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]  Vardeman & Gezelter, in progress (2009).                        
 */
#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:	1629
Committed:	Wed Sep 14 21:15:17 2011 UTC (13 years, 8 months ago) by gezelter
File size:	4346 byte(s)
Log Message:	Merging changes from old branch into development branch
#	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			* [4] Vardeman & Gezelter, in progress (2009).
40	tim	333	*/
41			#ifndef APPLICATIONS_DYNAMICPROPS_TIMECORRFUNC_HPP
42			#define APPLICATIONS_DYNAMICPROPS_TIMECORRFUNC_HPP
43
44			#include <string>
45			#include <vector>
46
47			#include "brains/SimInfo.hpp"
48			#include "brains/BlockSnapshotManager.hpp"
49
50			#include "primitives/StuntDouble.hpp"
51			#include "selection/SelectionEvaluator.hpp"
52			#include "selection/SelectionManager.hpp"
53
54	gezelter	1390	namespace OpenMD {
55	tim	333
56	gezelter	507	/**
57			* @class TimeCorrFunc TimeCorrFunc.hpp "applications/dynamicProps/TimeCorrFunc"
58			* @brief Base class for Correlation function
59			*/
60	tim	333
61	gezelter	507	class TimeCorrFunc {
62			public:
63			TimeCorrFunc(SimInfo* info, const std::string& filename,
64	gezelter	1629	const std::string& sele1, const std::string& sele2,
65			int storageLayout, long long int memSize);
66	tim	333
67	gezelter	507	void doCorrelate();
68	tim	333
69
70	gezelter	507	void setOutputName(const std::string& filename) {
71			outputFilename_ = filename;
72			}
73	tim	333
74	gezelter	507	const std::string& getOutputFileName() const {
75			return outputFilename_;
76			}
77	tim	333
78
79	gezelter	507	const std::string& getCorrFuncType() const {
80			return corrFuncType_;
81			}
82	tim	333
83	gezelter	507	void setCorrFuncType(const std::string& type) {
84			corrFuncType_ = type;
85			}
86	tim	333
87	gezelter	507	void setExtraInfo(const std::string& extra) {
88			extra_ = extra;
89			}
90	tim	333
91	gezelter	507	protected:
92	tim	333
93	gezelter	507	virtual void preCorrelate();
94			virtual void postCorrelate();
95			virtual void updateFrame(int frame);
96	tim	333
97	tim	963	RealType deltaTime_;
98	gezelter	507	int nTimeBins_;
99	tim	963	std::vector<RealType> histogram_;
100	gezelter	507	std::vector<int> count_;
101	gezelter	1629	std::vector<RealType> time_;
102	tim	333
103	gezelter	507	SimInfo* info_;
104			int storageLayout_;
105	gezelter	1629	long long int memSize_;
106	gezelter	507	std::string dumpFilename_;
107			SelectionManager seleMan1_;
108			SelectionManager seleMan2_;
109	tim	333
110	gezelter	507	BlockSnapshotManager* bsMan_;
111	tim	333
112	gezelter	507	private:
113	tim	333
114	gezelter	507	void correlateBlocks(int block1, int block2);
115			virtual void correlateFrames(int frame1, int frame2) = 0;
116	tim	333
117	gezelter	507	virtual void writeCorrelate();
118	tim	333
119	gezelter	507	virtual void validateSelection(const SelectionManager& seleMan) {}
120	tim	333
121
122	gezelter	507	std::string selectionScript1_;
123			std::string selectionScript2_;
124	tim	333
125	gezelter	507	SelectionEvaluator evaluator1_;
126			SelectionEvaluator evaluator2_;
127	tim	333
128
129	gezelter	507	std::string outputFilename_;
130	tim	333
131	gezelter	507	std::string corrFuncType_;
132			std::string extra_;
133			};
134	tim	333
135			}
136			#endif