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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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|
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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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#include "math/randomSPRNG.hpp" |
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|
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namespace oopse { |
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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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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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gaussianSPRNG gaussStream(info_->getSeed()); |
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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 * gaussStream.getGaussian(); |
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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 * gaussStream.getGaussian(); |
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vbar = sqrt(2.0 * kebar * I(n, n)); |
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aJ[n] = vbar * gaussStream.getGaussian(); |
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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 * gaussStream.getGaussian(); |
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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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|
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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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} |
| 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," |
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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. |
| 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 |
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> |
* 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 |
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> |
* 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 |
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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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#include "math/MersenneTwister.hpp" |
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namespace oopse { |
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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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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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#ifndef IS_MPI |
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MTRand randNumGen(info_->getSeed()); |
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#else |
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int nProcessors; |
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MPI_Comm_size(MPI_COMM_WORLD, &nProcessors); |
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MTRand randNumGen(info_->getSeed(), nProcessors, worldRank); |
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#endif |
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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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|
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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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} |
