VelocityAutoOutProductCorrFunc.cpp

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 * 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] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 * [5] Kuang & Gezelter, Mol. Phys., 110, 691-701 (2012).
 * [6] Lamichhane, Gezelter & Newman, J. Chem. Phys. 141, 134109 (2014).
 * [7] Lamichhane, Newman & Gezelter, J. Chem. Phys. 141, 134110 (2014).
 * [8] Bhattarai, Newman & Gezelter, Phys. Rev. B 99, 094106 (2019).
 */
 
#include "applications/dynamicProps/VelocityAutoOutProductCorrFunc.hpp"
 
#include "math/SquareMatrix3.hpp"
#include "utils/Revision.hpp"
 
namespace OpenMD {
  VelocityAutoOutProductCorrFunc::VelocityAutoOutProductCorrFunc(
      SimInfo* info, const std::string& filename, const std::string& sele1,
      const std::string& sele2) :
      ObjectACF<Mat3x3d>(info, filename, sele1, sele2) {
    setCorrFuncType(
        "Velocity - Velocity Auto Outer Product Correlation Function");
    setOutputName(getPrefix(dumpFilename_) + ".vaOutProdcorr");
 
    velocity_.resize(nFrames_);
    sumVelocity_   = V3Zero;
    velocityCount_ = 0;
    propertyTemp   = V3Zero;
  }
 
  int VelocityAutoOutProductCorrFunc::computeProperty1(int frame,
                                                       StuntDouble* sd) {
    Vector3d vel = sd->getVel();
    propertyTemp = vel;
 
    velocity_[frame].push_back(propertyTemp);
    sumVelocity_ += propertyTemp;
    velocityCount_++;
    return velocity_[frame].size() - 1;
  }
 
  Mat3x3d VelocityAutoOutProductCorrFunc::calcCorrVal(int frame1, int frame2,
                                                      int id1, int id2) {
    Mat3x3d tmpMat_1;
    tmpMat_1 = outProduct(velocity_[frame1][id1], velocity_[frame2][id2]);
    Mat3x3d tmpMat_2;
    tmpMat_2 = outProduct(velocity_[frame2][id2], velocity_[frame1][id1]);
    Mat3x3d tmpMat_3;
    tmpMat_3 = 0.5 * (tmpMat_1 + tmpMat_2);
    return tmpMat_3;
  }
 
  void VelocityAutoOutProductCorrFunc::postCorrelate() {
    // Gets the average of the velocities
    sumVelocity_ /= RealType(velocityCount_);
 
    Mat3x3d correlationOfAverages_ = outProduct(sumVelocity_, sumVelocity_);
 
    for (unsigned int i = 0; i < nTimeBins_; ++i) {
      if (count_[i] > 0) {
        histogram_[i] /= RealType(count_[i]);
 
        // The outerProduct correlation of the averages is subtracted
        // from the correlation value:
        histogram_[i] -= correlationOfAverages_;
      } else {
        histogram_[i] = M3Zero;
      }
    }
  }
 
}  // namespace OpenMD