| 1 |
xsun |
1183 |
/* |
| 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 |
xsun |
1183 |
* notice, this list of conditions and the following disclaimer. |
| 11 |
|
|
* |
| 12 |
gezelter |
1390 |
* 2. Redistributions in binary form must reproduce the above copyright |
| 13 |
xsun |
1183 |
* 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 |
xsun |
1183 |
*/ |
| 41 |
|
|
|
| 42 |
|
|
#include "applications/dynamicProps/FrameTimeCorrFunc.hpp" |
| 43 |
|
|
|
| 44 |
gezelter |
1390 |
namespace OpenMD { |
| 45 |
xsun |
1183 |
|
| 46 |
|
|
FrameTimeCorrFunc::FrameTimeCorrFunc(SimInfo * info, const std::string & filename, |
| 47 |
|
|
const std :: string & sele1, |
| 48 |
gezelter |
1629 |
const std :: string & sele2, |
| 49 |
|
|
int storageLayout, long long int memSize) |
| 50 |
|
|
: TimeCorrFunc(info, filename, sele1, sele2, storageLayout, memSize){ |
| 51 |
xsun |
1183 |
} |
| 52 |
|
|
|
| 53 |
|
|
void FrameTimeCorrFunc::correlateFrames(int frame1, int frame2) { |
| 54 |
|
|
Snapshot* snapshot1 = bsMan_->getSnapshot(frame1); |
| 55 |
|
|
Snapshot* snapshot2 = bsMan_->getSnapshot(frame2); |
| 56 |
|
|
assert(snapshot1 && snapshot2); |
| 57 |
|
|
|
| 58 |
|
|
RealType time1 = snapshot1->getTime(); |
| 59 |
|
|
RealType time2 = snapshot2->getTime(); |
| 60 |
|
|
|
| 61 |
|
|
int timeBin = int ((time2 - time1) /deltaTime_ + 0.5); |
| 62 |
|
|
|
| 63 |
|
|
RealType corrVal = calcCorrVal(frame1, frame2); |
| 64 |
|
|
histogram_[timeBin] += corrVal; |
| 65 |
|
|
} |
| 66 |
|
|
|
| 67 |
|
|
} |
| 68 |
|
|
|
