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/*
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
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*
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* The University of Notre Dame grants you ("Licensee") a
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* non-exclusive, royalty free, license to use, modify and
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* redistribute this software in source and binary code form, provided
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* that the following conditions are met:
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*
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* 1. Acknowledgement of the program authors must be made in any
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* publication of scientific results based in part on use of the
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* program. An acceptable form of acknowledgement is citation of
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* the article in which the program was described (Matthew
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
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* Parallel Simulation Engine for Molecular Dynamics,"
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* J. Comput. Chem. 26, pp. 252-271 (2005))
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*
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* 2. Redistributions of source code must retain the above copyright
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* notice, this list of conditions and the following disclaimer.
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*
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* 3. Redistributions in binary form must reproduce the above copyright
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* notice, this list of conditions and the following disclaimer in the
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* documentation and/or other materials provided with the
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* distribution.
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*
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* This software is provided "AS IS," without a warranty of any
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* kind. All express or implied conditions, representations and
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* warranties, including any implied warranty of merchantability,
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* fitness for a particular purpose or non-infringement, are hereby
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* excluded. The University of Notre Dame and its licensors shall not
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* be liable for any damages suffered by licensee as a result of
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* using, modifying or distributing the software or its
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* derivatives. In no event will the University of Notre Dame or its
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* licensors be liable for any lost revenue, profit or data, or for
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* direct, indirect, special, consequential, incidental or punitive
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* damages, however caused and regardless of the theory of liability,
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* arising out of the use of or inability to use software, even if the
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* University of Notre Dame has been advised of the possibility of
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* such damages.
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*/
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#include "integrators/Velocitizer.hpp"
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#include "math/SquareMatrix3.hpp"
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#include "primitives/Molecule.hpp"
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#include "primitives/StuntDouble.hpp"
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#ifndef IS_MPI
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#include "math/SeqRandNumGen.hpp"
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#else
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#include "math/ParallelRandNumGen.hpp"
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#endif
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/* Remove me after testing*/
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#include <cstdio>
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#include <iostream>
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/*End remove me*/
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namespace oopse {
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Velocitizer::Velocitizer(SimInfo* info) : info_(info) {
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int seedValue;
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Globals * simParams = info->getSimParams();
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#ifndef IS_MPI
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if (simParams->haveSeed()) {
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seedValue = simParams->getSeed();
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randNumGen_ = new SeqRandNumGen(seedValue);
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}else {
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randNumGen_ = new SeqRandNumGen();
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}
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#else
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if (simParams->haveSeed()) {
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seedValue = simParams->getSeed();
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randNumGen_ = new ParallelRandNumGen(seedValue);
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}else {
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randNumGen_ = new ParallelRandNumGen();
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}
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#endif
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}
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Velocitizer::~Velocitizer() {
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delete randNumGen_;
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}
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void Velocitizer::velocitize(RealType temperature) {
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Vector3d aVel;
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Vector3d aJ;
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Mat3x3d I;
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int l;
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int m;
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int n;
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Vector3d vdrift;
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RealType vbar;
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/**@todo refactory kb */
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const RealType kb = 8.31451e-7; // kb in amu, angstroms, fs, etc.
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RealType av2;
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RealType kebar;
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Globals * simParams = info_->getSimParams();
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SimInfo::MoleculeIterator i;
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Molecule::IntegrableObjectIterator j;
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Molecule * mol;
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StuntDouble * integrableObject;
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kebar = kb * temperature * info_->getNdfRaw() / (2.0 * info_->getNdf());
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for( mol = info_->beginMolecule(i); mol != NULL;
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mol = info_->nextMolecule(i) ) {
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for( integrableObject = mol->beginIntegrableObject(j);
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integrableObject != NULL;
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integrableObject = mol->nextIntegrableObject(j) ) {
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// uses equipartition theory to solve for vbar in angstrom/fs
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av2 = 2.0 * kebar / integrableObject->getMass();
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vbar = sqrt(av2);
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// picks random velocities from a gaussian distribution
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// centered on vbar
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for( int k = 0; k < 3; k++ ) {
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aVel[k] = vbar * randNumGen_->randNorm(0.0, 1.0);
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}
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integrableObject->setVel(aVel);
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if (integrableObject->isDirectional()) {
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I = integrableObject->getI();
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if (integrableObject->isLinear()) {
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l = integrableObject->linearAxis();
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m = (l + 1) % 3;
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n = (l + 2) % 3;
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aJ[l] = 0.0;
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vbar = sqrt(2.0 * kebar * I(m, m));
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aJ[m] = vbar * randNumGen_->randNorm(0.0, 1.0);
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vbar = sqrt(2.0 * kebar * I(n, n));
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aJ[n] = vbar * randNumGen_->randNorm(0.0, 1.0);
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} else {
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for( int k = 0; k < 3; k++ ) {
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vbar = sqrt(2.0 * kebar * I(k, k));
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aJ[k] = vbar *randNumGen_->randNorm(0.0, 1.0);
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}
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} // else isLinear
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integrableObject->setJ(aJ);
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} //isDirectional
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}
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} //end for (mol = beginMolecule(i); ...)
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removeComDrift();
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// Remove angular drift if we are not using periodic boundary conditions.
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if(!simParams->getUsePeriodicBoundaryConditions()) removeAngularDrift();
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}
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void Velocitizer::removeComDrift() {
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// Get the Center of Mass drift velocity.
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Vector3d vdrift = info_->getComVel();
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SimInfo::MoleculeIterator i;
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Molecule::IntegrableObjectIterator j;
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Molecule * mol;
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StuntDouble * integrableObject;
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// Corrects for the center of mass drift.
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// sums all the momentum and divides by total mass.
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for( mol = info_->beginMolecule(i); mol != NULL;
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mol = info_->nextMolecule(i) ) {
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for( integrableObject = mol->beginIntegrableObject(j);
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integrableObject != NULL;
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integrableObject = mol->nextIntegrableObject(j) ) {
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integrableObject->setVel(integrableObject->getVel() - vdrift);
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}
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}
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}
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void Velocitizer::removeAngularDrift() {
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// Get the Center of Mass drift velocity.
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Vector3d vdrift;
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Vector3d com;
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info_->getComAll(com,vdrift);
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Mat3x3d inertiaTensor;
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Vector3d angularMomentum;
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Vector3d omega;
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info_->getInertiaTensor(inertiaTensor,angularMomentum);
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// We now need the inverse of the inertia tensor.
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/*
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std::cerr << "Angular Momentum before is "
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<< angularMomentum << std::endl;
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std::cerr << "Inertia Tensor before is "
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<< inertiaTensor << std::endl;
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*/
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inertiaTensor =inertiaTensor.inverse();
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/*
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std::cerr << "Inertia Tensor after inverse is "
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<< inertiaTensor << std::endl;
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*/
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omega = inertiaTensor*angularMomentum;
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SimInfo::MoleculeIterator i;
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Molecule::IntegrableObjectIterator j;
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Molecule * mol;
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StuntDouble * integrableObject;
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Vector3d tempComPos;
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// Corrects for the center of mass angular drift.
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// sums all the angular momentum and divides by total mass.
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for( mol = info_->beginMolecule(i); mol != NULL;
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mol = info_->nextMolecule(i) ) {
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for( integrableObject = mol->beginIntegrableObject(j);
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integrableObject != NULL;
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integrableObject = mol->nextIntegrableObject(j) ) {
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tempComPos = integrableObject->getPos()-com;
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integrableObject->setVel((integrableObject->getVel() - vdrift)-cross(omega,tempComPos));
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}
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}
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angularMomentum = info_->getAngularMomentum();
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/*
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std::cerr << "Angular Momentum after is "
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<< angularMomentum << std::endl;
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*/
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}
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}
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