DirectionalAtom.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 "primitives/DirectionalAtom.hpp"
 
#include "types/DirectionalAdapter.hpp"
#include "types/MultipoleAdapter.hpp"
#include "utils/simError.h"
 
namespace OpenMD {
 
  DirectionalAtom::DirectionalAtom(AtomType* dAtomType) : Atom(dAtomType) {
    objType_ = otDAtom;
 
    DirectionalAdapter da = DirectionalAdapter(dAtomType);
    I_                    = da.getI();
 
    MultipoleAdapter ma = MultipoleAdapter(dAtomType);
    if (ma.isDipole()) { dipole_ = ma.getDipole(); }
    if (ma.isQuadrupole()) { quadrupole_ = ma.getQuadrupole(); }
 
    // Check if one of the diagonal inertia tensor of this directional
    // atom is zero:
    int nLinearAxis       = 0;
    Mat3x3d inertiaTensor = getI();
    for (int i = 0; i < 3; i++) {
      if (fabs(inertiaTensor(i, i)) < OpenMD::epsilon) {
        linear_     = true;
        linearAxis_ = i;
        ++nLinearAxis;
      }
    }
 
    if (nLinearAxis > 1) {
      snprintf(
          painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
          "Directional Atom warning.\n"
          "\tOpenMD found more than one axis in this directional atom with a "
          "vanishing \n"
          "\tmoment of inertia.");
      painCave.isFatal = 0;
      simError();
    }
  }
 
  Mat3x3d DirectionalAtom::getI() { return I_; }
 
  void DirectionalAtom::setPrevA(const RotMat3x3d& a) {
    ((snapshotMan_->getPrevSnapshot())->*storage_).aMat[localIndex_] = a;
 
    if (atomType_->isMultipole()) {
      RotMat3x3d atrans = a.transpose();
 
      if (atomType_->isDipole()) {
        ((snapshotMan_->getPrevSnapshot())->*storage_).dipole[localIndex_] =
            atrans * dipole_;
      }
 
      if (atomType_->isQuadrupole()) {
        ((snapshotMan_->getPrevSnapshot())->*storage_).quadrupole[localIndex_] =
            atrans * quadrupole_ * a;
      }
    }
  }
 
  void DirectionalAtom::setA(const RotMat3x3d& a) {
    ((snapshotMan_->getCurrentSnapshot())->*storage_).aMat[localIndex_] = a;
 
    if (atomType_->isMultipole()) {
      RotMat3x3d atrans = a.transpose();
 
      if (atomType_->isDipole()) {
        ((snapshotMan_->getCurrentSnapshot())->*storage_).dipole[localIndex_] =
            atrans * dipole_;
      }
 
      if (atomType_->isQuadrupole()) {
        ((snapshotMan_->getCurrentSnapshot())->*storage_)
            .quadrupole[localIndex_] = atrans * quadrupole_ * a;
      }
    }
  }
 
  void DirectionalAtom::setA(const RotMat3x3d& a, int snapshotNo) {
    ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).aMat[localIndex_] = a;
 
    if (atomType_->isMultipole()) {
      RotMat3x3d atrans = a.transpose();
 
      if (atomType_->isDipole()) {
        ((snapshotMan_->getSnapshot(snapshotNo))->*storage_)
            .dipole[localIndex_] = atrans * dipole_;
      }
 
      if (atomType_->isQuadrupole()) {
        ((snapshotMan_->getSnapshot(snapshotNo))->*storage_)
            .quadrupole[localIndex_] = atrans * quadrupole_ * a;
      }
    }
  }
 
  void DirectionalAtom::rotateBy(const RotMat3x3d& m) { setA(m * getA()); }
 
  std::vector<RealType> DirectionalAtom::getGrad() {
    std::vector<RealType> grad(6, 0.0);
    Vector3d force;
    Vector3d torque;
    Vector3d myEuler;
    RealType phi, theta;
    RealType cphi, sphi, ctheta, stheta;
    Vector3d ephi;
    Vector3d etheta;
    Vector3d epsi;
 
    force  = getFrc();
    torque = getTrq();
 
    myEuler = getA().toEulerAngles();
 
    phi   = myEuler[0];
    theta = myEuler[1];
 
    cphi   = cos(phi);
    sphi   = sin(phi);
    ctheta = cos(theta);
    stheta = sin(theta);
 
    if (fabs(stheta) < 1.0E-9) { stheta = 1.0E-9; }
 
    ephi[0] = -sphi * ctheta / stheta;
    ephi[1] = cphi * ctheta / stheta;
    ephi[2] = 1.0;
 
    etheta[0] = cphi;
    etheta[1] = sphi;
    etheta[2] = 0.0;
 
    epsi[0] = sphi / stheta;
    epsi[1] = -cphi / stheta;
    epsi[2] = 0.0;
 
    // gradient is equal to -force
    for (int j = 0; j < 3; j++)
      grad[j] = -force[j];
 
    for (int j = 0; j < 3; j++) {
      grad[3] -= torque[j] * ephi[j];
      grad[4] -= torque[j] * etheta[j];
      grad[5] -= torque[j] * epsi[j];
    }
 
    return grad;
  }
 
  void DirectionalAtom::accept(BaseVisitor* v) { v->visit(this); }
}  // namespace OpenMD