NVE.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).
 */
 
/**
 * @file NVE.cpp
 * @author tlin
 * @date 11/08/2004
 * @version 1.0
 */
 
#include "integrators/NVE.hpp"
 
#include "primitives/Molecule.hpp"
#include "utils/Constants.hpp"
 
namespace OpenMD {
 
  NVE::NVE(SimInfo* info) : VelocityVerletIntegrator(info) {}
 
  void NVE::moveA() {
    SimInfo::MoleculeIterator i;
    Molecule::IntegrableObjectIterator j;
    Molecule* mol;
    StuntDouble* sd;
    Vector3d vel;
    Vector3d pos;
    Vector3d frc;
    Vector3d Tb;
    Vector3d ji;
    RealType mass;
 
    for (mol = info_->beginMolecule(i); mol != NULL;
         mol = info_->nextMolecule(i)) {
      for (sd = mol->beginIntegrableObject(j); sd != NULL;
           sd = mol->nextIntegrableObject(j)) {
        vel  = sd->getVel();
        pos  = sd->getPos();
        frc  = sd->getFrc();
        mass = sd->getMass();
 
        // velocity half step
        vel += (dt2 / mass * Constants::energyConvert) * frc;
 
        // position whole step
        pos += dt * vel;
 
        sd->setVel(vel);
        sd->setPos(pos);
 
        if (sd->isDirectional()) {
          // get and convert the torque to body frame
 
          Tb = sd->lab2Body(sd->getTrq());
 
          // get the angular momentum, and propagate a half step
 
          ji = sd->getJ();
 
          ji += (dt2 * Constants::energyConvert) * Tb;
 
          rotAlgo_->rotate(sd, ji, dt);
 
          sd->setJ(ji);
        }
      }
    }
    flucQ_->moveA();
    rattle_->constraintA();
  }
 
  void NVE::moveB() {
    SimInfo::MoleculeIterator i;
    Molecule::IntegrableObjectIterator j;
    Molecule* mol;
    StuntDouble* sd;
    Vector3d vel;
    Vector3d frc;
    Vector3d Tb;
    Vector3d ji;
    RealType mass;
 
    for (mol = info_->beginMolecule(i); mol != NULL;
         mol = info_->nextMolecule(i)) {
      for (sd = mol->beginIntegrableObject(j); sd != NULL;
           sd = mol->nextIntegrableObject(j)) {
        vel  = sd->getVel();
        frc  = sd->getFrc();
        mass = sd->getMass();
 
        // velocity half step
        vel += (dt2 / mass * Constants::energyConvert) * frc;
 
        sd->setVel(vel);
 
        if (sd->isDirectional()) {
          // get and convert the torque to body frame
 
          Tb = sd->lab2Body(sd->getTrq());
 
          // get the angular momentum, and propagate a half step
 
          ji = sd->getJ();
 
          ji += (dt2 * Constants::energyConvert) * Tb;
 
          sd->setJ(ji);
        }
      }
    }
 
    flucQ_->moveB();
    rattle_->constraintB();
  }
 
  RealType NVE::calcConservedQuantity() { return thermo.getTotalEnergy(); }
 
}  // namespace OpenMD