--- trunk/src/applications/dynamicProps/DynamicPropsCmd.c	2007/01/03 20:47:00	1112
+++ trunk/src/applications/dynamicProps/DynamicPropsCmd.cpp	2013/07/29 17:55:17	1915
@@ -1,7 +1,7 @@
 /*
-  File autogenerated by gengetopt version 2.15
+  File autogenerated by gengetopt version 2.22.4
   generated with the following command:
-  gengetopt -u -i DynamicProps.ggo -F DynamicPropsCmd 
+  gengetopt --file-name=DynamicPropsCmd --unamed-opts 
 
   The developers of gengetopt consider the fixed text that goes in all
   gengetopt output files to be in the public domain:
@@ -17,17 +17,60 @@
 #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 "DynamicPropsCmd.h"
 
+const char *gengetopt_args_info_purpose = "";
+
+const char *gengetopt_args_info_usage = "Usage: DynamicProps [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",
+  "  -i, --input=filename          input dump file",
+  "  -o, --output=filename         output file name",
+  "      --sele1=selection script  select first stuntdouble set",
+  "      --sele2=selection script  select second stuntdouble set (if sele2 is not \n                                  set, use script from sele1)",
+  "      --order=INT               Lengendre Polynomial Order",
+  "  -z, --nzbins=INT              Number of Z bins  (default=`100')",
+  "  -m, --memory=memory specification\n                                Available memory (defaults to 2G)  \n                                  (default=`2G')",
+  "\n Group: dynamicProps\n   an option of this group is required",
+  "  -s, --selecorr                selection correlation function",
+  "  -r, --rcorr                   rmsd",
+  "  -v, --vcorr                   velocity correlation function",
+  "  -d, --dcorr                   dipole correlation function",
+  "  -l, --lcorr                   Lengendre correlation function",
+  "      --lcorrZ                  Lengendre correlation function binned by Z",
+  "  -M, --sdcorr                  System dipole correlation function",
+  "      --r_rcorr                 Radial rmsd",
+  "      --thetacorr               Angular rmsd",
+  "      --drcorr                  Directional rmsd for particles with unit \n                                  vectors",
+  "      --helfandEcorr            Helfand moment for thermal conductvity",
+  "  -p, --momentum                Helfand momentum for viscosity",
+  "      --stresscorr              Stress tensor correlation function",
+    0
+};
+
+typedef enum {ARG_NO
+  , ARG_STRING
+  , ARG_INT
+} 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);
@@ -45,18 +88,28 @@ void clear_given (struct gengetopt_args_info *args_inf
   args_info->sele1_given = 0 ;
   args_info->sele2_given = 0 ;
   args_info->order_given = 0 ;
+  args_info->nzbins_given = 0 ;
+  args_info->memory_given = 0 ;
+  args_info->selecorr_given = 0 ;
   args_info->rcorr_given = 0 ;
   args_info->vcorr_given = 0 ;
   args_info->dcorr_given = 0 ;
   args_info->lcorr_given = 0 ;
+  args_info->lcorrZ_given = 0 ;
+  args_info->sdcorr_given = 0 ;
   args_info->r_rcorr_given = 0 ;
   args_info->thetacorr_given = 0 ;
+  args_info->drcorr_given = 0 ;
+  args_info->helfandEcorr_given = 0 ;
+  args_info->momentum_given = 0 ;
+  args_info->stresscorr_given = 0 ;
   args_info->dynamicProps_group_counter = 0 ;
 }
 
 static
 void clear_args (struct gengetopt_args_info *args_info)
 {
+  FIX_UNUSED (args_info);
   args_info->input_arg = NULL;
   args_info->input_orig = NULL;
   args_info->output_arg = NULL;
@@ -66,35 +119,73 @@ void clear_args (struct gengetopt_args_info *args_info
   args_info->sele2_arg = NULL;
   args_info->sele2_orig = NULL;
   args_info->order_orig = NULL;
+  args_info->nzbins_arg = 100;
+  args_info->nzbins_orig = NULL;
+  args_info->memory_arg = gengetopt_strdup ("2G");
+  args_info->memory_orig = NULL;
   
 }
 
+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->input_help = gengetopt_args_info_help[2] ;
+  args_info->output_help = gengetopt_args_info_help[3] ;
+  args_info->sele1_help = gengetopt_args_info_help[4] ;
+  args_info->sele2_help = gengetopt_args_info_help[5] ;
+  args_info->order_help = gengetopt_args_info_help[6] ;
+  args_info->nzbins_help = gengetopt_args_info_help[7] ;
+  args_info->memory_help = gengetopt_args_info_help[8] ;
+  args_info->selecorr_help = gengetopt_args_info_help[10] ;
+  args_info->rcorr_help = gengetopt_args_info_help[11] ;
+  args_info->vcorr_help = gengetopt_args_info_help[12] ;
+  args_info->dcorr_help = gengetopt_args_info_help[13] ;
+  args_info->lcorr_help = gengetopt_args_info_help[14] ;
+  args_info->lcorrZ_help = gengetopt_args_info_help[15] ;
+  args_info->sdcorr_help = gengetopt_args_info_help[16] ;
+  args_info->r_rcorr_help = gengetopt_args_info_help[17] ;
+  args_info->thetacorr_help = gengetopt_args_info_help[18] ;
+  args_info->drcorr_help = gengetopt_args_info_help[19] ;
+  args_info->helfandEcorr_help = gengetopt_args_info_help[20] ;
+  args_info->momentum_help = gengetopt_args_info_help[21] ;
+  args_info->stresscorr_help = gengetopt_args_info_help[22] ;
+  
+}
+
 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: DynamicProps [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","  -i, --input=filename          input dump file");
-  printf("%s\n","  -o, --output=filename         output file name");
-  printf("%s\n","      --sele1=selection script  select first stuntdouble set");
-  printf("%s\n","      --sele2=selection script  select second stuntdouble set (if sele2 is not \n                                  set, use script from sele1)");
-  printf("%s\n","      --order=INT               Lengendre Polynomial Order");
-  printf("%s\n","\n Group: dynamicProps\n   an option of this group is required");
-  printf("%s\n","  -r, --rcorr                   rmsd");
-  printf("%s\n","  -v, --vcorr                   velocity correlation function");
-  printf("%s\n","  -d, --dcorr                   dipole correlation function");
-  printf("%s\n","  -l, --lcorr                   Lengendre correlation function");
-  printf("%s\n","      --r_rcorr                 Radial rmsd");
-  printf("%s\n","      --thetacorr               Angular rmsd");
-  
+  int i = 0;
+  print_help_common();
+  while (gengetopt_args_info_help[i])
+    printf("%s\n", gengetopt_args_info_help[i++]);
 }
 
 void
@@ -102,72 +193,147 @@ 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->input_arg)
+  if (*s)
     {
-      free (args_info->input_arg); /* free previous argument */
-      args_info->input_arg = 0;
+      free (*s);
+      *s = 0;
     }
-  if (args_info->input_orig)
-    {
-      free (args_info->input_orig); /* free previous argument */
-      args_info->input_orig = 0;
-    }
-  if (args_info->output_arg)
-    {
-      free (args_info->output_arg); /* free previous argument */
-      args_info->output_arg = 0;
-    }
-  if (args_info->output_orig)
-    {
-      free (args_info->output_orig); /* free previous argument */
-      args_info->output_orig = 0;
-    }
-  if (args_info->sele1_arg)
-    {
-      free (args_info->sele1_arg); /* free previous argument */
-      args_info->sele1_arg = 0;
-    }
-  if (args_info->sele1_orig)
-    {
-      free (args_info->sele1_orig); /* free previous argument */
-      args_info->sele1_orig = 0;
-    }
-  if (args_info->sele2_arg)
-    {
-      free (args_info->sele2_arg); /* free previous argument */
-      args_info->sele2_arg = 0;
-    }
-  if (args_info->sele2_orig)
-    {
-      free (args_info->sele2_orig); /* free previous argument */
-      args_info->sele2_orig = 0;
-    }
-  if (args_info->order_orig)
-    {
-      free (args_info->order_orig); /* free previous argument */
-      args_info->order_orig = 0;
-    }
+}
+
+
+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));
+  free_string_field (&(args_info->output_orig));
+  free_string_field (&(args_info->sele1_arg));
+  free_string_field (&(args_info->sele1_orig));
+  free_string_field (&(args_info->sele2_arg));
+  free_string_field (&(args_info->sele2_orig));
+  free_string_field (&(args_info->order_orig));
+  free_string_field (&(args_info->nzbins_orig));
+  free_string_field (&(args_info->memory_arg));
+  free_string_field (&(args_info->memory_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, const char *values[])
+{
+  FIX_UNUSED (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->input_given)
+    write_into_file(outfile, "input", args_info->input_orig, 0);
+  if (args_info->output_given)
+    write_into_file(outfile, "output", args_info->output_orig, 0);
+  if (args_info->sele1_given)
+    write_into_file(outfile, "sele1", args_info->sele1_orig, 0);
+  if (args_info->sele2_given)
+    write_into_file(outfile, "sele2", args_info->sele2_orig, 0);
+  if (args_info->order_given)
+    write_into_file(outfile, "order", args_info->order_orig, 0);
+  if (args_info->nzbins_given)
+    write_into_file(outfile, "nzbins", args_info->nzbins_orig, 0);
+  if (args_info->memory_given)
+    write_into_file(outfile, "memory", args_info->memory_orig, 0);
+  if (args_info->selecorr_given)
+    write_into_file(outfile, "selecorr", 0, 0 );
+  if (args_info->rcorr_given)
+    write_into_file(outfile, "rcorr", 0, 0 );
+  if (args_info->vcorr_given)
+    write_into_file(outfile, "vcorr", 0, 0 );
+  if (args_info->dcorr_given)
+    write_into_file(outfile, "dcorr", 0, 0 );
+  if (args_info->lcorr_given)
+    write_into_file(outfile, "lcorr", 0, 0 );
+  if (args_info->lcorrZ_given)
+    write_into_file(outfile, "lcorrZ", 0, 0 );
+  if (args_info->sdcorr_given)
+    write_into_file(outfile, "sdcorr", 0, 0 );
+  if (args_info->r_rcorr_given)
+    write_into_file(outfile, "r_rcorr", 0, 0 );
+  if (args_info->thetacorr_given)
+    write_into_file(outfile, "thetacorr", 0, 0 );
+  if (args_info->drcorr_given)
+    write_into_file(outfile, "drcorr", 0, 0 );
+  if (args_info->helfandEcorr_given)
+    write_into_file(outfile, "helfandEcorr", 0, 0 );
+  if (args_info->momentum_given)
+    write_into_file(outfile, "momentum", 0, 0 );
+  if (args_info->stresscorr_given)
+    write_into_file(outfile, "stresscorr", 0, 0 );
+  
+
+  i = EXIT_SUCCESS;
+  return i;
+}
+
+int
 cmdline_parser_file_save(const char *filename, struct gengetopt_args_info *args_info)
 {
   FILE *outfile;
@@ -181,69 +347,9 @@ 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->input_given) {
-    if (args_info->input_orig) {
-      fprintf(outfile, "%s=\"%s\"\n", "input", args_info->input_orig);
-    } else {
-      fprintf(outfile, "%s\n", "input");
-    }
-  }
-  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->sele1_given) {
-    if (args_info->sele1_orig) {
-      fprintf(outfile, "%s=\"%s\"\n", "sele1", args_info->sele1_orig);
-    } else {
-      fprintf(outfile, "%s\n", "sele1");
-    }
-  }
-  if (args_info->sele2_given) {
-    if (args_info->sele2_orig) {
-      fprintf(outfile, "%s=\"%s\"\n", "sele2", args_info->sele2_orig);
-    } else {
-      fprintf(outfile, "%s\n", "sele2");
-    }
-  }
-  if (args_info->order_given) {
-    if (args_info->order_orig) {
-      fprintf(outfile, "%s=\"%s\"\n", "order", args_info->order_orig);
-    } else {
-      fprintf(outfile, "%s\n", "order");
-    }
-  }
-  if (args_info->rcorr_given) {
-    fprintf(outfile, "%s\n", "rcorr");
-  }
-  if (args_info->vcorr_given) {
-    fprintf(outfile, "%s\n", "vcorr");
-  }
-  if (args_info->dcorr_given) {
-    fprintf(outfile, "%s\n", "dcorr");
-  }
-  if (args_info->lcorr_given) {
-    fprintf(outfile, "%s\n", "lcorr");
-  }
-  if (args_info->r_rcorr_given) {
-    fprintf(outfile, "%s\n", "r_rcorr");
-  }
-  if (args_info->thetacorr_given) {
-    fprintf(outfile, "%s\n", "thetacorr");
-  }
-  
+  i = cmdline_parser_dump(outfile, args_info);
   fclose (outfile);
 
-  i = EXIT_SUCCESS;
   return i;
 }
 
@@ -253,13 +359,11 @@ 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;
 
@@ -271,37 +375,64 @@ static void
 }
 
 static void
-reset_group_dynamicProps(struct gengetopt_args_info *args_info);
-
-static void
 reset_group_dynamicProps(struct gengetopt_args_info *args_info)
 {
   if (! args_info->dynamicProps_group_counter)
     return;
   
+  args_info->selecorr_given = 0 ;
   args_info->rcorr_given = 0 ;
   args_info->vcorr_given = 0 ;
   args_info->dcorr_given = 0 ;
   args_info->lcorr_given = 0 ;
+  args_info->lcorrZ_given = 0 ;
+  args_info->sdcorr_given = 0 ;
   args_info->r_rcorr_given = 0 ;
   args_info->thetacorr_given = 0 ;
+  args_info->drcorr_given = 0 ;
+  args_info->helfandEcorr_given = 0 ;
+  args_info->momentum_given = 0 ;
+  args_info->stresscorr_given = 0 ;
 
   args_info->dynamicProps_group_counter = 0;
 }
 
 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_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);
@@ -316,7 +447,7 @@ 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)
@@ -332,29 +463,161 @@ 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->input_given)
     {
       fprintf (stderr, "%s: '--input' ('-i') option required%s\n", prog_name, (additional_error ? additional_error : ""));
       error = 1;
     }
+  
   if (args_info->dynamicProps_group_counter == 0)
     {
-      fprintf (stderr, "%s: %d options of group dynamicProps were given. One is required.%s\n", prog_name, args_info->dynamicProps_group_counter, (additional_error ? additional_error : ""));
+      fprintf (stderr, "%s: %d options of group dynamicProps were given. One is required%s.\n", prog_name, args_info->dynamicProps_group_counter, (additional_error ? additional_error : ""));
       error = 1;
     }
   
 
+  /* checks for dependences among options */
+
   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, 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)
+{
+  char *stop_char = 0;
+  const char *val = value;
+  int found;
+  char **string_field;
+  FIX_UNUSED (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 */
+    }
+
+  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_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:
+    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 **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);
@@ -362,14 +625,13 @@ cmdline_parser_internal (int argc, char * const *argv,
   cmdline_parser_init (&local_args_info);
 
   optarg = 0;
-  optind = 1;
-  opterr = 1;
+  optind = 0;
+  opterr = params->print_errors;
   optopt = '?';
 
   while (1)
     {
       int option_index = 0;
-      char *stop_char;
 
       static struct option long_options[] = {
         { "help",	0, NULL, 'h' },
@@ -379,17 +641,25 @@ cmdline_parser_internal (int argc, char * const *argv,
         { "sele1",	1, NULL, 0 },
         { "sele2",	1, NULL, 0 },
         { "order",	1, NULL, 0 },
+        { "nzbins",	1, NULL, 'z' },
+        { "memory",	1, NULL, 'm' },
+        { "selecorr",	0, NULL, 's' },
         { "rcorr",	0, NULL, 'r' },
         { "vcorr",	0, NULL, 'v' },
         { "dcorr",	0, NULL, 'd' },
         { "lcorr",	0, NULL, 'l' },
+        { "lcorrZ",	0, NULL, 0 },
+        { "sdcorr",	0, NULL, 'M' },
         { "r_rcorr",	0, NULL, 0 },
         { "thetacorr",	0, NULL, 0 },
-        { NULL,	0, NULL, 0 }
+        { "drcorr",	0, NULL, 0 },
+        { "helfandEcorr",	0, NULL, 0 },
+        { "momentum",	0, NULL, 'p' },
+        { "stresscorr",	0, NULL, 0 },
+        { 0,  0, 0, 0 }
       };
 
-      stop_char = 0;
-      c = getopt_long (argc, argv, "hVi:o:rvdl", long_options, &option_index);
+      c = getopt_long (argc, argv, "hVi:o:z:m:srvdlMp", long_options, &option_index);
 
       if (c == -1) break;	/* Exit from `while (1)' loop.  */
 
@@ -406,197 +676,305 @@ cmdline_parser_internal (int argc, char * const *argv,
           exit (EXIT_SUCCESS);
 
         case 'i':	/* input dump file.  */
-          if (local_args_info.input_given)
-            {
-              fprintf (stderr, "%s: `--input' (`-i') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
-              goto failure;
-            }
-          if (args_info->input_given && ! override)
-            continue;
-          local_args_info.input_given = 1;
-          args_info->input_given = 1;
-          if (args_info->input_arg)
-            free (args_info->input_arg); /* free previous string */
-          args_info->input_arg = gengetopt_strdup (optarg);
-          if (args_info->input_orig)
-            free (args_info->input_orig); /* free previous string */
-          args_info->input_orig = gengetopt_strdup (optarg);
+        
+        
+          if (update_arg( (void *)&(args_info->input_arg), 
+               &(args_info->input_orig), &(args_info->input_given),
+              &(local_args_info.input_given), optarg, 0, 0, ARG_STRING,
+              check_ambiguity, override, 0, 0,
+              "input", 'i',
+              additional_error))
+            goto failure;
+        
           break;
-
         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 'z':	/* Number of Z bins.  */
+        
+        
+          if (update_arg( (void *)&(args_info->nzbins_arg), 
+               &(args_info->nzbins_orig), &(args_info->nzbins_given),
+              &(local_args_info.nzbins_given), optarg, 0, "100", ARG_INT,
+              check_ambiguity, override, 0, 0,
+              "nzbins", 'z',
+              additional_error))
+            goto failure;
+        
+          break;
+        case 'm':	/* Available memory (defaults to 2G).  */
+        
+        
+          if (update_arg( (void *)&(args_info->memory_arg), 
+               &(args_info->memory_orig), &(args_info->memory_given),
+              &(local_args_info.memory_given), optarg, 0, "2G", ARG_STRING,
+              check_ambiguity, override, 0, 0,
+              "memory", 'm',
+              additional_error))
+            goto failure;
+        
+          break;
+        case 's':	/* selection correlation function.  */
+        
+          if (args_info->dynamicProps_group_counter && override)
+            reset_group_dynamicProps (args_info);
+          args_info->dynamicProps_group_counter += 1;
+        
+          if (update_arg( 0 , 
+               0 , &(args_info->selecorr_given),
+              &(local_args_info.selecorr_given), optarg, 0, 0, ARG_NO,
+              check_ambiguity, override, 0, 0,
+              "selecorr", 's',
+              additional_error))
+            goto failure;
+        
+          break;
         case 'r':	/* rmsd.  */
-          if (local_args_info.rcorr_given)
-            {
-              fprintf (stderr, "%s: `--rcorr' (`-r') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
-              goto failure;
-            }
-          if (args_info->rcorr_given && ! override)
-            continue;
-          local_args_info.rcorr_given = 1;
-          args_info->rcorr_given = 1;
+        
           if (args_info->dynamicProps_group_counter && override)
             reset_group_dynamicProps (args_info);
           args_info->dynamicProps_group_counter += 1;
+        
+          if (update_arg( 0 , 
+               0 , &(args_info->rcorr_given),
+              &(local_args_info.rcorr_given), optarg, 0, 0, ARG_NO,
+              check_ambiguity, override, 0, 0,
+              "rcorr", 'r',
+              additional_error))
+            goto failure;
+        
           break;
-
         case 'v':	/* velocity correlation function.  */
-          if (local_args_info.vcorr_given)
-            {
-              fprintf (stderr, "%s: `--vcorr' (`-v') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
-              goto failure;
-            }
-          if (args_info->vcorr_given && ! override)
-            continue;
-          local_args_info.vcorr_given = 1;
-          args_info->vcorr_given = 1;
+        
           if (args_info->dynamicProps_group_counter && override)
             reset_group_dynamicProps (args_info);
           args_info->dynamicProps_group_counter += 1;
+        
+          if (update_arg( 0 , 
+               0 , &(args_info->vcorr_given),
+              &(local_args_info.vcorr_given), optarg, 0, 0, ARG_NO,
+              check_ambiguity, override, 0, 0,
+              "vcorr", 'v',
+              additional_error))
+            goto failure;
+        
           break;
-
         case 'd':	/* dipole correlation function.  */
-          if (local_args_info.dcorr_given)
-            {
-              fprintf (stderr, "%s: `--dcorr' (`-d') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
-              goto failure;
-            }
-          if (args_info->dcorr_given && ! override)
-            continue;
-          local_args_info.dcorr_given = 1;
-          args_info->dcorr_given = 1;
+        
           if (args_info->dynamicProps_group_counter && override)
             reset_group_dynamicProps (args_info);
           args_info->dynamicProps_group_counter += 1;
+        
+          if (update_arg( 0 , 
+               0 , &(args_info->dcorr_given),
+              &(local_args_info.dcorr_given), optarg, 0, 0, ARG_NO,
+              check_ambiguity, override, 0, 0,
+              "dcorr", 'd',
+              additional_error))
+            goto failure;
+        
           break;
-
         case 'l':	/* Lengendre correlation function.  */
-          if (local_args_info.lcorr_given)
-            {
-              fprintf (stderr, "%s: `--lcorr' (`-l') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
-              goto failure;
-            }
-          if (args_info->lcorr_given && ! override)
-            continue;
-          local_args_info.lcorr_given = 1;
-          args_info->lcorr_given = 1;
+        
           if (args_info->dynamicProps_group_counter && override)
             reset_group_dynamicProps (args_info);
           args_info->dynamicProps_group_counter += 1;
+        
+          if (update_arg( 0 , 
+               0 , &(args_info->lcorr_given),
+              &(local_args_info.lcorr_given), optarg, 0, 0, ARG_NO,
+              check_ambiguity, override, 0, 0,
+              "lcorr", 'l',
+              additional_error))
+            goto failure;
+        
           break;
+        case 'M':	/* System dipole correlation function.  */
+        
+          if (args_info->dynamicProps_group_counter && override)
+            reset_group_dynamicProps (args_info);
+          args_info->dynamicProps_group_counter += 1;
+        
+          if (update_arg( 0 , 
+               0 , &(args_info->sdcorr_given),
+              &(local_args_info.sdcorr_given), optarg, 0, 0, ARG_NO,
+              check_ambiguity, override, 0, 0,
+              "sdcorr", 'M',
+              additional_error))
+            goto failure;
+        
+          break;
+        case 'p':	/* Helfand momentum for viscosity.  */
+        
+          if (args_info->dynamicProps_group_counter && override)
+            reset_group_dynamicProps (args_info);
+          args_info->dynamicProps_group_counter += 1;
+        
+          if (update_arg( 0 , 
+               0 , &(args_info->momentum_given),
+              &(local_args_info.momentum_given), optarg, 0, 0, ARG_NO,
+              check_ambiguity, override, 0, 0,
+              "momentum", 'p',
+              additional_error))
+            goto failure;
+        
+          break;
 
-
         case 0:	/* Long option with no short option */
           /* select first stuntdouble set.  */
           if (strcmp (long_options[option_index].name, "sele1") == 0)
           {
-            if (local_args_info.sele1_given)
-              {
-                fprintf (stderr, "%s: `--sele1' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
-                goto failure;
-              }
-            if (args_info->sele1_given && ! override)
-              continue;
-            local_args_info.sele1_given = 1;
-            args_info->sele1_given = 1;
-            if (args_info->sele1_arg)
-              free (args_info->sele1_arg); /* free previous string */
-            args_info->sele1_arg = gengetopt_strdup (optarg);
-            if (args_info->sele1_orig)
-              free (args_info->sele1_orig); /* free previous string */
-            args_info->sele1_orig = gengetopt_strdup (optarg);
+          
+          
+            if (update_arg( (void *)&(args_info->sele1_arg), 
+                 &(args_info->sele1_orig), &(args_info->sele1_given),
+                &(local_args_info.sele1_given), optarg, 0, 0, ARG_STRING,
+                check_ambiguity, override, 0, 0,
+                "sele1", '-',
+                additional_error))
+              goto failure;
+          
           }
           /* select second stuntdouble set (if sele2 is not set, use script from sele1).  */
           else if (strcmp (long_options[option_index].name, "sele2") == 0)
           {
-            if (local_args_info.sele2_given)
-              {
-                fprintf (stderr, "%s: `--sele2' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
-                goto failure;
-              }
-            if (args_info->sele2_given && ! override)
-              continue;
-            local_args_info.sele2_given = 1;
-            args_info->sele2_given = 1;
-            if (args_info->sele2_arg)
-              free (args_info->sele2_arg); /* free previous string */
-            args_info->sele2_arg = gengetopt_strdup (optarg);
-            if (args_info->sele2_orig)
-              free (args_info->sele2_orig); /* free previous string */
-            args_info->sele2_orig = gengetopt_strdup (optarg);
+          
+          
+            if (update_arg( (void *)&(args_info->sele2_arg), 
+                 &(args_info->sele2_orig), &(args_info->sele2_given),
+                &(local_args_info.sele2_given), optarg, 0, 0, ARG_STRING,
+                check_ambiguity, override, 0, 0,
+                "sele2", '-',
+                additional_error))
+              goto failure;
+          
           }
           /* Lengendre Polynomial Order.  */
           else if (strcmp (long_options[option_index].name, "order") == 0)
           {
-            if (local_args_info.order_given)
-              {
-                fprintf (stderr, "%s: `--order' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
-                goto failure;
-              }
-            if (args_info->order_given && ! override)
-              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);
+          
+          
+            if (update_arg( (void *)&(args_info->order_arg), 
+                 &(args_info->order_orig), &(args_info->order_given),
+                &(local_args_info.order_given), optarg, 0, 0, ARG_INT,
+                check_ambiguity, override, 0, 0,
+                "order", '-',
+                additional_error))
               goto failure;
-            }
-            if (args_info->order_orig)
-              free (args_info->order_orig); /* free previous string */
-            args_info->order_orig = gengetopt_strdup (optarg);
+          
           }
+          /* Lengendre correlation function binned by Z.  */
+          else if (strcmp (long_options[option_index].name, "lcorrZ") == 0)
+          {
+          
+            if (args_info->dynamicProps_group_counter && override)
+              reset_group_dynamicProps (args_info);
+            args_info->dynamicProps_group_counter += 1;
+          
+            if (update_arg( 0 , 
+                 0 , &(args_info->lcorrZ_given),
+                &(local_args_info.lcorrZ_given), optarg, 0, 0, ARG_NO,
+                check_ambiguity, override, 0, 0,
+                "lcorrZ", '-',
+                additional_error))
+              goto failure;
+          
+          }
           /* Radial rmsd.  */
           else if (strcmp (long_options[option_index].name, "r_rcorr") == 0)
           {
-            if (local_args_info.r_rcorr_given)
-              {
-                fprintf (stderr, "%s: `--r_rcorr' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
-                goto failure;
-              }
-            if (args_info->r_rcorr_given && ! override)
-              continue;
-            local_args_info.r_rcorr_given = 1;
-            args_info->r_rcorr_given = 1;
+          
             if (args_info->dynamicProps_group_counter && override)
               reset_group_dynamicProps (args_info);
             args_info->dynamicProps_group_counter += 1;
-            break;
+          
+            if (update_arg( 0 , 
+                 0 , &(args_info->r_rcorr_given),
+                &(local_args_info.r_rcorr_given), optarg, 0, 0, ARG_NO,
+                check_ambiguity, override, 0, 0,
+                "r_rcorr", '-',
+                additional_error))
+              goto failure;
+          
           }
           /* Angular rmsd.  */
           else if (strcmp (long_options[option_index].name, "thetacorr") == 0)
           {
-            if (local_args_info.thetacorr_given)
-              {
-                fprintf (stderr, "%s: `--thetacorr' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
-                goto failure;
-              }
-            if (args_info->thetacorr_given && ! override)
-              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;
+          
+            if (update_arg( 0 , 
+                 0 , &(args_info->thetacorr_given),
+                &(local_args_info.thetacorr_given), optarg, 0, 0, ARG_NO,
+                check_ambiguity, override, 0, 0,
+                "thetacorr", '-',
+                additional_error))
+              goto failure;
+          
           }
+          /* Directional rmsd for particles with unit vectors.  */
+          else if (strcmp (long_options[option_index].name, "drcorr") == 0)
+          {
           
+            if (args_info->dynamicProps_group_counter && override)
+              reset_group_dynamicProps (args_info);
+            args_info->dynamicProps_group_counter += 1;
+          
+            if (update_arg( 0 , 
+                 0 , &(args_info->drcorr_given),
+                &(local_args_info.drcorr_given), optarg, 0, 0, ARG_NO,
+                check_ambiguity, override, 0, 0,
+                "drcorr", '-',
+                additional_error))
+              goto failure;
+          
+          }
+          /* Helfand moment for thermal conductvity.  */
+          else if (strcmp (long_options[option_index].name, "helfandEcorr") == 0)
+          {
+          
+            if (args_info->dynamicProps_group_counter && override)
+              reset_group_dynamicProps (args_info);
+            args_info->dynamicProps_group_counter += 1;
+          
+            if (update_arg( 0 , 
+                 0 , &(args_info->helfandEcorr_given),
+                &(local_args_info.helfandEcorr_given), optarg, 0, 0, ARG_NO,
+                check_ambiguity, override, 0, 0,
+                "helfandEcorr", '-',
+                additional_error))
+              goto failure;
+          
+          }
+          /* Stress tensor correlation function.  */
+          else if (strcmp (long_options[option_index].name, "stresscorr") == 0)
+          {
+          
+            if (args_info->dynamicProps_group_counter && override)
+              reset_group_dynamicProps (args_info);
+            args_info->dynamicProps_group_counter += 1;
+          
+            if (update_arg( 0 , 
+                 0 , &(args_info->stresscorr_given),
+                &(local_args_info.stresscorr_given), optarg, 0, 0, ARG_NO,
+                check_ambiguity, override, 0, 0,
+                "stresscorr", '-',
+                additional_error))
+              goto failure;
+          
+          }
+          
           break;
         case '?':	/* Invalid option.  */
           /* `getopt_long' already printed an error message.  */
@@ -610,7 +988,7 @@ cmdline_parser_internal (int argc, char * const *argv,
 
   if (args_info->dynamicProps_group_counter > 1)
     {
-      fprintf (stderr, "%s: %d options of group dynamicProps were given. One is required.%s\n", argv[0], args_info->dynamicProps_group_counter, (additional_error ? additional_error : ""));
+      fprintf (stderr, "%s: %d options of group dynamicProps were given. One is required%s.\n", argv[0], args_info->dynamicProps_group_counter, (additional_error ? additional_error : ""));
       error = 1;
     }
   
@@ -629,12 +1007,25 @@ 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;