applications/staticProps/HBondGeometric.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_HBONDGEOMETRIC_HPP
#define APPLICATIONS_STATICPROPS_HBONDGEOMETRIC_HPP
#include "selection/SelectionEvaluator.hpp"
#include "selection/SelectionManager.hpp"
#include "applications/staticProps/StaticAnalyser.hpp"

namespace OpenMD {

  /**
   * @class HBondGeometric
   * @brief Hydrogen Bonding statistics using geometric criteria
   *
   * Computes hydrogen bonding statistics using structural information:
   *
   *   "Hydrogen-bond dynamics for the extended simple point-carge
   *   model of water" by F. W. Starr, J. K. Nielsen, and
   *   H. E. Stanley, Phys. Rev. E 62(1), 579-587 (2000).
   *
   */
  class HBondGeometric : public StaticAnalyser {
  public:

    HBondGeometric(SimInfo* info, const std::string& filename, 
                   const std::string& sele1, const std::string& sele2,
                   double rCut, double thetaCut,
                   int nbins);
    
    virtual ~HBondGeometric();
    virtual void process();
   
  private:
    virtual void initializeHistogram();
    virtual void collectHistogram(int nHB, int nD, int nA);    
    void writeHistogram();

    Snapshot* currentSnapshot_;
    std::string selectionScript1_;
    SelectionManager seleMan1_;    
    SelectionEvaluator evaluator1_;
    std::string selectionScript2_;
    SelectionManager seleMan2_;    
    SelectionEvaluator evaluator2_;
    ForceField* ff_;
                
    RealType rCut_;
    RealType thetaCut_;
    int frameCounter_;
    int nBins_;
   
    std::vector<int> nHBonds_;
    std::vector<int> nDonor_;
    std::vector<int> nAcceptor_;
    int nSelected_;
  };
}

#endif

Revision:	2049
Committed:	Tue Jan 6 21:44:10 2015 UTC (10 years, 3 months ago) by gezelter
File size:	3962 byte(s)
Log Message:	Added Geometric HBond StaticProps module.
#	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	* [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_HBONDGEOMETRIC_HPP
48	#define APPLICATIONS_STATICPROPS_HBONDGEOMETRIC_HPP
49	#include "selection/SelectionEvaluator.hpp"
50	#include "selection/SelectionManager.hpp"
51	#include "applications/staticProps/StaticAnalyser.hpp"
52
53	namespace OpenMD {
54
55	/**
56	* @class HBondGeometric
57	* @brief Hydrogen Bonding statistics using geometric criteria
58	*
59	* Computes hydrogen bonding statistics using structural information:
60	*
61	* "Hydrogen-bond dynamics for the extended simple point-carge
62	* model of water" by F. W. Starr, J. K. Nielsen, and
63	* H. E. Stanley, Phys. Rev. E 62(1), 579-587 (2000).
64	*
65	*/
66	class HBondGeometric : public StaticAnalyser {
67	public:
68
69	HBondGeometric(SimInfo* info, const std::string& filename,
70	const std::string& sele1, const std::string& sele2,
71	double rCut, double thetaCut,
72	int nbins);
73
74	virtual ~HBondGeometric();
75	virtual void process();
76
77	private:
78	virtual void initializeHistogram();
79	virtual void collectHistogram(int nHB, int nD, int nA);
80	void writeHistogram();
81
82	Snapshot* currentSnapshot_;
83	std::string selectionScript1_;
84	SelectionManager seleMan1_;
85	SelectionEvaluator evaluator1_;
86	std::string selectionScript2_;
87	SelectionManager seleMan2_;
88	SelectionEvaluator evaluator2_;
89	ForceField* ff_;
90
91	RealType rCut_;
92	RealType thetaCut_;
93	int frameCounter_;
94	int nBins_;
95
96	std::vector<int> nHBonds_;
97	std::vector<int> nDonor_;
98	std::vector<int> nAcceptor_;
99	int nSelected_;
100	};
101	}
102
103	#endif
104