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#include "integrators/VelocityVerletIntegrator.hpp" |
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namespace oopse { |
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< |
VelocityVerletIntegrator::VelocityVerletIntegrator(SimInfo *info) { } |
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> |
VelocityVerletIntegrator::VelocityVerletIntegrator(SimInfo *info) : Integrator(info) { } |
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VelocityVerletIntegrator::~VelocityVerletIntegrator() { } |
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void VelocityVerletIntegrator::integrate() { |
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double runTime = info->run_time; |
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double runTime = info_->run_time; |
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|
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double sampleTime = info->sampleTime; |
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double statusTime = info->statusTime; |
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double thermalTime = info->thermalTime; |
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double resetTime = info->resetTime; |
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int calcPot; |
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int calcStress; |
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|
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double difference; |
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double currSample; |
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double currThermal; |
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double currStatus; |
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double currReset; |
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|
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int calcPot, |
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calcStress; |
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|
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tStats = new Thermo(info); |
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statOut = new StatWriter(info); |
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dumpOut = new DumpWriter(info); |
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|
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atoms = info->atoms; |
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|
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fullStep_ = info->dt; |
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fullStep_ = info_->dt; |
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halfStep_ = 0.5 * fullStep_; |
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readyCheck(); |
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constrainB(); |
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} |
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if (info->setTemp) { |
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if (info_->setTemp) { |
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thermalize(); |
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} |
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calcPot = 0; |
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calcStress = 0; |
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currSample = sampleTime + info->getTime(); |
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currThermal = thermalTime + info->getTime(); |
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currStatus = statusTime + info->getTime(); |
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currReset = resetTime + info->getTime(); |
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|
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dumpOut->writeDump(info->getTime()); |
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statOut->writeStat(info->getTime()); |
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tStats = new Thermo(info_); |
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statOut = new StatWriter(info_); |
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dumpOut = new DumpWriter(info_); |
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|
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dumpOut->writeDump(info_->getTime()); |
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statOut->writeStat(info_->getTime()); |
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#ifdef IS_MPI |
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#endif // is_mpi |
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while (info->getTime() < runTime && !stopIntegrator()) { |
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difference = info->getTime() + fullStep_ - currStatus; |
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while (info_->getTime() < runTime) { |
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difference = info_->getTime() + fullStep_ - currStatus; |
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if (difference > 0 || fabs(difference) < 1e - 4) { |
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calcPot = 1; |
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calcStress = 1; |
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} |
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#ifdef PROFILE |
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startProfile(pro1); |
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|
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#endif |
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|
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//notify before integrateStep |
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notify() |
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integrateStep(calcPot, calcStress); |
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#ifdef PROFILE |
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|
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endProfile(pro1); |
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startProfile(pro2); |
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#endif // profile |
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|
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info->incrTime(fullStep_); |
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|
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if (info->setTemp) { |
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if (info->getTime() >= currThermal) { |
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info_->incrTime(fullStep_); |
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|
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//notify after integratreStep |
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notify(); |
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|
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if (info_->setTemp) { |
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if (info_->getTime() >= currThermal) { |
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thermalize(); |
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currThermal += thermalTime; |
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} |
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} |
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if (info->getTime() >= currSample) { |
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dumpOut->writeDump(info->getTime()); |
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if (info_->getTime() >= currSample) { |
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dumpOut->writeDump(info_->getTime()); |
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currSample += sampleTime; |
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} |
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if (info->getTime() >= currStatus) { |
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statOut->writeStat(info->getTime()); |
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if (info_->getTime() >= currStatus) { |
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statOut->writeStat(info_->getTime()); |
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calcPot = 0; |
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calcStress = 0; |
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currStatus += statusTime; |
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} |
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if (info->resetIntegrator) { |
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if (info->getTime() >= currReset) { |
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if (info_->resetIntegrator) { |
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if (info_->getTime() >= currReset) { |
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this->resetIntegrator(); |
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currReset += resetTime; |
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} |
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} |
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#ifdef PROFILE |
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|
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endProfile(pro2); |
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#endif //profile |
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|
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#ifdef IS_MPI |
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strcpy(checkPointMsg, "successfully took a time step."); |
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} |
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dumpOut->writeFinal(info->getTime()); |
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dumpOut->writeFinal(info_->getTime()); |
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delete dumpOut; |
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delete statOut; |
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void VelocityVerletIntegrator::thermalize() { |
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if (!info_->have_target_temp) { |
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> |
if (!info__->have_target_temp) { |
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sprintf(painCave.errMsg, |
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"You can't resample the velocities without a targetTemp!\n"); |
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painCave.isFatal = 1; |
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} |
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void VelocityVerletIntegrator::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; // velocity randomizer loop counts |
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Vector3d vdrift; |
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double vbar; |
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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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std::vector<Molecule *>::iterator i; |
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std::vector<StuntDouble *>::iterator 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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// Get the Center of Mass drift velocity. |
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vdrift = info_->getComVel(); |
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|
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removeComDrift(vdrift); |
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|
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} |
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|
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|
void VelocityVerletIntegrator::calcForce(bool needPotential, |
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|
bool needStress) { } |
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|
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void VelocityVerletIntegrator::removeComDrift(const Vector3d& vdrift) { |
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|
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std::vector<Molecule *>::iterator i; |
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std::vector<StuntDouble *>::iterator 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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} //end namespace oopse |
