OpenMD 3.0
Molecular Dynamics in the Open
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LegendreCorrFuncZ.hpp
1/*
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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_LEGENDRECORRFUNCZ_HPP
46#define APPLICATIONS_DYNAMICPROPS_LEGENDRECORRFUNCZ_HPP
47
48#include "applications/dynamicProps/TimeCorrFunc.hpp"
49#include "math/Polynomial.hpp"
50#include "math/Vector3.hpp"
51
52using namespace std;
53namespace OpenMD {
54
55 class LegendreCorrFuncZ : public ObjectACF<Vector3d> {
56 public:
57 LegendreCorrFuncZ(SimInfo* info, const std::string& filename,
58 const std::string& sele1, const std::string& sele2,
59 int order, int nZbins, int axis = 2);
60
61 private:
62 virtual void validateSelection(SelectionManager& seleMan);
63 virtual void computeFrame(int frame);
64 virtual int computeProperty1(int frame, StuntDouble* sd);
65 virtual Vector3d calcCorrVal(int frame1, int frame2, int id1, int id2);
66 virtual void correlateFrames(int frame1, int frame2, int timeBin);
67 virtual void postCorrelate();
68 virtual void writeCorrelate();
69
70 DoublePolynomial legendre_;
71 unsigned int nZBins_;
72 RealType boxZ_, halfBoxZ_;
73 int axis_;
74 int xaxis_;
75 int yaxis_;
76 std::string axisLabel_;
77
78 std::vector<std::vector<RotMat3x3d>> rotMats_;
79 std::vector<std::vector<Vector3d>> histogram_;
80 std::vector<std::vector<int>> counts_;
81 std::vector<std::vector<int>> zbin_;
82 };
83} // namespace OpenMD
84
85#endif
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!"
This basic Periodic Table class was originally taken from the data.cpp file in OpenBabel.