NAMD
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#include <Controller.h>
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struct | checkpoint |
Public Member Functions | |
Controller (NamdState *s) | |
virtual | ~Controller (void) |
void | run (void) |
void | awaken (void) |
void | resumeAfterTraceBarrier (int) |
Public Attributes | |
BigReal | accelMDdV |
Friends | |
class | ScriptTcl |
class | Node |
class | CheckpointMsg |
Definition at line 39 of file Controller.h.
Controller::Controller | ( | NamdState * | s | ) |
Definition at line 128 of file Controller.C.
References SimParameters::accelMDOn, amd_reduction, avg_count, AVGXY, ControllerState::berendsenPressure_avg, ControllerState::berendsenPressure_count, BOLTZMANN, broadcast, checkpoint_stored, cumAlchWork, drudeBondTemp, drudeBondTempAvg, SimParameters::dt, groupPressure_avg, groupPressure_tavg, heat, Tensor::identity(), langevinPiston_origStrainRate, ControllerState::langevinPiston_strainRate, min_reduction, Node::molecule, MULTIGRATOR_REDUCTION_MAX_RESERVED, SimParameters::multigratorNoseHooverChainLength, multigratorNu, multigratorNuT, multigratorOmega, SimParameters::multigratorOn, multigratorReduction, SimParameters::multigratorTemperatureRelaxationTime, SimParameters::multigratorTemperatureTarget, multigratorXi, multigratorZeta, Molecule::num_deg_freedom(), numPatches, PatchMap::Object(), Node::Object(), ReductionMgr::Object(), origLattice, ppbonded, ppint, ppnonbonded, pressure_avg, pressure_tavg, SimParameters::pressureProfileAtomTypes, pressureProfileAverage, pressureProfileCount, SimParameters::pressureProfileEwaldOn, SimParameters::pressureProfileFreq, SimParameters::pressureProfileOn, pressureProfileSlabs, SimParameters::pressureProfileSlabs, random, SimParameters::randomSeed, reduction, REDUCTIONS_AMD, REDUCTIONS_BASIC, REDUCTIONS_MINIMIZER, REDUCTIONS_MULTIGRATOR, REDUCTIONS_PPROF_BONDED, REDUCTIONS_PPROF_INTERNAL, REDUCTIONS_PPROF_NONBONDED, rescaleVelocities_numTemps, rescaleVelocities_sumTemps, simParams, ControllerState::smooth2_avg, Random::split(), state, stochRescale_count, SimParameters::stochRescaleFreq, SimParameters::stochRescaleOn, SimParameters::stochRescalePeriod, stochRescaleTimefactor, SimParameters::strainRate, SimParameters::strainRate2, submit_reduction, Tensor::symmetric(), tavg_count, temp_avg, totalEnergy0, SimParameters::useConstantRatio, SimParameters::useFlexibleCell, ReductionMgr::willRequire(), ReductionMgr::willSubmit(), and XXXBIGREAL.
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Definition at line 248 of file Controller.C.
References amd_reduction, broadcast, min_reduction, multigratorReduction, ppbonded, ppint, ppnonbonded, pressureProfileAverage, random, reduction, and submit_reduction.
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Definition at line 2351 of file Controller.C.
References adaptTempAutoDt, SimParameters::adaptTempAutoDt, adaptTempBetaMax, adaptTempBetaMin, adaptTempBetaN, adaptTempBins, SimParameters::adaptTempBins, adaptTempCg, SimParameters::adaptTempCgamma, adaptTempDBeta, adaptTempDt, SimParameters::adaptTempDt, adaptTempDTave, adaptTempDTavenum, adaptTempDtMax, adaptTempDtMin, SimParameters::adaptTempInFile, SimParameters::adaptTempOn, adaptTempPotEnergyAve, adaptTempPotEnergyAveDen, adaptTempPotEnergyAveNum, adaptTempPotEnergySamples, adaptTempPotEnergyVar, adaptTempPotEnergyVarNum, adaptTempRestartFile, SimParameters::adaptTempRestartFile, SimParameters::adaptTempRestartFreq, adaptTempT, SimParameters::adaptTempTmax, SimParameters::adaptTempTmin, endi(), iINFO(), SimParameters::initialTemp, iout, SimParameters::langevinOn, SimParameters::langevinTemp, NAMD_backup_file(), NAMD_die(), ofstream_namd::open(), SimParameters::rescaleFreq, SimParameters::rescaleTemp, and simParams.
Referenced by adaptTempUpdate().
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Definition at line 2477 of file Controller.C.
References adaptTempAutoDt, adaptTempBetaMax, adaptTempBetaMin, adaptTempBetaN, adaptTempBin, adaptTempBins, adaptTempCg, adaptTempDBeta, SimParameters::adaptTempDebug, adaptTempDt, adaptTempDTave, adaptTempDTavenum, adaptTempDtMax, adaptTempDtMin, ControllerBroadcasts::adaptTemperature, SimParameters::adaptTempFreq, adaptTempInit(), SimParameters::adaptTempLastStep, SimParameters::adaptTempOn, SimParameters::adaptTempOutFreq, adaptTempPotEnergyAve, adaptTempPotEnergyAveDen, adaptTempPotEnergyAveNum, adaptTempPotEnergySamples, adaptTempPotEnergyVar, adaptTempPotEnergyVarNum, SimParameters::adaptTempRandom, adaptTempT, adaptTempWriteRestart(), BOLTZMANN, broadcast, endi(), SimParameters::firstTimestep, Random::gaussian(), iout, iWARN(), kineticEnergy, SimpleBroadcastObject< T >::publish(), random, simParams, totalEnergy, and Random::uniform().
Referenced by integrate().
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Definition at line 2451 of file Controller.C.
References adaptTempBetaMax, adaptTempBetaMin, adaptTempBins, adaptTempCg, adaptTempDt, SimParameters::adaptTempOn, adaptTempPotEnergyAve, adaptTempPotEnergyAveDen, adaptTempPotEnergyAveNum, adaptTempPotEnergySamples, adaptTempPotEnergyVar, adaptTempPotEnergyVarNum, adaptTempRestartFile, SimParameters::adaptTempRestartFreq, adaptTempT, endi(), ofstream_namd::flush(), iout, and simParams.
Referenced by adaptTempUpdate().
Definition at line 281 of file Controller.C.
References BackEnd::awaken(), broadcast, checkpoint_lattice, checkpoint_state, checkpoint_stored, checkpoints, END_OF_RUN, endi(), enqueueCollections(), EVAL_MEASURE, FILE_OUTPUT, SimParameters::firstTimestep, FORCE_OUTPUT, SimpleBroadcastObject< T >::get(), if(), SimParameters::initialTemp, integrate(), iout, Controller::checkpoint::lattice, minimize(), NAMD_bug(), NAMD_die(), Node::Object(), outputExtendedSystem(), 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_RESCALESOLUTECHARGES, SCRIPT_RESCALEVELS, SCRIPT_REVERT, SCRIPT_RUN, SimParameters::scriptArg1, ControllerBroadcasts::scriptBarrier, SimParameters::scriptIntArg1, SimParameters::scriptStringArg1, Node::sendCheckpointReq(), simParams, state, Controller::checkpoint::state, msm::swap(), and terminate().
Definition at line 45 of file Controller.h.
Referenced by LdbCoordinator::awakenSequencers(), resumeAfterTraceBarrier(), and run().
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Definition at line 950 of file Controller.C.
References ControllerState::berendsenPressure_avg, ControllerState::berendsenPressure_count, SimParameters::berendsenPressureCompressibility, SimParameters::berendsenPressureFreq, SimParameters::berendsenPressureOn, SimParameters::berendsenPressureRelaxationTime, SimParameters::berendsenPressureTarget, broadcast, controlPressure, Tensor::diagonal(), SimParameters::dt, endi(), Tensor::identity(), iERROR(), iout, LIMIT_SCALING, ControllerBroadcasts::positionRescaleFactor, SimpleBroadcastObject< T >::publish(), Lattice::rescale(), simParams, state, Tensor::xx, Tensor::yy, and Tensor::zz.
Referenced by integrate().
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Definition at line 1598 of file Controller.C.
References SimParameters::accelMDOn, AVGXY, controlPressure, controlPressure_nbond, controlPressure_normal, controlPressure_slow, Tensor::diagonal(), SimParameters::getCurrentLambda(), Molecule::getVirialTailCorr(), groupPressure, groupPressure_nbond, groupPressure_normal, groupPressure_slow, Tensor::identity(), SimParameters::LJcorrection, Node::molecule, NAMD_bug(), nbondFreq, Node::Object(), Lattice::origin(), outer(), pressure, pressure_amd, pressure_nbond, pressure_normal, pressure_slow, Node::simParameters, slowFreq, state, SimParameters::useConstantRatio, SimParameters::useFlexibleCell, SimParameters::useGroupPressure, virial_amd, and Lattice::volume().
Referenced by multigratorPressure(), and receivePressure().
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Definition at line 2775 of file Controller.C.
References computeChecksum, endi(), SimParameters::fullElectFrequency, SimParameters::goGroPair, iERROR(), iINFO(), iout, RequireReduction::item(), iWARN(), marginViolations, Node::molecule, SimParameters::mollyOn, NAMD_bug(), Molecule::numAtoms, Molecule::numCalcAngles, Molecule::numCalcAnisos, Molecule::numCalcBonds, Molecule::numCalcCrossterms, Molecule::numCalcDihedrals, Molecule::numCalcExclusions, Molecule::numCalcFullExclusions, Molecule::numCalcImpropers, Molecule::numCalcTholes, Node::Object(), SimParameters::outputPairlists, pairlistWarnings, SimParameters::qmForcesOn, reduction, REDUCTION_ANGLE_CHECKSUM, REDUCTION_ANISO_CHECKSUM, REDUCTION_ATOM_CHECKSUM, REDUCTION_BOND_CHECKSUM, REDUCTION_COMPUTE_CHECKSUM, REDUCTION_CROSSTERM_CHECKSUM, REDUCTION_DIHEDRAL_CHECKSUM, REDUCTION_EXCLUSION_CHECKSUM, REDUCTION_EXCLUSION_CHECKSUM_CUDA, REDUCTION_IMPROPER_CHECKSUM, REDUCTION_MARGIN_VIOLATIONS, REDUCTION_PAIRLIST_WARNINGS, REDUCTION_STRAY_CHARGE_ERRORS, REDUCTION_THOLE_CHECKSUM, simParams, and slowFreq.
Referenced by printDynamicsEnergies(), and printMinimizeEnergies().
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Definition at line 3879 of file Controller.C.
References bondedEnergy_ti_1, bondedEnergy_ti_2, electEnergy_ti_1, electEnergy_ti_2, electEnergyPME_ti_1, electEnergyPME_ti_2, electEnergySlow_ti_1, electEnergySlow_ti_2, SimParameters::getBondLambda(), SimParameters::getCurrentLambda(), SimParameters::getElecLambda(), SimParameters::getVdwLambda(), ljEnergy_ti_1, ljEnergy_ti_2, and simParams.
Referenced by printEnergies().
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Definition at line 1255 of file Controller.C.
References broadcast, endi(), iERROR(), iout, RequireReduction::item(), Vector::length2(), ControllerBroadcasts::momentumCorrection, NAMD_die(), SimpleBroadcastObject< T >::publish(), reduction, REDUCTION_MOMENTUM_MASS, slowFreq, Vector::x, Vector::y, and Vector::z.
Referenced by integrate().
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Definition at line 3664 of file Controller.C.
References collection, Output::coordinateNeeded(), CollectionMaster::enqueueForces(), CollectionMaster::enqueuePositions(), CollectionMaster::enqueueVelocities(), Output::forceNeeded(), state, and Output::velocityNeeded().
Referenced by algorithm(), integrate(), and minimize().
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Definition at line 429 of file Controller.C.
References adaptTempUpdate(), berendsenPressure(), correctMomentum(), cycleBarrier(), enqueueCollections(), SimParameters::firstTimestep, SimParameters::fullElectFrequency, langevinPiston1(), langevinPiston2(), multigratorPressure(), multigratorTemperature(), SimParameters::N, nbondFreq, SimParameters::nonbondedFrequency, SimParameters::numTraceSteps, Node::Object(), outputExtendedSystem(), outputFepEnergy(), outputTiEnergy(), printDynamicsEnergies(), printFepMessage(), printTiMessage(), reassignVelocities(), rebalanceLoad(), receivePressure(), rescaleaccelMD(), rescaleVelocities(), SCRIPT_RUN, simParams, slowFreq, SimParameters::statsOn, SimParameters::stepsPerCycle, stochRescaleVelocities(), tcoupleVelocities(), traceBarrier(), SimParameters::traceStartStep, and SimParameters::zeroMomentum.
Referenced by algorithm().
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Definition at line 987 of file Controller.C.
References BOLTZMANN, broadcast, Lattice::c(), controlNumDegFreedom, controlPressure, controlPressure_nbond, controlPressure_slow, Tensor::diagonal(), SimParameters::dt, SimParameters::fixCellDims, SimParameters::fixCellDimX, SimParameters::fixCellDimY, SimParameters::fixCellDimZ, Random::gaussian(), Random::gaussian_vector(), Tensor::identity(), iINFO(), iout, ControllerState::langevinPiston_strainRate, SimParameters::langevinPistonBarrier, SimParameters::langevinPistonDecay, SimParameters::langevinPistonOn, SimParameters::langevinPistonPeriod, SimParameters::langevinPistonTarget, SimParameters::langevinPistonTemp, nbondFreq, ControllerBroadcasts::positionRescaleFactor, positionRescaleFactor, SimpleBroadcastObject< T >::publish(), random, Lattice::rescale(), simParams, slowFreq, state, strainRate_old, SimParameters::surfaceTensionTarget, SimParameters::useConstantArea, SimParameters::useConstantRatio, SimParameters::useFlexibleCell, Lattice::volume(), Tensor::xx, Tensor::yy, Vector::z, and Tensor::zz.
Referenced by integrate().
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Definition at line 1142 of file Controller.C.
References BOLTZMANN, Lattice::c(), controlNumDegFreedom, controlPressure, controlPressure_nbond, controlPressure_slow, Tensor::diagonal(), SimParameters::dt, SimParameters::fixCellDims, SimParameters::fixCellDimX, SimParameters::fixCellDimY, SimParameters::fixCellDimZ, Random::gaussian(), Random::gaussian_vector(), Tensor::identity(), iINFO(), iout, ControllerState::langevinPiston_strainRate, SimParameters::langevinPistonDecay, SimParameters::langevinPistonOn, SimParameters::langevinPistonPeriod, SimParameters::langevinPistonTarget, SimParameters::langevinPistonTemp, nbondFreq, random, simParams, slowFreq, state, SimParameters::surfaceTensionTarget, SimParameters::useConstantRatio, SimParameters::useFlexibleCell, Lattice::volume(), Tensor::xx, Tensor::yy, Vector::z, and Tensor::zz.
Referenced by integrate().
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Definition at line 594 of file Controller.C.
References broadcast, CALCULATE, minpoint::dudx, endi(), enqueueCollections(), SimParameters::firstTimestep, iout, RequireReduction::item(), min_energy, min_f_dot_f, min_f_dot_v, min_huge_count, min_reduction, min_v_dot_v, ControllerBroadcasts::minimizeCoefficient, SimParameters::minLineGoal, SimParameters::minVerbose, MOVETO, SimParameters::N, nbondFreq, minpoint::noGradient, PRINT_BRACKET, SimpleBroadcastObject< T >::publish(), RequireReduction::require(), simParams, slowFreq, minpoint::u, x, and minpoint::x.
Referenced by algorithm().
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Definition at line 919 of file Controller.C.
References BOLTZMANN, controlNumDegFreedom, kineticEnergy, Node::molecule, SimParameters::multigratorNoseHooverChainLength, multigratorNu, multigratorOmega, SimParameters::multigratorPressureRelaxationTime, SimParameters::multigratorPressureTarget, SimParameters::multigratorTemperatureTarget, multigratorXi, multigratorZeta, numDegFreedom, Node::Object(), Node::simParameters, simParams, state, and Lattice::volume().
Referenced by printEnergies().
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Definition at line 778 of file Controller.C.
References BOLTZMANN, broadcast, calcPressure(), controlNumDegFreedom, controlPressure, SimParameters::dt, GET_TENSOR, GET_VECTOR, Tensor::identity(), RequireReduction::item(), kineticEnergy, momentumSqrSum, SimParameters::multigratorOn, SimParameters::multigratorPressureFreq, SimParameters::multigratorPressureRelaxationTime, SimParameters::multigratorPressureTarget, SimParameters::multigratorTemperatureTarget, multigratorXi, multigratorXiT, numDegFreedom, ControllerBroadcasts::positionRescaleFactor, ControllerBroadcasts::positionRescaleFactor2, SimpleBroadcastObject< T >::publish(), reduction, REDUCTION_CENTERED_KINETIC_ENERGY, RequireReduction::require(), Lattice::rescale(), simParams, state, temperature, ControllerBroadcasts::velocityRescaleTensor, ControllerBroadcasts::velocityRescaleTensor2, and Lattice::volume().
Referenced by integrate().
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Definition at line 853 of file Controller.C.
References BOLTZMANN, broadcast, SimParameters::dt, GET_TENSOR, RequireReduction::item(), kineticEnergy, momentumSqrSum, MULTIGRATOR_REDUCTION_KINETIC_ENERGY, SimParameters::multigratorNoseHooverChainLength, multigratorNu, multigratorNuT, multigratorOmega, SimParameters::multigratorOn, SimParameters::multigratorPressureFreq, multigratorReduction, SimParameters::multigratorTemperatureFreq, SimParameters::multigratorTemperatureRelaxationTime, SimParameters::multigratorTemperatureTarget, multigratorZeta, numDegFreedom, SimpleBroadcastObject< T >::publish(), RequireReduction::require(), simParams, temperature, ControllerBroadcasts::velocityRescaleFactor, and ControllerBroadcasts::velocityRescaleFactor2.
Referenced by integrate().
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Definition at line 3968 of file Controller.C.
References ofstream_namd::clear(), ofstream_namd::close(), END_OF_RUN, endi(), FILE_OUTPUT, SimParameters::firstTimestep, ofstream_namd::flush(), iout, ofstream_namd::is_open(), SimParameters::N, NAMD_backup_file(), NAMD_err(), ofstream_namd::open(), SimParameters::outputFilename, SimParameters::restartFilename, SimParameters::restartFrequency, SimParameters::restartSave, simParams, writeExtendedSystemData(), writeExtendedSystemLabels(), xstFile, SimParameters::xstFilename, and SimParameters::xstFrequency.
Referenced by algorithm(), and integrate().
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Definition at line 3676 of file Controller.C.
References SimParameters::alchEnsembleAvg, SimParameters::alchEquilSteps, SimParameters::alchFepOn, SimParameters::alchIDWSFreq, SimParameters::alchLambda, SimParameters::alchLambda2, SimParameters::alchLambdaIDWS, SimParameters::alchOn, SimParameters::alchOutFile, SimParameters::alchOutFreq, SimParameters::alchTemp, BOLTZMANN, bondedEnergyDiff_f, dE, dG, electEnergy, electEnergy_f, electEnergySlow, electEnergySlow_f, endi(), exp_dE_ByRT, fepFile, FepNo, fepSum, SimParameters::firstTimestep, ofstream_namd::flush(), iout, ofstream_namd::is_open(), ljEnergy, ljEnergy_f, SimParameters::N, NAMD_backup_file(), net_dE, ofstream_namd::open(), simParams, and writeFepEnergyData().
Referenced by integrate().
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Definition at line 3750 of file Controller.C.
References SimParameters::alchEquilSteps, SimParameters::alchLambda, SimParameters::alchLambdaFreq, SimParameters::alchOn, SimParameters::alchOutFile, SimParameters::alchOutFreq, SimParameters::alchTemp, SimParameters::alchThermIntOn, alchWork, bondedEnergy_ti_1, bondedEnergy_ti_2, electEnergy_ti_1, electEnergy_ti_2, electEnergyPME_ti_1, electEnergyPME_ti_2, electEnergySlow_ti_1, electEnergySlow_ti_2, endi(), SimParameters::firstTimestep, ofstream_namd::flush(), FORMAT(), SimParameters::getBondLambda(), SimParameters::getCurrentLambda2(), SimParameters::getElecLambda(), SimParameters::getLambdaDelta(), SimParameters::getVdwLambda(), iout, ofstream_namd::is_open(), ljEnergy_ti_1, ljEnergy_ti_2, NAMD_backup_file(), net_dEdl_bond_1, net_dEdl_bond_2, net_dEdl_elec_1, net_dEdl_elec_2, net_dEdl_lj_1, net_dEdl_lj_2, ofstream_namd::open(), recent_alchWork, recent_dEdl_bond_1, recent_dEdl_bond_2, recent_dEdl_elec_1, recent_dEdl_elec_2, recent_dEdl_lj_1, recent_dEdl_lj_2, recent_TiNo, simParams, tiFile, TiNo, and writeTiEnergyData().
Referenced by integrate().
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Definition at line 3023 of file Controller.C.
References compareChecksums(), Node::molecule, Node::Object(), printEnergies(), Node::simParameters, and state.
Referenced by integrate().
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Definition at line 3035 of file Controller.C.
References Lattice::a(), Lattice::a_p(), SimParameters::alchEquilSteps, SimParameters::alchFepOn, SimParameters::alchLambdaFreq, SimParameters::alchOn, SimParameters::alchThermIntOn, alchWork, avg_count, Lattice::b(), Lattice::b_p(), bondedEnergy_ti_1, bondedEnergy_ti_2, bondedEnergyDiff_f, Lattice::c(), Lattice::c_p(), CALLBACKDATA, CALLBACKLIST, computeAlchWork(), cumAlchWork, drudeBondTemp, drudeBondTempAvg, SimParameters::drudeOn, SimParameters::dt, IMDEnergies::Eangle, IMDEnergies::Ebond, IMDEnergies::Edihe, IMDEnergies::Eelec, IMDEnergies::Eimpr, electEnergy, electEnergy_f, electEnergy_ti_1, electEnergy_ti_2, electEnergyPME_ti_1, electEnergyPME_ti_2, electEnergySlow, electEnergySlow_f, electEnergySlow_ti_1, electEnergySlow_ti_2, endi(), IMDEnergies::Epot, ETITLE(), IMDEnergies::Etot, IMDEnergies::Evdw, FEPTITLE2(), fflush_count, SimParameters::firstLdbStep, SimParameters::firstTimestep, FORMAT(), IMDOutput::gather_energies(), GET_VECTOR, SimParameters::getCurrentLambda(), SimParameters::getCurrentLambda2(), PressureProfileReduction::getData(), Molecule::getEnergyTailCorr(), Node::getScript(), SimParameters::goForcesOn, SimParameters::goGroPair, goNativeEnergy, goNonnativeEnergy, goTotalEnergy, groGaussEnergy, groLJEnergy, groupPressure, groupPressure_avg, groupPressure_tavg, heat, iERROR(), iINFO(), Node::imd, SimParameters::IMDfreq, SimParameters::IMDon, iout, RequireReduction::item(), iWARN(), kineticEnergy, kineticEnergyCentered, kineticEnergyHalfstep, SimParameters::LJcorrection, ljEnergy, ljEnergy_f, ljEnergy_ti_1, ljEnergy_ti_2, marginViolations, memusage_MB(), SimParameters::mergeCrossterms, Node::molecule, multigatorCalcEnthalpy(), SimParameters::multigratorOn, SimParameters::N, NAMD_bug(), nbondFreq, Node::Object(), Lattice::origin(), SimParameters::outputEnergies, SimParameters::outputEnergiesPrecision, SimParameters::outputMomenta, SimParameters::outputPairlists, SimParameters::outputPressure, SimParameters::pairInteractionOn, pairlistWarnings, SimParameters::PMEOn, ppbonded, ppint, ppnonbonded, pressure, pressure_avg, pressure_tavg, PRESSUREFACTOR, pressureProfileAverage, pressureProfileCount, SimParameters::pressureProfileFreq, pressureProfileSlabs, printTiming(), SimParameters::qmForcesOn, reduction, REDUCTION_ANGLE_ENERGY, REDUCTION_BC_ENERGY, REDUCTION_BOND_ENERGY, REDUCTION_BONDED_ENERGY_F, REDUCTION_BONDED_ENERGY_TI_1, REDUCTION_BONDED_ENERGY_TI_2, REDUCTION_CROSSTERM_ENERGY, REDUCTION_DIHEDRAL_ENERGY, REDUCTION_ELECT_ENERGY, REDUCTION_ELECT_ENERGY_F, REDUCTION_ELECT_ENERGY_PME_TI_1, REDUCTION_ELECT_ENERGY_PME_TI_2, REDUCTION_ELECT_ENERGY_SLOW, REDUCTION_ELECT_ENERGY_SLOW_F, REDUCTION_ELECT_ENERGY_SLOW_TI_1, REDUCTION_ELECT_ENERGY_SLOW_TI_2, REDUCTION_ELECT_ENERGY_TI_1, REDUCTION_ELECT_ENERGY_TI_2, REDUCTION_GO_NATIVE_ENERGY, REDUCTION_GO_NONNATIVE_ENERGY, REDUCTION_GRO_GAUSS_ENERGY, REDUCTION_GRO_LJ_ENERGY, REDUCTION_IMPROPER_ENERGY, REDUCTION_LJ_ENERGY, REDUCTION_LJ_ENERGY_F, REDUCTION_LJ_ENERGY_TI_1, REDUCTION_LJ_ENERGY_TI_2, REDUCTION_MISC_ENERGY, Node::simParameters, simParams, slowFreq, ControllerState::smooth2_avg, state, stepInFullRun, SimParameters::stochRescaleHeat, SimParameters::stochRescaleOn, IMDEnergies::T, tavg_count, temp_avg, temperature, TITITLE(), totalEnergy, totalEnergy0, IMDEnergies::tstep, values, Lattice::volume(), Vector::x, XXXBIGREAL, Vector::y, and Vector::z.
Referenced by printDynamicsEnergies(), and printMinimizeEnergies().
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Definition at line 1274 of file Controller.C.
References SimParameters::alchEquilSteps, SimParameters::alchFepOn, SimParameters::alchLambda, SimParameters::alchLambda2, SimParameters::alchLambdaFreq, SimParameters::alchLambdaIDWS, SimParameters::alchOn, SimParameters::alchTemp, endi(), iout, and simParams.
Referenced by integrate().
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Definition at line 3004 of file Controller.C.
References compareChecksums(), RequireReduction::item(), min_energy, min_f_dot_f, min_f_dot_v, min_huge_count, min_v_dot_v, Node::molecule, Node::Object(), printEnergies(), receivePressure(), reduction, REDUCTION_MIN_F_DOT_F, REDUCTION_MIN_F_DOT_V, REDUCTION_MIN_HUGE_COUNT, REDUCTION_MIN_V_DOT_V, rescaleaccelMD(), and totalEnergy.
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Definition at line 1294 of file Controller.C.
References SimParameters::alchEquilSteps, SimParameters::alchLambda, SimParameters::alchLambdaFreq, SimParameters::alchOn, SimParameters::alchThermIntOn, endi(), iout, and simParams.
Referenced by integrate().
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Definition at line 2967 of file Controller.C.
References endi(), fflush_count, SimParameters::firstTimestep, iout, iWARN(), memusage_MB(), SimParameters::N, SimParameters::outputEnergies, SimParameters::outputTiming, and simParams.
Referenced by printEnergies().
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Definition at line 1308 of file Controller.C.
References endi(), if(), iout, SimParameters::reassignFreq, SimParameters::reassignHold, SimParameters::reassignIncr, SimParameters::reassignTemp, and simParams.
Referenced by integrate().
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Definition at line 4126 of file Controller.C.
References fflush_count, LdbCoordinator::getNumStepsToRun(), ldbSteps, Node::Object(), LdbCoordinator::Object(), Node::outputPatchComputeMaps(), and LdbCoordinator::rebalance().
Referenced by integrate().
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Definition at line 1420 of file Controller.C.
References SimParameters::accelMDDebugOn, SimParameters::accelMDOn, SimParameters::accelMDOutFreq, BOLTZMANN, calcPressure(), SimParameters::comMove, controlNumDegFreedom, controlPressure, controlPressure_nbond, controlPressure_normal, controlPressure_slow, drudeBondTemp, SimParameters::drudeOn, endi(), SimParameters::fixCellDims, SimParameters::fixCellDimX, SimParameters::fixCellDimY, SimParameters::fixCellDimZ, SimParameters::fixedAtomsOn, GET_TENSOR, GET_VECTOR, groupPressure, groupPressure_nbond, groupPressure_normal, groupPressure_slow, iINFO(), iout, RequireReduction::item(), kineticEnergy, kineticEnergyCentered, kineticEnergyHalfstep, SimParameters::langevinOn, Node::molecule, momentumSqrSum, Molecule::num_deg_freedom(), Molecule::num_fixed_atoms(), Molecule::num_fixed_groups(), Molecule::num_group_deg_freedom(), Molecule::numAtoms, Molecule::numConstraints, numDegFreedom, Molecule::numDrudeAtoms, Molecule::numFepInitial, Molecule::numFixedAtoms, Molecule::numFixedGroups, Molecule::numFixedRigidBonds, Molecule::numHydrogenGroups, Molecule::numLonepairs, Molecule::numRigidBonds, Node::Object(), SimParameters::pairInteractionOn, pressure, pressure_amd, pressure_nbond, pressure_normal, pressure_slow, PRESSUREFACTOR, reduction, REDUCTION_CENTERED_KINETIC_ENERGY, REDUCTION_DRUDEBOND_CENTERED_KINETIC_ENERGY, REDUCTION_DRUDECOM_CENTERED_KINETIC_ENERGY, REDUCTION_HALFSTEP_KINETIC_ENERGY, REDUCTION_INT_CENTERED_KINETIC_ENERGY, REDUCTION_INT_HALFSTEP_KINETIC_ENERGY, RequireReduction::require(), Node::simParameters, simParams, state, temperature, and SimParameters::useGroupPressure.
Referenced by integrate(), and printMinimizeEnergies().
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Definition at line 4117 of file Controller.C.
References checkpoint_task, Controller::checkpoint::lattice, SCRIPT_CHECKPOINT_LOAD, SCRIPT_CHECKPOINT_SWAP, state, and Controller::checkpoint::state.
Referenced by Node::recvCheckpointAck().
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Definition at line 4087 of file Controller.C.
References checkpoints, NAMD_die(), SCRIPT_CHECKPOINT_FREE, SCRIPT_CHECKPOINT_LOAD, SCRIPT_CHECKPOINT_STORE, SCRIPT_CHECKPOINT_SWAP, and msm::swap().
Referenced by Node::recvCheckpointReq().
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Definition at line 1839 of file Controller.C.
References SimParameters::accelMDalpha, SimParameters::accelMDDebugOn, SimParameters::accelMDdihe, SimParameters::accelMDdual, accelMDdV, accelMDdVAverage, SimParameters::accelMDE, SimParameters::accelMDFirstStep, SimParameters::accelMDG, SimParameters::accelMDGcMDPrepSteps, SimParameters::accelMDGcMDSteps, SimParameters::accelMDGEquiPrepSteps, SimParameters::accelMDGEquiSteps, SimParameters::accelMDGiE, SimParameters::accelMDGresetVaftercmd, SimParameters::accelMDGRestart, SimParameters::accelMDGRestartFile, SimParameters::accelMDGSigma0D, SimParameters::accelMDGSigma0P, SimParameters::accelMDGStatWindow, SimParameters::accelMDLastStep, SimParameters::accelMDOn, SimParameters::accelMDOutFreq, ControllerBroadcasts::accelMDRescaleFactor, SimParameters::accelMDTalpha, SimParameters::accelMDTE, amd_reduction, broadcast, calc_accelMDG_E_k(), calc_accelMDG_force_factor(), calc_accelMDG_mean_std(), electEnergy, electEnergySlow, endi(), SimParameters::firstTimestep, GET_TENSOR, goNativeEnergy, goNonnativeEnergy, goTotalEnergy, groGaussEnergy, groLJEnergy, iout, SubmitReduction::item(), RequireReduction::item(), iWARN(), SimParameters::LJcorrection, ljEnergy, Node::molecule, SimParameters::N, NAMD_die(), nbondFreq, Node::Object(), PRESSUREFACTOR, SimpleBroadcastObject< T >::publish(), REDUCTION_ANGLE_ENERGY, REDUCTION_BC_ENERGY, REDUCTION_BOND_ENERGY, REDUCTION_CROSSTERM_ENERGY, REDUCTION_DIHEDRAL_ENERGY, REDUCTION_ELECT_ENERGY, REDUCTION_ELECT_ENERGY_SLOW, REDUCTION_GO_NATIVE_ENERGY, REDUCTION_GO_NONNATIVE_ENERGY, REDUCTION_GRO_GAUSS_ENERGY, REDUCTION_GRO_LJ_ENERGY, REDUCTION_IMPROPER_ENERGY, REDUCTION_LJ_ENERGY, REDUCTION_MAX_RESERVED, REDUCTION_MISC_ENERGY, RequireReduction::require(), SimParameters::restartFrequency, simParams, slowFreq, state, SubmitReduction::submit(), submit_reduction, Molecule::tail_corr_ener, virial_amd, Lattice::volume(), and write_accelMDG_rest_file().
Referenced by integrate(), and printMinimizeEnergies().
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Definition at line 1233 of file Controller.C.
References SimParameters::adaptTempFirstStep, SimParameters::adaptTempLastStep, SimParameters::adaptTempOn, SimParameters::adaptTempRescale, adaptTempT, broadcast, SimpleBroadcastObject< T >::publish(), SimParameters::rescaleFreq, SimParameters::rescaleTemp, rescaleVelocities_numTemps, rescaleVelocities_sumTemps, simParams, temperature, and ControllerBroadcasts::velocityRescaleFactor.
Referenced by integrate().
void Controller::resumeAfterTraceBarrier | ( | int | step | ) |
Definition at line 4157 of file Controller.C.
References awaken(), broadcast, SimpleBroadcastObject< T >::publish(), and ControllerBroadcasts::traceBarrier.
Referenced by Node::resumeAfterTraceBarrier().
Definition at line 268 of file Controller.C.
References awaken(), CTRL_STK_SZ, and DebugM.
Referenced by NamdState::runController().
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Calculate new coefficient for stochastic velocity rescaling and update heat.
Definition at line 1364 of file Controller.C.
References BOLTZMANN, Random::gaussian(), heat, numDegFreedom, random, simParams, SimParameters::stochRescaleTemp, stochRescaleTimefactor, Random::sum_of_squared_gaussians(), and temperature.
Referenced by stochRescaleVelocities().
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The Controller routine for stochastic velocity rescaling uses the most recent temperature reduction to calculate the velocity rescaling coefficient that is then broadcast to all patches.
Generate and broadcast the scale factor for stochastic velocity rescaling.
Stochastic velocity rescaling couples the system to a heat bath by globally scaling the velocites by a single factor. This factor is chosen based on the instantaneous and bath temperatures, a user-defined time scale, and a stochastic component linked to the number of degrees of freedom in the system. All of this information is combined here and sent to the Sequencer for the actual rescaling.
step | the current timestep |
Definition at line 1348 of file Controller.C.
References broadcast, SimpleBroadcastObject< T >::publish(), simParams, stochRescale_count, ControllerBroadcasts::stochRescaleCoefficient, stochRescaleCoefficient(), SimParameters::stochRescaleFreq, and SimParameters::stochRescaleOn.
Referenced by integrate().
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Definition at line 1326 of file Controller.C.
References broadcast, SimpleBroadcastObject< T >::publish(), simParams, ControllerBroadcasts::tcoupleCoefficient, SimParameters::tCoupleOn, SimParameters::tCoupleTemp, and temperature.
Referenced by integrate().
Definition at line 4178 of file Controller.C.
References BackEnd::awaken().
Referenced by algorithm().
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Definition at line 4150 of file Controller.C.
Referenced by integrate().
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Definition at line 1781 of file Controller.C.
References endi(), iout, iWARN(), NAMD_backup_file(), and simParams.
Referenced by rescaleaccelMD().
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Definition at line 3643 of file Controller.C.
References Lattice::a(), Lattice::a_p(), Lattice::b(), Lattice::b_p(), Lattice::c(), Lattice::c_p(), ControllerState::langevinPiston_strainRate, SimParameters::langevinPistonOn, Lattice::origin(), simParams, state, Vector::x, Vector::y, and Vector::z.
Referenced by outputExtendedSystem().
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Definition at line 3630 of file Controller.C.
References Lattice::a_p(), Lattice::b_p(), Lattice::c_p(), SimParameters::langevinPistonOn, simParams, and state.
Referenced by outputExtendedSystem().
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Definition at line 3908 of file Controller.C.
References SimParameters::alchEnsembleAvg, SimParameters::alchIDWSFreq, SimParameters::alchLambda, SimParameters::alchLambdaIDWS, SimParameters::alchTemp, BOLTZMANN, dE, dG, electEnergy, electEnergy_f, electEnergySlow, electEnergySlow_f, exp_dE_ByRT, fepFile, FepNo, FEPTITLE(), FEPTITLE_BACK(), SimParameters::firstTimestep, FORMAT(), ljEnergy, ljEnergy_f, net_dE, simParams, and temperature.
Referenced by outputFepEnergy().
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Definition at line 3944 of file Controller.C.
References SimParameters::alchLambdaFreq, cumAlchWork, FORMAT(), net_dEdl_bond_1, net_dEdl_bond_2, net_dEdl_elec_1, net_dEdl_elec_2, net_dEdl_lj_1, net_dEdl_lj_2, recent_alchWork, recent_dEdl_bond_1, recent_dEdl_bond_2, recent_dEdl_elec_1, recent_dEdl_elec_2, recent_dEdl_lj_1, recent_dEdl_lj_2, recent_TiNo, simParams, tiFile, TiNo, and TITITLE().
Referenced by outputTiEnergy().
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Definition at line 55 of file Controller.h.
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Definition at line 54 of file Controller.h.
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Definition at line 53 of file Controller.h.
BigReal Controller::accelMDdV |
Definition at line 50 of file Controller.h.
Referenced by rescaleaccelMD().
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Definition at line 301 of file Controller.h.
Referenced by rescaleaccelMD().
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Definition at line 324 of file Controller.h.
Referenced by adaptTempInit(), and adaptTempUpdate().
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Definition at line 318 of file Controller.h.
Referenced by adaptTempInit(), adaptTempUpdate(), and adaptTempWriteRestart().
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Definition at line 317 of file Controller.h.
Referenced by adaptTempInit(), adaptTempUpdate(), and adaptTempWriteRestart().
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Definition at line 313 of file Controller.h.
Referenced by adaptTempInit(), and adaptTempUpdate().
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Definition at line 319 of file Controller.h.
Referenced by adaptTempUpdate().
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Definition at line 320 of file Controller.h.
Referenced by adaptTempInit(), adaptTempUpdate(), and adaptTempWriteRestart().
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Definition at line 322 of file Controller.h.
Referenced by adaptTempInit(), adaptTempUpdate(), and adaptTempWriteRestart().
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Definition at line 321 of file Controller.h.
Referenced by adaptTempInit(), and adaptTempUpdate().
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Definition at line 323 of file Controller.h.
Referenced by adaptTempInit(), adaptTempUpdate(), and adaptTempWriteRestart().
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Definition at line 315 of file Controller.h.
Referenced by adaptTempInit(), and adaptTempUpdate().
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Definition at line 316 of file Controller.h.
Referenced by adaptTempInit(), and adaptTempUpdate().
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Definition at line 326 of file Controller.h.
Referenced by adaptTempInit(), and adaptTempUpdate().
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Definition at line 325 of file Controller.h.
Referenced by adaptTempInit(), and adaptTempUpdate().
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Definition at line 310 of file Controller.h.
Referenced by adaptTempInit(), adaptTempUpdate(), and adaptTempWriteRestart().
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Definition at line 308 of file Controller.h.
Referenced by adaptTempInit(), adaptTempUpdate(), and adaptTempWriteRestart().
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Definition at line 307 of file Controller.h.
Referenced by adaptTempInit(), adaptTempUpdate(), and adaptTempWriteRestart().
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Definition at line 312 of file Controller.h.
Referenced by adaptTempInit(), adaptTempUpdate(), and adaptTempWriteRestart().
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Definition at line 311 of file Controller.h.
Referenced by adaptTempInit(), adaptTempUpdate(), and adaptTempWriteRestart().
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Definition at line 309 of file Controller.h.
Referenced by adaptTempInit(), adaptTempUpdate(), and adaptTempWriteRestart().
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Definition at line 327 of file Controller.h.
Referenced by adaptTempInit(), and adaptTempWriteRestart().
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Definition at line 314 of file Controller.h.
Referenced by adaptTempInit(), adaptTempUpdate(), adaptTempWriteRestart(), and rescaleVelocities().
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Definition at line 151 of file Controller.h.
Referenced by outputTiEnergy(), and printEnergies().
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Definition at line 238 of file Controller.h.
Referenced by Controller(), rescaleaccelMD(), and ~Controller().
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Definition at line 84 of file Controller.h.
Referenced by Controller(), and printEnergies().
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Definition at line 126 of file Controller.h.
Referenced by computeAlchWork(), outputTiEnergy(), and printEnergies().
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Definition at line 127 of file Controller.h.
Referenced by computeAlchWork(), outputTiEnergy(), and printEnergies().
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Definition at line 113 of file Controller.h.
Referenced by outputFepEnergy(), and printEnergies().
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Definition at line 251 of file Controller.h.
Referenced by adaptTempUpdate(), algorithm(), berendsenPressure(), Controller(), correctMomentum(), cycleBarrier(), langevinPiston1(), minimize(), multigratorPressure(), multigratorTemperature(), rescaleaccelMD(), rescaleVelocities(), resumeAfterTraceBarrier(), stochRescaleVelocities(), tcoupleVelocities(), and ~Controller().
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Definition at line 269 of file Controller.h.
Referenced by algorithm().
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Definition at line 270 of file Controller.h.
Referenced by algorithm().
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Definition at line 268 of file Controller.h.
Referenced by algorithm(), and Controller().
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Definition at line 277 of file Controller.h.
Referenced by recvCheckpointAck().
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Definition at line 276 of file Controller.h.
Referenced by algorithm(), and recvCheckpointReq().
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Definition at line 249 of file Controller.h.
Referenced by enqueueCollections().
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Definition at line 89 of file Controller.h.
Referenced by compareChecksums().
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Definition at line 169 of file Controller.h.
Referenced by langevinPiston1(), langevinPiston2(), multigatorCalcEnthalpy(), multigratorPressure(), and receivePressure().
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Definition at line 170 of file Controller.h.
Referenced by berendsenPressure(), calcPressure(), langevinPiston1(), langevinPiston2(), multigratorPressure(), and receivePressure().
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Definition at line 77 of file Controller.h.
Referenced by calcPressure(), langevinPiston1(), langevinPiston2(), and receivePressure().
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Definition at line 76 of file Controller.h.
Referenced by calcPressure(), and receivePressure().
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Definition at line 78 of file Controller.h.
Referenced by calcPressure(), langevinPiston1(), langevinPiston2(), and receivePressure().
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Definition at line 140 of file Controller.h.
Referenced by Controller(), printEnergies(), and writeTiEnergyData().
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Definition at line 119 of file Controller.h.
Referenced by outputFepEnergy(), and writeFepEnergyData().
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Definition at line 121 of file Controller.h.
Referenced by outputFepEnergy(), and writeFepEnergyData().
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Definition at line 155 of file Controller.h.
Referenced by Controller(), printEnergies(), and receivePressure().
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Definition at line 156 of file Controller.h.
Referenced by Controller(), and printEnergies().
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Definition at line 104 of file Controller.h.
Referenced by outputFepEnergy(), printEnergies(), rescaleaccelMD(), and writeFepEnergyData().
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Definition at line 114 of file Controller.h.
Referenced by outputFepEnergy(), printEnergies(), and writeFepEnergyData().
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Definition at line 128 of file Controller.h.
Referenced by computeAlchWork(), outputTiEnergy(), and printEnergies().
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Definition at line 131 of file Controller.h.
Referenced by computeAlchWork(), outputTiEnergy(), and printEnergies().
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Definition at line 141 of file Controller.h.
Referenced by computeAlchWork(), outputTiEnergy(), and printEnergies().
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Definition at line 142 of file Controller.h.
Referenced by computeAlchWork(), outputTiEnergy(), and printEnergies().
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Definition at line 105 of file Controller.h.
Referenced by outputFepEnergy(), printEnergies(), rescaleaccelMD(), and writeFepEnergyData().
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Definition at line 115 of file Controller.h.
Referenced by outputFepEnergy(), printEnergies(), and writeFepEnergyData().
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Definition at line 129 of file Controller.h.
Referenced by computeAlchWork(), outputTiEnergy(), and printEnergies().
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Definition at line 132 of file Controller.h.
Referenced by computeAlchWork(), outputTiEnergy(), and printEnergies().
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Definition at line 118 of file Controller.h.
Referenced by outputFepEnergy(), and writeFepEnergyData().
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Definition at line 258 of file Controller.h.
Referenced by outputFepEnergy(), and writeFepEnergyData().
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Definition at line 122 of file Controller.h.
Referenced by outputFepEnergy(), and writeFepEnergyData().
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Definition at line 124 of file Controller.h.
Referenced by outputFepEnergy().
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Definition at line 222 of file Controller.h.
Referenced by printEnergies(), printTiming(), and rebalanceLoad().
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Definition at line 109 of file Controller.h.
Referenced by printEnergies(), and rescaleaccelMD().
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Definition at line 110 of file Controller.h.
Referenced by printEnergies(), and rescaleaccelMD().
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Definition at line 111 of file Controller.h.
Referenced by printEnergies(), and rescaleaccelMD().
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Definition at line 108 of file Controller.h.
Referenced by printEnergies(), and rescaleaccelMD().
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Definition at line 107 of file Controller.h.
Referenced by printEnergies(), and rescaleaccelMD().
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Definition at line 168 of file Controller.h.
Referenced by calcPressure(), printEnergies(), and receivePressure().
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Definition at line 83 of file Controller.h.
Referenced by Controller(), and printEnergies().
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Definition at line 74 of file Controller.h.
Referenced by calcPressure(), and receivePressure().
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Definition at line 73 of file Controller.h.
Referenced by calcPressure(), and receivePressure().
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Definition at line 75 of file Controller.h.
Referenced by calcPressure(), and receivePressure().
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Definition at line 86 of file Controller.h.
Referenced by Controller(), and printEnergies().
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heat exchanged with the thermostat since firstTimestep
Definition at line 162 of file Controller.h.
Referenced by Controller(), printEnergies(), and stochRescaleCoefficient().
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Definition at line 158 of file Controller.h.
Referenced by adaptTempUpdate(), multigatorCalcEnthalpy(), multigratorPressure(), multigratorTemperature(), printEnergies(), and receivePressure().
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Definition at line 160 of file Controller.h.
Referenced by printEnergies(), and receivePressure().
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Definition at line 159 of file Controller.h.
Referenced by printEnergies(), and receivePressure().
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Definition at line 204 of file Controller.h.
Referenced by Controller().
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Definition at line 220 of file Controller.h.
Referenced by rebalanceLoad().
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Definition at line 106 of file Controller.h.
Referenced by outputFepEnergy(), printEnergies(), rescaleaccelMD(), and writeFepEnergyData().
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Definition at line 116 of file Controller.h.
Referenced by outputFepEnergy(), printEnergies(), and writeFepEnergyData().
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Definition at line 117 of file Controller.h.
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Definition at line 130 of file Controller.h.
Referenced by computeAlchWork(), outputTiEnergy(), and printEnergies().
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Definition at line 133 of file Controller.h.
Referenced by computeAlchWork(), outputTiEnergy(), and printEnergies().
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Definition at line 90 of file Controller.h.
Referenced by compareChecksums(), and printEnergies().
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Definition at line 94 of file Controller.h.
Referenced by minimize(), and printMinimizeEnergies().
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Definition at line 95 of file Controller.h.
Referenced by minimize(), and printMinimizeEnergies().
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Definition at line 96 of file Controller.h.
Referenced by minimize(), and printMinimizeEnergies().
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Definition at line 98 of file Controller.h.
Referenced by minimize(), and printMinimizeEnergies().
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Definition at line 60 of file Controller.h.
Referenced by Controller(), minimize(), and ~Controller().
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Definition at line 97 of file Controller.h.
Referenced by minimize(), and printMinimizeEnergies().
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Definition at line 211 of file Controller.h.
Referenced by multigratorPressure(), multigratorTemperature(), and receivePressure().
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Definition at line 213 of file Controller.h.
Referenced by Controller(), multigatorCalcEnthalpy(), and multigratorTemperature().
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Definition at line 214 of file Controller.h.
Referenced by Controller(), and multigratorTemperature().
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Definition at line 215 of file Controller.h.
Referenced by Controller(), multigatorCalcEnthalpy(), and multigratorTemperature().
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Definition at line 217 of file Controller.h.
Referenced by Controller(), multigratorTemperature(), and ~Controller().
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Definition at line 209 of file Controller.h.
Referenced by Controller(), multigatorCalcEnthalpy(), and multigratorPressure().
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Definition at line 210 of file Controller.h.
Referenced by multigratorPressure().
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Definition at line 216 of file Controller.h.
Referenced by Controller(), multigatorCalcEnthalpy(), and multigratorTemperature().
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Definition at line 79 of file Controller.h.
Referenced by calcPressure(), integrate(), langevinPiston1(), langevinPiston2(), minimize(), printEnergies(), and rescaleaccelMD().
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Definition at line 120 of file Controller.h.
Referenced by outputFepEnergy(), and writeFepEnergyData().
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Definition at line 134 of file Controller.h.
Referenced by outputTiEnergy(), and writeTiEnergyData().
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Definition at line 135 of file Controller.h.
Referenced by outputTiEnergy(), and writeTiEnergyData().
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Definition at line 136 of file Controller.h.
Referenced by outputTiEnergy(), and writeTiEnergyData().
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Definition at line 137 of file Controller.h.
Referenced by outputTiEnergy(), and writeTiEnergyData().
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Definition at line 138 of file Controller.h.
Referenced by outputTiEnergy(), and writeTiEnergyData().
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Definition at line 139 of file Controller.h.
Referenced by outputTiEnergy(), and writeTiEnergyData().
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Definition at line 101 of file Controller.h.
Referenced by multigatorCalcEnthalpy(), multigratorPressure(), multigratorTemperature(), receivePressure(), and stochRescaleCoefficient().
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Definition at line 281 of file Controller.h.
Referenced by Controller().
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Definition at line 91 of file Controller.h.
Referenced by compareChecksums(), and printEnergies().
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Definition at line 206 of file Controller.h.
Referenced by langevinPiston1().
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Definition at line 242 of file Controller.h.
Referenced by Controller(), printEnergies(), and ~Controller().
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Definition at line 244 of file Controller.h.
Referenced by Controller(), printEnergies(), and ~Controller().
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Definition at line 243 of file Controller.h.
Referenced by Controller(), printEnergies(), and ~Controller().
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Definition at line 167 of file Controller.h.
Referenced by calcPressure(), printEnergies(), and receivePressure().
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Definition at line 71 of file Controller.h.
Referenced by calcPressure(), and receivePressure().
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Definition at line 82 of file Controller.h.
Referenced by Controller(), and printEnergies().
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Definition at line 69 of file Controller.h.
Referenced by calcPressure(), and receivePressure().
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Definition at line 68 of file Controller.h.
Referenced by calcPressure(), and receivePressure().
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Definition at line 70 of file Controller.h.
Referenced by calcPressure(), and receivePressure().
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Definition at line 85 of file Controller.h.
Referenced by Controller(), and printEnergies().
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Definition at line 247 of file Controller.h.
Referenced by Controller(), printEnergies(), and ~Controller().
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Definition at line 246 of file Controller.h.
Referenced by Controller(), and printEnergies().
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Definition at line 245 of file Controller.h.
Referenced by Controller(), and printEnergies().
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Definition at line 234 of file Controller.h.
Referenced by adaptTempUpdate(), Controller(), langevinPiston1(), langevinPiston2(), stochRescaleCoefficient(), and ~Controller().
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Definition at line 150 of file Controller.h.
Referenced by outputTiEnergy(), and writeTiEnergyData().
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Definition at line 144 of file Controller.h.
Referenced by outputTiEnergy(), and writeTiEnergyData().
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Definition at line 145 of file Controller.h.
Referenced by outputTiEnergy(), and writeTiEnergyData().
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Definition at line 146 of file Controller.h.
Referenced by outputTiEnergy(), and writeTiEnergyData().
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Definition at line 147 of file Controller.h.
Referenced by outputTiEnergy(), and writeTiEnergyData().
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Definition at line 148 of file Controller.h.
Referenced by outputTiEnergy(), and writeTiEnergyData().
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Definition at line 149 of file Controller.h.
Referenced by outputTiEnergy(), and writeTiEnergyData().
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Definition at line 152 of file Controller.h.
Referenced by outputTiEnergy(), and writeTiEnergyData().
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Definition at line 237 of file Controller.h.
Referenced by compareChecksums(), Controller(), correctMomentum(), multigratorPressure(), printEnergies(), printMinimizeEnergies(), receivePressure(), and ~Controller().
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Definition at line 175 of file Controller.h.
Referenced by Controller(), and rescaleVelocities().
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Definition at line 174 of file Controller.h.
Referenced by Controller(), and rescaleVelocities().
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Definition at line 235 of file Controller.h.
Referenced by adaptTempInit(), adaptTempUpdate(), adaptTempWriteRestart(), algorithm(), berendsenPressure(), compareChecksums(), computeAlchWork(), Controller(), integrate(), langevinPiston1(), langevinPiston2(), minimize(), multigatorCalcEnthalpy(), multigratorPressure(), multigratorTemperature(), outputExtendedSystem(), outputFepEnergy(), outputTiEnergy(), printEnergies(), printFepMessage(), printTiMessage(), printTiming(), reassignVelocities(), receivePressure(), rescaleaccelMD(), rescaleVelocities(), stochRescaleCoefficient(), stochRescaleVelocities(), tcoupleVelocities(), writeExtendedSystemData(), writeExtendedSystemLabels(), writeFepEnergyData(), and writeTiEnergyData().
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Definition at line 80 of file Controller.h.
Referenced by calcPressure(), compareChecksums(), correctMomentum(), integrate(), langevinPiston1(), langevinPiston2(), minimize(), printEnergies(), and rescaleaccelMD().
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Definition at line 166 of file Controller.h.
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Definition at line 236 of file Controller.h.
Referenced by algorithm(), berendsenPressure(), calcPressure(), Controller(), enqueueCollections(), langevinPiston1(), langevinPiston2(), multigatorCalcEnthalpy(), multigratorPressure(), printDynamicsEnergies(), printEnergies(), receivePressure(), recvCheckpointAck(), rescaleaccelMD(), writeExtendedSystemData(), and writeExtendedSystemLabels().
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Definition at line 102 of file Controller.h.
Referenced by printEnergies().
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Count time steps until next stochastic velocity rescaling.
Definition at line 192 of file Controller.h.
Referenced by Controller(), and stochRescaleVelocities().
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The timefactor for stochastic velocity rescaling depends on fixed configuration parameters, so can be precomputed.
Definition at line 195 of file Controller.h.
Referenced by Controller(), and stochRescaleCoefficient().
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Definition at line 205 of file Controller.h.
Referenced by langevinPiston1().
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Definition at line 239 of file Controller.h.
Referenced by Controller(), rescaleaccelMD(), and ~Controller().
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Definition at line 87 of file Controller.h.
Referenced by Controller(), and printEnergies().
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Definition at line 81 of file Controller.h.
Referenced by Controller(), and printEnergies().
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Definition at line 161 of file Controller.h.
Referenced by multigratorPressure(), multigratorTemperature(), printEnergies(), receivePressure(), rescaleVelocities(), stochRescaleCoefficient(), tcoupleVelocities(), and writeFepEnergyData().
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Definition at line 262 of file Controller.h.
Referenced by outputTiEnergy(), and writeTiEnergyData().
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Definition at line 143 of file Controller.h.
Referenced by outputTiEnergy(), and writeTiEnergyData().
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Definition at line 103 of file Controller.h.
Referenced by adaptTempUpdate(), printEnergies(), and printMinimizeEnergies().
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totalEnergy at firstTimestep
Definition at line 164 of file Controller.h.
Referenced by Controller(), and printEnergies().
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Definition at line 72 of file Controller.h.
Referenced by calcPressure(), and rescaleaccelMD().
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Definition at line 252 of file Controller.h.
Referenced by outputExtendedSystem().