OpenMD 3.0
Molecular Dynamics in the Open
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AtomData.hpp
1/*
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31 * SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
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 VISITOR_ATOMDATA_HPP
46#define VISITOR_ATOMDATA_HPP
47
48#include <memory>
49#include <string>
50#include <vector>
51
52#include "math/Vector3.hpp"
53#include "utils/GenericData.hpp"
54
55namespace OpenMD {
56
57 struct AtomInfo {
58 AtomInfo() :
59 pos(V3Zero), vec(V3Zero), vel(V3Zero), frc(V3Zero), eField(V3Zero),
60 charge(0.0), hasCharge(false), hasVector(false), hasVelocity(false),
61 hasForce(false), hasElectricField(false), hasGlobalID(false) {}
62
63 std::string atomTypeName;
64 int globalID;
65 Vector3d pos;
66 Vector3d vec;
67 Vector3d vel;
68 Vector3d frc;
69 Vector3d eField;
70 RealType charge;
71 bool hasCharge;
72 bool hasVector;
73 bool hasVelocity;
74 bool hasForce;
75 bool hasElectricField;
76 bool hasGlobalID;
77 };
78
79 class AtomData : public GenericData {
80 public:
81 AtomData(const std::string& id = "ATOMDATA") : GenericData(id) {}
82
83 void addAtomInfo(std::shared_ptr<AtomInfo> info) { data.push_back(info); }
84
85 void clearAllAtomInfo();
86
87 std::shared_ptr<AtomInfo> beginAtomInfo(
88 std::vector<std::shared_ptr<AtomInfo>>::iterator& i) {
89 i = data.begin();
90 return i != data.end() ? *i : nullptr;
91 }
92
93 std::shared_ptr<AtomInfo> nextAtomInfo(
94 std::vector<std::shared_ptr<AtomInfo>>::iterator& i) {
95 ++i;
96 return i != data.end() ? *i : nullptr;
97 }
98
99 std::vector<std::shared_ptr<AtomInfo>> getData() { return data; }
100
101 size_t getSize() { return data.size(); }
102
103 protected:
104 std::vector<std::shared_ptr<AtomInfo>> data;
105 };
106} // namespace OpenMD
107
108#endif // VISITOR_ATOMDATA_HPP
@ class GenericData GenericData.hpp "utils/GenericData.hpp"
This basic Periodic Table class was originally taken from the data.cpp file in OpenBabel.