applications/dynamicProps/CrossTimeCorrFunc.cpp

/*
 * 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.
 */
 
#include "applications/dynamicProps/CrossTimeCorrFunc.hpp"

namespace oopse {

  CrossTimeCorrFunc::CrossTimeCorrFunc(SimInfo * info, const  std::string & filename,
                                       const std :: string & sele1, const std :: string & sele2, int storageLayout) 
    : TimeCorrFunc(info, filename, sele1, sele2, storageLayout) {
    
      nSelected1_ = seleMan1_.getSelectionCount();  
      nSelected2_ = seleMan2_.getSelectionCount();  
      nSelectedPairs_ = nSelected1_ * nSelected2_;
    }

  void CrossTimeCorrFunc::correlateFrames(int frame1, int frame2) {
    Snapshot* snapshot1 = bsMan_->getSnapshot(frame1);
    Snapshot* snapshot2 = bsMan_->getSnapshot(frame2);
    assert(snapshot1 && snapshot2);

    double time1 = snapshot1->getTime();
    double time2 = snapshot2->getTime();

    int timeBin = int ((time2 - time1) /deltaTime_ + 0.5);
    count_[timeBin] += nSelectedPairs_ ;    

    int i;
    int j;
    StuntDouble* sd1;
    StuntDouble* sd2;
    for (sd1 = seleMan1_.beginSelected(i); sd1 != NULL; sd1 = seleMan1_.nextSelected(i)) {

      for (sd2 = seleMan2_.beginSelected(j); sd2 != NULL; sd2 = seleMan2_.nextSelected(j)) {
        double corrVal = calcCorrVal(frame1, frame2, sd1, sd2);
        histogram_[timeBin] += corrVal;    
      }            
    }
  }

}
Revision:	2204
Committed:	Fri Apr 15 22:04:00 2005 UTC (19 years, 3 months ago) by gezelter
File size:	3346 byte(s)
Log Message:	xemacs has been drafted to perform our indentation services
#	User	Rev	Content
1	tim	2017	/*
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
42			#include "applications/dynamicProps/CrossTimeCorrFunc.hpp"
43
44			namespace oopse {
45
46	gezelter	2204	CrossTimeCorrFunc::CrossTimeCorrFunc(SimInfo * info, const std::string & filename,
47			const std :: string & sele1, const std :: string & sele2, int storageLayout)
48	tim	2017	: TimeCorrFunc(info, filename, sele1, sele2, storageLayout) {
49
50	gezelter	2204	nSelected1_ = seleMan1_.getSelectionCount();
51			nSelected2_ = seleMan2_.getSelectionCount();
52			nSelectedPairs_ = nSelected1_ * nSelected2_;
53			}
54	tim	2017
55	gezelter	2204	void CrossTimeCorrFunc::correlateFrames(int frame1, int frame2) {
56	tim	2017	Snapshot* snapshot1 = bsMan_->getSnapshot(frame1);
57			Snapshot* snapshot2 = bsMan_->getSnapshot(frame2);
58			assert(snapshot1 && snapshot2);
59
60			double time1 = snapshot1->getTime();
61			double time2 = snapshot2->getTime();
62
63			int timeBin = int ((time2 - time1) /deltaTime_ + 0.5);
64			count_[timeBin] += nSelectedPairs_ ;
65
66			int i;
67			int j;
68			StuntDouble* sd1;
69			StuntDouble* sd2;
70			for (sd1 = seleMan1_.beginSelected(i); sd1 != NULL; sd1 = seleMan1_.nextSelected(i)) {
71
72	gezelter	2204	for (sd2 = seleMan2_.beginSelected(j); sd2 != NULL; sd2 = seleMan2_.nextSelected(j)) {
73			double corrVal = calcCorrVal(frame1, frame2, sd1, sd2);
74			histogram_[timeBin] += corrVal;
75			}
76	tim	2017	}
77	gezelter	2204	}
78	tim	2017
79			}