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root/OpenMD/trunk/src/applications/dynamicProps/BondCorrFunc.cpp
Revision: 1962
Committed: Wed Jan 15 22:26:18 2014 UTC (11 years, 7 months ago) by gezelter
File size: 3643 byte(s)
Log Message:
Some potential bug fixes.

File Contents

# User Rev Content
1 gezelter 1953 /*
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. Redistributions of source code must retain the above copyright
10     * notice, this list of conditions and the following disclaimer.
11     *
12     * 2. Redistributions in binary form must reproduce the above copyright
13     * 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     *
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, 234107 (2008).
39     * [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40     * [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41     */
42    
43     #include "applications/dynamicProps/BondCorrFunc.hpp"
44    
45     namespace OpenMD {
46     BondCorrFunc::BondCorrFunc(SimInfo* info, const std::string& filename,
47     const std::string& sele1, long long int memSize)
48     : InteractionTimeCorrFunc(info, filename, sele1,
49     DataStorage::dslPosition, memSize){
50    
51     setCorrFuncType("Bond Correlation Function");
52     setOutputName(getPrefix(dumpFilename_) + ".bondcorr");
53     nSelectedBonds_ = seleMan1_.getBondSelectionCount();
54     }
55    
56    
57     void BondCorrFunc::correlateFrames(int frame1, int frame2) {
58 gezelter 1962 snapshot1 = bsMan_->getSnapshot(frame1);
59     snapshot2 = bsMan_->getSnapshot(frame2);
60 gezelter 1953 assert(snapshot1 && snapshot2);
61    
62     RealType time1 = snapshot1->getTime();
63     RealType time2 = snapshot2->getTime();
64    
65     int timeBin = int ((time2 - time1) /deltaTime_ + 0.5);
66     count_[timeBin] += nSelectedBonds_;
67    
68     int i;
69    
70     for (bond = seleMan1_.beginSelectedBond(i);
71     bond != NULL ;
72     bond = seleMan1_.nextSelectedBond(i)) {
73    
74     RealType corrVal = calcCorrVal(frame1, frame2, bond);
75     histogram_[timeBin] += corrVal;
76     }
77     }
78    
79     RealType BondCorrFunc::calcCorrVal(int frame1, int frame2, ShortRangeInteraction* sri) {
80 gezelter 1962 bond = dynamic_cast<Bond*>(sri);
81     re = bond->getBondType()->getEquilibriumBondLength();
82     val1 = bond->getValue(frame1) - re;
83     val2 = bond->getValue(frame2) - re;
84 gezelter 1953 return val1 * val2;
85     }
86     }
87    

Properties

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svn:eol-style native