NAMD
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#include <Sequencer.h>
Public Member Functions | |
Sequencer (HomePatch *p) | |
virtual | ~Sequencer (void) |
void | run (void) |
void | awaken (void) |
void | suspend (void) |
Protected Member Functions | |
virtual void | algorithm (void) |
void | integrate_CUDA_SOA (int scriptTask) |
void | initialize_integrate_CUDA_SOA (int scriptTask, int step, BigReal timestep, int numberOfSteps, int nbondstep, int slowstep, int maxForceUsed) |
void | suspendULTs () |
void | wakeULTs () |
void | runComputeObjectsCUDA (int doMigration, int doGlobal, int pairlists, int nstep, int startup) |
void | constructDevicePatchMap () |
void | updateDevicePatchMap (int startup) |
void | printDevicePatchMap () |
void | clearDevicePatchMap () |
void | updateDeviceData (const int startup, const int maxForceUsed, const int doGlobal) |
void | doMigrationGPU (const int startup, const int doGlobal, const int updatePatchMap) |
void | monteCarloPressureControl (const int step, const int doMigration, const int doEnergy, const int doVirial, const int maxForceNumber, const int doGlobal) |
void | integrate_SOA (int) |
void | rattle1_SOA (BigReal, int) |
void | addForceToMomentum_SOA (const double scaling, double dt_normal, double dt_nbond, double dt_slow, int maxForceNumber) |
void | addVelocityToPosition_SOA (const double dt) |
void | submitHalfstep_SOA () |
void | submitReductions_SOA () |
void | submitCollections_SOA (int step, int zeroVel=0) |
void | maximumMove_SOA (const double dt, const double maxvel2) |
void | langevinVelocitiesBBK1_SOA (BigReal timestep) |
void | langevinVelocitiesBBK2_SOA (BigReal timestep) |
void | berendsenPressure_SOA (int step) |
void | langevinPiston_SOA (int step) |
void | stochRescaleVelocities_SOA (int step) |
void | runComputeObjects_SOA (int migration, int pairlists, int step) |
void | integrate (int) |
void | minimize () |
void | runComputeObjects (int migration=1, int pairlists=0, int pressureStep=0) |
void | calcFixVirial (Tensor &fixVirialNormal, Tensor &fixVirialNbond, Tensor &fixVirialSlow, Vector &fixForceNormal, Vector &fixForceNbond, Vector &fixForceSlow) |
void | submitReductions (int) |
void | submitHalfstep (int) |
void | submitMinimizeReductions (int, BigReal fmax2) |
void | submitCollections (int step, int zeroVel=0) |
void | submitMomentum (int step) |
void | correctMomentum (int step, BigReal drifttime) |
void | saveForce (const int ftag=Results::normal) |
void | addForceToMomentum (BigReal, const int ftag=Results::normal, const int useSaved=0) |
void | addForceToMomentum3 (const BigReal timestep1, const int ftag1, const int useSaved1, const BigReal timestep2, const int ftag2, const int useSaved2, const BigReal timestep3, const int ftag3, const int useSaved3) |
void | addVelocityToPosition (BigReal) |
void | addRotDragToPosition (BigReal) |
void | addMovDragToPosition (BigReal) |
void | minimizeMoveDownhill (BigReal fmax2) |
void | newMinimizeDirection (BigReal) |
void | newMinimizePosition (BigReal) |
void | quenchVelocities () |
void | hardWallDrude (BigReal, int) |
void | rattle1 (BigReal, int) |
void | maximumMove (BigReal) |
void | minimizationQuenchVelocity (void) |
void | reloadCharges () |
void | rescaleSoluteCharges (BigReal) |
void | adaptTempUpdate (int) |
void | rescaleVelocities (int) |
void | rescaleaccelMD (int, int, int) |
void | reassignVelocities (BigReal, int) |
void | reinitVelocities (void) |
void | rescaleVelocitiesByFactor (BigReal) |
void | tcoupleVelocities (BigReal, int) |
void | stochRescaleVelocities (int) |
void | berendsenPressure (int) |
void | langevinPiston (int) |
void | newtonianVelocities (BigReal, const BigReal, const BigReal, const BigReal, const int, const int, const int) |
void | langevinVelocities (BigReal) |
void | langevinVelocitiesBBK1 (BigReal) |
void | langevinVelocitiesBBK2 (BigReal) |
void | scalePositionsVelocities (const Tensor &posScale, const Tensor &velScale) |
void | multigratorPressure (int step, int callNumber) |
void | scaleVelocities (const BigReal velScale) |
BigReal | calcKineticEnergy () |
void | multigratorTemperature (int step, int callNumber) |
void | cycleBarrier (int, int) |
void | traceBarrier (int) |
void | terminate (void) |
void | rebalanceLoad (int timestep) |
Protected Attributes | |
SubmitReduction * | min_reduction |
int | pairlistsAreValid |
int | pairlistsAge |
int | pairlistsAgeLimit |
BigReal | adaptTempT |
int | rescaleVelocities_numTemps |
int | stochRescale_count |
int | berendsenPressure_count |
int | checkpoint_berendsenPressure_count |
int | slowFreq |
SubmitReduction * | multigratorReduction |
int | doKineticEnergy |
int | doMomenta |
Random * | random |
SimParameters *const | simParams |
HomePatch *const | patch |
SubmitReduction * | reduction |
SubmitReduction * | pressureProfileReduction |
CollectionMgr *const | collection |
ControllerBroadcasts * | broadcast |
int | ldbSteps |
bool | masterThread |
Friends | |
class | HomePatch |
class | SequencerCUDA |
Definition at line 45 of file Sequencer.h.
Sequencer::Sequencer | ( | HomePatch * | p | ) |
Definition at line 171 of file Sequencer.C.
References SimParameters::accelMDOn, berendsenPressure_count, broadcast, constructDevicePatchMap(), SimParameters::CUDASOAintegrateMode, deviceCUDA, DeviceCUDA::getDeviceID(), Patch::getPatchID(), HomePatch::ldObjHandle, masterThread, min_reduction, MULTIGRATOR_REDUCTION_MAX_RESERVED, SimParameters::multigratorOn, multigratorReduction, PatchData::nodeBroadcast, PatchMap::numPatches(), PatchMap::Object(), GlobalGPUMgr::Object(), SynchronousCollectives::Object(), LdbCoordinator::Object(), ReductionMgr::Object(), pairlistsAgeLimit, SimParameters::pairlistsPerCycle, patch, SimParameters::pressureProfileAtomTypes, SimParameters::pressureProfileOn, pressureProfileReduction, SimParameters::pressureProfileSlabs, random, SimParameters::randomSeed, reduction, REDUCTIONS_AMD, REDUCTIONS_BASIC, REDUCTIONS_MINIMIZER, REDUCTIONS_MULTIGRATOR, REDUCTIONS_PPROF_INTERNAL, rescaleSoluteCharges(), rescaleVelocities_numTemps, SequencerCUDA, simParams, SimParameters::soluteScalingFactorCharge, SimParameters::soluteScalingOn, Random::split(), SimParameters::stepsPerCycle, stochRescale_count, and ReductionMgr::willSubmit().
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Definition at line 245 of file Sequencer.C.
References broadcast, clearDevicePatchMap(), SimParameters::CUDASOAintegrateMode, min_reduction, multigratorReduction, pressureProfileReduction, random, reduction, and simParams.
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Definition at line 5450 of file Sequencer.C.
References ControllerBroadcasts::adaptTemperature, SimParameters::adaptTempFreq, SimParameters::adaptTempLastStep, SimParameters::adaptTempOn, adaptTempT, broadcast, SimParameters::firstTimestep, SimpleBroadcastObject< T >::get(), SimParameters::langevinOn, SimParameters::langevinTemp, and simParams.
Referenced by integrate().
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Definition at line 5609 of file Sequencer.C.
References HomePatch::addForceToMomentum(), ResizeArray< Elem >::begin(), ResizeArray< Elem >::const_begin(), Patch::f, Patch::flags, NAMD_EVENT_RANGE_2, Patch::numAtoms, patch, and TIMEFACTOR.
Referenced by newtonianVelocities().
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Definition at line 5624 of file Sequencer.C.
References HomePatch::addForceToMomentum3(), ResizeArray< Elem >::begin(), ResizeArray< Elem >::const_begin(), Patch::f, Patch::flags, NAMD_EVENT_RANGE_2, Patch::numAtoms, patch, and TIMEFACTOR.
Referenced by newtonianVelocities().
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Definition at line 2726 of file Sequencer.C.
References PatchDataSOA::f_nbond_x, PatchDataSOA::f_nbond_y, PatchDataSOA::f_nbond_z, PatchDataSOA::f_normal_x, PatchDataSOA::f_normal_y, PatchDataSOA::f_normal_z, PatchDataSOA::f_slow_x, PatchDataSOA::f_slow_y, PatchDataSOA::f_slow_z, Patch::flags, NAMD_EVENT_RANGE_2, Results::nbond, Results::normal, PatchDataSOA::numAtoms, patch, PatchDataSOA::pos_x, PatchDataSOA::pos_y, PatchDataSOA::pos_z, PatchDataSOA::recipMass, Results::slow, PatchDataSOA::vel_x, PatchDataSOA::vel_y, and PatchDataSOA::vel_z.
Referenced by integrate_SOA().
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Definition at line 4397 of file Sequencer.C.
References CompAtomExt::atomFixed, ResizeArray< Elem >::begin(), SimParameters::fixedAtomsOn, Molecule::get_movdrag_params(), CompAtomExt::id, Molecule::is_atom_movdragged(), Node::molecule, SimParameters::movDragGlobVel, Patch::numAtoms, Node::Object(), patch, CompAtom::position, simParams, and TIMEFACTOR.
Referenced by integrate().
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Definition at line 4416 of file Sequencer.C.
References CompAtomExt::atomFixed, ResizeArray< Elem >::begin(), SimParameters::fixedAtomsOn, Molecule::get_rotdrag_params(), CompAtomExt::id, Molecule::is_atom_rotdragged(), Vector::length(), Node::molecule, Patch::numAtoms, Node::Object(), patch, CompAtom::position, SimParameters::rotDragGlobVel, simParams, and TIMEFACTOR.
Referenced by integrate().
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Definition at line 5648 of file Sequencer.C.
References HomePatch::addVelocityToPosition(), ResizeArray< Elem >::begin(), Patch::flags, NAMD_EVENT_RANGE_2, Patch::numAtoms, patch, and TIMEFACTOR.
Referenced by integrate().
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dt | scaled timestep |
Definition at line 2829 of file Sequencer.C.
References Patch::flags, NAMD_EVENT_RANGE_2, PatchDataSOA::numAtoms, patch, PatchDataSOA::pos_x, PatchDataSOA::pos_y, PatchDataSOA::pos_z, PatchDataSOA::vel_x, PatchDataSOA::vel_y, and PatchDataSOA::vel_z.
Referenced by integrate_SOA().
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Definition at line 289 of file Sequencer.C.
References berendsenPressure_count, broadcast, HomePatch::checkpoint(), checkpoint_berendsenPressure_count, SimParameters::CUDASOAintegrate, END_OF_RUN, EVAL_MEASURE, HomePatch::exchangeAtoms(), HomePatch::exchangeCheckpoint(), FILE_OUTPUT, FORCE_OUTPUT, SimpleBroadcastObject< T >::get(), integrate(), integrate_CUDA_SOA(), integrate_SOA(), minimize(), NAMD_bug(), NAMD_die(), pairlistsAreValid, patch, reinitVelocities(), reloadCharges(), rescaleSoluteCharges(), rescaleVelocitiesByFactor(), HomePatch::revert(), SCRIPT_ATOMRECV, SCRIPT_ATOMSEND, SCRIPT_ATOMSENDRECV, SCRIPT_CHECKPOINT, SCRIPT_CHECKPOINT_FREE, SCRIPT_CHECKPOINT_LOAD, SCRIPT_CHECKPOINT_STORE, SCRIPT_CHECKPOINT_SWAP, SCRIPT_CONTINUE, SCRIPT_END, SCRIPT_FORCEOUTPUT, SCRIPT_MEASURE, SCRIPT_MINIMIZE, SCRIPT_OUTPUT, SCRIPT_REINITVELS, SCRIPT_RELOADCHARGES, SCRIPT_RESCALESOLUTECHARGES, SCRIPT_RESCALEVELS, SCRIPT_REVERT, SCRIPT_RUN, SimParameters::scriptArg1, ControllerBroadcasts::scriptBarrier, simParams, SimParameters::SOAintegrateOn, SimParameters::soluteScalingFactorCharge, submitCollections(), and terminate().
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Definition at line 55 of file Sequencer.h.
References PRIORITY_SIZE.
Referenced by LdbCoordinator::awakenSequencers(), HomePatch::boxClosed(), HomePatch::depositMigration(), HomePatch::receiveResult(), and run().
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Definition at line 5244 of file Sequencer.C.
References Lattice::apply_transform(), CompAtomExt::atomFixed, ResizeArray< Elem >::begin(), berendsenPressure_count, SimParameters::berendsenPressureFreq, SimParameters::berendsenPressureOn, broadcast, SimParameters::fixedAtomsOn, SimpleBroadcastObject< T >::get(), CompAtomExt::groupFixed, CompAtom::hydrogenGroupSize, Patch::lattice, FullAtom::mass, Patch::numAtoms, patch, CompAtom::position, ControllerBroadcasts::positionRescaleFactor, Lattice::rescale(), simParams, and SimParameters::useGroupPressure.
Referenced by integrate().
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Definition at line 3409 of file Sequencer.C.
References berendsenPressure_count, SimParameters::berendsenPressureFreq, broadcast, SimpleBroadcastObject< T >::get(), PatchDataSOA::hydrogenGroupSize, Patch::lattice, PatchDataSOA::mass, namd_reciprocal, PatchDataSOA::numAtoms, Lattice::origin(), patch, PatchDataSOA::pos_x, PatchDataSOA::pos_y, PatchDataSOA::pos_z, ControllerBroadcasts::positionRescaleFactor, Lattice::rescale(), simParams, SimParameters::useGroupPressure, Vector::x, Tensor::xx, Tensor::xy, Tensor::xz, Vector::y, Tensor::yx, Tensor::yy, Tensor::yz, Vector::z, Tensor::zx, Tensor::zy, and Tensor::zz.
Referenced by integrate_SOA().
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Definition at line 5946 of file Sequencer.C.
References CompAtomExt::atomFixed, ResizeArray< Elem >::begin(), Patch::f, SimParameters::fixedAtomsOn, FullAtom::fixedPosition, Results::nbond, Results::normal, Patch::numAtoms, Tensor::outerAdd(), patch, simParams, and Results::slow.
Referenced by multigratorPressure(), submitMinimizeReductions(), and submitReductions().
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Definition at line 4937 of file Sequencer.C.
References ResizeArray< Elem >::begin(), Vector::length2(), FullAtom::mass, Patch::numAtoms, SimParameters::pairInteractionOn, SimParameters::pairInteractionSelf, partition(), patch, simParams, and FullAtom::velocity.
Referenced by multigratorTemperature().
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Referenced by ~Sequencer().
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Referenced by Sequencer().
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Definition at line 4726 of file Sequencer.C.
References ResizeArray< Elem >::begin(), broadcast, SimParameters::fixedAtomsOn, SimpleBroadcastObject< T >::get(), ControllerBroadcasts::momentumCorrection, NAMD_die(), Patch::numAtoms, patch, simParams, TIMEFACTOR, and SimParameters::zeroMomentumAlt.
Referenced by integrate().
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Definition at line 5660 of file Sequencer.C.
References ADD_TENSOR_OBJECT, SimParameters::drudeHardWallOn, Node::enableEarlyExit(), endi(), HomePatch::hardWallDrude(), iERROR(), iout, Node::Object(), patch, pressureProfileReduction, reduction, simParams, and terminate().
Referenced by integrate().
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Definition at line 3870 of file Sequencer.C.
References SimParameters::accelMDdihe, SimParameters::accelMDdual, SimParameters::accelMDOn, SimParameters::adaptTempOn, adaptTempT, adaptTempUpdate(), addMovDragToPosition(), addRotDragToPosition(), addVelocityToPosition(), SimParameters::alchOn, SimParameters::alchOutFreq, Results::amdf, Patch::atomMapper, ResizeArray< Elem >::begin(), berendsenPressure(), SimParameters::colvarsOn, SimParameters::commOnly, SimParameters::computeEnergies, ComputeMgr::computeGlobalObject, Node::computeMgr, correctMomentum(), cycleBarrier(), D_MSG, DebugM, Flags::doEnergy, Flags::doFullDispersion, Flags::doFullElectrostatics, Flags::doGBIS, doKineticEnergy, Flags::doLCPO, Flags::doLoweAndersen, Flags::doMolly, doMomenta, Flags::doNonbonded, Flags::doVirial, SimParameters::dt, ResizeArray< Elem >::end(), endi(), eventEndOfTimeStep, NamdProfileEvent::EventsCount, SimParameters::firstTimestep, Patch::flags, SimParameters::fullElectFrequency, SimParameters::GBISOn, Patch::getPatchID(), hardWallDrude(), SimParameters::initialTemp, SimParameters::langevin_useBAOAB, SimParameters::langevinOn, langevinPiston(), SimParameters::langevinPistonOn, SimParameters::langevinTemp, langevinVelocities(), langevinVelocitiesBBK1(), langevinVelocitiesBBK2(), SimParameters::LCPOOn, SimParameters::LJPMEOn, SimParameters::LJPMESerialRealSpaceOn, SimParameters::lonepairs, SimParameters::loweAndersenOn, Flags::maxForceMerged, Flags::maxForceUsed, maximumMove(), minimizationQuenchVelocity(), SimParameters::mollyOn, SimParameters::movDragOn, SimParameters::MTSAlgorithm, SimParameters::multigratorOn, multigratorPressure(), SimParameters::multigratorPressureFreq, multigratorTemperature(), SimParameters::multigratorTemperatureFreq, SimParameters::N, NAIVE, NAMD_EVENT_START, NAMD_EVENT_START_EX, NAMD_EVENT_STOP, NAMD_gcd(), NAMD_PROFILE_START, NAMD_PROFILE_STOP, NamdProfileEventStr, Results::nbond, newtonianVelocities(), SimParameters::nonbondedFrequency, Results::normal, SimParameters::numTraceSteps, Node::Object(), SimParameters::outputMomenta, SimParameters::outputPressure, patch, Patch::patchID, rattle1(), SimParameters::reassignFreq, reassignVelocities(), rebalanceLoad(), AtomMapper::registerIDsFullAtom(), rescaleaccelMD(), SimParameters::rescaleFreq, SimParameters::rescaleTemp, rescaleVelocities(), SimParameters::rotDragOn, runComputeObjects(), saveForce(), ComputeGlobal::saveTotalForces(), SCRIPT_RUN, simParams, SimParameters::singleTopology, Results::slow, slowFreq, SPECIAL_PATCH_ID, SimParameters::statsOn, Flags::step, SimParameters::stepsPerCycle, SimParameters::stochRescaleOn, stochRescaleVelocities(), submitCollections(), submitHalfstep(), submitMomentum(), submitReductions(), SimParameters::tclForcesOn, tcoupleVelocities(), TIMER_DONE, TIMER_INIT_WIDTH, TIMER_REPORT, TIMER_START, TIMER_STOP, traceBarrier(), SimParameters::traceStartStep, and SimParameters::zeroMomentum.
Referenced by algorithm().
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Referenced by algorithm().
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Definition at line 2051 of file Sequencer.C.
References addForceToMomentum_SOA(), addVelocityToPosition_SOA(), SimParameters::alchOn, SimParameters::alchOutFreq, berendsenPressure_SOA(), SimParameters::berendsenPressureOn, CheckStep::check(), SimParameters::colvarsOn, SimParameters::computeEnergies, ComputeMgr::computeGlobalObject, Node::computeMgr, SimParameters::cutoff, SimParameters::dcdFrequency, Molecule::dcdSelectionParams, DebugM, Flags::doEnergy, Flags::doFullElectrostatics, Flags::doGBIS, doKineticEnergy, Flags::doLCPO, Flags::doLoweAndersen, Flags::doMolly, doMomenta, Flags::doNonbonded, Flags::doVirial, SimParameters::dt, endi(), PatchDataSOA::f_nbond_x, PatchDataSOA::f_nbond_y, PatchDataSOA::f_nbond_z, PatchDataSOA::f_normal_x, PatchDataSOA::f_normal_y, PatchDataSOA::f_normal_z, PatchDataSOA::f_slow_x, PatchDataSOA::f_slow_y, PatchDataSOA::f_slow_z, SimParameters::firstTimestep, Patch::flags, SimParameters::forceDcdFrequency, dcd_params::frequency, SimParameters::fullElectFrequency, PatchDataSOA::gaussrand_x, PatchDataSOA::gaussrand_y, PatchDataSOA::gaussrand_z, Patch::getPatchID(), PatchDataSOA::hydrogenGroupSize, PatchDataSOA::id, SimParameters::IMDfreq, CheckStep::init(), PatchDataSOA::langevinParam, langevinPiston_SOA(), SimParameters::langevinPistonOn, langevinVelocitiesBBK1_SOA(), langevinVelocitiesBBK2_SOA(), PatchDataSOA::langScalRandBBK2, PatchDataSOA::langScalVelBBK2, PatchDataSOA::mass, Flags::maxForceMerged, Flags::maxForceUsed, maximumMove_SOA(), Node::molecule, SimParameters::N, NAMD_EVENT_START, NAMD_EVENT_START_EX, NAMD_EVENT_STOP, NAMD_gcd(), NAMD_PROFILE_START, NAMD_PROFILE_STOP, NamdProfileEventStr, Results::nbond, SimParameters::nonbondedFrequency, Results::normal, PatchDataSOA::numAtoms, Node::Object(), patch, Patch::patchID, CheckStep::period, PatchDataSOA::pos_x, PatchDataSOA::pos_y, PatchDataSOA::pos_z, rattle1_SOA(), rebalanceLoad(), RECIP_TIMEFACTOR, PatchDataSOA::recipMass, SimParameters::restartFrequency, runComputeObjects_SOA(), ComputeGlobal::saveTotalForces(), SCRIPT_RUN, simParams, Results::slow, slowFreq, SOA_SIMPLIFY_PARAMS, SPECIAL_PATCH_ID, Flags::step, SimParameters::stepsPerCycle, SimParameters::stochRescaleOn, stochRescaleVelocities_SOA(), submitCollections_SOA(), submitHalfstep_SOA(), submitReductions_SOA(), SimParameters::tclForcesOn, TIMER_DONE, TIMER_INIT_WIDTH, TIMER_REPORT, TIMER_START, TIMER_STOP, PatchDataSOA::vel_x, PatchDataSOA::vel_y, PatchDataSOA::vel_z, SimParameters::velDcdFrequency, Vector::x, Vector::y, and Vector::z.
Referenced by algorithm().
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Definition at line 5308 of file Sequencer.C.
References Lattice::apply_transform(), CompAtomExt::atomFixed, ResizeArray< Elem >::begin(), broadcast, SimParameters::fixedAtomsOn, for(), SimpleBroadcastObject< T >::get(), CompAtomExt::groupFixed, CompAtom::hydrogenGroupSize, CompAtomExt::id, Molecule::is_atom_exPressure(), SimParameters::langevinPistonOn, Patch::lattice, FullAtom::mass, Node::molecule, Patch::numAtoms, Node::Object(), patch, CompAtom::position, ControllerBroadcasts::positionRescaleFactor, Lattice::rescale(), simParams, slowFreq, TIMER_START, TIMER_STOP, SimParameters::useGroupPressure, FullAtom::velocity, Vector::x, Tensor::xx, Vector::y, Tensor::yy, Vector::z, and Tensor::zz.
Referenced by integrate().
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Definition at line 3508 of file Sequencer.C.
References broadcast, SimpleBroadcastObject< T >::get(), PatchDataSOA::hydrogenGroupSize, Patch::lattice, PatchDataSOA::mass, namd_reciprocal, PatchDataSOA::numAtoms, Lattice::origin(), patch, PatchDataSOA::pos_x, PatchDataSOA::pos_y, PatchDataSOA::pos_z, ControllerBroadcasts::positionRescaleFactor, Lattice::rescale(), simParams, TIMER_START, TIMER_STOP, SimParameters::useGroupPressure, PatchDataSOA::vel_x, PatchDataSOA::vel_y, PatchDataSOA::vel_z, Vector::x, Tensor::xx, Tensor::xy, Tensor::xz, Vector::y, Tensor::yx, Tensor::yy, Tensor::yz, Vector::z, Tensor::zx, Tensor::zy, and Tensor::zz.
Referenced by integrate_SOA().
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Definition at line 5027 of file Sequencer.C.
References SimParameters::adaptTempLangevin, SimParameters::adaptTempOn, adaptTempT, ResizeArray< Elem >::begin(), BOLTZMANN, Random::gaussian_vector(), SimParameters::langevin_useBAOAB, SimParameters::langevinOn, FullAtom::langevinParam, SimParameters::langevinTemp, SimParameters::lesFactor, SimParameters::lesOn, SimParameters::lesReduceTemp, Node::molecule, Patch::numAtoms, Node::Object(), partition(), patch, random, simParams, and FullAtom::velocity.
Referenced by integrate().
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Definition at line 5064 of file Sequencer.C.
References ResizeArray< Elem >::begin(), SimParameters::drudeOn, Patch::flags, SimParameters::langevin_useBAOAB, SimParameters::langevinOn, FullAtom::langevinParam, FullAtom::mass, Node::molecule, NAMD_EVENT_RANGE_2, Patch::numAtoms, Node::Object(), patch, simParams, and FullAtom::velocity.
Referenced by integrate().
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Definition at line 3280 of file Sequencer.C.
References Patch::flags, SimParameters::langevinOn, PatchDataSOA::langevinParam, NAMD_EVENT_RANGE_2, PatchDataSOA::numAtoms, patch, simParams, TIMEFACTOR, PatchDataSOA::vel_x, PatchDataSOA::vel_y, and PatchDataSOA::vel_z.
Referenced by integrate_SOA().
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Definition at line 5137 of file Sequencer.C.
References SimParameters::adaptTempLangevin, SimParameters::adaptTempOn, adaptTempT, ResizeArray< Elem >::begin(), BOLTZMANN, SimParameters::drudeOn, SimParameters::drudeTemp, Patch::flags, Random::gaussian_vector(), SimParameters::langevin_useBAOAB, SimParameters::langevinOn, FullAtom::langevinParam, SimParameters::langevinTemp, SimParameters::lesFactor, SimParameters::lesOn, SimParameters::lesReduceTemp, FullAtom::mass, Node::molecule, NAMD_EVENT_RANGE_2, Patch::numAtoms, Node::Object(), partition(), patch, random, rattle1(), simParams, TIMER_START, TIMER_STOP, and FullAtom::velocity.
Referenced by integrate().
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Definition at line 3326 of file Sequencer.C.
References Patch::flags, Random::gaussian_array_f(), Random::gaussian_vector(), PatchDataSOA::gaussrand_x, PatchDataSOA::gaussrand_y, PatchDataSOA::gaussrand_z, SimParameters::langevinGammasDiffer, SimParameters::langevinOn, PatchDataSOA::langevinParam, PatchDataSOA::langScalRandBBK2, PatchDataSOA::langScalVelBBK2, NAMD_EVENT_RANGE_2, PatchDataSOA::numAtoms, patch, random, rattle1_SOA(), simParams, TIMEFACTOR, TIMER_START, TIMER_STOP, PatchDataSOA::vel_x, PatchDataSOA::vel_y, PatchDataSOA::vel_z, Vector::x, Vector::y, and Vector::z.
Referenced by integrate_SOA().
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Definition at line 5732 of file Sequencer.C.
References ResizeArray< Elem >::begin(), SimParameters::cutoff, Node::enableEarlyExit(), endi(), Patch::flags, CompAtomExt::id, iERROR(), iout, Vector::length(), Vector::length2(), SimParameters::maximumMove, NAMD_EVENT_RANGE_2, Patch::numAtoms, Node::Object(), patch, Patch::patchID, PDBVELFACTOR, simParams, terminate(), TIMEFACTOR, and FullAtom::velocity.
Referenced by integrate().
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dt | scaled timestep |
maxvel2 | square of bound on velocity |
Definition at line 3222 of file Sequencer.C.
References ResizeArray< Elem >::begin(), Node::enableEarlyExit(), endi(), Patch::flags, CompAtomExt::id, iERROR(), iout, NAMD_EVENT_RANGE_2, PatchDataSOA::numAtoms, Node::Object(), patch, Patch::patchID, PDBVELFACTOR, terminate(), PatchDataSOA::vel_x, PatchDataSOA::vel_y, and PatchDataSOA::vel_z.
Referenced by integrate_SOA().
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Definition at line 5777 of file Sequencer.C.
References ResizeArray< Elem >::begin(), SimParameters::minimizeOn, Patch::numAtoms, patch, simParams, and FullAtom::velocity.
Referenced by integrate().
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Definition at line 4439 of file Sequencer.C.
References Patch::atomMapper, ResizeArray< Elem >::begin(), broadcast, SimParameters::colvarsOn, ComputeMgr::computeGlobalObject, Node::computeMgr, SimParameters::CUDASOAintegrateMode, Flags::doEnergy, Flags::doFullElectrostatics, Flags::doGBIS, Flags::doLCPO, Flags::doLoweAndersen, Flags::doMinimize, Flags::doMolly, Flags::doNonbonded, ResizeArray< Elem >::end(), SimParameters::firstTimestep, Patch::flags, SimParameters::fullElectFrequency, SimParameters::GBISOn, SimpleBroadcastObject< T >::get(), SimParameters::LCPOOn, SimParameters::lonepairs, Flags::maxForceMerged, Flags::maxForceUsed, ControllerBroadcasts::minimizeCoefficient, minimizeMoveDownhill(), SimParameters::mollyOn, SimParameters::N, Results::nbond, newMinimizeDirection(), newMinimizePosition(), Results::normal, Node::Object(), patch, quenchVelocities(), HomePatch::rattle1(), rebalanceLoad(), AtomMapper::registerIDsFullAtom(), runComputeObjects(), saveForce(), ComputeGlobal::saveTotalForces(), simParams, SimParameters::singleTopology, Results::slow, Flags::step, SimParameters::stepsPerCycle, submitCollections(), submitMinimizeReductions(), SimParameters::tclForcesOn, TIMEFACTOR, and SimParameters::useDeviceMigration.
Referenced by algorithm().
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Definition at line 4585 of file Sequencer.C.
References CompAtomExt::atomFixed, ResizeArray< Elem >::begin(), Patch::f, SimParameters::fixedAtomsOn, CompAtom::hydrogenGroupSize, Vector::length2(), Results::normal, Patch::numAtoms, patch, CompAtom::position, HomePatch::rattle1(), simParams, and Vector::unit().
Referenced by minimize().
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(stepstepsPerCycle)
Definition at line 4794 of file Sequencer.C.
References ADD_TENSOR_OBJECT, ADD_VECTOR_OBJECT, ResizeArray< Elem >::begin(), broadcast, calcFixVirial(), Flags::doFullElectrostatics, Patch::f, SimParameters::fixedAtomsOn, Patch::flags, SimpleBroadcastObject< T >::get(), CompAtom::hydrogenGroupSize, Tensor::identity(), SubmitReduction::item(), Patch::lattice, Vector::length2(), HomePatch::marginViolations, FullAtom::mass, SimParameters::multigratorOn, SimParameters::multigratorPressureFreq, SimParameters::N, NAMD_bug(), Results::nbond, Results::normal, Patch::numAtoms, Tensor::outerAdd(), SimParameters::pairInteractionOn, SimParameters::pairInteractionSelf, partition(), patch, CompAtom::position, ControllerBroadcasts::positionRescaleFactor, ControllerBroadcasts::positionRescaleFactor2, reduction, REDUCTION_ATOM_CHECKSUM, REDUCTION_CENTERED_KINETIC_ENERGY, REDUCTION_MARGIN_VIOLATIONS, Lattice::rescale(), runComputeObjects(), scalePositionsVelocities(), simParams, Results::slow, SimParameters::stepsPerCycle, SubmitReduction::submit(), SimParameters::useGroupPressure, FullAtom::velocity, ControllerBroadcasts::velocityRescaleTensor, and ControllerBroadcasts::velocityRescaleTensor2.
Referenced by integrate().
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Definition at line 4957 of file Sequencer.C.
References ADD_TENSOR_OBJECT, ResizeArray< Elem >::begin(), broadcast, calcKineticEnergy(), SimpleBroadcastObject< T >::get(), CompAtom::hydrogenGroupSize, SubmitReduction::item(), FullAtom::mass, MULTIGRATOR_REDUCTION_KINETIC_ENERGY, SimParameters::multigratorOn, SimParameters::multigratorPressureFreq, multigratorReduction, SimParameters::multigratorTemperatureFreq, Patch::numAtoms, Tensor::outerAdd(), patch, CompAtom::position, scaleVelocities(), simParams, SubmitReduction::submit(), SimParameters::useGroupPressure, FullAtom::velocity, ControllerBroadcasts::velocityRescaleFactor, and ControllerBroadcasts::velocityRescaleFactor2.
Referenced by integrate().
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Definition at line 4607 of file Sequencer.C.
References ResizeArray< Elem >::begin(), SimParameters::drudeHardWallOn, Patch::f, SimParameters::fixedAtomsOn, CompAtom::hydrogenGroupSize, Vector::length2(), SubmitReduction::max(), min_reduction, HomePatch::minimize_rattle2(), Results::normal, Patch::numAtoms, patch, simParams, SubmitReduction::submit(), TIMEFACTOR, and FullAtom::velocity.
Referenced by minimize().
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Definition at line 4666 of file Sequencer.C.
References ResizeArray< Elem >::begin(), SimParameters::drudeHardWallOn, Patch::numAtoms, patch, CompAtom::position, HomePatch::rattle1(), simParams, and FullAtom::velocity.
Referenced by minimize().
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Definition at line 5003 of file Sequencer.C.
References addForceToMomentum(), addForceToMomentum3(), Patch::flags, NAMD_EVENT_RANGE_2, Results::nbond, Results::normal, patch, and Results::slow.
Referenced by integrate().
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Definition at line 4694 of file Sequencer.C.
References ResizeArray< Elem >::begin(), Patch::numAtoms, patch, and FullAtom::velocity.
Referenced by minimize().
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Definition at line 5675 of file Sequencer.C.
References ADD_TENSOR_OBJECT, ResizeArray< Elem >::const_begin(), Node::enableEarlyExit(), endi(), Patch::f, Patch::flags, iERROR(), iout, NAMD_EVENT_RANGE_2, Results::normal, Patch::numAtoms, Node::Object(), patch, CompAtom::position, pressureProfileReduction, HomePatch::rattle1(), reduction, RIGID_NONE, SimParameters::rigidBonds, simParams, terminate(), FullAtom::velocity, Tensor::xx, Tensor::xy, Tensor::xz, Vector::y, Tensor::yx, Tensor::yy, Tensor::yz, Vector::z, Tensor::zx, Tensor::zy, and Tensor::zz.
Referenced by integrate(), and langevinVelocitiesBBK2().
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Definition at line 3637 of file Sequencer.C.
References ADD_TENSOR_OBJECT, Node::enableEarlyExit(), endi(), Patch::flags, iERROR(), iout, NAMD_EVENT_RANGE_2, Node::Object(), patch, pressureProfileReduction, HomePatch::rattle1_SOA(), reduction, RIGID_NONE, SimParameters::rigidBonds, simParams, and terminate().
Referenced by integrate_SOA(), and langevinVelocitiesBBK2_SOA().
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Definition at line 5466 of file Sequencer.C.
References CompAtomExt::atomFixed, ResizeArray< Elem >::begin(), BOLTZMANN, SimParameters::fixedAtomsOn, Random::gaussian_vector(), SimParameters::lesFactor, SimParameters::lesOn, SimParameters::lesReduceTemp, FullAtom::mass, NAMD_bug(), Patch::numAtoms, partition(), patch, random, SimParameters::reassignFreq, SimParameters::reassignHold, SimParameters::reassignIncr, SimParameters::reassignTemp, simParams, and FullAtom::velocity.
Referenced by integrate().
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Definition at line 6624 of file Sequencer.C.
References LdbCoordinator::getNumStepsToRun(), Patch::getPatchID(), ldbSteps, LdbCoordinator::Object(), pairlistsAreValid, patch, LdbCoordinator::rebalance(), and HomePatch::submitLoadStats().
Referenced by integrate(), integrate_SOA(), and minimize().
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Definition at line 5498 of file Sequencer.C.
References CompAtomExt::atomFixed, ResizeArray< Elem >::begin(), BOLTZMANN, SimParameters::drudeOn, SimParameters::fixedAtomsOn, Random::gaussian_vector(), SimParameters::initialTemp, SimParameters::lesFactor, SimParameters::lesOn, SimParameters::lesReduceTemp, FullAtom::mass, Patch::numAtoms, partition(), patch, random, simParams, and FullAtom::velocity.
Referenced by algorithm().
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Definition at line 5531 of file Sequencer.C.
References Molecule::atomcharge(), ResizeArray< Elem >::begin(), CompAtom::charge, Node::molecule, Patch::numAtoms, Node::Object(), and patch.
Referenced by algorithm().
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Definition at line 5407 of file Sequencer.C.
References SimParameters::accelMDdihe, SimParameters::accelMDdual, SimParameters::accelMDLastStep, SimParameters::accelMDOn, ControllerBroadcasts::accelMDRescaleFactor, Results::amdf, broadcast, Patch::f, SimpleBroadcastObject< T >::get(), NAMD_die(), Results::nbond, Results::normal, Patch::numAtoms, patch, simParams, and Results::slow.
Referenced by integrate().
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Definition at line 5543 of file Sequencer.C.
References Molecule::atomcharge(), ResizeArray< Elem >::begin(), CompAtom::charge, PatchDataSOA::charge, Molecule::get_ss_type(), CompAtomExt::id, Node::molecule, Patch::numAtoms, Node::Object(), patch, simParams, and SimParameters::SOAintegrateOn.
Referenced by algorithm(), and Sequencer().
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Definition at line 5388 of file Sequencer.C.
References ResizeArray< Elem >::begin(), broadcast, SimpleBroadcastObject< T >::get(), Patch::numAtoms, patch, SimParameters::rescaleFreq, rescaleVelocities_numTemps, simParams, FullAtom::velocity, and ControllerBroadcasts::velocityRescaleFactor.
Referenced by integrate().
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Definition at line 5521 of file Sequencer.C.
References ResizeArray< Elem >::begin(), Patch::numAtoms, patch, and FullAtom::velocity.
Referenced by algorithm().
void Sequencer::run | ( | void | ) |
Definition at line 269 of file Sequencer.C.
References awaken(), DebugM, Patch::getPatchID(), patch, PATCH_PRIORITY, and SEQ_STK_SZ.
Referenced by HomePatch::runSequencer().
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Definition at line 6410 of file Sequencer.C.
References ADD_TENSOR_OBJECT, ResizeArray< Elem >::begin(), COMPUTE_HOME_PRIORITY, Flags::doFullElectrostatics, Flags::doGBIS, Flags::doLoweAndersen, Flags::doMolly, Flags::doNonbonded, Patch::f, Patch::flags, SimParameters::fullElectFrequency, GB1_COMPUTE_HOME_PRIORITY, GB2_COMPUTE_HOME_PRIORITY, HomePatch::gbisComputeAfterP1(), HomePatch::gbisComputeAfterP2(), Patch::getPatchID(), SimParameters::lonepairs, HomePatch::loweAndersenFinish(), HomePatch::mollyMollify(), Results::nbond, Results::normal, Patch::numAtoms, Patch::p, pairlistsAge, pairlistsAgeLimit, pairlistsAreValid, patch, PATCH_PRIORITY, Patch::pExt, HomePatch::positionsReady(), reduction, Flags::savePairlists, Flags::sequence, simParams, SimParameters::singleTopology, Results::slow, suspend(), SWM4, TIP4, Flags::usePairlists, SimParameters::usePairlists, and SimParameters::watmodel.
Referenced by integrate(), minimize(), and multigratorPressure().
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Definition at line 3654 of file Sequencer.C.
References PatchDataSOA::charge, COMPUTE_HOME_PRIORITY, SimParameters::CUDASOAintegrate, Flags::doFullElectrostatics, Flags::doNonbonded, PatchDataSOA::f_nbond_x, PatchDataSOA::f_nbond_y, PatchDataSOA::f_nbond_z, PatchDataSOA::f_normal_x, PatchDataSOA::f_normal_y, PatchDataSOA::f_normal_z, PatchDataSOA::f_slow_x, PatchDataSOA::f_slow_y, PatchDataSOA::f_slow_z, Patch::flags, SimParameters::fullElectFrequency, Patch::getPatchID(), Patch::numAtoms, PatchDataSOA::numAtoms, pairlistsAge, pairlistsAgeLimit, pairlistsAreValid, patch, PATCH_PRIORITY, Patch::patchID, PatchDataSOA::pos_x, PatchDataSOA::pos_y, PatchDataSOA::pos_z, HomePatch::positionsReady_SOA(), Flags::savePairlists, Flags::sequence, simParams, Flags::step, suspend(), Flags::usePairlists, and SimParameters::usePairlists.
Referenced by integrate_SOA().
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Definition at line 5598 of file Sequencer.C.
References patch, and HomePatch::saveForce().
Referenced by integrate(), and minimize().
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Definition at line 4757 of file Sequencer.C.
References ResizeArray< Elem >::begin(), SimParameters::fixedAtomsOn, CompAtom::hydrogenGroupSize, Patch::lattice, FullAtom::mass, NAMD_bug(), Patch::numAtoms, Lattice::origin(), patch, CompAtom::position, simParams, SimParameters::useGroupPressure, and FullAtom::velocity.
Referenced by multigratorPressure().
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Definition at line 4929 of file Sequencer.C.
References ResizeArray< Elem >::begin(), Patch::numAtoms, patch, and FullAtom::velocity.
Referenced by multigratorTemperature().
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When doing stochastic velocity rescaling, every stochRescaleFreq steps we receive the globally computed rescaling coefficient and apply it to the velocities of all the atoms in our patch.
Rescale velocities with the scale factor sent from the Controller.
step | The current timestep |
Definition at line 5582 of file Sequencer.C.
References ResizeArray< Elem >::begin(), broadcast, DebugM, SimpleBroadcastObject< T >::get(), Patch::numAtoms, patch, simParams, stochRescale_count, ControllerBroadcasts::stochRescaleCoefficient, SimParameters::stochRescaleFreq, and FullAtom::velocity.
Referenced by integrate().
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Rescale velocities with the scale factor sent from the Controller.
step | The current timestep |
Definition at line 3840 of file Sequencer.C.
References broadcast, DebugM, SimpleBroadcastObject< T >::get(), PatchDataSOA::numAtoms, patch, simParams, stochRescale_count, ControllerBroadcasts::stochRescaleCoefficient, SimParameters::stochRescaleFreq, PatchDataSOA::vel_x, PatchDataSOA::vel_y, and PatchDataSOA::vel_z.
Referenced by integrate_SOA().
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Definition at line 6373 of file Sequencer.C.
References broadcast, collection, Output::coordinateNeeded(), IMDSessionInfo::energies_switch, Patch::f, SimParameters::firstTimestep, Patch::flags, Output::forceNeeded(), SimpleBroadcastObject< T >::get(), SimParameters::IMDfreq, SimParameters::IMDon, SimParameters::IMDsendsettings, ControllerBroadcasts::IMDTimeEnergyBarrier, IMDv3, SimParameters::IMDversion, Patch::lattice, Flags::maxForceUsed, NAMD_EVENT_RANGE_2, patch, simParams, Results::slow, CollectionMgr::submitForces(), CollectionMgr::submitPositions(), CollectionMgr::submitVelocities(), IMDSessionInfo::time_switch, and Output::velocityNeeded().
Referenced by algorithm(), integrate(), and minimize().
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Definition at line 3173 of file Sequencer.C.
References collection, Output::coordinateNeeded(), Patch::f, Patch::flags, Output::forceNeeded(), Patch::lattice, Flags::maxForceUsed, NAMD_EVENT_RANGE_2, patch, simParams, Results::slow, CollectionMgr::submitForces(), CollectionMgr::submitPositions(), CollectionMgr::submitVelocities(), SimParameters::useDeviceMigration, and Output::velocityNeeded().
Referenced by integrate_SOA().
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Definition at line 5788 of file Sequencer.C.
References ADD_TENSOR_OBJECT, ResizeArray< Elem >::begin(), Lattice::c(), doKineticEnergy, Flags::doVirial, Patch::flags, CompAtom::hydrogenGroupSize, SubmitReduction::item(), Patch::lattice, Vector::length2(), FullAtom::mass, SimParameters::multigratorOn, NAMD_EVENT_RANGE_2, Patch::numAtoms, Lattice::origin(), Tensor::outerAdd(), SimParameters::pairInteractionOn, SimParameters::pairInteractionSelf, partition(), CompAtom::partition, patch, CompAtom::position, pressureProfileReduction, SimParameters::pressureProfileSlabs, reduction, REDUCTION_HALFSTEP_KINETIC_ENERGY, REDUCTION_INT_HALFSTEP_KINETIC_ENERGY, simParams, SimParameters::useGroupPressure, FullAtom::velocity, Vector::x, Vector::y, and Vector::z.
Referenced by integrate().
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Definition at line 2868 of file Sequencer.C.
References ADD_TENSOR_OBJECT, Patch::flags, PatchDataSOA::hydrogenGroupSize, SubmitReduction::item(), PatchDataSOA::mass, NAMD_EVENT_RANGE_2, PatchDataSOA::numAtoms, patch, reduction, REDUCTION_HALFSTEP_KINETIC_ENERGY, REDUCTION_INT_HALFSTEP_KINETIC_ENERGY, PatchDataSOA::vel_x, PatchDataSOA::vel_y, PatchDataSOA::vel_z, Tensor::xx, Tensor::xy, Tensor::xz, Tensor::yx, Tensor::yy, Tensor::yz, Tensor::zx, Tensor::zy, and Tensor::zz.
Referenced by integrate_SOA().
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Definition at line 6224 of file Sequencer.C.
References ADD_TENSOR_OBJECT, ADD_VECTOR_OBJECT, CompAtomExt::atomFixed, ResizeArray< Elem >::begin(), calcFixVirial(), SimParameters::drudeBondLen, SimParameters::drudeHardWallOn, Patch::f, SimParameters::fixedAtomsOn, Patch::flags, CompAtom::hydrogenGroupSize, SubmitReduction::item(), Vector::length2(), FullAtom::mass, HomePatch::minimize_rattle2(), Results::nbond, Results::normal, Patch::numAtoms, Tensor::outerAdd(), patch, Patch::pExt, CompAtom::position, SimParameters::printBadContacts, reduction, REDUCTION_ATOM_CHECKSUM, REDUCTION_MIN_F_DOT_F, REDUCTION_MIN_F_DOT_V, REDUCTION_MIN_HUGE_COUNT, REDUCTION_MIN_V_DOT_V, Flags::sequence, simParams, Results::slow, SubmitReduction::submit(), TIMEFACTOR, Vector::unit(), FullAtom::velocity, Vector::y, and Vector::z.
Referenced by minimize().
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Definition at line 4703 of file Sequencer.C.
References ADD_VECTOR_OBJECT, ResizeArray< Elem >::begin(), SubmitReduction::item(), FullAtom::mass, Patch::numAtoms, patch, reduction, REDUCTION_MOMENTUM_MASS, simParams, FullAtom::velocity, and SimParameters::zeroMomentumAlt.
Referenced by integrate().
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Definition at line 5966 of file Sequencer.C.
References ADD_TENSOR_OBJECT, ADD_VECTOR_OBJECT, ResizeArray< Elem >::begin(), Lattice::c(), calcFixVirial(), doKineticEnergy, doMomenta, Flags::doVirial, SimParameters::drudeOn, Patch::f, SimParameters::fixedAtomsOn, Patch::flags, CompAtom::hydrogenGroupSize, SubmitReduction::item(), Patch::lattice, Vector::length2(), HomePatch::marginViolations, FullAtom::mass, NAMD_EVENT_RANGE_2, Results::nbond, Results::normal, Patch::numAtoms, Lattice::origin(), Tensor::outerAdd(), SimParameters::pairInteractionOn, SimParameters::pairInteractionSelf, partition(), CompAtom::partition, patch, CompAtom::position, pressureProfileReduction, SimParameters::pressureProfileSlabs, reduction, REDUCTION_ATOM_CHECKSUM, REDUCTION_CENTERED_KINETIC_ENERGY, REDUCTION_DRUDEBOND_CENTERED_KINETIC_ENERGY, REDUCTION_DRUDECOM_CENTERED_KINETIC_ENERGY, REDUCTION_INT_CENTERED_KINETIC_ENERGY, REDUCTION_MARGIN_VIOLATIONS, simParams, Results::slow, SubmitReduction::submit(), SimParameters::useGroupPressure, FullAtom::velocity, Vector::x, Tensor::xx, Tensor::xy, Tensor::xz, Vector::y, Tensor::yx, Tensor::yy, Tensor::yz, Vector::z, Tensor::zx, Tensor::zy, and Tensor::zz.
Referenced by integrate().
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Definition at line 2968 of file Sequencer.C.
References ADD_TENSOR_OBJECT, ADD_VECTOR_OBJECT, PatchDataSOA::f_nbond_x, PatchDataSOA::f_nbond_y, PatchDataSOA::f_nbond_z, PatchDataSOA::f_normal_x, PatchDataSOA::f_normal_y, PatchDataSOA::f_normal_z, PatchDataSOA::f_slow_x, PatchDataSOA::f_slow_y, PatchDataSOA::f_slow_z, Patch::flags, PatchDataSOA::hydrogenGroupSize, SubmitReduction::item(), Patch::lattice, HomePatch::marginViolations, PatchDataSOA::mass, NAMD_EVENT_RANGE_2, namd_reciprocal, PatchDataSOA::numAtoms, Lattice::origin(), patch, PatchDataSOA::pos_x, PatchDataSOA::pos_y, PatchDataSOA::pos_z, reduction, REDUCTION_ATOM_CHECKSUM, REDUCTION_CENTERED_KINETIC_ENERGY, REDUCTION_INT_CENTERED_KINETIC_ENERGY, REDUCTION_MARGIN_VIOLATIONS, SubmitReduction::submit(), PatchDataSOA::vel_x, PatchDataSOA::vel_y, PatchDataSOA::vel_z, Vector::x, Tensor::xx, Tensor::xy, Tensor::xz, Vector::y, Tensor::yx, Tensor::yy, Tensor::yz, Vector::z, Tensor::zx, Tensor::zy, and Tensor::zz.
Referenced by integrate_SOA().
void Sequencer::suspend | ( | void | ) |
Definition at line 279 of file Sequencer.C.
References HomePatch::ldObjHandle, LdbCoordinator::Object(), patch, LdbCoordinator::pauseWork(), and LdbCoordinator::startWork().
Referenced by HomePatch::doAtomMigration(), LdbCoordinator::rebalance(), runComputeObjects(), and runComputeObjects_SOA().
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Definition at line 5559 of file Sequencer.C.
References ResizeArray< Elem >::begin(), broadcast, SimpleBroadcastObject< T >::get(), Node::molecule, Patch::numAtoms, Node::Object(), patch, simParams, ControllerBroadcasts::tcoupleCoefficient, SimParameters::tCoupleOn, and FullAtom::velocity.
Referenced by integrate().
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Definition at line 6655 of file Sequencer.C.
References HomePatch::ldObjHandle, LdbCoordinator::Object(), patch, and LdbCoordinator::pauseWork().
Referenced by algorithm(), hardWallDrude(), maximumMove(), maximumMove_SOA(), rattle1(), and rattle1_SOA().
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Definition at line 6643 of file Sequencer.C.
References broadcast, SimpleBroadcastObject< T >::get(), and ControllerBroadcasts::traceBarrier.
Referenced by integrate().
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Definition at line 47 of file Sequencer.h.
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Definition at line 49 of file Sequencer.h.
Referenced by Sequencer().
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Definition at line 272 of file Sequencer.h.
Referenced by adaptTempUpdate(), integrate(), langevinVelocities(), and langevinVelocitiesBBK2().
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Definition at line 294 of file Sequencer.h.
Referenced by algorithm(), berendsenPressure(), berendsenPressure_SOA(), HomePatch::recvCheckpointLoad(), and Sequencer().
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Definition at line 328 of file Sequencer.h.
Referenced by adaptTempUpdate(), algorithm(), berendsenPressure(), berendsenPressure_SOA(), correctMomentum(), cycleBarrier(), langevinPiston(), langevinPiston_SOA(), minimize(), multigratorPressure(), multigratorTemperature(), rescaleaccelMD(), rescaleVelocities(), Sequencer(), stochRescaleVelocities(), stochRescaleVelocities_SOA(), submitCollections(), tcoupleVelocities(), traceBarrier(), and ~Sequencer().
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Definition at line 295 of file Sequencer.h.
Referenced by algorithm().
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Definition at line 327 of file Sequencer.h.
Referenced by submitCollections(), and submitCollections_SOA().
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Definition at line 310 of file Sequencer.h.
Referenced by integrate(), integrate_SOA(), submitHalfstep(), and submitReductions().
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Definition at line 311 of file Sequencer.h.
Referenced by integrate(), integrate_SOA(), and submitReductions().
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Definition at line 330 of file Sequencer.h.
Referenced by rebalanceLoad().
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Definition at line 331 of file Sequencer.h.
Referenced by Sequencer().
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Definition at line 228 of file Sequencer.h.
Referenced by newMinimizeDirection(), Sequencer(), and ~Sequencer().
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Definition at line 309 of file Sequencer.h.
Referenced by multigratorTemperature(), Sequencer(), and ~Sequencer().
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Definition at line 232 of file Sequencer.h.
Referenced by runComputeObjects(), and runComputeObjects_SOA().
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Definition at line 233 of file Sequencer.h.
Referenced by runComputeObjects(), runComputeObjects_SOA(), and Sequencer().
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Definition at line 231 of file Sequencer.h.
Referenced by algorithm(), rebalanceLoad(), runComputeObjects(), and runComputeObjects_SOA().
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Definition at line 323 of file Sequencer.h.
Referenced by addForceToMomentum(), addForceToMomentum3(), addForceToMomentum_SOA(), addMovDragToPosition(), addRotDragToPosition(), addVelocityToPosition(), addVelocityToPosition_SOA(), algorithm(), berendsenPressure(), berendsenPressure_SOA(), calcFixVirial(), calcKineticEnergy(), correctMomentum(), hardWallDrude(), integrate(), integrate_SOA(), langevinPiston(), langevinPiston_SOA(), langevinVelocities(), langevinVelocitiesBBK1(), langevinVelocitiesBBK1_SOA(), langevinVelocitiesBBK2(), langevinVelocitiesBBK2_SOA(), maximumMove(), maximumMove_SOA(), minimizationQuenchVelocity(), minimize(), minimizeMoveDownhill(), multigratorPressure(), multigratorTemperature(), newMinimizeDirection(), newMinimizePosition(), newtonianVelocities(), quenchVelocities(), rattle1(), rattle1_SOA(), reassignVelocities(), rebalanceLoad(), reinitVelocities(), reloadCharges(), rescaleaccelMD(), rescaleSoluteCharges(), rescaleVelocities(), rescaleVelocitiesByFactor(), run(), runComputeObjects(), runComputeObjects_SOA(), saveForce(), scalePositionsVelocities(), scaleVelocities(), Sequencer(), stochRescaleVelocities(), stochRescaleVelocities_SOA(), submitCollections(), submitCollections_SOA(), submitHalfstep(), submitHalfstep_SOA(), submitMinimizeReductions(), submitMomentum(), submitReductions(), submitReductions_SOA(), suspend(), tcoupleVelocities(), and terminate().
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Definition at line 325 of file Sequencer.h.
Referenced by hardWallDrude(), rattle1(), rattle1_SOA(), Sequencer(), submitHalfstep(), submitReductions(), and ~Sequencer().
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Definition at line 321 of file Sequencer.h.
Referenced by langevinVelocities(), langevinVelocitiesBBK2(), langevinVelocitiesBBK2_SOA(), reassignVelocities(), reinitVelocities(), Sequencer(), and ~Sequencer().
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Definition at line 324 of file Sequencer.h.
Referenced by hardWallDrude(), multigratorPressure(), rattle1(), rattle1_SOA(), runComputeObjects(), Sequencer(), submitHalfstep(), submitHalfstep_SOA(), submitMinimizeReductions(), submitMomentum(), submitReductions(), submitReductions_SOA(), and ~Sequencer().
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Definition at line 277 of file Sequencer.h.
Referenced by rescaleVelocities(), and Sequencer().
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Definition at line 322 of file Sequencer.h.
Referenced by adaptTempUpdate(), addMovDragToPosition(), addRotDragToPosition(), algorithm(), berendsenPressure(), berendsenPressure_SOA(), calcFixVirial(), calcKineticEnergy(), correctMomentum(), hardWallDrude(), integrate(), integrate_SOA(), langevinPiston(), langevinPiston_SOA(), langevinVelocities(), langevinVelocitiesBBK1(), langevinVelocitiesBBK1_SOA(), langevinVelocitiesBBK2(), langevinVelocitiesBBK2_SOA(), maximumMove(), minimizationQuenchVelocity(), minimize(), minimizeMoveDownhill(), multigratorPressure(), multigratorTemperature(), newMinimizeDirection(), newMinimizePosition(), rattle1(), rattle1_SOA(), reassignVelocities(), reinitVelocities(), rescaleaccelMD(), rescaleSoluteCharges(), rescaleVelocities(), runComputeObjects(), runComputeObjects_SOA(), scalePositionsVelocities(), Sequencer(), stochRescaleVelocities(), stochRescaleVelocities_SOA(), submitCollections(), submitCollections_SOA(), submitHalfstep(), submitMinimizeReductions(), submitMomentum(), submitReductions(), tcoupleVelocities(), and ~Sequencer().
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Definition at line 297 of file Sequencer.h.
Referenced by integrate(), integrate_SOA(), and langevinPiston().
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Count time steps until next stochastic velocity rescaling.
Definition at line 290 of file Sequencer.h.
Referenced by Sequencer(), stochRescaleVelocities(), and stochRescaleVelocities_SOA().