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. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. 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.
 */
#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 oopse {

  /**
   * @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);
        
    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_;
    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:	1104
Committed:	Fri Dec 29 21:43:18 2006 UTC (18 years, 4 months ago) by gezelter
Original Path:	*trunk/src/applications/dynamicProps/TimeCorrFunc.hpp*
File size:	4237 byte(s)
Log Message:	Adding the ability to compute Center of Mass properties on reading in a dump file. DumpReader must be told if it needs to do this, however.
#	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			* 1. Acknowledgement of the program authors must be made in any
10			* publication of scientific results based in part on use of the
11			* program. An acceptable form of acknowledgement is citation of
12			* the article in which the program was described (Matthew
13			* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14			* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15			* Parallel Simulation Engine for Molecular Dynamics,"
16			* J. Comput. Chem. 26, pp. 252-271 (2005))
17			*
18			* 2. Redistributions of source code must retain the above copyright
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
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			namespace oopse {
55
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			const std::string& sele1, const std::string& sele2, int storageLayout);
65	tim	333
66	gezelter	507	void doCorrelate();
67	tim	333
68
69	gezelter	507	void setOutputName(const std::string& filename) {
70			outputFilename_ = filename;
71			}
72	tim	333
73	gezelter	507	const std::string& getOutputFileName() const {
74			return outputFilename_;
75			}
76	tim	333
77
78	gezelter	507	const std::string& getCorrFuncType() const {
79			return corrFuncType_;
80			}
81	tim	333
82	gezelter	507	void setCorrFuncType(const std::string& type) {
83			corrFuncType_ = type;
84			}
85	tim	333
86	gezelter	507	void setExtraInfo(const std::string& extra) {
87			extra_ = extra;
88			}
89	tim	333
90	gezelter	507	protected:
91	tim	333
92	gezelter	507	virtual void preCorrelate();
93			virtual void postCorrelate();
94			virtual void updateFrame(int frame);
95	tim	333
96	tim	963	RealType deltaTime_;
97	gezelter	507	int nTimeBins_;
98	tim	963	std::vector<RealType> histogram_;
99	gezelter	507	std::vector<int> count_;
100	gezelter	1104	std::vector<RealType> time_;
101	tim	333
102	gezelter	507	SimInfo* info_;
103			int storageLayout_;
104			std::string dumpFilename_;
105			SelectionManager seleMan1_;
106			SelectionManager seleMan2_;
107	tim	333
108	gezelter	507	BlockSnapshotManager* bsMan_;
109	tim	333
110	gezelter	507	private:
111	tim	333
112	gezelter	507	void correlateBlocks(int block1, int block2);
113			virtual void correlateFrames(int frame1, int frame2) = 0;
114	tim	333
115	gezelter	507	virtual void writeCorrelate();
116	tim	333
117	gezelter	507	virtual void validateSelection(const SelectionManager& seleMan) {}
118	tim	333
119
120	gezelter	507	std::string selectionScript1_;
121			std::string selectionScript2_;
122	tim	333
123	gezelter	507	SelectionEvaluator evaluator1_;
124			SelectionEvaluator evaluator2_;
125	tim	333
126
127	gezelter	507	std::string outputFilename_;
128	tim	333
129	gezelter	507	std::string corrFuncType_;
130			std::string extra_;
131			};
132	tim	333
133			}
134			#endif