applications/staticProps/NitrileFrequencyMap.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]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).                     
 *
 */
#ifndef APPLICATIONS_STATICPROPS_NITRILEFREQUENCYMAP_HPP
#define APPLICATIONS_STATICPROPS_NITRILEFREQUENCYMAP_HPP

#include <string>
#include <vector>
#include "selection/SelectionEvaluator.hpp"
#include "selection/SelectionManager.hpp"
#include "utils/NumericConstant.hpp"
#include "applications/staticProps/StaticAnalyser.hpp"
#include "nonbonded/Electrostatic.hpp"

using namespace std;
namespace OpenMD {
  
  class NitrileFrequencyMap : public StaticAnalyser {
    
  public:
    NitrileFrequencyMap(SimInfo* info, const string& filename, 
                        const string& sele1, int nbins);
        
    virtual void process();
    
  private:
    bool excludeAtomPair(int atom1, int atom2);
    void processHistogram();
    void writeProbs();
        
    SimInfo* info_;
    Snapshot* currentSnapshot_;

    string selectionScript1_;
    SelectionManager seleMan1_;
    SelectionEvaluator evaluator1_;

    int nProcessed_;    
    vector<int> count_;
    vector<RealType> histogram_;
    vector<RealType> freqs_;
    map<string, RealType> frequencyMap_;
    RealType minFreq_;
    RealType maxFreq_;
    int nBins_;
    vector<vector<int> > excludesForAtom;
    Electrostatic* electrostatic_;
    Vector3d EF_;


  };
  
}
#endif


Revision:	1994
Committed:	Wed Apr 30 18:50:45 2014 UTC (11 years ago) by gezelter
File size:	3391 byte(s)
Log Message:	Added NitrileFrequencyMap module to staticProps
#	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] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
40	*
41	*/
42	#ifndef APPLICATIONS_STATICPROPS_NITRILEFREQUENCYMAP_HPP
43	#define APPLICATIONS_STATICPROPS_NITRILEFREQUENCYMAP_HPP
44
45	#include <string>
46	#include <vector>
47	#include "selection/SelectionEvaluator.hpp"
48	#include "selection/SelectionManager.hpp"
49	#include "utils/NumericConstant.hpp"
50	#include "applications/staticProps/StaticAnalyser.hpp"
51	#include "nonbonded/Electrostatic.hpp"
52
53	using namespace std;
54	namespace OpenMD {
55
56	class NitrileFrequencyMap : public StaticAnalyser {
57
58	public:
59	NitrileFrequencyMap(SimInfo* info, const string& filename,
60	const string& sele1, int nbins);
61
62	virtual void process();
63
64	private:
65	bool excludeAtomPair(int atom1, int atom2);
66	void processHistogram();
67	void writeProbs();
68
69	SimInfo* info_;
70	Snapshot* currentSnapshot_;
71
72	string selectionScript1_;
73	SelectionManager seleMan1_;
74	SelectionEvaluator evaluator1_;
75
76	int nProcessed_;
77	vector<int> count_;
78	vector<RealType> histogram_;
79	vector<RealType> freqs_;
80	map<string, RealType> frequencyMap_;
81	RealType minFreq_;
82	RealType maxFreq_;
83	int nBins_;
84	vector<vector<int> > excludesForAtom;
85	Electrostatic* electrostatic_;
86	Vector3d EF_;
87
88
89	};
90
91	}
92	#endif
93
94
95