OpenMD 3.0
Molecular Dynamics in the Open
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PairList.hpp
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32 * research, please cite the appropriate papers when you publish your
33 * work. Good starting points are:
34 *
35 * [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
36 * [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
37 * [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
38 * [4] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
39 * [5] Kuang & Gezelter, Mol. Phys., 110, 691-701 (2012).
40 * [6] Lamichhane, Gezelter & Newman, J. Chem. Phys. 141, 134109 (2014).
41 * [7] Lamichhane, Newman & Gezelter, J. Chem. Phys. 141, 134110 (2014).
42 * [8] Bhattarai, Newman & Gezelter, Phys. Rev. B 99, 094106 (2019).
43 */
44
45#ifndef BRAINS_PAIRLIST_HPP
46
47#define BRAINS_PAIRLIST_HPP
48
49#include <iostream>
50#include <set>
51#include <utility>
52#include <vector>
53
54namespace OpenMD {
55
56 /**
57 * @class PairList PairList.hpp "brains/PairList.hpp"
58 * @brief PairList class maintains a general purpose list of atom
59 * pairs using the global indices of the atoms. This structure is
60 * the general form for exclude lists as well as 1-4, 1-3, and 1-2
61 * lists.
62 */
63 class PairList {
64 public:
65 PairList() : modified_(false) {}
66
67 /** Adds a pair into this PairList class */
68 void addPair(int i, int j);
69
70 void addPairs(std::set<int>& set1, std::set<int>& set2);
71 template<typename IterType1, typename IterType2>
72 void addPairs(IterType1 iter1_first, IterType1 iter1_last,
73 IterType2 iter2_first, IterType2 iter2_last);
74
75 /** Remove a pair from PairList class */
76 void removePair(int i, int j);
77
78 void removePairs(std::set<int>& set1, std::set<int>& set2);
79 template<typename IterType1, typename IterType2>
80 void removePairs(IterType1 iter1_first, IterType1 iter1_last,
81 IterType2 iter2_first, IterType2 iter2_last);
82
83 /** Checks whether pair (i, j) is in this PairList class */
84 bool hasPair(int i, int j);
85
86 /** Returns the number of pairs in the list */
87 int getSize();
88
89 /** Returns the size of PairList */
91
92 /** Returns the pairs in a plain array*/
93 int* getPairList();
94
95 /** write out the exclusion list to an ostream */
96 friend std::ostream& operator<<(std::ostream& o, PairList& e);
97
98 private:
99 std::set<std::pair<int, int>> pairSet_;
100 std::vector<int> pairList_;
101 bool modified_;
102 };
103} // namespace OpenMD
104
105#endif // __PAIRLIST_H__
PairList class maintains a general purpose list of atom pairs using the global indices of the atoms.
Definition PairList.hpp:63
friend std::ostream & operator<<(std::ostream &o, PairList &e)
write out the exclusion list to an ostream
Definition PairList.cpp:154
int * getPairList()
Returns the pairs in a plain array.
Definition PairList.cpp:53
int getSizeOfPairList()
Returns the size of PairList.
bool hasPair(int i, int j)
Checks whether pair (i, j) is in this PairList class.
Definition PairList.cpp:140
void addPair(int i, int j)
Adds a pair into this PairList class.
Definition PairList.cpp:68
void removePair(int i, int j)
Remove a pair from PairList class.
Definition PairList.cpp:104
int getSize()
Returns the number of pairs in the list.
Definition PairList.cpp:152
This basic Periodic Table class was originally taken from the data.cpp file in OpenBabel.