applications/dynamicProps/cOHz.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).
 */
#ifndef APPLICATIONS_DYNAMICPROPS_COHZ_HPP
#define APPLICATIONS_DYNAMICPROPS_COHZ_HPP

#include "math/Polynomial.hpp"
#include "math/Vector3.hpp"
#include "applications/dynamicProps/ParticleTimeCorrFunc.hpp"

using namespace std;
namespace OpenMD {

  class COHZ : public ParticleTimeCorrFunc {
  public:
    COHZ(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, int order, int nZbins, long long int memSize);   

  private:
    virtual void correlateFrames(int frame1, int frame2);
    virtual RealType calcCorrVal(int frame1, int frame2, StuntDouble* sd1,  StuntDouble* sd2) { return 0.0; }
    virtual Vector3d calcCorrVals(int frame1, int frame2, StuntDouble* sd1, StuntDouble* sd2);
    virtual void writeCorrelate();

    virtual void validateSelection(const SelectionManager& seleMan);


    void setOutputName1(const std::string& filename) {
      outputFilename1_ = filename;
    }
    const std::string& getOutputFileName1() const {
      return outputFilename1_;
    }

    void setOutputName2(const std::string& filename) {
      outputFilename2_ = filename;
    }
    const std::string& getOutputFileName2() const {
      return outputFilename2_;
    }


    int order_;
    DoublePolynomial legendre_;

  protected:
    virtual void preCorrelate();
    virtual void postCorrelate();
    vector<vector<Vector3d> > histogram_;
    vector<vector<int> > counts_;
    int nZBins_;
    std::string outputFilename1_;
    std::string outputFilename2_;

  };

}
#endif
Revision:	1934
Committed:	Mon Aug 26 14:15:09 2013 UTC (11 years, 8 months ago) by gezelter
File size:	3703 byte(s)
Log Message:	Added OH bond time correlation function
#	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	*/
42	#ifndef APPLICATIONS_DYNAMICPROPS_COHZ_HPP
43	#define APPLICATIONS_DYNAMICPROPS_COHZ_HPP
44
45	#include "math/Polynomial.hpp"
46	#include "math/Vector3.hpp"
47	#include "applications/dynamicProps/ParticleTimeCorrFunc.hpp"
48
49	using namespace std;
50	namespace OpenMD {
51
52	class COHZ : public ParticleTimeCorrFunc {
53	public:
54	COHZ(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, int order, int nZbins, long long int memSize);
55
56	private:
57	virtual void correlateFrames(int frame1, int frame2);
58	virtual RealType calcCorrVal(int frame1, int frame2, StuntDouble* sd1, StuntDouble* sd2) { return 0.0; }
59	virtual Vector3d calcCorrVals(int frame1, int frame2, StuntDouble* sd1, StuntDouble* sd2);
60	virtual void writeCorrelate();
61
62	virtual void validateSelection(const SelectionManager& seleMan);
63
64
65	void setOutputName1(const std::string& filename) {
66	outputFilename1_ = filename;
67	}
68	const std::string& getOutputFileName1() const {
69	return outputFilename1_;
70	}
71
72	void setOutputName2(const std::string& filename) {
73	outputFilename2_ = filename;
74	}
75	const std::string& getOutputFileName2() const {
76	return outputFilename2_;
77	}
78
79
80	int order_;
81	DoublePolynomial legendre_;
82
83	protected:
84	virtual void preCorrelate();
85	virtual void postCorrelate();
86	vector<vector<Vector3d> > histogram_;
87	vector<vector<int> > counts_;
88	int nZBins_;
89	std::string outputFilename1_;
90	std::string outputFilename2_;
91
92	};
93
94	}
95	#endif