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:	1596
Committed:	Mon Jul 25 17:30:53 2011 UTC (14 years, 1 month ago) by gezelter
File size:	4347 byte(s)
Log Message:	Updated the BlockSnapshotManager to use a specified memory footprint in constructor and not to rely on physmem and residentMem to figure out free memory. DynamicProps is the only program that uses the BlockSnapshotManager, so substantial changes were needed there as well.
#	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	1596	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	1596	std::vector<RealType> time_;
102	tim	333
103	gezelter	507	SimInfo* info_;
104			int storageLayout_;
105	gezelter	1596	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