StressCorrFunc.cpp

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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] 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/StressCorrFunc.hpp"
 
#include <string>
 
#include "applications/dynamicProps/TimeCorrFunc.hpp"
#include "math/SquareMatrix3.hpp"
#include "math/Vector3.hpp"
#include "utils/Constants.hpp"
#include "utils/Revision.hpp"
#include "utils/StringUtils.hpp"
 
namespace OpenMD {
 
  // We need all of the positions, velocities, etc. so that we can
  // recalculate pressures and actions on the fly:
  StressCorrFunc::StressCorrFunc(SimInfo* info, const std::string& filename,
                                 const std::string& sele1,
                                 const std::string& sele2) :
      SystemACF<Mat3x3d>(info, filename, sele1, sele2) {
    setCorrFuncType("StressCorrFunc");
    setOutputName(getPrefix(dumpFilename_) + ".action");
    setLabelString("Txx\tTxy\tTxz\tTyx\tTyy\tTyz\tTzx\tTzy\tTzz");
 
    // We'll need the force manager to compute forces for the average pressure
    forceMan_ = new ForceManager(info_);
 
    // We'll need thermo to compute the pressures from the virial
    thermo_ = new Thermo(info_);
 
    action_.resize(nTimeBins_);
    time_.resize(nTimeBins_);
  }
 
  void StressCorrFunc::computeProperty1(int frame) {
    forceMan_->calcForces();
    RealType vol      = thermo_->getVolume();
    RealType pressure = thermo_->getPressure() / Constants::pressureConvert;
 
    int i;
    StuntDouble* sd;
 
    for (sd = seleMan1_.beginSelected(i); sd != NULL;
         sd = seleMan1_.nextSelected(i)) {
      Vector3d r = sd->getPos();
      Vector3d v = sd->getVel();
      RealType m = sd->getMass();
 
      action_[frame] += m * outProduct(r, v);
    }
 
    action_[frame] /= vol;
    time_[frame] = info_->getSnapshotManager()->getCurrentSnapshot()->getTime();
 
    pressure_.add(pressure);
  }
 
  Mat3x3d StressCorrFunc::calcCorrVal(int frame1, int frame2) {
    Mat3x3d corrTensor(0.0);
    RealType thisTerm;
 
    RealType pAve = pressure_.getAverage();
 
    for (unsigned int i = 0; i < 3; i++) {
      for (unsigned int j = 0; j < 3; j++) {
        if (i == j) {
          thisTerm = (action_[frame2](i, j) - action_[frame1](i, j) -
                      pAve * (time_[frame2] - time_[frame1]));
        } else {
          thisTerm = (action_[frame2](i, j) - action_[frame1](i, j));
        }
        corrTensor(i, j) += thisTerm * thisTerm;
      }
    }
    return corrTensor;
  }
}  // namespace OpenMD