applications/staticProps/TetrahedralityParam.hpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
 * [4] Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). *
 *  Created by J. Daniel Gezelter on 09/26/06
 *  @author  J. Daniel Gezelter 
 *  @version $Id: BondOrderParameter.hpp 1442 2010-05-10 17:28:26Z gezelter $
 *
 */

#ifndef APPLICATIONS_STATICPROPS_TETRAHEDRALITYPARAM_HPP
#define APPLICATIONS_STATICPROPS_TETRAHEDRALITYPARAM_HPP
#include "selection/SelectionEvaluator.hpp"
#include "selection/SelectionManager.hpp"
#include "applications/staticProps/StaticAnalyser.hpp"
#include "math/Vector3.hpp"

namespace OpenMD {

  /**
   * @class TetrahedralityParam
   * @brief Tetrahedrality Parameter
   *
   * Computes local tetrahedral order parameter Q as introduced in:
   *
   *   "A new order parameter for tetrahedral configurations," by P.-L. Chau and 
   *    A.J. Hardwick, Mol. Phys. 93, pp. 511-518 (1998).
   *
   *
   * Note that we use a rescaled version of the tetrahedral order
   * parameter 'Q' such that a perfectly tetrahedral configuration has a Q value
   * of 1 and an ideal gas configuration has a Q value of 0. This rescaled
   * version of the tetrahedrality parameter was first introduced in:
   *
   *   "Relationship between structural order and the anomalies of liquid water,"
   *    by J.R. Errington and P.G. Debenedetti, Nature 409, pp. 318-321 (2001).
   * 
   *
   * Characterization of the spatial correlations of the the local order parameter Q
   * are done according to the procedure outlined in:
   *
   *   "Space-time correlations in the orientational order parameter and the
   *    orientational entropy of water," by P. Kumar, S.V. Buldyrev, and H.E. Stanley,
   *    arXiv:0807.4699v1 [cond-mat.soft] 29 Jul 2008.
   *
   */
  class TetrahedralityParam : public StaticAnalyser{
  public:
    TetrahedralityParam(SimInfo* info, const std::string& filename, 
                        const std::string& sele, double rCut, int nbins);
    
    virtual ~TetrahedralityParam();
    virtual void process();
    
  private:
    virtual void initializeHistogram();
    virtual void collectHistogram(RealType Qk);    
    void writeOrderParameter();

    Snapshot* currentSnapshot_;
    std::string selectionScript_;
    SelectionManager seleMan_;    
    SelectionEvaluator evaluator_;           
            
    RealType rCut_;
    int frameCounter_;
    int nBins_;
   
    RealType MinQ_;
    RealType MaxQ_;
    RealType deltaQ_;
    std::vector<int> Q_histogram_;
    std::vector<StuntDouble*> Distorted_;
    std::vector<StuntDouble*> Tetrahedral_;
  };
}

#endif

Revision:	1785
Committed:	Wed Aug 22 18:43:27 2012 UTC (12 years, 8 months ago) by jmichalk
File size:	4602 byte(s)
Log Message:	Trunk: The changes in this commit are confined to applications/staticProps and for the most part deal with a misspelling of initialize. The one other change took place in StaticProps.cpp and deals with the default treatment of sele2. It had previously been set to 'select all' which seems to go against what would be desired by not specifying it with regard to proper operations of many of the analysis programs ( g of r's especially)
#	Content
1	/*
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_TETRAHEDRALITYPARAM_HPP
48	#define APPLICATIONS_STATICPROPS_TETRAHEDRALITYPARAM_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 TetrahedralityParam
58	* @brief Tetrahedrality Parameter
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 TetrahedralityParam : public StaticAnalyser{
84	public:
85	TetrahedralityParam(SimInfo* info, const std::string& filename,
86	const std::string& sele, double rCut, int nbins);
87
88	virtual ~TetrahedralityParam();
89	virtual void process();
90
91	private:
92	virtual void initializeHistogram();
93	virtual void collectHistogram(RealType Qk);
94	void writeOrderParameter();
95
96	Snapshot* currentSnapshot_;
97	std::string selectionScript_;
98	SelectionManager seleMan_;
99	SelectionEvaluator evaluator_;
100
101	RealType rCut_;
102	int frameCounter_;
103	int nBins_;
104
105	RealType MinQ_;
106	RealType MaxQ_;
107	RealType deltaQ_;
108	std::vector<int> Q_histogram_;
109	std::vector<StuntDouble*> Distorted_;
110	std::vector<StuntDouble*> Tetrahedral_;
111	};
112	}
113
114	#endif
115