Here is a list of all documented class members with links to the class documentation for each member:
- r -
- r
: t_pargs
, gmx::SelectionParserValue
, t_compare_value
, t_methoddata_kwint
, gmx_ana_selvalue_t
, t_methoddata_kwreal
- r1
: gmx::SelectionParserValue
- r2
: gmx::SelectionParserValue
- radacc
: anonymous_namespace{edsam.cpp}::t_edvecs
- radcon
: anonymous_namespace{edsam.cpp}::t_edvecs
- radfix
: anonymous_namespace{edsam.cpp}::t_edvecs
- radius
: anonymous_namespace{edsam.cpp}::t_eigvec
- randomSeed
: ReplicaExchangeParameters
- Range()
: gmx::Range< T >
- range
: gmx::test::SimdMathTest::CompareSettings
, gmx::AnalysisHistogramSettingsInitializer
- rangeEnd
: VsiteThread
- RangeError()
: gmx::RangeError
- rangeStart
: VsiteThread
- rank()
: gmx::detail::extents_analyse< R, E0, StaticExtents...>
, gmx::detail::extents_analyse< R, dynamic_extent, StaticExtents...>
, gmx::detail::extents_analyse< 0 >
, gmx::extents< StaticExtents >
, gmx::basic_mdspan< ElementType, Extents, LayoutPolicy, AccessorPolicy >
- rank_
: gmx::PhysicalNodeCommunicator
, gmx::test::MultiSimTest
- rank_dynamic()
: gmx::basic_mdspan< ElementType, Extents, LayoutPolicy, AccessorPolicy >
, gmx::detail::extents_analyse< R, E0, StaticExtents...>
, gmx::detail::extents_analyse< R, dynamic_extent, StaticExtents...>
, gmx::detail::extents_analyse< 0 >
, gmx::extents< StaticExtents >
- rankId
: PpRanks
- rankOrder
: gmx::DomdecOptions
- RawArray
: gmx::BasicVector< ValueType >
- rawIndex()
: gmx::RangePartitioning
- rb
: PreprocessResidue
, MoleculePatchDatabase
- rbegin()
: gmx::ArrayRef< T >
, gmx::EnumerationArray< EnumType, DataType, ArraySize >
, gmx::FixedCapacityVector< T, capacity >
- rcoulomb_sq
: cu_nbparam
, cl_nbparam
, cl_nbparam_params
- rcut_coulomb
: pme_setup_t
- RdfModuleData()
: gmx::analysismodules::anonymous_namespace{rdf.cpp}::RdfModuleData
- readAll()
: gmx::TextReader
- readCheckpointDataOnMaster()
: gmx::anonymous_namespace{densityfitting.cpp}::DensityFitting
- readCommand()
: gmx::ImdSession::Impl
- readDouble()
: gmx::test::TestReferenceChecker
- readFileToString()
: gmx::TextReader
- readFloat()
: gmx::test::TestReferenceChecker
- reading()
: gmx::FileIOXdrSerializer
, gmx::ISerializer
- readInt32()
: gmx::test::TestReferenceChecker
- readInt64()
: gmx::test::TestReferenceChecker
- readInteger()
: gmx::test::TestReferenceChecker
- readInternalParametersFromKvt()
: gmx::DensityFittingOptions
- readLength
: MD5Checksum
- readLine()
: gmx::StringInputStream
, gmx::TextReader
, gmx::TextInputStream
, gmx::StandardInputStream
, gmx::TextInputFile
- readNextFrame()
: gmx::TrajectoryAnalysisRunnerCommon
, gmx::test::EnergyFrameReader
, gmx::test::TrajectoryFrameReader
- readReferenceDensityFromFile()
: gmx::anonymous_namespace{densityfitting.cpp}::DensityFittingSimulationParameterSetup
- readString()
: gmx::test::TestReferenceChecker
- readUChar()
: gmx::test::TestReferenceChecker
- readVmdForces()
: gmx::ImdSession::Impl
- readWriteFlags()
: gmx::FileNameOption
- Real
: SoftCoreReal< softCoreTreatment >
, SoftCoreReal< SoftCoreTreatment::RPower48 >
- real_fft
: gmx_fft_mkl
- real_transform
: gmx_fft_fftw3
- realddxyz
: gmx::LegacyMdrunOptions
- realGridSize
: PmeGpuGridParams
, PmeGpuSpecific
- realGridSizeAlloc
: PmeGpuSpecific
- realGridSizeFP
: PmeGpuGridParams
- realGridSizePadded
: PmeGpuGridParams
- realMemory_
: gmx::test::anonymous_namespace{simd_floatingpoint_util.cpp}::SimdFloatingpointUtilTest
- recalculateSplines
: PmeGpuSettings
- receiveForceFromPmeCudaDirect()
: gmx::PmePpCommGpu
, gmx::PmePpCommGpu::Impl
- recipBox
: PmeGpuDynamicParams
- recordCycles_
: SearchCycleCounting
- redirector_
: gmx::FileNameOptionManager::Impl
- redirectStringToStdin()
: gmx::test::StdioTestHelper
- reduceNumBlocks()
: gmx::RangePartitioning
- reduceTask
: InterdependentTask
- ref
: gmx_slabdata
- refcount
: t_compiler_data
, gmx_ana_poscalc_t
- refCountArray_
: gmx::analysismodules::anonymous_namespace{pairdist.cpp}::PairDistanceModuleData
- refData_
: gmx::test::anonymous_namespace{energyoutput.cpp}::EnergyOutputTest
, gmx::test::anonymous_namespace{leapfrog.cpp}::LeapFrogTest
, gmx::test::anonymous_namespace{settle.cpp}::SettleTest
- reference
: gmx::MultiDimArray< TContainer, Extents, LayoutPolicy >
, gmx::accessor_basic< ElementType >
, gmx::basic_mdspan< ElementType, Extents, LayoutPolicy, AccessorPolicy >
, gmx::internal::SimdArrayRef< T >
, gmx::ArrayRef< T >
, gmx::FixedCapacityVector< T, capacity >
- referenceDensity()
: gmx::anonymous_namespace{densityfitting.cpp}::DensityFittingSimulationParameterSetup
- referenceDensityFileName()
: gmx::DensityFittingOptions
- referenceFileNames_
: gmx::test::anonymous_namespace{periodicactions.cpp}::PeriodicActionsTest
- referenceProjectionSlope
: anonymous_namespace{edsam.cpp}::t_edflood
- referenceSquaredSum
: gmx::anonymous_namespace{densityfit.cpp}::CrossCorrelationEvaluationHelperValues
- refid
: gmx_ana_indexmap_t
- refId()
: gmx::SelectionPosition
- refIds()
: gmx::Selection
- refIndex()
: gmx::AnalysisNeighborhoodPair
- refproj
: anonymous_namespace{edsam.cpp}::t_eigvec
- refreshMassesAndCharges()
: gmx::internal::SelectionData
- refreshName()
: gmx::internal::SelectionData
- registerAnalysisDataset()
: gmx::TrajectoryAnalysisModule
- registerAwhWithPull()
: gmx::Awh
- registerBasicDataset()
: gmx::TrajectoryAnalysisModule
- registerClient()
: gmx::TopologyHolder
- registerEnergyCallback()
: gmx::IEnergySignallerClient
- registerLastStepCallback()
: gmx::ILastStepSignallerClient
- registerLoggingCallback()
: gmx::ILoggingSignallerClient
- registerModule()
: gmx::TrajectoryAnalysisCommandLineRunner
, gmx::CommandLineModuleManager
- registerModuleDirect()
: gmx::ICommandLineOptionsModule
- registerModuleFactory()
: gmx::ICommandLineOptionsModule
- registerNSCallback()
: gmx::INeighborSearchSignallerClient
- registerOption()
: gmx::SelectionOptionManager
- registerSignallerClient()
: gmx::SignallerBuilder< Signaller >
, gmx::TrajectoryElementBuilder
- registerStopCondition()
: gmx::StopHandlerBuilder
- registerSubTopic()
: gmx::AbstractCompositeHelpTopic
- registerTrajectorySignallerCallback()
: gmx::ITrajectorySignallerClient
- registerTrajectoryWriterCallback()
: gmx::ITrajectoryWriterClient
- registerWriterClient()
: gmx::TrajectoryElementBuilder
- reinit()
: gmx::PmePpCommGpu
, gmx::PmePpCommGpu::Impl
- reinitHalo()
: gmx::GpuHaloExchange
- relativeLatency
: gmx::HardwareTopology::Numa
- relativeToleranceAsFloatingPoint()
: gmx::test::FloatingPointTolerance
- relativeToleranceAsPrecisionDependentFloatingPoint()
: gmx::test::FloatingPointTolerance
- relativeToleranceAsPrecisionDependentUlp()
: gmx::test::FloatingPointTolerance
- relativeToleranceAsUlp()
: gmx::test::FloatingPointTolerance
- releaser
: gmx::OpenClTraits< cl_context >
, gmx::OpenClTraits< cl_command_queue >
, gmx::OpenClTraits< cl_program >
, gmx::OpenClTraits< cl_kernel >
- ReleaserType
: gmx::OpenClTraitsBase< cl_type >
- removeCalculation()
: gmx::PositionCalculationCollection::Impl
- removeFiles()
: gmx::test::TestFileManager::Impl
- removeMolecularShifts()
: gmx::ImdSession::Impl
- removeTerminatingLineFeed()
: gmx::anonymous_namespace{exceptions.cpp}::MessageWriterString
- rend()
: gmx::ArrayRef< T >
, gmx::FixedCapacityVector< T, capacity >
- renumberTypes()
: PreprocessingAtomTypes
- reopenRegionCpu()
: DDBalanceRegionHandler
- RepeatingOptionSection()
: gmx::RepeatingOptionSection< T >
- RepeatingOptionSectionHandle()
: gmx::RepeatingOptionSectionHandle< T >
- RepeatingOptionSectionHandle< T >
: gmx::RepeatingOptionSectionStorage< T >
- RepeatingOptionSectionStorage()
: gmx::RepeatingOptionSectionStorage< T >
- RepeatingOptionSectionStorage< T >
: gmx::RepeatingOptionSection< T >
- repl
: gmx_repl_ex
- replaceLinks()
: gmx::HelpWriterContext::Impl
- ReplaceList
: gmx::HelpWriterContext::Impl
- replacements_
: gmx::HelpWriterContext::Impl
- replExParams
: gmx::ISimulator
, gmx::LegacyMdrunOptions
- reportGpuUsage()
: gmx::GpuTaskAssignments
- reppow
: gmx_ffparams_t
- representativeItem()
: gmx::UnionFinder
- representativeValue()
: gmx::MappedUnionFinder
- reproducible
: gmx::MdrunOptions
- repulsion_shift
: cu_nbparam
, cl_nbparam
, cl_nbparam_params
- req
: gmx_pme_pp
- requestFrame()
: gmx::test::TopologyManager
- RequestList
: gmx::SelectionOptionManager::Impl
- requestOptionDelayedParsing()
: gmx::SelectionOptionManager
- requests_
: gmx::SelectionOptionManager::Impl
- RequestsClearer()
: gmx::SelectionOptionManager::Impl::RequestsClearer
- requestStorage()
: gmx::AbstractAnalysisData
, gmx::AnalysisDataStorage
- requestStorageInternal()
: gmx::AbstractAnalysisData
- requestUnsetRequiredOptions()
: gmx::SelectionOptionManager::Impl
- required()
: gmx::OptionTemplate< T, U >
- required_span_size()
: gmx::layout_right::mapping< Extents >
- requiredAtoms_
: gmx::SelectionCollection::Impl
- RequiredTopologyInfo
: gmx::PositionCalculationCollection
- requiredTopologyInfoForType()
: gmx::PositionCalculationCollection
- requiredTopologyProperties()
: gmx::SelectionCollection
, gmx::SelectionTreeElement
- requiredTopologyPropertiesForPositionType()
: gmx::SelectionCollection::Impl
- requirementsBuilder_
: gmx::test::FlagTest
- requirePbcHandling
: gmx::test::TrajectoryFrameMatchSettings
- requiresIndexGroups()
: gmx::SelectionCollection
, gmx::SelectionTreeElement
- rerun
: gmx::MdrunOptions
- rerunConstructVsites
: gmx::MdrunOptions
- res_a_
: gmx::analysismodules::anonymous_namespace{sasa.cpp}::SasaModuleData
- resampleDoubleBinWidth()
: gmx::AbstractAverageHistogram
- reserve()
: gmx::MDAtoms
, gmx::internal::EnumIndexStore< EnumType >
, gmx::IOptionValueStore< T >
, gmx::OptionValueStoreNull< T >
, anonymous_namespace{evaluate.cpp}::MempoolSelelemReserver
, anonymous_namespace{evaluate.cpp}::MempoolGroupReserver
- ReservedSymbol
: gmx::SelectionParserSymbol
- reserveWithPadding()
: gmx::PaddedVector< T, Allocator >
- reset()
: gmx::AnalysisNeighborhoodSearch
, gmx::NormalDistribution< RealType >
, GpuRegionTimerWrapper< GpuRegionTimerImpl >
, GpuRegionTimerImpl
, gmx::ExponentialDistribution< RealType >
, gmx::GammaDistribution< RealType >
, gmx::TabulatedNormalDistribution< RealType, tableBits >
, gmx::UniformIntDistribution< IntType >
, gmx::UniformRealDistribution< RealType >
, gmx::PrivateImplPointer< Impl >
- reset_time_stamp
: gmx_walltime_accounting
- reset_time_stamp_per_thread
: gmx_walltime_accounting
- resetCounters()
: gmx::ResetHandler
- resetHalfway
: gmx::TimingOptions
- ResetHandler()
: gmx::ResetHandler
- resetStep
: gmx::TimingOptions
- residueName
: BaseEntry
, ResidueTypeEntry
, AtomProxy
- residueNumber()
: AtomProxy
- residueNumberStart
: MoleculeBlockIndices
- residueType
: ResidueTypeEntry
- ResidueTypeEntry()
: ResidueTypeEntry
- resize()
: gmx::MDAtoms
, gmx::MultiDimArray< TContainer, Extents, LayoutPolicy >
- resizeWithPadding()
: gmx::PaddedVector< T, Allocator >
- resname
: VirtualSiteTopology
, PreprocessResidue
- resno
: t_bb
- resolveExternalGroups()
: gmx::SelectionCollection::Impl
- resolveIndexGroupReference()
: gmx::SelectionTreeElement
- restart()
: gmx::ThreeFry2x64General< rounds, internalCounterBits >
- restartWithAppending
: gmx_enfrot
- restoreFromHistory()
: gmx::CorrelationTensor
, gmx::BiasState
, gmx::CoordState
, gmx::CorrelationBlockData
, gmx::HistogramSize
- restoreOriginalPositions()
: gmx::internal::SelectionData
- restoreStateFromHistory()
: gmx::CorrelationGrid
, gmx::Bias
, gmx::Awh
- restraint_
: gmx::RestraintManager::Impl
- RestraintForceProvider()
: gmx::RestraintForceProvider
- RestraintManager()
: gmx::RestraintManager
- RestraintMDModule()
: gmx::RestraintMDModule
- RestraintMDModuleImpl()
: gmx::RestraintMDModuleImpl
- restype()
: AtomProperties
, AtomProperties::Impl
- result()
: gmx::anonymous_namespace{helpwritercontext.cpp}::WrapperToVector
, gmx::anonymous_namespace{helpwritercontext.cpp}::WrapperToString
, gmx::anonymous_namespace{exceptions.cpp}::MessageWriterString
- result_type
: gmx::NormalDistribution< RealType >
, gmx::TabulatedNormalDistribution< RealType, tableBits >
, gmx::UniformRealDistribution< RealType >
, gmx::ExponentialDistribution< RealType >
, gmx::UniformIntDistribution< IntType >
, gmx::GammaDistribution< RealType >
, gmx::ThreeFry2x64General< rounds, internalCounterBits >
- reverse_iterator
: gmx::FixedCapacityVector< T, capacity >
, gmx::ArrayRef< T >
, gmx::internal::SimdArrayRef< T >
- reverseBoolean_
: gmx::OptionsAssigner::Impl
- rgb
: t_mapping
- right
: t_methoddata_compare
- rlistInner
: PairlistParams
, pme_setup_t
- rlistInner_sq
: cl_nbparam
, cl_nbparam_params
, cu_nbparam
- rlistOuter
: pme_setup_t
, PairlistParams
- rlistOuter_sq
: cu_nbparam
, cl_nbparam_params
, cl_nbparam
- rms_
: gmx::MrcDataStatistics
- rmsa
: t_bb
- rmsd()
: gmx::Constraints
- rmsdData
: gmx::Lincs
, gmx::Constraints
- rng
: t_UmbrellaOptions
- rollingPrune_k
: Nbnxm::gpu_timers_t::Interaction
- root
: gmx_ana_selcollection_t
- rootChecker()
: gmx::test::CommandLineTestBase
, gmx::test::TestReferenceData
- rootChecker_
: gmx::test::MockAnalysisDataModule::Impl
- rootContext_
: gmx::HelpManager::Impl
- rootElement()
: gmx::internal::SelectionData
- rootGroup_
: gmx::internal::OptionSectionImpl
- rootHelp
: gmx_ana_selcollection_t
- RootHelpTopic()
: gmx::anonymous_namespace{cmdlinehelpmodule.cpp}::RootHelpTopic
- rootObject()
: gmx::KeyValueTreeBuilder
- rootSection()
: gmx::Options
- rootSection_
: gmx::internal::OptionsImpl
- rot
: gmx_enfrot
- rotateBuffer()
: gmx::internal::AnalysisDataStorageImpl
- rotg
: gmx_enfrotgrp
- rotmat
: gmx_enfrotgrp
, gmx_potfit
- roundRange()
: gmx::AnalysisHistogramSettingsInitializer
- rowCount()
: gmx::AbstractAnalysisArrayData
- rperm
: t_methoddata_permute
- rpost_
: gmx::SelectionCollection::Impl
- RstParagraphIterator()
: gmx::RstParagraphIterator
- rules()
: gmx::KeyValueTreeTransformRulesScoped
- run()
: gmx::anonymous_namespace{cmdlinemodulemanager.cpp}::CMainCommandLineModule
, gmx::CommandLineModuleManager
, gmx::ISimulator
, gmx::ImdSession::Impl
, gmx::CommandLineHelpModule
, gmx::CheckpointHelper
, anonymous_namespace{minimize.cpp}::EnergyEvaluator
, anonymous_namespace{legacymodules.cpp}::ObsoleteToolModule
, gmx::ModularSimulator
, gmx::LegacySimulator
, gmx::PmeLoadBalanceHelper
, gmx::ICommandLineModule
, gmx::DomDecHelper
, gmx::ICommandLineOptionsModule
- runAsMain()
: gmx::TrajectoryAnalysisCommandLineRunner
, gmx::ICommandLineOptionsModule
- runAsMainCMain()
: gmx::CommandLineModuleManager
- runAsMainCMainWithSettings()
: gmx::CommandLineModuleManager
- runAsMainSingleModule()
: gmx::CommandLineModuleManager
- runExitsNormallyTest()
: gmx::test::MultiSimTest
- runFirstMdrun()
: gmx::test::TerminationHelper
- runMaxhTest()
: gmx::test::MultiSimTest
- runMode
: PmeShared
- RunModesList
: gmx::test::anonymous_namespace{pmetest.cpp}::PmeTest
- runModuleDirect()
: gmx::test::CommandLineTestHelper
- runModuleFactory()
: gmx::test::CommandLineTestHelper
- runner_
: gmx::test::MdrunTestFixture
, gmx::test::TerminationHelper
- runners_
: gmx::test::anonymous_namespace{settle.cpp}::SettleTest
- runScheduleWork
: gmx::ISimulator
, anonymous_namespace{minimize.cpp}::EnergyEvaluator
- runSecondMdrun()
: gmx::test::TerminationHelper
- runSecondMdrunWithNoAppend()
: gmx::test::TerminationHelper
- runTest()
: gmx::test::anonymous_namespace{pmesolvetest.cpp}::PmeSolveTest
, gmx::test::anonymous_namespace{pmegathertest.cpp}::PmeGatherTest
, gmx::anonymous_namespace{shake.cpp}::ShakeTest
, gmx::test::anonymous_namespace{pmetest.cpp}::PmeTest
, gmx::test::anonymous_namespace{tpitest.cpp}::TpiTest
, gmx::test::anonymous_namespace{pmesplinespreadtest.cpp}::PmeSplineAndSpreadTest
, gmx::test::anonymous_namespace{pmebsplinetest.cpp}::PmeBSplineModuliTest
, gmx::test::ModuleTest
, gmx::test::AbstractTrajectoryAnalysisModuleTestFixture
, anonymous_namespace{grompp.cpp}::GromppTest
- rv
: t_pargs
- rvdw_sq
: cl_nbparam
, cu_nbparam
, cl_nbparam_params
- rvdw_switch
: cu_nbparam
, cl_nbparam
, cl_nbparam_params
- rvec_array()
: gmx::PaddedVector< T, Allocator >
- rvecBuffer
: AtomDistribution
- RVecMatcher()
: gmx::test::RVecMatcher< FloatType >