applications/staticProps/TetrahedralityParamXYZ.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).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 * [6]  Kuang & Gezelter, Mol. Phys., 110, 691-701 (2012).
 */

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

namespace OpenMD {

  /**
   * @class TetrahedralityParamXYZ
   * @brief Tetrahedrality Parameter XYZ
   *
   * 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 TetrahedralityParamXYZ : public StaticAnalyser{
  public:
    TetrahedralityParamXYZ(SimInfo* info, const std::string& filename, 
                           const std::string& sele1, const std::string& sele2, 
                           RealType rCut, RealType voxelSize, RealType gaussWidth);

    virtual ~TetrahedralityParamXYZ();
    virtual void process();
    
  private:
    void writeQxyz();

    Snapshot* currentSnapshot_;
    std::string selectionScript1_;
    std::string selectionScript2_;
    SelectionManager seleMan1_;
    SelectionEvaluator evaluator1_;
    SelectionManager seleMan2_;
    SelectionEvaluator evaluator2_;

    RealType rCut_;
    RealType voxelSize_;
    RealType gaussWidth_;

    Vector3i nBins_;
    std::vector<std::vector<std::vector<RealType> > > count_;
    std::vector<std::vector<std::vector<RealType> > > hist_;

  };
}
#endif

Revision:	2015
Committed:	Wed Aug 13 20:42:43 2014 UTC (10 years, 9 months ago) by gezelter
File size:	4590 byte(s)
Log Message:	Changes to include the volume-resolved tetrahedrality parameter.
#	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, 234107 (2008).
39	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40	* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	* [6] Kuang & Gezelter, Mol. Phys., 110, 691-701 (2012).
42	*/
43
44	#ifndef APPLICATIONS_STATICPROPS_TETRAHEDRALITYPARAMXYZ_HPP
45	#define APPLICATIONS_STATICPROPS_TETRAHEDRALITYPARAMXYZ_HPP
46	#include "selection/SelectionEvaluator.hpp"
47	#include "selection/SelectionManager.hpp"
48	#include "applications/staticProps/StaticAnalyser.hpp"
49	#include "math/Vector3.hpp"
50
51	namespace OpenMD {
52
53	/**
54	* @class TetrahedralityParamXYZ
55	* @brief Tetrahedrality Parameter XYZ
56	*
57	* Computes local tetrahedral order parameter Q as introduced in:
58	*
59	* "A new order parameter for tetrahedral configurations," by P.-L. Chau and
60	* A.J. Hardwick, Mol. Phys. 93, pp. 511-518 (1998).
61	*
62	*
63	* Note that we use a rescaled version of the tetrahedral order
64	* parameter 'Q' such that a perfectly tetrahedral configuration has a Q value
65	* of 1 and an ideal gas configuration has a Q value of 0. This rescaled
66	* version of the tetrahedrality parameter was first introduced in:
67	*
68	* "Relationship between structural order and the anomalies of liquid water,"
69	* by J.R. Errington and P.G. Debenedetti, Nature 409, pp. 318-321 (2001).
70	*
71	*
72	* Characterization of the spatial correlations of the the local
73	* order parameter Q are done according to the procedure outlined
74	* in:
75	*
76	* "Space-time correlations in the orientational order parameter and the
77	* orientational entropy of water," by P. Kumar, S.V. Buldyrev, and
78	* H.E. Stanley, arXiv:0807.4699v1 [cond-mat.soft] 29 Jul 2008.
79	*
80	*/
81	class TetrahedralityParamXYZ : public StaticAnalyser{
82	public:
83	TetrahedralityParamXYZ(SimInfo* info, const std::string& filename,
84	const std::string& sele1, const std::string& sele2,
85	RealType rCut, RealType voxelSize, RealType gaussWidth);
86
87	virtual ~TetrahedralityParamXYZ();
88	virtual void process();
89
90	private:
91	void writeQxyz();
92
93	Snapshot* currentSnapshot_;
94	std::string selectionScript1_;
95	std::string selectionScript2_;
96	SelectionManager seleMan1_;
97	SelectionEvaluator evaluator1_;
98	SelectionManager seleMan2_;
99	SelectionEvaluator evaluator2_;
100
101	RealType rCut_;
102	RealType voxelSize_;
103	RealType gaussWidth_;
104
105	Vector3i nBins_;
106	std::vector<std::vector<std::vector<RealType> > > count_;
107	std::vector<std::vector<std::vector<RealType> > > hist_;
108
109	};
110	}
111	#endif
112