applications/dynamicProps/TimeCorrFunc.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, 24107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
#ifndef APPLICATIONS_DYNAMICPROPS_TIMECORRFUNC_HPP
#define APPLICATIONS_DYNAMICPROPS_TIMECORRFUNC_HPP

#include <string>
#include <vector>

#include "brains/SimInfo.hpp"
#include "brains/BlockSnapshotManager.hpp"

#include "primitives/StuntDouble.hpp"
#include "selection/SelectionEvaluator.hpp"
#include "selection/SelectionManager.hpp"

namespace OpenMD {

  /**
   * @class TimeCorrFunc TimeCorrFunc.hpp "applications/dynamicProps/TimeCorrFunc"
   * @brief Base class for Correlation function
   */
 
  class TimeCorrFunc {
  public:
    TimeCorrFunc(SimInfo* info, const std::string& filename, 
                 const std::string& sele1, const std::string& sele2,
                 int storageLayout, long long int memSize);
        
    void doCorrelate();


    void setOutputName(const std::string& filename) {
      outputFilename_ = filename;
    }

    const std::string& getOutputFileName() const {
      return outputFilename_;
    }


    const std::string& getCorrFuncType() const {
      return corrFuncType_;
    }

    void setCorrFuncType(const std::string& type) {
      corrFuncType_ = type;
    }

    void setExtraInfo(const std::string& extra) {
      extra_ = extra;
    }
            
  protected:
        
    virtual void preCorrelate();        
    virtual void postCorrelate();
    virtual void updateFrame(int frame);

    RealType deltaTime_;
    int nTimeBins_;
    std::vector<RealType> histogram_;
    std::vector<int> count_;
    std::vector<RealType> time_;
        
    SimInfo* info_;
    int storageLayout_;
    long long int memSize_;
    std::string dumpFilename_;        
    SelectionManager seleMan1_;
    SelectionManager seleMan2_;          

    BlockSnapshotManager* bsMan_;       
        
  private:

    void correlateBlocks(int block1, int block2);
    virtual void correlateFrames(int frame1, int frame2) = 0;       
        
    virtual void writeCorrelate();

    virtual void validateSelection(const SelectionManager& seleMan) {}


    std::string selectionScript1_;
    std::string selectionScript2_;
        
    SelectionEvaluator evaluator1_;
    SelectionEvaluator evaluator2_;
 

    std::string outputFilename_;

    std::string corrFuncType_;
    std::string extra_;
  };

}
#endif
Revision:	1665
Committed:	Tue Nov 22 20:38:56 2011 UTC (13 years, 6 months ago) by gezelter
File size:	4412 byte(s)
Log Message:	updated copyright notices
#	User	Rev	Content
1	tim	333	/*
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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	tim	333	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	tim	333	* 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	gezelter	1390	*
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, 24107 (2008).
39	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	tim	333	*/
42			#ifndef APPLICATIONS_DYNAMICPROPS_TIMECORRFUNC_HPP
43			#define APPLICATIONS_DYNAMICPROPS_TIMECORRFUNC_HPP
44
45			#include <string>
46			#include <vector>
47
48			#include "brains/SimInfo.hpp"
49			#include "brains/BlockSnapshotManager.hpp"
50
51			#include "primitives/StuntDouble.hpp"
52			#include "selection/SelectionEvaluator.hpp"
53			#include "selection/SelectionManager.hpp"
54
55	gezelter	1390	namespace OpenMD {
56	tim	333
57	gezelter	507	/**
58			* @class TimeCorrFunc TimeCorrFunc.hpp "applications/dynamicProps/TimeCorrFunc"
59			* @brief Base class for Correlation function
60			*/
61	tim	333
62	gezelter	507	class TimeCorrFunc {
63			public:
64			TimeCorrFunc(SimInfo* info, const std::string& filename,
65	gezelter	1629	const std::string& sele1, const std::string& sele2,
66			int storageLayout, long long int memSize);
67	tim	333
68	gezelter	507	void doCorrelate();
69	tim	333
70
71	gezelter	507	void setOutputName(const std::string& filename) {
72			outputFilename_ = filename;
73			}
74	tim	333
75	gezelter	507	const std::string& getOutputFileName() const {
76			return outputFilename_;
77			}
78	tim	333
79
80	gezelter	507	const std::string& getCorrFuncType() const {
81			return corrFuncType_;
82			}
83	tim	333
84	gezelter	507	void setCorrFuncType(const std::string& type) {
85			corrFuncType_ = type;
86			}
87	tim	333
88	gezelter	507	void setExtraInfo(const std::string& extra) {
89			extra_ = extra;
90			}
91	tim	333
92	gezelter	507	protected:
93	tim	333
94	gezelter	507	virtual void preCorrelate();
95			virtual void postCorrelate();
96			virtual void updateFrame(int frame);
97	tim	333
98	tim	963	RealType deltaTime_;
99	gezelter	507	int nTimeBins_;
100	tim	963	std::vector<RealType> histogram_;
101	gezelter	507	std::vector<int> count_;
102	gezelter	1629	std::vector<RealType> time_;
103	tim	333
104	gezelter	507	SimInfo* info_;
105			int storageLayout_;
106	gezelter	1629	long long int memSize_;
107	gezelter	507	std::string dumpFilename_;
108			SelectionManager seleMan1_;
109			SelectionManager seleMan2_;
110	tim	333
111	gezelter	507	BlockSnapshotManager* bsMan_;
112	tim	333
113	gezelter	507	private:
114	tim	333
115	gezelter	507	void correlateBlocks(int block1, int block2);
116			virtual void correlateFrames(int frame1, int frame2) = 0;
117	tim	333
118	gezelter	507	virtual void writeCorrelate();
119	tim	333
120	gezelter	507	virtual void validateSelection(const SelectionManager& seleMan) {}
121	tim	333
122
123	gezelter	507	std::string selectionScript1_;
124			std::string selectionScript2_;
125	tim	333
126	gezelter	507	SelectionEvaluator evaluator1_;
127			SelectionEvaluator evaluator2_;
128	tim	333
129
130	gezelter	507	std::string outputFilename_;
131	tim	333
132	gezelter	507	std::string corrFuncType_;
133			std::string extra_;
134			};
135	tim	333
136			}
137			#endif