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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. 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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* 2. 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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* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
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* research, please cite the appropriate papers when you publish your |
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* work. Good starting points are: |
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* |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
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* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
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* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). |
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* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
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* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
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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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namespace OpenMD { |
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|
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Velocitizer::Velocitizer(SimInfo* info) : info_(info), thermo(info) { |
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|
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|
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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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int 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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int 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(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, m, n; |
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Vector3d vdrift; |
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RealType vbar; |
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/**@todo refactor 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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|
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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 * sd; |
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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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|
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for( sd = mol->beginIntegrableObject(j); sd != NULL; |
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sd = 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 / sd->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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sd->setVel(aVel); |
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|
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if (sd->isDirectional()) { |
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I = sd->getI(); |
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|
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if (sd->isLinear()) { |
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l = sd->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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} |
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|
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sd->setJ(aJ); |
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} |
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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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// Remove angular drift if we are not using periodic boundary |
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// conditions: |
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|
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if(!simParams->getUsePeriodicBoundaryConditions()) removeAngularDrift(); |
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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 = thermo.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 * sd; |
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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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|
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for( sd = mol->beginIntegrableObject(j); sd != NULL; |
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sd = mol->nextIntegrableObject(j) ) { |
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|
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sd->setVel(sd->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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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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thermo.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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thermo.getInertiaTensor(inertiaTensor, angularMomentum); |
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|
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// We now need the inverse of the inertia tensor. |
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inertiaTensor = inertiaTensor.inverse(); |
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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* sd; |
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Vector3d tempComPos; |
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|
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// Corrects for the center of mass angular drift by summing all |
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// the angular momentum and dividing by the total mass. |
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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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|
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for( sd = mol->beginIntegrableObject(j); sd != NULL; |
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sd = mol->nextIntegrableObject(j) ) { |
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|
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tempComPos = sd->getPos() - com; |
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sd->setVel((sd->getVel() - vdrift) - cross(omega, tempComPos)); |
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|
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} |
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} |
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} |
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} |
