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, 234107 (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:	1879
Committed:	Sun Jun 16 15:15:42 2013 UTC (12 years, 4 months ago) by gezelter
File size:	4603 byte(s)
Log Message:	MERGE OpenMD development 1783:1878 into trunk
#	User	Rev	Content
1	kstocke1	1524	/*
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	gezelter	1879	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	gezelter	1782	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). *
41	kstocke1	1524	* 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	jmichalk	1785	virtual void initializeHistogram();
93	kstocke1	1524	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