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* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. |
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* |
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*/ |
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|
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/** |
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* @file VelocityVerletIntegrator.cpp |
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* @author tlin |
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* @date 11/09/2004 |
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* @time 16:16am |
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* @version 1.0 |
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*/ |
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|
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/** |
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* @file VelocityVerletIntegrator.cpp |
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* @author tlin |
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* @date 11/09/2004 |
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* @time 16:16am |
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* @version 1.0 |
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*/ |
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|
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#include "integrators/VelocityVerletIntegrator.hpp" |
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|
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namespace oopse { |
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VelocityVerletIntegrator::VelocityVerletIntegrator(SimInfo *info) { } |
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|
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VelocityVerletIntegrator::~VelocityVerletIntegrator() { } |
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|
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VelocityVerletIntegrator::VelocityVerletIntegrator(SimInfo* info){ |
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void VelocityVerletIntegrator::integrate() { |
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double runTime = info->run_time; |
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|
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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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|
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VelocityVerletIntegrator::~VelocityVerletIntegrator() { |
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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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} |
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int calcPot, |
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calcStress; |
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|
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void VelocityVerletIntegrator::integrate() { |
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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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} |
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atoms = info->atoms; |
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|
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void VelocityVerletIntegrator::integrateStep() { |
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fullStep_ = info->dt; |
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halfStep_ = 0.5 * fullStep_; |
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|
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} |
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readyCheck(); |
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|
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void VelocityVerletIntegrator::moveA() { |
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// remove center of mass drift velocity (in case we passed in a configuration |
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// that was drifting |
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tStats->removeCOMdrift(); |
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|
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} |
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// initialize the forces before the first step |
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|
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void VelocityVerletIntegrator::moveB() { |
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calcForce(1, 1); |
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|
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//execute constraint algorithm to make sure at the very beginning the system is constrained |
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if (nConstrained) { |
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constrainA(); |
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calcForce(1, 1); |
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constrainB(); |
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} |
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|
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if (info->setTemp) { |
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thermalize(); |
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} |
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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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|
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#ifdef IS_MPI |
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|
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strcpy(checkPointMsg, "The integrator is ready to go."); |
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MPIcheckPoint(); |
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|
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#endif // is_mpi |
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|
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while (info->getTime() < runTime && !stopIntegrator()) { |
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difference = info->getTime() + fullStep_ - currStatus; |
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|
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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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|
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#ifdef PROFILE |
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|
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startProfile(pro1); |
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|
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#endif |
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|
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integrateStep(calcPot, calcStress); |
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|
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#ifdef PROFILE |
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|
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endProfile(pro1); |
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|
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startProfile(pro2); |
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|
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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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thermalize(); |
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currThermal += thermalTime; |
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} |
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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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currSample += sampleTime; |
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} |
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|
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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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|
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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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|
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#ifdef PROFILE |
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|
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endProfile(pro2); |
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|
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#endif //profile |
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|
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#ifdef IS_MPI |
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|
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strcpy(checkPointMsg, "successfully took a time step."); |
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MPIcheckPoint(); |
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|
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#endif // is_mpi |
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|
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} |
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|
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dumpOut->writeFinal(info->getTime()); |
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|
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delete dumpOut; |
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delete statOut; |
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} |
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|
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void VelocityVerletIntegrator::integrateStep() { } |
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|
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|
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void VelocityVerletIntegrator::thermalize() { |
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|
|
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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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painCave.severity = OOPSE_ERROR; |
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simError(); |
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return; |
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} |
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|
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} |
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|
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< |
void VelocityVerletIntegrator::velocitize() { |
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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, m, n; // velocity randomizer loop counts |
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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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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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double temperature; |
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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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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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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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); |
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painCave.isFatal = 1; |
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painCave.severity = OOPSE_ERROR; |
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simError(); |
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return; |
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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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temperature = info_->target_temp; |
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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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kebar = kb * temperature * info_->getNdfRaw() / ( 2.0 * info_->getNdf()); |
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|
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|
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for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) { |
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for (integrableObject = mol->beginIntegrableObject(j); 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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> |
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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> |
for( int k = 0; k < 3; k++ ) { |
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|
aVel[k] = vbar * gaussStream.getGaussian(); |
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|
} |
116 |
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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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> |
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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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; |
244 |
< |
vbar = sqrt( 2.0 * kebar * I(m, m) ); |
244 |
> |
vbar = sqrt(2.0 * kebar * I(m, m)); |
245 |
|
aJ[m] = vbar * gaussStream.getGaussian(); |
246 |
< |
vbar = sqrt( 2.0 * kebar * I(n, n) ); |
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> |
vbar = sqrt(2.0 * kebar * I(n, n)); |
247 |
|
aJ[n] = vbar * gaussStream.getGaussian(); |
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– |
|
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|
} else { |
249 |
< |
|
250 |
< |
for (int k = 0 ; k < 3; k++) { |
138 |
< |
vbar = sqrt( 2.0 * kebar * I(k, k) ); |
249 |
> |
for( int k = 0; k < 3; k++ ) { |
250 |
> |
vbar = sqrt(2.0 * kebar * I(k, k)); |
251 |
|
aJ[k] = vbar * gaussStream.getGaussian(); |
252 |
< |
} |
141 |
< |
|
252 |
> |
} |
253 |
|
} // else isLinear |
254 |
|
|
255 |
< |
integrableObject->setJ( aJ ); |
255 |
> |
integrableObject->setJ(aJ); |
256 |
> |
} //isDirectional |
257 |
> |
} |
258 |
> |
} //end for (mol = beginMolecule(i); ...) |
259 |
|
|
146 |
– |
}//isDirectional |
147 |
– |
|
148 |
– |
} |
149 |
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}//end for (mol = beginMolecule(i); ...) |
150 |
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|
260 |
|
// Get the Center of Mass drift velocity. |
261 |
|
vdrift = info_->getComVel(); |
153 |
– |
|
154 |
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// Corrects for the center of mass drift. |
155 |
– |
// sums all the momentum and divides by total mass. |
156 |
– |
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
157 |
– |
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
158 |
– |
integrableObject = mol->nextIntegrableObject(j)) { |
262 |
|
|
263 |
< |
aVel = integrableObject->getVel(); |
161 |
< |
aVel -= vdrift; |
162 |
< |
integrableObject->setVel( aVel ); |
163 |
< |
} |
164 |
< |
} |
165 |
< |
|
166 |
< |
} |
263 |
> |
removeComDrift(vdrift); |
264 |
|
|
168 |
– |
void VelocityVerletIntegrator::calcForce(int needPotential, int needStress){ |
169 |
– |
|
265 |
|
} |
266 |
|
|
267 |
< |
void VelocityVerletIntegrator::velocitize() { |
267 |
> |
void VelocityVerletIntegrator::calcForce(bool needPotential, |
268 |
> |
bool needStress) { } |
269 |
|
|
270 |
< |
} |
270 |
> |
void VelocityVerletIntegrator::removeComDrift(const Vector3d& vdrift) { |
271 |
|
|
272 |
< |
void removeComDrift(){ |
272 |
> |
std::vector<Molecule *>::iterator i; |
273 |
> |
std::vector<StuntDouble *>::iterator j; |
274 |
> |
Molecule * mol; |
275 |
> |
StuntDouble * integrableObject; |
276 |
> |
|
277 |
> |
// Corrects for the center of mass drift. |
278 |
> |
// sums all the momentum and divides by total mass. |
279 |
> |
for( mol = info_->beginMolecule(i); mol != NULL; |
280 |
> |
mol = info_->nextMolecule(i) ) { |
281 |
> |
for( integrableObject = mol->beginIntegrableObject(j); |
282 |
> |
integrableObject != NULL; |
283 |
> |
integrableObject = mol->nextIntegrableObject(j) ) { |
284 |
> |
integrableObject->setVel(integrableObject->getVel() - vdrift); |
285 |
> |
} |
286 |
> |
} |
287 |
|
|
288 |
|
} |
289 |
+ |
|
290 |
+ |
} //end namespace oopse |