Atom.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/Atom.hpp"
 
#include "types/FluctuatingChargeAdapter.hpp"
 
namespace OpenMD {
 
  Atom::Atom(AtomType* at) :
      StuntDouble(otAtom, &Snapshot::atomData), atomType_(at) {
    mass_ = at->getMass();
    if (at->isFluctuatingCharge()) {
      FluctuatingChargeAdapter fca = FluctuatingChargeAdapter(at);
      chargeMass_                  = fca.getChargeMass();
    } else {
      chargeMass_ = std::numeric_limits<RealType>::infinity();
    }
  }
 
  Mat3x3d Atom::getI() { return Mat3x3d::identity(); }
 
  std::vector<RealType> Atom::getGrad() {
    std::vector<RealType> grad(3, 0.0);
 
    Vector3d force = getFrc();
 
    grad[0] = -force[0];
    grad[1] = -force[1];
    grad[2] = -force[2];
 
    return grad;
  }
 
  void Atom::accept(BaseVisitor* v) { v->visit(this); }
}  // namespace OpenMD