--- trunk/src/applications/dump2Xyz/Dump2XYZCmd.c	2004/09/28 23:24:25	12
+++ trunk/src/applications/dump2Xyz/Dump2XYZCmd.c	2010/05/10 17:28:26	1442
@@ -1,28 +1,97 @@
 /*
-  File autogenerated by gengetopt version 2.11
+  File autogenerated by gengetopt version 2.15
   generated with the following command:
-  /home/maul/gezelter/tim/program/gengetopt-2.11/src/gengetopt --file-name=Dump2XYZCmd 
+  gengetopt -i Dump2XYZ.ggo -F Dump2XYZCmd 
 
   The developers of gengetopt consider the fixed text that goes in all
   gengetopt output files to be in the public domain:
   we make no copyright claims on it.
 */
 
-
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-
 /* If we use autoconf.  */
 #ifdef HAVE_CONFIG_H
 #include "config.h"
 #endif
 
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
 
 #include "getopt.h"
 
-#include "applications/dump2Xyz/Dump2XYZCmd.h"
+#include "Dump2XYZCmd.h"
 
+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);
+
+static int
+cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error);
+
+static char *
+gengetopt_strdup (const char *s);
+
+static
+void clear_given (struct gengetopt_args_info *args_info)
+{
+  args_info->help_given = 0 ;
+  args_info->version_given = 0 ;
+  args_info->input_given = 0 ;
+  args_info->output_given = 0 ;
+  args_info->frame_given = 0 ;
+  args_info->water_given = 0 ;
+  args_info->periodicBox_given = 0 ;
+  args_info->zconstraint_given = 0 ;
+  args_info->rigidbody_given = 0 ;
+  args_info->watertype_given = 0 ;
+  args_info->selection_given = 0 ;
+  args_info->originsele_given = 0 ;
+  args_info->refsele_given = 0 ;
+  args_info->repeatX_given = 0 ;
+  args_info->repeatY_given = 0 ;
+  args_info->repeatZ_given = 0 ;
+  args_info->gb_given = 0 ;
+  args_info->basetype_given = 0 ;
+  args_info->printPosOnly_given = 0 ;
+}
+
+static
+void clear_args (struct gengetopt_args_info *args_info)
+{
+  args_info->input_arg = NULL;
+  args_info->input_orig = NULL;
+  args_info->output_arg = NULL;
+  args_info->output_orig = NULL;
+  args_info->frame_arg = 1;
+  args_info->frame_orig = NULL;
+  args_info->water_flag = 0;
+  args_info->periodicBox_flag = 0;
+  args_info->zconstraint_flag = 0;
+  args_info->rigidbody_flag = 0;
+  args_info->watertype_flag = 1;
+  args_info->selection_arg = NULL;
+  args_info->selection_orig = NULL;
+  args_info->originsele_arg = NULL;
+  args_info->originsele_orig = NULL;
+  args_info->refsele_arg = NULL;
+  args_info->refsele_orig = NULL;
+  args_info->repeatX_arg = 0;
+  args_info->repeatX_orig = NULL;
+  args_info->repeatY_arg = 0;
+  args_info->repeatY_orig = NULL;
+  args_info->repeatZ_arg = 0;
+  args_info->repeatZ_orig = NULL;
+  args_info->gb_arg = NULL;
+  args_info->gb_orig = NULL;
+  args_info->basetype_flag = 0;
+  args_info->printPosOnly_flag = 0;
+  
+}
+
 void
 cmdline_parser_print_version (void)
 {
@@ -33,35 +102,259 @@ cmdline_parser_print_help (void)
 cmdline_parser_print_help (void)
 {
   cmdline_parser_print_version ();
-  printf("\n"
-  "Usage: %s [OPTIONS]...\n", CMDLINE_PARSER_PACKAGE);
-  printf("\n");
-  printf("  -h, --help             Print help and exit\n");
-  printf("  -V, --version          Print version and exit\n");
-  printf("  -i, --input=filename   input dump file\n");
-  printf("  -o, --output=filename  output file name\n");
-  printf("  -n, --frame=INT        print every n frame  (default=`1')\n");
-  printf("  -d, --dipole           print the dipole moments  (default=off)\n");
-  printf("  -w, --water            skip the the waters  (default=off)\n");
-  printf("  -m, --periodicBox      map to the periodic box  (default=off)\n");
-  printf("  -z, --zconstraint      replace the atom types of zconstraint molecules  \n                           (default=off)\n");
-  printf("  -r, --rigidbody        add a pseudo COM atom to rigidbody  (default=off)\n");
-  printf("  -t, --watertype        replace the atom type of water model  (default=on)\n");
-  printf("  -s, --ignore=atomtype  ignore the atom types\n");
-  printf("      --repeatX=INT      The number of images to repeat in the x direction  \n                           (default=`0')\n");
-  printf("      --repeatY=INT      The number of images to repeat in the y direction  \n                           (default=`0')\n");
-  printf("      --repeatZ=INT      The number of images to repeat in the z direction  \n                           (default=`0')\n");
+  printf("\nUsage: Dump2XYZ [OPTIONS]...\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","  -n, --frame=INT               print every n frame  (default=`1')");
+  printf("%s\n","  -w, --water                   skip the the waters  (default=off)");
+  printf("%s\n","  -m, --periodicBox             map to the periodic box  (default=off)");
+  printf("%s\n","  -z, --zconstraint             replace the atom types of zconstraint molecules \n                                   (default=off)");
+  printf("%s\n","  -r, --rigidbody               add a pseudo COM atom to rigidbody  \n                                  (default=off)");
+  printf("%s\n","  -t, --watertype               replace the atom type of water model  \n                                  (default=on)");
+  printf("%s\n","  -s, --selection=selection script\n                                general selection syntax");
+  printf("%s\n","      --originsele=selection script\n                                select origin");
+  printf("%s\n","      --refsele=selection script\n                                select reference");
+  printf("%s\n","      --repeatX=INT             The number of images to repeat in the x \n                                  direction  (default=`0')");
+  printf("%s\n","      --repeatY=INT             The number of images to repeat in the y \n                                  direction  (default=`0')");
+  printf("%s\n","      --repeatZ=INT             The number of images to repeat in the z \n                                  direction  (default=`0')");
+  printf("%s\n","      --gb=atomtype             Replace the Gay-Berne atom with four linear \n                                  atoms");
+  printf("%s\n","  -b, --basetype                Convert to base atom type  (default=off)");
+  printf("%s\n","      --printPosOnly            Print only positions in xyz file  (default=off)");
+  
 }
 
+void
+cmdline_parser_init (struct gengetopt_args_info *args_info)
+{
+  clear_given (args_info);
+  clear_args (args_info);
+}
 
-static char *gengetopt_strdup (const char *s);
+static void
+cmdline_parser_release (struct gengetopt_args_info *args_info)
+{
+  
+  if (args_info->input_arg)
+    {
+      free (args_info->input_arg); /* free previous argument */
+      args_info->input_arg = 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->frame_orig)
+    {
+      free (args_info->frame_orig); /* free previous argument */
+      args_info->frame_orig = 0;
+    }
+  if (args_info->selection_arg)
+    {
+      free (args_info->selection_arg); /* free previous argument */
+      args_info->selection_arg = 0;
+    }
+  if (args_info->selection_orig)
+    {
+      free (args_info->selection_orig); /* free previous argument */
+      args_info->selection_orig = 0;
+    }
+  if (args_info->originsele_arg)
+    {
+      free (args_info->originsele_arg); /* free previous argument */
+      args_info->originsele_arg = 0;
+    }
+  if (args_info->originsele_orig)
+    {
+      free (args_info->originsele_orig); /* free previous argument */
+      args_info->originsele_orig = 0;
+    }
+  if (args_info->refsele_arg)
+    {
+      free (args_info->refsele_arg); /* free previous argument */
+      args_info->refsele_arg = 0;
+    }
+  if (args_info->refsele_orig)
+    {
+      free (args_info->refsele_orig); /* free previous argument */
+      args_info->refsele_orig = 0;
+    }
+  if (args_info->repeatX_orig)
+    {
+      free (args_info->repeatX_orig); /* free previous argument */
+      args_info->repeatX_orig = 0;
+    }
+  if (args_info->repeatY_orig)
+    {
+      free (args_info->repeatY_orig); /* free previous argument */
+      args_info->repeatY_orig = 0;
+    }
+  if (args_info->repeatZ_orig)
+    {
+      free (args_info->repeatZ_orig); /* free previous argument */
+      args_info->repeatZ_orig = 0;
+    }
+  if (args_info->gb_arg)
+    {
+      free (args_info->gb_arg); /* free previous argument */
+      args_info->gb_arg = 0;
+    }
+  if (args_info->gb_orig)
+    {
+      free (args_info->gb_orig); /* free previous argument */
+      args_info->gb_orig = 0;
+    }
+  
+  clear_given (args_info);
+}
 
+int
+cmdline_parser_file_save(const char *filename, struct gengetopt_args_info *args_info)
+{
+  FILE *outfile;
+  int i = 0;
+
+  outfile = fopen(filename, "w");
+
+  if (!outfile)
+    {
+      fprintf (stderr, "%s: cannot open file for writing: %s\n", CMDLINE_PARSER_PACKAGE, filename);
+      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->frame_given) {
+    if (args_info->frame_orig) {
+      fprintf(outfile, "%s=\"%s\"\n", "frame", args_info->frame_orig);
+    } else {
+      fprintf(outfile, "%s\n", "frame");
+    }
+  }
+  if (args_info->water_given) {
+    fprintf(outfile, "%s\n", "water");
+  }
+  if (args_info->periodicBox_given) {
+    fprintf(outfile, "%s\n", "periodicBox");
+  }
+  if (args_info->zconstraint_given) {
+    fprintf(outfile, "%s\n", "zconstraint");
+  }
+  if (args_info->rigidbody_given) {
+    fprintf(outfile, "%s\n", "rigidbody");
+  }
+  if (args_info->watertype_given) {
+    fprintf(outfile, "%s\n", "watertype");
+  }
+  if (args_info->selection_given) {
+    if (args_info->selection_orig) {
+      fprintf(outfile, "%s=\"%s\"\n", "selection", args_info->selection_orig);
+    } else {
+      fprintf(outfile, "%s\n", "selection");
+    }
+  }
+  if (args_info->originsele_given) {
+    if (args_info->originsele_orig) {
+      fprintf(outfile, "%s=\"%s\"\n", "originsele", args_info->originsele_orig);
+    } else {
+      fprintf(outfile, "%s\n", "originsele");
+    }
+  }
+  if (args_info->refsele_given) {
+    if (args_info->refsele_orig) {
+      fprintf(outfile, "%s=\"%s\"\n", "refsele", args_info->refsele_orig);
+    } else {
+      fprintf(outfile, "%s\n", "refsele");
+    }
+  }
+  if (args_info->repeatX_given) {
+    if (args_info->repeatX_orig) {
+      fprintf(outfile, "%s=\"%s\"\n", "repeatX", args_info->repeatX_orig);
+    } else {
+      fprintf(outfile, "%s\n", "repeatX");
+    }
+  }
+  if (args_info->repeatY_given) {
+    if (args_info->repeatY_orig) {
+      fprintf(outfile, "%s=\"%s\"\n", "repeatY", args_info->repeatY_orig);
+    } else {
+      fprintf(outfile, "%s\n", "repeatY");
+    }
+  }
+  if (args_info->repeatZ_given) {
+    if (args_info->repeatZ_orig) {
+      fprintf(outfile, "%s=\"%s\"\n", "repeatZ", args_info->repeatZ_orig);
+    } else {
+      fprintf(outfile, "%s\n", "repeatZ");
+    }
+  }
+  if (args_info->gb_given) {
+    if (args_info->gb_orig) {
+      fprintf(outfile, "%s=\"%s\"\n", "gb", args_info->gb_orig);
+    } else {
+      fprintf(outfile, "%s\n", "gb");
+    }
+  }
+  if (args_info->basetype_given) {
+    fprintf(outfile, "%s\n", "basetype");
+  }
+  if (args_info->printPosOnly_given) {
+    fprintf(outfile, "%s\n", "printPosOnly");
+  }
+  
+  fclose (outfile);
+
+  i = EXIT_SUCCESS;
+  return i;
+}
+
+void
+cmdline_parser_free (struct gengetopt_args_info *args_info)
+{
+  cmdline_parser_release (args_info);
+}
+
+
 /* gengetopt_strdup() */
 /* strdup.c replacement of strdup, which is not standard */
 char *
 gengetopt_strdup (const char *s)
 {
-  char *result = (char*)malloc(strlen(s) + 1);
+  char *result = NULL;
+  if (!s)
+    return result;
+
+  result = (char*)malloc(strlen(s) + 1);
   if (result == (char*)0)
     return (char*)0;
   strcpy(result, s);
@@ -71,50 +364,69 @@ cmdline_parser (int argc, char * const *argv, struct g
 int
 cmdline_parser (int argc, char * const *argv, struct gengetopt_args_info *args_info)
 {
-  int c;	/* Character of the parsed option.  */
-  int i;        /* Counter */
-  struct ignore_list
-  {
-    char * ignore_arg;
-    struct ignore_list * next;
-  };
-  struct ignore_list * ignore_list = NULL,* ignore_new = NULL;
+  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)
+{
+  int result;
+
+  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);
+    }
   
-  int missing_required_options = 0;
+  return result;
+}
 
-  args_info->help_given = 0 ;
-  args_info->version_given = 0 ;
-  args_info->input_given = 0 ;
-  args_info->output_given = 0 ;
-  args_info->frame_given = 0 ;
-  args_info->dipole_given = 0 ;
-  args_info->water_given = 0 ;
-  args_info->periodicBox_given = 0 ;
-  args_info->zconstraint_given = 0 ;
-  args_info->rigidbody_given = 0 ;
-  args_info->watertype_given = 0 ;
-  args_info->ignore_given = 0 ;
-  args_info->repeatX_given = 0 ;
-  args_info->repeatY_given = 0 ;
-  args_info->repeatZ_given = 0 ;
-#define clear_args() { \
-  args_info->input_arg = NULL; \
-  args_info->output_arg = NULL; \
-  args_info->frame_arg = 1 ;\
-  args_info->dipole_flag = 0;\
-  args_info->water_flag = 0;\
-  args_info->periodicBox_flag = 0;\
-  args_info->zconstraint_flag = 0;\
-  args_info->rigidbody_flag = 0;\
-  args_info->watertype_flag = 1;\
-  args_info->ignore_arg = NULL; \
-  args_info->repeatX_arg = 0 ;\
-  args_info->repeatY_arg = 0 ;\
-  args_info->repeatZ_arg = 0 ;\
+int
+cmdline_parser_required (struct gengetopt_args_info *args_info, const char *prog_name)
+{
+  int result = EXIT_SUCCESS;
+
+  if (cmdline_parser_required2(args_info, prog_name, NULL) > 0)
+    result = EXIT_FAILURE;
+
+  if (result == EXIT_FAILURE)
+    {
+      cmdline_parser_free (args_info);
+      exit (EXIT_FAILURE);
+    }
+  
+  return result;
 }
 
-  clear_args();
+int
+cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error)
+{
+  int error = 0;
 
+  if (! args_info->input_given)
+    {
+      fprintf (stderr, "%s: '--input' ('-i') option required%s\n", prog_name, (additional_error ? additional_error : ""));
+      error = 1;
+    }
+
+  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)
+{
+  int c;	/* Character of the parsed option.  */
+
+  int error = 0;
+  struct gengetopt_args_info local_args_info;
+
+  if (initialize)
+    cmdline_parser_init (args_info);
+
+  cmdline_parser_init (&local_args_info);
+
   optarg = 0;
   optind = 1;
   opterr = 1;
@@ -131,216 +443,356 @@ cmdline_parser (int argc, char * const *argv, struct g
         { "input",	1, NULL, 'i' },
         { "output",	1, NULL, 'o' },
         { "frame",	1, NULL, 'n' },
-        { "dipole",	0, NULL, 'd' },
         { "water",	0, NULL, 'w' },
         { "periodicBox",	0, NULL, 'm' },
         { "zconstraint",	0, NULL, 'z' },
         { "rigidbody",	0, NULL, 'r' },
         { "watertype",	0, NULL, 't' },
-        { "ignore",	1, NULL, 's' },
+        { "selection",	1, NULL, 's' },
+        { "originsele",	1, NULL, 0 },
+        { "refsele",	1, NULL, 0 },
         { "repeatX",	1, NULL, 0 },
         { "repeatY",	1, NULL, 0 },
         { "repeatZ",	1, NULL, 0 },
+        { "gb",	1, NULL, 0 },
+        { "basetype",	0, NULL, 'b' },
+        { "printPosOnly",	0, NULL, 0 },
         { NULL,	0, NULL, 0 }
       };
 
       stop_char = 0;
-      c = getopt_long (argc, argv, "hVi:o:n:dwmzrts:", long_options, &option_index);
+      c = getopt_long (argc, argv, "hVi:o:n:wmzrts:b", long_options, &option_index);
 
       if (c == -1) break;	/* Exit from `while (1)' loop.  */
 
       switch (c)
         {
         case 'h':	/* Print help and exit.  */
-          clear_args ();
           cmdline_parser_print_help ();
+          cmdline_parser_free (&local_args_info);
           exit (EXIT_SUCCESS);
 
         case 'V':	/* Print version and exit.  */
-          clear_args ();
           cmdline_parser_print_version ();
+          cmdline_parser_free (&local_args_info);
           exit (EXIT_SUCCESS);
 
         case 'i':	/* input dump file.  */
-          if (args_info->input_given)
+          if (local_args_info.input_given)
             {
-              fprintf (stderr, "%s: `--input' (`-i') option given more than once\n", CMDLINE_PARSER_PACKAGE);
-              clear_args ();
-              exit (EXIT_FAILURE);
+              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);
           break;
 
         case 'o':	/* output file name.  */
-          if (args_info->output_given)
+          if (local_args_info.output_given)
             {
-              fprintf (stderr, "%s: `--output' (`-o') option given more than once\n", CMDLINE_PARSER_PACKAGE);
-              clear_args ();
-              exit (EXIT_FAILURE);
+              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);
           break;
 
         case 'n':	/* print every n frame.  */
-          if (args_info->frame_given)
+          if (local_args_info.frame_given)
             {
-              fprintf (stderr, "%s: `--frame' (`-n') option given more than once\n", CMDLINE_PARSER_PACKAGE);
-              clear_args ();
-              exit (EXIT_FAILURE);
+              fprintf (stderr, "%s: `--frame' (`-n') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
+              goto failure;
             }
+          if (args_info->frame_given && ! override)
+            continue;
+          local_args_info.frame_given = 1;
           args_info->frame_given = 1;
-          args_info->frame_arg = strtol (optarg,&stop_char,0);
+          args_info->frame_arg = strtol (optarg, &stop_char, 0);
+          if (!(stop_char && *stop_char == '\0')) {
+            fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
+            goto failure;
+          }
+          if (args_info->frame_orig)
+            free (args_info->frame_orig); /* free previous string */
+          args_info->frame_orig = gengetopt_strdup (optarg);
           break;
 
-        case 'd':	/* print the dipole moments.  */
-          if (args_info->dipole_given)
-            {
-              fprintf (stderr, "%s: `--dipole' (`-d') option given more than once\n", CMDLINE_PARSER_PACKAGE);
-              clear_args ();
-              exit (EXIT_FAILURE);
-            }
-          args_info->dipole_given = 1;
-          args_info->dipole_flag = !(args_info->dipole_flag);
-          break;
-
         case 'w':	/* skip the the waters.  */
-          if (args_info->water_given)
+          if (local_args_info.water_given)
             {
-              fprintf (stderr, "%s: `--water' (`-w') option given more than once\n", CMDLINE_PARSER_PACKAGE);
-              clear_args ();
-              exit (EXIT_FAILURE);
+              fprintf (stderr, "%s: `--water' (`-w') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
+              goto failure;
             }
+          if (args_info->water_given && ! override)
+            continue;
+          local_args_info.water_given = 1;
           args_info->water_given = 1;
           args_info->water_flag = !(args_info->water_flag);
           break;
 
         case 'm':	/* map to the periodic box.  */
-          if (args_info->periodicBox_given)
+          if (local_args_info.periodicBox_given)
             {
-              fprintf (stderr, "%s: `--periodicBox' (`-m') option given more than once\n", CMDLINE_PARSER_PACKAGE);
-              clear_args ();
-              exit (EXIT_FAILURE);
+              fprintf (stderr, "%s: `--periodicBox' (`-m') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
+              goto failure;
             }
+          if (args_info->periodicBox_given && ! override)
+            continue;
+          local_args_info.periodicBox_given = 1;
           args_info->periodicBox_given = 1;
           args_info->periodicBox_flag = !(args_info->periodicBox_flag);
           break;
 
         case 'z':	/* replace the atom types of zconstraint molecules.  */
-          if (args_info->zconstraint_given)
+          if (local_args_info.zconstraint_given)
             {
-              fprintf (stderr, "%s: `--zconstraint' (`-z') option given more than once\n", CMDLINE_PARSER_PACKAGE);
-              clear_args ();
-              exit (EXIT_FAILURE);
+              fprintf (stderr, "%s: `--zconstraint' (`-z') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
+              goto failure;
             }
+          if (args_info->zconstraint_given && ! override)
+            continue;
+          local_args_info.zconstraint_given = 1;
           args_info->zconstraint_given = 1;
           args_info->zconstraint_flag = !(args_info->zconstraint_flag);
           break;
 
         case 'r':	/* add a pseudo COM atom to rigidbody.  */
-          if (args_info->rigidbody_given)
+          if (local_args_info.rigidbody_given)
             {
-              fprintf (stderr, "%s: `--rigidbody' (`-r') option given more than once\n", CMDLINE_PARSER_PACKAGE);
-              clear_args ();
-              exit (EXIT_FAILURE);
+              fprintf (stderr, "%s: `--rigidbody' (`-r') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
+              goto failure;
             }
+          if (args_info->rigidbody_given && ! override)
+            continue;
+          local_args_info.rigidbody_given = 1;
           args_info->rigidbody_given = 1;
           args_info->rigidbody_flag = !(args_info->rigidbody_flag);
           break;
 
         case 't':	/* replace the atom type of water model.  */
-          if (args_info->watertype_given)
+          if (local_args_info.watertype_given)
             {
-              fprintf (stderr, "%s: `--watertype' (`-t') option given more than once\n", CMDLINE_PARSER_PACKAGE);
-              clear_args ();
-              exit (EXIT_FAILURE);
+              fprintf (stderr, "%s: `--watertype' (`-t') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
+              goto failure;
             }
+          if (args_info->watertype_given && ! override)
+            continue;
+          local_args_info.watertype_given = 1;
           args_info->watertype_given = 1;
           args_info->watertype_flag = !(args_info->watertype_flag);
           break;
 
-        case 's':	/* ignore the atom types.  */
-          args_info->ignore_given++;
-          ignore_new = (struct ignore_list *) malloc (sizeof (struct ignore_list));
-          ignore_new->next = ignore_list;
-          ignore_list = ignore_new;
-          ignore_new->ignore_arg = gengetopt_strdup (optarg);
+        case 's':	/* general selection syntax.  */
+          if (local_args_info.selection_given)
+            {
+              fprintf (stderr, "%s: `--selection' (`-s') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
+              goto failure;
+            }
+          if (args_info->selection_given && ! override)
+            continue;
+          local_args_info.selection_given = 1;
+          args_info->selection_given = 1;
+          if (args_info->selection_arg)
+            free (args_info->selection_arg); /* free previous string */
+          args_info->selection_arg = gengetopt_strdup (optarg);
+          if (args_info->selection_orig)
+            free (args_info->selection_orig); /* free previous string */
+          args_info->selection_orig = gengetopt_strdup (optarg);
           break;
 
+        case 'b':	/* Convert to base atom type.  */
+          if (local_args_info.basetype_given)
+            {
+              fprintf (stderr, "%s: `--basetype' (`-b') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
+              goto failure;
+            }
+          if (args_info->basetype_given && ! override)
+            continue;
+          local_args_info.basetype_given = 1;
+          args_info->basetype_given = 1;
+          args_info->basetype_flag = !(args_info->basetype_flag);
+          break;
 
+
         case 0:	/* Long option with no short option */
-          /* The number of images to repeat in the x direction.  */
-          if (strcmp (long_options[option_index].name, "repeatX") == 0)
+          /* select origin.  */
+          if (strcmp (long_options[option_index].name, "originsele") == 0)
           {
-            if (args_info->repeatX_given)
+            if (local_args_info.originsele_given)
               {
-                fprintf (stderr, "%s: `--repeatX' option given more than once\n", CMDLINE_PARSER_PACKAGE);
-                clear_args ();
-                exit (EXIT_FAILURE);
+                fprintf (stderr, "%s: `--originsele' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
+                goto failure;
               }
+            if (args_info->originsele_given && ! override)
+              continue;
+            local_args_info.originsele_given = 1;
+            args_info->originsele_given = 1;
+            if (args_info->originsele_arg)
+              free (args_info->originsele_arg); /* free previous string */
+            args_info->originsele_arg = gengetopt_strdup (optarg);
+            if (args_info->originsele_orig)
+              free (args_info->originsele_orig); /* free previous string */
+            args_info->originsele_orig = gengetopt_strdup (optarg);
+          }
+          /* select reference.  */
+          else if (strcmp (long_options[option_index].name, "refsele") == 0)
+          {
+            if (local_args_info.refsele_given)
+              {
+                fprintf (stderr, "%s: `--refsele' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
+                goto failure;
+              }
+            if (args_info->refsele_given && ! override)
+              continue;
+            local_args_info.refsele_given = 1;
+            args_info->refsele_given = 1;
+            if (args_info->refsele_arg)
+              free (args_info->refsele_arg); /* free previous string */
+            args_info->refsele_arg = gengetopt_strdup (optarg);
+            if (args_info->refsele_orig)
+              free (args_info->refsele_orig); /* free previous string */
+            args_info->refsele_orig = gengetopt_strdup (optarg);
+          }
+          /* The number of images to repeat in the x direction.  */
+          else if (strcmp (long_options[option_index].name, "repeatX") == 0)
+          {
+            if (local_args_info.repeatX_given)
+              {
+                fprintf (stderr, "%s: `--repeatX' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
+                goto failure;
+              }
+            if (args_info->repeatX_given && ! override)
+              continue;
+            local_args_info.repeatX_given = 1;
             args_info->repeatX_given = 1;
-            args_info->repeatX_arg = strtol (optarg,&stop_char,0);
-            break;
+            args_info->repeatX_arg = strtol (optarg, &stop_char, 0);
+            if (!(stop_char && *stop_char == '\0')) {
+              fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
+              goto failure;
+            }
+            if (args_info->repeatX_orig)
+              free (args_info->repeatX_orig); /* free previous string */
+            args_info->repeatX_orig = gengetopt_strdup (optarg);
           }
-          
           /* The number of images to repeat in the y direction.  */
           else if (strcmp (long_options[option_index].name, "repeatY") == 0)
           {
-            if (args_info->repeatY_given)
+            if (local_args_info.repeatY_given)
               {
-                fprintf (stderr, "%s: `--repeatY' option given more than once\n", CMDLINE_PARSER_PACKAGE);
-                clear_args ();
-                exit (EXIT_FAILURE);
+                fprintf (stderr, "%s: `--repeatY' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
+                goto failure;
               }
+            if (args_info->repeatY_given && ! override)
+              continue;
+            local_args_info.repeatY_given = 1;
             args_info->repeatY_given = 1;
-            args_info->repeatY_arg = strtol (optarg,&stop_char,0);
-            break;
+            args_info->repeatY_arg = strtol (optarg, &stop_char, 0);
+            if (!(stop_char && *stop_char == '\0')) {
+              fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
+              goto failure;
+            }
+            if (args_info->repeatY_orig)
+              free (args_info->repeatY_orig); /* free previous string */
+            args_info->repeatY_orig = gengetopt_strdup (optarg);
           }
-          
           /* The number of images to repeat in the z direction.  */
           else if (strcmp (long_options[option_index].name, "repeatZ") == 0)
           {
-            if (args_info->repeatZ_given)
+            if (local_args_info.repeatZ_given)
               {
-                fprintf (stderr, "%s: `--repeatZ' option given more than once\n", CMDLINE_PARSER_PACKAGE);
-                clear_args ();
-                exit (EXIT_FAILURE);
+                fprintf (stderr, "%s: `--repeatZ' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
+                goto failure;
               }
+            if (args_info->repeatZ_given && ! override)
+              continue;
+            local_args_info.repeatZ_given = 1;
             args_info->repeatZ_given = 1;
-            args_info->repeatZ_arg = strtol (optarg,&stop_char,0);
-            break;
+            args_info->repeatZ_arg = strtol (optarg, &stop_char, 0);
+            if (!(stop_char && *stop_char == '\0')) {
+              fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
+              goto failure;
+            }
+            if (args_info->repeatZ_orig)
+              free (args_info->repeatZ_orig); /* free previous string */
+            args_info->repeatZ_orig = gengetopt_strdup (optarg);
           }
+          /* Replace the Gay-Berne atom with four linear atoms.  */
+          else if (strcmp (long_options[option_index].name, "gb") == 0)
+          {
+            if (local_args_info.gb_given)
+              {
+                fprintf (stderr, "%s: `--gb' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
+                goto failure;
+              }
+            if (args_info->gb_given && ! override)
+              continue;
+            local_args_info.gb_given = 1;
+            args_info->gb_given = 1;
+            if (args_info->gb_arg)
+              free (args_info->gb_arg); /* free previous string */
+            args_info->gb_arg = gengetopt_strdup (optarg);
+            if (args_info->gb_orig)
+              free (args_info->gb_orig); /* free previous string */
+            args_info->gb_orig = gengetopt_strdup (optarg);
+          }
+          /* Print only positions in xyz file.  */
+          else if (strcmp (long_options[option_index].name, "printPosOnly") == 0)
+          {
+            if (local_args_info.printPosOnly_given)
+              {
+                fprintf (stderr, "%s: `--printPosOnly' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
+                goto failure;
+              }
+            if (args_info->printPosOnly_given && ! override)
+              continue;
+            local_args_info.printPosOnly_given = 1;
+            args_info->printPosOnly_given = 1;
+            args_info->printPosOnly_flag = !(args_info->printPosOnly_flag);
+          }
           
-
+          break;
         case '?':	/* Invalid option.  */
           /* `getopt_long' already printed an error message.  */
-          exit (EXIT_FAILURE);
+          goto failure;
 
         default:	/* bug: option not considered.  */
-          fprintf (stderr, "%s: option unknown: %c\n", CMDLINE_PARSER_PACKAGE, c);
+          fprintf (stderr, "%s: option unknown: %c%s\n", CMDLINE_PARSER_PACKAGE, c, (additional_error ? additional_error : ""));
           abort ();
         } /* switch */
     } /* while */
 
 
-  if (! args_info->input_given)
-    {
-      fprintf (stderr, "%s: '--input' ('-i') option required\n", CMDLINE_PARSER_PACKAGE);
-      missing_required_options = 1;
-    }
-  if ( missing_required_options )
-    exit (EXIT_FAILURE);
 
-  if (args_info->ignore_given)
+  if (check_required)
     {
-      args_info->ignore_arg = (char * *) malloc (args_info->ignore_given * sizeof (char *));
-      for (i = 0; i < args_info->ignore_given; i++)
-        {
-          args_info->ignore_arg [i] = ignore_list->ignore_arg;
-          ignore_list = ignore_list->next;
-        }
+      error += cmdline_parser_required2 (args_info, argv[0], additional_error);
     }
-  
+
+  cmdline_parser_release (&local_args_info);
+
+  if ( error )
+    return (EXIT_FAILURE);
+
   return 0;
+
+failure:
+  
+  cmdline_parser_release (&local_args_info);
+  return (EXIT_FAILURE);
 }