ForceAutoCorrFunc.cpp

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 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the following paper when you publish your work:
 *
 * [1] Drisko et al., J. Open Source Softw. 9, 7004 (2024).
 *
 * Good starting points for code and simulation methodology are:
 *
 * [2] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
 * [3] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
 * [4] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
 * [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 * [6] Kuang & Gezelter, Mol. Phys., 110, 691-701 (2012).
 * [7] Lamichhane, Gezelter & Newman, J. Chem. Phys. 141, 134109 (2014).
 * [8] Bhattarai, Newman & Gezelter, Phys. Rev. B 99, 094106 (2019).
 * [9] Drisko & Gezelter, J. Chem. Theory Comput. 20, 4986-4997 (2024).
 */
 
#include "applications/dynamicProps/ForceAutoCorrFunc.hpp"
 
#include "math/SquareMatrix3.hpp"
#include "utils/Revision.hpp"
 
namespace OpenMD {
  ForceAutoCorrFunc::ForceAutoCorrFunc(SimInfo* info,
                                       const std::string& filename,
                                       const std::string& sele1,
                                       const std::string& sele2) :
      ObjectACF<Mat3x3d>(info, filename, sele1, sele2) {
    setCorrFuncType("Force - Force Auto Correlation Function");
    setOutputName(getPrefix(dumpFilename_) + ".facorr");
 
    forces_.resize(nFrames_);
    sumForces_   = V3Zero;
    forcesCount_ = 0;
  }
 
  int ForceAutoCorrFunc::computeProperty1(int frame, StuntDouble* sd) {
    if (sd->isDirectional()) {
      Mat3x3d A    = sd->getA();
      Vector3d f   = sd->getFrc();
      propertyTemp = A * f;
    } else {
      Vector3d f   = sd->getFrc();
      propertyTemp = f;
    }
    forces_[frame].push_back(propertyTemp);
    sumForces_ += propertyTemp;
    forcesCount_++;
    return forces_[frame].size() - 1;
  }
 
  Mat3x3d ForceAutoCorrFunc::calcCorrVal(int frame1, int frame2, int id1,
                                         int id2) {
    return outProduct(forces_[frame1][id1], forces_[frame2][id2]);
  }
 
  void ForceAutoCorrFunc::postCorrelate() {
    // Gets the average of the forces_
    sumForces_ /= RealType(forcesCount_);
 
    Mat3x3d correlationOfAverages_ = outProduct(sumForces_, sumForces_);
    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