OpenMD 3.2
Molecular Dynamics in the Open
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AtomStamp.hpp
1/*
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17 * this software without specific prior written permission.
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31 * SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
32 * research, please cite the following paper when you publish your work:
33 *
34 * [1] Drisko et al., J. Open Source Softw. 9, 7004 (2024).
35 *
36 * Good starting points for code and simulation methodology are:
37 *
38 * [2] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
39 * [3] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
40 * [4] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
41 * [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
42 * [6] Kuang & Gezelter, Mol. Phys., 110, 691-701 (2012).
43 * [7] Lamichhane, Gezelter & Newman, J. Chem. Phys. 141, 134109 (2014).
44 * [8] Bhattarai, Newman & Gezelter, Phys. Rev. B 99, 094106 (2019).
45 * [9] Drisko & Gezelter, J. Chem. Theory Comput. 20, 4986-4997 (2024).
46 */
47
48#ifndef TYPES_ATOMSTAMP_HPP
49#define TYPES_ATOMSTAMP_HPP
50
51#include <set>
52#include <vector>
53
54#include "types/DataHolder.hpp"
55
56namespace OpenMD {
57
58 class AtomStamp : public DataHolder {
59 DeclareParameter(Type, std::string);
60
61 public:
62 AtomStamp(int index);
63
64 public:
65 bool setPosition(const std::vector<RealType>& pos);
66 bool setOrientation(const std::vector<RealType>& ort);
67 bool havePosition() { return havePos_; }
68 bool haveOrientation() { return haveOrt_; }
69 RealType getPosX() { return position_[0]; }
70 RealType getPosY() { return position_[1]; }
71 RealType getPosZ() { return position_[2]; }
72 RealType getEulerPhi() { return orientation_[0]; }
73 RealType getEulerTheta() { return orientation_[1]; }
74 RealType getEulerPsi() { return orientation_[2]; }
75 int getIndex() { return index_; }
76 virtual void validate();
77 using AtomIter = std::set<int>::iterator;
78 using BondIter = std::vector<int>::iterator;
79 int getFirstBondedAtom(AtomIter& ai) {
80 ai = bondedAtoms_.begin();
81 return ai != bondedAtoms_.end() ? *ai : -1;
82 }
83 int getNextBondedAtom(AtomIter& ai) {
84 ++ai;
85 return ai != bondedAtoms_.end() ? *ai : -1;
86 }
87 int getFirstBond(BondIter& bi) {
88 bi = bonds_.begin();
89 return bi != bonds_.end() ? *bi : -1;
90 }
91 int getNextBond(BondIter& bi) {
92 ++bi;
93 return bi != bonds_.end() ? *bi : -1;
94 }
95 void addBond(int bondIndex) { bonds_.push_back(bondIndex); }
96 void addBondedAtom(int atomIndex) { bondedAtoms_.insert(atomIndex); }
97 size_t getCoordination() { return bonds_.size(); }
98 void overrideCharge(RealType c) {
99 orCharge_ = c;
100 hasOverride_ = true;
101 }
102
103 bool hasOverride() { return hasOverride_; }
104 RealType getOverrideCharge() { return orCharge_; }
105
106 private:
107 Vector3d position_;
108 Vector3d orientation_;
109 RealType orCharge_;
110 bool havePos_;
111 bool haveOrt_;
112 bool hasOverride_;
113 int index_;
114 std::vector<int> bonds_;
115 std::set<int> bondedAtoms_;
116 };
117} // namespace OpenMD
118
119#endif
OpenMD
This basic Periodic Table class was originally taken from the data.cpp file in OpenBabel.
Definition ActionCorrFunc.cpp:63