applications/dynamicProps/ParticleTimeCorrFunc.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. 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).
 */
 
#include "applications/dynamicProps/ParticleTimeCorrFunc.hpp"

namespace OpenMD {

  ParticleTimeCorrFunc::ParticleTimeCorrFunc(SimInfo * info, 
                                             const std::string & filename, 
                                             const std :: string & sele1, 
                                             const std :: string & sele2,
                                             int storageLayout,
                                             long long int memSize) 
    : TimeCorrFunc(info, filename, sele1, sele2, storageLayout, memSize){
    
    
    nSelected_ =   seleMan1_.getSelectionCount();  
    assert(  nSelected_ == seleMan2_.getSelectionCount());
  }
  
  void ParticleTimeCorrFunc::correlateFrames(int frame1, int frame2) {
    Snapshot* snapshot1 = bsMan_->getSnapshot(frame1);
    Snapshot* snapshot2 = bsMan_->getSnapshot(frame2);
    assert(snapshot1 && snapshot2);

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

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

    int i;
    int j;
    StuntDouble* sd1;
    StuntDouble* sd2;

    for (sd1 = seleMan1_.beginSelected(i), sd2 = seleMan2_.beginSelected(j);
         sd1 != NULL && sd2 != NULL;
         sd1 = seleMan1_.nextSelected(i), sd2 = seleMan2_.nextSelected(j)) {

      RealType corrVal = calcCorrVal(frame1, frame2, sd1, sd2);
      histogram_[timeBin] += corrVal;    
    }
    
  }

}

Revision:	1665
Committed:	Tue Nov 22 20:38:56 2011 UTC (13 years, 6 months ago) by gezelter
File size:	3627 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
43			#include "applications/dynamicProps/ParticleTimeCorrFunc.hpp"
44
45	gezelter	1390	namespace OpenMD {
46	tim	333
47	gezelter	1629	ParticleTimeCorrFunc::ParticleTimeCorrFunc(SimInfo * info,
48			const std::string & filename,
49			const std :: string & sele1,
50			const std :: string & sele2,
51			int storageLayout,
52			long long int memSize)
53			: TimeCorrFunc(info, filename, sele1, sele2, storageLayout, memSize){
54
55
56			nSelected_ = seleMan1_.getSelectionCount();
57			assert( nSelected_ == seleMan2_.getSelectionCount());
58			}
59
60	gezelter	507	void ParticleTimeCorrFunc::correlateFrames(int frame1, int frame2) {
61	tim	333	Snapshot* snapshot1 = bsMan_->getSnapshot(frame1);
62			Snapshot* snapshot2 = bsMan_->getSnapshot(frame2);
63			assert(snapshot1 && snapshot2);
64
65	tim	963	RealType time1 = snapshot1->getTime();
66			RealType time2 = snapshot2->getTime();
67	tim	333
68			int timeBin = int ((time2 - time1) /deltaTime_ + 0.5);
69			count_[timeBin] += nSelected_;
70
71			int i;
72			int j;
73			StuntDouble* sd1;
74			StuntDouble* sd2;
75
76			for (sd1 = seleMan1_.beginSelected(i), sd2 = seleMan2_.beginSelected(j);
77	gezelter	507	sd1 != NULL && sd2 != NULL;
78			sd1 = seleMan1_.nextSelected(i), sd2 = seleMan2_.nextSelected(j)) {
79	tim	333
80	tim	963	RealType corrVal = calcCorrVal(frame1, frame2, sd1, sd2);
81	gezelter	507	histogram_[timeBin] += corrVal;
82	tim	333	}
83
84	gezelter	507	}
85	tim	333
86			}
87