--- branches/development/src/applications/randomBuilder/randomBuilderCmd.c	2010/07/09 23:08:25	1465
+++ branches/development/src/applications/randomBuilder/randomBuilderCmd.c	2011/09/14 21:40:12	1630
@@ -1,7 +1,7 @@
 /*
-  File autogenerated by gengetopt version 2.16
+  File autogenerated by gengetopt version 2.22.4
   generated with the following command:
-  gengetopt -F randomBuilderCmd --unamed-opts 
+  gengetopt -F randomBuilderCmd -u 
 
   The developers of gengetopt consider the fixed text that goes in all
   gengetopt output files to be in the public domain:
@@ -17,28 +17,50 @@
 #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 "randomBuilderCmd.h"
 
+const char *gengetopt_args_info_purpose = "";
+
+const char *gengetopt_args_info_usage = "Usage: randomBuilder [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",
+  "  -o, --output=STRING       Output file name",
+  "      --density=DOUBLE      density (g/cm^3)",
+  "      --nx=INT              number of unit cells in x",
+  "      --ny=INT              number of unit cells in y",
+  "      --nz=INT              number of unit cells in z",
+  "      --molFraction=DOUBLE  (Default) Builds a multi-component random mixed \n                              nanoparticle. Mole Fraction must be specified for \n                              each componet > 1 in MD file.",
+    0
+};
+
+typedef enum {ARG_NO
+  , ARG_STRING
+  , ARG_INT
+  , 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 **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);
 
-struct molFraction_list
-{
-  double molFraction_arg;
-  char *molFraction_orig;
-  struct molFraction_list * next;
-};
-
 static char *
 gengetopt_strdup (const char *s);
 
@@ -58,6 +80,7 @@ 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->density_orig = NULL;
@@ -69,26 +92,54 @@ void clear_args (struct gengetopt_args_info *args_info
   
 }
 
+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] ;
+  args_info->density_help = gengetopt_args_info_help[3] ;
+  args_info->nx_help = gengetopt_args_info_help[4] ;
+  args_info->ny_help = gengetopt_args_info_help[5] ;
+  args_info->nz_help = gengetopt_args_info_help[6] ;
+  args_info->molFraction_help = gengetopt_args_info_help[7] ;
+  args_info->molFraction_min = 0;
+  args_info->molFraction_max = 0;
+  
+}
+
 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) {
+  cmdline_parser_print_version ();
+
+  if (strlen(gengetopt_args_info_purpose) > 0)
+    printf("\n%s\n", gengetopt_args_info_purpose);
+
+  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\n", gengetopt_args_info_description);
+}
+
 void
 cmdline_parser_print_help (void)
 {
-  cmdline_parser_print_version ();
-  printf("\nUsage: randomBuilder [OPTIONS]... [FILES]...\n\n");
-  printf("%s\n","  -h, --help                Print help and exit");
-  printf("%s\n","  -V, --version             Print version and exit");
-  printf("%s\n","  -o, --output=STRING       Output file name");
-  printf("%s\n","      --density=DOUBLE      density (g/cm^3)");
-  printf("%s\n","      --nx=INT              number of unit cells in x");
-  printf("%s\n","      --ny=INT              number of unit cells in y");
-  printf("%s\n","      --nz=INT              number of unit cells in z");
-  printf("%s\n","      --molFraction=DOUBLE  (Default) Builds a multi-component random mixed \n                              nanoparticle. Mole Fraction must be specified for \n                              each componet > 1 in MD file.");
-  
+  int i = 0;
+  print_help_common();
+  while (gengetopt_args_info_help[i])
+    printf("%s\n", gengetopt_args_info_help[i++]);
 }
 
 void
@@ -96,69 +147,165 @@ cmdline_parser_init (struct gengetopt_args_info *args_
 {
   clear_given (args_info);
   clear_args (args_info);
+  init_args_info (args_info);
 
-  args_info->inputs = NULL;
+  args_info->inputs = 0;
   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->density_orig)
-    {
-      free (args_info->density_orig); /* free previous argument */
-      args_info->density_orig = 0;
-    }
-  if (args_info->nx_orig)
-    {
-      free (args_info->nx_orig); /* free previous argument */
-      args_info->nx_orig = 0;
-    }
-  if (args_info->ny_orig)
-    {
-      free (args_info->ny_orig); /* free previous argument */
-      args_info->ny_orig = 0;
-    }
-  if (args_info->nz_orig)
-    {
-      free (args_info->nz_orig); /* free previous argument */
-      args_info->nz_orig = 0;
-    }
-  if (args_info->molFraction_arg)
-    {
-      for (i = 0; i < args_info->molFraction_given; ++i)
-        {
-          if (args_info->molFraction_orig [i])
-            {
-              free (args_info->molFraction_orig [i]); /* free previous argument */
-              args_info->molFraction_orig [i] = 0;
-            }
-        }
-      free (args_info->molFraction_arg); /* free previous argument */
-      args_info->molFraction_arg = 0;
-      free (args_info->molFraction_orig); /* free previous argument */
-      args_info->molFraction_orig = 0;
-    }
+}
+
+/** @brief generic value variable */
+union generic_value {
+    int int_arg;
+    double double_arg;
+    char *string_arg;
+    const char *default_string_arg;
+};
+
+/** @brief holds temporary values for multiple options */
+struct generic_list
+{
+  union generic_value arg;
+  char *orig;
+  struct generic_list *next;
+};
+
+/**
+ * @brief add a node at the head of the list 
+ */
+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 = 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)
+{
+  unsigned int i;
+  if (arg) {
+    for (i = 0; i < len; ++i)
+      {
+        free_string_field(&((*orig)[i]));
+      }
+
+    free (arg);
+    free (*orig);
+    *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->density_orig));
+  free_string_field (&(args_info->nx_orig));
+  free_string_field (&(args_info->ny_orig));
+  free_string_field (&(args_info->nz_orig));
+  free_multiple_field (args_info->molFraction_given, (void *)(args_info->molFraction_arg), &(args_info->molFraction_orig));
+  args_info->molFraction_arg = 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);
+}
+
+
+static void
+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 {
+    fprintf(outfile, "%s\n", opt);
+  }
+}
+
+static void
+write_multiple_into_file(FILE *outfile, int len, const char *opt, char **arg, const char *values[])
+{
+  int i;
+  
+  for (i = 0; i < len; ++i)
+    write_into_file(outfile, opt, (arg ? arg[i] : 0), values);
+}
+
+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->density_given)
+    write_into_file(outfile, "density", args_info->density_orig, 0);
+  if (args_info->nx_given)
+    write_into_file(outfile, "nx", args_info->nx_orig, 0);
+  if (args_info->ny_given)
+    write_into_file(outfile, "ny", args_info->ny_orig, 0);
+  if (args_info->nz_given)
+    write_into_file(outfile, "nz", args_info->nz_orig, 0);
+  write_multiple_into_file(outfile, args_info->molFraction_given, "molFraction", args_info->molFraction_orig, 0);
+  
+
+  i = EXIT_SUCCESS;
+  return i;
 }
 
 int
@@ -175,61 +322,9 @@ 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->density_given) {
-    if (args_info->density_orig) {
-      fprintf(outfile, "%s=\"%s\"\n", "density", args_info->density_orig);
-    } else {
-      fprintf(outfile, "%s\n", "density");
-    }
-  }
-  if (args_info->nx_given) {
-    if (args_info->nx_orig) {
-      fprintf(outfile, "%s=\"%s\"\n", "nx", args_info->nx_orig);
-    } else {
-      fprintf(outfile, "%s\n", "nx");
-    }
-  }
-  if (args_info->ny_given) {
-    if (args_info->ny_orig) {
-      fprintf(outfile, "%s=\"%s\"\n", "ny", args_info->ny_orig);
-    } else {
-      fprintf(outfile, "%s\n", "ny");
-    }
-  }
-  if (args_info->nz_given) {
-    if (args_info->nz_orig) {
-      fprintf(outfile, "%s=\"%s\"\n", "nz", args_info->nz_orig);
-    } else {
-      fprintf(outfile, "%s\n", "nz");
-    }
-  }
-  if (args_info->molFraction_orig)
-    {
-      for (i = 0; i < args_info->molFraction_given; ++i)
-        {
-          if (args_info->molFraction_orig [i])
-            {
-              fprintf(outfile, "%s=\"%s\"\n", "molFraction", args_info->molFraction_orig [i]);
-            }
-        }
-    }
-  
+  i = cmdline_parser_dump(outfile, args_info);
   fclose (outfile);
 
-  i = EXIT_SUCCESS;
   return i;
 }
 
@@ -239,13 +334,11 @@ 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)
 {
-  char *result = NULL;
+  char *result = 0;
   if (!s)
     return result;
 
@@ -259,55 +352,174 @@ get_multiple_arg_token(const char *arg)
 static char *
 get_multiple_arg_token(const char *arg)
 {
-  char *tok, *ret;
-  size_t len;
+  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;
 
+  /* make sure it is not escaped */
+  while (tok)
+    {
+      if (*(tok-1) == '\\')
+        {
+          /* find the next one */
+          tok = strchr (tok+1, ',');
+          ++num_of_escape;
+        }
+      else
+        break;
+    }
+
   if (tok)
     len = (size_t)(tok - arg + 1);
   else
     len = strlen (arg) + 1;
 
+  len -= num_of_escape;
+
   ret = (char *) malloc (len);
-  strncpy (ret, arg, len-1);
+
+  i = 0;
+  j = 0;
+  while (arg[i] && (j < len-1))
+    {
+      if (arg[i] == '\\' && 
+	  arg[ i + 1 ] && 
+	  arg[ i + 1 ] == ',')
+        ++i;
+
+      ret[j++] = arg[i++];
+    }
+
   ret[len-1] = '\0';
 
   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, ',');
 
+  /* make sure it is not escaped */
+  while (tok)
+    {
+      if (*(tok-1) == '\\')
+        {
+          /* find the next one */
+          tok = strchr (tok+1, ',');
+        }
+      else
+        break;
+    }
+
   if (! tok || strlen(tok) == 1)
     return 0;
 
   return tok+1;
 }
 
+static int
+check_multiple_option_occurrences(const char *prog_name, unsigned int option_given, unsigned int min, unsigned int max, const char *option_desc);
+
 int
-cmdline_parser (int argc, char * const *argv, struct gengetopt_args_info *args_info)
+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 (min > 0 && max > 0)
+        {
+          if (min == max)
+            {
+              /* specific occurrences */
+              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 < (unsigned int) min
+                || option_given > (unsigned int) max)
+            {
+              /* range occurrences */
+              fprintf (stderr, "%s: %s option occurrences must be between %d and %d\n",
+                prog_name, option_desc, min, max);
+              error = 1;
+            }
+        }
+      else if (min > 0)
+        {
+          /* at least check */
+          if (option_given < min)
+            {
+              fprintf (stderr, "%s: %s option occurrences must be at least %d\n",
+                prog_name, option_desc, min);
+              error = 1;
+            }
+        }
+      else if (max > 0)
+        {
+          /* at most check */
+          if (option_given > max)
+            {
+              fprintf (stderr, "%s: %s option occurrences must be at most %d\n",
+                prog_name, option_desc, max);
+              error = 1;
+            }
+        }
+    }
+    
+  return error;
+}
+int
+cmdline_parser (int argc, char **argv, struct gengetopt_args_info *args_info)
+{
   return cmdline_parser2 (argc, argv, args_info, 0, 1, 1);
 }
 
 int
-cmdline_parser2 (int argc, char * const *argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required)
+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, 0);
 
-  result = cmdline_parser_internal (argc, argv, args_info, override, initialize, check_required, NULL);
+  if (result == EXIT_FAILURE)
+    {
+      cmdline_parser_free (args_info);
+      exit (EXIT_FAILURE);
+    }
+  
+  return result;
+}
 
+int
+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;
+  
+  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, &params, 0);
+
   if (result == EXIT_FAILURE)
     {
       cmdline_parser_free (args_info);
@@ -322,7 +534,7 @@ 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)
@@ -338,47 +550,328 @@ 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)
     {
       fprintf (stderr, "%s: '--output' ('-o') option required%s\n", prog_name, (additional_error ? additional_error : ""));
       error = 1;
     }
+  
   if (! args_info->density_given)
     {
       fprintf (stderr, "%s: '--density' option required%s\n", prog_name, (additional_error ? additional_error : ""));
       error = 1;
     }
+  
   if (! args_info->nx_given)
     {
       fprintf (stderr, "%s: '--nx' option required%s\n", prog_name, (additional_error ? additional_error : ""));
       error = 1;
     }
+  
   if (! args_info->ny_given)
     {
       fprintf (stderr, "%s: '--ny' option required%s\n", prog_name, (additional_error ? additional_error : ""));
       error = 1;
     }
+  
   if (! args_info->nz_given)
     {
       fprintf (stderr, "%s: '--nz' option required%s\n", prog_name, (additional_error ? additional_error : ""));
       error = 1;
     }
+  
+  if (check_multiple_option_occurrences(prog_name, args_info->molFraction_given, args_info->molFraction_min, args_info->molFraction_max, "'--molFraction'"))
+     error = 1;
+  
+  
+  /* checks for dependences among options */
 
   return error;
 }
 
-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)
+
+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, 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,
+               const char *long_opt, char short_opt,
+               const char *additional_error)
 {
-  int c;	/* Character of the parsed option.  */
-  char *multi_token, *multi_next; /* for multiple options */
+  char *stop_char = 0;
+  const char *val = value;
+  int found;
+  char **string_field;
+  FIX_UNUSED (field);
 
-  int i;        /* Counter */
+  stop_char = 0;
+  found = 0;
 
-  struct molFraction_list * molFraction_list = NULL,* molFraction_new = NULL;
+  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 */
+    }
+
+  FIX_UNUSED (default_value);
+    
+  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_INT:
+    if (val) *((int *)field) = strtol (val, &stop_char, 0);
+    break;
+  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_INT:
+  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 */
+}
+
+/**
+ * @brief store information about a multiple option in a temporary list
+ * @param list where to (temporarily) store multiple options
+ */
+static
+int update_multiple_arg_temp(struct generic_list **list,
+               unsigned int *prev_given, const char *val,
+               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)
+{
+  /* store single arguments */
+  char *multi_token;
+  const char *multi_next;
+
+  if (arg_type == ARG_NO) {
+    (*prev_given)++;
+    return 0; /* OK */
+  }
+
+  multi_token = get_multiple_arg_token(val);
+  multi_next = get_multiple_arg_token_next (val);
+
+  while (1)
+    {
+      add_node (list);
+      if (update_arg((void *)&((*list)->arg), &((*list)->orig), 0,
+          prev_given, multi_token, possible_values, default_value, 
+          arg_type, 0, 1, 1, 1, long_opt, short_opt, additional_error)) {
+        if (multi_token) free(multi_token);
+        return 1; /* failure */
+      }
+
+      if (multi_next)
+        {
+          multi_token = get_multiple_arg_token(multi_next);
+          multi_next = get_multiple_arg_token_next (multi_next);
+        }
+      else
+        break;
+    }
+
+  return 0; /* OK */
+}
+
+/**
+ * @brief free the passed list (including possible string argument)
+ */
+static
+void free_list(struct generic_list *list, short string_arg)
+{
+  if (list) {
+    struct generic_list *tmp;
+    while (list)
+      {
+        tmp = list;
+        if (string_arg && list->arg.string_arg)
+          free (list->arg.string_arg);
+        if (list->orig)
+          free (list->orig);
+        list = list->next;
+        free (tmp);
+      }
+  }
+}
+
+/**
+ * @brief updates a multiple option starting from the passed list
+ */
+static
+void update_multiple_arg(void *field, char ***orig_field,
+               unsigned int field_given, unsigned int prev_given, union generic_value *default_value,
+               cmdline_parser_arg_type arg_type,
+               struct generic_list *list)
+{
+  int i;
+  struct generic_list *tmp;
+
+  if (prev_given && list) {
+    *orig_field = (char **) realloc (*orig_field, (field_given + prev_given) * sizeof (char *));
+
+    switch(arg_type) {
+    case ARG_INT:
+      *((int **)field) = (int *)realloc (*((int **)field), (field_given + prev_given) * sizeof (int)); break;
+    case ARG_DOUBLE:
+      *((double **)field) = (double *)realloc (*((double **)field), (field_given + prev_given) * sizeof (double)); break;
+    case ARG_STRING:
+      *((char ***)field) = (char **)realloc (*((char ***)field), (field_given + prev_given) * sizeof (char *)); break;
+    default:
+      break;
+    };
+    
+    for (i = (prev_given - 1); i >= 0; --i)
+      {
+        tmp = list;
+        
+        switch(arg_type) {
+        case ARG_INT:
+          (*((int **)field))[i + field_given] = tmp->arg.int_arg; break;
+        case ARG_DOUBLE:
+          (*((double **)field))[i + field_given] = tmp->arg.double_arg; break;
+        case ARG_STRING:
+          (*((char ***)field))[i + field_given] = tmp->arg.string_arg; break;
+        default:
+          break;
+        }        
+        (*orig_field) [i + field_given] = list->orig;
+        list = list->next;
+        free (tmp);
+      }
+  } else { /* set the default value */
+    if (default_value && ! field_given) {
+      switch(arg_type) {
+      case ARG_INT:
+        if (! *((int **)field)) {
+          *((int **)field) = (int *)malloc (sizeof (int));
+          (*((int **)field))[0] = default_value->int_arg; 
+        }
+        break;
+      case ARG_DOUBLE:
+        if (! *((double **)field)) {
+          *((double **)field) = (double *)malloc (sizeof (double));
+          (*((double **)field))[0] = default_value->double_arg;
+        }
+        break;
+      case ARG_STRING:
+        if (! *((char ***)field)) {
+          *((char ***)field) = (char **)malloc (sizeof (char *));
+          (*((char ***)field))[0] = gengetopt_strdup(default_value->string_arg);
+        }
+        break;
+      default: break;
+      }
+      if (!(*orig_field)) {
+        *orig_field = (char **) malloc (sizeof (char *));
+        (*orig_field)[0] = 0;
+      }
+    }
+  }
+}
+
+int
+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.  */
+
+  struct generic_list * molFraction_list = NULL;
   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);
@@ -387,13 +880,12 @@ 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' },
@@ -404,10 +896,9 @@ cmdline_parser_internal (int argc, char * const *argv,
         { "ny",	1, NULL, 0 },
         { "nz",	1, NULL, 0 },
         { "molFraction",	1, NULL, 0 },
-        { NULL,	0, NULL, 0 }
+        { 0,  0, 0, 0 }
       };
 
-      stop_char = 0;
       c = getopt_long (argc, argv, "hVo:", long_options, &option_index);
 
       if (c == -1) break;	/* Exit from `while (1)' loop.  */
@@ -425,139 +916,85 @@ 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 0:	/* Long option with no short option */
           /* density (g/cm^3).  */
           if (strcmp (long_options[option_index].name, "density") == 0)
           {
-            if (local_args_info.density_given)
-              {
-                fprintf (stderr, "%s: `--density' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
-                goto failure;
-              }
-            if (args_info->density_given && ! override)
-              continue;
-            local_args_info.density_given = 1;
-            args_info->density_given = 1;
-            args_info->density_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->density_arg), 
+                 &(args_info->density_orig), &(args_info->density_given),
+                &(local_args_info.density_given), optarg, 0, 0, ARG_DOUBLE,
+                check_ambiguity, override, 0, 0,
+                "density", '-',
+                additional_error))
               goto failure;
-            }
-            if (args_info->density_orig)
-              free (args_info->density_orig); /* free previous string */
-            args_info->density_orig = gengetopt_strdup (optarg);
+          
           }
           /* number of unit cells in x.  */
           else if (strcmp (long_options[option_index].name, "nx") == 0)
           {
-            if (local_args_info.nx_given)
-              {
-                fprintf (stderr, "%s: `--nx' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
-                goto failure;
-              }
-            if (args_info->nx_given && ! override)
-              continue;
-            local_args_info.nx_given = 1;
-            args_info->nx_given = 1;
-            args_info->nx_arg = strtol (optarg, &stop_char, 0);
-            if (!(stop_char && *stop_char == '\0')) {
-              fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
+          
+          
+            if (update_arg( (void *)&(args_info->nx_arg), 
+                 &(args_info->nx_orig), &(args_info->nx_given),
+                &(local_args_info.nx_given), optarg, 0, 0, ARG_INT,
+                check_ambiguity, override, 0, 0,
+                "nx", '-',
+                additional_error))
               goto failure;
-            }
-            if (args_info->nx_orig)
-              free (args_info->nx_orig); /* free previous string */
-            args_info->nx_orig = gengetopt_strdup (optarg);
+          
           }
           /* number of unit cells in y.  */
           else if (strcmp (long_options[option_index].name, "ny") == 0)
           {
-            if (local_args_info.ny_given)
-              {
-                fprintf (stderr, "%s: `--ny' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
-                goto failure;
-              }
-            if (args_info->ny_given && ! override)
-              continue;
-            local_args_info.ny_given = 1;
-            args_info->ny_given = 1;
-            args_info->ny_arg = strtol (optarg, &stop_char, 0);
-            if (!(stop_char && *stop_char == '\0')) {
-              fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
+          
+          
+            if (update_arg( (void *)&(args_info->ny_arg), 
+                 &(args_info->ny_orig), &(args_info->ny_given),
+                &(local_args_info.ny_given), optarg, 0, 0, ARG_INT,
+                check_ambiguity, override, 0, 0,
+                "ny", '-',
+                additional_error))
               goto failure;
-            }
-            if (args_info->ny_orig)
-              free (args_info->ny_orig); /* free previous string */
-            args_info->ny_orig = gengetopt_strdup (optarg);
+          
           }
           /* number of unit cells in z.  */
           else if (strcmp (long_options[option_index].name, "nz") == 0)
           {
-            if (local_args_info.nz_given)
-              {
-                fprintf (stderr, "%s: `--nz' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
-                goto failure;
-              }
-            if (args_info->nz_given && ! override)
-              continue;
-            local_args_info.nz_given = 1;
-            args_info->nz_given = 1;
-            args_info->nz_arg = strtol (optarg, &stop_char, 0);
-            if (!(stop_char && *stop_char == '\0')) {
-              fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
+          
+          
+            if (update_arg( (void *)&(args_info->nz_arg), 
+                 &(args_info->nz_orig), &(args_info->nz_given),
+                &(local_args_info.nz_given), optarg, 0, 0, ARG_INT,
+                check_ambiguity, override, 0, 0,
+                "nz", '-',
+                additional_error))
               goto failure;
-            }
-            if (args_info->nz_orig)
-              free (args_info->nz_orig); /* free previous string */
-            args_info->nz_orig = gengetopt_strdup (optarg);
+          
           }
           /* (Default) Builds a multi-component random mixed nanoparticle. Mole Fraction must be specified for each componet > 1 in MD file..  */
           else if (strcmp (long_options[option_index].name, "molFraction") == 0)
           {
-            local_args_info.molFraction_given++;
           
-            multi_token = get_multiple_arg_token(optarg);
-            multi_next = get_multiple_arg_token_next (optarg);
+            if (update_multiple_arg_temp(&molFraction_list, 
+                &(local_args_info.molFraction_given), optarg, 0, 0, ARG_DOUBLE,
+                "molFraction", '-',
+                additional_error))
+              goto failure;
           
-            while (1)
-              {
-                molFraction_new = (struct molFraction_list *) malloc (sizeof (struct molFraction_list));
-                molFraction_new->next = molFraction_list;
-                molFraction_list = molFraction_new;
-                molFraction_new->molFraction_arg = strtod (multi_token, &stop_char);
-                if (!(stop_char && *stop_char == '\0')) {
-                  fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], multi_token);
-                  goto failure;
-                }
-                molFraction_new->molFraction_orig = multi_token;
-          
-                if (multi_next)
-                  {
-                    multi_token = get_multiple_arg_token(multi_next);
-                    multi_next = get_multiple_arg_token_next (multi_next);
-                    local_args_info.molFraction_given++;
-                  }
-                else
-                  break;
-              }
-            break;
           }
           
           break;
@@ -572,21 +1009,10 @@ cmdline_parser_internal (int argc, char * const *argv,
     } /* while */
 
 
-  if (local_args_info.molFraction_given && molFraction_list)
-    {
-      struct molFraction_list *tmp;
-      args_info->molFraction_arg = (double *) realloc (args_info->molFraction_arg, (args_info->molFraction_given + local_args_info.molFraction_given) * sizeof (double));
-      args_info->molFraction_orig = (char **) realloc (args_info->molFraction_orig, (args_info->molFraction_given + local_args_info.molFraction_given) * sizeof (char *));
-      for (i = (local_args_info.molFraction_given - 1); i >= 0; --i)
-        {
-          tmp = molFraction_list;
-          args_info->molFraction_arg [i + args_info->molFraction_given] = molFraction_list->molFraction_arg;
-          args_info->molFraction_orig [i + args_info->molFraction_given] = molFraction_list->molFraction_orig;
-          molFraction_list = molFraction_list->next;
-          free (tmp);
-        }
-    }
-  
+  update_multiple_arg((void *)&(args_info->molFraction_arg),
+    &(args_info->molFraction_orig), args_info->molFraction_given,
+    local_args_info.molFraction_given, 0,
+    ARG_DOUBLE, molFraction_list);
 
   args_info->molFraction_given += local_args_info.molFraction_given;
   local_args_info.molFraction_given = 0;
@@ -604,28 +1030,31 @@ cmdline_parser_internal (int argc, char * const *argv,
   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) */
 
-      args_info->inputs_num = argc - optind ;
+      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)
-        args_info->inputs[ i++ ] = gengetopt_strdup (argv[optind++]) ;
+        if (argv[optind++] != argv[0])
+          args_info->inputs[ i++ ] = gengetopt_strdup (argv[optind-1]) ;
     }
 
   return 0;
 
 failure:
-  if (molFraction_list)
-    {
-      struct molFraction_list *tmp;
-      while (molFraction_list)
-        {
-          tmp = molFraction_list;
-          free (molFraction_list->molFraction_orig);
-          molFraction_list = molFraction_list->next;
-          free (tmp);
-        }
-    }
+  free_list (molFraction_list, 0 );
   
   cmdline_parser_release (&local_args_info);
   return (EXIT_FAILURE);