--- trunk/OOPSE/utils/Dump2XYZCmd.c	2004/04/19 03:52:27	1118
+++ trunk/OOPSE/utils/Dump2XYZCmd.c	2004/04/20 05:39:38	1126
@@ -38,12 +38,14 @@ cmdline_parser_print_help (void)
   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=STRING    output file name\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("  -r, --replace          replace the atom types of zconstraint molecules  \n                           (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");
@@ -87,7 +89,9 @@ cmdline_parser (int argc, char * const *argv, struct g
   args_info->dipole_given = 0 ;
   args_info->water_given = 0 ;
   args_info->periodicBox_given = 0 ;
-  args_info->replace_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 ;
@@ -99,7 +103,9 @@ cmdline_parser (int argc, char * const *argv, struct g
   args_info->dipole_flag = 0;\
   args_info->water_flag = 0;\
   args_info->periodicBox_flag = 0;\
-  args_info->replace_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 ;\
@@ -127,7 +133,9 @@ cmdline_parser (int argc, char * const *argv, struct g
         { "dipole",	0, NULL, 'd' },
         { "water",	0, NULL, 'w' },
         { "periodicBox",	0, NULL, 'm' },
-        { "replace",	0, NULL, 'r' },
+        { "zconstraint",	0, NULL, 'z' },
+        { "rigidbody",	0, NULL, 'r' },
+        { "watertype",	0, NULL, 't' },
         { "ignore",	1, NULL, 's' },
         { "repeatX",	1, NULL, 0 },
         { "repeatY",	1, NULL, 0 },
@@ -136,7 +144,7 @@ cmdline_parser (int argc, char * const *argv, struct g
       };
 
       stop_char = 0;
-      c = getopt_long (argc, argv, "hVi:o:n:dwmrs:", long_options, &option_index);
+      c = getopt_long (argc, argv, "hVi:o:n:dwmzrts:", long_options, &option_index);
 
       if (c == -1) break;	/* Exit from `while (1)' loop.  */
 
@@ -218,17 +226,39 @@ cmdline_parser (int argc, char * const *argv, struct g
           args_info->periodicBox_flag = !(args_info->periodicBox_flag);
           break;
 
-        case 'r':	/* replace the atom types of zconstraint molecules.  */
-          if (args_info->replace_given)
+        case 'z':	/* replace the atom types of zconstraint molecules.  */
+          if (args_info->zconstraint_given)
             {
-              fprintf (stderr, "%s: `--replace' (`-r') option given more than once\n", CMDLINE_PARSER_PACKAGE);
+              fprintf (stderr, "%s: `--zconstraint' (`-z') option given more than once\n", CMDLINE_PARSER_PACKAGE);
+              clear_args ();
+              exit (EXIT_FAILURE);
+            }
+          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)
+            {
+              fprintf (stderr, "%s: `--rigidbody' (`-r') option given more than once\n", CMDLINE_PARSER_PACKAGE);
               clear_args ();
               exit (EXIT_FAILURE);
             }
-          args_info->replace_given = 1;
-          args_info->replace_flag = !(args_info->replace_flag);
+          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)
+            {
+              fprintf (stderr, "%s: `--watertype' (`-t') option given more than once\n", CMDLINE_PARSER_PACKAGE);
+              clear_args ();
+              exit (EXIT_FAILURE);
+            }
+          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));