Here is a list of all documented class members with links to the class documentation for each member:
- a -
- a
: BondedInteraction
, MoleculePatch
, gmx::UniformIntDistribution< IntType >
, gmx::UniformRealDistribution< RealType >::param_type
, gmx::UniformIntDistribution< IntType >::param_type
, gmx::UniformRealDistribution< RealType >
- absoluteTolerance()
: gmx::test::FloatingPointTolerance
- AbstractAnalysisArrayData()
: gmx::AbstractAnalysisArrayData
- AbstractAnalysisData()
: gmx::AbstractAnalysisData
- AbstractAverageHistogram()
: gmx::AbstractAverageHistogram
- AbstractOption()
: gmx::AbstractOption
- AbstractOptionSection()
: gmx::AbstractOptionSection
- AbstractOptionSectionHandle()
: gmx::AbstractOptionSectionHandle
- AbstractOptionStorage()
: gmx::AbstractOptionStorage
, gmx::AbstractOption
- AbstractPlotModule()
: gmx::AbstractPlotModule
- acceptOptions()
: gmx::OptionsIterator
, gmx::OptionsModifyingIterator
- acceptSections()
: gmx::OptionsIterator
, gmx::OptionsModifyingIterator
- access()
: gmx::accessor_basic< ElementType >
- accessor()
: gmx::basic_mdspan< ElementType, Extents, LayoutPolicy, AccessorPolicy >
- accessor_type
: gmx::basic_mdspan< ElementType, Extents, LayoutPolicy, AccessorPolicy >
- accum_m
: df_history_t
- accum_m2
: df_history_t
- accum_p
: df_history_t
- accum_p2
: df_history_t
- accumulate()
: ForeignLambdaTerms
- add()
: gmx::GaussTransform3D
, gmx::MDModules
, gmx::SimulatorBuilder
, gmx::OptionManagerContainer
, gmx::LocalAtomSetManager
- addAdapter()
: gmx::OutputAdapterContainer
- addAndCheckGuarantee()
: gmx::ProcessFrameConversion
- addArray()
: gmx::KeyValueTreeObjectBuilder
- addBehavior()
: gmx::OptionsBehaviorCollection
- addBondAtomType()
: PreprocessingBondAtomType
- addBondedTaskAssignment()
: gmx::MdrunnerBuilder
- addCastConversion()
: gmx::OptionValueConverterSimple< OutType >
- addCogs()
: gmx::UpdateGroupsCog
- addColumn()
: gmx::TextTableFormatter
- addColumnHelpTextBlock()
: gmx::TextTableFormatter
- addColumnLine()
: gmx::TextTableFormatter
- addColumnModule()
: gmx::AbstractAnalysisData
- addConverter()
: gmx::OptionValueConverterSimple< OutType >
- addCurrentExceptionAsNested()
: gmx::ExceptionInitializer
- addDefaultFileNameOption()
: gmx::FileNameOptionManager
- addDomainDecomposition()
: gmx::MdrunnerBuilder
- addElectrostatics()
: gmx::MdrunnerBuilder
- addEntry()
: t_state
- addError()
: WarningHandler
, gmx::EnergyCalculationFrequencyErrors
- addExistingFile()
: gmx::test::TestFileInputRedirector
- addFilenames()
: gmx::MdrunnerBuilder
- addForceProvider()
: gmx::ForceProviders
- addFrame()
: gmx::test::AnalysisDataTestInput
, gmx::EnergyTerm
- addFrameConverter()
: gmx::ProcessFrameConversion
- addFrameWithValueAndError()
: gmx::test::AnalysisDataTestInput
- addFrameWithValues()
: gmx::test::AnalysisDataTestInput
- addGroup()
: gmx::AbstractOptionSectionHandle
, gmx::IOptionsContainer
, gmx::Options
- addHardwareDetectionResult()
: gmx::MdrunnerBuilder
- addHardwareOptions()
: gmx::MdrunnerBuilder
- addHelpTopic()
: gmx::CommandLineModuleManager
- addInput()
: gmx::MdrunnerBuilder
- addLink()
: gmx::HelpLinks
- addLogFile()
: gmx::MdrunnerBuilder
- addManager()
: gmx::Options
- addModule()
: gmx::AnalysisDataModuleManager
, gmx::CommandLineModuleManager
, gmx::CommandLineModuleGroup
, gmx::AbstractAnalysisData
- addModuleCMain()
: gmx::CommandLineModuleManager
- addModuleCMainWithSettings()
: gmx::CommandLineModuleManager
- addModuleGroup()
: gmx::CommandLineModuleManager
- addModuleWithDescription()
: gmx::CommandLineModuleGroup
- addNeighborList()
: gmx::MdrunnerBuilder
- addNested()
: gmx::ExceptionInitializer
- addNonBonded()
: gmx::MdrunnerBuilder
- addNote()
: WarningHandler
- addObject()
: gmx::KeyValueTreeObjectArrayBuilder
, gmx::KeyValueTreeObjectBuilder
- addObjectArray()
: gmx::KeyValueTreeObjectBuilder
- addOption()
: gmx::test::CommandLine
, gmx::IOptionsContainer
- addOptionForSelection()
: gmx::test::ModuleSelection
- addOptionImpl()
: gmx::IOptionsContainer
- addOptionsBehavior()
: gmx::ICommandLineOptionsModuleSettings
- addOutputEnvironment()
: gmx::MdrunnerBuilder
- addPointSet()
: gmx::test::AnalysisDataTestInputFrame
- addPointSetWithValueAndError()
: gmx::test::AnalysisDataTestInputFrame
- addPointSetWithValues()
: gmx::test::AnalysisDataTestInputFrame
- addPotential()
: gmx::Mdrunner
- addRawValue()
: gmx::KeyValueTreeObjectBuilder
- addReferenceCheckerModule()
: gmx::test::AnalysisDataTestFixture
- addRegexToSkip()
: gmx::test::FilteringExactTextMatch
- addReplicaExchange()
: gmx::MdrunnerBuilder
- addRule()
: gmx::IKeyValueTreeTransformRules
- addSection()
: gmx::IOptionsContainerWithSections
- addSectionImpl()
: gmx::IOptionsContainerWithSections
- addSimulationMethod()
: gmx::MdrunnerBuilder
- addStaticCheckerModule()
: gmx::test::AnalysisDataTestFixture
- addStaticColumnCheckerModule()
: gmx::test::AnalysisDataTestFixture
- addStaticParallelCheckerModule()
: gmx::test::AnalysisDataTestFixture
- addStaticStorageCheckerModule()
: gmx::test::AnalysisDataTestFixture
- addStopHandlerBuilder()
: gmx::MdrunnerBuilder
- addString()
: StringTableBuilder
- addSubscriber()
: gmx::ObservablesReducerBuilder
- addSubTopic()
: gmx::AbstractCompositeHelpTopic
- addTargetFile()
: gmx::LoggerBuilder
- addTargetStream()
: gmx::LoggerBuilder
- addTimeUnitOption()
: gmx::TimeUnitBehavior
- addTopology()
: gmx::test::ModuleTest
- addToSpec()
: gmx::RestraintManager
- addType()
: PreprocessingAtomTypes
- addUniformArray()
: gmx::KeyValueTreeObjectBuilder
- addUpdateTaskAssignment()
: gmx::MdrunnerBuilder
- addValue()
: gmx::test::AnalysisDataTestInputPointSet
, gmx::OptionStorageTemplate< T >
, gmx::KeyValueTreeUniformArrayBuilder< T >
, gmx::KeyValueTreeObjectBuilder
- addValueWithError()
: gmx::test::AnalysisDataTestInputPointSet
- addVirialContribution()
: gmx::ForceWithVirial
- addWarning()
: WarningHandler
- adjustInputrecBasedOnModules()
: gmx::MDModules
- AffineTransformation()
: gmx::AffineTransformation
- AfterFrom()
: gmx::KeyValueTreeTransformRuleBuilder::AfterFrom< FromType >
- ai()
: InteractionOfType
, BondedInteraction
, MoleculePatch
- aj()
: BondedInteraction
, MoleculePatch
- ak()
: BondedInteraction
, MoleculePatch
- al()
: BondedInteraction
, MoleculePatch
- alignment()
: gmx::HostAllocationPolicy
, gmx::AlignedAllocationPolicy
, gmx::PageAlignedAllocationPolicy
- allocate()
: gmx::Allocator< T, AllocationPolicy >
- allocateValues()
: gmx::AbstractAnalysisArrayData
- Allocator()
: gmx::Allocator< T, AllocationPolicy >
- allowedValues()
: gmx::StringOptionInfo
, gmx::EnumOptionInfo
- allowEmpty()
: gmx::SelectionOption
- allowMissing()
: gmx::FileNameOption
, gmx::FileNameOptionInfo
- allowMultiple()
: gmx::OptionTemplate< T, U >
- allowPositionalArguments()
: gmx::CommandLineParser
- allPresent()
: gmx::AnalysisDataPointSetRef
, gmx::AnalysisDataFrameRef
- allSizes()
: gmx::UnionFinder
, gmx::MappedUnionFinder
- alpha()
: gmx::GammaDistribution< RealType >::param_type
, gmx::GammaDistribution< RealType >
- altloc()
: PdbAtomEntry
- AlwaysAtomSelections
: gmx::SelectionCollection
- am()
: BondedInteraction
- Amd
: gmx::CpuInfo
- amplitude_
: gmx::GaussianSpreadKernelParameters::PositionAndAmplitude
- AnalysisArrayData()
: gmx::AnalysisArrayData
- AnalysisData
: gmx::AnalysisDataHandle
, gmx::AnalysisData
- AnalysisDataBinAverageModule()
: gmx::AnalysisDataBinAverageModule
- AnalysisDataFrameHeader()
: gmx::AnalysisDataFrameHeader
- AnalysisDataFrameRef()
: gmx::AnalysisDataFrameRef
- AnalysisDataHandle()
: gmx::AnalysisDataHandle
- AnalysisDataParallelOptions()
: gmx::AnalysisDataParallelOptions
- AnalysisDataPlotModule()
: gmx::AnalysisDataPlotModule
- AnalysisDataPlotSettings()
: gmx::AnalysisDataPlotSettings
- AnalysisDataPointSetRef()
: gmx::AnalysisDataPointSetRef
- AnalysisDataSimpleHistogramModule()
: gmx::AnalysisDataSimpleHistogramModule
- AnalysisDataStorage()
: gmx::AnalysisDataStorage
- AnalysisDataTestInput
: gmx::test::AnalysisDataTestInputFrame
, gmx::test::AnalysisDataTestInput
- AnalysisDataTestInputFrame
: gmx::test::AnalysisDataTestInputPointSet
- AnalysisDataValue()
: gmx::AnalysisDataValue
- AnalysisDataVectorPlotModule()
: gmx::AnalysisDataVectorPlotModule
- AnalysisDataWeightedHistogramModule()
: gmx::AnalysisDataWeightedHistogramModule
- AnalysisHistogramSettings()
: gmx::AnalysisHistogramSettings
- AnalysisHistogramSettingsInitializer()
: gmx::AnalysisHistogramSettingsInitializer
- AnalysisNeighborhood()
: gmx::AnalysisNeighborhood
- AnalysisNeighborhoodPair()
: gmx::AnalysisNeighborhoodPair
- AnalysisNeighborhoodPairSearch()
: gmx::AnalysisNeighborhoodPairSearch
- AnalysisNeighborhoodPositions()
: gmx::AnalysisNeighborhoodPositions
- AnalysisNeighborhoodSearch()
: gmx::AnalysisNeighborhoodSearch
- analyzeFrame()
: gmx::IEnergyAnalysis
, gmx::TrajectoryAnalysisModule
- Angles
: ListedForces
- anisotropy()
: PdbAtomEntry
- Any()
: gmx::Any
- APIError()
: gmx::APIError
- append()
: gmx::KeyValueTreePath
, gmx::MessageStringCollector
, gmx::KeyValueTreePath
, gmx::test::CommandLine
, gmx::MessageStringCollector
, gmx::test::CommandLine
- appendBlock()
: gmx::RangePartitioning
- appendIf()
: gmx::MessageStringCollector
- appendLegend()
: gmx::AbstractPlotModule
- appendListOfLists()
: gmx::ListOfLists< typename >
- appendOption
: gmx::LegacyMdrunOptions
- appendText()
: gmx::LogEntryWriter
- appendTextFormatted()
: gmx::LogEntryWriter
- appendValue()
: gmx::AbstractOptionStorage
, gmx::OptionsAssigner
- apply()
: gmx::Constraints
- applyBiasForcesAndUpdateBias()
: gmx::Awh
- applyModule()
: gmx::AnalysisDataModuleManager
, gmx::AbstractAnalysisData
- arg()
: gmx::test::CommandLine
- argc()
: gmx::test::CommandLine
- argumentOf()
: gmx::test::CommandLine
- argv()
: gmx::test::CommandLine
- Arm
: gmx::CpuInfo
- Arm_Neon
: gmx::CpuInfo
- Arm_NeonAsimd
: gmx::CpuInfo
- Arm_Sve
: gmx::CpuInfo
- ArrayRef()
: gmx::ArrayRef< typename >
- arrayRefFromArray()
: gmx::ArrayRef< typename >
- ArrayRefWithPadding()
: gmx::ArrayRefWithPadding< typename >
- arrayRefWithPadding()
: gmx::PaddedVector< T, Allocator >
- ArrayRefWithPadding()
: gmx::ArrayRefWithPadding< typename >
- as_vec()
: gmx::BasicVector< ValueType >
- asAbsolute()
: gmx::test::FloatingPointDifference
- asConstView()
: gmx::MultiDimArray< TContainer, Extents, LayoutPolicy >
- asParagraph()
: gmx::LogEntryWriter
- assignOptionsToModules()
: gmx::MDModules
- associativity
: gmx::HardwareTopology::Cache
- asUlps()
: gmx::test::FloatingPointDifference
- asView()
: gmx::MultiDimArray< TContainer, Extents, LayoutPolicy >
- at()
: gmx::ListOfLists< typename >
, gmx::ArrayRef< typename >
, gmx_ga2la_t
, gmx::FixedCapacityVector< typename, size_t >
, StringTable
, gmx::FixedCapacityVector< typename, size_t >
- atnr
: gmx_ffparams_t
- atom
: PreprocessResidue
, AtomProxy
, MoleculePatch
- atom2constraints_moltype()
: gmx::Constraints
- atom2settle_moltype()
: gmx::Constraints
- atomChargeFromAtomType()
: PreprocessingAtomTypes
- atomCount()
: gmx::Selection
, gmx::SelectionPosition
- atomdata_add_nbat_f_to_f()
: nonbonded_verlet_t
- atomdata_init_copy_x_to_nbat_x_gpu()
: nonbonded_verlet_t
- atomDensity
: Nbnxm::Grid::Dimensions
- atomIndices()
: gmx::SelectionPosition
, gmx::Selection
- atomInfoAllVdw
: gmx::BenchmarkSystem
- atomInfoOxygenVdw
: gmx::BenchmarkSystem
- AtomIterator()
: AtomIterator
- atomMassFromAtomType()
: PreprocessingAtomTypes
- atomname
: PreprocessResidue
- atomName()
: PdbAtomEntry
, AtomProxy
- atomNameFromAtomType()
: PreprocessingAtomTypes
- atomNameFromBondAtomType()
: PreprocessingBondAtomType
- atomNonBondedParamFromAtomType()
: PreprocessingAtomTypes
- atomNumber
: gmx::ExclusionBlock
- atomnumber()
: SimulationParticle
- atomNumberFromAtomType()
: PreprocessingAtomTypes
- atomNumberFromElement()
: AtomProperties
- atomNumberInMol()
: AtomProxy
- atomParticleTypeFromAtomType()
: PreprocessingAtomTypes
- AtomProperties()
: AtomProperties
- AtomProxy()
: AtomProxy
- AtomRange()
: AtomRange
- atoms
: MoleculeInformation
, gmx::TopologyInformation
, gmx_moltype_t
, InteractionOfType
, gmx::OutputRequirements
, InteractionOfType
- atomSerialNumber()
: PdbAtomEntry
- atomTypeFromName()
: PreprocessingAtomTypes
- atomTypes
: gmx::BenchmarkSystem
- average()
: gmx::EnergyTerm
, gmx::AnalysisDataAverageModule
- averageMCycles()
: nbnxn_cycle_t
- averager()
: gmx::AnalysisDataWeightedHistogramModule
, gmx::AnalysisDataSimpleHistogramModule
- Awh()
: gmx::Awh
- awhHistory
: t_state
- axis_x
: t_matrix
- axis_y
: t_matrix