--- trunk/src/applications/nanoparticleBuilder/nanoparticleBuilderCmd.c	2009/11/25 20:02:06	1390
+++ branches/development/src/applications/nanoparticleBuilder/nanoparticleBuilderCmd.cpp	2011/10/03 20:32:45	1655
@@ -1,7 +1,7 @@
 /*
-  File autogenerated by gengetopt version 2.22
+  File autogenerated by gengetopt version 2.22.4
   generated with the following command:
-  gengetopt -u -F nanoparticleBuilderCmd 
+  gengetopt -F nanoparticleBuilderCmd -u 
 
   The developers of gengetopt consider the fixed text that goes in all
   gengetopt output files to be in the public domain:
@@ -17,8 +17,12 @@
 #include <stdlib.h>
 #include <string.h>
 
-#include "getopt.h"
+#ifndef FIX_UNUSED
+#define FIX_UNUSED(X) (void) (X) /* avoid warnings for unused params */
+#endif
 
+#include <getopt.h>
+
 #include "nanoparticleBuilderCmd.h"
 
 const char *gengetopt_args_info_purpose = "Builds spherical random or core-shell nanoparticles and outputs an OpenMD \nstartup file";
@@ -52,7 +56,7 @@ static int
 void clear_args (struct gengetopt_args_info *args_info);
 
 static int
-cmdline_parser_internal (int argc, char * const *argv, struct gengetopt_args_info *args_info,
+cmdline_parser_internal (int argc, char **argv, struct gengetopt_args_info *args_info,
                         struct cmdline_parser_params *params, const char *additional_error);
 
 static int
@@ -79,6 +83,7 @@ void clear_args (struct gengetopt_args_info *args_info
 static
 void clear_args (struct gengetopt_args_info *args_info)
 {
+  FIX_UNUSED (args_info);
   args_info->output_arg = NULL;
   args_info->output_orig = NULL;
   args_info->latticeConstant_orig = NULL;
@@ -104,11 +109,11 @@ void init_args_info(struct gengetopt_args_info *args_i
   args_info->latticeConstant_help = gengetopt_args_info_help[3] ;
   args_info->radius_help = gengetopt_args_info_help[4] ;
   args_info->shellRadius_help = gengetopt_args_info_help[5] ;
-  args_info->shellRadius_min = -1;
-  args_info->shellRadius_max = -1;
+  args_info->shellRadius_min = 0;
+  args_info->shellRadius_max = 0;
   args_info->molFraction_help = gengetopt_args_info_help[6] ;
-  args_info->molFraction_min = -1;
-  args_info->molFraction_max = -1;
+  args_info->molFraction_min = 0;
+  args_info->molFraction_max = 0;
   args_info->vacancyPercent_help = gengetopt_args_info_help[7] ;
   args_info->vacancyInnerRadius_help = gengetopt_args_info_help[8] ;
   args_info->vacancyOuterRadius_help = gengetopt_args_info_help[9] ;
@@ -118,7 +123,9 @@ cmdline_parser_print_version (void)
 void
 cmdline_parser_print_version (void)
 {
-  printf ("%s %s\n", CMDLINE_PARSER_PACKAGE, CMDLINE_PARSER_VERSION);
+  printf ("%s %s\n",
+     (strlen(CMDLINE_PARSER_PACKAGE_NAME) ? CMDLINE_PARSER_PACKAGE_NAME : CMDLINE_PARSER_PACKAGE),
+     CMDLINE_PARSER_VERSION);
 }
 
 static void print_help_common(void) {
@@ -133,7 +140,7 @@ static void print_help_common(void) {
   printf("\n");
 
   if (strlen(gengetopt_args_info_description) > 0)
-    printf("%s\n", gengetopt_args_info_description);
+    printf("%s\n\n", gengetopt_args_info_description);
 }
 
 void
@@ -152,7 +159,7 @@ cmdline_parser_init (struct gengetopt_args_info *args_
   clear_args (args_info);
   init_args_info (args_info);
 
-  args_info->inputs = NULL;
+  args_info->inputs = 0;
   args_info->inputs_num = 0;
 }
 
@@ -192,6 +199,7 @@ union generic_value {
 union generic_value {
     double double_arg;
     char *string_arg;
+    const char *default_string_arg;
 };
 
 /** @brief holds temporary values for multiple options */
@@ -209,22 +217,24 @@ static void add_node(struct generic_list **list) {
   struct generic_list *new_node = (struct generic_list *) malloc (sizeof (struct generic_list));
   new_node->next = *list;
   *list = new_node;
-  new_node->arg.string_arg = NULL;
-  new_node->orig = NULL;
+  new_node->arg.string_arg = 0;
+  new_node->orig = 0;
 }
 
+/**
+ * The passed arg parameter is NOT set to 0 from this function
+ */
 static void
-free_multiple_field(unsigned int len, void **arg, char ***orig)
+free_multiple_field(unsigned int len, void *arg, char ***orig)
 {
   unsigned int i;
-  if (*arg) {
+  if (arg) {
     for (i = 0; i < len; ++i)
       {
         free_string_field(&((*orig)[i]));
       }
 
-    free (*arg);
-    *arg = 0;
+    free (arg);
     free (*orig);
     *orig = 0;
   }
@@ -239,8 +249,10 @@ cmdline_parser_release (struct gengetopt_args_info *ar
   free_string_field (&(args_info->output_orig));
   free_string_field (&(args_info->latticeConstant_orig));
   free_string_field (&(args_info->radius_orig));
-  free_multiple_field (args_info->shellRadius_given, (void **)&(args_info->shellRadius_arg), &(args_info->shellRadius_orig));
-  free_multiple_field (args_info->molFraction_given, (void **)&(args_info->molFraction_arg), &(args_info->molFraction_orig));
+  free_multiple_field (args_info->shellRadius_given, (void *)(args_info->shellRadius_arg), &(args_info->shellRadius_orig));
+  args_info->shellRadius_arg = 0;
+  free_multiple_field (args_info->molFraction_given, (void *)(args_info->molFraction_arg), &(args_info->molFraction_orig));
+  args_info->molFraction_arg = 0;
   free_string_field (&(args_info->vacancyPercent_orig));
   free_string_field (&(args_info->vacancyInnerRadius_orig));
   free_string_field (&(args_info->vacancyOuterRadius_orig));
@@ -257,8 +269,9 @@ static void
 
 
 static void
-write_into_file(FILE *outfile, const char *opt, const char *arg, char *values[])
+write_into_file(FILE *outfile, const char *opt, const char *arg, const char *values[])
 {
+  FIX_UNUSED (values);
   if (arg) {
     fprintf(outfile, "%s=\"%s\"\n", opt, arg);
   } else {
@@ -267,7 +280,7 @@ static void
 }
 
 static void
-write_multiple_into_file(FILE *outfile, int len, const char *opt, char **arg, char *values[])
+write_multiple_into_file(FILE *outfile, int len, const char *opt, char **arg, const char *values[])
 {
   int i;
   
@@ -340,7 +353,7 @@ gengetopt_strdup (const char *s)
 char *
 gengetopt_strdup (const char *s)
 {
-  char *result = NULL;
+  char *result = 0;
   if (!s)
     return result;
 
@@ -354,11 +367,12 @@ get_multiple_arg_token(const char *arg)
 static char *
 get_multiple_arg_token(const char *arg)
 {
-  char *tok, *ret;
+  const char *tok;
+  char *ret;
   size_t len, num_of_escape, i, j;
 
   if (!arg)
-    return NULL;
+    return 0;
 
   tok = strchr (arg, ',');
   num_of_escape = 0;
@@ -402,13 +416,13 @@ get_multiple_arg_token(const char *arg)
   return ret;
 }
 
-static char *
+static const char *
 get_multiple_arg_token_next(const char *arg)
 {
-  char *tok;
+  const char *tok;
 
   if (!arg)
-    return NULL;
+    return 0;
 
   tok = strchr (arg, ',');
 
@@ -431,29 +445,29 @@ static int
 }
 
 static int
-check_multiple_option_occurrences(const char *prog_name, unsigned int option_given, int min, int max, const char *option_desc);
+check_multiple_option_occurrences(const char *prog_name, unsigned int option_given, unsigned int min, unsigned int max, const char *option_desc);
 
 int
-check_multiple_option_occurrences(const char *prog_name, unsigned int option_given, int min, int max, const char *option_desc)
+check_multiple_option_occurrences(const char *prog_name, unsigned int option_given, unsigned int min, unsigned int max, const char *option_desc)
 {
   int error = 0;
 
-  if (option_given && ! (min < 0 && max < 0))
+  if (option_given && (min > 0 || max > 0))
     {
-      if (min >= 0 && max >= 0)
+      if (min > 0 && max > 0)
         {
           if (min == max)
             {
               /* specific occurrences */
-              if (option_given != min)
+              if (option_given != (unsigned int) min)
                 {
                   fprintf (stderr, "%s: %s option occurrences must be %d\n",
                     prog_name, option_desc, min);
                   error = 1;
                 }
             }
-          else if (option_given < min
-              || option_given > max)
+          else if (option_given < (unsigned int) min
+                || option_given > (unsigned int) max)
             {
               /* range occurrences */
               fprintf (stderr, "%s: %s option occurrences must be between %d and %d\n",
@@ -461,7 +475,7 @@ check_multiple_option_occurrences(const char *prog_nam
               error = 1;
             }
         }
-      else if (min >= 0)
+      else if (min > 0)
         {
           /* at least check */
           if (option_given < min)
@@ -471,7 +485,7 @@ check_multiple_option_occurrences(const char *prog_nam
               error = 1;
             }
         }
-      else if (max >= 0)
+      else if (max > 0)
         {
           /* at most check */
           if (option_given > max)
@@ -486,17 +500,17 @@ int
   return error;
 }
 int
-cmdline_parser (int argc, char * const *argv, struct gengetopt_args_info *args_info)
+cmdline_parser (int argc, char **argv, struct gengetopt_args_info *args_info)
 {
   return cmdline_parser2 (argc, argv, args_info, 0, 1, 1);
 }
 
 int
-cmdline_parser_ext (int argc, char * const *argv, struct gengetopt_args_info *args_info,
+cmdline_parser_ext (int argc, char **argv, struct gengetopt_args_info *args_info,
                    struct cmdline_parser_params *params)
 {
   int result;
-  result = cmdline_parser_internal (argc, argv, args_info, params, NULL);
+  result = cmdline_parser_internal (argc, argv, args_info, params, 0);
 
   if (result == EXIT_FAILURE)
     {
@@ -508,7 +522,7 @@ int
 }
 
 int
-cmdline_parser2 (int argc, char * const *argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required)
+cmdline_parser2 (int argc, char **argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required)
 {
   int result;
   struct cmdline_parser_params params;
@@ -519,7 +533,7 @@ cmdline_parser2 (int argc, char * const *argv, struct 
   params.check_ambiguity = 0;
   params.print_errors = 1;
 
-  result = cmdline_parser_internal (argc, argv, args_info, &params, NULL);
+  result = cmdline_parser_internal (argc, argv, args_info, &params, 0);
 
   if (result == EXIT_FAILURE)
     {
@@ -535,7 +549,7 @@ cmdline_parser_required (struct gengetopt_args_info *a
 {
   int result = EXIT_SUCCESS;
 
-  if (cmdline_parser_required2(args_info, prog_name, NULL) > 0)
+  if (cmdline_parser_required2(args_info, prog_name, 0) > 0)
     result = EXIT_FAILURE;
 
   if (result == EXIT_FAILURE)
@@ -551,6 +565,7 @@ cmdline_parser_required2 (struct gengetopt_args_info *
 cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error)
 {
   int error = 0;
+  FIX_UNUSED (additional_error);
 
   /* checks for required options */
   if (! args_info->output_given)
@@ -607,7 +622,8 @@ int update_arg(void *field, char **orig_field,
 static
 int update_arg(void *field, char **orig_field,
                unsigned int *field_given, unsigned int *prev_given, 
-               char *value, char *possible_values[], const char *default_value,
+               char *value, const char *possible_values[],
+               const char *default_value,
                cmdline_parser_arg_type arg_type,
                int check_ambiguity, int override,
                int no_free, int multiple_option,
@@ -618,6 +634,7 @@ int update_arg(void *field, char **orig_field,
   const char *val = value;
   int found;
   char **string_field;
+  FIX_UNUSED (field);
 
   stop_char = 0;
   found = 0;
@@ -635,6 +652,7 @@ int update_arg(void *field, char **orig_field,
       return 1; /* failure */
     }
 
+  FIX_UNUSED (default_value);
     
   if (field_given && *field_given && ! override)
     return 0;
@@ -699,12 +717,14 @@ int update_multiple_arg_temp(struct generic_list **lis
 static
 int update_multiple_arg_temp(struct generic_list **list,
                unsigned int *prev_given, const char *val,
-               char *possible_values[], const char *default_value,
+               const char *possible_values[], const char *default_value,
                cmdline_parser_arg_type arg_type,
                const char *long_opt, char short_opt,
                const char *additional_error)
 {
-  char *multi_token, *multi_next; /* store single arguments */
+  /* store single arguments */
+  char *multi_token;
+  const char *multi_next;
 
   if (arg_type == ARG_NO) {
     (*prev_given)++;
@@ -816,14 +836,15 @@ void update_multiple_arg(void *field, char ***orig_fie
       }
       if (!(*orig_field)) {
         *orig_field = (char **) malloc (sizeof (char *));
-        (*orig_field)[0] = NULL;
+        (*orig_field)[0] = 0;
       }
     }
   }
 }
 
 int
-cmdline_parser_internal (int argc, char * const *argv, struct gengetopt_args_info *args_info,
+cmdline_parser_internal (
+  int argc, char **argv, struct gengetopt_args_info *args_info,
                         struct cmdline_parser_params *params, const char *additional_error)
 {
   int c;	/* Character of the parsed option.  */
@@ -870,7 +891,7 @@ cmdline_parser_internal (int argc, char * const *argv,
         { "vacancyPercent",	1, NULL, 0 },
         { "vacancyInnerRadius",	1, NULL, 0 },
         { "vacancyOuterRadius",	1, NULL, 0 },
-        { NULL,	0, NULL, 0 }
+        { 0,  0, 0, 0 }
       };
 
       c = getopt_long (argc, argv, "hVo:", long_options, &option_index);
@@ -1010,11 +1031,11 @@ cmdline_parser_internal (int argc, char * const *argv,
 
   update_multiple_arg((void *)&(args_info->shellRadius_arg),
     &(args_info->shellRadius_orig), args_info->shellRadius_given,
-    local_args_info.shellRadius_given, 0 , 
+    local_args_info.shellRadius_given, 0,
     ARG_DOUBLE, shellRadius_list);
   update_multiple_arg((void *)&(args_info->molFraction_arg),
     &(args_info->molFraction_orig), args_info->molFraction_given,
-    local_args_info.molFraction_given, 0 , 
+    local_args_info.molFraction_given, 0,
     ARG_DOUBLE, molFraction_list);
 
   args_info->shellRadius_given += local_args_info.shellRadius_given;