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:
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 * 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
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 * licensors be liable for any lost revenue, profit or data, or for
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 *
 * 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, 234107 (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);
 
    int i;
    int j;
    StuntDouble* sd1;
    StuntDouble* sd2;
    
    int id1, id2;
 
    for (sd1 = seleMan1_.beginSelected(i), sd2 = seleMan2_.beginSelected(j); 
         sd1 != NULL && sd2 != NULL;
         sd1 = seleMan1_.nextSelected(i), sd2 = seleMan2_.nextSelected(j) ) {
      
      id1 = sd1->getGlobalIndex();
      id2 = sd2->getGlobalIndex();
 
      // If the selections are dynamic, they might not have the same
      // objects in both frames, so we need to roll either of the
      // selections until we have the same particle to correlate.
 
      while (id1 < id2 && sd1 != NULL) {
        sd1 = seleMan1_.nextSelected(i);
        if (sd1 != NULL) id1 = sd1->getGlobalIndex();
      }
      while (id2 < id1 && sd2 != NULL) {
        sd2 = seleMan2_.nextSelected(j);
        if (sd2 != NULL) id2 = sd2->getGlobalIndex();
      }
     
      if (sd1 == NULL || sd2 == NULL) break;
 
      RealType corrVal = calcCorrVal(frame1, frame2, sd1, sd2);
 
      histogram_[timeBin] += corrVal;
      count_[timeBin]++;
      
    }
  }    
}