1 |
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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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* |
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* The University of Notre Dame grants you ("Licensee") a |
5 |
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* non-exclusive, royalty free, license to use, modify and |
6 |
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* redistribute this software in source and binary code form, provided |
7 |
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* that the following conditions are met: |
8 |
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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 |
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 |
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* Parallel Simulation Engine for Molecular Dynamics," |
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* J. Comput. Chem. 26, pp. 252-271 (2005)) |
17 |
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* |
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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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* |
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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 |
23 |
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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 |
28 |
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* warranties, including any implied warranty of merchantability, |
29 |
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* fitness for a particular purpose or non-infringement, are hereby |
30 |
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* excluded. The University of Notre Dame and its licensors shall not |
31 |
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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 |
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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," |
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 |
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|
42 |
> |
#include "integrators/Velocitizer.hpp" |
43 |
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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 |
73 |
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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 |
80 |
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} |
81 |
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|
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Velocitizer::~Velocitizer() { |
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delete randNumGen_; |
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} |
85 |
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|
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void Velocitizer::velocitize(RealType temperature) { |
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Vector3d aVel; |
88 |
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Vector3d aJ; |
89 |
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Mat3x3d I; |
90 |
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int l; |
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int m; |
92 |
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int n; |
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Vector3d vdrift; |
94 |
> |
RealType vbar; |
95 |
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/**@todo refactory kb */ |
96 |
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const RealType kb = 8.31451e-7; // kb in amu, angstroms, fs, etc. |
97 |
> |
RealType av2; |
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> |
RealType kebar; |
99 |
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|
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Globals * simParams = info_->getSimParams(); |
101 |
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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; |
106 |
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|
107 |
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|
108 |
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|
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kebar = kb * temperature * info_->getNdfRaw() / (2.0 * info_->getNdf()); |
110 |
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|
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for( mol = info_->beginMolecule(i); mol != NULL; |
112 |
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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) ) { |
116 |
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|
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// uses equipartition theory to solve for vbar in angstrom/fs |
118 |
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|
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av2 = 2.0 * kebar / integrableObject->getMass(); |
120 |
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vbar = sqrt(av2); |
121 |
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|
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// picks random velocities from a gaussian distribution |
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// centered on vbar |
124 |
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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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} |
128 |
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|
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integrableObject->setVel(aVel); |
130 |
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|
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if (integrableObject->isDirectional()) { |
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I = integrableObject->getI(); |
133 |
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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; |
138 |
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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)); |
143 |
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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++ ) { |
146 |
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vbar = sqrt(2.0 * kebar * I(k, k)); |
147 |
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aJ[k] = vbar *randNumGen_->randNorm(0.0, 1.0); |
148 |
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} |
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} // else isLinear |
150 |
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|
151 |
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integrableObject->setJ(aJ); |
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} //isDirectional |
153 |
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} |
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} //end for (mol = beginMolecule(i); ...) |
155 |
> |
|
156 |
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|
157 |
> |
|
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removeComDrift(); |
159 |
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// Remove angular drift if we are not using periodic boundary conditions. |
160 |
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if(!simParams->getUsePeriodicBoundaryConditions()) removeAngularDrift(); |
161 |
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|
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} |
163 |
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|
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|
165 |
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|
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> |
void Velocitizer::removeComDrift() { |
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// Get the Center of Mass drift velocity. |
168 |
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Vector3d vdrift = info_->getComVel(); |
169 |
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|
170 |
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SimInfo::MoleculeIterator i; |
171 |
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Molecule::IntegrableObjectIterator j; |
172 |
> |
Molecule * mol; |
173 |
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StuntDouble * integrableObject; |
174 |
> |
|
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// Corrects for the center of mass drift. |
176 |
> |
// sums all the momentum and divides by total mass. |
177 |
> |
for( mol = info_->beginMolecule(i); mol != NULL; |
178 |
> |
mol = info_->nextMolecule(i) ) { |
179 |
> |
for( integrableObject = mol->beginIntegrableObject(j); |
180 |
> |
integrableObject != NULL; |
181 |
> |
integrableObject = mol->nextIntegrableObject(j) ) { |
182 |
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integrableObject->setVel(integrableObject->getVel() - vdrift); |
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} |
184 |
> |
} |
185 |
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|
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> |
} |
187 |
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|
188 |
> |
|
189 |
> |
void Velocitizer::removeAngularDrift() { |
190 |
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// Get the Center of Mass drift velocity. |
191 |
> |
|
192 |
> |
Vector3d vdrift; |
193 |
> |
Vector3d com; |
194 |
> |
|
195 |
> |
info_->getComAll(com,vdrift); |
196 |
> |
|
197 |
> |
Mat3x3d inertiaTensor; |
198 |
> |
Vector3d angularMomentum; |
199 |
> |
Vector3d omega; |
200 |
> |
|
201 |
> |
|
202 |
> |
|
203 |
> |
info_->getInertiaTensor(inertiaTensor,angularMomentum); |
204 |
> |
// We now need the inverse of the inertia tensor. |
205 |
> |
/* |
206 |
> |
std::cerr << "Angular Momentum before is " |
207 |
> |
<< angularMomentum << std::endl; |
208 |
> |
std::cerr << "Inertia Tensor before is " |
209 |
> |
<< inertiaTensor << std::endl; |
210 |
> |
*/ |
211 |
> |
|
212 |
> |
inertiaTensor =inertiaTensor.inverse(); |
213 |
> |
/* |
214 |
> |
std::cerr << "Inertia Tensor after inverse is " |
215 |
> |
<< inertiaTensor << std::endl; |
216 |
> |
*/ |
217 |
> |
omega = inertiaTensor*angularMomentum; |
218 |
> |
|
219 |
> |
SimInfo::MoleculeIterator i; |
220 |
> |
Molecule::IntegrableObjectIterator j; |
221 |
> |
Molecule * mol; |
222 |
> |
StuntDouble * integrableObject; |
223 |
> |
Vector3d tempComPos; |
224 |
> |
|
225 |
> |
// Corrects for the center of mass angular drift. |
226 |
> |
// sums all the angular momentum and divides by total mass. |
227 |
> |
for( mol = info_->beginMolecule(i); mol != NULL; |
228 |
> |
mol = info_->nextMolecule(i) ) { |
229 |
> |
for( integrableObject = mol->beginIntegrableObject(j); |
230 |
> |
integrableObject != NULL; |
231 |
> |
integrableObject = mol->nextIntegrableObject(j) ) { |
232 |
> |
tempComPos = integrableObject->getPos()-com; |
233 |
> |
integrableObject->setVel((integrableObject->getVel() - vdrift)-cross(omega,tempComPos)); |
234 |
> |
} |
235 |
> |
} |
236 |
> |
|
237 |
> |
angularMomentum = info_->getAngularMomentum(); |
238 |
> |
/* |
239 |
> |
std::cerr << "Angular Momentum after is " |
240 |
> |
<< angularMomentum << std::endl; |
241 |
> |
*/ |
242 |
> |
|
243 |
> |
} |
244 |
> |
|
245 |
> |
|
246 |
> |
|
247 |
> |
|
248 |
> |
} |