt -i StaticProps.ggo -F StaticPropsCmd -c cpp 
 
   The developers of gengetopt consider the fixed text that goes in all
   gengetopt output files to be in the public domain:
@@ -21,17 +21,13 @@
 #define FIX_UNUSED(X) (void) (X) /* avoid warnings for unused params */
 #endif
 
-#ifdef WIN32
-#include "utils/wingetopt.h"
-#else
 #include <getopt.h>
-#endif
 
 #include "StaticPropsCmd.h"
 
 const char *gengetopt_args_info_purpose = "";
 
-const char *gengetopt_args_info_usage = "Usage: StaticProps [OPTIONS]... [FILES]...";
+const char *gengetopt_args_info_usage = "Usage: StaticProps [OPTIONS]...";
 
 const char *gengetopt_args_info_description = "";
 
@@ -97,6 +93,7 @@ const char *gengetopt_args_info_help[] = {
   "      --rnemdrt                 shell and angle-resolved RNEMD statistics \n                                  (temperature, density, angular velocity)",
   "      --nitrile                 electrostatic potential to frequency map based \n                                  on the Cho nitrile fits",
   "  -m, --multipole               average multipole moments contained within \n                                  cutoff spheres as a function of radius",
+  "      --surfDiffusion           X, Y, and R (surface diffusion if Z exposed and \n                                  bulk immobile) diffusion",
     0
 };
 
@@ -184,6 +181,7 @@ void clear_given (struct gengetopt_args_info *args_inf
   args_info->rnemdrt_given = 0 ;
   args_info->nitrile_given = 0 ;
   args_info->multipole_given = 0 ;
+  args_info->surfDiffusion_given = 0 ;
   args_info->staticProps_group_counter = 0 ;
 }
 
@@ -300,6 +298,7 @@ void init_args_info(struct gengetopt_args_info *args_i
   args_info->rnemdrt_help = gengetopt_args_info_help[58] ;
   args_info->nitrile_help = gengetopt_args_info_help[59] ;
   args_info->multipole_help = gengetopt_args_info_help[60] ;
+  args_info->surfDiffusion_help = gengetopt_args_info_help[61] ;
   
 }
 
@@ -341,9 +340,6 @@ cmdline_parser_init (struct gengetopt_args_info *args_
   clear_given (args_info);
   clear_args (args_info);
   init_args_info (args_info);
-
-  args_info->inputs = 0;
-  args_info->inputs_num = 0;
 }
 
 void
@@ -382,7 +378,7 @@ 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));
@@ -419,11 +415,6 @@ cmdline_parser_release (struct gengetopt_args_info *ar
   free_string_field (&(args_info->gaussWidth_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);
 }
@@ -572,6 +563,8 @@ cmdline_parser_dump(FILE *outfile, struct gengetopt_ar
     write_into_file(outfile, "nitrile", 0, 0 );
   if (args_info->multipole_given)
     write_into_file(outfile, "multipole", 0, 0 );
+  if (args_info->surfDiffusion_given)
+    write_into_file(outfile, "surfDiffusion", 0, 0 );
   
 
   i = EXIT_SUCCESS;
@@ -657,6 +650,7 @@ reset_group_staticProps(struct gengetopt_args_info *ar
   args_info->rnemdrt_given = 0 ;
   args_info->nitrile_given = 0 ;
   args_info->multipole_given = 0 ;
+  args_info->surfDiffusion_given = 0 ;
 
   args_info->staticProps_group_counter = 0;
 }
@@ -962,6 +956,7 @@ cmdline_parser_internal (
         { "rnemdrt",	0, NULL, 0 },
         { "nitrile",	0, NULL, 0 },
         { "multipole",	0, NULL, 'm' },
+        { "surfDiffusion",	0, NULL, 0 },
         { 0,  0, 0, 0 }
       };
 
@@ -1855,6 +1850,23 @@ cmdline_parser_internal (
                 &(local_args_info.nitrile_given), optarg, 0, 0, ARG_NO,
                 check_ambiguity, override, 0, 0,
                 "nitrile", '-',
+                additional_error))
+              goto failure;
+          
+          }
+          /* X, Y, and R (surface diffusion if Z exposed and bulk immobile) diffusion.  */
+          else if (strcmp (long_options[option_index].name, "surfDiffusion") == 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->surfDiffusion_given),
+                &(local_args_info.surfDiffusion_given), optarg, 0, 0, ARG_NO,
+                check_ambiguity, override, 0, 0,
+                "surfDiffusion", '-',
                 additional_error))
               goto failure;
           
@@ -1889,30 +1901,6 @@ cmdline_parser_internal (
   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: