src/utils/Utility.hpp

/*
 * 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).
 */
 
#ifndef UTILS_UTILITY_HPP
#define UTILS_UTILITY_HPP
#include <vector>
#include <math.h>
#include "config.h"
#include "utils/next_combination.hpp"

using namespace std;
namespace OpenMD {
  inline RealType roundMe( const 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
   * 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(vector<string>::iterator i = resultString.begin(); 
   *          i != resultString.end(); ++i) {
   *         cout << *i << "\t";
   *     }
   *     cout << 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(vector<vector<string>::iterator>& cont,
                           vector<string>& sequence, vector<string>& result, 
                           const string& wildCard = "X");
}
#endif

Revision:	1896
Committed:	Tue Jul 2 20:02:31 2013 UTC (12 years, 4 months ago) by gezelter
File size:	4005 byte(s)
Log Message:	Speedup tests
#	User	Rev	Content
1	gezelter	507	/*
2	gezelter	246	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3			*
4			* The University of Notre Dame grants you ("Licensee") a
5			* non-exclusive, royalty free, license to use, modify and
6			* redistribute this software in source and binary code form, provided
7			* that the following conditions are met:
8			*
9	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	gezelter	246	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	gezelter	246	* notice, this list of conditions and the following disclaimer in the
14			* documentation and/or other materials provided with the
15			* distribution.
16			*
17			* This software is provided "AS IS," without a warranty of any
18			* kind. All express or implied conditions, representations and
19			* warranties, including any implied warranty of merchantability,
20			* fitness for a particular purpose or non-infringement, are hereby
21			* excluded. The University of Notre Dame and its licensors shall not
22			* be liable for any damages suffered by licensee as a result of
23			* using, modifying or distributing the software or its
24			* derivatives. In no event will the University of Notre Dame or its
25			* licensors be liable for any lost revenue, profit or data, or for
26			* direct, indirect, special, consequential, incidental or punitive
27			* damages, however caused and regardless of the theory of liability,
28			* arising out of the use of or inability to use software, even if the
29			* University of Notre Dame has been advised of the possibility of
30			* such damages.
31	gezelter	1390	*
32			* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33			* research, please cite the appropriate papers when you publish your
34			* work. Good starting points are:
35			*
36			* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37			* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	gezelter	1879	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	gezelter	1782	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	gezelter	246	*/
42
43			#ifndef UTILS_UTILITY_HPP
44			#define UTILS_UTILITY_HPP
45	gezelter	2	#include <vector>
46			#include <math.h>
47	tim	963	#include "config.h"
48	gezelter	246	#include "utils/next_combination.hpp"
49
50	gezelter	1782	using namespace std;
51	gezelter	1390	namespace OpenMD {
52	gezelter	1896	inline RealType roundMe( const RealType &x ){
53	gezelter	507	return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
54			}
55	gezelter	246
56	gezelter	507	/**
57			* @brief iteratively replace the sequence with wild cards
58	gezelter	1782	* @return true if more combination sequence is avaliable, otherwise
59			* return true
60			* @param cont iterator container, if expect the whole series of
61			* combinations, pass an empty iterator container. The user should
62			* not modify this iterator container
63	gezelter	507	* @param sequence the whole sequence used to generate combination
64			* @param result a possible combination sequence which is set on return
65			* @param wildCard the wild card string. Its value is "X" by default
66	gezelter	1782	* @note since next_combination never returns an empty sequence,
67			* replaceWildCard will not generate one special combination, which
68			* is n identical wild cards (n is equal to the size of the passing
69			* sequence)
70	gezelter	507	*
71			* @code
72	gezelter	1782	* vector<string> sv;
73			* vector<vector<string>::iterator> sic;
74			* vector<string> resultString;
75	gezelter	507	* sv.push_back("H");
76			* sv.push_back("C");
77			* sv.push_back("N");
78	gezelter	246
79	gezelter	507	* while (replaceWithWildCard(sic, sv, resultString)) {
80	gezelter	1782	* for(vector<string>::iterator i = resultString.begin();
81			* i != resultString.end(); ++i) {
82			* cout << *i << "\t";
83	gezelter	507	* }
84	gezelter	1782	* cout << endl;
85	gezelter	507	* }
86			* //output
87			* //H X X
88			* //X C X
89			* //X X N
90			* //H C X
91			* //H X N
92			* //X C N
93			* //H C N
94			* @endcode
95			*/
96	gezelter	1782	bool replaceWithWildCard(vector<vector<string>::iterator>& cont,
97			vector<string>& sequence, vector<string>& result,
98			const string& wildCard = "X");
99	gezelter	246	}
100	gezelter	2	#endif
101	gezelter	246