--- trunk/src/utils/Utility.hpp	2005/01/12 22:41:40	246
+++ trunk/src/utils/Utility.hpp	2009/11/25 20:02:06	1390
@@ -1,4 +1,4 @@
- /*
+/*
  * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
  *
  * The University of Notre Dame grants you ("Licensee") a
@@ -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.
@@ -37,56 +28,66 @@
  * 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, 24107 (2008).          
+ * [4]  Vardeman & Gezelter, in progress (2009).                        
  */
  
 #ifndef UTILS_UTILITY_HPP
 #define UTILS_UTILITY_HPP
 #include <vector>
 #include <math.h>
+#include "config.h"
 #include "utils/next_combination.hpp"
 
-namespace oopse {
-inline double roundMe( double x ){
-  return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
-}
+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
- * @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)
- * 
- * @code
- * std::vector<std::string> sv;
- * std::vector<std::vector<std::string>::iterator> sic;
- * std::vector<std::string> resultString;
- * sv.push_back("H");
- * sv.push_back("C");
- * sv.push_back("N");
+  /**
+   * @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
+   * @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)
+   * 
+   * @code
+   * std::vector<std::string> sv;
+   * std::vector<std::vector<std::string>::iterator> sic;
+   * std::vector<std::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";
- *     }
- *     std::cout << std::endl;
- * }
- * //output
- * //H X X
- * //X C X
- * //X X N
- * //H C X
- * //H X N
- * //X C N
- * //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");
+   * while (replaceWithWildCard(sic, sv, resultString)) {   
+   *     for(std::vector<std::string>::iterator i = resultString.begin(); i != resultString.end(); ++i) {
+   *         std::cout << *i << "\t";
+   *     }
+   *     std::cout << std::endl;
+   * }
+   * //output
+   * //H X X
+   * //X C X
+   * //X X N
+   * //H C X
+   * //H X N
+   * //X C N
+   * //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");
 }
 #endif