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/* |
| 2 |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
| 3 |
< |
* |
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< |
* The University of Notre Dame grants you ("Licensee") a |
| 5 |
< |
* non-exclusive, royalty free, license to use, modify and |
| 6 |
< |
* redistribute this software in source and binary code form, provided |
| 7 |
< |
* that the following conditions are met: |
| 8 |
< |
* |
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< |
* 1. Acknowledgement of the program authors must be made in any |
| 10 |
< |
* publication of scientific results based in part on use of the |
| 11 |
< |
* program. An acceptable form of acknowledgement is citation of |
| 12 |
< |
* the article in which the program was described (Matthew |
| 13 |
< |
* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
| 14 |
< |
* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
| 15 |
< |
* Parallel Simulation Engine for Molecular Dynamics," |
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< |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
| 17 |
< |
* |
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< |
* 2. Redistributions of source code must retain the above copyright |
| 19 |
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* notice, this list of conditions and the following disclaimer. |
| 20 |
< |
* |
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< |
* 3. Redistributions in binary form must reproduce the above copyright |
| 22 |
< |
* notice, this list of conditions and the following disclaimer in the |
| 23 |
< |
* documentation and/or other materials provided with the |
| 24 |
< |
* distribution. |
| 25 |
< |
* |
| 26 |
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* This software is provided "AS IS," without a warranty of any |
| 27 |
< |
* kind. All express or implied conditions, representations and |
| 28 |
< |
* warranties, including any implied warranty of merchantability, |
| 29 |
< |
* fitness for a particular purpose or non-infringement, are hereby |
| 30 |
< |
* excluded. The University of Notre Dame and its licensors shall not |
| 31 |
< |
* be liable for any damages suffered by licensee as a result of |
| 32 |
< |
* using, modifying or distributing the software or its |
| 33 |
< |
* derivatives. In no event will the University of Notre Dame or its |
| 34 |
< |
* licensors be liable for any lost revenue, profit or data, or for |
| 35 |
< |
* direct, indirect, special, consequential, incidental or punitive |
| 36 |
< |
* damages, however caused and regardless of the theory of liability, |
| 37 |
< |
* arising out of the use of or inability to use software, even if the |
| 38 |
< |
* University of Notre Dame has been advised of the possibility of |
| 39 |
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* such damages. |
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< |
*/ |
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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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|
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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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|
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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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|
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namespace oopse { |
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|
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Velocitizer::Velocitizer(SimInfo* info) : info_(info) { |
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|
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int seedValue; |
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Globals * simParams = info->getSimParams(); |
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|
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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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|
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Velocitizer::~Velocitizer() { |
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delete randNumGen_; |
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} |
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|
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void Velocitizer::velocitize(double 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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double vbar; |
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/**@todo refactory kb */ |
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const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc. |
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double av2; |
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double kebar; |
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|
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Globals * simParams = info_->getSimParams(); |
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|
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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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|
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|
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|
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kebar = kb * temperature * info_->getNdfRaw() / (2.0 * info_->getNdf()); |
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|
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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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|
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// uses equipartition theory to solve for vbar in angstrom/fs |
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|
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av2 = 2.0 * kebar / integrableObject->getMass(); |
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vbar = sqrt(av2); |
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|
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// picks random velocities from a gaussian distribution |
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// centered on vbar |
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|
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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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|
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integrableObject->setVel(aVel); |
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|
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if (integrableObject->isDirectional()) { |
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I = integrableObject->getI(); |
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|
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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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|
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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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|
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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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|
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|
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|
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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->getPBC()) removeAngularDrift(); |
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|
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} |
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|
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|
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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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|
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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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|
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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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} |
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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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|
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Vector3d vdrift; |
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Vector3d com; |
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|
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info_->getComAll(com,vdrift); |
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|
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Mat3x3d inertiaTensor; |
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Vector3d angularMomentum; |
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Vector3d omega; |
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|
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|
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|
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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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|
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inertiaTensor =inertiaTensor.inverse(); |
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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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|
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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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|
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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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|
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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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|
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|
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|
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|
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} |
| 1 |
> |
/* |
| 2 |
> |
* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
| 3 |
> |
* |
| 4 |
> |
* The University of Notre Dame grants you ("Licensee") a |
| 5 |
> |
* non-exclusive, royalty free, license to use, modify and |
| 6 |
> |
* redistribute this software in source and binary code form, provided |
| 7 |
> |
* that the following conditions are met: |
| 8 |
> |
* |
| 9 |
> |
* 1. Acknowledgement of the program authors must be made in any |
| 10 |
> |
* publication of scientific results based in part on use of the |
| 11 |
> |
* program. An acceptable form of acknowledgement is citation of |
| 12 |
> |
* the article in which the program was described (Matthew |
| 13 |
> |
* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
| 14 |
> |
* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
| 15 |
> |
* Parallel Simulation Engine for Molecular Dynamics," |
| 16 |
> |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
| 17 |
> |
* |
| 18 |
> |
* 2. Redistributions of source code must retain the above copyright |
| 19 |
> |
* notice, this list of conditions and the following disclaimer. |
| 20 |
> |
* |
| 21 |
> |
* 3. Redistributions in binary form must reproduce the above copyright |
| 22 |
> |
* notice, this list of conditions and the following disclaimer in the |
| 23 |
> |
* documentation and/or other materials provided with the |
| 24 |
> |
* distribution. |
| 25 |
> |
* |
| 26 |
> |
* This software is provided "AS IS," without a warranty of any |
| 27 |
> |
* kind. All express or implied conditions, representations and |
| 28 |
> |
* warranties, including any implied warranty of merchantability, |
| 29 |
> |
* fitness for a particular purpose or non-infringement, are hereby |
| 30 |
> |
* excluded. The University of Notre Dame and its licensors shall not |
| 31 |
> |
* be liable for any damages suffered by licensee as a result of |
| 32 |
> |
* using, modifying or distributing the software or its |
| 33 |
> |
* derivatives. In no event will the University of Notre Dame or its |
| 34 |
> |
* licensors be liable for any lost revenue, profit or data, or for |
| 35 |
> |
* direct, indirect, special, consequential, incidental or punitive |
| 36 |
> |
* damages, however caused and regardless of the theory of liability, |
| 37 |
> |
* arising out of the use of or inability to use software, even if the |
| 38 |
> |
* University of Notre Dame has been advised of the possibility of |
| 39 |
> |
* such damages. |
| 40 |
> |
*/ |
| 41 |
> |
|
| 42 |
> |
#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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> |
|
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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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> |
|
| 53 |
> |
/* Remove me after testing*/ |
| 54 |
> |
#include <cstdio> |
| 55 |
> |
#include <iostream> |
| 56 |
> |
/*End remove me*/ |
| 57 |
> |
|
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> |
namespace oopse { |
| 59 |
> |
|
| 60 |
> |
Velocitizer::Velocitizer(SimInfo* info) : info_(info) { |
| 61 |
> |
|
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> |
int seedValue; |
| 63 |
> |
Globals * simParams = info->getSimParams(); |
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> |
|
| 65 |
> |
#ifndef IS_MPI |
| 66 |
> |
if (simParams->haveSeed()) { |
| 67 |
> |
seedValue = simParams->getSeed(); |
| 68 |
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randNumGen_ = new SeqRandNumGen(seedValue); |
| 69 |
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}else { |
| 70 |
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randNumGen_ = new SeqRandNumGen(); |
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} |
| 72 |
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#else |
| 73 |
> |
if (simParams->haveSeed()) { |
| 74 |
> |
seedValue = simParams->getSeed(); |
| 75 |
> |
randNumGen_ = new ParallelRandNumGen(seedValue); |
| 76 |
> |
}else { |
| 77 |
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randNumGen_ = new ParallelRandNumGen(); |
| 78 |
> |
} |
| 79 |
> |
#endif |
| 80 |
> |
} |
| 81 |
> |
|
| 82 |
> |
Velocitizer::~Velocitizer() { |
| 83 |
> |
delete randNumGen_; |
| 84 |
> |
} |
| 85 |
> |
|
| 86 |
> |
void Velocitizer::velocitize(RealType temperature) { |
| 87 |
> |
Vector3d aVel; |
| 88 |
> |
Vector3d aJ; |
| 89 |
> |
Mat3x3d I; |
| 90 |
> |
int l; |
| 91 |
> |
int m; |
| 92 |
> |
int n; |
| 93 |
> |
Vector3d vdrift; |
| 94 |
> |
RealType vbar; |
| 95 |
> |
/**@todo refactory kb */ |
| 96 |
> |
const RealType kb = 8.31451e-7; // kb in amu, angstroms, fs, etc. |
| 97 |
> |
RealType av2; |
| 98 |
> |
RealType kebar; |
| 99 |
> |
|
| 100 |
> |
Globals * simParams = info_->getSimParams(); |
| 101 |
> |
|
| 102 |
> |
SimInfo::MoleculeIterator i; |
| 103 |
> |
Molecule::IntegrableObjectIterator j; |
| 104 |
> |
Molecule * mol; |
| 105 |
> |
StuntDouble * integrableObject; |
| 106 |
> |
|
| 107 |
> |
kebar = kb * temperature * info_->getNdfRaw() / (2.0 * info_->getNdf()); |
| 108 |
> |
for( mol = info_->beginMolecule(i); mol != NULL; |
| 109 |
> |
mol = info_->nextMolecule(i) ) { |
| 110 |
> |
for( integrableObject = mol->beginIntegrableObject(j); |
| 111 |
> |
integrableObject != NULL; |
| 112 |
> |
integrableObject = mol->nextIntegrableObject(j) ) { |
| 113 |
> |
|
| 114 |
> |
// uses equipartition theory to solve for vbar in angstrom/fs |
| 115 |
> |
|
| 116 |
> |
av2 = 2.0 * kebar / integrableObject->getMass(); |
| 117 |
> |
vbar = sqrt(av2); |
| 118 |
> |
|
| 119 |
> |
// picks random velocities from a gaussian distribution |
| 120 |
> |
// centered on vbar |
| 121 |
> |
|
| 122 |
> |
for( int k = 0; k < 3; k++ ) { |
| 123 |
> |
aVel[k] = vbar * randNumGen_->randNorm(0.0, 1.0); |
| 124 |
> |
} |
| 125 |
> |
integrableObject->setVel(aVel); |
| 126 |
> |
|
| 127 |
> |
if (integrableObject->isDirectional()) { |
| 128 |
> |
I = integrableObject->getI(); |
| 129 |
> |
|
| 130 |
> |
if (integrableObject->isLinear()) { |
| 131 |
> |
l = integrableObject->linearAxis(); |
| 132 |
> |
m = (l + 1) % 3; |
| 133 |
> |
n = (l + 2) % 3; |
| 134 |
> |
|
| 135 |
> |
aJ[l] = 0.0; |
| 136 |
> |
vbar = sqrt(2.0 * kebar * I(m, m)); |
| 137 |
> |
aJ[m] = vbar * randNumGen_->randNorm(0.0, 1.0); |
| 138 |
> |
vbar = sqrt(2.0 * kebar * I(n, n)); |
| 139 |
> |
aJ[n] = vbar * randNumGen_->randNorm(0.0, 1.0); |
| 140 |
> |
} else { |
| 141 |
> |
for( int k = 0; k < 3; k++ ) { |
| 142 |
> |
vbar = sqrt(2.0 * kebar * I(k, k)); |
| 143 |
> |
aJ[k] = vbar *randNumGen_->randNorm(0.0, 1.0); |
| 144 |
> |
} |
| 145 |
> |
} // else isLinear |
| 146 |
> |
|
| 147 |
> |
integrableObject->setJ(aJ); |
| 148 |
> |
} //isDirectional |
| 149 |
> |
} |
| 150 |
> |
} //end for (mol = beginMolecule(i); ...) |
| 151 |
> |
|
| 152 |
> |
|
| 153 |
> |
|
| 154 |
> |
removeComDrift(); |
| 155 |
> |
// Remove angular drift if we are not using periodic boundary conditions. |
| 156 |
> |
if(!simParams->getUsePeriodicBoundaryConditions()) removeAngularDrift(); |
| 157 |
> |
|
| 158 |
> |
} |
| 159 |
> |
|
| 160 |
> |
|
| 161 |
> |
|
| 162 |
> |
void Velocitizer::removeComDrift() { |
| 163 |
> |
// Get the Center of Mass drift velocity. |
| 164 |
> |
Vector3d vdrift = info_->getComVel(); |
| 165 |
> |
|
| 166 |
> |
SimInfo::MoleculeIterator i; |
| 167 |
> |
Molecule::IntegrableObjectIterator j; |
| 168 |
> |
Molecule * mol; |
| 169 |
> |
StuntDouble * integrableObject; |
| 170 |
> |
|
| 171 |
> |
// Corrects for the center of mass drift. |
| 172 |
> |
// sums all the momentum and divides by total mass. |
| 173 |
> |
for( mol = info_->beginMolecule(i); mol != NULL; |
| 174 |
> |
mol = info_->nextMolecule(i) ) { |
| 175 |
> |
for( integrableObject = mol->beginIntegrableObject(j); |
| 176 |
> |
integrableObject != NULL; |
| 177 |
> |
integrableObject = mol->nextIntegrableObject(j) ) { |
| 178 |
> |
integrableObject->setVel(integrableObject->getVel() - vdrift); |
| 179 |
> |
} |
| 180 |
> |
} |
| 181 |
> |
|
| 182 |
> |
} |
| 183 |
> |
|
| 184 |
> |
|
| 185 |
> |
void Velocitizer::removeAngularDrift() { |
| 186 |
> |
// Get the Center of Mass drift velocity. |
| 187 |
> |
|
| 188 |
> |
Vector3d vdrift; |
| 189 |
> |
Vector3d com; |
| 190 |
> |
|
| 191 |
> |
info_->getComAll(com,vdrift); |
| 192 |
> |
|
| 193 |
> |
Mat3x3d inertiaTensor; |
| 194 |
> |
Vector3d angularMomentum; |
| 195 |
> |
Vector3d omega; |
| 196 |
> |
|
| 197 |
> |
|
| 198 |
> |
|
| 199 |
> |
info_->getInertiaTensor(inertiaTensor,angularMomentum); |
| 200 |
> |
// We now need the inverse of the inertia tensor. |
| 201 |
> |
/* |
| 202 |
> |
std::cerr << "Angular Momentum before is " |
| 203 |
> |
<< angularMomentum << std::endl; |
| 204 |
> |
std::cerr << "Inertia Tensor before is " |
| 205 |
> |
<< inertiaTensor << std::endl; |
| 206 |
> |
*/ |
| 207 |
> |
inertiaTensor =inertiaTensor.inverse(); |
| 208 |
> |
/* |
| 209 |
> |
std::cerr << "Inertia Tensor after inverse is " |
| 210 |
> |
<< inertiaTensor << std::endl; |
| 211 |
> |
*/ |
| 212 |
> |
omega = inertiaTensor*angularMomentum; |
| 213 |
> |
|
| 214 |
> |
SimInfo::MoleculeIterator i; |
| 215 |
> |
Molecule::IntegrableObjectIterator j; |
| 216 |
> |
Molecule * mol; |
| 217 |
> |
StuntDouble * integrableObject; |
| 218 |
> |
Vector3d tempComPos; |
| 219 |
> |
|
| 220 |
> |
// Corrects for the center of mass angular drift. |
| 221 |
> |
// sums all the angular momentum and divides by total mass. |
| 222 |
> |
for( mol = info_->beginMolecule(i); mol != NULL; |
| 223 |
> |
mol = info_->nextMolecule(i) ) { |
| 224 |
> |
for( integrableObject = mol->beginIntegrableObject(j); |
| 225 |
> |
integrableObject != NULL; |
| 226 |
> |
integrableObject = mol->nextIntegrableObject(j) ) { |
| 227 |
> |
tempComPos = integrableObject->getPos()-com; |
| 228 |
> |
integrableObject->setVel((integrableObject->getVel() - vdrift)-cross(omega,tempComPos)); |
| 229 |
> |
} |
| 230 |
> |
} |
| 231 |
> |
|
| 232 |
> |
angularMomentum = info_->getAngularMomentum(); |
| 233 |
> |
/* |
| 234 |
> |
std::cerr << "Angular Momentum after is " |
| 235 |
> |
<< angularMomentum << std::endl; |
| 236 |
> |
*/ |
| 237 |
> |
|
| 238 |
> |
} |
| 239 |
> |
|
| 240 |
> |
|
| 241 |
> |
|
| 242 |
> |
|
| 243 |
> |
} |
