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• packCoordinateSendBuffer() : gmx::DomainCommBackward
• packedBoundingBoxes() : gmx::Grid
• paddedArrayRef() : gmx::ArrayRefWithPadding< typename >
• paddedConstArrayRef() : gmx::ArrayRefWithPadding< typename >
• paddedNumAtomsInColumn() : gmx::Grid
• paddedSize() : gmx::PaddedVector< T, Allocator >
• PaddedVector() : gmx::PaddedVector< T, Allocator >
• PairDistanceModuleData() : gmx::analysismodules::anonymous_namespace{pairdist.cpp}::PairDistanceModuleData
• pairlistInnerRadius() : gmx::nonbonded_verlet_t
• pairlistIsSimple() : gmx::nonbonded_verlet_t
• pairlistOuterRadius() : gmx::nonbonded_verlet_t
• PairlistParams() : gmx::PairlistParams
• pairlistSet() : gmx::PairlistSets
• PairlistSet() : gmx::PairlistSet
• PairlistSets() : gmx::PairlistSets
• pairlistSets() : gmx::nonbonded_verlet_t
• PairSearch() : gmx::PairSearch
• paragraphBreak() : gmx::HelpWriterContext
• ParallelConsistencyError() : gmx::ParallelConsistencyError
• parallelDataStarted() : gmx::AnalysisDataProxy , gmx::IAnalysisDataModule , gmx::AnalysisDataModuleParallel , gmx::AnalysisDataSimpleHistogramModule , gmx::AnalysisDataWeightedHistogramModule
• parallelizationFactor() : gmx::AnalysisDataParallelOptions
• parallelSelection() : gmx::TrajectoryAnalysisModuleData
• parallelSelections() : gmx::TrajectoryAnalysisModuleData
• param() : gmx::ExponentialDistribution< RealType > , gmx::GammaDistribution< RealType > , gmx::NormalDistribution< RealType > , gmx::TabulatedNormalDistribution< RealType, tableBits > , gmx::UniformIntDistribution< IntType > , gmx::UniformRealDistribution< RealType >
• param_type() : gmx::ExponentialDistribution< RealType >::param_type , gmx::GammaDistribution< RealType >::param_type , gmx::NormalDistribution< RealType >::param_type , gmx::TabulatedNormalDistribution< RealType, tableBits >::param_type , gmx::UniformIntDistribution< IntType >::param_type , gmx::UniformRealDistribution< RealType >::param_type
• parameters() : gmx::QMMMOptions
• parametersAllMasses1() : gmx::SettleData
• parametersMassWeighted() : gmx::SettleData
• params() : gmx::Bias , gmx::nbnxn_atomdata_t , gmx::PairlistSet , gmx::PairlistSets
• Params() : gmx::nbnxn_atomdata_t::Params
• paramsDeprecated() : gmx::nbnxn_atomdata_t
• pargsToOptions() : gmx::anonymous_namespace{pargs.cpp}::OptionsAdapter
• ParrinelloRahmanBarostat() : gmx::ParrinelloRahmanBarostat
• parse() : gmx::CommandLineParser
• parseFromFile() : gmx::SelectionCollection
• parseFromStdin() : gmx::SelectionCollection
• parseFromString() : gmx::SelectionCollection
• parseInteractive() : gmx::SelectionCollection
• parseRequestedFromFile() : gmx::SelectionOptionManager
• parseRequestedFromStdin() : gmx::SelectionOptionManager
• parseRequestedFromString() : gmx::SelectionOptionManager
• partialCleanUp() : MoleculeInformation
• particleName() : SimulationParticle
• particleTypeNameA() : SimulationParticle
• particleTypeNameB() : SimulationParticle
• pbc() : gmx::TrajectoryFrame
• pbcType() : gmx::TopologyInformation
• PdbAtomEntry() : PdbAtomEntry
• perform3dFft() : gmx::Gpu3dFft , gmx::Gpu3dFft::ImplCuFft , gmx::Gpu3dFft::ImplCuFftMp , gmx::Gpu3dFft::ImplHipRocfft , gmx::Gpu3dFft::ImplHipVkFft , gmx::Gpu3dFft::Impl , gmx::Gpu3dFft::ImplOcl , gmx::Gpu3dFft::ImplOclVkfft , gmx::Gpu3dFft::ImplSycl , gmx::Gpu3dFft::ImplSyclBbfft , gmx::Gpu3dFft::ImplSyclMkl , gmx::Gpu3dFft::ImplSyclRocfft , gmx::Gpu3dFft::ImplSyclVkfft
• performPatternSearch() : gmx::analysismodules::anonymous_namespace{dssp.cpp}::SecondaryStructures
• performPreviouslySkippedUpdates() : gmx::PointState
• period() : gmx::GridAxis
• periodicBoundaryConditionType() : gmx::ColvarsSimulationsParameters , gmx::anonymous_namespace{densityfitting.cpp}::DensityFittingSimulationParameterSetup , gmx::anonymous_namespace{qmmm.cpp}::QMMMSimulationParameterSetup
• permitSeparatePmeRanks() : gmx::SeparatePmeRanksPermitted
• PhysicalNodeCommunicator() : gmx::PhysicalNodeCommunicator
• pinningPolicy() : gmx::HostAllocationPolicy , gmx::ForceBuffers
• placeSelectionsInRequests() : gmx::SelectionOptionManager::Impl
• plainPairlist() : gmx::nonbonded_verlet_t , gmx::PairlistSets
• PlainPairlistRanges() : gmx::PlainPairlistRanges
• plotFormat() : gmx::AnalysisDataPlotSettings
• plotSettings() : gmx::TrajectoryAnalysisSettings
• PlumedForceProvider() : gmx::PlumedForceProvider
• PlumedMDModule() : gmx::anonymous_namespace{plumedMDModule.cpp}::PlumedMDModule , gmx::anonymous_namespace{plumedMDModule_stub.cpp}::PlumedMDModule
• PmeAtomComm() : PmeAtomComm
• PmeCoordinateReceiverGpu() : gmx::PmeCoordinateReceiverGpu
• PmeForceSenderGpu() : gmx::PmeForceSenderGpu
• PmeGpuProgram() : PmeGpuProgram
• PmeGpuProgramImpl() : PmeGpuProgramImpl
• PmeGpuSpecific() : PmeGpuSpecific
• PmeLoadBalanceHelper() : gmx::PmeLoadBalanceHelper
• PmeLoadBalancing() : gmx::PmeLoadBalancing
• PmePpCommGpu() : gmx::PmePpCommGpu
• pmePrinting() : gmx::PmeLoadBalanceHelper
• PmeSolve() : PmeSolve
• point() : gmx::BiasGrid
• points() : gmx::BiasState
• pointsAdded() : gmx::AnalysisDataSimpleHistogramModule , gmx::AnalysisDataWeightedHistogramModule , gmx::AnalysisDataBinAverageModule , gmx::AnalysisDataLifetimeModule , gmx::AbstractPlotModule , gmx::AnalysisDataPlotModule , gmx::AnalysisDataVectorPlotModule , gmx::AnalysisDataProxy , gmx::internal::BasicAverageHistogramModule , gmx::analysismodules::anonymous_namespace{select.cpp}::IndexFileWriterModule , gmx::IAnalysisDataModule , gmx::AnalysisDataModuleSerial , gmx::AnalysisDataModuleParallel , gmx::AnalysisDataAverageModule , gmx::AnalysisDataFrameAverageModule , gmx::AnalysisDataDisplacementModule
• pointSet() : gmx::internal::AnalysisDataStorageFrameData , gmx::test::AnalysisDataTestInputFrame , gmx::AnalysisDataFrameRef
• pointSetCount() : gmx::internal::AnalysisDataStorageFrameData , gmx::test::AnalysisDataTestInputFrame , gmx::AnalysisDataFrameRef
• PointState() : gmx::PointState
• pop_back() : gmx::KeyValueTreePath , gmx::FixedCapacityVector< typename, size_t >
• pop_last() : gmx::KeyValueTreePath
• popIEntryWhenEmpty() : gmx::AtomPairlist
• posCount() : gmx::internal::SelectionData , gmx::Selection
• position() : gmx::H5mdParticleBlock , gmx::Selection
• position_distance() : gmx::ColvarProxyGromacs
• PositionCalculationCollection() : gmx::PositionCalculationCollection
• positionScalingCallback() : gmx::Propagator< integrationStage >
• positionsView() : gmx::StatePropagatorData
• potential() : gmx::AwhParams
• PotentialPointData() : gmx::PotentialPointData
• ppCommAtomRange() : gmx::PmeCoordinateReceiverGpu , gmx::PmeCoordinateReceiverGpu::Impl
• ppCommNumRanksSendingParticles() : gmx::PmeCoordinateReceiverGpu::Impl , gmx::PmeCoordinateReceiverGpu
• ppCommStream() : gmx::PmeCoordinateReceiverGpu , gmx::PmeCoordinateReceiverGpu::Impl
• prepareAndTransformCoordinates() : gmx::ProcessFrameConversion
• prepareAndWriteFrame() : gmx::TrajectoryFrameWriter
• prepareForPositionAssembly() : gmx::ImdSession::Impl
• prepareMainSocket() : gmx::ImdSession::Impl
• prepareMDForces() : gmx::ImdSession::Impl
• prepareMoleculesInImdGroup() : gmx::ImdSession::Impl
• prepareReferenceData() : gmx::test::PeriodicActionsTest
• prepareTest() : gmx::test::SetAtomsUnSupportedFiles , gmx::test::SetAtomsSupportedFiles , gmx::test::AnyOutputSupportedFiles , gmx::test::NoOptionalOutput , gmx::test::OutputSelectorDeathTest , gmx::test::SetVelocityUnSupportedFiles , gmx::test::SetForceSupportedFiles , gmx::test::SetForceUnSupportedFiles , gmx::test::SetPrecisionSupportedFiles , gmx::test::SetPrecisionUnSupportedFiles , gmx::test::SetVelocitySupportedFiles
• prepareVmdForces() : gmx::ImdSession::Impl
• prependContext() : gmx::anonymous_namespace{exceptions.cpp}::ErrorMessage , gmx::GromacsException
• preprocess() : gmx::NNPotTopologyPreprocessor
• PreprocessingAtomTypes() : PreprocessingAtomTypes
• present() : gmx::test::AnalysisDataTestInputPointSet , gmx::AnalysisDataFrameRef , gmx::AnalysisDataPointSetRef
• presentAllData() : gmx::test::AnalysisDataTestFixture
• presentData() : gmx::AnalysisDataModuleManager::Impl
• presentDataFrame() : gmx::test::AnalysisDataTestFixture
• pressure() : gmx::EnergyData
• previousBlockIndex() : gmx::CorrelationBlockData
• previousBox() : gmx::StatePropagatorData
• previousPositionsView() : gmx::StatePropagatorData
• printCycles() : gmx::SearchCycleCounting
• printDebugInfo() : gmx::Selection
• printInfo() : gmx::Selection
• printInitializationToLog() : gmx::Bias
• printSettings() : gmx::PmeLoadBalancing
• printStringTableStorageToFile() : StringTable
• printThanks() : gmx::CommandLineModuleManager::Impl
• printTree() : gmx::PositionCalculationCollection , gmx::SelectionCollection
• printXvgrInfo() : gmx::SelectionCollection
• process() : gmx::OutputRequirementOptionDirector
• processAll() : gmx::OptionStorageTemplate< T > , gmx::AbstractOptionStorage
• processAtomsRedistributedSignal() : gmx::ColvarsForceProvider
• processAwhFrame() : AwhReader
• processCommonOptions() : gmx::CommandLineModuleManager::Impl
• processCoordinates() : gmx::ColvarsOptions , gmx::QMMMOptions
• processEdrFilename() : gmx::ColvarsOptions
• processFrame() : gmx::SetBox , gmx::SetForces , gmx::SetVelocities , gmx::SetTimeStep , gmx::SetPrecision , gmx::SetStartTime , gmx::IOutputAdapter , gmx::OutputSelector , gmx::SetAtoms
• ProcessFrameConversion() : gmx::ProcessFrameConversion
• processId() : gmx::BinaryInformationSettings
• processItem() : gmx::test::TestReferenceChecker::Impl
• processMarkup() : gmx::HelpWriterContext::Impl
• processSet() : gmx::OptionStorageTemplate< T > , gmx::AbstractOptionStorage
• processSetValues() : gmx::OptionStorageTemplate< T >
• processTemperature() : gmx::ColvarsOptions
• processTopology() : gmx::ColvarsOptions
• processTprFilename() : gmx::QMMMOptions
• processValue() : gmx::OptionStorageTemplateSimple< T >
• Profiling() : gmx::Profiling
• programName() : gmx::IProgramContext , gmx::test::anonymous_namespace{testinit.cpp}::TestProgramContext , gmx::CommandLineProgramContext , gmx::anonymous_namespace{programcontext.cpp}::DefaultProgramContext
• prop() : AtomProperties
• Propagator() : gmx::Propagator< integrationStage >
• propagatorCallback() : gmx::MttkData , gmx::MttkPropagatorConnection
• PropagatorTag() : gmx::PropagatorTag
• prScalingCallback() : gmx::Propagator< integrationStage >
• ptr() : gmx::BoundingBox::Corner
• ptype() : SimulationParticle
• pull_coord_work_t() : pull_coord_work_t
• pull_group_work_t() : pull_group_work_t
• PullCoordExpressionParser() : gmx::PullCoordExpressionParser
• pullDimParams() : gmx::DimParams
• PullElement() : gmx::PullElement
• push_back() : gmx::JClusterList , InteractionList , gmx::FixedCapacityVector< typename, size_t > , gmx::PackedJClusterList , InteractionList
• pushBack() : gmx::ListOfLists< typename >
• pushBackListOfSize() : gmx::ListOfLists< typename >
• putAtomsOnGrid() : gmx::nonbonded_verlet_t
• putOnGrid() : gmx::PairSearch , gmx::GridSet