--- trunk/src/applications/sequentialProps/SequentialPropsCmd.cpp	2014/11/06 14:31:32	2039
+++ trunk/src/applications/sequentialProps/SequentialPropsCmd.cpp	2015/03/17 18:22:18	2081
@@ -44,6 +44,8 @@ const char *gengetopt_args_info_help[] = {
   "      --sele2=selection script  select second stuntdouble set (if sele2 is not \n                                  set, use script from sele1)",
   "  -b, --nbins=INT               number of bins (general purpose)  \n                                  (default=`100')",
   "      --nbins_z=INT             number of bins in z axis  (default=`100')",
+  "  -x, --centroidX=DOUBLE        Location of droplet centroid in x",
+  "  -y, --centroidY=DOUBLE        Location of droplet centroid in y",
   "  -z, --referenceZ=DOUBLE       Reference z-height of solid surface",
   "  -r, --dropletR=DOUBLE         Droplet radius in angstroms",
   "      --threshDens=DOUBLE       Threshold Density in g/cm^3",
@@ -87,6 +89,8 @@ void clear_given (struct gengetopt_args_info *args_inf
   args_info->sele2_given = 0 ;
   args_info->nbins_given = 0 ;
   args_info->nbins_z_given = 0 ;
+  args_info->centroidX_given = 0 ;
+  args_info->centroidY_given = 0 ;
   args_info->referenceZ_given = 0 ;
   args_info->dropletR_given = 0 ;
   args_info->threshDens_given = 0 ;
@@ -113,6 +117,8 @@ void clear_args (struct gengetopt_args_info *args_info
   args_info->nbins_orig = NULL;
   args_info->nbins_z_arg = 100;
   args_info->nbins_z_orig = NULL;
+  args_info->centroidX_orig = NULL;
+  args_info->centroidY_orig = NULL;
   args_info->referenceZ_orig = NULL;
   args_info->dropletR_orig = NULL;
   args_info->threshDens_orig = NULL;
@@ -133,13 +139,15 @@ void init_args_info(struct gengetopt_args_info *args_i
   args_info->sele2_help = gengetopt_args_info_help[5] ;
   args_info->nbins_help = gengetopt_args_info_help[6] ;
   args_info->nbins_z_help = gengetopt_args_info_help[7] ;
-  args_info->referenceZ_help = gengetopt_args_info_help[8] ;
-  args_info->dropletR_help = gengetopt_args_info_help[9] ;
-  args_info->threshDens_help = gengetopt_args_info_help[10] ;
-  args_info->bufferLength_help = gengetopt_args_info_help[11] ;
-  args_info->com_help = gengetopt_args_info_help[13] ;
-  args_info->ca1_help = gengetopt_args_info_help[14] ;
-  args_info->ca2_help = gengetopt_args_info_help[15] ;
+  args_info->centroidX_help = gengetopt_args_info_help[8] ;
+  args_info->centroidY_help = gengetopt_args_info_help[9] ;
+  args_info->referenceZ_help = gengetopt_args_info_help[10] ;
+  args_info->dropletR_help = gengetopt_args_info_help[11] ;
+  args_info->threshDens_help = gengetopt_args_info_help[12] ;
+  args_info->bufferLength_help = gengetopt_args_info_help[13] ;
+  args_info->com_help = gengetopt_args_info_help[15] ;
+  args_info->ca1_help = gengetopt_args_info_help[16] ;
+  args_info->ca2_help = gengetopt_args_info_help[17] ;
   
 }
 
@@ -233,6 +241,8 @@ cmdline_parser_release (struct gengetopt_args_info *ar
   free_string_field (&(args_info->sele2_orig));
   free_string_field (&(args_info->nbins_orig));
   free_string_field (&(args_info->nbins_z_orig));
+  free_string_field (&(args_info->centroidX_orig));
+  free_string_field (&(args_info->centroidY_orig));
   free_string_field (&(args_info->referenceZ_orig));
   free_string_field (&(args_info->dropletR_orig));
   free_string_field (&(args_info->threshDens_orig));
@@ -288,6 +298,10 @@ cmdline_parser_dump(FILE *outfile, struct gengetopt_ar
     write_into_file(outfile, "nbins", args_info->nbins_orig, 0);
   if (args_info->nbins_z_given)
     write_into_file(outfile, "nbins_z", args_info->nbins_z_orig, 0);
+  if (args_info->centroidX_given)
+    write_into_file(outfile, "centroidX", args_info->centroidX_orig, 0);
+  if (args_info->centroidY_given)
+    write_into_file(outfile, "centroidY", args_info->centroidY_orig, 0);
   if (args_info->referenceZ_given)
     write_into_file(outfile, "referenceZ", args_info->referenceZ_orig, 0);
   if (args_info->dropletR_given)
@@ -611,6 +625,8 @@ cmdline_parser_internal (
         { "sele2",	1, NULL, 0 },
         { "nbins",	1, NULL, 'b' },
         { "nbins_z",	1, NULL, 0 },
+        { "centroidX",	1, NULL, 'x' },
+        { "centroidY",	1, NULL, 'y' },
         { "referenceZ",	1, NULL, 'z' },
         { "dropletR",	1, NULL, 'r' },
         { "threshDens",	1, NULL, 0 },
@@ -621,7 +637,7 @@ cmdline_parser_internal (
         { 0,  0, 0, 0 }
       };
 
-      c = getopt_long (argc, argv, "hVi:o:b:z:r:c", long_options, &option_index);
+      c = getopt_long (argc, argv, "hVi:o:b:x:y:z:r:c", long_options, &option_index);
 
       if (c == -1) break;	/* Exit from `while (1)' loop.  */
 
@@ -669,10 +685,34 @@ cmdline_parser_internal (
               &(local_args_info.nbins_given), optarg, 0, "100", ARG_INT,
               check_ambiguity, override, 0, 0,
               "nbins", 'b',
+              additional_error))
+            goto failure;
+        
+          break;
+        case 'x':	/* Location of droplet centroid in x.  */
+        
+        
+          if (update_arg( (void *)&(args_info->centroidX_arg), 
+               &(args_info->centroidX_orig), &(args_info->centroidX_given),
+              &(local_args_info.centroidX_given), optarg, 0, 0, ARG_DOUBLE,
+              check_ambiguity, override, 0, 0,
+              "centroidX", 'x',
               additional_error))
             goto failure;
         
           break;
+        case 'y':	/* Location of droplet centroid in y.  */
+        
+        
+          if (update_arg( (void *)&(args_info->centroidY_arg), 
+               &(args_info->centroidY_orig), &(args_info->centroidY_given),
+              &(local_args_info.centroidY_given), optarg, 0, 0, ARG_DOUBLE,
+              check_ambiguity, override, 0, 0,
+              "centroidY", 'y',
+              additional_error))
+            goto failure;
+        
+          break;
         case 'z':	/* Reference z-height of solid surface.  */