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root/OpenMD/branches/development/src/utils/Utility.hpp

Comparing:
trunk/src/utils/Utility.hpp (file contents), Revision 246 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
branches/development/src/utils/Utility.hpp (file contents), Revision 1562 by gezelter, Thu May 12 17:00:14 2011 UTC

#	Line 1 | Line 1
1	<	/*
1	>	/*
2		* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3		*
4		* The University of Notre Dame grants you ("Licensee") a
#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
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	+	*
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	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	+	* [4]  Vardeman & Gezelter, in progress (2009).
40		*/
41
42		#ifndef UTILS_UTILITY_HPP
43		#define UTILS_UTILITY_HPP
44		#include <vector>
45		#include <math.h>
46	+	#include "config.h"
47		#include "utils/next_combination.hpp"
48
49	<	namespace oopse {
50	<	inline double roundMe( double x ){
51	<	return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
52	<	}
49	>	using namespace std;
50	>	namespace OpenMD {
51	>	inline RealType roundMe( RealType x ){
52	>	return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
53	>	}
54
55	<	/**
56	<	* @brief iteratively replace the sequence with wild cards
57	<	* @return true if more combination sequence is avaliable, otherwise return true
58	<	* @param cont iterator container, if expect the whole series of combinations,  pass an empty iterator
59	<	* container. The user should not modify this iterator container
60	<	* @param sequence the whole sequence used to generate combination
61	<	* @param result a possible combination sequence which is set on return
62	<	* @param wildCard the wild card string. Its value is "X" by default
63	<	* @note since next_combination never returns an empty sequence, replaceWildCard will not generate
64	<	* one special combination, which is n identical wild cards (n is equal to the size of the passing sequence)
65	<	*
66	<	* @code
67	<	* std::vector<std::string> sv;
68	<	* std::vector<std::vector<std::string>::iterator> sic;
69	<	* std::vector<std::string> resultString;
70	<	* sv.push_back("H");
71	<	* sv.push_back("C");
72	<	* sv.push_back("N");
55	>	/**
56	>	* @brief iteratively replace the sequence with wild cards
57	>	* @return true if more combination sequence is avaliable, otherwise
58	>	* return true
59	>	* @param cont iterator container, if expect the whole series of
60	>	* combinations, pass an empty iterator container. The user should
61	>	* not modify this iterator container
62	>	* @param sequence the whole sequence used to generate combination
63	>	* @param result a possible combination sequence which is set on return
64	>	* @param wildCard the wild card string. Its value is "X" by default
65	>	* @note since next_combination never returns an empty sequence,
66	>	* replaceWildCard will not generate one special combination, which
67	>	* is n identical wild cards (n is equal to the size of the passing
68	>	* sequence)
69	>	*
70	>	* @code
71	>	* vector<string> sv;
72	>	* vector<vector<string>::iterator> sic;
73	>	* vector<string> resultString;
74	>	* sv.push_back("H");
75	>	* sv.push_back("C");
76	>	* sv.push_back("N");
77
78	<	* while (replaceWithWildCard(sic, sv, resultString)) {
79	<	*     for(std::vector<std::string>::iterator i = resultString.begin(); i != resultString.end(); ++i) {
80	<	*         std::cout << *i << "\t";
81	<	*     }
82	<	*     std::cout << std::endl;
83	<	* }
84	<	* //output
85	<	* //H X X
86	<	* //X C X
87	<	* //X X N
88	<	* //H C X
89	<	* //H X N
90	<	* //X C N
91	<	* //H C N
92	<	* @endcode
93	<	*/
94	<	bool replaceWithWildCard(std::vector<std::vector<std::string>::iterator>& cont,
95	<	std::vector<std::string>& sequence, std::vector<std::string>& result, const std::string& wildCard = "X");
78	>	* while (replaceWithWildCard(sic, sv, resultString)) {
79	>	*     for(vector<string>::iterator i = resultString.begin();
80	>	*          i != resultString.end(); ++i) {
81	>	*         cout << *i << "\t";
82	>	*     }
83	>	*     cout << endl;
84	>	* }
85	>	* //output
86	>	* //H X X
87	>	* //X C X
88	>	* //X X N
89	>	* //H C X
90	>	* //H X N
91	>	* //X C N
92	>	* //H C N
93	>	* @endcode
94	>	*/
95	>	bool replaceWithWildCard(vector<vector<string>::iterator>& cont,
96	>	vector<string>& sequence, vector<string>& result,
97	>	const string& wildCard = "X");
98		}
99		#endif
100

Comparing:
trunk/src/utils/Utility.hpp (property svn:keywords), Revision 246 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
branches/development/src/utils/Utility.hpp (property svn:keywords), Revision 1562 by gezelter, Thu May 12 17:00:14 2011 UTC

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