OpenMD 3.0
Molecular Dynamics in the Open
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HBondJump.hpp
1/*
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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 APPLICATIONS_DYNAMICPROPS_HBONDJUMP_HPP
46#define APPLICATIONS_DYNAMICPROPS_HBONDJUMP_HPP
47
48#include "applications/dynamicProps/TimeCorrFunc.hpp"
49
50#define HONKING_LARGE_VALUE 1.0e10
51
52namespace OpenMD {
53
54 class HBondJump : public TimeCorrFunc<RealType> {
55 public:
56 HBondJump(SimInfo* info, const std::string& filename,
57 const std::string& sele1, const std::string& sele2, double OOCut,
58 double thetaCut, double OHCut);
59
60 protected:
61 virtual void correlation();
62 virtual void computeFrame(int istep);
63
64 virtual void computeProperty1(int) { return; }
65 virtual void computeProperty2(int) { return; }
66 virtual int computeProperty1(int, Molecule*) { return -1; }
67 virtual int computeProperty1(int, StuntDouble*) { return -1; }
68 virtual int computeProperty1(int, Bond*) { return -1; }
69 virtual int computeProperty2(int, Molecule*) { return -1; }
70 virtual int computeProperty2(int, StuntDouble*) { return -1; }
71 virtual int computeProperty2(int, Bond*) { return -1; }
72
73 virtual RealType calcCorrVal(int, int, int, int) { return 0.0; }
74 virtual RealType calcCorrVal(int, int) { return 0.0; }
75
76 virtual void postCorrelate();
77
78 virtual int registerHydrogen(int frame, int hIndex);
79 virtual void findHBonds(int frame);
80 bool isHBond(Vector3d donorPos, Vector3d hPos, Vector3d acceptorPos);
81 void registerHydrogenBond(int frame, int index, int hIndex, int aIndex);
82 void processNonOverlapping(int frame, SelectionManager& sman1,
83 SelectionManager& sman2);
84 void processOverlapping(int frame, SelectionManager& sman);
85
86 std::vector<std::vector<int>> GIDtoH_;
87 std::vector<std::vector<int>> hydrogen_;
88 std::vector<std::vector<int>> acceptor_;
89 std::vector<std::vector<int>> lastAcceptor_;
90 std::vector<std::vector<bool>> selected_;
91 std::vector<std::vector<int>> acceptorStartFrame_;
92
93 RealType OOCut_;
94 RealType thetaCut_;
95 RealType OHCut_;
96
97 SelectionManager sele1_minus_common_;
98 SelectionManager sele2_minus_common_;
99 SelectionManager common_;
100 };
101
102 class HBondJumpZ : public HBondJump {
103 public:
104 HBondJumpZ(SimInfo* info, const std::string& filename,
105 const std::string& sele1, const std::string& sele2, double OOCut,
106 double thetaCut, double OHCut, int nZbins, int axis = 2);
107 virtual int registerHydrogen(int frame, int hIndex);
108 virtual void findHBonds(int frame);
109 virtual void correlation();
110 virtual void postCorrelate();
111 virtual void writeCorrelate();
112
113 private:
114 std::vector<std::vector<RealType>> histogram_;
115 std::vector<std::vector<int>> counts_;
116 std::vector<std::vector<int>> zbin_;
117 unsigned int nZBins_;
118 int axis_;
119 std::string axisLabel_;
120 };
121
122 class HBondJumpR : public HBondJump {
123 public:
124 HBondJumpR(SimInfo* info, const std::string& filename,
125 const std::string& sele1, const std::string& sele2,
126 const std::string& sele3, double OOCut, RealType thetaCut,
127 RealType OHCut, RealType len, int nRbins);
128 virtual int registerHydrogen(int frame, int hIndex);
129 virtual void findHBonds(int frame);
130 virtual void correlation();
131 virtual void postCorrelate();
132 virtual void writeCorrelate();
133
134 private:
135 RealType len_;
136 unsigned int nRBins_;
137 RealType deltaR_;
138 SelectionManager seleMan3_;
139 std::string selectionScript3_;
140 SelectionEvaluator evaluator3_;
141
142 std::vector<std::vector<RealType>> histogram_;
143 std::vector<std::vector<int>> counts_;
144 std::vector<std::vector<int>> rbin_;
145 };
146} // namespace OpenMD
147
148#endif
"selection/SelectionEvaluator"
One of the heavy-weight classes of OpenMD, SimInfo maintains objects and variables relating to the cu...
Definition SimInfo.hpp:93
"Don't move, or you're dead! Stand up! Captain, we've got them!"
Computes a correlation function by scanning a trajectory once to precompute quantities to be correlat...
This basic Periodic Table class was originally taken from the data.cpp file in OpenBabel.