MPFrameTimeCorrFunc.cpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
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 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
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 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
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 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
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 *    distribution.
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 * 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
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 * using, modifying or distributing the software or its
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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/MPFrameTimeCorrFunc.hpp"
#include "math/DynamicVector.hpp"
 
namespace OpenMD {
 
  template<typename T>
  MPFrameTimeCorrFunc<T>::MPFrameTimeCorrFunc(SimInfo* info, 
                                              const std::string & filename, 
                                              const std::string & sele1, 
                                              const std::string & sele2, 
                                              int storageLayout)
    : MultipassCorrFunc<T>(info, filename, sele1, sele2, storageLayout) {
    this->autoCorrFunc_ = true;
  }
  
  template<typename T>
  void MPFrameTimeCorrFunc<T>::computeFrame(int istep) {
    
    if (this->evaluator1_.isDynamic()) {
      this->seleMan1_.setSelectionSet(this->evaluator1_.evaluate());
      this->validateSelection(this->seleMan1_);
    }
 
    if (this->uniqueSelections_ && this->evaluator2_.isDynamic()) {
      this->seleMan2_.setSelectionSet(this->evaluator2_.evaluate());
      this->validateSelection(this->seleMan2_);
    }
 
    computeProperty(istep);
  }
 
  template<typename T>
  void MPFrameTimeCorrFunc<T>::correlateFrames(int frame1, int frame2,
                                               int timeBin) {
 
    T corrVal(0.0);
 
    corrVal = calcCorrVal(frame1, frame2);
    this->histogram_[timeBin] += corrVal;
    this->count_[timeBin]++;
  }
 
  template class MPFrameTimeCorrFunc<RealType>;
  template class MPFrameTimeCorrFunc<Vector3d>;  
  template class MPFrameTimeCorrFunc<Mat3x3d>;
  template class MPFrameTimeCorrFunc<DynamicVector<RealType> >;
}