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root/OpenMD/trunk/src/applications/staticProps/TetrahedralityParamZ.hpp
Revision: 1767
Committed: Fri Jul 6 22:01:58 2012 UTC (12 years, 10 months ago) by gezelter
Original Path: branches/development/src/applications/staticProps/TetrahedralityParamZ.hpp
File size: 4864 byte(s)
Log Message:
Various fixes required to compile OpenMD with the MS Visual C++ compiler

File Contents

# User Rev Content
1 plouden 1762 /*
2     * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3     *
4     * The University of Notre Dame grants you ("Licensee") a
5     * non-exclusive, royalty free, license to use, modify and
6     * redistribute this software in source and binary code form, provided
7     * that the following conditions are met:
8     *
9     * 1. Redistributions of source code must retain the above copyright
10     * notice, this list of conditions and the following disclaimer.
11     *
12     * 2. Redistributions in binary form must reproduce the above copyright
13     * notice, this list of conditions and the following disclaimer in the
14     * documentation and/or other materials provided with the
15     * distribution.
16     *
17     * This software is provided "AS IS," without a warranty of any
18     * kind. All express or implied conditions, representations and
19     * warranties, including any implied warranty of merchantability,
20     * fitness for a particular purpose or non-infringement, are hereby
21     * excluded. The University of Notre Dame and its licensors shall not
22     * be liable for any damages suffered by licensee as a result of
23     * using, modifying or distributing the software or its
24     * derivatives. In no event will the University of Notre Dame or its
25     * licensors be liable for any lost revenue, profit or data, or for
26     * direct, indirect, special, consequential, incidental or punitive
27     * damages, however caused and regardless of the theory of liability,
28     * arising out of the use of or inability to use software, even if the
29     * University of Notre Dame has been advised of the possibility of
30     * such damages.
31     *
32     * SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33     * research, please cite the appropriate papers when you publish your
34     * work. Good starting points are:
35     *
36     * [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37     * [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38     * [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39     * [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40     * [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). *
41     * Created by J. Daniel Gezelter on 09/26/06
42     * @author J. Daniel Gezelter
43     * @version $Id: BondOrderParameter.hpp 1442 2010-05-10 17:28:26Z gezelter $
44     *
45     */
46    
47     #ifndef APPLICATIONS_STATICPROPS_TETRAHEDRALITYPARAMZ_HPP
48     #define APPLICATIONS_STATICPROPS_TETRAHEDRALITYPARAMZ_HPP
49     #include "selection/SelectionEvaluator.hpp"
50     #include "selection/SelectionManager.hpp"
51     #include "applications/staticProps/StaticAnalyser.hpp"
52     #include "math/Vector3.hpp"
53    
54     namespace OpenMD {
55    
56     /**
57     * @class TetrahedralityParamZ
58     * @brief Tetrahedrality ParameterZ
59     *
60     * Computes local tetrahedral order parameter Q as introduced in:
61     *
62     * "A new order parameter for tetrahedral configurations," by P.-L. Chau and
63     * A.J. Hardwick, Mol. Phys. 93, pp. 511-518 (1998).
64     *
65     *
66     * Note that we use a rescaled version of the tetrahedral order
67     * parameter 'Q' such that a perfectly tetrahedral configuration has a Q value
68     * of 1 and an ideal gas configuration has a Q value of 0. This rescaled
69     * version of the tetrahedrality parameter was first introduced in:
70     *
71     * "Relationship between structural order and the anomalies of liquid water,"
72     * by J.R. Errington and P.G. Debenedetti, Nature 409, pp. 318-321 (2001).
73     *
74     *
75     * Characterization of the spatial correlations of the the local order parameter Q
76     * are done according to the procedure outlined in:
77     *
78     * "Space-time correlations in the orientational order parameter and the
79     * orientational entropy of water," by P. Kumar, S.V. Buldyrev, and H.E. Stanley,
80     * arXiv:0807.4699v1 [cond-mat.soft] 29 Jul 2008.
81     *
82     */
83     class TetrahedralityParamZ : public StaticAnalyser{
84     public:
85     TetrahedralityParamZ(SimInfo* info, const std::string& filename,
86     const std::string& sele, double rCut, int nzbins);
87     int getNZBins(){
88     return nZBins_;
89     }
90    
91     virtual ~TetrahedralityParamZ();
92     virtual void process();
93    
94     private:
95     virtual void initalizeHistogram();
96     virtual void collectHistogram(RealType Qk);
97     void writeOrderParameter();
98    
99     Snapshot* currentSnapshot_;
100     std::string selectionScript_;
101     SelectionManager seleMan1_;
102     SelectionManager seleMan2_;
103     SelectionEvaluator evaluator_;
104    
105     RealType rCut_;
106     int frameCounter_;
107     int nZBins_;
108     int nProcessed_;
109    
110     RealType MinQ_;
111     RealType MaxQ_;
112     RealType deltaQ_;
113     std::vector<int> Q_histogram_;
114     std::vector<StuntDouble*> Distorted_;
115     std::vector<StuntDouble*> Tetrahedral_;
116     std::vector<RealType> zBox_;
117 gezelter 1767 std::vector<RealType> Qave_;
118     std::vector<RealType> count_;
119 plouden 1762 std::vector<std::vector<RealType> > sliceSDLists_;
120     };
121     }
122    
123     #endif
124    

Properties

Name Value
svn:executable *