--- trunk/src/utils/Utility.hpp	2006/05/17 21:51:42	963
+++ trunk/src/utils/Utility.hpp	2013/06/16 15:15:42	1879
@@ -6,19 +6,10 @@
  * redistribute this software in source and binary code form, provided
  * that the following conditions are met:
  *
- * 1. Acknowledgement of the program authors must be made in any
- *    publication of scientific results based in part on use of the
- *    program.  An acceptable form of acknowledgement is citation of
- *    the article in which the program was described (Matthew
- *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
- *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
- *    Parallel Simulation Engine for Molecular Dynamics,"
- *    J. Comput. Chem. 26, pp. 252-271 (2005))
- *
- * 2. Redistributions of source code must retain the above copyright
+ * 1. Redistributions of source code must retain the above copyright
  *    notice, this list of conditions and the following disclaimer.
  *
- * 3. Redistributions in binary form must reproduce the above copyright
+ * 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.
@@ -37,6 +28,16 @@
  * 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).
  */
  
 #ifndef UTILS_UTILITY_HPP
@@ -46,35 +47,41 @@
 #include "config.h"
 #include "utils/next_combination.hpp"
 
-namespace oopse {
+using namespace std;
+namespace OpenMD {
   inline RealType roundMe( RealType x ){
     return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
   }
 
   /**
    * @brief iteratively replace the sequence with wild cards
-   * @return true if more combination sequence is avaliable, otherwise return true
-   * @param cont iterator container, if expect the whole series of combinations,  pass an empty iterator 
-   * container. The user should not modify this iterator container
+   * @return true if more combination sequence is avaliable, otherwise
+   * return true
+   * @param cont iterator container, if expect the whole series of
+   * combinations, pass an empty iterator container. The user should
+   * not modify this iterator container
    * @param sequence the whole sequence used to generate combination
    * @param result a possible combination sequence which is set on return
    * @param wildCard the wild card string. Its value is "X" by default
-   * @note since next_combination never returns an empty sequence, replaceWildCard will not generate 
-   * one special combination, which is n identical wild cards (n is equal to the size of the passing sequence)
+   * @note since next_combination never returns an empty sequence,
+   * replaceWildCard will not generate one special combination, which
+   * is n identical wild cards (n is equal to the size of the passing
+   * sequence)
    * 
    * @code
-   * std::vector<std::string> sv;
-   * std::vector<std::vector<std::string>::iterator> sic;
-   * std::vector<std::string> resultString;
+   * vector<string> sv;
+   * vector<vector<string>::iterator> sic;
+   * vector<string> resultString;
    * sv.push_back("H");
    * sv.push_back("C");
    * sv.push_back("N");
 
    * while (replaceWithWildCard(sic, sv, resultString)) {   
-   *     for(std::vector<std::string>::iterator i = resultString.begin(); i != resultString.end(); ++i) {
-   *         std::cout << *i << "\t";
+   *     for(vector<string>::iterator i = resultString.begin(); 
+   *          i != resultString.end(); ++i) {
+   *         cout << *i << "\t";
    *     }
-   *     std::cout << std::endl;
+   *     cout << endl;
    * }
    * //output
    * //H X X
@@ -86,8 +93,9 @@ namespace oopse {
    * //H C N
    * @endcode
    */
-  bool replaceWithWildCard(std::vector<std::vector<std::string>::iterator>& cont,
-			   std::vector<std::string>& sequence, std::vector<std::string>& result, const std::string& wildCard = "X");
+  bool replaceWithWildCard(vector<vector<string>::iterator>& cont,
+			   vector<string>& sequence, vector<string>& result, 
+                           const string& wildCard = "X");
 }
 #endif