--- trunk/src/applications/thermalizer/thermalizerCmd.c	2006/10/20 14:59:05	1083
+++ trunk/src/applications/thermalizer/thermalizerCmd.c	2009/11/25 20:02:06	1390
@@ -1,7 +1,7 @@
 /*
-  File autogenerated by gengetopt version 2.17
+  File autogenerated by gengetopt version 2.22
   generated with the following command:
-  gengetopt -F thermalizerCmd --unamed-opts 
+  gengetopt -u -F thermalizerCmd 
 
   The developers of gengetopt consider the fixed text that goes in all
   gengetopt output files to be in the public domain:
@@ -21,10 +21,12 @@
 
 #include "thermalizerCmd.h"
 
-const char *gengetopt_args_info_purpose = "Resamples the velocities for all the integrable objects in an OOPSE file from a \nMaxwell-Boltzmann distribution.";
+const char *gengetopt_args_info_purpose = "Resamples the velocities for all the integrable objects in an OpenMD file from \na Maxwell-Boltzmann distribution.";
 
 const char *gengetopt_args_info_usage = "Usage: thermalizer [OPTIONS]... [FILES]...";
 
+const char *gengetopt_args_info_description = "";
+
 const char *gengetopt_args_info_help[] = {
   "  -h, --help                Print help and exit",
   "  -V, --version             Print version and exit",
@@ -33,13 +35,19 @@ const char *gengetopt_args_info_help[] = {
     0
 };
 
+typedef enum {ARG_NO
+  , ARG_STRING
+  , ARG_DOUBLE
+} cmdline_parser_arg_type;
+
 static
 void clear_given (struct gengetopt_args_info *args_info);
 static
 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, int override, int initialize, int check_required, const char *additional_error);
+cmdline_parser_internal (int argc, char * const *argv, struct gengetopt_args_info *args_info,
+                        struct cmdline_parser_params *params, const char *additional_error);
 
 static int
 cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error);
@@ -68,6 +76,8 @@ void init_args_info(struct gengetopt_args_info *args_i
 static
 void init_args_info(struct gengetopt_args_info *args_info)
 {
+
+
   args_info->help_help = gengetopt_args_info_help[0] ;
   args_info->version_help = gengetopt_args_info_help[1] ;
   args_info->output_help = gengetopt_args_info_help[2] ;
@@ -81,16 +91,26 @@ cmdline_parser_print_version (void)
   printf ("%s %s\n", CMDLINE_PARSER_PACKAGE, CMDLINE_PARSER_VERSION);
 }
 
-void
-cmdline_parser_print_help (void)
-{
-  int i = 0;
+static void print_help_common(void) {
   cmdline_parser_print_version ();
 
   if (strlen(gengetopt_args_info_purpose) > 0)
     printf("\n%s\n", gengetopt_args_info_purpose);
 
-  printf("\n%s\n\n", gengetopt_args_info_usage);
+  if (strlen(gengetopt_args_info_usage) > 0)
+    printf("\n%s\n", gengetopt_args_info_usage);
+
+  printf("\n");
+
+  if (strlen(gengetopt_args_info_description) > 0)
+    printf("%s\n", gengetopt_args_info_description);
+}
+
+void
+cmdline_parser_print_help (void)
+{
+  int i = 0;
+  print_help_common();
   while (gengetopt_args_info_help[i])
     printf("%s\n", gengetopt_args_info_help[i++]);
 }
@@ -106,37 +126,95 @@ cmdline_parser_init (struct gengetopt_args_info *args_
   args_info->inputs_num = 0;
 }
 
+void
+cmdline_parser_params_init(struct cmdline_parser_params *params)
+{
+  if (params)
+    { 
+      params->override = 0;
+      params->initialize = 1;
+      params->check_required = 1;
+      params->check_ambiguity = 0;
+      params->print_errors = 1;
+    }
+}
+
+struct cmdline_parser_params *
+cmdline_parser_params_create(void)
+{
+  struct cmdline_parser_params *params = 
+    (struct cmdline_parser_params *)malloc(sizeof(struct cmdline_parser_params));
+  cmdline_parser_params_init(params);  
+  return params;
+}
+
 static void
-cmdline_parser_release (struct gengetopt_args_info *args_info)
+free_string_field (char **s)
 {
-  
-  unsigned int i;
-  if (args_info->output_arg)
+  if (*s)
     {
-      free (args_info->output_arg); /* free previous argument */
-      args_info->output_arg = 0;
+      free (*s);
+      *s = 0;
     }
-  if (args_info->output_orig)
-    {
-      free (args_info->output_orig); /* free previous argument */
-      args_info->output_orig = 0;
-    }
-  if (args_info->temperature_orig)
-    {
-      free (args_info->temperature_orig); /* free previous argument */
-      args_info->temperature_orig = 0;
-    }
+}
+
+
+static void
+cmdline_parser_release (struct gengetopt_args_info *args_info)
+{
+  unsigned int i;
+  free_string_field (&(args_info->output_arg));
+  free_string_field (&(args_info->output_orig));
+  free_string_field (&(args_info->temperature_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);
 }
 
+
+static void
+write_into_file(FILE *outfile, const char *opt, const char *arg, char *values[])
+{
+  if (arg) {
+    fprintf(outfile, "%s=\"%s\"\n", opt, arg);
+  } else {
+    fprintf(outfile, "%s\n", opt);
+  }
+}
+
+
 int
+cmdline_parser_dump(FILE *outfile, struct gengetopt_args_info *args_info)
+{
+  int i = 0;
+
+  if (!outfile)
+    {
+      fprintf (stderr, "%s: cannot dump options to stream\n", CMDLINE_PARSER_PACKAGE);
+      return EXIT_FAILURE;
+    }
+
+  if (args_info->help_given)
+    write_into_file(outfile, "help", 0, 0 );
+  if (args_info->version_given)
+    write_into_file(outfile, "version", 0, 0 );
+  if (args_info->output_given)
+    write_into_file(outfile, "output", args_info->output_orig, 0);
+  if (args_info->temperature_given)
+    write_into_file(outfile, "temperature", args_info->temperature_orig, 0);
+  
+
+  i = EXIT_SUCCESS;
+  return i;
+}
+
+int
 cmdline_parser_file_save(const char *filename, struct gengetopt_args_info *args_info)
 {
   FILE *outfile;
@@ -150,30 +228,9 @@ cmdline_parser_file_save(const char *filename, struct 
       return EXIT_FAILURE;
     }
 
-  if (args_info->help_given) {
-    fprintf(outfile, "%s\n", "help");
-  }
-  if (args_info->version_given) {
-    fprintf(outfile, "%s\n", "version");
-  }
-  if (args_info->output_given) {
-    if (args_info->output_orig) {
-      fprintf(outfile, "%s=\"%s\"\n", "output", args_info->output_orig);
-    } else {
-      fprintf(outfile, "%s\n", "output");
-    }
-  }
-  if (args_info->temperature_given) {
-    if (args_info->temperature_orig) {
-      fprintf(outfile, "%s=\"%s\"\n", "temperature", args_info->temperature_orig);
-    } else {
-      fprintf(outfile, "%s\n", "temperature");
-    }
-  }
-  
+  i = cmdline_parser_dump(outfile, args_info);
   fclose (outfile);
 
-  i = EXIT_SUCCESS;
   return i;
 }
 
@@ -183,9 +240,7 @@ cmdline_parser_free (struct gengetopt_args_info *args_
   cmdline_parser_release (args_info);
 }
 
-
-/* gengetopt_strdup() */
-/* strdup.c replacement of strdup, which is not standard */
+/** @brief replacement of strdup, which is not standard */
 char *
 gengetopt_strdup (const char *s)
 {
@@ -207,11 +262,34 @@ int
 }
 
 int
+cmdline_parser_ext (int argc, char * const *argv, struct gengetopt_args_info *args_info,
+                   struct cmdline_parser_params *params)
+{
+  int result;
+  result = cmdline_parser_internal (argc, argv, args_info, params, NULL);
+
+  if (result == EXIT_FAILURE)
+    {
+      cmdline_parser_free (args_info);
+      exit (EXIT_FAILURE);
+    }
+  
+  return result;
+}
+
+int
 cmdline_parser2 (int argc, char * const *argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required)
 {
   int result;
+  struct cmdline_parser_params params;
+  
+  params.override = override;
+  params.initialize = initialize;
+  params.check_required = check_required;
+  params.check_ambiguity = 0;
+  params.print_errors = 1;
 
-  result = cmdline_parser_internal (argc, argv, args_info, override, initialize, check_required, NULL);
+  result = cmdline_parser_internal (argc, argv, args_info, &params, NULL);
 
   if (result == EXIT_FAILURE)
     {
@@ -263,13 +341,136 @@ cmdline_parser_required2 (struct gengetopt_args_info *
   return error;
 }
 
+
+static char *package_name = 0;
+
+/**
+ * @brief updates an option
+ * @param field the generic pointer to the field to update
+ * @param orig_field the pointer to the orig field
+ * @param field_given the pointer to the number of occurrence of this option
+ * @param prev_given the pointer to the number of occurrence already seen
+ * @param value the argument for this option (if null no arg was specified)
+ * @param possible_values the possible values for this option (if specified)
+ * @param default_value the default value (in case the option only accepts fixed values)
+ * @param arg_type the type of this option
+ * @param check_ambiguity @see cmdline_parser_params.check_ambiguity
+ * @param override @see cmdline_parser_params.override
+ * @param no_free whether to free a possible previous value
+ * @param multiple_option whether this is a multiple option
+ * @param long_opt the corresponding long option
+ * @param short_opt the corresponding short option (or '-' if none)
+ * @param additional_error possible further error specification
+ */
+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,
+               cmdline_parser_arg_type arg_type,
+               int check_ambiguity, int override,
+               int no_free, int multiple_option,
+               const char *long_opt, char short_opt,
+               const char *additional_error)
+{
+  char *stop_char = 0;
+  const char *val = value;
+  int found;
+  char **string_field;
+
+  stop_char = 0;
+  found = 0;
+
+  if (!multiple_option && prev_given && (*prev_given || (check_ambiguity && *field_given)))
+    {
+      if (short_opt != '-')
+        fprintf (stderr, "%s: `--%s' (`-%c') option given more than once%s\n", 
+               package_name, long_opt, short_opt,
+               (additional_error ? additional_error : ""));
+      else
+        fprintf (stderr, "%s: `--%s' option given more than once%s\n", 
+               package_name, long_opt,
+               (additional_error ? additional_error : ""));
+      return 1; /* failure */
+    }
+
+    
+  if (field_given && *field_given && ! override)
+    return 0;
+  if (prev_given)
+    (*prev_given)++;
+  if (field_given)
+    (*field_given)++;
+  if (possible_values)
+    val = possible_values[found];
+
+  switch(arg_type) {
+  case ARG_DOUBLE:
+    if (val) *((double *)field) = strtod (val, &stop_char);
+    break;
+  case ARG_STRING:
+    if (val) {
+      string_field = (char **)field;
+      if (!no_free && *string_field)
+        free (*string_field); /* free previous string */
+      *string_field = gengetopt_strdup (val);
+    }
+    break;
+  default:
+    break;
+  };
+
+  /* check numeric conversion */
+  switch(arg_type) {
+  case ARG_DOUBLE:
+    if (val && !(stop_char && *stop_char == '\0')) {
+      fprintf(stderr, "%s: invalid numeric value: %s\n", package_name, val);
+      return 1; /* failure */
+    }
+    break;
+  default:
+    ;
+  };
+
+  /* store the original value */
+  switch(arg_type) {
+  case ARG_NO:
+    break;
+  default:
+    if (value && orig_field) {
+      if (no_free) {
+        *orig_field = value;
+      } else {
+        if (*orig_field)
+          free (*orig_field); /* free previous string */
+        *orig_field = gengetopt_strdup (value);
+      }
+    }
+  };
+
+  return 0; /* OK */
+}
+
+
 int
-cmdline_parser_internal (int argc, char * const *argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required, const char *additional_error)
+cmdline_parser_internal (int argc, char * const *argv, struct gengetopt_args_info *args_info,
+                        struct cmdline_parser_params *params, const char *additional_error)
 {
   int c;	/* Character of the parsed option.  */
 
   int error = 0;
   struct gengetopt_args_info local_args_info;
+  
+  int override;
+  int initialize;
+  int check_required;
+  int check_ambiguity;
+  
+  package_name = argv[0];
+  
+  override = params->override;
+  initialize = params->initialize;
+  check_required = params->check_required;
+  check_ambiguity = params->check_ambiguity;
 
   if (initialize)
     cmdline_parser_init (args_info);
@@ -278,13 +479,12 @@ cmdline_parser_internal (int argc, char * const *argv,
 
   optarg = 0;
   optind = 0;
-  opterr = 1;
+  opterr = params->print_errors;
   optopt = '?';
 
   while (1)
     {
       int option_index = 0;
-      char *stop_char;
 
       static struct option long_options[] = {
         { "help",	0, NULL, 'h' },
@@ -294,7 +494,6 @@ cmdline_parser_internal (int argc, char * const *argv,
         { NULL,	0, NULL, 0 }
       };
 
-      stop_char = 0;
       c = getopt_long (argc, argv, "hVo:t:", long_options, &option_index);
 
       if (c == -1) break;	/* Exit from `while (1)' loop.  */
@@ -312,44 +511,30 @@ cmdline_parser_internal (int argc, char * const *argv,
           exit (EXIT_SUCCESS);
 
         case 'o':	/* Output file name.  */
-          if (local_args_info.output_given)
-            {
-              fprintf (stderr, "%s: `--output' (`-o') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
-              goto failure;
-            }
-          if (args_info->output_given && ! override)
-            continue;
-          local_args_info.output_given = 1;
-          args_info->output_given = 1;
-          if (args_info->output_arg)
-            free (args_info->output_arg); /* free previous string */
-          args_info->output_arg = gengetopt_strdup (optarg);
-          if (args_info->output_orig)
-            free (args_info->output_orig); /* free previous string */
-          args_info->output_orig = gengetopt_strdup (optarg);
+        
+        
+          if (update_arg( (void *)&(args_info->output_arg), 
+               &(args_info->output_orig), &(args_info->output_given),
+              &(local_args_info.output_given), optarg, 0, 0, ARG_STRING,
+              check_ambiguity, override, 0, 0,
+              "output", 'o',
+              additional_error))
+            goto failure;
+        
           break;
-
         case 't':	/* temperature (K).  */
-          if (local_args_info.temperature_given)
-            {
-              fprintf (stderr, "%s: `--temperature' (`-t') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
-              goto failure;
-            }
-          if (args_info->temperature_given && ! override)
-            continue;
-          local_args_info.temperature_given = 1;
-          args_info->temperature_given = 1;
-          args_info->temperature_arg = strtod (optarg, &stop_char);
-          if (!(stop_char && *stop_char == '\0')) {
-            fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
+        
+        
+          if (update_arg( (void *)&(args_info->temperature_arg), 
+               &(args_info->temperature_orig), &(args_info->temperature_given),
+              &(local_args_info.temperature_given), optarg, 0, 0, ARG_DOUBLE,
+              check_ambiguity, override, 0, 0,
+              "temperature", 't',
+              additional_error))
             goto failure;
-          }
-          if (args_info->temperature_orig)
-            free (args_info->temperature_orig); /* free previous string */
-          args_info->temperature_orig = gengetopt_strdup (optarg);
+        
           break;
 
-
         case 0:	/* Long option with no short option */
         case '?':	/* Invalid option.  */
           /* `getopt_long' already printed an error message.  */