MagneticField.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 "perturbations/MagneticField.hpp"
 
#include "brains/ForceModifier.hpp"
#include "nonbonded/NonBondedInteraction.hpp"
#include "primitives/Molecule.hpp"
#include "types/FixedChargeAdapter.hpp"
#include "types/MultipoleAdapter.hpp"
#include "utils/Constants.hpp"
 
namespace OpenMD {
 
  MagneticField::MagneticField(SimInfo* info) :
      ForceModifier {info}, initialized {false}, doMagneticField {false} {
    simParams = info_->getSimParams();
  }
 
  void MagneticField::initialize() {
    std::vector<RealType> mf;
 
    if (simParams->haveMagneticField()) {
      doMagneticField = true;
      mf              = simParams->getMagneticField();
    }
    if (mf.size() != 3) {
      snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
               "MagneticField: Incorrect number of parameters specified.\n"
               "\tthere should be 3 parameters, but %zu were specified.\n",
               mf.size());
      painCave.isFatal = 1;
      simError();
    }
    MF.x() = mf[0];
    MF.y() = mf[1];
    MF.z() = mf[2];
 
    initialized = true;
  }
 
  void MagneticField::modifyForces() {
    if (!initialized) initialize();
 
    SimInfo::MoleculeIterator i;
    Molecule::AtomIterator j;
    Molecule* mol;
    Atom* atom;
    AtomType* atype;
 
    int l, m, n;
    RealType C;
    Vector3d v;
    Vector3d f;
    Vector3d r;
    Vector3d t;
    Vector3d D;
    Vector3d AngMomentum;
    Vector3d omega;
    Mat3x3d I;
    bool isCharge;
 
    if (doMagneticField) {
      for (mol = info_->beginMolecule(i); mol != NULL;
           mol = info_->nextMolecule(i)) {
        for (atom = mol->beginAtom(j); atom != NULL; atom = mol->nextAtom(j)) {
          isCharge = false;
          C        = 0.0;
 
          atype = atom->getAtomType();
          r     = atom->getPos();
          v     = atom->getVel();
 
          FixedChargeAdapter fca = FixedChargeAdapter(atype);
          if (fca.isFixedCharge()) {
            isCharge = true;
            C        = fca.getCharge();
          }
 
          C *= Constants::chargeFieldConvert;
 
          if (isCharge) {
            f = cross(v, MF) * C * Constants::magneticFieldConvert;
            atom->addFrc(f);
          }
 
          MultipoleAdapter ma = MultipoleAdapter(atype);
          if (ma.isDipole()) {
            D = atom->getDipole() * Constants::dipoleFieldConvert;
 
            t = cross(D, cross(v, MF));
            atom->addTrq(t);
 
            AngMomentum = atom->getJ();
            I           = atom->getI();
            if (atom->isLinear()) {
              l        = atom->linearAxis();
              m        = (l + 1) % 3;
              n        = (l + 2) % 3;
              omega[l] = 0;
              omega[m] = AngMomentum[m] / I(m, m);
              omega[n] = AngMomentum[n] / I(n, n);
            } else {
              omega = I.inverse() * AngMomentum;
            }
 
            f = cross(cross(omega, D), MF);
            atom->addFrc(f);
          }
        }
      }
    }
  }
}  // namespace OpenMD