OpenMD 3.1
Molecular Dynamics in the Open
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TranslationalOrderParamZ.hpp
1/*
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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_STATICPROPS_TRANSLATIONALORDERPARAMZ_HPP
46#define APPLICATIONS_STATICPROPS_TRANSLATIONALORDERPARAMZ_HPP
47
48#include "applications/staticProps/RadialDistrFunc.hpp"
49
50namespace OpenMD {
51
52 /**
53 * @class TranslationalOrderParamZ
54 * @brief TranslationalOrder ParameterZ
55 *
56 * Computes local translational order parameter t as introduced in:
57 *
58 * "Towards a quantification of disorder in materials: Distinguishing
59 * equilibrium and glassy sphere packings," by T. M. Truskett, S. Torquato,
60 * and P. G. Debenedetti, Phys. Rev. E 62(1), pp. 994-1001 (2000).
61 *
62 * and in:
63 *
64 * "Molecular structural order and anomalies in liquid silica," by
65 * M. Scott Shell, Pablo G. Debenedetti, and Athanassios
66 * Z. Panagiotopoulos, Phys. Rev. E 66, 011202 (2002).
67 */
69 public:
70 TranslationalOrderParamZ(SimInfo* info, const std::string& filename,
71 const std::string& sele1, const std::string& sele2,
72 double rCut, int nrbins, int nzbins, RealType len,
73 RealType zlen, int axis = 2);
74
75 int getNRBins() { return nRBins_; }
76 RealType getLength() { return len_; }
77 int getNZBins() { return nZBins_; }
78
79 private:
80 virtual void preProcess();
81 virtual void initializeHistogram();
82 virtual void processHistogram();
83 virtual void collectHistogram(StuntDouble* sd1, StuntDouble* sd2);
84 virtual void postProcess();
85 virtual void writeRdf();
86
87 RealType len_;
88 RealType zLen_;
89 int nRBins_;
90 RealType deltaR_;
91 int nZBins_;
92 RealType deltaZ_;
93 RealType rCut_;
94
95 std::vector<std::vector<int>> histogram_;
96 std::vector<std::vector<RealType>> avgGofr_;
97 std::vector<RealType> Tz_;
98 std::vector<RealType> zBox_;
99
100 int axis_;
101 std::string axisLabel_;
102 int xaxis_;
103 int yaxis_;
104 };
105} // namespace OpenMD
106
107#endif
Radial Distribution Function.
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.