ChargeKineticCorrFunc.cpp

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 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
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 * [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/ChargeKineticCorrFunc.hpp"
 
#include "primitives/Molecule.hpp"
#include "types/FixedChargeAdapter.hpp"
#include "types/FluctuatingChargeAdapter.hpp"
 
namespace OpenMD {
  ChargeKineticCorrFunc::ChargeKineticCorrFunc(SimInfo* info,
                                               const std::string& filename,
                                               const std::string& sele1,
                                               const std::string& sele2,
                                               const RealType cutoff) :
      ObjectCCF<RealType>(info, filename, sele1, sele2),
      rcut_(cutoff) {
    setCorrFuncType("Charge - Kinetic Cross Correlation Function");
    setOutputName(getPrefix(dumpFilename_) + ".QKcorr");
 
    charges_.resize(nFrames_);
    kinetic_.resize(nFrames_);
 
    sumCharge_    = 0;
    sumKinetic_   = 0;
    chargeCount_  = 0;
    kineticCount_ = 0;
  }
 
  void ChargeKineticCorrFunc::validateSelection(SelectionManager& seleMan) {
    StuntDouble* sd;
    int i;
 
    for (sd = seleMan.beginSelected(i); sd != NULL;
         sd = seleMan.nextSelected(i)) {
      Atom* atom                   = static_cast<Atom*>(sd);
      AtomType* atomType           = atom->getAtomType();
      FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atomType);
 
      if (!sd->isDirectional() && !fqa.isFluctuatingCharge()) {
        snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
                 "ChargeKineticCorrFunc::validateSelection Error: selection "
                 "%d (%s)\n"
                 "\t is not a Directional object\n",
                 sd->getGlobalIndex(), sd->getType().c_str());
        painCave.isFatal = 1;
        simError();
      }
    }
  }
 
  int ChargeKineticCorrFunc::computeProperty1(int frame, StuntDouble* sd) {
    RealType q = 0.0;
    pos1_      = sd->getPos();
    Atom* atom = static_cast<Atom*>(sd);
 
    AtomType* atomType = atom->getAtomType();
 
    FixedChargeAdapter fca = FixedChargeAdapter(atomType);
    if (fca.isFixedCharge()) { q += fca.getCharge(); }
 
    FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atomType);
    if (fqa.isFluctuatingCharge()) { q += atom->getFlucQPos(); }
 
    propertyTemp = q;
    charges_[frame].push_back(propertyTemp);
    sumCharge_ += propertyTemp;
    chargeCount_++;
    return charges_[frame].size() - 1;
  }
 
  int ChargeKineticCorrFunc::computeProperty2(int frame, StuntDouble* sd) {
    RealType kinetic(0.0);
    pos2_ = sd->getPos();
 
    RealType mass = sd->getMass();
    Vector3d vel  = sd->getVel();
 
    kinetic += mass * (vel[0] * vel[0] + vel[1] * vel[1] + vel[2] * vel[2]);
 
    Vector3d angMom;
    Mat3x3d I;
    int i, j, k;
 
    if (sd->isDirectional()) {
      angMom = sd->getJ();
      I      = sd->getI();
 
      if (sd->isLinear()) {
        i = sd->linearAxis();
        j = (i + 1) % 3;
        k = (i + 2) % 3;
        kinetic +=
            angMom[j] * angMom[j] / I(j, j) + angMom[k] * angMom[k] / I(k, k);
      } else {
        kinetic += angMom[0] * angMom[0] / I(0, 0) +
                   angMom[1] * angMom[1] / I(1, 1) +
                   angMom[2] * angMom[2] / I(2, 2);
      }
    }
    propertyTemp = 0.5 * kinetic;
    kinetic_[frame].push_back(propertyTemp);
    sumKinetic_ += propertyTemp;
    kineticCount_++;
    return kinetic_[frame].size() - 1;
  }
 
  RealType ChargeKineticCorrFunc::calcCorrVal(int frame1, int frame2, int id1,
                                              int id2) {
    Vector3d sep      = pos1_ - pos2_;
    RealType distance = sep.length();
    if (distance <= rcut_)
      return 0;
    else
      return charges_[frame1][id1] * kinetic_[frame2][id2];
  }
 
  void ChargeKineticCorrFunc::postCorrelate() {
    // gets the average of the charges
    sumCharge_ /= RealType(chargeCount_);
 
    // gets the average of the kinetic energy
    sumKinetic_ /= RealType(kineticCount_);
 
    RealType correlationOfAverages_ = sumCharge_ * sumKinetic_;
    for (unsigned int i = 0; i < nTimeBins_; ++i) {
      if (count_[i] > 0) {
        histogram_[i] /= RealType(count_[i]);
 
        // The  correlation of the averages is subtracted
        // from the correlation value:
        histogram_[i] -= correlationOfAverages_;
      } else {
        histogram_[i] = 0;
      }
    }
  }
}  // namespace OpenMD