--- trunk/src/utils/Utility.cpp	2004/09/24 16:27:58	3
+++ branches/development/src/utils/Utility.cpp	2013/02/20 15:39:39	1850
@@ -1,24 +1,68 @@
+/*
+ * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
+ *
+ * The University of Notre Dame grants you ("Licensee") a
+ * non-exclusive, royalty free, license to use, modify and
+ * redistribute this software in source and binary code form, provided
+ * that the following conditions are met:
+ *
+ * 1. Redistributions of source code must retain the above copyright
+ *    notice, this list of conditions and the following disclaimer.
+ *
+ * 2. Redistributions in binary form must reproduce the above copyright
+ *    notice, this list of conditions and the following disclaimer in the
+ *    documentation and/or other materials provided with the
+ *    distribution.
+ *
+ * This software is provided "AS IS," without a warranty of any
+ * kind. All express or implied conditions, representations and
+ * warranties, including any implied warranty of merchantability,
+ * fitness for a particular purpose or non-infringement, are hereby
+ * excluded.  The University of Notre Dame and its licensors shall not
+ * be liable for any damages suffered by licensee as a result of
+ * using, modifying or distributing the software or its
+ * derivatives. In no event will the University of Notre Dame or its
+ * licensors be liable for any lost revenue, profit or data, or for
+ * direct, indirect, special, consequential, incidental or punitive
+ * damages, however caused and regardless of the theory of liability,
+ * arising out of the use of or inability to use software, even if the
+ * University of Notre Dame has been advised of the possibility of
+ * such damages.
+ *
+ * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
+ * research, please cite the appropriate papers when you publish your
+ * work.  Good starting points are:
+ *                                                                      
+ * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
+ * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
+ * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
+ * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
+ * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
+ */
+ 
+
 #include "utils/Utility.hpp"
-#include <vector>
-#include <iostream>
-#include <math.h>
-using namespace std;
 
-double dotProduct(vector<double>& v1, vector<double>& v2){
-  double sum;
+namespace OpenMD {
 
-  sum = 0;
+  bool replaceWithWildCard(std::vector<std::vector<std::string>::iterator>& cont,
+			   std::vector<std::string>& sequence, std::vector<std::string>& result, const std::string& wildCard) {
+    if (cont.size() > sequence.size()) {
+      std::cerr << "the size of iterator container is greater than the size of sequence";
+    }
 
-  if(v1.size() != v2.size()){
-    cerr << "Utility Error: dimension of two vectors are not matched" << endl;
-    exit(-1);
-  }
-  
-   for(int  i = 0; i < v1.size(); i++)
-     sum += v1[i]*v2[i];
-   return sum;
-}
+    bool hasMoreCombination = next_combination(cont, sequence.begin(), sequence.end());
+    if (hasMoreCombination) {
+      result.clear();
+      result.insert(result.begin(), sequence.size(), wildCard);
+      std::vector<std::vector<std::string>::iterator>::iterator i;
+      for ( i = cont.begin(); i != cont.end(); i++){
+	result[*i - sequence.begin()] = **i;
+      }
+    }
 
-double norm2(vector<double>& x){
-  return sqrt(dotProduct(x, x));
-}	
+    return hasMoreCombination;
+    
+  }//end replaceWildCard
+
+}