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, 6 months ago) by gezelter
File size:	3962 byte(s)
Log Message:	Added Geometric HBond StaticProps module.
#	User	Rev	Content
1	gezelter	2049	/*
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