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]  Vardeman & Gezelter, in progress (2009).                        
 *
 *  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 initalizeHistogram();
    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:	1524
Committed:	Fri Nov 19 20:48:18 2010 UTC (14 years, 6 months ago) by kstocke1
File size:	4546 byte(s)
Log Message:	added missing files
#	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] Vardeman & Gezelter, in progress (2009).
40	*
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 initalizeHistogram();
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