--- trunk/SHAPES/shaperCmd.c	2004/06/25 22:16:39	1311
+++ trunk/SHAPES/shaperCmd.c	2004/06/26 15:32:12	1312
@@ -39,6 +39,7 @@ void clear_given (struct gengetopt_args_info *args_inf
   args_info->version_given = 0 ;
   args_info->input_given = 0 ;
   args_info->bandwidth_given = 0 ;
+  args_info->tolerance_given = 0 ;
   args_info->charmm_given = 0 ;
   args_info->amber_given = 0 ;
   args_info->lj_given = 0 ;
@@ -52,6 +53,7 @@ void clear_args (struct gengetopt_args_info *args_info
 {
   args_info->input_arg = NULL;
   args_info->bandwidth_arg = 8 ;
+  args_info->tolerance_arg = 0.01 ;
 }
 
 void
@@ -67,17 +69,18 @@ cmdline_parser_print_help (void)
   printf("\n"
   "Usage: %s [OPTIONS]...\n", CMDLINE_PARSER_PACKAGE);
   printf("\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 file name");
-  printf("%s\n","  -b, --bandwidth=INT   The step detail for the potential grids - typically a \n                          power of 2  (default=`8')");
+  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 file name");
+  printf("%s\n","  -b, --bandwidth=INT     The step detail for the potential grids - typically \n                            a power of 2  (default=`8')");
+  printf("%s\n","  -t, --tolerance=DOUBLE  The tolerance for recognition of spherical harmonic \n                            terms  (default=`0.01')");
   printf("\n");
   printf(" Group: ForceField A Force Field must be specified\n");
-  printf("%s\n","  -c, --charmm          Use CHARMM 27 parameters");
-  printf("%s\n","  -a, --amber           Use Amber99 parameters");
-  printf("%s\n","  -l, --lj              Use Lennard-Jones parameters");
-  printf("%s\n","  -g, --gaff            Use GAFF parameters");
-  printf("%s\n","  -o, --opls            Use OPLS/AA parameters");
+  printf("%s\n","  -c, --charmm            Use CHARMM 27 parameters");
+  printf("%s\n","  -a, --amber             Use Amber99 parameters");
+  printf("%s\n","  -l, --lj                Use Lennard-Jones parameters");
+  printf("%s\n","  -g, --gaff              Use GAFF parameters");
+  printf("%s\n","  -o, --opls              Use OPLS/AA parameters");
 }
 
 void
@@ -184,6 +187,7 @@ cmdline_parser_internal (int argc, char * const *argv,
         { "version",	0, NULL, 'V' },
         { "input",	1, NULL, 'i' },
         { "bandwidth",	1, NULL, 'b' },
+        { "tolerance",	1, NULL, 't' },
         { "charmm",	0, NULL, 'c' },
         { "amber",	0, NULL, 'a' },
         { "lj",	0, NULL, 'l' },
@@ -193,7 +197,7 @@ cmdline_parser_internal (int argc, char * const *argv,
       };
 
       stop_char = 0;
-      c = getopt_long (argc, argv, "hVi:b:calgo", long_options, &option_index);
+      c = getopt_long (argc, argv, "hVi:b:t:calgo", long_options, &option_index);
 
       if (c == -1) break;	/* Exit from `while (1)' loop.  */
 
@@ -233,6 +237,19 @@ cmdline_parser_internal (int argc, char * const *argv,
           local_args_info.bandwidth_given = 1;
           args_info->bandwidth_given = 1;
           args_info->bandwidth_arg = strtol (optarg,&stop_char,0);
+          break;
+
+        case 't':	/* The tolerance for recognition of spherical harmonic terms.  */
+          if (local_args_info.tolerance_given)
+            {
+              fprintf (stderr, "%s: `--tolerance' (`-t') option given more than once%s\n", CMDLINE_PARSER_PACKAGE, (additional_error ? additional_error : ""));
+              goto failure;
+            }
+          if (args_info->tolerance_given && ! override)
+            continue;
+          local_args_info.tolerance_given = 1;
+          args_info->tolerance_given = 1;
+          args_info->tolerance_arg = strtod (optarg, NULL);
           break;
 
         case 'c':	/* Use CHARMM 27 parameters.  */