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/* |
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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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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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*/ |
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#include "integrators/Velocitizer.hpp" |
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#include "math/SquareMatrix3.hpp" |
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#include "primitives/Molecule.hpp" |
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#include "primitives/StuntDouble.hpp" |
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namespace oopse { |
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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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Velocitizer::Velocitizer(SimInfo* info) { |
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namespace oopse { |
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Velocitizer::Velocitizer(SimInfo* info) : info_(info) { |
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int seedValue; |
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Globals * simParams = info->getSimParams(); |
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#ifndef IS_MPI |
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if (simParams->haveSeed()) { |
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seedValue = simParams->getSeed(); |
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randNumGen_ = new MTRand(seedValue); |
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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 MTRand(); |
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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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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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randNumGen_ = new ParallelRandNumGen(); |
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} |
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#endif |
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} |
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Velocitizer::~Velocitizer() { |
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} |
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Velocitizer::~Velocitizer() { |
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delete randNumGen_; |
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} |
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void Velocitizer::velocitize(double temperature) { |
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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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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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SimInfo::MoleculeIterator i; |
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Molecule::IntegrableObjectIterator j; |
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Molecule * mol; |
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StuntDouble * integrableObject; |
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kebar = kb * temperature * info_->getNdfRaw() / (2.0 * info_->getNdf()); |
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for( mol = info_->beginMolecule(i); mol != NULL; |
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mol = info_->nextMolecule(i) ) { |
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for( integrableObject = mol->beginIntegrableObject(j); |
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integrableObject != NULL; |
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integrableObject = mol->nextIntegrableObject(j) ) { |
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// uses equipartition theory to solve for vbar in angstrom/fs |
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av2 = 2.0 * kebar / integrableObject->getMass(); |
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vbar = sqrt(av2); |
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// picks random velocities from a gaussian distribution |
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// centered on vbar |
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for( int k = 0; k < 3; k++ ) { |
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aVel[k] = vbar * randNumGen_->randNorm(0.0, 1.0); |
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} |
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integrableObject->setVel(aVel); |
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if (integrableObject->isDirectional()) { |
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I = integrableObject->getI(); |
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if (integrableObject->isLinear()) { |
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l = integrableObject->linearAxis(); |
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m = (l + 1) % 3; |
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n = (l + 2) % 3; |
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aJ[l] = 0.0; |
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vbar = sqrt(2.0 * kebar * I(m, m)); |
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aJ[m] = vbar * randNumGen_->randNorm(0.0, 1.0); |
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vbar = sqrt(2.0 * kebar * I(n, n)); |
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aJ[n] = vbar * randNumGen_->randNorm(0.0, 1.0); |
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} else { |
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for( int k = 0; k < 3; k++ ) { |
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vbar = sqrt(2.0 * kebar * I(k, k)); |
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aJ[k] = vbar *randNumGen_->randNorm(0.0, 1.0); |
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} |
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} // else isLinear |
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integrableObject->setJ(aJ); |
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} //isDirectional |
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} |
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mol = info_->nextMolecule(i) ) { |
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for( integrableObject = mol->beginIntegrableObject(j); |
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integrableObject != NULL; |
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integrableObject = mol->nextIntegrableObject(j) ) { |
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// uses equipartition theory to solve for vbar in angstrom/fs |
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av2 = 2.0 * kebar / integrableObject->getMass(); |
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vbar = sqrt(av2); |
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// picks random velocities from a gaussian distribution |
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// centered on vbar |
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for( int k = 0; k < 3; k++ ) { |
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aVel[k] = vbar * randNumGen_->randNorm(0.0, 1.0); |
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} |
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integrableObject->setVel(aVel); |
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if (integrableObject->isDirectional()) { |
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I = integrableObject->getI(); |
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if (integrableObject->isLinear()) { |
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l = integrableObject->linearAxis(); |
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m = (l + 1) % 3; |
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n = (l + 2) % 3; |
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aJ[l] = 0.0; |
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vbar = sqrt(2.0 * kebar * I(m, m)); |
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aJ[m] = vbar * randNumGen_->randNorm(0.0, 1.0); |
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vbar = sqrt(2.0 * kebar * I(n, n)); |
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aJ[n] = vbar * randNumGen_->randNorm(0.0, 1.0); |
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} else { |
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for( int k = 0; k < 3; k++ ) { |
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vbar = sqrt(2.0 * kebar * I(k, k)); |
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aJ[k] = vbar *randNumGen_->randNorm(0.0, 1.0); |
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} |
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} // else isLinear |
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integrableObject->setJ(aJ); |
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} //isDirectional |
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} |
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} //end for (mol = beginMolecule(i); ...) |
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removeComDrift(); |
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} |
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void Velocitizer::removeComDrift() { |
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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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// 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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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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} |